bluuebunny/crossref_metadata_2025 huggingface dataset:
Scaling analysis of single‐plume convection from a hydrothermal source
Authors: Soler Marianna , Serra Teresa , Colomer Jordi
Published: May 2008

The characteristics of a convective single plume developing from a hydrothermal lake source of radius R have been investigated. The study was motivated by the aim of estimating velocity and buoyancy scaling laws obtained from numerical models of convection from isolated sources of finite extent. This has been done for the case R/H < 0.7, where H is the water column depth, and for the case of baroclinically stable convection. The single plume described hereafter presents the following characteristics: 0.35 < R/H < 0.64, RD/R > 25.8, where RD is the Rossby radius of deformation. From the results, the density anomaly scales with the buoyancy flux Bo applied over the source and the depth according to g′ = (3.81 ± 0.06) Bo2/3/H1/3, and a single vortex is maintained around the forcing disk with a mean radial velocity scaling according to Ur = (1.57 ± 0.43) Bo1/3R/H2/3. The experimental results described here will be compared to the results found for the numerical model by Okada et al. (2004).
Long‐term remote sensing database, Walnut Gulch Experimental Watershed, Arizona, United States
Authors: Moran M. S. , Holifield Collins C. D. , Goodrich D. C. , Qi J. , Shannon D. T. , Olsson A.
Published: May 2008

The USDA Agricultural Research Service, Southwest Watershed Research Center, Walnut Gulch Experimental Watershed (WGEW), is located in the San Pedro Valley of southeastern Arizona. It is one of the most highly instrumented semiarid experimental watersheds in the world and has one of the largest published collections of spectral imagery with coordinated ground observations. The WGEW Image and Ground Data Archive produced in 2006 (WIDGA06) is a collection of images from satellite‐ and aircraft‐based sensors dating back to 1990 with ancillary ground‐based measurements archived with each image. This report provides background information on the collection and archiving of this data set and contact information for obtaining copies of the image and data files. Many images are available in the University of Arizona, Arizona Regional Image Archive (ARIA) (http://aria.arizona.edu). Metadata are available via the U.S. Department of Agriculture, Agricultural Research Service, Southwest Watershed Research Center (SWRC) (http://www.tucson.ars.ag.gov/dap/).
Multispacecraft observation of electron beam in reconnection region
Authors: Åsnes A. , Taylor M. G. G. T. , Borg A. L. , Lavraud B. , Friedel R. W. H. , Escoubet C. P. , Laakso H. , Daly P. , Fazakerley A. N.
Published: May 2008

On the 18th of August 2002, during a crossing of the near‐Earth plasma sheet Cluster observed an ion flow burst, caused by a near‐Earth reconnection event. Cluster observed a tailward bulk flow which reverse to earthward flow, indicating a close passage of the diffusion region. We show that reversals in BZ and BY are consistent with reconnection. During the event, a short duration burst of electrons in the range of a few keV up to more than 100 keV are observed streaming away from the reconnection region. The accelerated electrons were aligned with the magnetic field, streaming tailward, and were observed simultaneously by all four spacecraft located on both the northern and southern side of the current sheet. The four Cluster spacecraft, separated by ∼3700 km, observe the electrons for a time period of ∼60 s, indicating the burst to be a temporal rather than localized feature. A second burst of tailward accelerated electrons observed for ∼40 s was observed by Cluster 1 and 2 upon entering the earthward outflow region. The second beam thus appear to be directed toward the X‐line. The flux levels of the energetic electron bursts exceed those of the ambient plasma sheet by a factor 2–4. In general, the highest energetic electron fluxes during this event were observed in the earthward outflow region. Observations indicate that reconnection operates on closed plasma sheet field lines in this event and does not reach lobe field lines.
Statistical morphology of ENA emissions at Saturn
Authors: Carbary J. F. , Mitchell D. G. , Brandt P. , Roelof E. C. , Krimigis S. M.
Published: May 2008

The Magnetospheric Imaging Instrument (MIMI) on the Cassini spacecraft is providing the first energetic neutral particle (ENA) measurements in the magnetosphere of Saturn. Advantageous spacecraft orbits during the first 120 days of 2007 allowed ENA observations to be mapped to the equatorial plane of the planet and surveyed as a statistical ensemble in a Sun‐synchronous coordinate system. When projected onto the equatorial plane, emissions from both energetic hydrogen atoms (20–50 keV) and energetic oxygen atoms (64–144 keV) form toroidal distributions nearly concentric with the planet. The hydrogen torus is continuous in local time, but the oxygen torus has a gap from dawn to noon. When fitted to circles, the H torus has a mean radius of 11.0 ± 0.5 RS, while the O torus has a mean radius of 7.9 ± 0.8 RS (1 RS = 60268 km). Both tori display peaks at just before midnight at local times of 23.6 h (H) and 21.8 h (O). These maxima seem to be regular features over the 120‐day interval surveyed, suggesting the hot spot may be caused by injection of particles from Saturn's magnetotail, as would be the case during substorms. However, the persistence of the ENA emissions suggests they are continuously driven by processes internal to Saturn's magnetosphere. When mapped along magnetic field lines to Saturn's ionosphere, both H and O emissions appear equatorward of the aurora and are distinct from it.
Ion heat flux and energy transport near the magnetotail neutral sheet
Authors: Kaufmann Richard L. , Paterson William R.
Published: May 2008

