bluuebunny/crossref_metadata_2025 huggingface dataset:
Transform and rift structure of Paleogene crust near Resolution Ridge, Tasman Sea, southwest New Zealand
Authors: Barker Daniel H. N. , Wood Ray , Sutherland Rupert
Published: July 2008

Multibeam bathymetry, seismic reflection, magnetic anomaly, and gravity anomaly data show that most of the Resolution Ridge System is Tasman Sea oceanic crust, deformed by Eocene rift faulting associated with the initiation of the modern Australia‐Pacific plate boundary. Resolution Ridge, the most eastern ridge of the system, is inferred to be continental crust that was plucked from the southwest corner of the Campbell Plateau during Eocene rift propagation. Rift propagation proceeded through sequential northward steps between weak points in the lithosphere: young fossil spreading centers, fracture zones, and the western margin of the continental Campbell Plateau. Fracture zones guided the large‐scale geometry of the rift, but there is not always a close surface correspondence between transform and rift faults. This may be because transform faults were subvertical, whereas rift faults evolved to be moderately dipping. The very good correspondence of fracture zones, rift faults, and magnetic anomalies from the Resolution Ridge System with their conjugates southwest of the Campbell Plateau allows precise prerift reconstruction of the Australia‐Pacific plate boundary at a time (circa 48 Ma) of significant global plate reorganization and profound change in Pacific plate motion. This precise plate reconstruction better constrains plate motion chains that connect the Pacific and Indo‐Atlantic hemispheres, thus contributing to debate of global scientific issues such as what caused the bend in the Emperor‐Hawaii seamount chain.
Electron structure of the magnetopause boundary layer: Cluster/Double Star observations
Authors: Dunlop M. W. , Taylor M. G. G. T. , Bogdanova Y. V. , Shen C. , Pitout F. , Pu Z. , Davies J. A. , Zhang Q.‐H. , Wang J. , Lavraud B. , Fazakerley A. N. , Walsh A. , Owen C. J. , Laakso H. , Zong Q.‐G. , Liu Z.‐X. , Escoubet C. P. , Carr C. M. , Rème H.
Published: July 2008

We present a comparison of two events, monitored by the Double Star and Cluster spacecraft at separate locations on the dayside magnetopause, which exhibit distinct properties at high and low latitudes in the magnetopause boundary layer during the occurrence of low‐latitude reconnection. On 6 April 2004, the four Cluster and TC‐1 spacecraft were on near‐coincident, outbound transits of the dawnside magnetosphere at north and south midlatitudes, respectively. The observations show a series of oppositely directed flux transfer events (FTEs), fed by a low‐latitude reconnection line located between the spacecraft. Although both spacecraft locations were nearly equidistant from the active reconnection region, the associated magnetopause boundary layer was maintained at TC‐1 but not at Cluster. We suggest an asymmetric north and south extent of the LLBL so as to be more extensive at TC‐1, where the local magnetic shear across the magnetopause is small. On 4 January 2005, the Cluster and TC‐1 spacecraft all repeatedly traverse the northern, duskside magnetopause almost simultaneously, before and after a strong reversal in the IMF from northward to southward during a period of turbulent solar wind. Open flux tubes are observed within minutes of the southward turning, arising from the sudden formation of a nearby subsolar reconnection line. Before the IMF change, a complex and energized boundary layer, largely absent at the lower latitudes of TC‐1, and containing an energetic (>40 keV) electron population of locally trapped and field‐aligned distributions, is present at the high‐latitude Cluster locations. Following reconnection onset after the IMF reversal, the boundary layer is seen to extend to TC‐1, and the electron distribution, which depends on position through the boundary layer, develops as an energetic, field‐aligned (bistreaming) distribution. The analysis is utilizes an extended electron distribution for energies ranging from a few to 400 keV and by reordering the transition through the magnetopause to the electron distribution.
Rupture process of the 2004 Parkfield earthquake from near‐fault seismic waveform and geodetic records
Authors: Kim Ahyi , Dreger Douglas S.
Published: July 2008

The 28 September 2004 Parkfield earthquake, arguably the best recorded earthquake ever, allows for detailed investigation of finite‐source models and their resolution. We have developed finite‐source models using GPS and interferometric synthetic aperture radar geodetic data and seismic strong motion waveform data (f ≤ 0.5 Hz) both independently and combined. The preferred model shows that the rupture is predominantly unilateral to the NW with a small component to the SE. Slip is concentrated into two primary patches, one near the hypocenter and the other between 10 and 23 km to the NW within a narrow depth range (5–13 km). The scalar seismic moment is 1.3 × 1018 N m (Mw 6.0), the overall rupture length is 23 km, the peak slip is 0.45 m, and the rupture velocity is 2.6 km/s. The average static stress drop obtained from the spatially distributed slip model is 2.3 MPa, and peak values are 10 MPa. A detailed sensitivity and resolution analysis shows that the recovered slip, the average rupture velocity, risetime, and slip velocity are well resolved.
Electrical conductivity beneath the Bolivian Orocline and its relation to subduction processes at the South American continental margin
Authors: Brasse Heinrich , Eydam Diane
Published: July 2008

