bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluid dynamical implications of anastomosing slope streaks on Mars
Authors: Miyamoto Hideaki , Dohm James M. , Beyer Ross A. , Baker Victor R.
Published: June 2004

The Mars Global Surveyor mission has imaged slope streaks, some of which have formed in periods as short as 109 days. These features are one of the most currently active surface processes on Mars. Some slope streaks have flow‐like morphologic characteristics, which include anastomosing patterns influenced by small topographic barriers. In order to understand what processes gave rise to these specific features, we applied viscoplastic flow numerical modeling techniques to simulated Martian surfaces. We simulate Martian surfaces with observed slope streaks by using Mars Orbiter Laser Altimeter measurements to obtain large‐scale slope measurements and a photoclinometry technique on Mars Orbiter Camera images to obtain meter‐scale topographic information. Our numerical simulations of slow‐moving plastic flows show that a fluid rheology and a short formation period are necessary to explain these features. We estimate that the typical values of bulk viscosity and bulk yield strength are less than 10 Pa s and less than 10 Pa, respectively. The fluid rheology can be explained by a water‐related flow with a solid content less than about 20%. An alternative explanation is a dry grain flow with extremely low cohesion and friction angle supported by dispersive pressure or a lubricant, such as electric conditions of particles. The continuous nature of anastomosing slope streaks that originate from point sources is best explained by continuous discharges of material or lubricant. In this case, the estimated flow rate is less than several cubic meters per second, and the flow duration is estimated to be less than a day.
Diurnal variability of subglacial drainage conditions as revealed by tracer experiments
Authors: Schuler T. , Fischer U. H. , Gudmundsson G. H.
Published: June 2004

The morphology of the drainage system of Unteraargletscher, Switzerland, and the diurnal variability of drainage conditions were investigated by conducting a series of tracer tests over a number of discharge cycles during the ablation season 2000. Dye injections into a moulin were repeated at intervals of a few hours and were accompanied by simultaneous measurements of discharge of supraglacial meltwater draining into the moulin and bulk runoff in the proglacial stream. Fast transit velocities in conjunction with low dispersion values suggest that the tracer was routed through a hydraulically efficient, channelized drainage system. However, detailed analyses reveal a large diurnal variability in terms of transit velocity and dispersion coefficient. This finding underlines the difficulty of detecting a possible drainage system evolution based on single tracer tests conducted at coarse temporal intervals. Furthermore, the obtained velocity‐discharge relationships display pronounced hysteresis. We suggest that the evolution of the cross‐sectional area of an ice‐walled conduit and the modulation of inflow at the junction of a tributary moulin to a main subglacial channel are responsible for the observed behavior.
Dust‐induced changes in phytoplankton composition in the Tasman Sea during the last four glacial cycles
Authors: Calvo Eva , Pelejero Carles , Logan Graham A. , De Deckker Patrick
Published: June 2004

An increase in iron supply associated with enhanced dust inputs could be responsible for higher marine phytoplankton production leading to the typically lower glacial atmospheric CO2 concentrations, as suggested by the “iron hypothesis.” The enhanced dust supply may also have provided the oceans with significant amounts of silica, which would have favored the growth of diatoms over coccolithophores, as suggested by the “silica hypothesis.” Here we present new data on molecular biomarkers in a sediment core from the midlatitudes of the Southern Hemisphere, which reveal dust‐induced changes in the relative contribution of the phytoplankton to total productivity. Our results illustrate a shift in the relative abundance of siliceous over calcareous organisms during glacial times, when terrestrial aeolian input was enhanced. Although we did not detect a significant glacial decrease in coccolithophorid productivity, the decrease in the CaCO3/Corg rain ratio could have still contributed to some extent in lowering atmospheric CO2 levels.
Interference suppression factor characteristics of complementary codes for ST/MST radar applications
Authors: Ghebrebrhan Ogubazghi , Luce Hubert , Yamamoto Mamoru , Fukao Shoichiro
Published: June 2004