Ten‐year averages of energy transport rates near the neutral sheet showed that the enthalpy flux density or thermal energy term QT = (5/2)PV was the largest, where P is the isotropic pressure and V is the bulk flow velocity. The ion heat flux, qi, was the next largest term. Sorting data using a magnetic flux transport parameter showed that qi could become dominant during periods of slow flow. Both qi and the ion bulk velocity Vi were duskward on the dusk side of the neutral sheet. This relationship is characteristic of cross‐tail drift and a heat flux that can be attributed to the energy dependent gradient and curvature drifts. The qi and Vi vectors often pointed in different directions on the dawn side. The x component of qi on the dawn side pointed tailward, suggesting entry through the magnetopause of a suprathermal ion component. On the dusk side the qix plots that were sorted using a magnetic flux transport parameter showed evidence of plasma sheet reconnection. The long‐term averaged x component of QT pointed earthward almost everywhere in the neutral sheet, and was attributed to periods of very fast plasma flow. The cross‐tail component of QT was separated into two contributions. One part of QTy involved a common drift away from midnight during both earthward and tailward fast flows. This feature suggests that thermal energy and plasma flow from the outer plasma sheet toward the neutral sheet near midnight, and then toward the flanks. The other part of QTy involved a differential duskward drift during fast earthward flows and a dawnward drift during fast tailward flows. The incremental E fields that would produce such convection point tailward during the fastest earthward flows and earthward during the fastest tailward flows. The dependencies of Vi, qi and QT on the interplanetary magnetic field (IMF) clock angle also were studied. Both Vi and QT were reduced when the IMF was northward and the neutral sheet plasma became cold and dense. However, no dependence of qi on the IMF direction was seen. This shows that the generation of a cold dense plasma sheet does not substantially change the distribution of the suprathermal ions that are most important in the production of qi.
Observations of Kuroshio flow variations in the East China Sea
Authors: Andres M. , Wimbush M. , Park J.‐H. , Chang K.‐I. , Lim B.‐H. , Watts D. R. , Ichikawa H. , Teague W. J.
Published: May 2008

Kuroshio velocity structure and transport in the East China Sea (ECS) were investigated as part of a 23‐month study using inverted echo sounders and acoustic Doppler current profilers (ADCPs) along the regularly sampled PN‐line. Flow toward the northeast is concentrated near the continental shelf with the mean surface velocity maximum located 30 km offshore from the shelf break (taken as the 170 m isobath). There are two regions of southwestward flow: a deep countercurrent over the continental slope beneath the Kuroshio axis and a recirculation offshore which extends throughout the whole water column. There is a bimodal distribution to the depth of maximum velocity with occurrence peaks at the surface and 210 dbar. When the maximum velocity is located within the top 80 m of the water column, it ranges between 0.36 m/s and 2.02 m/s; when the maximum velocity is deeper than 80 m, it ranges between 0.31 m/s and 1.11 m/s. The 13‐month mean net absolute transport of the Kuroshio in the ECS is 18.5 ± 0.8 Sv (standard deviation, σ = 4.0 Sv). The mean positive and negative portions of this net flow are 24.0 ± 0.9 Sv and −5.4 ± 0.3 Sv, respectively.
Assessment of three dynamical climate downscaling methods using the Weather Research and Forecasting (WRF) model
Authors: Lo Jeff Chun‐Fung , Yang Zong‐Liang , Pielke Roger A.
Published: May 2008

The common methodology in dynamical regional climate downscaling employs a continuous integration of a limited‐area model with a single initialization of the atmospheric fields and frequent updates of lateral boundary conditions based on general circulation model outputs or reanalysis data sets. This study suggests alternative methods that can be more skillful than the traditional one in obtaining high‐resolution climate information. We use the Weather Research and Forecasting (WRF) model with a grid spacing at 36 km over the conterminous U.S. to dynamically downscale the 1‐degree NCEP Global Final Analysis (FNL). We perform three types of experiments for the entire year of 2000: (1) continuous integrations with a single initialization as usually done, (2) consecutive integrations with frequent re‐initializations, and (3) as (1) but with a 3‐D nudging being applied. The simulations are evaluated in a high temporal scale (6‐hourly) by comparison with the 32‐km NCEP North American Regional Reanalysis (NARR). Compared to NARR, the downscaling simulation using the 3‐D nudging shows the highest skill, and the continuous run produces the lowest skill. While the re‐initialization runs give an intermediate skill, a run with a more frequent (e.g., weekly) re‐initialization outperforms that with the less frequent re‐initialization (e.g., monthly). Dynamical downscaling outperforms bi‐linear interpolation, especially for meteorological fields near the surface over the mountainous regions. The 3‐D nudging generates realistic regional‐scale patterns that are not resolved by simply updating the lateral boundary conditions as done traditionally, therefore significantly improving the accuracy of generating regional climate information.
Spectrally resolved fluxes derived from collocated AIRS and CERES measurements and their application in model evaluation: Clear sky over the tropical oceans
Authors: Huang Xianglei , Yang Wenze , Loeb Norman G. , Ramaswamy V.
Published: May 2008

