bluuebunny/crossref_metadata_2025 huggingface dataset:
A geophysical study of oceanic core complexes and surrounding terrain, Mid‐Atlantic Ridge 13°N–14°N
Authors: Mallows C. , Searle R. C.
Published: May 2012

We describe a geophysical study of oceanic core complexes (OCC) and surrounding seafloor on the Mid‐Atlantic Ridge at 13°N–14°N and off‐axis to ∼1.9 Myr. Data include a detailed, deep‐towed side scan sonar, magnetic field and bathymetry survey, supplemented by concurrent sea‐surface bathymetry, magnetic field and gravity measurements. Using side scan and bathymetry, we infer areas and relative ages of seafloor volcanism, revealing a complex pattern of melt accretion across the median valley including close to its walls. We estimate tectonic and magmatic extension throughout the area, and find that average tectonic extension since chron 2 on plates containing OCCs is up to three times that on their conjugates. Deep‐towed magnetic data reveal asymmetric spreading (faster on OCC‐containing plates) and crustal magnetization that is highly heterogeneous on a scale of ∼5 km, suggesting that exhumed domes of OCCs have highly variable lithologies, perhaps comprising both serpentinized peridotite and gabbro. Improved fits to magnetic data are provided by models incorporating ∼45°of OCC footwall rotation. An axial zone of normal magnetization, of presumed Brunhes epoch, has highly variable width and amplitude, with parts of the ridge axis displaying very low or apparently reversed magnetization. Gravity requires that OCCs have dense cores capped by lower density zones several kilometers thick. Gravity data indicate longer term patterns of crustal thickness and melt distribution that are broadly consistent with numerical models of OCC formation and show that waxing magmatism may terminate OCCs.
Multiple expressions of plume‐ridge interaction in the Galápagos: Volcanic lineaments and ridge jumps
Authors: Mittelstaedt E. , Soule S. , Harpp K. , Fornari D. , McKee C. , Tivey M. , Geist D. , Kurz M. D. , Sinton C. , Mello C.
Published: May 2012

Anomalous volcanism and tectonics between near‐ridge mantle plumes and mid‐ocean ridges provide important insights into the mechanics of plume‐lithosphere interaction. We present new observations and analysis of multibeam, side scan sonar, sub‐bottom chirp, and total magnetic field data collected during the R/V Melville FLAMINGO cruise (MV1007; May–June, 2010) to the Northern Galápagos Volcanic Province (NGVP), the region between the Galápagos Archipelago and the Galápagos Spreading Center (GSC) on the Nazca Plate, and to the region east of the Galápagos Transform Fault (GTF) on the Cocos Plate. The NGVP exhibits pervasive off‐axis volcanism related to the nearby Galápagos hot spot, which has dominated the tectonic evolution of the region. Observations indicate that ∼94% of the excess volcanism in our survey area occurs on the Nazca Plate in three volcanic lineaments. Identified faults in the NGVP are consistent with normal ridge spreading except for those within a ∼60 km wide swath of transform‐oblique faults centered on the GTF. These transform‐oblique faults are sub‐parallel to the elongation direction of larger lineament volcanoes, suggesting that lineament formation is influenced by the lithospheric stress field. We evaluate current models for lineament formation using existing and new observations as well as numerical models of mantle upwelling and melting. The data support a model where the lithospheric stress field controls the location of volcanism along the lineaments while several processes likely supply melt to these eruptions. Synthetic magnetic models and an inversion for crustal magnetization are used to determine the tectonic history of the study area. Results are consistent with creation of the GTF by two southward ridge jumps, part of a series of jumps that have maintained a plume‐ridge separation distance of 145 km to 215 km since ∼5 Ma.
Recent mass changes of glaciers in the Russian High Arctic
Authors: Moholdt Geir , Wouters Bert , Gardner Alex S.
Published: May 2012

Glaciers and ice caps are known to contribute significantly to present‐day sea level rise, but there are still glaciated regions where little is known about modern changes in glacier mass. One of these regions is the Russian High Arctic archipelagos which has a total glaciated area of 51,500 km2. We have assessed the glacier mass budget of this region for a 6‐year period between October 2003 and October 2009 using independent ICESat laser altimetry and GRACE gravimetry. Over this period we found that the archipelagos have lost ice at a rate of −9.1 ± 2.0 Gt a−1, which corresponds to a sea level contribution of 0.025 mm a−1. Approximately 80% of the ice loss came from Novaya Zemlya with the remaining 20% coming from Franz Josef Land and Severnaya Zemlya. Meteorological records of temperature and precipitation for the period 1980–2009 suggest that the recent climatic mass budget is not substantially different from the longer‐term trend.
Does subducting lithosphere weaken as it enters the lower mantle?
Authors: Zhao S. , Jin Z. , Zhang J. , Xu H. , Xia G. , Green H. W.
Published: May 2012

The boundary between the upper and lower mantles of Earth corresponds to breakdown of (Mg,Fe)2SiO4, spinel (ringwoodite), into (Mg,Fe)SiO3perovskite (pv) + (Mg,Fe)O, magnesiowüstite (mw). The rheology of these materials is important for understanding deeply subducted slabs, the termination of deep earthquakes, mantle convection, post‐glacial rebound, etc. It has been proposed that decomposition of ringwoodite as subducting slabs enter the lower mantle leads to very fine‐grained material that is inherently weak because it flows by grain‐boundary sliding. Such abrupt and great weakening would have important geophysical implications. Here we test whether products from such decomposition are weak, using a realistic analogue high‐pressure system (Co2TiO4). Our results show that spinel breakdown products are complicated intergrowths (symplectites) that flow by dislocation creep, rather than fine‐grained domains that flow by diffusion creep as is commonly assumed from very fine phase domains seen in two dimensions. Application to Earth strongly suggests that ringwoodite breakdown is likely to strengthen the slab, reflecting the inherently greater viscosity of the uppermost lower mantle revealed by geophysical measurements.
Sensitivity of internal tide generation in Hawaii
Authors: Powell B. S. , Janeković I. , Carter G. S. , Merrifield M. A.
Published: May 2012