In a coding system that uses complementary codes, the decoding process favors the geophysical signal and other radar returns which have been coded by the radar system, while interference signals may be attenuated. The attenuation is relative to the geophysical signal and is dependent on the spectral characteristics of the interference signal and the code used. An interference suppression factor (ISF) is defined as the ratio (in dB) of the power gains of the interference to that of the geophysical signals, as both traverse the coherent integration and decoding stages of the radar signal processor. ISF values of codes, in and around the zero Doppler frequency band, are obtained analytically, while the corresponding values for other frequency bands are estimated from simulations performed using the sinusoidal interference signal. The results show that codes having an equal number of opposite elements have superior performances over other codes as they have better values of ISF in and around the zero Doppler frequency band, a segment of the spectrum where the geophysical signal is expected. This is confirmed by the observations made using the middle and upper atmosphere radar in Japan, where other experiments intended to study the effectiveness of different codes have also been performed, and the results are reported.
F region plasma density estimation at Jicamarca using the complex cross‐correlation of orthogonal polarized backscatter fields
Authors: Feng Zhaomei , Kudeki Erhan , Woodman Ronald F. , Chau Jorge , Milla Marco
Published: June 2004

The differential‐phase method for Jicamarca F region density measurements has been modified to fit the real and imaginary components of the cross‐correlation of orthogonally polarized radar returns. The original method [Kudeki et al., 2003; Feng et al., 2003] based on fitting the cross‐correlation phase could only make use of correlation data from lower F region heights since the phase noise in low‐SNR upper F region returns is typically non‐Gaussian. However, upper F region correlation data become useful in the modified method since the fluctuations in real and imaginary parts of cross‐correlation remain Gaussian even under low‐SNR conditions.
Inverse modeling of large‐scale spatially distributed vadose zone properties using global optimization
Authors: Vrugt Jasper A. , Schoups Gerrit , Hopmans Jan W. , Young Chuck , Wallender Wesley W. , Harter Thomas , Bouten Willem
Published: June 2004

Computational capabilities have evolved to a point where it is possible to use multidimensional physically based hydrologic models to study spatial and temporal patterns of water flow in the vadose zone. However, models based on multidimensional governing equations have only received limited attention, in particular because of their computational, distributed input, and parameter estimation requirements. The aim of the present paper is to explore the usefulness and applicability of the inverse method to estimate vadose zone properties using the solution of a physically based, distributed three‐dimensional model combined with spatially distributed measured tile drainage data from the 3880‐ha Broadview Water District (BWD) in the San Joaquin Valley of California. The inverse problem is posed within a single‐criterion Bayesian framework and solved by means of the computerized Shuffled Complex Evolution Metropolis global optimization algorithm. To study the benefits of using a spatially distributed three‐dimensional vadose zone model, the results of the 3‐D model were compared with those obtained using a simple storage‐based bucket model and a spatially averaged one‐dimensional unsaturated water flow model for a 2‐year period. District‐wide results demonstrate that measured spatially distributed patterns of drainage data contain only limited information for the identification of vadose zone model parameters and are particularly inadequate to identify the soil hydraulic properties. In contrast, the drain conductance and a soil matrix bypass coefficient were well determined, indicating that the dominant hydrology of the BWD was determined by drain system properties and preferential flow. Despite the significant CPU time needed for model calibration, results suggest that there are advantages in using physically based hydrologic models to study spatial and temporal patterns of water flow at the scale of a watershed. These models not only generate consistent forecasts of spatially distributed drainage data during the calibration and validation period but also possess unbiased predictive capabilities with respect to measured groundwater table depths not included in the calibration.
Breathing of coastal vadose zone induced by sea level fluctuations
Authors: Jiao Jiu J. , Li Hailong
Published: June 2004