A long‐period magnetotelluric data set was obtained during 2002 and 2004 in the central Andes to study the deep electrical conductivity structure in the region of the Bolivian Orocline between latitudes 17°S and 19°S. The profile extends from the Coastal Cordillera in northernmost Chile, crosses the volcanic arc and the Altiplano high plateau in central Bolivia, and ends in the Eastern Cordillera. Two‐dimensional inversion revealed several well‐defined conductivity anomalies: in upper crustal levels the conductive sedimentary basins of the central Altiplano and the resistive Arequipa block beneath the western Altiplano are imaged. Earlier seismological and magnetotelluric investigations on the southern Altiplano inferred a large, highly conductive (partially molten) body in the mid to deep crust. It was assumed that this structure would be underlying the entire plateau, but this is not the case according to the new models. Instead, the most prominent feature in the new investigation area is a high‐conductivity zone at upper mantle depths below the high plateau, which may be interpreted as an image of partial melts and fluids triggered by water supply from the subducting Nazca slab. This conductor would be in accordance with the standard subduction scenario; it is, however, laterally offset by almost 100 km from the volcanic arc. In contrast, the deep crust and upper mantle beneath the arc is moderately resistive. Both observations may hint at an emerging shift of the magmatic/fluid system in the central Andes.
Grain size variations in the Earth's mantle and the evolution of primordial chemical heterogeneities
Authors: Solomatov V. S. , Reese C. C.
Published: July 2008

Chemical heterogeneities with relatively high viscosity are known to be poorly mixed by mantle convection. One of the factors which can cause viscosity variations is the grain size. Analysis of various physical processes in the Earth's mantle suggests that variation in the grain size can be extremely large even outside of subducting slabs. The largest grains are formed in the early molten Earth where Ostwald ripening is controlled by liquid‐state diffusion. The smallest grains are formed due to recrystallization by the spinel‐perovskite phase transformation in downwelling flow and subsequent Ostwald ripening. The viscosity contrast between primordial, large grain size material and recrystallized material is likely to be many orders of magnitude. Preliminary numerical simulations show that strongly time‐dependent mantle convection can process primordial large‐grain size heterogeneities through the spinel‐perovskite phase boundary only after a few overturns. This reduces the viscosity contrasts and leads to rapid mixing by mantle convection. A more steady flow in the lower mantle may lead to the formation of stagnant, poorly mixed regions which may never have had a chance to cross the 660‐km discontinuity and be recrystallized by the spinel‐perovskite phase transformation. Heterogeneities can also avoid grain size reduction and mixing if their density is slightly larger than the surrounding mantle. In this case, they accumulate at the core‐mantle boundary.
Role of ozone in the solar cycle modulation of the North Atlantic Oscillation
Authors: Kuroda Yuhji , Yamazaki Koji , Shibata Kiyotaka
Published: July 2008

The effect of ozone on the 11‐year solar cycle modulation of the winter‐mean North Atlantic Oscillation (NAO) is examined through analyses of observed meteorological and ozone data from 1978 to 2000. It is found that a significant ozone anomaly associated with the winter NAO is created in winter in high solar (HS) years only and the anomaly persists from spring to summer, creating a large temperature anomaly in the lower stratosphere through radiative heating. Such a temperature anomaly in the stratosphere creates anomalous temperature of opposite sign at lower heights and anomalous zonal wind in the polar area of the troposphere in summer. The associated surface signal is very similar to the summer Arctic Oscillation (Summer‐AO). The mechanism for the formation of the Summer‐AO is also discussed.
An observational study of the relationship between cloud, aerosol and meteorology in broken low‐level cloud conditions
Authors: Loeb Norman G. , Schuster Gregory L.
Published: July 2008

Global satellite analyses showing strong correlations between aerosol optical depth and cloud cover have stirred much debate recently. While it is tempting to interpret the results as evidence of aerosol enhancement of cloud cover, other factors such as the influence of meteorology on both the aerosol and cloud distributions can also play a role, as both aerosols and clouds depend upon local meteorology. This study uses satellite observations to examine aerosol‐cloud relationships for broken low‐level cloud regions off the coast of Africa. The analysis approach minimizes the influence of large‐scale meteorology by restricting the spatial and temporal domains in which the aerosol and cloud properties are compared. While distributions of several meteorological variables within 5° × 5° latitude‐longitude regions are nearly identical under low and high aerosol optical depth, the corresponding distributions of single‐layer low cloud properties and top‐of‐atmosphere radiative fluxes differ markedly, consistent with earlier studies showing increased cloud cover with aerosol optical depth. Furthermore, fine‐mode fraction and Angstrom Exponent are also larger in conditions of higher aerosol optical depth, even though no evidence of systematic latitudinal or longitudinal gradients between the low and high aerosol optical depth populations are observed. When the analysis is repeated for all 5° × 5° latitude‐longitude regions over the global oceans (after removing cases in which significant meteorological differences are found between the low and high aerosol populations), results are qualitatively similar to those off the coast of Africa.
Temperature, pressure, and wind instrumentation in the Phoenix meteorological package
Authors: Taylor Peter A. , Catling David C. , Daly Mike , Dickinson Cameron S. , Gunnlaugsson Haraldur P. , Harri Ari‐Matti , Lange Carlos F.
Published: July 2008

