bluuebunny/crossref_metadata_2025 huggingface dataset:
Smoke over haze: Comparative analysis of satellite, surface radiometer, and airborne in situ measurements of aerosol optical properties and radiative forcing over the eastern United States
Authors: Vant‐Hull Brian , Li Zhanqing , Taubman Brett F. , Levy Robert , Marufu Lackson , Chang Fu‐Lung , Doddridge Bruce G. , Dickerson Russell R.
Published: February 2005

In July 2002 Canadian forest fires produced a major smoke episode that blanketed the east coast of the United States. Properties of the smoke aerosol were measured in situ from aircraft, complementing operational Aerosol Robotic Network (AERONET), and Moderate Resolution Imaging Spectroradiometer (MODIS) remotely sensed aerosol retrievals. This study compares single scattering albedo and phase function derived from the in situ measurements and AERONET retrievals in order to evaluate their consistency for application to satellite retrievals of optical depth and radiative forcing. These optical properties were combined with MODIS reflectance observations to calculate optical depth. The use of AERONET optical properties yielded optical depths 2–16% lower than those directly measured by AERONET. The use of in situ–derived optical properties resulted in optical depths 22–43% higher than AERONET measurements. These higher optical depths are attributed primarily to the higher absorption measured in situ, which is roughly twice that retrieved by AERONET. The resulting satellite retrieved optical depths were in turn used to calculate integrated radiative forcing at both the surface and top of atmosphere. Comparisons to surface (Surface Radiation Budget Network (SURFRAD) and ISIS) and to satellite (Clouds and Earth Radiant Energy System CERES) broadband radiometer measurements demonstrate that the use of optical properties derived from the aircraft measurements provided a better broadband forcing estimate (21% error) than those derived from AERONET (33% error). Thus AERONET‐derived optical properties produced better fits to optical depth measurements, while in situ properties resulted in better fits to forcing measurements. These apparent inconsistencies underline the significant challenges facing the aerosol community in achieving column closure between narrow and broadband measurements and calculations.
A comparison and summary of aerosol optical properties as observed in situ from aircraft, ship, and land during ACE‐Asia
Authors: Doherty Sarah J. , Quinn Patricia K. , Jefferson Anne , Carrico Christian M. , Anderson Theodore L. , Hegg Dean
Published: February 2005

During the ACE‐Asia campaign in March–May 2001, in situ measurements of aerosol optical properties were made from multiple airborne and land‐ or ship‐based platforms. Using a suite of direct interplatform comparisons and a campaign‐wide statistical comparison, we test the precision of these measurements, and we determine whether the platforms sampled similar aerosol. Data included in the study are from the National Center for Atmospheric Research C‐130 aircraft; the CIRPAS Twin Otter aircraft; the National Oceanographic and Atmospheric Administration (NOAA) ship R.V. Ronald H. Brown; and the Gosan surface station on Jeju Island, located off the southern tip of South Korea. Comparisons were made of total and submicron light scattering at 450, 550, and 700 nm; total and submicron absorption at 550 nm; the Ångström exponent; single scatter albedo of the total aerosol, submicron and supermicron aerosol at 550 nm; hemispheric backscatter fraction at 550 nm; and light scattering hygroscopic growth at 550 nm. For the campaign‐wide comparison, the data are broken down by light scattering fine mode fraction since the aerosol in the ACE‐Asia study region were a variable mix of pollution, dust, and sea salt. Finally, we calculate how the observed uncertainties in the aerosol optical properties propagate to uncertainties in top‐of‐atmosphere radiative forcing. Single scatter albedo showed excellent agreement among all platforms other than the Twin Otter, with discrepancies generally <0.02. These data sets combine to give campaign‐wide values of single scatter albedo of 0.885 ± 0.023 for the submicron aerosol (i.e. pollution) and 0.957 ± 0.031 for the supermicron aerosol (which, for these data, was predominantly dust). The data also indicated that, as expected, the Low Turbulent Inlet on the C‐130 produced enhanced concentrations of coarse mode aerosol. There also may have been significant coarse mode particle losses on the other platforms. These effects combined to produce generally lower fine mode fractions and Ångström exponents on the C‐130 than on the other platforms. Large discrepancies in hemispheric backscatter fraction and light scattering hygroscopic growth were observed in both the side‐by‐side and statistical comparisons. We are not able to explain these differences, though possible causes are discussed. Studies of the TSI, Inc. nephelometer backscatter measurement and of the two methods used here to measure hygroscopic growth are needed to clarify the source of these observed discrepancies. A better understanding of the effects of nonsphericity on hemispheric backscatter fraction is also needed.
Provenance of present‐day eolian dust collected off NW Africa
Authors: Stuut Jan‐Berend , Zabel Matthias , Ratmeyer Volker , Helmke Peer , Schefuß Enno , Lavik Gaute , Schneider Ralph
Published: February 2005