Spectrally resolved outgoing thermal‐IR flux, the integrand of the outgoing longwave radiation (OLR), has a unique value in evaluating model simulations. Here we describe an algorithm for deriving such clear‐sky outgoing spectral flux through the entire thermal‐IR spectrum from the collocated Atmospheric Infrared Sounder (AIRS) and the Clouds and the Earth's Radiant Energy System (CERES) measurements over the tropical oceans. On the basis of the predefined scene types in the CERES Single Satellite Footprint (SSF) data set, spectrally dependent ADMs are developed and used to estimate the spectral flux each AIRS channel. A multivariate linear prediction scheme is then used to estimate spectral fluxes at frequencies not covered by the AIRS instrument. The whole algorithm is validated using synthetic spectra as well as the CERES OLR measurements. Using the GFDL AM2 model simulation as a case study, applications of the derived clear‐sky outgoing spectral fluxes in model evaluation are illustrated. By comparing the observed spectral fluxes and simulated ones for the year of 2004, compensating errors in the simulated OLR from different absorption bands are revealed, along with the errors from frequencies within a given absorption band. Discrepancies between the simulated and observed spatial distributions and seasonal evolutions of the spectral fluxes are further discussed. The methodology described in this study can be applied to other surface types as well as cloudy‐sky observations and also to corresponding model evaluations.
A self‐replication model for long channelized lava flows on the Mars plains
Authors: Baloga S. M. , Glaze L. S.
Published: May 2008

A model is presented for channelized lava flows emplaced by a self‐replicating, levee‐building process over long distances on the plains of Mars. Such flows may exhibit morphologic evidence of stagnation, overspills, and upstream breakouts. However, these processes do not inhibit the formation and persistence of a prominent central channel that can often be traced for more than 100 km. The two central assumptions of the self‐replication model are (1) the flow advances at the average upstream velocity of the molten core and (2) the fraction of the lava that travels faster than the average upstream velocity forms stationary margins in the advancing distal zone to preserve the self‐replication process. For an exemplary 300 km long flow north of Pavonis Mons, the model indicates that ∼8 m of crust must have formed during emplacement, as determined from the channel and levee dimensions. When combined with independent thermal dynamic estimates for the crustal growth rate, relatively narrow constraints are obtained for the flow rate (2250 m3 s−1), emplacement duration (600 d), and the lava viscosity of the molten interior (106 Pa s). Minor, transient overspills and breakouts increase the emplacement time by only a factor of 2. The primary difference between the prodigious channelized Martian flows and their smaller terrestrial counterparts is that high volumetric flow rates must have persisted for many hundreds of days on Mars, in contrast to a few hours or days on Earth.
Mineralization of ancient carbon in the subsurface of riparian forests
Authors: Gurwick Noel P. , McCorkle Daniel M. , Groffman Peter M. , Gold Arthur J. , Kellogg D. Q. , Seitz‐Rundlett Peter
Published: May 2008

Microbial activity in saturated, subsurface sediments in riparian forests may be supported by recent photosynthate or ancient (>500 ybp) soil organic carbon (SOC) in buried horizons. Metabolism of ancient SOC may be particularly important in riparian zones, considered denitrification hot spots, because denitrification in the riparian subsurface is often C‐limited, because buried horizons intersect deep flow paths, and because low C mineralization rates can support ecosystem‐relevant rates of denitrification. Buried horizons are common where alluvial processes (stream migration, overbank flow) have dominated riparian evolution. Our objectives were to determine: (1) the extent to which ancient SOC directly supports subsurface microbial activity; (2) whether different C sources support microbial activity in alluvial versus glaciofluvial riparian zones; and (3) how microbial use of ancient SOC varies with depth. In situ groundwater incubations and 14C dating of dissolved inorganic carbon revealed that ancient SOC mineralization was common, and that it constituted 31–100% of C mineralization 2.6 m deep at one site, at rates sufficient to influence landscape N budgets. Our data failed to reveal consistent spatial patterns of microbially available ancient C. Although mineralized C age increased with depth at one alluvial site, we observed ancient C metabolism 150 cm deep at a glaciofluvial site, suggesting that subsurface microbial activity in riparian zones does not vary systematically between alluvial and glaciofluvial hydrogeologic settings. These findings underscore the relevance of ancient C to contemporary ecosystem processes and the challenge of using mappable surface features to identify subsurface ecosystem characteristics or riparian zone N‐sink strength.
Program Studies the Kuroshio Extension
Authors: Donohue Kathleen , Watts D. Randolph , Tracey Karen , Wimbush Mark , Park Jae‐Hun , Bond Nicholas , Cronin Meghan , Chen Shuiming , Qiu Bo , Hacker Peter , Hogg Nelson , Jayne Steven , McClean Julie , Rainville Luc , Mitsudera Humio , Tanimoto Youichi , Xie Shang‐Ping
Published: May 2008

The Kuroshio Extension system links to North Pacific climate through its role in subtropical‐subpolar exchange, the formation and distribution of mode waters, and the intensification of the extratropical storm track across the North Pacific. The Kuroshio Extension System Study (KESS) offers a window into these processes through integrated measurements of the ocean and atmosphere and through modeling efforts (Figure 1).