The meteorological package (MET) on the Phoenix Lander is designed to provide information on the daily and seasonal variations in Mars near‐polar weather during Martian late spring and summer. The present paper provides some background on the temperature, pressure, and wind instrumentation on the Phoenix MET station and their characterization. A separate paper addresses the MET lidar instrument. Laboratory studies in a Mars wind tunnel confirm estimates that the time constant of the thermocouples should be less than 0.5 s for wind speeds of 5 m s−1 or greater. Solar radiation falling on the thermocouples could raise the reported temperatures by up to 0.7 K for wind speeds of 5 m s−1. The increase will be wind speed dependent and will increase to 0.8 K at U = 3 m s−1 under peak solar radiation. Pressure sensors will give Mars surface pressures accurate to 10 Pa or better while Telltale deflections should provide reliable wind speed information up to at least 10 m s−1. The paper also discusses, to a limited extent, how the MET instruments will be used in conjunction with other instruments on the Phoenix Lander to provide an enhanced meteorological data set. We also describe instrumentation related to the Atmospheric Structure Experiment during entry, descent, and landing (EDL). These instruments will provide deceleration data. Together with drag coefficient information and a surface pressure measurement from MET, these data will allow us to infer the density, pressure, and temperature structure throughout the vertical column during EDL.
How alpine plant growth is linked to snow cover and climate variability
Authors: Jonas Tobias , Rixen Christian , Sturm Matthew , Stoeckli Veronika
Published: July 2008

Recent climate models predict future changes in temperature and precipitation in the Alps. To assess the potential response of alpine plant communities to climate change, we analyzed specific and combined effects of temperature, precipitation, and snow season timing on the growth of plants. This analysis is based on data from 17 snow meteorological stations and includes plant growth records from the same sites over 10 years. Using multiple regression and path analysis, we found that plant growth was primarily driven by climatic factors controlled by the timing of the snow season. Air temperature and precipitation before snow‐up and after melt‐out yielded the greatest direct impact on maximum plant height as well as growth rates. The variability of environmental drivers between sites versus between years had different effects on plant growth: e.g., sites with early melt‐out dates hosted plant communities with tall, slow‐growing vegetation. But interannual variations in melt‐out dates at a given site did not produce measurable differences in plant growth performance. However, high temperatures after melt‐out invariably resulted in a shortened growth period. We speculate that the plant growth patterns we observed in response to climate variation between sites are indicative of the long‐term responses of alpine plant communities to persistent climate changes. With most climate models indicating shorter winters, we thus expect alpine grasslands in the Alps to display an enhanced biomass production in the future.
Estimation of energy and moisture fluxes for dynamic vegetation using coupled SVAT and crop‐growth models
Authors: Casanova Joaquin J. , Judge Jasmeet
Published: July 2008

A Soil Vegetation Atmosphere Transfer (SVAT) model, viz. Land Surface Process (LSP) model, is coupled with a widely used crop‐growth model, DSSAT, to estimate energy and moisture fluxes at the land surface and in the vadose zone for growing vegetation. In this study, we present detailed observations of soil and crop characteristics, and various components of energy and water balance during a season‐long field experiment for sweet corn. The data set is used to calibrate the LSP with Latin Hypercube Sampling and Pareto ranking. We compare the observations with model estimates of crop growth and development, land surface fluxes, soil moisture and temperature profiles from both the stand‐alone LSP and coupled LSP‐DSSAT models. We find that the model estimates of radiation fluxes, soil moisture, and soil temperature, by both the LSP and LSP‐DSSAT are very similar, indicating that the LSP‐DSSAT model can be used to simulate fluxes for dynamic vegetation without the need of in situ vegetation observations. Moreover, because coupling was achieved without structurally changing either of the models, the methodology in this study can be extended to coupling other SVAT and vegetation growth models.
An automatic, stagnation point based algorithm for the delineation of Wellhead Protection Areas
Authors: Tosco Tiziana , Sethi Rajandrea , Di Molfetta Antonio
Published: July 2008

Time‐related capture areas are usually delineated using the backward particle tracking method, releasing circles of equally spaced particles around each well. In this way, an accurate delineation often requires both a very high number of particles and a manual capture zone encirclement. The aim of this work was to propose an Automatic Protection Area (APA) delineation algorithm, which can be coupled with any model of flow and particle tracking. The computational time is here reduced, thanks to the use of a limited number of nonequally spaced particles. The particle starting positions are determined coupling forward particle tracking from the stagnation point, and backward particle tracking from the pumping well. The pathlines are postprocessed for a completely automatic delineation of closed perimeters of time‐related capture zones. The APA algorithm was tested for a two‐dimensional geometry, in homogeneous and nonhomogeneous aquifers, steady state flow conditions, single and multiple wells. Results show that the APA algorithm is robust and able to automatically and accurately reconstruct protection areas with a very small number of particles, also in complex scenarios.
Asfaw Receives 2008 New International Award
Authors: Whaler Kathryn A. , Asfaw Laike Mariam
Published: July 2008

Laike Mariam Asfaw became the director of the Addis Ababa Geophysical Observatory (AAO) at Addis Ababa University, Ethiopia, in 1978. His quiet calm and dedication have ensured a continuous, high‐quality data stream throughout the often politically turbulent period since. He is also deeply involved in the geophysical education of his country's science students, understanding, awareness‐raising, and advising on its seismic and related hazards, and the promotion of its science on the international stage.