Energy from the barotropic tide is transferred into the baroclinic tide over topographic gradients, which provides a mechanism for the ocean boundaries to communicate with the deep ocean, to close energy budgets, and as a source of flux affecting nutrient supply and larval transport. Understanding the temporal variability of the conversion from barotropic to baroclinic tides is critical to our understanding of these processes. Using a numerical model and its adjoint, we examine the sensitivity of tidal conversion at Kaena Ridge in Hawaii. We find a sensitivity to changes in the upper ocean due to a phase difference between the pressure anomaly and tidal velocity caused by internal waves generated on the opposite slope of the ridge; however, we also find that conversion is equally as sensitive to local, deep stratification changes.
Utility of coarse and downscaled soil moisture products at L‐band for hydrologic modeling at the catchment scale
Authors: Mascaro Giuseppe , Vivoni Enrique R.
Published: May 2012

Demonstrating the utility of satellite‐based soil moisture (θ) products for hydrologic modeling at high resolution is a critical component of mission design. In this study, we utilize aircraft and ground θdata collected during the SMEX04 experiment in Sonora (Mexico) to compare two downscaling frameworks using C‐band and L‐band sensors. We show that the L‐band framework, which mimics the disaggregation of SMAP products, has considerably better performance than the C‐band framework simulating the downscaling of AMSR‐E. Disaggregated L‐bandθ fields are able to characterize with reasonable accuracy the θvariability at multiple extent scales, including the SMAP footprint and the catchment scale, and along an elevation transect. We then test the utility of coarse and downscaled C‐ and L‐bandθestimates for hydrologic simulations through data assimilation experiments using a distributed hydrologic model. Results reveal that the model prognostic capability is significantly enhanced when using L‐bandθfields at the SMAP scale and, to a greater extent, when downscaled L‐bandθfields are assimilated. L‐band data assimilation leads to higher model fidelity relative to ground data as well as more realistic soil moisture patterns at the catchment scale. This study indicates the potential value of satellite‐based L‐band sensors for hydrologic modeling when coupled with a statistical downscaling algorithm.
Significant concentrations of nitryl chloride observed in rural continental Europe associated with the influence of sea salt chloride and anthropogenic emissions
Authors: Phillips G. J. , Tang M. J. , Thieser J. , Brickwedde B. , Schuster G. , Bohn B. , Lelieveld J. , Crowley J. N.
Published: May 2012

We present the first measurements of nitryl chloride (ClNO2) over continental Europe. Significant quantities of ClNO2, up to 800 pptv, were measured at a mountaintop field site in Hessen, southwest Germany. ClNO2 was detected during the majority of nights between the 15th August and 16th September 2011, its largest mixing ratios being associated with air masses influenced by sea salt and anthropogenic NOx emissions. ClNO2 persisted in measurable quantities until early afternoons on days with low photolysis frequencies. As a consequence, early morning production rates of Cl atoms could significantly exceed the production of OH via ozone photolysis, likely leading to increased O3 production.
Near infrared and ultraviolet spectra of TLEs
Authors: Gordillo‐Vázquez F. J. , Luque A. , Simek M.
Published: May 2012

We have found that sprites, beads and halos have similar optical spectra, but measurable differences in the near IR and near UV spectra. In particular, near infrared (NIR) and ultraviolet (UV) spectra of sprites, halos and beads corresponding to the first (1PG) and second positive (2PG) bands of N2 have been calculated for different observation altitudes from mountains (3.25 km) to airplanes (14 km), balloons (35 km) and space (nadir) platforms. The calculated non‐equilibrium vibrational distribution functions (VDF) of the N2(B3Πg) states in halos and beads show that the calculated NIR emissions produced through strong N2‐1PG (B3Πg → A3Σu+) transitions differ from the calculated sprite spectral emission patterns at ∼888 nm but particularly pronounced differences are found in the NIR spectral region at ∼1046 nm and ∼1231 nm corresponding to the N2‐1PG (0,0) and (0,1) transitions, respectively. The blue ‐ near UV spectra from N2‐2PG (C3Πu → B3Πg) transitions in halos and beads also exhibits slightly different spectral features when compared to the blue ‐ near UV spectrum of sprites for bands originating from higher v‐levels (v > 0) although they might not be above electronic noise level to be distinguished.
THEMIS observations and modeling of multiple ion species and EMIC waves: Implications for a vanishing He+ stop band
Authors: Lee Justin H. , Chen Lunjin , Angelopoulos Vassilis , Thorne Richard M.
Published: May 2012