Atmospheric dust samples collected along a transect off the West African coast have been investigated for their physical (grain‐size distribution), mineralogical, and chemical (major elements) composition. On the basis of these data the samples were grouped into sets of samples that most likely originated from the same source area. In addition, shipboard‐collected atmospheric meteorological data, modeled 4‐day back trajectories for each sampling day and location, and Total Ozone Mapping Spectrometer aerosol index data for the time period of dust collection (February–March 1998) were combined and used to reconstruct the sources of the groups of dust samples. On the basis of these data we were able to determine the provenance of the various dust samples. It appears that the bulk of the wind‐blown sediments that are deposited in the proximal equatorial Atlantic Ocean are transported in the lower level (≳900 hPa) NE trade wind layer, which is a very dominant feature north of the Intertropical Convergence Zone (ITCZ). However, south of the surface expression of the ITCZ, down to 5°S, where surface winds are southwesterly, we still collected sediments that originated from the north and east, carried there by the NE trade wind layer, as well as by easterly winds from higher altitudes. The fact that the size of the wind‐blown dust depends not only on the wind strength of the transporting agent but also on the distance to the source hampers a direct comparison of the dust's size distributions and measured wind strengths. However, a comparison between eolian dust and terrigenous sediments collected in three submarine sediment traps off the west coast of NW Africa shows that knowledge of the composition of eolian dust is a prerequisite for the interpretation of paleorecords obtained from sediment cores in the equatorial Atlantic.
Linearization of vector radiative transfer with respect to aerosol properties and its use in satellite remote sensing
Authors: Hasekamp Otto P. , Landgraf Jochen
Published: February 2005

We present a plane parallel radiative transfer model for polarized light that provides the intensity vector field as well as analytical derivatives of the four Stokes parameters at the top of the atmosphere with respect to physical properties of spherical aerosols. The linearization consists of two steps: (1) calculation of the derivatives of the four Stokes parameters at the top of the atmosphere with respect to scattering coefficient, extinction coefficient, and expansion coefficients of the scattering phase matrix. These derivatives are calculated employing the forward‐adjoint perturbation theory. General expressions are presented that can be applied for the linearization of any vector radiative transfer model that calculates the internal radiation field in the model atmosphere. (2) The second step is calculation of the derivatives of the scattering coefficient, extinction coefficient, and the expansion coefficients of the scattering phase matrix, with respect to the real and imaginary part of the refractive index, and parameters describing the size distribution (e.g., effective radius, effective variance). These derivatives are analytically calculated following Mie theory. The use of the developed linearized radiative transfer model for the retrieval of aerosol properties is demonstrated using synthetic measurements of intensity and polarization of the Global Ozone Monitoring Experiment‐2 (GOME‐2). Here it is shown that an iterative retrieval approach based on the linearized radiative transfer model is suited to solve the nonlinear aerosol retrieval problem, and additionally allows a solid error analysis.
Structure and Tertiary tectonic history of the Mulhouse High, Upper Rhine Graben: Block faulting modified by changes in the Alpine stress regime
Authors: Rotstein Y. , Schaming M. , Rousse S.
Published: February 2005

The Mulhouse High (Horst) is situated in the southernmost Upper Rhine Graben, and changes in its tectonic history record the interaction with the adjacent Alpine front. Recently released seismic data show that the Mulhouse High consists of the Sierentz and the Altkirch tilted blocks, separated by the Ferrette fault zone with a throw of several hundred meters. During the Eocene‐early Rupelian main rifting phase, the Mulhouse High was the elevated flank of the Dannemarie basin with sedimentation affected by the nearby southern boundary of the Rhine Graben. The Miocene Jura compression extended into the Mulhouse High, creating a series of semiparallel buried folds with no evidence for thin skin tectonics. The change to a NW‐SE regional compressive stress reactivated the main graben faults as wrench faults. It also resulted in transpression on the NE‐SW trending faults, particularly the northern segment of the Illfurth fault zone. Consequently, the northern part of the Mulhouse High was uplifted. Strike‐slip motion along the Ferrette fault zone is shown to be small.
Parameter estimation using the falling head infiltration model: Simulation and field experiment
Authors: Zeleke Takele B. , Si Bing C.
Published: February 2005

Soil hydraulic parameters have high spatial variability. A large number of measurements are needed to characterize these parameters in a field. Therefore there is a need to develop quicker and cheaper methods to determine soil hydraulic parameters. The objective of this study was to examine the uniqueness of the Kfs (field saturated hydraulic conductivity) and α (inverse macroscopic capillary length scale) parameters obtained through inverting the falling head infiltration model. Five simulated scenarios were imposed on the cumulative infiltration data [L(t)] during the inverse procedure. The uniqueness of the Kfs and α estimates under each scenario was studied. In situ infiltration data were used to verify the scenario that provided unique parameter estimates. It appears that the falling head infiltration model can be used to simultaneously estimate the Kfs and α parameters when estimates (or published values) of the α parameter for the site are available.
Economic impact of alternative policy responses to prolonged and severe drought in the Rio Grande Basin
Authors: Booker James F. , Michelsen Ari M. , Ward Frank A.
Published: February 2005

In the Rio Grande Basin, water is overallocated, demands are growing, and river flows and uses are vulnerable to drought and climate change. Currently, the basin is in the third year of severe drought; irrigation and municipal water diversions have been severely curtailed; extensive diversions threaten endangered species, and reservoir volumes are nearly depleted. A central challenge is development of policies that efficiently and equitably allocate the basin's water resources among competing uses across political and institutional jurisdictions. A basin‐wide, nonlinear programming model optimizes resource allocations and water use levels for the upper part of the Rio Grande Basin to test whether institutional adjustments can reduce damages caused by drought. Compared to existing institutions, we find that future drought damages could be reduced by 20 and 33% per year through intracompact and interstate water markets, respectively, that would allow water transfers across water management jurisdictions. Results reveal economic tradeoffs among water uses, regions, and drought control strategies.
Examination of mitochondrial protein targeting of haem synthetic enzymes: in vivo identification of three functional haem-responsive motifs in 5-aminolaevulinate synthase
Authors: DAILEY Tamara A. , WOODRUFF John H. , DAILEY Harry A.
Published: February 2005