The northward flowing waters of the Kuroshio western boundary current leave the Japanese coast to flow eastward as a free jet—the Kuroshio Extension. The Extension forms a vigorously meandering boundary between the warm subtropical and cold northern waters.
Geodetic Observations Help Scientists Understand Geohazards and Mitigate Disasters: The GGOS Contribution to GEOSS and an Observing System for Geohazards and Disaster Prevention; Frascati, Italy, 5–6 October 2007
Authors: Plag Hans‐Peter , Zerbini Susanna
Published: May 2008

Modern space‐geodetic observations have revolutionized our understanding of geohazards, and these observations have a great potential for further scientific discovery and applications, including early warning.

To discuss this, about 50 scientists from the geodetic and geohazards communities took part in a workshop organized by the Global Geodetic Observing System (GGOS) of the International Association of Geodesy (IAG) as a contribution to the intergovernmental Group on Earth Observations (GEO). Highest‐level representatives of space agencies (European Space Agency, NASA, and Agenzia Spaziale Italiana) emphasized the fundamental importance of the geodetic reference frames for satellite missions and Earth observation. Although high, the present accuracy of these reference frames still is a key limitation in quantifying global change processes such as changes in ice sheets and sea level. Improvements of the reference frame are a pivotal step toward a better understanding of these processes and their impact on society. The representative of GEO identified GGOS as a core element in the Global Earth Observation System of Systems (GEOSS), which aims to integrate Earth observations in order to better serve users in a number of societal benefit areas, including disasters.
South American Dust and Its Role in Past and Present Climate: Multidisciplinary Workshop on Southern South American Dust; Puerto Madryn, Argentina, 3–5 October 2007
Authors: Gassó Santiago , Gaiero Diego , Koren Ilan , Del Valle Héctor F.
Published: May 2008

Recent studies have emphasized the impact of dust emissions from southern South American (SSA) deserts (in particular the Patagonian desert) on past and present climate, as well as possible links to marine biology and carbon uptake in the high‐latitude southern oceans. However, understanding is hindered by the lack of observations about dust activity, its composition, and its long‐range transport. Although model simulations are in general agreement with the limited observations of Southern Hemisphere dust aerosols, many of the modeling efforts addressing aerosol transport and ocean biogeochemistry in the Southern Ocean rely on measurements and parameterizations from Northern Hemisphere locations.
Organizations Urge Caution on Ocean Fertilization Experiments
Authors: Urban Ed , Haag Fredrik
Published: May 2008

The idea of stimulating ocean primary production to draw down atmospheric carbon dioxide and/or enhance production at higher trophic levels is not new. However, recent proposals to fertilize the ocean with iron or urea as part of commercial carbon sequestration and/or food production schemes have stimulated the ocean science community to publish papers and other statements documenting the community's views on this topic [see Buesseler et al., 2008; Glibert et al., 2008]. While some are upbeat that commercial carbon sequestration through stimulating ocean primary production will help offset fossil fuel emissions, others worry that fertilizing the ocean will not result in the hoped for sequestration and/or will have significant adverse environmental consequences.
Dynamics of late autumn rainfall reduction over southeastern Australia
Authors: Cai Wenju , Cowan Tim
Published: May 2008

During 1950–2006, austral autumn rainfall over the south‐eastern Australian state of Victoria decreased by about 40% from its long‐term seasonal average. The dynamics of this decline are not understood. We show that the reduction predominantly occurs in May, with variations of rainfall linked to two sources of sea surface temperature (SST) variability. A higher SST in the Indonesian Throughflow region, which occurs as the Indo‐Pacific system enters into La Niña‐like conditions, is associated with a rainfall increase over northern Victoria. An SST variability pattern with a positive anomaly in the central southern Indian Ocean (IO) and a negative anomaly in the subtropical IO are linked to atmospheric wave‐trains, with a low pressure center over Victoria, is conducive to a rainfall increase. The weakening of the wave‐trains since 1950, and an increase (reduction) in El Niño (La Niña) events, contribute to the rainfall decline. Possible influences from climate change forcing are discussed.
The histamine H3receptor: an attractive target for the treatment of cognitive disorders
Authors: Esbenshade T A , Browman K E , Bitner R S , Strakhova M , Cowart M D , Brioni J D
Published: May 2008

The histamine H3receptor, first described in 1983 as a histamine autoreceptor and later shown to also function as a heteroreceptor that regulates the release of other neurotransmitters, has been the focus of research by numerous laboratories as it represents an attractive drug target for a number of indications including cognition. The purpose of this review is to acquaint the reader with the current understanding of H3receptor localization and function as a modulator of neurotransmitter release and its effects on cognitive processes, as well as to provide an update on selected H3antagonists in various states of preclinical and clinical advancement. Blockade of centrally localized H3receptors by selective H3receptor antagonists has been shown to enhance the release of neurotransmitters such as histamine, ACh, dopamine and norepinephrine, among others, which play important roles in cognitive processes. The cognitive‐enhancing effects of H3antagonists across multiple cognitive domains in a wide number of preclinical cognition models also bolster confidence in this therapeutic approach for the treatment of attention deficit hyperactivity disorder, Alzheimer's disease and schizophrenia. However, although a number of clinical studies examining the efficacy of H3receptor antagonists for a variety of cognitive disorders are currently underway, no clinical proof of concept for an H3receptor antagonist has been reported to date. The discovery of effective H3antagonists as therapeutic agents for the novel treatment of cognitive disorders will only be accomplished through continued research efforts that further our insights into the functions of the H3receptor.