The AAO was founded in the International Geophysical Year (IGY) as a geomagnetic observatory, still one of the few in Africa. Originally using paper records, hourly mean data have been produced since the observatory's inception; minute mean values have been available since 2000. It is now an International Real‐Time Magnetic Observatory Network (INTERMAGNET) observatory, indicating that it adheres to the highest standards of operation and, through satellite communication, provides data in near real time. Seismometer installation took place in 1959 and was upgraded with digital equipment in 1997. The AAO now also manages the Incorporated Research Institutions for Seismology (IRIS) broadband and other short‐period digital seismic stations in Ethiopia, and is an auxiliary Comprehensive Nuclear‐Test‐Ban Treaty Organization station. A continuously running GPS receiver has recently augmented the instrument base, and AAO is an International Global Navigation Satellite System (GNSS) Service station. The observatory's development and expansion and commitment of overseas funds would not have happened without Laike's leadership. He also ensures that AAO staff and students are actively involved in research based on the observatory's data.
Groundwater Science and Policy: An International Overview
Authors: Robins Nick
Published: July 2008

While global demand for water increases, the risks from pollution and the uncertainty of climate heighten the threat to available resources. One fifth of the world's freshwater reserves lie underground in the form of groundwater, whereas surface water systems account for a mere two hundredths of the global reserve, and the remainder is locked up—for the moment—in the polar ice caps. However, because groundwater is out of sight, to many this means out of mind. As a result, much of the world's groundwater is poorly managed and exploited for short‐term gain at the expense of longer‐term protection.

In response to requirements that had been outlined in the European Commission's Water Framework Directive (2000/60/EC) of 2000, the Commission's European “daughter,” Groundwater Directive (2006/118/EC, adopted in December 2006) clarifies the objectives outlined in the Water Framework Directive for groundwater protection in Europe.
Consistent changes in twenty‐first century daily precipitation from regional climate simulations for Korea using two convection parameterizations
Authors: Im E.‐S. , Gutowski W. J. , Giorgi F.
Published: July 2008

We present an analysis of the projected daily precipitation over Korea from regional climate change scenarios (1971–2080) implementing different convection schemes (Grell vs. MIT‐Emanuel) within the RegCM3 double‐nested system. Daily precipitation characteristics are investigated in terms of the normalized frequency and amount of precipitation and the extreme precipitation above the 95th percentile. For reference period (1971–2000), the MIT‐Emanuel simulation is superior to the Grell simulation for daily precipitation regardless of frequency and intensity. However, future changes tend to be similar. This behavior can be explained partly by a constraint on the normalized distribution of precipitation that separates increasing from decreasing contributions to the normalized spectrum. Precipitation with intensity above the 50th percentile tends to increase its contribution to total precipitation while precipitation of lower intensity tends to yield a reduced contribution. The change signal of winter precipitation is clearer, showing a well‐defined pattern of more intense precipitation.
A global climatology of ionospheric irregularities derived from GPS radio occultation
Authors: Arras C. , Wickert J. , Beyerle G. , Heise S. , Schmidt T. , Jacobi C.
Published: July 2008

GPS radio occultation measurements from CHAMP, GRACE‐A and FORMOSAT‐3/COSMIC are used to derive global information on small‐scale ionospheric irregularities such as sporadic E layers between January 2002 and December 2007. The investigations are based on the analysis of amplitude variations of the GPS radio occultation signals. The global distribution of ionospheric irregularities shows strong seasonal variations with highest occurrence rates during summer in the middle latitudes. The long‐term data set of CHAMP allows for first climatological studies, while the data coverage increases significantly with the combination of CHAMP, GRACE and FORMOSAT‐3/COSMIC measurements. This allows for global maps of sporadic E occurrence rates of very high spatial resolution where the influence of the Earth's magnetic field becomes visible in global sporadic E maps for the first time.
Global distributions of carbonyl sulfide in the upper troposphere and stratosphere
Authors: Barkley Michael P. , Palmer Paul I. , Boone Chris D. , Bernath Peter F. , Suntharalingam Parvadha
Published: July 2008

We present the first upper tropospheric and stratospheric global distributions of carbonyl sulfide (OCS) observed from space using solar occultation measurements made by the Atmospheric Chemistry Experiment (ACE) satellite Fourier transform spectrometer during 2004–2006. We observe high OCS mixing ratios (>400 pptv) within the tropical stratosphere owing to convected tropospheric air. Stratospheric mixing ratios decrease more rapidly with altitude moving away from the Equator, creating a poleward gradient. Elevated OCS concentrations observed at low southern latitudes are consistent with a significant pyrogenic source. Using coincident ACE measurements of CFC‐11 and CFC‐12 we determine a global OCS stratospheric lifetime of 64 ± 21 years corresponding to a stratospheric sink of 63–124 Gg OCS yr−1.
First direct measurements of enthalpy flux in the hurricane boundary layer: The CBLAST results
Authors: Zhang Jun A. , Black Peter G. , French Jeffrey R. , Drennan William M.
Published: July 2008