The initial and the terminal three enzymes of the mammalian haem biosynthetic pathway are nuclear encoded, cytoplasmically synthesized and post-translationally translocated into the mitochondrion. The first enzyme, ALAS (5-aminolaevulinate synthase), occurs as an isoenzyme encoded on different chromosomes and is synthesized either as a housekeeping protein (ALAS-1) in all non-erythroid cell types, or only in differentiating erythroid precursor cells (ALAS-2). Both ALAS proteins possess mitochondrial targeting sequences that have putative haem-binding motifs. In the present study, evidence is presented demonstrating that two haem-binding motifs in the leader sequence, as well as one present in the N-terminus of the mature ALAS-1 function in vivo in the haem-regulated translocation of ALAS-1. Coproporphyrinogen oxidase, the antepenultimate pathway enzyme, possesses a leader sequence that is approx. 120 residues long. In contrast with an earlier report suggesting that only 30 residues were required for translocation of the coproporphyrinogen oxidase, we report that the complete leader is necessary for translocation and that this process is not haem-sensitive in vivo. PPO (protoporphyrinogen oxidase) lacks a typical mitochondrial targeting leader sequence and was found to be effectively targeted by just 17 N-terminal residues. Bacillus subtilis PPO, which is very similar to human PPO at its N-terminal end, is not targeted to the mitochondrion when expressed in mammalian cells, demonstrating that the translocation is highly specific with regard to both the length and spacing of charged residues in this targeting region. Ferrochelatase, the terminal enzyme, possesses a typical N-terminal leader sequence and no evidence of a role for the C-terminus was found in mitochondrial targeting.
Stimulation of hepatocytic AMP-activated protein kinase by okadaic acid and other autophagy-suppressive toxins
Authors: SAMARI Hamid R. , MØLLER Michael T. N. , HOLDEN Lise , ASMYHR Tonje , SEGLEN Per O.
Published: February 2005

Autophagic activity in isolated rat hepatocytes is strongly suppressed by OA (okadaic acid) and other PP (protein phosphatase)-inhibitory toxins as well as by AICAR (5-aminoimidazole-4-carboxamide riboside), a direct activator of AMPK (AMP-activated protein kinase). To investigate whether AMPK is a mediator of the effects of the toxin, a phosphospecific antibody directed against the activation of phosphorylation of the AMPK α (catalytic)-subunit at Thr172 was used to assess the activation status of this enzyme. AICAR as well as all the toxins tested (OA, microcystin-LR, calyculin A, cantharidin and tautomycin) induced strong, dose-dependent AMPKα phosphorylation, correlating with AMPK activity in situ (in intact hepatocytes) as measured by the AMPK-dependent phosphorylation of acetyl-CoA carboxylase at Ser79. All treatments induced the appearance of multiple, phosphatase-sensitive, low-mobility forms of the AMPK α-subunit, consistent with phosphorylation at several sites other than Thr172. The flavonoid naringin, an effective antagonist of OA-induced autophagy suppression, inhibited the AMPK phosphorylation and mobility shifting induced by AICAR, OA or microcystin, but not the changes induced by calyculin A or cantharidin. AMPK may thus be activated both by a naringin-sensitive and a naringin-resistant mechanism, probably involving the PPs PP2A and PP1 respectively. Neither the Thr172-phosphorylating protein kinase LKB1 nor the Thr172-dephosphorylating PP, PP2C, were mobility-shifted after treatment with toxins or AICAR, whereas a slight mobility shifting of the regulatory AMPK β-subunit was indicated. Immunoblotting with a phosphospecific antibody against pSer108 at the β-subunit revealed a naringin-sensitive phosphorylation induced by OA, microcystin and AICAR and a naringin-resistant phosphorylation induced by calyculin A and cantharidin, suggesting that β-subunit phosphorylation could play a role in AMPK activation. Naringin antagonized the autophagy-suppressive effects of AICAR and OA, but not the autophagy suppression caused by cantharidin, consistent with AMPK-mediated inhibition of autophagy by toxins as well as by AICAR.
Compartmentalization of transport and phosphorylation of glucose in a hepatoma cell line
Authors: WHITESELL Richard R. , ARDEHALI Hossein , BEECHEM Joseph M. , POWERS Alvin C. , VAN DER MEER Wieb , PERRIOTT Laureta M. , GRANNER Daryl K.
Published: February 2005

The first steps of glucose metabolism are carried out by members of the families of GLUTs (glucose transporters) and HKs (hexokinases). Previous experiments using the inhibitor of glucose transport, CB (cytochalasin B), revealed that compartmentalization of GLUTs and HKs is a major factor in the control of glucose uptake in L6 myotubes [Whitesell, Ardehali, Printz, Beechem, Knobel, Piston, Granner, Van Der Meer, Perriott and May (2003) Biochem. J. 370, 47–56]. In the present paper, we evaluate compartmentalization of GLUTs and HKs in a hepatoma cell line, H4IIE, which is characterized by excess GLUT activity, HKI in a particulate and a cytosolic fraction, and insignificant G6Pase (glucose-6-phosphatase) activity. The measured activity of glucose transport exceeded the rate of phosphorylation approx. 30-fold. Treatment with 25 μM CB (Ki∼3 μM in H4IIE cells) paradoxically increased the excess of GLUTs over phosphorylation (GLUTs are inhibited 80%, while phosphorylation is inhibited 98%). The global relationships of the data could be reconciled most simply by a two-compartment model. In this model, phosphorylation of glucose is carried out by a subset of HK molecules supplied by a subset of GLUTs that are more sensitive to CB than the other GLUTs. The agent, DCC (dicyclohexylcarbodi-imide) caused HKI to translocate from the particulate compartment to the cytosolic compartment and potently inhibited glucose phosphorylation. The particulate compartment may represent the mitochondria, to which the more CB-sensitive GLUTs may control the transport of glucose.
Direct oxidation of polymeric substrates by multifunctional manganese peroxidase isoenzyme from Pleurotus ostreatus without redox mediators
Authors: KAMITSUJI Hisatoshi , WATANABE Takashi , HONDA Yoichi , KUWAHARA Masaaki
Published: February 2005