British Journal of Pharmacology(2008)154, 1166–1181; doi:10.1038/bjp.2008.147; published online 12 May 2008
The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection
Authors: Hersleth Hans-Petter , Hsiao Ya-Wen , Ryde Ulf , Görbitz Carl Henrik , Andersson K. Kristoffer
Published: May 2008

Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallographic data collection. We have generated and solved the 1.30 Å (1 Å=0.1 nm) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe–O distance of 1.8 Å and O–O bond of 1.3 Å in accordance with a FeII–O–O− (or FeIII–O–O2−) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metalloproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O–O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.
Trafficking properties and activity regulation of the neuronal glycine transporter GLYT2 by protein kinase C
Authors: Fornés Amparo , Núñez Enrique , Alonso-Torres Pablo , Aragón Carmen , López-Corcuera Beatriz
Published: May 2008

The neuronal glycine transporter GLYT2 controls the availability of the neurotransmitter in glycinergic synapses, and the modulation of its function may influence synaptic transmission. The active transporter is located in membrane rafts and reaches the cell surface through intracellular trafficking. In the present study we prove that GLYT2 constitutively recycles between the cell interior and the plasma membrane by means of a monensin-sensitive trafficking pathway. Also, a regulated trafficking can be triggered by PMA. We demonstrate that PMA inhibits GLYT2 transport by causing net accumulation of the protein in internal compartments through an increase of the internalization rate. In addition, a small increase of plasma membrane delivery and a redistribution of the transporter to non-raft domains is triggered by PMA. A previously identified phorbol-ester-resistant mutant (K422E) displaying an acidic substitution in a regulatory site, exhibits constitutive traffic but, in contrast with the wild-type, fails to show glycine uptake inhibition, membrane raft redistribution and trafficking modulation by PMA. We prove that the action of PMA on GLYT2 involves PKC (protein kinase C)-dependent and -independent pathways, although an important fraction of the effects are PKC-mediated. We show the additional participation of signalling pathways triggered by the small GTPase Rac1 on PMA action. GLYT2 inhibition by PMA and monensin also take place in brainstem primary neurons and synaptosomes, pointing to a GLYT2 trafficking regulation in the central nervous system.
The zinc-binding motif of human RECQ5β suppresses the intrinsic strand-annealing activity of its DExH helicase domain and is essential for the helicase activity of the enzyme
Authors: Ren Hua , Dou Shuo-Xing , Zhang Xing-Dong , Wang Peng-Ye , Kanagaraj Radhakrishnan , Liu Jie-lin , Janscak Pavel , Hu Jin-Shan , Xi Xu Guang
Published: May 2008

RecQ family helicases, functioning as caretakers of genomic integrity, contain a zinc-binding motif which is highly conserved among these helicases, but does not have a substantial structural similarity with any other known zinc-finger folds. In the present study, we show that a truncated variant of the human RECQ5β helicase comprised of the conserved helicase domain only, a splice variant named RECQ5α, possesses neither ATPase nor DNA-unwinding activities, but surprisingly displays a strong strand-annealing activity. In contrast, fragments of RECQ5β including the intact zinc-binding motif, which is located immediately downstream of the helicase domain, exhibit much reduced strand-annealing activity but are proficient in DNA unwinding. Quantitative measurements indicate that the regulatory role of the zinc-binding motif is achieved by enhancing the DNA-binding affinity of the enzyme. The novel intramolecular modulation of RECQ5β catalytic activity mediated by the zinc-binding motif may represent a universal regulation mode for all RecQ family helicases.
Cathepsin L expression is up-regulated by hypoxia in human melanoma cells: role of its 5′-untranslated region
Authors: Jean Didier , Rousselet Nathalie , Frade Raymond
Published: May 2008

Overexpression of cathepsin L, a cysteine protease, and consequently procathepsin L secretion switch the phenotype of human melanoma cells to highly tumorigenic and strongly metastatic. This led us to identify the DNA regulatory sequences involved in the regulation of cathepsin L expression in highly metastatic human melanoma cells. The results of the present study demonstrated the presence of regulatory sequences in the 3′ region downstream of the cathepsin L gene and in the 3′- and 5′-flanking regions of GC/CCAAT sites of its promoter. In addition, we established that the 5′-UTR (untranslated region) was the most important region for cathepsin L expression. This 5′-UTR integrated an alternative promoter and sequences involved in post-transcriptional regulation. Transfection experiments of bicistronic reporter vectors and RNAs demonstrated that the cathepsin L 5′-UTR contained a functional IRES (internal ribosome entry site). This complete IRES was present only in one of the three splice variants, which differed in their 5′-UTR. Then, we analysed cathepsin L expression in this human melanoma cell line grown under hypoxia. We demonstrated that under moderate hypoxic conditions (1% O2) intracellular expression of cathepsin L was up-regulated. Hypoxia significantly increased only the expression of the transcript which contains the complete IRES, but inhibited promoter activity. These results suggest that the presence of an IRES allowed cathepsin L mRNA translation to be efficient under hypoxic conditions. Altogether, our results indicated that in vivo a tumour hypoxic environment up-regulates cathepsin L expression which promotes tumour progression.
Alternative metabolic fates of phosphatidylinositol produced by phosphatidylinositol synthase isoforms in Arabidopsis thaliana
Authors: Löfke Christian , Ischebeck Till , König Sabine , Freitag Sabine , Heilmann Ingo
Published: May 2008