Observations of left‐hand polarized electro‐magnetic ion cyclotron (EMIC) waves with significant wave power across fHe+ are presented. Concurrent field and particle measurements reveal pitch angle scattering of thermal ions during the interval of maximum wave power. The observations suggest the presence of multiple cold ion species (H+, He+) at this time, below the sum of spacecraft potential and minimum energy of the ion instrument (i.e., <∼20 eV). Fortuitously, immediately following the most intense wave activity, the ambient plasma flow velocity became sufficiently large such that cold ions can be accelerated into the energy range of the particle instrument. Thus, two low energy ion components are revealed in the particle measurements at energies consistent with cold protons and He+. Maxwellian fits provide approximations of these cold ion species component densities and temperatures. The linear dispersion relation of parallel propagating EMIC waves for the observed conditions shows a vanishing cold plasma He+ stop band, consistent with the wave measurements during this interval. These results provide the first observational evidence of the importance of the cool ion species temperature/density in controlling linear wave growth through the heavy ion stop bands in warm plasma theory.
On the signature of the quasi‐3‐day wave in the thermosphere during the January 2010 URSI World Day Campaign
Authors: England Scott L. , Liu Guiping , Zhou Qihou , Immel Thomas J. , Kumar Karanam K. , Ramkumar Geetha
Published: May 2012

Ultra‐fast Kelvin waves with periods of 3–5 days are important in the coupling of the lower atmosphere to the thermosphere and ionosphere. Here we focus on the observations and effects of a 3‐day wave during January 2010. As this time period coincides with a stratospheric warming event, a coordinated set of observations with incoherent scatter radars are available. While there is no evidence that the occurrence of this 3‐day wave is connected with this event, these observations offer an unprecedented glimpse of the thermospheric conditions during this period, including the first‐ever detection of a 3‐day wave with an incoherent scatter radar. Using a combination of ground‐ and space‐based observations, we identify an eastward moving zonal wave number‐one 3‐day equatorial wave that is comprised of a Kelvin wave at the lowest latitudes and a Rossby‐gravity wave at higher latitudes. In the equatorial region, the vertical wavelength is ∼40 km and the wave peaks in amplitude around 95–100 km altitude. The wave observed here is only seen to propagate to around 105 km altitude. Evidence of an interaction between this wave and the diurnal tide is seen between 82–88 km. The resultant 3‐day periodicity in the diurnal tide is seen to propagate up to altitudes of ∼150 km. This could have a significant impact on the ionosphere via modulation of the E‐region dynamo, thus carrying the 3‐day periodicity to higher altitudes.
Turbulence production by nonbreaking waves: Laboratory and numerical simulations
Authors: Savelyev Ivan B. , Maxeiner Eric , Chalikov Dmitry
Published: May 2012

This paper investigates the effect of wave motion on the turbulence in close proximity to the surface. Some existing theories suggest mechanisms by which the energy is transferred from waves to turbulence. However, scarce empirical results struggle to establish the existence of such energy transfer and are not sufficient for thorough validation of existing theories. The present investigation relies on both experimental and numerical approaches. Turbulent velocities at the water surface were measured in a laboratory wave tank with high precision using the thermal‐marking velocimetry technique. Numerically, a fully nonlinear model for the wave motion was coupled with Large Eddy Simulation for the turbulent motion. The results confirm the turbulence production due to wave motion. The turbulent kinetic energy was found to be a function of time, wave steepness, wave phase, and initial turbulent conditions. Additionally, turbulent motion near the surface was found to be horizontally anisotropic due to the formation of near‐surface eddies, elongated in the direction of wave propagation.
The impact of spring subsurface soil temperature anomaly in the western U.S. on North American summer precipitation: A case study using regional climate model downscaling
Authors: Xue Yongkang , Vasic Ratko , Janjic Zavisa , Liu Y. M. , Chu Peter C.
Published: May 2012

This study explores the impact of spring subsurface soil temperature (SUBT) anomaly in the western U.S. on North American summer precipitation, mainly southeastern U.S., and possible mechanisms using a regional climate Eta model and a general circulation model (GCM). The GCM produces the lateral boundary condition (LBC) for the Eta model. Two initial SUBT conditions (one cold and another warm) on May 1st were assigned for the GCM runs and the corresponding Eta runs. The results suggest that antecedent May 1st warm initial SUBT in the western U.S. contributes positive June precipitation over the southern U.S. and less precipitation to the north, consistent with the observed anomalies between a year with a warm spring and a year with a cold spring in the western U.S. The anomalous cyclone induced by the surface heating due to SUBT anomaly propagated eastward through Rossby waves in westerly mean flow. In addition, the steering flow also contributed to the dissipation of perturbation in the northeastern U.S. and its enhancement in southeastern U.S. However, these results were obtained only when the Eta model run was driven by the corresponding GCM run. When the same reanalysis data were applied for both (cold and warm initial SUBT) Eta runs' LBCs, the precipitation anomalies could not be properly produced, indicating the intimate dependence of the regional climate sensitivity downscaling on the imposed global climate forcing, especially when the impact was through wave propagation in the large‐scale atmospheric flow.
Characterization of an acetyltransferase that detoxifies aromatic chemicals in Legionella pneumophila
Authors: Kubiak Xavier , Dervins-Ravault Delphine , Pluvinage Benjamin , Chaffotte Alain F. , Gomez-Valero Laura , Dairou Julien , Busi Florent , Dupret Jean-Marie , Buchrieser Carmen , Rodrigues-Lima Fernando
Published: May 2012