VPs (versatile peroxidases) sharing the functions of LiP (lignin peroxidase) and MnP (manganese peroxidase) have been described in basidiomycetous fungi Pleurotus and Bjerkandera. Despite the importance of this enzyme in polymer degradation, its reactivity with polymeric substrates remains poorly understood. In the present study, we first report that, unlike LiP, VP from Pleurotus ostreatus directly oxidized two polymeric substrates, bovine pancreatic RNase and Poly R-478, through a long-range electron pathway without redox mediators. P. ostreatus produces several MnP isoenzymes, including the multifunctional enzyme MnP2 (VP) and a typical MnP isoenzyme MnP3. MnP2 (VP) depolymerized a polymeric azo dye, Poly R-478, to complete its catalytic cycle. Reduction of the oxidized intermediates of MnP2 (VP) to its resting state was also observed for RNase. RNase inhibited the oxidation of VA (veratryl alcohol) in a competitive manner. Blocking of the exposed tryptophan by N-bromosuccinimide inhibited the oxidation of RNase and VA by MnP2 (VP), but its Mn2+-oxidizing activity was retained, suggesting that Trp-170 exposed on an enzyme surface is a substrate-binding site both for VA and the polymeric substrates. The direct oxidation of RNase and Poly R by MnP2 (VP) is in sharp contrast with redox mediator-dependent oxidation of these polymers by LiP from Phanerochaete chrysosporium. Molecular modelling of MnP2 (VP) revealed that the differences in the dependence on redox mediators in polymer oxidation by MnP2 (VP) and LiP were explained by the anionic microenvironment surrounding the exposed tryptophan.
Cephalopod vision involves dicarboxylic amino acids: D-aspartate, L-aspartate and L-glutamate
Authors: D'ANIELLO Salvatore , SPINELLI Patrizia , FERRANDINO Gabriele , PETERSON Kevin , TSESARSKIA Mara , FISHER George , D'ANIELLO Antimo
Published: February 2005

In the present study, we report the finding of high concentrations of D-Asp (D-aspartate) in the retina of the cephalopods Sepia officinalis, Loligo vulgaris and Octopus vulgaris. D-Asp increases in concentration in the retina and optic lobes as the animal develops. In neonatal S. officinalis, the concentration of D-Asp in the retina is 1.8±0.2 μmol/g of tissue, and in the optic lobes it is 5.5±0.4 μmol/g of tissue. In adult animals, D-Asp is found at a concentration of 3.5±0.4 μmol/g in retina and 16.2±1.5 μmol/g in optic lobes (1.9-fold increased in the retina, and 2.9-fold increased in the optic lobes). In the retina and optic lobes of S. officinalis, the concentration of D-Asp, L-Asp (L-aspartate) and L-Glu (L-glutamate) is significantly influenced by the light/dark environment. In adult animals left in the dark, these three amino acids fall significantly in concentration in both retina (approx. 25% less) and optic lobes (approx. 20% less) compared with the control animals (animals left in a diurnal/nocturnal physiological cycle). The reduction in concentration is in all cases statistically significant (P=0.01–0.05). Experiments conducted in S. officinalis by using D-[2,3-3H]Asp have shown that D-Asp is synthesized in the optic lobes and is then transported actively into the retina. D-aspartate racemase, an enzyme which converts L-Asp into D-Asp, is also present in these tissues, and it is significantly decreased in concentration in animals left for 5 days in the dark compared with control animals. Our hypothesis is that the dicarboxylic amino acids, D-Asp, L-Asp and L-Glu, play important roles in vision.
Kinetic investigation of human dipeptidyl peptidase II (DPPII)-mediated hydrolysis of dipeptide derivatives and its identification as quiescent cell proline dipeptidase (QPP)/dipeptidyl peptidase 7 (DPP7)
Authors: MAES Marie-Berthe , LAMBEIR Anne-Marie , GILANY Kambiz , SENTEN Kristel , VAN der VEKEN Pieter , LEITING Barbara , AUGUSTYNS Koen , SCHARPÉ Simon , DE MEESTER Ingrid
Published: February 2005