Tide‐induced variations in subsurface air pressure, mainly between −1.0 to 2.0 kPa, are observed in coastal areas in Hong Kong. A two‐dimensional model which couples the two‐phase air‐water flow in unsaturated and saturated zones successfully reproduces the observed air pressure under no rain conditions. The simulation reveals that significant increases in air pressure depend on the tidal rate, not necessarily on the amplitude of the sea level fluctuation. With rainfall, abnormal air pressure 2–9 times greater than without rainfall can be generated when the geological structure, the period and intensity of rain, and the timing of rainfall with respect to the maximum tidal rate combine favorably. This study provides a better understanding of the interactions among the sea tides, barometric pressure variations, groundwater and air‐water flow, and rainfall. This natural coastal breathing phenomenon has relevance to the transfer of gases across the soil‐seawater‐atmosphere interface and to coastal environments around the world.
Seasonal mass balance of halogens in simulated rice paddies
Authors: Redeker K. R. , Manley S. L. , Brothers L. , McDuffee K. , Walser M. , Cicerone R. J.
Published: June 2004

Halogens released from soil reservoirs to the atmosphere play important roles in atmospheric chemistry, including ozone loss and aerosol formation. Closed system experiments to determine controlling factors in halogen movement between the pedosphere, hydrosphere, terrestrial biosphere, and atmosphere are needed. This paper presents results from a closed system experiment on simulated rice paddies. It was observed that most water‐extractable (bioavailable), halogens were swept downward from the surface during the initial watering pulse (∼50, 70, and 75% of chloride, bromide, and iodide in unadulterated soils). Soil halogens were sequestered by rice plants with 28, 4, and 24% of the remaining bioavailable chlorine, bromine, and iodine processed by the plant tissue by the end of the season. Of the bioavailable halogens taken into the rice plant, less than 1% of chlorine or bromine is volatilized as a methyl halide while over 90% of iodide is emitted as gaseous CH3I.
234Th deficit and excess in the Southern Ocean during spring 2001: Particle export and remineralization
Authors: Savoye N. , Buesseler K. O. , Cardinal D. , Dehairs F.
Published: June 2004

234Th deficit and excess were examined in the upper 500 m of the Southern Ocean from Sub‐Antarctic to Seasonal Ice Zones (Australian sector) during austral spring 2001.234Th fluxes at 100 m indicate that particle export was low in the North (46.9–51.0°S), minimal in the Polar and Inter‐Polar Frontal Zones and high in the South (≥61°S). These results are in tight agreement with new production estimates from the same cruise. Our data indicate that Polar and Inter‐Polar Frontal Zones were not zones of intense export in the Australian sector at this time of year, in contrast with other sectors of the Southern Ocean. Also, we highlight the usefulness of234Th excess below the mixed layer as a tool to study mesopelagic remineralization.
Deep seismic structure of the Atacama basin, northern Chile
Authors: Schurr B. , Rietbrock A.
Published: June 2004

The Atacama basin is a prominent morphological anomaly in the Central Andean forearc. 3D seismic structure beneath the depression and its surroundings has been determined from local earthquake tomography. Depth maps of P‐wave velocity and attenuation (1/Qp) through the lithosphere reveal a rheologically strong (high Qp and vp) lithospheric block beneath the basin, surrounded by weak regions (low Qp and vp) beneath Pre‐ and Western Cordilleras. The anomalous lithospheric structure appears to bar hot asthenospheric mantle from penetrating trenchward, and hence causes the volcanic front to be deflected by the Salar de Atacama basin. The cold block may also influence the thermal structure of the subducted slab causing reduced Benioff seismicity and less hydration of mantle rocks evident from reduced vp/vs ratios. Seismic data are hard to reconcile with extension and lithospheric thinning as a mechanism for subsidence of the basin. Instead, high strength of the Atacama lithospheric block may contribute to basin formation by focussing deformation and uplift along the block's weak edges.
The pattern of northern hemisphere surface air temperature during prolonged periods of low solar output
Authors: Ruzmaikin Alexander , Feynman Joan , Jiang Xun , Noone David C. , Waple Anne M. , Yung Yuk L.
Published: June 2004

We show that the reconstructed sensitivity of the sea level temperature to long term solar forcing in the Northern Hemisphere is in very good agreement with the empirical temperature pattern corresponding to changes of the North Annular Mode (NAM). This implies that long‐term variations of solar output affect climate predominantly through the NAM that extends throughout the stratosphere and troposphere.
Does the Taiwan warm current exist in winter?
Authors: Zhu Jianrong , Chen Changsheng , Ding Pingxing , Li Chunyan , Lin Huichan
Published: June 2004