Legionella pneumophila is an opportunistic pathogen and the causative agent of Legionnaires' disease. Despite being exposed to many chemical compounds in its natural and man-made habitats (natural aquatic biotopes and man-made water systems), L. pneumophila is able to adapt and survive in these environments. The molecular mechanisms by which this bacterium detoxifies these chemicals remain poorly understood. In particular, the expression and functions of XMEs (xenobiotic-metabolizing enzymes) that could contribute to chemical detoxification in L. pneumophila have been poorly documented at the molecular and functional levels. In the present paper we report the identification and biochemical and functional characterization of a unique acetyltransferase that metabolizes aromatic amine chemicals in three characterized clinical strains of L. pneumophila (Paris, Lens and Philadelphia). Strain-specific sequence variations in this enzyme, an atypical member of the arylamine N-acetyltransferase family (EC 2.3.1.5), produce enzymatic variants with different structural and catalytic properties. Functional inactivation and complementation experiments showed that this acetyltransferase allows L. pneumophila to detoxify aromatic amine chemicals and grow in their presence. The present study provides a new enzymatic mechanism by which the opportunistic pathogen L. pneumophila biotransforms and detoxifies toxic aromatic chemicals. These data also emphasize the role of XMEs in the environmental adaptation of certain prokaryotes.
Dromion in space and laboratory dusty plasma
Authors: Annou K. , Annou R.
Published: May 2012

The nonlinear evolution of dust acoustic wave in magnetized dusty plasma was shown to obey the Davey-Stewartson I equation, which admits the so called dromion solutions.
Optimization of resistive switching performance of metal-manganite oxide interfaces by a multipulse protocol
Authors: Ghenzi N. , Sánchez M. J. , Rozenberg M. J. , Stoliar P. , Marlasca F. G. , Rubi D. , Levy P.
Published: May 2012

We explore different resistance states of La0.325Pr0.300Ca0.375MnO3-Ti interfaces as prototypes of non-volatile memory devices at room temperature. In addition to high and low resistance states accessible through bipolar pulsing with one pulse, higher resistance states can be obtained by repeatedly pulsing with a single polarity. The accumulative action of successive pulsing drives the resistance towards saturation, the time constant being a strong function of the pulsing amplitude. The experiments reveal that the pulsing amplitude and the number of applied pulses necessary to reach a target high resistance value appear to be in an exponential relationship, with a rate that results independent of the resistance value. Model simulations confirm these results and provide the oxygen vacancy profiles associated to the high resistance states obtained in the experiments.
Interface tension of silica hydroxylated nanoparticle with brine: A combined experimental and molecular dynamics study
Authors: de Lara Lucas S. , Michelon Mateus F. , Metin Cigdem O. , Nguyen Quoc P. , Miranda Caetano R.
Published: May 2012

We have used molecular dynamics simulations to calculate the interfacial tension of hydroxylated SiO2 nanoparticles under different temperatures and solutions (helium and brine with monovalent and divalent salts). In order to benchmark the atomistic model, quartz SiO2 interfacial tension was measured based on inverse gas chromatography under He atmosphere. The experimental interfacial tension values for quartz were found between 0.512 and 0.617 N/m. Our calculated results for the interfacial tension of silica nanoparticles within helium atmosphere was 0.676 N/m, which is higher than the value found for the system containing He/α-quartz (0.478 N/m), but it is similar to the one found for amorphous silica surface. We have also studied the interfacial tension of the nanoparticles in electrolyte aqueous solution for different types and salts concentrations (NaCl, CaCl2, and MgCl2). Our calculations indicate that adsorption properties and salt solutions greatly influence the interfacial tension in an order of CaCl2 > MgCl2 > NaCl. This effect is due to the difference in distribution of ions in solution, which modifies the hydration and electrostatic potential of those ions near the nanoparticle.
A six-dimensional wave packet study of the vibrational overtone induced decomposition of hydrogen peroxide
Authors: Wang Chunrui , Zhang Dong H. , Skodje Rex T.
Published: May 2012

A converged quantum wave packet study is presented for the unimolecular reaction HOOH → OH+OH induced by the fifth OH-overtone excitation employing an ab initio potential energy surface. All six internal vibrational degrees of freedom are explicitly represented in this simulation for total angular momentum zero. It is found that the decay of the survival probability and of the autocorrelation function is non-exponential and that the long time dynamics is likely due to the superposition of a number of resonance states. The simulated overtone spectrum and rotational product distribution is in good agreement with experimental measurements. It is concluded that: (1) the reaction dynamics is non-statistical on a 30 ps timescale, (2) the observed line width is roughly a factor of 1.7 larger than implied by the reactive lifetimes suggesting that a significant portion of the linewidth is due to intramolecular vibrational energy relaxation, and (3) the quantum reaction rate is suppressed by about a factor of two relative to its classical counterpart.
Defect energy levels and electronic behavior of Ni-, Co-, and As-doped synthetic pyrite (FeS2)
Authors: Lehner S. W. , Newman N. , van Schilfgaarde M. , Bandyopadhyay S. , Savage K. , Buseck P. R.
Published: May 2012

This work investigates the properties of Ni, Co, and As dopants in pyrite. Optical transmission spectroscopy and temperature-dependent Hall measurements were performed on doped pyrite crystals grown by chemical-vapor transport (CVT). The energy position(s) of the defect levels within the bandgap were determined from the optical spectrum. These values were then used to infer the concentration and occupancy of the defect levels from a statistical model fit to the temperature-dependent Hall concentration results. Doping pyrite with Ni atoms introduces partly filled, NiFe donor levels at 0.37 and 0.42 eV below the conduction band minimum (CBM). Doping with Co introduces a partially filled CoFe donor level at 0.09 eV below the CBM. Doping with As modifies the valence bands, which are of Fe d character. It reduces the gap slightly, and adds a hole. The Ni-doped, As-doped and undoped pyrite all have an absorption peak at 0.13 eV. Self-consistent GW electronic-structure calculations provide reliable conduction and valence band DOS for interpreting the optical spectra and fitting the data with the statistical model.
Photonic band structures of 1-D plasma photonic crystal with time-variation plasma density
Authors: Guo B. , Xie M. Q. , Qiu X. M. , Peng L.
Published: May 2012