The presence of DPPII (dipeptidyl peptidase II; E.C. 3.4.14.2) has been demonstrated in various mammalian tissues. However, a profound molecular and catalytic characterization, including substrate selectivity, kinetics and pH-dependence, has not been conducted. In the present study, DPPII was purified from human seminal plasma to apparent homogeneity with a high yield (40%) purification scheme, including an inhibitor-based affinity chromatographic step. The inhibitor lysyl-piperidide (Ki~0.9 μM at pH 5.5) was chosen, as it provided a favourable affinity/recovery ratio. The human enzyme appeared as a 120 kDa homodimer. Mass spectrometric analysis after tryptic digestion together with a kinetic comparison indicate strongly its identity with QPP (quiescent cell proline dipeptidase), also called dipeptidyl peptidase 7. pH profiles of both kcat and kcat/Km clearly demonstrated that DPPII/QPP possesses an acidic and not a neutral optimum as was reported for QPP. Kinetic parameters of the human natural DPPII for dipeptide-derived chromogenic [pNA (p-nitroanilide)] and fluorogenic [4Me2NA (4-methoxy-2-naphthylamide)] substrates were determined under different assay conditions. DPPII preferred the chromogenic pNA-derived substrates over the fluorogenic 4Me2NA-derived substrates. Natural human DPPII showed high efficiency towards synthetic substrates containing proline at the P1 position and lysine at P2. The importance of the P1′ group for P2 and P1 selectivity was revealed, explaining many discrepancies in the literature. Furthermore, substrate preferences of human DPPII and dipeptidyl peptidase IV were compared based on their selectivity constants (kcat/Km). Lys-Pro-pNA (kcat/Km 4.1×106 s−1·M−1) and Ala-Pro-pNA (kcat/Km 2.6×106 s−1· M−1) were found to be the most sensitive chromogenic substrates for human DPPII, but were less selective than Lys-Ala-pNA (kcat/Km 0.4×106 s−1·M−1).
Essential role of ATF-1 in induction of NOX1, a catalytic subunit of NADPH oxidase: involvement of mitochondrial respiratory chain
Authors: KATSUYAMA Masato , FAN ChunYuan , ARAKAWA Noriaki , NISHINAKA Toru , MIYAGISHI Makoto , TAIRA Kazunari , YABE-NISHIMURA Chihiro
Published: February 2005

NADPH oxidase is the major source of superoxide production in cardiovascular tissues. We and others reported that PG (prostaglandin) F2α, PDGF (platelet-derived growth factor) and angiotensin II cause hypertrophy of vascular smooth muscle cells by induction of NOX1 (NADPH oxidase 1), a catalytic subunit of NADPH oxidase. We found DPI (diphenylene iodonium), an inhibitor of flavoproteins, including NADPH oxidase itself, almost completely suppressed induction of NOX1 mRNA by PGF2α or PDGF in a rat vascular smooth muscle cell line, A7r5. Exploration into the site of action of DPI using various inhibitors suggested the involvement of mitochondrial oxidative phosphorylation in PGF2α- or PDGF-induced increase in NOX1 mRNA. In a luciferase reporter assay, activation of the CRE (cAMP-response element)-dependent gene transcription by PGF2α was attenuated by oligomycin, an inhibitor of mitochondrial FoF1-ATPase. Oligomycin and other mitochondrial inhibitors also suppressed PGF2α-induced phosphorylation of ATF (activating transcription factor)-1, a transcription factor of the CREB (CRE-binding protein)/ATF family. Silencing of the ATF-1 gene by RNA interference significantly reduced the induction of NOX1 by PGF2α or PDGF, while overexpression of ATF-1 recovered NOX1 induction suppressed by oligomycin. Taken together, ATF-1 may play a pivotal role in the up-regulation of NOX1 in rat vascular smooth muscle cells.
Human xylosyltransferase I: functional and biochemical characterization of cysteine residues required for enzymic activity
Authors: MÜLLER Sandra , SCHÖTTLER Manuela , SCHÖN Sylvia , PRANTE Christian , BRINKMANN Thomas , KUHN Joachim , GÖTTING Christian , KLEESIEK Knut
Published: February 2005

XT-I (xylosyltransferase I) is the initial enzyme in the post-translational biosynthesis of glycosaminoglycan chains in proteoglycans. To gain insight into the structure–function relationship of the enzyme, a soluble active form of human XT-I was expressed in High Five insect cells with an apparent molecular mass of 90 kDa. Analysis of the electrophoretic mobility of the protein under non-reducing and reducing conditions indicated that soluble XT-I does not form homodimers through disulphide bridges. In addition, the role of the cysteine residues was investigated by site-directed mutagenesis combined with chemical modifications of XT-I by N-phenylmaleimide. Replacement of Cys471 or Cys574 with alanine led to a complete loss of catalytic activity, indicating the necessity of these residues for maintaining an active conformation of soluble recombinant XT-I by forming disulphide bonds. On the other hand, N-phenylmaleimide treatment showed no effect on wild-type XT-I but strongly inactivated the cysteine mutants in a dose-dependant manner, indicating that seven intramolecular disulphide bridges are formed in wild-type XT-I. The inhibitory effect of UDP on the XT-I activity of C561A (Cys561→Ala) mutant enzyme was significantly reduced compared with all other tested cysteine mutants. In addition, we tested for binding to UDP-agarose beads. The inactive mutants revealed no significantly different nucleotide-binding properties. Our study demonstrates that recombinant XT-I is organized as a monomer with no free thiol groups and strongly suggests that the catalytic activity does not depend on the presence of free thiol groups, furthermore, we identified five cysteine residues which are critical for enzyme activity.
Zebrafish (Danio rerio) matrilins: shared and divergent characteristics with their mammalian counterparts
Authors: KO Ya-Ping , KOBBE Birgit , PAULSSON Mats , WAGENER Raimund
Published: February 2005