It has been argued for many years whether the Taiwan Warm Current (TWC) exists in winter, though there is no question about its existence in summer. A regional CTD survey and anchored ADCP measurements were conducted off the mouth of the Changjiang on the western shelf of the East China Sea from 24 February to 10 March 2001. Both hydrographic and current data showed an evidence of the TWC, which flowed northeastward along the 50‐m isobath and intruded into the submerged river valley off the Changjiang. This current is sub‐surface intensified, with a maximum velocity of 30 cm/s occurring at a depth of 30 m below the surface. This finding was consistent with the satellite‐derived SST image received on 26–30 January 1986 and MODIS SST image received on 18 February 2001. It suggests that the TWC is at least an episodic feature in the East China Sea and its occurrence and duration might vary due to meandering of the Kuroshio around the Taiwan Strait.
Radio emission from mini‐magnetospheres on the Moon
Authors: Kuncic Zdenka , Cairns Iver H.
Published: June 2004

Small‐scale, localized magnetic anomalies on the surface of planetary satellites effectively create “mini‐magnetospheres”, which can lead to standoff shocks analogous to planetary bow shocks. This gives rise to the tantalizing possibility that radio emission can be produced in the vicinity of such mini‐magnetospheres, since it is well known that radio emissions are directly associated with the foreshock regions of planetary bow shocks and travelling interplanetary shocks. In this letter, we generalize a theoretical model for foreshock radio emissions in order to determine whether observable radio fluxes can also be generated near mini‐magnetospheres. We show that, when applied specifically to the Moon, this model predicts that mini‐magnetospheres should produce radio fluxes above current instrument sensitivity limits. Moreover, the predicted strong dependence of the radio emission on the upstream plasma properties may have important implications for the model's applicability to other planetary satellites.
The West Philippine Basin and the initiation of subduction, revisited
Authors: Taylor Brian , Goodliffe Andrew M.
Published: June 2004

New swath bathymetry plus existing geophysical data reveal that the direction of West Philippine Basin (WPB) seafloor spreading rotated 100° counter‐clockwise between 49 Ma and 33 Ma. The curvilinear and multi‐stranded Mindanao Fracture Zone separates the WPB from the Palau Basin to the south. WPB opening was contemporaneous with, and behind, early Izu‐Bonin‐Mariana (IBM) subduction, whose arc volcanism began by 50 Ma. This produced over 1000 km of arc parallel spreading (or stretching plus magmatism) in the Mariana segment of the Eocene IBM arc/forearc. The initial IBM subduction cut across, rather than followed, pre‐existing structures (remnant arcs, fracture zones and spreading fabric). New models of subduction initiation are required to reproduce such characteristics.
Transport extremum through Denmark Strait
Authors: Stern Melvin E.
Published: June 2004

A single layer of fluid with thickness h(x) and geostrophic velocity u = (g′/f)∂(h + M)/∂x is conventionally used to model the flow of a density current over a sill/contraction, where M(x) is the cross‐stream (x) bottom elevation, g′ = gΔρ/ρ is reduced gravity, and f is the Coriolis parameter. The interface [h] intersects the parabolic bottom at two points x = ξ,L, with M(L) = H given. A new extremum for the volume discharge Q is obtained which is approximately half that of the Killworth‐Whitehead upper bound, and which agrees with measurements in the Denmark Strait.
Ground/satellite signatures of field line resonance: A test of theoretical predictions
Authors: Vellante M. , Lühr H. , Zhang T. L. , Wesztergom V. , Villante U. , De Lauretis M. , Piancatelli A. , Rother M. , Schwingenschuh K. , Koren W. , Magnes W.
Published: June 2004