The photonic band structures of one-dimensional plasma photonic crystal (1-D PPC) with time-variation plasma density are studied by using differential transfer matrix method. Taking an exponential functional form of time as an illustration of the time-varying plasma density, we examine the photonic band structures of the 1-D PPC. The results show that the photonic band structures can be tuned correspondingly by changing the time which modifies the plasma dielectric constant in different frequency regions, especially in the range of 0<ω<ωp0; whereas well above ωp0, the effects of the time-variation are small. The parameter dependence of the effects is also calculated and discussed.
Thermal nonlinearity in silicon microcylindrical resonators
Authors: Vukovic Natasha , Healy Noel , Mehta Priyanth , Day Todd D. , Sazio Pier J. A. , Badding John V. , Peacock Anna C.
Published: May 2012

We explore the thermally induced nonlinearity in hydrogenated amorphous silicon microcylindrical resonators that are fabricated from the silicon optical fiber platform. In particular, we use a pump-probe technique to experimentally demonstrate thermally induced optical modulation and determine the response time. Through characterization of the thermal properties and the associated resonance wavelength shifts, we will show that it is possible to infer the material absorption coefficient for a range of whispering gallery mode resonators.
Large area Co nanoring arrays fabricated on silicon substrate by anodic aluminum oxide template-assisted electrodeposition
Authors: Li Y. L. , Tang S. L , Xia W. B. , Chen L. Y. , Wang Y. , Tang T. , Du Y. W.
Published: May 2012

A simple approach based on anodic aluminum oxide template-assisted electrodeposition was developed to fabricate large-area Co nanoring arrays on silicon substrate. The ring outer diameter and interspace can be modulated by varying the anodization parameters. Magnetic measurements and micromagnetic simulation revealed that the onion to vortex (O-V) transition is strongly diameter dependent. With increasing the outer diameter from 100 nm to 300 nm, the O-V switching field gradually changes from positive value to negative value. This was also proved by in situ observation of the magnetic states of the rings under different external fields using magnetic force microscope.
Ripple formation on a nickel electrode during a glow discharge in a solution
Authors: Saito Genki , Hosokai Sou , Tsubota Masakatsu , Akiyama Tomohiro
Published: May 2012

We investigated ripple formation on a nickel electrode during a glow discharge in a solution. A nickel wire was partially melted to produce nanoparticles during glow discharge electrolysis. When the electrolysis time was over 30 min, a ripple pattern was formed on the electrode surface, and particle size increased. In this study, we investigated the relationship between the ripple formation and crystal orientation of the electrode. As a result, the ripple patterns were formed on all planes, except (111)- and (100)-oriented planes; their direction was [001].
Transcription factors c-Myc and CDX2 mediate E-selectin ligand expression in colon cancer cells undergoing EGF/bFGF-induced epithelial–mesenchymal transition
Authors: Sakuma Keiichiro , Aoki Masahiro , Kannagi Reiji
Published: May 2012

Sialyl Lewis x (sLe
x
) and sialyl Lewis a (sLe
a
) glycans are expressed on highly metastatic colon cancer cells. They promote extravasation of cancer cells and tumor angiogenesis via interacting with E-selectin on endothelial cells. Recently, epithelial–mesenchymal transition (EMT) has been noted as a critical phenotypic alteration in metastatic cancer cells. To address the association between sLe
x/a
expression and EMT, we assessed whether sLe
x/a
are highly expressed on colon cancer cells undergoing EMT. Treatment of HT29 and DLD-1 cells with EGF and/or basic FGF (bFGF) induced EMT and significantly increased sLe
x/a
expression resulting in enhanced E-selectin binding activity. The transcript levels of the glycosyltransferase genes
ST3GAL1
/
3
/
4
and
FUT3
were significantly elevated and that of
FUT2
was significantly suppressed by the treatment. We provide evidence that
ST3GAL1
/
3
/
4
and
FUT3
are transcriptionally up-regulated by c-Myc with probable involvement of Ser62 phosphorylation, and that
FUT2
is transcriptionally down-regulated through the attenuation of CDX2. The contribution of c-Myc and CDX2 to the sLe
x/a
induction was proved to be significant by knockdown or forced expression experiments. Interestingly, the cells undergoing EMT exhibited significantly increased VEGF secretion, which can promote tumor angiogenesis in cooperation with sLe
x/a
. Finally, immunohistological study indicated high E-selectin ligand expression on cancer cells undergoing EMT in vivo, supporting their coexistence observed in vitro. These results suggest a significant link between sLe
x/a
expression and EMT in colon cancer cells and a pivotal role of c-Myc and CDX2 in regulating sLe
x/a
expression during EMT.
Maturation cleavage of the murine leukemia virus Env precursor separates the transmembrane subunits to prime it for receptor triggering
Authors: Löving Robin , Wu Shang-Rung , Sjöberg Mathilda , Lindqvist Birgitta , Garoff Henrik
Published: May 2012