We have cloned the cDNAs of the zebrafish (Danio rerio) members of the matrilin family of extracellular adaptor proteins. In contrast to mammals, no orthologue of matrilin-2 was found in zebrafish, either by RT (reverse-transcriptase) PCR using degenerated primers or by screeening the databases (Ensembl and NCBI); however, two forms of matrilin-3, matrilin-3a and -3b, were present. The identity with the mammalian matrilins is from more than 70% for the VWA (von Willebrand factor A)-like domains to only 28% for the coiled-coil domains of matrilin-3a and -3b. In all zebrafish matrilins we found a greater variety of splice variants than in mammals, with splicing mainly affecting the number of EGF (epidermal growth factor)-like repeats. The exon–intron organization is nearly identical with that of mammals, and also the characteristic AT–AC intron interrupting the exons coding for the coiled-coil domain is conserved. In the matrilin-3b gene a unique exon codes for a proline- and serine/threonine-rich domain, possibly having mucin-like properties. The matrilin-1 and -3a genes were mapped to chomosome 19 and 20 respectively by the radiation hybrid method. The temporal and spatial expression of zebrafish matrilins is similar to that seen in the mouse. Zebrafish matrilin-4 is highly expressed as early as 24 hpf (h post fertilization), whereas the other matrilins show peak expression at 72 hpf. By immunostaining of whole mounts and sections, we found that matrilin-1 and -3a show predominantly skeletal staining, whereas matrilin-4 is more widespread, with the protein also being present in loose connective tissues and epithelia.
Regulation of adenylate cyclase type VIII splice variants by acute and chronic Gi/o-coupled receptor activation
Authors: STEINER Debora , AVIDOR-REISS Tomer , SCHALLMACH Ester , BUTOVSKY Elena , LEV Nirit , VOGEL Zvi
Published: February 2005

We previously reported that acute agonist activation of Gi/o-coupled receptors inhibits adenylate cyclase (AC) type VIII activity, whereas agonist withdrawal following chronic activation of these receptors induces AC-VIII superactivation. Three splice variants of AC-VIII have been identified, which are called AC-VIII-A, -B and -C (with AC-VIII-B missing the glycosylation domain and AC-VIII-C lacking most of the C1b area). We report here that AC-VIII-A and -B, but not -C, are inhibited by acute μ-opioid and dopaminergic type D2 receptor activation, indicating that the C1b area of AC-VIII has an important role in AC inhibition by Gi/o-coupled receptor activation. On the other hand the glycosylation sites in AC-VIII did not play a role in AC-VIII regulation. Although AC-VIII-A and -C differed in their capacity to be inhibited by acute agonist exposure, agonist withdrawal after prolonged treatment led to a similar superactivation of all three splice variants, with no significant change in AC-VIII expression. AC-VIII superactivation was not affected by pre-incubation with a cell permeable cAMP analogue, indicating that the superactivation does not depend on the agonist-induced reduction in cAMP levels. The superactivated AC-VIII-A, -B and -C were similarly re-inhibited by re-application of agonist (morphine or quinpirole), returning the activity to control levels. These results demonstrate marked differences in the agonist inhibition of the AC-VIII splice variants before, but not after, superactivation.
Drosophila melanogaster NEP2 is a new soluble member of the neprilysin family of endopeptidases with implications for reproduction and renal function
Authors: THOMAS Josie E. , RYLETT Caroline M. , CARHAN Ahmet , BLAND Nicholas D. , BINGHAM Richard J. , SHIRRAS Alan D. , TURNER Anthony J. , ISAAC R. Elwyn
Published: February 2005

The mammalian neprilysin (NEP) family members are typically type II membrane endopeptidases responsible for the activation/inactivation of neuropeptides and peptide hormones. Differences in substrate specificity and subcellular localization of the seven mammalian NEPs contribute to their functional diversity. The sequencing of the Drosophila melanogaster genome has revealed a large expansion of this gene family, resulting in over 20 fly NEP-like genes, suggesting even greater diversity in structure and function than seen in mammals. We now report that one of these genes (Nep2) codes for a secreted endopeptidase with a highly restricted pattern of expression. D. melanogaster NEP2 is expressed in the specialized stellate cells of the renal tubules and in the cyst cells that surround the elongating spermatid bundles in adult testis, suggesting roles for the peptidase in renal function and in spermatogenesis. D. melanogaster NEP2 was found in vesicle-like structures in the syncytial cytoplasm of the spermatid bundles, suggesting that the protein was acquired by endocytosis of protein secreted from the cyst cells. Expression of NEP2 cDNA in D. melanogaster S2 cells confirmed that the peptidase is secreted and is only weakly inhibited by thiorphan, a potent inhibitor of human NEP. D. melanogaster NEP2 also differs from human NEP in the manner in which the peptidase cleaves the tachykinin, GPSGFYGVR-amide. Molecular modelling suggests that there are important structural differences between D. melanogaster NEP2 and human NEP in the S1′ and S2′ ligand-binding subsites, which might explain the observed differences in inhibitor and substrate specificities. A soluble isoform of a mouse NEP-like peptidase is strongly expressed in spermatids, suggesting an evolutionarily conserved role for a soluble endopeptidase in spermatogenesis.
Characterization of a new family of cyclin-dependent kinase activators
Authors: DINARINA Ana , PEREZ Laurent H. , DAVILA Amparo , SCHWAB Markus , HUNT Tim , NEBREDA Angel R.
Published: February 2005