Hurricanes extract energy from the warm ocean through enthalpy fluxes. As part of the Coupled Boundary Layer Air‐Sea Transfer (CBLAST) experiment, flights were conducted to measure turbulent fluxes in the high‐wind boundary layer of hurricanes. Here we present the first field observations of sensible heat and enthalpy flux for 10m wind speeds to 30 ms−1. The analyses indicate no statistically significant dependence of these bulk exchange coefficients on wind speed. As a measure of hurricane development potential, we compute the mean ratio of the exchange coefficient for enthalpy to that for momentum and find it to be significantly below the lowest threshold estimated by previous investigators. This suggests that the enthalpy flux required for hurricane development may come from sources other than turbulent fluxes, such as lateral fluxes from the vortex warm core, or sea spray. Alternatively, it demands a re‐evaluation of the theoretical models used to derive the threshold.
Remote measurements of ion temperatures in the terrestrial magnetotail
Authors: Keesee Amy M. , Scime Earl , Moldwin Mark B.
Published: July 2008

Time‐resolved remote ion temperature measurements of the magnetosphere from 10 RE to −60 RE are presented for the first 48 h of the storm of 4–7 October 2000. Ion temperatures are calculated from Maxwellian fits to data from the Medium Energetic Neutral Atom instrument aboard the Imager for Magnetopause‐to‐Aurora Global Exploration spacecraft. The calculated ion temperatures in the magnetotail are consistent with in situ measurements from multiple geosynchronous spacecraft and Geotail at x = −9 RE. The measurements indicate two separate instances of an earthward propagating increase in ion temperature during the storm. Ion heating is observed coincident with substorm injections at 0600 UT and 1720 UT on 4 October. At −12 RE, the remotely measured ion temperatures are consistent with predictions of a solar wind velocity correlation equation only when the solar wind–magnetospheric coupling is strong. At other times, the measured ion temperature is 2–3 times larger than the predicted value.
MCPH1/BRIT1 cooperates with E2F1 in the activation of checkpoint, DNA repair and apoptosis
Authors: Yang Shan‐Zhong , Lin Fang‐Tsyr , Lin Weei‐Chin
Published: July 2008

Microcephalin (MCPH1) has a crucial role in the DNA damage response by promoting the expression of Checkpoint kinase 1 (CHK1) and Breast cancer susceptibility gene 1 (BRCA1); however, the mechanism of this regulation remains unclear. Here, we show that MCPH1 regulates CHK1 and BRCA1 through the interaction with E2F1 on the promoters of both genes. MCPH1 also regulates other E2F target genes involved in DNA repair and apoptosis such as RAD51, DDB2, TOPBP1, p73 and caspases. MCPH1 interacts with E2F1 on the p73 promoter, and regulates p73 induction and E2F1‐induced apoptosis as a result of DNA damage. MCPH1 forms oligomers through the second and third BRCT domains. An MCPH1 mutant containing only its oligomerization domain has a dominant‐negative role by blocking MCPH1 binding to E2F1. It also inhibits p73 induction in DNA damage and E2F1‐dependent apoptosis. Taken together, MCPH1 cooperates with E2F1 to regulate genes involved in DNA repair, checkpoint and apoptosis, and might participate in the maintenance of genomic integrity.
PCSK9 is required for the disposal of non‐acetylated intermediates of the nascent membrane protein BACE1
Authors: Jonas Mary Cabell , Costantini Claudio , Puglielli Luigi
Published: July 2008

We have recently identified a new form of post‐translational regulation of BACE1 (β‐site amyloid precursor protein (APP)‐cleaving enzyme 1), a membrane protein that acts as the rate‐limiting enzyme in the generation of the Alzheimer disease amyloid β‐peptide (Aβ). Specifically, BACE1 is transiently acetylated on seven lysine residues in the lumen of the endoplasmic reticulum/endoplasmic reticulum–Golgi intermediate compartment (ER/ERGIC). The acetylated intermediates of the nascent protein are able to reach the Golgi apparatus, whereas the non‐acetylated ones are retained and degraded in a post‐ER compartment. Here, we report that the serine protease PCSK9 (proprotein convertase subtilisin kexin type 9) contributes to the disposal of non‐acetylated BACE1. Both overexpression and small interfering RNA‐mediated downregulation of PCSK9 affected the levels of BACE1. The downregulation of PCSK9 affected the levels of the loss‐of‐acetylation mutants (BACE1Ala and BACE1Arg) but not those of the gain‐of‐acetylation mutant (BACE1Gln). In addition, Pcsk9−/− mice showed increased levels of BACE1 and Aβ in the brain. Finally, we found that nascent low‐density lipoprotein receptor, a known substrate of PCSK9, is also acetylated.
Tyrosine phosphorylation in semaphorin signalling: shifting into overdrive
Authors: Franco Mélanie , Tamagnone Luca
Published: July 2008

The semaphorins constitute a large family of molecular signals with regulatory functions in neuronal development, angiogenesis, cancer progression and immune responses. Accumulating data indicate that semaphorins might trigger multiple signalling pathways, and mediate different and sometimes opposing effects, depending on the cellular context and the particular plexin‐associated subunits of the receptor complex, which can include receptor‐type or cytoplasmic tyrosine kinases such as MET, ERBB2, VEGFR2, FYN, FES, PYK2 and SRC. It has also been shown that a specific plexin can alternatively associate with different tyrosine kinase receptors, eliciting divergent signalling pathways and functional outcomes. Tyrosine phosphorylation is a pivotal post‐translational protein modification that regulates intracellular signalling. Therefore, phosphorylation of tyrosines in the intracellular domain of plexins could determine or modify their interactions with additional signal transducers. Here, we discuss the potential relevance of tyrosine phosphorylation in semaphorin‐induced signalling, with an emphasis on its probable role in dictating the choice between multiple pathways and functional outcomes. The identification of implicated tyrosine kinases will pave the way to target individual semaphorin‐mediated functions.
Cisplatin-mediated impairment of mitochondrial DNA metabolism inversely correlates with glutathione levels
Authors: Garrido Nuria , Pérez-Martos Acisclo , Faro Mercedes , Lou-Bonafonte José Manuel , Fernández-Silva Patricio , López-Pérez Manuel José , Montoya Julio , Enríquez José Antonio
Published: July 2008