PtdIns is an important precursor for inositol-containing lipids, including polyphosphoinositides, which have multiple essential functions in eukaryotic cells. It was previously proposed that different regulatory functions of inositol-containing lipids may be performed by independent lipid pools; however, it remains unclear how such subcellular pools are established and maintained. In the present paper, a previously uncharacterized Arabidopsis gene product with similarity to the known Arabidopsis PIS (PtdIns synthase), PIS1, is shown to be an active enzyme, PIS2, capable of producing PtdIns in vitro. PIS1 and PIS2 diverged slightly in substrate preferences for CDP-DAG [cytidinediphospho-DAG (diacylglycerol)] species differing in fatty acid composition, PIS2 preferring unsaturated substrates in vitro. Transient expression of fluorescently tagged PIS1 or PIS2 in onion epidermal cells indicates localization of both enzymes in the ER (endoplasmic reticulum) and, possibly, Golgi, as was reported previously for fungal and mammalian homologues. Constitutive ectopic overexpression of PIS1 or PIS2 in Arabidopsis plants resulted in elevated levels of PtdIns in leaves. PIS2-overexpressors additionally exhibited significantly elevated levels of PtdIns(4)P and PtdIns(4,5)P2, whereas polyphosphoinositides were not elevated in plants overexpressing PIS1. In contrast, PIS1-overexpressors contained significantly elevated levels of DAG and PtdEtn (phosphatidylethanolamine), an effect not observed in plants overexpressing PIS2. Biochemical analysis of transgenic plants with regards to fatty acids associated with relevant lipids indicates that lipids increasing with PIS1 overexpression were enriched in saturated or monounsaturated fatty acids, whereas lipids increasing with PIS2 overexpression, including polyphosphoinositides, contained more unsaturated fatty acids. The results indicate that PtdIns populations originating from different PIS isoforms may enter alternative routes of metabolic conversion, possibly based on specificity and immediate metabolic context of the biosynthetic enzymes.
Characterization of an ideal amphipathic peptide as a procoagulant agent
Authors: Ganopolsky Jorge G. , Charbonneau Sophie , Peng Henry T. , Shek Pang N. , Blostein Mark D.
Published: May 2008

On the basis of previous evidence that amphipathic helical peptides accelerate Factor IXa activation of Factor X [Blostein, Rigby, Furie, Furie and Gilbert (2000) Biochemistry 39, 12000–12006], the present study was designed to assess the procoagulant activity of an IAP (ideal amphipathic peptide) of Lys7Leu15 composition. The results show that IAP accelerates Factor X activation by Factor IXa in a concentration-dependent manner and accelerates thrombin generation by Factor Xa with a comparable peptide- and substrate-concentration-dependence. A scrambled helical peptide with the same amino acid composition as IAP, but with its amphipathicity abolished, eliminated most of the aforementioned effects. The Gla (γ-carboxyglutamic acid)-rich domain of Factor X is required for IAP activity, suggesting that this peptide behaves as a phospholipid membrane. This hypothesis was confirmed, using fluorescence spectroscopy, by demonstrating direct binding between IAP and the Gla-rich domain of Factor X. In addition, the catalytic efficiencies of the tenase and prothrombinase enzymatic complexes, containing cofactors Factor VIIIa and Factor Va respectively, are enhanced by IAP. Finally, we show that IAP delays clot lysis in vitro. In summary, these observations demonstrate that IAP not only enhances essential procoagulant reactions required for fibrin generation, but also inhibits fibrinolysis, suggesting a potential role for IAP as a haemostatic agent.
New members of the glutathione transferase family discovered in red and brown algae
Authors: Hervé Cécile , de Franco Pierre-Olivier , Groisillier Agnès , Tonon Thierry , Boyen Catherine
Published: May 2008

The GSTs (glutathione transferases) are involved in the detoxification of a wide variety of hydrophobic substrates. These enzymes have been found in virtually all types of organisms, including plants, animals, nematodes and bacteria. In the present study, we report the molecular and biochemical characterization of algal GSTs. Phylogenetic analysis showed that most of them were distinct from previously described GST classes, but were most closely related to the Sigma class. Profiling of GST genes from the red alga Chondrus crispus and brown alga Laminaria digitata was undertaken after different chemical treatments and showed that they displayed contrasting patterns of transcription. Recombinant algal GST from both species showed transferase activities against the common substrates aryl halides, but also on the α,β-unsaturated carbonyl 4-hydroxynonenal. Also, they exhibit significant peroxidation towards organic hydroperoxides, including oxygenated derivatives of polyunsaturated fatty acids. Among a range of compounds tested, Cibacron Blue was the most efficient inhibitor of algal GSTs identified.
Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase: a novel metallophosphoesterase family preferentially expressed in rodent immune cells
Authors: Canales José , Fernández Ascensión , Ribeiro João Meireles , Cabezas Alicia , Rodrigues Joaquim Rui , Cameselle José Carlos , Costas María Jesús
Published: May 2008