Progression through the cell cycle is regulated by CDKs (cyclin-dependent kinases), which associate with activating partners, named cyclins, to efficiently phosphorylate substrates. We previously reported the identification of RINGO, a Xenopus protein that can activate CDK1 and CDK2 despite lack of sequence similarity to cyclins, which plays a role in the regulation of the meiotic cell cycle in oocytes. In the present study we report the characterization of four mammalian RINGO proteins, which are 53–68% identical with Xenopus RINGO in a central core of about 75 residues. We show that all RINGO family members can bind to and activate CDK1 and CDK2, albeit with different efficiencies, but they do not bind to CDK4 or CDK6. The core RINGO sequences are critical for CDK activation. We also identified key residues in CDK2 that are required for RINGO binding. All RINGO proteins can also bind the CDK inhibitor p27Kip1, but with an inverse efficiency of their ability to bind to CDK1. Our results identify a new family of mammalian proteins that can activate CDKs and therefore potentially function as cell cycle regulators. The ability of RINGO proteins to activate CDK1 and CDK2 suggest also cyclin-independent roles for these kinases.
Enhanced tunability and phase transition studies in compositionally varying lead magnesium niobate–lead titanate multilayered thin films
Authors: Ranjith R. , Laha Apurba , Krupanidhi S. B.
Published: February 2005

Multilayers of (1−x)Pb(Mg1∕3Nb2∕3)O3–xPbTiO3 thin films were prepared with a compositional variation of PbTiO3 on each layer across the film by pulsed laser ablation technique. The fabricated films were found to possess an enhanced diffusiveness in the dielectric phase transition, which actually seemed to be an envelope of the phase transition of the individual layer relaxor ferroelectrics of a particular composition. They also showed a very high nonlinear dielectric response and hence a high tunability about 70%, an increase of about 40% than that observed for single layer composition. This increase in tunability has been attributed to the lattice strain and the artificially enhanced chemical heterogeneity of the system. These multilayer films also showed a slim hysteresis loop characteristic with a saturation and remnant polarization of 20 and 6μC∕cm2, respectively.
Molecular wave packet interferometry and quantum entanglement
Authors: Martínez-Galicia Ricardo , Romero-Rochín Víctor
Published: February 2005

We study wave packet interferometry (WPI) considering the laser pulse fields both classical and quantum mechanically. WPI occurs in a molecule after subjecting it to the interaction with a sequence of phase-locked ultrashort laser pulses. Typically, the measured quantity is the fluorescence of the molecule from an excited electronic state. This signal has imprinted the interference of the vibrational wave packets prepared by the different laser pulses of the sequence. The consideration of the pulses as quantum entities in the analysis allows us to study the entanglement of the laser pulse states with the molecular states. With a simple model for the molecular system, plus several justified approximations, we solve for the fully quantum mechanical molecule-electromagnetic field state. We then study the reduced density matrices of the molecule and the laser pulses separately. We calculate measurable corrections to the case where the fields are treated classically.
Density functional theory based molecular-dynamics study of aqueous fluoride solvation
Authors: Heuft J. M. , Meijer E. J.
Published: February 2005

We use density functional theory based molecular-dynamics simulations to study the aqueous solvation of the fluoride anion. Our studies are focused on the first solvation shell and have resulted in detailed information on its structural and dynamical properties. The fluoride ion leads to the formation of a rigid solvation shell, qualitatively consistent with simulation and experimental studies, classifying fluoride as a “structure making” particle. However, quantitatively we find the solvation shell to be less structured and more mobile than predicted from empirical force-field simulation. The influence on the intramolecular electronical and structural properties of water is minimal, as observed for other halogens. We propose two distinct mechanisms for the exchange of bulk and first solvation shell water molecules.
Two-dimensional connective nanostructures of electrodeposited Zn on Au (111) induced by spinodal decomposition
Authors: Dogel J. , Tsekov R. , Freyland W.
Published: February 2005

Phase formation of surface alloying by spinodal decomposition has been studied at an electrified interface. For this aim Zn was electrodeposited on Au(111) from the ionic liquid AlCl3-MBIC (58:42) containing 1 mM Zn(II) at different potentials in the underpotential range corresponding to submonolayer up to monolayer coverage. Structure evolution was observed by in situ electrochemical scanning tunneling microscopy (STM) at different times after starting the deposition via potential jumps and at temperatures of 298 and 323 K. Spinodal or labyrinth two-dimensional structures predominate at middle coverage, both in deposition and in dissolution experiments. They are characterized by a length scale of typically 5 nm which has been determined from the power spectral density of STM images. Structure formation and surface alloying are governed by slow kinetics with a rate constant k with activation energy of 120 meV and preexponential factor of 0.17s−1. The evolution of the structural features is described by a continuum model and is found to be in good agreement with the STM observations. From the experimental and model calculation results we conclude that the two-dimensional phase formation in the Zn on Au(111) system is dominated by surface alloying. The phase separation of a Zn-rich and a Zn-Au alloy phase is governed by two-dimensional spinodal decomposition.
Water adsorption in disordered mesoporous silica (Vycor) at 300K and 650K: A Grand Canonical Monte Carlo simulation study of hysteresis
Authors: Puibasset Joël , Pellenq Roland J.-M.
Published: February 2005

This numerical simulation paper focuses on the adsorption/desorption of water in disordered mesoporous silica glasses (Vycor-like). The numerical adsorbent was previously obtained by off lattice method, and was shown to reproduce quite well the micro- and mesotextural properties of real Vycor, as well as morphological (pore size distribution) and topological (pore interconnections) disorder. The water-water interactions are described by the SPC model while water-silica interactions are calculated in the framework of the PN-TrAZ model. The water adsorption/desorption isotherms and the configurational energies are calculated by the Grand Canonical Monte Carlo simulation method. The low pressure results compare well with experiments, showing the good transferability of the intermolecular potential. It is shown that if the hysteresis loop observed in the adsorption/desorption isotherm is considered as a true phase transition (which is actually still an open question in the case of disordered porous materials), then it is possible to calculate the grand potential by applying the thermodynamic integration scheme. The grand potential is shown to be multivalued for low (subcritical) temperature, and continuous for high (supercritical) temperature. A coexistence point is found within the hysteresis loop, actually close to the vertical desorption line. Below the equilibrium chemical potential, the gaslike branch is stable whereas the liquidlike branch is metastable. The situation is reversed above the coexistence point.
Dynamics and scaling of polymers in a dilute solution:  Analytical treatment in two and higher dimensions
Authors: Punkkinen O. , Falck E. , Vattulainen I. , Ala-Nissila T.
Published: February 2005