Cisplatin accumulates in mitochondria, which are a major target for this drug in cancer cells. Thus alterations in mitochondrial function have been implicated in cancer cell resistance to chemotherapeutic agents. Moreover, cisplatin toxic side effects seem to be associated with mitochondrial injury in vivo and in vitro. In order to clarify the potential effect of cisplatin in mtDNA (mitochondrial DNA) maintenance and expression, we have analysed rat liver mtDNA and mtRNA (mitochondrial RNA) synthesis as well as their stability under the influence of in vivo treatment or in vitro exposure to cisplatin. We show that cisplatin causes a direct and significant impairment of mtDNA and mtRNA synthesis and decreases steady-state levels of mtRNAs in isolated mitochondria. Furthermore, in vivo treatment of the animals with cisplatin exerts a protective effect from the impairment of mtRNA metabolism caused by in vitro exposure to the drug, by means of increased mitochondrial GSH levels after in vivo cisplatin treatment.
Effects of substitutions in the CXXC active-site motif of the extracytoplasmic thioredoxin ResA
Authors: Lewin Allison , Crow Allister , Hodson Christopher T. C. , Hederstedt Lars , Le Brun Nick E.
Published: July 2008

The thiol–disulfide oxidoreductase ResA from Bacillus subtilis fulfils a reductive role in cytochrome c maturation. The pKa values for the CEPC (one-letter code) active-site cysteine residues of ResA are unusual for thioredoxin-like proteins in that they are both high (>8) and within 0.5 unit of each other. To determine the contribution of the inter-cysteine dipeptide of ResA to its redox and acid–base properties, three variants (CPPC, CEHC and CPHC) were generated representing a stepwise conversion into the active-site sequence of the high-potential DsbA protein from Escherichia coli. The substitutions resulted in large decreases in the pKa values of both the active-site cysteine residues: in CPHC (DsbA-type) ResA, ΔpKa values of −2.5 were measured for both cysteine residues. Increases in midpoint reduction potentials were also observed, although these were comparatively small: CPHC (DsbA-type) ResA exhibited an increase of +40 mV compared with the wild-type protein. Unfolding studies revealed that, despite the observed differences in the properties of the reduced proteins, changes in stability were largely confined to the oxidized state. High-resolution structures of two of the variants (CEHC and CPHC ResA) in their reduced states were determined and are discussed in terms of the observed changes in properties. Finally, the in vivo functional properties of CEHC ResA are shown to be significantly affected compared with those of the wild-type protein.
Targeting human glutathione transferase A3-3 attenuates progesterone production in human steroidogenic cells
Authors: Raffalli-Mathieu Françoise , Orre Carolina , Stridsberg Mats , Hansson Edalat Maryam , Mannervik Bengt
Published: July 2008

hGSTA3-3 (human Alpha-class glutathione transferase 3-3) efficiently catalyses steroid Δ5–Δ4 double-bond isomerization in vitro, using glutathione as a cofactor. This chemical transformation is an obligatory reaction in the biosynthesis of steroid hormones and follows the oxidation of 3β-hydroxysteroids catalysed by 3β-HSD (3β-hydroxysteroid dehydrogenase). The isomerization has commonly been ascribed to a supplementary function of 3β-HSD. The present study is the first to provide evidence that hGSTA3-3 contributes to this step in steroid hormone biosynthesis in complex cellular systems. First, we find glutathione-dependent Δ5–Δ4 isomerase activity in whole-cell extracts prepared from human steroidogenic cells. Secondly, effective inhibitors of hGSTA3-3 dramatically decrease the conversion of Δ5-androstene-3,17-dione into Δ4-androstene-3,17-dione in cell lysates. Thirdly, we show that RNAi (RNA interference) targeting hGSTA3-3 expression decreases by 30% the forskolin-stimulated production of the steroid hormone progesterone in a human placental cell line. This effect is achieved at low concentrations of two small interfering RNAs directed against distinct regions of hGSTA3-3 mRNA, and is weaker in unstimulated cells, in which hGSTA3-3 expression is low. The results concordantly show that hGSTA3-3 makes a significant contribution to the double-bond isomerization necessary for steroid hormone biosynthesis and thereby complements the indispensable 3β-hydroxysteroid oxidoreductase activity of 3β-HSD. The results indicate that the lower isomerase activity of 3β-HSD is insufficient for maximal rate of cellular sex hormone production and identify hGSTA3-3 as a possible target for pharmaceutical intervention in steroid hormone-dependent diseases.
Phenolic substrates and suicide inactivation of tyrosinase: kinetics and mechanism
Authors: Muñoz-Muñoz Jose L. , García-Molina Francisco , García-Ruiz Pedro A. , Molina-Alarcón Milagros , Tudela Jose , García-Cánovas Francisco , Rodríguez-López Jose N.
Published: July 2008