During June–July 2002 the low‐altitude (h ∼ 400 km) Challenging Minisatellite Payload (CHAMP) satellite passed approximately every 2nd day close to the South European Geomagnetic Array (SEGMA, 1.56 < L < 1.88) during daytime hours. We present here the analysis of a Pc3 geomagnetic pulsation event observed simultaneously in space and at the ground array during the conjunction of 6 July 2002. Both compressional and transverse oscillations were identified in CHAMP magnetic measurements. A close correspondence between the compressional component and the ground signals is observed. The behavior of the CHAMP azimuthal component shows evidence for the occurrence of a field line resonance at L ≅ 1.6. The frequency of these azimuthal oscillations is ∼20% higher than the frequency of both the compressional oscillation and the ground pulsations. Such a difference is explained in terms of a sort of Doppler shift caused by the fast movement of the satellite across the resonance region where the phase signal changes rapidly. A further analysis verifies for the first time by space measurements the theoretical pattern of the wave polarization sense in the resonance region. The comparison with corresponding SEGMA measurements also provides an unprecedented direct confirmation of the well‐known 90° rotation of the ULF wave polarization ellipse through the ionosphere.
First spaceborne observations of Antarctic stratospheric ClONO2 recovery: Austral spring 2002
Authors: Höpfner M. , von Clarmann T. , Fischer H. , Glatthor N. , Grabowski U. , Kellmann S. , Kiefer M. , Linden A. , Mengistu Tsidu G. , Milz M. , Steck T. , Stiller G. P. , Wang D. Y. , Funke B.
Published: June 2004

We report on the first spaceborne observations of ClONO2 recovery in the springtime Antarctic polar vortex, performed by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) from 8 September to 13 October 2002. ClONO2 was retrieved by constrained nonlinear least squares fit from MIPAS measurements with a vertical resolution of 3.3–3.8 km and an estimated accuracy of 6–11% in the lower stratosphere (18–27 km). During the end of September 2002 an unusual major stratospheric warming affected the polar vortex. At the 475 K potential temperature level, ClONO2 showed a pronounced collar structure with high mixing ratios at the vortex edge and values of 0.5–0.6 ppbv in the inner region from 8 to 17 September. During the following 8 days, mean inner vortex ClONO2 increased by 0.8 ppbv accompanied by a decrease of ClO. Thus from 18 to 25 September the conversion into ClONO2 was a major pathway for chlorine deactivation at 475 K. After 25 September, ClONO2 decreased because of conversion into HCl. The onset of chlorine deactivation at 475 K is consistent with the latest polar stratospheric clouds detected by MIPAS on 18 September. At 625 K, mean inner vortex ClONO2 mixing ratios decreased from 2 to 1.35 ppbv from 8 September to 13 October. This evolution was interrupted by temporary chlorine activation from 12 to 16 September when values of 1.55 ppbv were reached. Comparison with previous measurements and model results of 1992 show similar chlorine partitioning at 475 K before the major warming in 2002. However, there is indication that in 2002 the evolution of chlorine deactivation at 475 K was characterized by a faster and more pronounced increase of ClONO2 compared with 1992.
Spatial synchrony of local populations has increased in association with the recent Northern Hemisphere climate trend
Authors: Post Eric , Forchhammer Mads C.
Published: June 2004

According to ecological theory, populations whose dynamics are entrained by environmental correlation face increased extinction risk as environmental conditions become more synchronized spatially. This prediction is highly relevant to the study of ecological consequences of climate change. Recent empirical studies have indicated, for example, that large-scale climate synchronizes trophic interactions and population dynamics over broad spatial scales in freshwater and terrestrial systems. Here, we present an analysis of century-scale, spatially replicated data on local weather and the population dynamics of caribou in Greenland. Our results indicate that spatial autocorrelation in local weather has increased with large-scale climatic warming. This increase in spatial synchrony of environmental conditions has been matched, in turn, by an increase in the spatial synchrony of local caribou populations toward the end of the 20th century. Our results indicate that spatial synchrony in environmental conditions and the populations influenced by them are highly variable through time and can increase with climatic warming. We suggest that if future warming can increase population synchrony, it may also increase extinction risk.
Modulation of the polyamine biosynthetic pathway in transgenic rice confers tolerance to drought stress
Authors: Capell Teresa , Bassie Ludovic , Christou Paul
Published: June 2004