We consider the dynamical scaling of a single polymer chain in good solvent. In the case of two-dimensional systems, Shannon and Choy [Phys. Rev. Lett. 79, 1455 (1997)] have suggested that the dynamical scaling for a dilute polymer solution breaks down. Using scaling arguments and analytical calculations based on the Zimm model, we show that the dynamical scaling of a dilute two-dimensional polymer system holds when the relevant dynamical quantities are properly extracted from finite systems. Most important, the polymer diffusion coefficient in two dimensions scales logarithmically with system size, in excellent agreement with our extensive computer simulations. This scaling is the reason for the failure of the previous attempts to resolve the dynamical scaling of dilute two-dimensional polymer systems. In three and higher dimensions our analytic calculations are in agreement with previous results in the literature.
Mixed quantum-classical equilibrium
Authors: Parandekar Priya V. , Tully John C.
Published: February 2005

We present an analysis of the equilibrium limits of the two most widely used approaches for simulating the dynamics of molecular systems that combine both quantum and classical degrees of freedom. For a two-level quantum system connected to an infinite number of classical particles, we derive a simple analytical expression for the equilibrium mean energy attained by the self-consistent-field (Ehrenfest) method and show that it deviates substantially from Boltzmann. By contrast, “fewest switches” surface hopping achieves Boltzmann quantum state populations. We verify these analytical results with simulations.
Dynamics of coupled Bohmian and phase-space variables: A moment approach to mixed quantum-classical dynamics
Authors: Burghardt Irene
Published: February 2005

The theoretical framework of the mixed quantum-classical description given by Burghardt and Parlant [J. Chem. Phys. 120, 3055 (2004)] is detailed. A representation in terms of partial hydrodynamic moments is developed, the dynamics of which is determined by a hierarchy of equations derived from the quantum Liouville equation. Exact equations of motion are obtained, whose quantum-classical approximants are associated with a fluid-dynamical trajectory representation which couples classical variables to quantum hydrodynamic variables. The latter evolve under a generalized hydrodynamic force which also depends upon the classical phase-space variables. The hydrodynamic moment description is shown to be closely connected to mixed quantum-classical phase-space methods.
Inverted deposition and high-velocity spinning to develop buried planar chalcogenide glass waveguides for highly nonlinear integrated optics
Authors: Mairaj A. K. , Curry R. J. , Hewak D. W.
Published: February 2005

We report on buried planar waveguides in a highly nonlinear infrared transmitting chalcogenide glass, fabricated using a combination of inverted deposition of the molten glass phase and high-velocity spinning. Films of gallium lanthanum sulphide (Ga:La:S) glass were deposited onto an expansion coefficient matched Ga:La:S cladding substrate. These amorphous films, with an optimized composition designed to be resistant against crystallization, were observed to have an excellent interface quality and uniformity. The designed planar chip had a buried core, 6μm thick in the vertical direction, in single-mode operation at 1.064μm and a measured propagation loss of <0.2dBcm−1. Through this technique waveguides from Ga:La:S glass, a highly versatile optical semiconductor material, can potentially be used in nonlinear applications as well as provide passive and active integrated optic functionality into the infrared beyond 5μm.
Diffusion coefficient of ionic solvation shell molecules
Authors: Masia Marco , Rey Rossend
Published: February 2005

It is shown that, for a tightly bound ion-solvation shell complex, the mean square displacement for solvation molecules is characterized by a long lasting transitory. This initial portion is related to the rotational relaxation of the complex and can reach up to several hundred picoseconds for a representative example such as the Mg2+ ion in water. As the diffusion coefficient is usually fitted using much shorter time spans, unnoticed overestimations are possible. It is argued that, instead of computing the aforementioned diffusion coefficient from the mean square displacement, it should be defined taking as a basic guideline the ratio between the rotational relaxation time of the complex and the lifetime within the first solvation shell.
Film cooling effectiveness on a large angle blunt cone flying at hypersonic speed
Authors: Sahoo Niranjan , Kulkarni Vinayak , Saravanan S. , Jagadeesh G. , Reddy K. P. J.
Published: February 2005

Effectiveness of film cooling technique to reduce convective heating rates for a large angle blunt cone flying at hypersonic Mach number and its effect on the aerodynamic characteristics is investigated experimentally by measuring surface heat-transfer rates and aerodynamic drag coefficient simultaneously. The test model is a 60° apex-angle blunt cone with an internally mounted accelerometer balance system for measuring aerodynamic drag and an array of surface mounted platinum thin film gauges for measuring heat-transfer rates. The coolant gas (air, carbon dioxide, and/or helium) is injected into the hypersonic flow at the nose of the test model. The experiments are performed at a flow free stream Mach number of 5.75 and 0° angle of attack for stagnation enthalpies of 1.16MJ∕kg and 1.6MJ∕kg with and without gas injection. About 30%–45% overall reduction in heat-transfer rates is observed with helium as coolant gas except at stagnation regions. With all other coolants, the reduction in surface heat-transfer rate is between 10%–25%. The aerodynamic drag coefficient is found to increase by 12% with helium injection whereas with other gases this increase is about 27%.