The suicide inactivation mechanism of tyrosinase acting on its substrates has been studied. The kinetic analysis of the proposed mechanism during the transition phase provides explicit analytical expressions for the concentrations of o-quinone against time. The electronic, steric and hydrophobic effects of the substrates influence the enzymatic reaction, increasing the catalytic speed by three orders of magnitude and the inactivation by one order of magnitude. To explain the suicide inactivation, we propose a mechanism in which the enzymatic form Eox (oxy-tyrosinase) is responsible for such inactivation. A key step might be the transfer of the C-1 hydroxyl group proton to the peroxide, which would act as a general base. Another essential step might be the axial attack of the o-diphenol on the copper atom. The rate constant of this reaction would be directly related to the strength of the nucleophilic attack of the C-1 hydroxyl group, which depends on the chemical shift of the carbon C-1 (δ1) obtained by 13C-NMR. Protonation of the peroxide would bring the copper atoms together and encourage the diaxial nucleophilic attack of the C-2 hydroxyl group, facilitating the co-planarity with the ring of the copper atoms and the concerted oxidation/reduction reaction, and giving rise to an o-quinone. The suicide inactivation would occur if the C-2 hydroxyl group transferred the proton to the protonated peroxide, which would again act as a general base. In this case, the co-planarity between the copper atom, the oxygen of the C-1 and the ring would only permit the oxidation/reduction reaction on one copper atom, giving rise to copper(0), hydrogen peroxide and an o-quinone, which would be released, thus inactivating the enzyme.
Regulation of natriuretic peptide receptor-A gene expression and stimulation of its guanylate cyclase activity by transcription factor Ets-1
Authors: Kumar Prerna , Bolden Gevoni , Arise Kiran K. , Krazit Stephen T. , Pandey Kailash N.
Published: July 2008

ANP (atrial natriuretic peptide) exerts its biological effects by binding to GC (guanylate cyclase)-A/NPR (natriuretic peptide receptor)-A, which generates the second messenger cGMP. The molecular mechanism mediating Npr1 (coding for GC-A/NPRA) gene regulation and expression is not well understood. The objective of the present study was to elucidate the mechanism by which Ets-1 [Ets (E twenty-six) transformation-specific sequence] contributes to the regulation of Npr1 gene transcription and expression. Chromatin immunoprecipitation and gel-shift assays confirmed the in vivo and in vitro binding of Ets-1 to the Npr1 promoter. Overexpression of Ets-1 enhanced significantly Npr1 mRNA levels, protein expression, GC activity and ANP-stimulated intracellular accumulation of cGMP in transfected cells. Depletion of endogenous Ets-1 by siRNA (small interfering RNA) dramatically decreased promoter activity by 80%. Moreover, methylation of the Npr1 promoter region (−356 to +55) reduced significantly the promoter activity and hypermethylation around the Ets-1 binding sites directly reduced Ets-1 binding to the Npr1 promoter. Collectively, the present study demonstrates that Npr1 gene transcription and GC activity of the receptor are critically controlled by Ets-1 in target cells.
Granular L1 FePt:TiO2 (001) nanocomposite thin films with 5nm grains for high density magnetic recording
Authors: Ding Y. F. , Chen J. S. , Lim B. C. , Hu J. F. , Liu B. , Ju G.
Published: July 2008

Fe Pt : Ti O 2 (001) thin films were deposited on CrRu∕MgO underlayers by dc magnetron cosputtering. The effects of TiO2 content on microstructure and magnetic properties of the epitaxial FePt (001) films were studied. Experimental results showed that even with 20vol% TiO2 doping, FePt films could keep a (001) preferred orientation and perpendicular anisotropy. The FePt:TiO2 (001) film with 5nm grain size, adjustable coercivity, and reduced exchange coupling was obtained by doping 20vol% TiO2 into FePt film, showing great potential as low noise ultrahigh density perpendicular magnetic recording media.
Inverse molecular design in a tight-binding framework
Authors: Xiao Dequan , Yang Weitao , Beratan David N.
Published: July 2008

The number of chemical species of modest molecular weight that can be accessed with known synthetic methods is astronomical. An open challenge is to explore this space in a manner that will enable the discovery of molecular species and materials with optimized properties. Recently, an inverse molecular design strategy, the linear combination of atomic potentials (LCAP) approach [J. Am. Chem. Soc. 128, 3228 (2006)] was developed to optimize electronic polarizabilities and first hyperpolarizabilities. Here, using a simple tight-binding (TB) approach, we show that continuous optimization can be carried out on the LCAP surface successfully to explore vast chemical libraries of 102 to 1016 extended aromatic compounds. We show that the TB-LCAP optimization is not only effective in locating globally optimal structures based on their electronic polarizabilities and first hyperpolarizabilities, but also is straightforwardly extended to optimize transition dipole moments and HOMO-LUMO energy gaps. This approach finds optimal structures among 104 candidates with about 40 individual molecular property calculations. As such, for structurally similar molecular candidates, the TB-LCAP approach may provide an effective means to identify structures with optimal properties.
Do thermal fluctuations influence the recoil loops of nanocomposite magnets?
Authors: Rong Chuan-bing , Liu Yuzi , Liu J. Ping
Published: July 2008