We have generated transgenic rice plants expressing the
Datura stramonium adc
gene and investigated their response to drought stress. We monitored the steady-state mRNA levels of genes involved in polyamine biosynthesis (
Datura adc
, rice
adc
, and rice
samdc
) and polyamine levels. Wild-type plants responded to the onset of drought stress by increasing endogenous putrescine levels, but this was insufficient to trigger the conversion of putrescine into spermidine and spermine (the agents that are believed to protect plants under stress). In contrast, transgenic plants expressing
Datura adc
produced much higher levels of putrescine under stress, promoting spermidine and spermine synthesis and ultimately protecting the plants from drought. We demonstrate clearly that the manipulation of polyamine biosynthesis in plants can produce drought-tolerant germplasm, and we propose a model consistent with the role of polyamines in the protection of plants against abiotic stress.
Multimerization and interaction of Toll and Spätzle in
Drosophila
Authors: Hu Xiaodi , Yagi Yoshimasa , Tanji Takahiro , Zhou Sili , Ip Y. Tony
Published: June 2004

The Toll family of receptors is required for innate immune response to pathogen-associated molecules, but the mechanism of signaling is not entirely clear. In
Drosophila
the prototypic Toll regulates both embryonic development and adult immune response. We demonstrate here that the host protein Spätzle can function as a ligand for Toll because Spätzle forms a complex with Toll in transgenic fly extracts and stimulates the expression of a Toll-dependent immunity gene,
drosomycin
, in adult flies. We also show that constitutively active mutants of Toll form multimers that contain intermolecular disulfide linkages. These disulfide linkages are critical for the activity of one of these mutant receptors, indicating that multimerization is essential for the constitutive activity. Furthermore, systematic mutational analysis revealed that a conserved cysteine-containing motif, different from the cysteines used for the intermolecular disulfide linkages, serves as a self-inhibitory module of Toll. Deleting or mutating this cysteine-containing motif leads to constitutive activity. This motif is located just outside the transmembrane domain and may provide a structural hindrance for multimerization and activation of Toll. Together, our results suggest that multimerization may be a regulated, essential step for Toll-receptor activation.
A simulation method for calculating the absolute entropy and free energy of fluids: Application to liquid argon and water
Authors: White Ronald P. , Meirovitch Hagai
Published: June 2004

The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy and free energy by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics techniques. With HS applied to a fluid, each configurationiof the sample is reconstructed by adding its atoms gradually to the initially empty volume, i.e., by placing them in their positions atiusing transition probabilities (TPs). At each step of the process, the volume is divided into two parts, the already visited part (the “past”) and the “future” part, where obtaining the TP requires calculating partition functions over the future part in the presence of the frozen past. In recent publications, the TPs were calculated approximately by taking into account only partial future. Here we present a “complete HSMC” procedure, where the TPs are calculated from MC simulations carried out over the complete future. The complete HSMC method is applied to systems of liquid argon and the TIP3P model of water, and very good results for the free energy are obtained, as compared with results obtained by thermodynamic integration.
Ezrin regulates NHE3 translocation and activation after Na
+
-glucose cotransport
Authors: Zhao Huiren , Shiue Harn , Palkon Sara , Wang Yingmin , Cullinan Patrick , Burkhardt Janis K. , Musch Mark W. , Chang Eugene B. , Turner Jerrold R.
Published: June 2004