The Env protein of murine leukemia virus matures by two cleavage events. First, cellular furin separates the receptor binding surface (SU) subunit from the fusion-active transmembrane (TM) subunit and then, in the newly assembled particle, the viral protease removes a 16-residue peptide, the R-peptide from the endodomain of the TM. Both cleavage events are required to prime the Env for receptor-triggered activation. Cryoelectron microscopy (cryo-EM) analyses have shown that the mature Env forms an open cage-like structure composed of three SU–TM complexes, where the TM subunits formed separated Env legs. Here we have studied the structure of the R-peptide precursor Env by cryo-EM. TM cleavage in Moloney murine leukemia virus was inhibited by amprenavir, and the Envs were solubilized in Triton X-100 and isolated by sedimentation in a sucrose gradient. We found that the legs of the R-peptide Env were held together by trimeric interactions at the very bottom of the Env. This suggested that the R-peptide ties the TM legs together and that this prevents the activation of the TM for fusion. The model was supported by further cryo-EM studies using an R-peptide Env mutant that was fusion-competent despite an uncleaved R-peptide. The Env legs of this mutant were found to be separated, like in the mature Env. This shows that it is the TM leg separation, normally caused by R-peptide cleavage, that primes the Env for receptor triggering.
Trapping and structure determination of an intermediate in the allosteric transition of aspartate transcarbamoylase
Authors: Guo Wenyue , West Jay M. , Dutton Andrew S. , Tsuruta Hiro , Kantrowitz Evan R.
Published: May 2012

X-ray crystallography and small-angle X-ray scattering (SAXS) in solution have been used to show that a mutant aspartate transcarbamoylase exists in an intermediate quaternary structure between the canonical T and R structures. Additionally, the SAXS data indicate a pH-dependent structural alteration consistent with either a pH-induced conformational change or a pH-induced alteration in the T to R equilibrium. These data indicate that this mutant is not a model for the R state, as has been proposed, but rather represents the enzyme trapped along the path of the allosteric transition between the T and R states.
Amino acid coevolution induces an evolutionary Stokes shift
Authors: Pollock David D. , Thiltgen Grant , Goldstein Richard A.
Published: May 2012

The process of amino acid replacement in proteins is context-dependent, with substitution rates influenced by local structure, functional role, and amino acids at other locations. Predicting how these differences affect replacement processes is difficult. To make such inference easier, it is often assumed that the acceptabilities of different amino acids at a position are constant. However, evolutionary interactions among residue positions will tend to invalidate this assumption. Here, we use simulations of purple acid phosphatase evolution to show that amino acid propensities at a position undergo predictable change after an amino acid replacement at that position. After a replacement, the new amino acid and similar amino acids tend to become gradually more acceptable over time at that position. In other words, proteins tend to equilibrate to the presence of an amino acid at a position through replacements at other positions. Such a shift is reminiscent of the spectroscopy effect known as the Stokes shift, where molecules receiving a quantum of energy and moving to a higher electronic state will adjust to the new state and emit a smaller quantum of energy whenever they shift back down to the original ground state. Predictions of changes in stability in real proteins show that mutation reversals become less favorable over time, and thus, broadly support our results. The observation of an evolutionary Stokes shift has profound implications for the study of protein evolution and the modeling of evolutionary processes.
Bergmann glia modulate cerebellar Purkinje cell bistability via Ca
2+
-dependent K
+
uptake
Authors: Wang Fushun , Xu Qiwu , Wang Weishan , Takano Takahiro , Nedergaard Maiken
Published: May 2012

Recent studies have shown that cerebellar Bergmann glia display coordinated Ca
2+
transients in live mice. However, the functional significance of Bergmann glial Ca
2+
signaling remains poorly understood. Using transgenic mice that allow selective stimulation of glial cells, we report here that cytosolic Ca
2+
regulates uptake of K
+
by Bergmann glia, thus providing a powerful mechanism for control of Purkinje cell-membrane potential. The decline in extracellular K
+
evoked by agonist-induced Ca
2+
in Bergmann glia transiently increased spike activity of Purkinje cells in cerebellar slices as well as in live anesthetized mice. Thus, Bergmann glia play a previously unappreciated role in controlling the membrane potential and thereby the activity of adjacent Purkinje cells.
Nanodiamonds and wildfire evidence in the Usselo horizon postdate the Allerød-Younger Dryas boundary
Authors: van Hoesel Annelies , Hoek Wim Z. , Braadbaart Freek , van der Plicht Johannes , Pennock Gillian M. , Drury Martyn R.
Published: May 2012

The controversial Younger Dryas impact hypothesis suggests that at the onset of the Younger Dryas an extraterrestrial impact over North America caused a global catastrophe. The main evidence for this impact—after the other markers proved to be neither reproducible nor consistent with an impact—is the alleged occurrence of several nanodiamond polymorphs, including the proposed presence of lonsdaleite, a shock polymorph of diamond. We examined the Usselo soil horizon at Geldrop-Aalsterhut (The Netherlands), which formed during the Allerød/Early Younger Dryas and would have captured such impact material. Our accelerator mass spectrometry radiocarbon dates of 14 individual charcoal particles are internally consistent and show that wildfires occurred well after the proposed impact. In addition we present evidence for the occurrence of cubic diamond in glass-like carbon. No lonsdaleite was found. The relation of the cubic nanodiamonds to glass-like carbon, which is produced during wildfires, suggests that these nanodiamonds might have formed after, rather than at the onset of, the Younger Dryas. Our analysis thus provides no support for the Younger Dryas impact hypothesis.
Common patterns and disease-related signatures in tuberculosis and sarcoidosis
Authors: Maertzdorf Jeroen , Weiner January , Mollenkopf Hans-Joachim , Network TBornotTB , Bauer Torsten , Prasse Antje , Müller-Quernheim Joachim , Kaufmann Stefan H. E. , Bellinger Oswald , Diel Roland , Ehlers Stefan , Heykes-Uden Helga , Hölscher Christoph , Kaufmann Stefan H. E. , Lange Christoph , Meyer Christian , Niemann Stefan , Nöthlings Ute , Reiling Norbert , Schaberg Tom , Stenger Steffen
Published: May 2012