ADPRibase-Mn (Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase) was earlier isolated from rat liver supernatants after separation from ADPRibase-I and ADPRibase-II (Mg2+-activated ADP-ribose pyrophosphatases devoid of CDP-alcohol pyrophosphatase activity). The last mentioned are putative Nudix hydrolases, whereas the molecular identity of ADPRibase-Mn is unknown. MALDI (matrix-assisted laser-desorption ionization) MS data from rat ADPRibase-Mn pointed to a hypothetical protein that was cloned and expressed and showed the expected specificity. It is encoded by the RGD1309906 rat gene, which so far has been annotated simply as ‘hydrolase’. ADPRibase-Mn is not a Nudix hydrolase, but it shows the sequence and structural features typical of the metallophosphoesterase superfamily. It may constitute a protein family of its own, the members of which appear to be specific to vertebrates, plants and algae. ADP-ribose was successfully docked to a model of rat ADPRibase-Mn, revealing its putative active centre. Microarray data from the GEO (Gene Expression Omnibus) database indicated that the mouse gene 2310004I24Rik, an orthologue of RGD1309906, is preferentially expressed in immune cells. This was confirmed by Northern-blot and activity assay of ADPRibase-Mn in rat tissues. A possible role of ADPRibase-Mn in immune cell signalling is suggested by the second-messenger role of ADP-ribose, which activates TRPM2 (transient receptor potential melastatin channel-2) ion channels as a mediator of oxidative/nitrosative stress, and by the signalling function assigned to many of the microarray profile neighbours of 2310004I24Rik. Furthermore, the influence of ADPRibase-Mn on the CDP-choline or CDP-ethanolamine pathways of phospholipid biosynthesis cannot be discounted.
Effect of glycosylation on the extracellular domain of the Ag43 bacterial autotransporter: enhanced stability and reduced cellular aggregation
Authors: Knudsen Stine K. , Stensballe Allan , Franzmann Magnus , Westergaard Uffe B. , Otzen Daniel E.
Published: May 2008

Autotransporters constitute the biggest group of secreted proteins in Gram-negative bacteria and contain a membrane-bound β-domain and a passenger domain secreted to the extracellular environment via an unusually long N-terminal sequence. Several passenger domains are known to be glycosylated by cytosolic glycosyl transferases, promoting bacterial attachment to mammalian cells. In the present study we describe the effect of glycosylation on the extracellular passenger domain of the Escherichia coli autotransporter Ag43α, which induces frizzy colony morphology and cell settling. We identify 16 glycosylation sites and suggest two possible glycosylation motifs for serine and threonine residues. Glycosylation stabilizes against thermal and chemical denaturation and increases refolding kinetics. Unexpectedly, glycosylation also reduces the stabilizing effect of Ca2+ ions, removes the ability of Ca2+ to promote cell adhesion, reduces the ability of Ag43α-containing cells to form bacterial amyloid and increases the susceptibility of the resulting amyloid to proteolysis. In addition, our results indicate that Ag43α folds without a stable intermediate, unlike pertactin, indicating that autotransporters may arrive at the native state by a variety of different mechanisms despite a common overall structure. A small but significant fraction of Ag43α can survive intact in the periplasm if expressed without the β-domain, suggesting that it is able to adopt a protease-resistant structure prior to translocation across the membrane. The present study demonstrates that glycosylation may play significant roles in structural and functional properties of bacterial autotransporters at many different levels.
Calmodulin binding to cellular FLICE-like inhibitory protein modulates Fas-induced signalling
Authors: Pawar Pritish S. , Micoli Keith J. , Ding Haitao , Cook William J. , Kappes John C. , Chen Yabing , McDonald Jay M.
Published: May 2008

We and others have demonstrated that Fas-mediated apoptosis is a potential therapeutic target for cholangiocarcinoma. Previously, we reported that CaM (calmodulin) antagonists induced apoptosis in cholangiocarcinoma cells through Fas-related mechanisms. Further, we identified a direct interaction between CaM and Fas with recruitment of CaM into the Fas-mediated DISC (death-inducing signalling complex), suggesting a novel role for CaM in Fas signalling. Therefore we characterized the interaction of CaM with proteins recruited into the Fas-mediated DISC, including FADD (Fas-associated death domain)-containing protein, caspase 8 and c-FLIP {cellular FLICE [FADD (Fas-associated death domain)-like interleukin 1β-converting enzyme]-like inhibitory protein}. A Ca2+-dependent direct interaction between CaM and FLIPL, but not FADD or caspase 8, was demonstrated. Furthermore, a 37.3±5.7% increase (n=6, P=0.001) in CaM–FLIP binding was observed at 30 min after Fas stimulation, which returned to the baseline after 60 min and correlated with a Fas-induced increase in intracellular Ca2+ that reached a peak at 30 min and decreased gradually over 60 min in cholangiocarcinoma cells. A CaM antagonist, TFP (trifluoperazine), inhibited the Fas-induced increase in CaM–FLIP binding concurrent with inhibition of ERK (extracellular-signal-regulated kinase) phosphorylation, a downstream signal of FLIP. Direct binding between CaM and FLIPL was demonstrated using recombinant proteins, and a CaM-binding region was identified in amino acids 197–213 of FLIPL. Compared with overexpression of wild-type FLIPL that resulted in decreased spontaneous as well as Fas-induced apoptosis, mutant FLIPL with deletion of the CaM-binding region resulted in increased spontaneous and Fas-induced apoptosis in cholangiocarcinoma cells. Understanding the biology of CaM–FLIP binding may provide new therapeutic targets for cholangiocarcinoma and possibly other cancers.
Negative-feedback regulation of FGF signalling by DUSP6/MKP-3 is driven by ERK1/2 and mediated by Ets factor binding to a conserved site within the DUSP6/MKP-3 gene promoter
Authors: Ekerot Maria , Stavridis Marios P. , Delavaine Laurent , Mitchell Michael P. , Staples Christopher , Owens David M. , Keenan Iain D. , Dickinson Robin J. , Storey Kate G. , Keyse Stephen M.
Published: May 2008