An exchange-coupled FePt∕Fe3Pt nanocomposite system with well defined hard/soft two-phase morphology was prepared by reducing chemically synthesized FePt∕Fe3O4 bimagnetic nanoparticles. It was interesting to observe that the recoil loop openness is strongly dependent on the sweep rate of applied fields. A quantitative analysis shows a linear relation between the openness of recoil loops and the reciprocal activation volume, indicating that the recoil loops are intimately related to thermal fluctuation. The large open area of the recoil loops for nanocomposite magnets compared to that of single phase magnets is attributed to the unstable magnetic moments in the soft phase.
Temperature independence of pressure-induced amorphization of the phase-change memory alloy Ge2Sb2Te5
Authors: Krbal M. , Kolobov A. V. , Haines J. , Pradel A. , Ribes M. , Fons P. , Tominaga J. , Levelut C. , Le Parc R. , Hanfland M.
Published: July 2008

In the temperature range from room temperature to about 150°C, the prototypic phase-change material Ge2Sb2Te5 becomes amorphous upon hydrostatic compression. In the studied temperature range, the onset of amorphization is at about 15GPa and the material completely amorphizes at 25GPa; these values do not depend on temperature. Upon decompression, the amorphous phase is stable at lower temperatures, yet at higher temperatures (145°C), the initial fcc phase is recovered upon decompression. A possible mechanism of pressure-induced amorphization and its implications for phase-change memories are discussed.
Generalization of some integrals over unitary matrices by character expansion of groups
Authors: Ghaderipoor Alireza , Tellambura Chintha
Published: July 2008

The character expansion method was introduced by Balantekin [Phys. Rev. D 62, 085017 (2000)] for integration over the unitary group and, in particular, for calculating the well-known Harish–Chandra–Itzykson–Zuber integral where the coefficient matrices in the integrand are square matrices with nonzero determinants. However, in some applications such as the capacity analysis of multiple-input multiple-output channels in wireless communications and information theory, or applying the color-flavor transformation to lattice quantum chromodynamics in physics, or the theory of random matrices in mathematics, the integration over the unitary group is required where general rectangular complex matrices appear in the integrand. In this paper, we use the character expansion of groups to generalize two integrals over the unitary group that have general rectangular complex matrices in the integrand. Although we consider only two integrals, we believe that the integration framework presented here can be used for other integrals over unitary matrices.
Extended Hückel tight-binding approach to electronic excitations
Authors: Rincón Luis , Hasmy Anwar , Gonzalez Carlos A. , Almeida Rafael
Published: July 2008

In this work, we propose the application of a self-consistent extended Hückel tight-binding (EHTB) method in the computation of the absorption optical spectrum of molecules within the linear response time dependent density functional formalism. The EHTB approach is presented as an approximation to the Kohn–Sham energy functional. The method is applied to the computation of excitation energies and oscillator strengths of benzene, pyridine, naphthalene, diazines, and the fullerenes: C60(Ih), C70(D5h), and C80(D2). The very good agreement with experimental data is very encouraging and suggests the possibility of using the EHTB as a computational efficient and reliable tool to study optical properties of a wide variety of molecular systems.
Effects of oxygen, fluorine, and hydroxyl passivation on electronic properties of ⟨001⟩-oriented silicon nanowires
Authors: Migas D. B. , Borisenko V. E.
Published: July 2008

By means of ab initio calculations we show possible ways to band gap engineering in the ⟨001⟩-oriented silicon nanowires with a diameter of about 1.5 nm and terminated by hydrogen, oxygen, fluorine, and hydroxyl. The fluorine and hydroxyl functional groups are found to effectively decrease the gap value, if their coverage exceeds more than 50%, and to mostly preserve the direct nature of the gap in such nanostructures. Saturation by oxygen affects band dispersion near the gap region depending on the type of the bond between silicon and oxygen atoms. Estimates of the dipole matrix elements of the first direct transition mainly indicate marginal oscillator strength, however, some cases of silicon nanowires with the specific surface termination display the direct nature of the gap with appreciable oscillator strength. We also discuss the role of different terminating functional groups in the photoluminescence process from porous silicon considered as an ensemble of nanowires.
Asymptotic structure of steady nonlinear reaction-diffusion-Marangoni convection fronts
Authors: Rongy L. , De Wit A. , Homsy G. M.
Published: July 2008

Chemical fronts propagating in horizontal liquid layers with a free surface can induce localized steady Marangoni flow. Numerical integration of the Stokes equations coupled to a reaction-diffusion-convection equation for the concentration of the surface-active reaction product shows that the system reaches an asymptotic dynamic state characterized by a deformed front surrounded by a steady convection roll traveling at a constant speed. To understand the basic balances determining this steady dynamics, we present here an asymptotic analysis of the system based on the numerically obtained scalings at high Marangoni numbers M quantifying the interaction between reaction-diffusion processes and Marangoni convection. M is positive (negative) when the product decreases (increases) the surface tension behind the front. We obtain a semianalytical solution for the product concentration for large M>0, showing that the key balances are between reaction, convection, and vertical (rather than axial) diffusion. For M<0, we present evidence of a multiscale structure of the front resulting from more complex balances.