In light of the marked global health impact of tuberculosis (TB), strong focus has been on identifying biosignatures. Gene expression profiles in blood cells identified so far are indicative of a persistent activation of the immune system and chronic inflammatory pathology in active TB. Definition of a biosignature with unique specificity for TB demands that identified profiles can differentiate diseases with similar pathology, like sarcoidosis (SARC). Here, we present a detailed comparison between pulmonary TB and SARC, including whole-blood gene expression profiling, microRNA expression, and multiplex serum analytes. Our analysis reveals that previously disclosed gene expression signatures in TB show highly similar patterns in SARC, with a common up-regulation of proinflammatory pathways and IFN signaling and close similarity to TB-related signatures. microRNA expression also presented a highly similar pattern in both diseases, whereas cytokines in the serum of TB patients revealed a slightly elevated proinflammatory pattern compared with SARC and controls. Our results indicate several differences in expression between the two diseases, with increased metabolic activity and significantly higher antimicrobial defense responses in TB. However, matrix metallopeptidase 14 was identified as the most distinctive marker of SARC. Described communalities as well as unique signatures in blood profiles of two distinct inflammatory pulmonary diseases not only have considerable implications for the design of TB biosignatures and future diagnosis, but they also provide insights into biological processes underlying chronic inflammatory disease entities of different etiology.
Inversion of neurovascular coupling by subarachnoid blood depends on large-conductance Ca
2+
-activated K
+
(BK) channels
Authors: Koide Masayo , Bonev Adrian D. , Nelson Mark T. , Wellman George C.
Published: May 2012

The cellular events that cause ischemic neurological damage following aneurysmal subarachnoid hemorrhage (SAH) have remained elusive. We report that subarachnoid blood profoundly impacts communication within the neurovascular unit—neurons, astrocytes, and arterioles—causing inversion of neurovascular coupling. Elevation of astrocytic endfoot Ca
2+
to ∼400 nM by neuronal stimulation or to ∼300 nM by Ca
2+
uncaging dilated parenchymal arterioles in control brain slices but caused vasoconstriction in post-SAH brain slices. Inhibition of K
+
efflux via astrocytic endfoot large-conductance Ca
2+
-activated K
+
(BK) channels prevented both neurally evoked vasodilation (control) and vasoconstriction (SAH). Consistent with the dual vasodilator/vasoconstrictor action of extracellular K
+
([K
+
]
o
), [K
+
]
o
<10 mM dilated and [K
+
]
o
>20 mM constricted isolated brain cortex parenchymal arterioles with or without SAH. Notably, elevation of external K
+
to 10 mM caused vasodilation in brain slices from control animals but caused a modest constriction in brain slices from SAH model rats; this latter effect was reversed by BK channel inhibition, which restored K
+
-induced dilations. Importantly, the amplitude of spontaneous astrocytic Ca
2+
oscillations was increased after SAH, with peak Ca
2+
reaching ∼490 nM. Our data support a model in which SAH increases the amplitude of spontaneous astrocytic Ca
2+
oscillations sufficiently to activate endfoot BK channels and elevate [K
+
]
o
in the restricted perivascular space. Abnormally elevated basal [K
+
]
o
combined with further K
+
efflux stimulated by neuronal activity elevates [K
+
]
o
above the dilation/constriction threshold, switching the polarity of arteriolar responses to vasoconstriction. Inversion of neurovascular coupling may contribute to the decreased cerebral blood flow and development of neurological deficits that commonly follow SAH.
Hydrodynamic stretching of single cells for large population mechanical phenotyping
Authors: Gossett Daniel R. , Tse Henry T. K. , Lee Serena A. , Ying Yong , Lindgren Anne G. , Yang Otto O. , Rao Jianyu , Clark Amander T. , Di Carlo Dino
Published: May 2012

Cell state is often assayed through measurement of biochemical and biophysical markers. Although biochemical markers have been widely used, intrinsic biophysical markers, such as the ability to mechanically deform under a load, are advantageous in that they do not require costly labeling or sample preparation. However, current techniques that assay cell mechanical properties have had limited adoption in clinical and cell biology research applications. Here, we demonstrate an automated microfluidic technology capable of probing single-cell deformability at approximately 2,000 cells/s. The method uses inertial focusing to uniformly deliver cells to a stretching extensional flow where cells are deformed at high strain rates, imaged with a high-speed camera, and computationally analyzed to extract quantitative parameters. This approach allows us to analyze cells at throughputs orders of magnitude faster than previously reported biophysical flow cytometers and single-cell mechanics tools, while creating easily observable larger strains and limiting user time commitment and bias through automation. Using this approach we rapidly assay the deformability of native populations of leukocytes and malignant cells in pleural effusions and accurately predict disease state in patients with cancer and immune activation with a sensitivity of 91% and a specificity of 86%. As a tool for biological research, we show the deformability we measure is an early biomarker for pluripotent stem cell differentiation and is likely linked to nuclear structural changes. Microfluidic deformability cytometry brings the statistical accuracy of traditional flow cytometric techniques to label-free biophysical biomarkers, enabling applications in clinical diagnostics, stem cell characterization, and single-cell biophysics.
Subcortical encoding of sound is enhanced in bilinguals and relates to executive function advantages
Authors: Krizman Jennifer , Marian Viorica , Shook Anthony , Skoe Erika , Kraus Nina
Published: May 2012