Initiation of Na
+
-glucose cotransport in intestinal epithelial cells leads to activation of the apical Na
+
-H
+
exchanger NHE3 and subsequent increases in cytoplasmic pH (pH
i
). This process requires activation of p38 mitogen-activated protein (MAP) kinase, but additional signaling intermediates have not been identified. One candidate is the cytoskeletal linker protein ezrin, which interacts with NHE3 via specific regulatory proteins. The data show that initiation of Na
+
-glucose cotransport resulted in rapid increases in both apical membrane-associated NHE3 and cytoskeletal-associated ezrin and occurred in parallel with ezrin phosphorylation at threonine 567. Phosphorylation at this site is known to activate ezrin and increase its association with actin. Consistent with a central role for ezrin activation in this NHE3 regulation, an N-terminal dominant negative ezrin construct inhibited both NHE3 recruitment and pH
i
increases after Na
+
-glucose cotransport. Ezrin phosphorylation occurred in parallel with p38 MAP kinase activation, and the latter proceeded normally in cells expressing dominant negative ezrin. In contrast, inhibition of p38 MAP kinase prevented increases in ezrin phosphorylation after initiation of Na
+
-glucose cotransport. Thus, ezrin phosphorylation after Na
+
-glucose cotransport requires p38 MAP kinase activity, but p38 MAP kinase activation does not require ezrin function. These data describe a specific role for ezrin in the coordinate regulation of Na
+
-glucose cotransport and Na
+
-H
+
exchange. Intact ezrin function is necessary for NHE3 recruitment to the apical membrane and NHE3-dependent pH
i
increases triggered by Na
+
-glucose cotransport. The data also define a pathway of p38 MAP kinase-dependent ezrin activation.
Pattern formation by vascular mesenchymal cells
Authors: Garfinkel Alan , Tintut Yin , Petrasek Danny , Boström Kristina , Demer Linda L.
Published: June 2004

In embryogenesis, immature mesenchymal cells aggregate and organize into patterned tissues. Later in life, a pathological recapitulation of this process takes place in atherosclerotic lesions, when vascular mesenchymal cells organize into trabecular bone tissue within the artery wall. Here we show that multipotential adult vascular mesenchymal cells self-organize
in vitro
into patterns that are predicted by a mathematical model based on molecular morphogens interacting in a reaction-diffusion process. We identify activator and inhibitor morphogens for stripe, spot, and labyrinthine patterns and confirm the model predictions
in vitro
. Thus, reaction-diffusion principles may play a significant role in morphogenetic processes in adult mesenchymal cells.
Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from
Escherichia coli
-expressed libraries
Authors: Harvey Barrett R. , Georgiou George , Hayhurst Andrew , Jeong Ki Jun , Iverson Brent L. , Rogers Geoffrey K.
Published: June 2004

Anchored periplasmic expression (APEx) is a technology for the isolation of ligand-binding proteins from combinatorial libraries anchored on the periplasmic face of the inner membrane of
Escherichia coli
. After disruption of the outer membrane by Tris-EDTA-lysozyme, the inner-membrane-anchored proteins readily bind fluorescently labeled ligands as large as 240 kDa. Fluorescently labeled cells are isolated by flow cytometry, and the DNA of isolated clones is rescued by PCR. By using two rounds of APEx, the affinity of a neutralizing antibody to the
Bacillus anthracis
protective antigen was improved >200-fold, exhibiting a final
K
D
of 21 pM. This approach has several technical advantages compared with previous library screening technologies, including the unique ability to screen for ligand-binding proteins that bind endogenously expressed ligands fused to a short-lived GFP. Further, APEx is able to display proteins either as an N
-
terminal fusion to a six-residue sequence derived from the native
E. coli
lipoprotein NlpA, or as a C-terminal fusion to the phage gene three minor coat protein of M13. The latter fusions allow hybrid phage display/APEx strategies without the need for further subcloning.
Therapeutic immunization protects dopaminergic neurons in a mouse model of Parkinson's disease
Authors: Benner Eric J. , Mosley R. Lee , Destache Chris J. , Lewis Travis B. , Jackson-Lewis Vernice , Gorantla Santhi , Nemachek Craig , Green Steven R. , Przedborski Serge , Gendelman Howard E.
Published: June 2004

Degeneration of the nigrostriatal dopaminergic pathway, the hallmark of Parkinson's disease, can be recapitulated in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-intoxicated mice. Herein, we demonstrate that adoptive transfer of copolymer-1 immune cells to MPTP recipient mice leads to T cell accumulation within the substantia nigra pars compacta, suppression of microglial activation, and increased local expression of astrocyte-associated glial cell line-derived neurotrophic factor. This immunization strategy resulted in significant protection of nigrostriatal neurons against MPTP-induced neurodegeneration that was abrogated by depletion of donor T cells. Such vaccine treatment strategies may provide benefit for Parkinson's disease.
Identification of the amino acid sequence in Sindbis virus nsP4 that binds to the promoter for the synthesis of the subgenomic RNA
Authors: Li Mei-Ling , Stollar Victor
Published: June 2004