DUSP6 (dual-specificity phosphatase 6), also known as MKP-3 [MAPK (mitogen-activated protein kinase) phosphatase-3] specifically inactivates ERK1/2 (extracellular-signal-regulated kinase 1/2) in vitro and in vivo. DUSP6/MKP-3 is inducible by FGF (fibroblast growth factor) signalling and acts as a negative regulator of ERK activity in key and discrete signalling centres that direct outgrowth and patterning in early vertebrate embryos. However, the molecular mechanism by which FGFs induce DUSP6/MKP-3 expression and hence help to set ERK1/2 signalling levels is unknown. In the present study, we demonstrate, using pharmacological inhibitors and analysis of the murine DUSP6/MKP-3 gene promoter, that the ERK pathway is critical for FGF-induced DUSP6/MKP-3 transcription. Furthermore, we show that this response is mediated by a conserved binding site for the Ets (E twenty-six) family of transcriptional regulators and that the Ets2 protein, a known target of ERK signalling, binds to the endogenous DUSP6/MKP-3 promoter. Finally, the murine DUSP6/MKP-3 promoter coupled to EGFP (enhanced green fluorescent protein) recapitulates the specific pattern of endogenous DUSP6/MKP-3 mRNA expression in the chicken neural plate, where its activity depends on FGFR (FGF receptor) and MAPK signalling and an intact Ets-binding site. These findings identify a conserved Ets-factor-dependent mechanism by which ERK signalling activates DUSP6/MKP-3 transcription to deliver ERK1/2-specific negative-feedback control of FGF signalling.
Dihydropteroate synthase from Streptococcus pneumoniae: structure, ligand recognition and mechanism of sulfonamide resistance
Authors: Levy Colin , Minnis David , Derrick Jeremy P.
Published: May 2008

DHPS (dihydropteroate synthase) catalyses an essential step in the biosynthesis of folic acid and is the target for the sulfonamide group of antimicrobial drugs. In the present paper we report two crystal structures of DHPS from the respiratory pathogen Streptococcus pneumoniae: the apoenzyme at 1.8 Å (1 Å=0.1 nm) resolution and a complex with DHPP (6-hydroxymethyl-7,8-dihydropterin monophosphate) at 2.4 Å resolution. The enzyme forms a α/β barrel structure, with a highly conserved binding pocket for recognition of the pterin substrate, DHPPP (6-hydroxymethyl-7,8-dihydropterin pyrophosphate). There is a fixed order of substrate binding: DHPPP binds first, followed by the second substrate, pABA (p-aminobenzoic acid). Binding of PPi also allows the enzyme to recognize pABA or sulfonamide drugs, which act as pABA analogues. Using equilibrium and pre-steady state kinetic fluorescence measurements, we show that the on-rate for DHPPP binding to the enzyme is relatively low (2.6×105 M−1·s−1) and propose that binding of this substrate induces a large scale movement of the second loop in the enzyme structure to participate in the formation of the pABA-binding site. Two mutations which confer resistance to sulfonamide drugs do not affect DHPPP binding, but have a substantial effect on pABA and sulfonamide recognition. The results show that binding of DHPPP and pABA are separate distinguishable events in the reaction cycle, and that mutations which confer resistance to sulfonamide drugs act exclusively on the second step in the binding process.
Differential effects of N-glycans on surface expression suggest structural differences between the acid-sensing ion channel (ASIC) 1a and ASIC1b
Authors: Kadurin Ivan , Golubovic Andjelko , Leisle Lilia , Schindelin Hermann , Gründer Stefan
Published: May 2008

ASICs (acid-sensing ion channels) are H+-gated Na+ channels with a widespread expression pattern in the central and the peripheral nervous system. ASICs have a simple topology with two transmembrane domains, cytoplasmic termini and a large ectodomain between the transmembrane domains; this topology has been confirmed by the crystal structure of chicken ASIC1. ASIC1a and ASIC1b are two variants encoded by the asic1 gene. The variable part of the protein includes the cytoplasmic N-terminus, the first transmembrane domain and approximately the first third of the ectodomain. Both variants contain two consensus sequences for N-linked glycosylation in the common, distal part of the ectodomain. In contrast with ASIC1a, ASIC1b contains two additional consensus sequences in the variable, proximal part of the ectodomain. Here we show that all the extracellular asparagine residues within the putative consensus sequences for N-glycosylation carry glycans. The two common distal glycans increase surface expression of the channels, but are no absolute requirement for channel activity. In sharp contrast, the presence of at least one of the two proximal glycans, which are specific to ASIC1b, is an absolute requirement for surface expression of ASIC1b. This result suggests substantial differences in the structure of the proximal ectodomain between the two ASIC1 variants.