Bilingualism profoundly affects the brain, yielding functional and structural changes in cortical regions dedicated to language processing and executive function [Crinion J, et al. (2006)
Science
312:1537–1540; Kim KHS, et al. (1997)
Nature
388:171–174]. Comparatively, musical training, another type of sensory enrichment, translates to expertise in cognitive processing and refined biological processing of sound in both cortical and subcortical structures. Therefore, we asked whether bilingualism can also promote experience-dependent plasticity in subcortical auditory processing. We found that adolescent bilinguals, listening to the speech syllable [da], encoded the stimulus more robustly than age-matched monolinguals. Specifically, bilinguals showed enhanced encoding of the fundamental frequency, a feature known to underlie pitch perception and grouping of auditory objects. This enhancement was associated with executive function advantages. Thus, through experience-related tuning of attention, the bilingual auditory system becomes highly efficient in automatically processing sound. This study provides biological evidence for system-wide neural plasticity in auditory experts that facilitates a tight coupling of sensory and cognitive functions.
Regulators of G protein signaling RGS7 and RGS11 determine the onset of the light response in ON bipolar neurons
Authors: Cao Yan , Pahlberg Johan , Sarria Ignacio , Kamasawa Naomi , Sampath Alapakkam P. , Martemyanov Kirill A.
Published: May 2012

The time course of signaling via heterotrimeric G proteins is controlled through their activation by G-protein coupled receptors and deactivation through the action of GTPase accelerating proteins (GAPs). Here we identify RGS7 and RGS11 as the key GAPs in the mGluR6 pathway of retinal rod ON bipolar cells that set the sensitivity and time course of light-evoked responses. We showed using electroretinography and single cell recordings that the elimination of RGS7 did not influence dark-adapted light-evoked responses, but the concurrent elimination of RGS11 severely reduced their magnitude and dramatically slowed the onset of the response. In RGS7/RGS11 double-knockout mice, light-evoked responses in rod ON bipolar cells were only observed during persistent activation of rod photoreceptors that saturate rods. These observations are consistent with persistently high G-protein activity in rod ON bipolar cell dendrites caused by the absence of the dominant GAP, biasing TRPM1 channels to the closed state.
Requirement of Rad18 protein for replication through DNA lesions in mouse and human cells
Authors: Yoon Jung-Hoon , Prakash Satya , Prakash Louise
Published: May 2012

In yeast, the Rad6-Rad18 ubiquitin conjugating enzyme plays a critical role in promoting replication although DNA lesions by translesion synthesis (TLS). In striking contrast, a number of studies have indicated that TLS can occur in the absence of Rad18 in human and other mammalian cells, and also in chicken cells. In this study, we determine the role of Rad18 in TLS that occurs during replication in human and mouse cells, and show that in the absence of Rad18, replication of duplex plasmids containing a
cis-syn
TT dimer or a (6-4) TT photoproduct is severely inhibited in human cells and that mutagenesis resulting from TLS opposite cyclobutane pyrimidine dimers and (6-4) photoproducts formed at the TT, TC, and CC dipyrimidine sites in the chromosomal
cII
gene in UV-irradiated mouse cells is abolished. From these and other observations with Rad18, we conclude that the Rad6-Rad18 enzyme plays an essential role in promoting replication through DNA lesions by TLS in mammalian cells. In contrast, the dispensability of Rad18 for TLS in chicken DT40 cells would suggest that the role of the Rad6-Rad18 enzyme complex has diverged considerably between chicken and mammals, raising the possibility that TLS mechanisms differ among them.
Apoptotic marginal zone deletion of anti-Sm/ribonucleoprotein B cells
Authors: Kishi Yusuke , Higuchi Tetsuya , Phoon Shirly , Sakamaki Yasuo , Kamiya Koki , Riemekasten Gabriela , Akiyoshi Kazunari , Weigert Martin G. , Tsubata Takeshi
Published: May 2012

CD40L is excessively produced in both human and murine lupus and plays a role in lupus pathogenesis. To address how excess CD40L induces autoantibody production, we crossed CD40L-transgenic mice with the anti-DNA H-chain transgenic mouse lines 3H9 and 56R, well-characterized models for studying B-cell tolerance to nuclear antigens. Excess CD40L did not induce autoantibody production in 3H9 mice in which anergy maintains self-tolerance, nor did it perturb central tolerance, including deletion and receptor editing, of anti-DNA B cells in 56R mice. In contrast, CD40L/56R mice restored a large number of marginal zone (MZ) B cells reactive to Sm/ribonucleoprotein (RNP) and produced autoantibody, whereas these B cells were deleted by apoptosis in MZ of 56R mice. Thus, excess CD40L efficiently blocked tolerance of Sm/RNP-reactive MZ B cells, leading to production of anti-Sm/RNP antibody implicated in the pathogenesis of lupus. These results suggest that self-reactive B cells such as anti-Sm/RNP B cells, which somehow escape tolerance in the bone marrow and migrate to MZ, are tolerized by apoptotic deletion in MZ and that a break in this tolerance may play a role in the pathogenesis of lupus.