A gel mobility-shift assay was used to demonstrate the binding of the Sindbis virus transcriptase to the promoter for the synthesis of subgenomic (SG) RNA. The assay made use of a P15 fraction (the cell fraction that is pelleted at 15,000 ×
g
) from cells infected with recombinant vaccinia virions expressing various Sindbis virus nonstructural proteins (nsPs) and a
32
P-labeled 24-mer oligoribonucleotide representing the minimal sequence with SG promoter activity. By itself, nsP4, the viral RNA-dependent RNA polymerase, did not bind to the SG promoter; rather, all four nsPs were required for the binding of the transcriptase to the promoter. UV crosslinking of the transcriptase to a thiouridine-containing SG promoter, followed by V8 protease digestion of the complex, generated a peptide fragment that was bound to the SG promoter. This peptide fragment contained a sequence that corresponded to residues 329–334 of nsP4. This peptide may be in the fingers domain of nsP4. The peptide that was identified contained Arg residues at positions 331 and 332. Another Arg is present at position 327. By changing each of the Arg residues to Ala, we demonstrated that only the Arg residues at positions 331 and 332 were required for binding nsP4 to the SG promoter.
Activation of cAMP-response-element-binding protein (CREB) after focal cerebral ischemia stimulates neurogenesis in the adult dentate gyrus
Authors: Zhu Dong Ya , Lau Lorraine , Liu Shu Hong , Wei Jian She , Lu You Ming
Published: June 2004

New neurons are generated in adult mammalians and may contribute to repairing the brain after injury. Here, we show that the number of new neurons in the dentate gyrus of adult rats increased in cerebral ischemic stroke and correlated with activation of the cAMP-response-element-binding protein (CREB). Inhibition of endogenous CREB by expression of a dominant-negative mutant of CREB (CREB-S133A or CREB-R287L) blocked ischemia-induced neurogenesis in the dentate gyrus of adult rats, whereas expression of constitutively active CREB, VP16-CREB, increased the number of new neurons. Thus, our findings provide roles and regulatory mechanisms for CREB in adult neurogenesis and possibly suggest a practical strategy for replacing dead neurons in brain injury.
Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex
Authors: Kiel C. , Selzer T. , Shaul Y. , Schreiber G. , Herrmann C.
Published: June 2004

Association of two proteins can be described as a two-step process, with the formation of an encounter complex followed by desolvation and establishment of a tight complex. Here, by using the computer algorithm
pare
, we designed a set of mutants of the Ras effector protein Ral guanine nucleotide dissociation stimulator (RalGDS) with optimized electrostatic steering. The fastest binding RalGDS mutant, M26K,D47K,E54K, binds Ras 14-fold faster and 25-fold tighter compared with WT. A linear correlation was found between the calculated and experimental data, with a correlation coefficient of 0.97 and a slope of 0.65 for the 24 mutants produced. The data suggest that increased electrostatic steering specifically stabilizes the encounter complex and transition state. This conclusion is backed up by Φ analysis of the encounter complex and transition state of the RalGDS
M26K,D47K,E54K
/Ras complex, with both values being close to 1. Upon further formation of the final complex, the increased Coulombic interactions are probably counterbalanced by the cost of desolvation of charges, keeping the dissociation rate constant almost unchanged. This mechanism is also reflected by the mutual compensation of enthalpy and entropy changes quantified by isothermal titration calorimetry. The binding constants of the faster binding RalGDS mutants toward Ras are similar to those of Raf, the most prominent Ras effector, suggesting that the design methodology may be used to switch between signal transduction pathways.
Sex pheromone of the pink hibiscus mealybug,
Maconellicoccus hirsutus
, contains an unusual cyclobutanoid monoterpene
Authors: Zhang Aijun , Amalin Divina , Shirali Shyam , Serrano Miguel S. , Franqui Rosa A. , Oliver James E. , Klun Jerome A. , Aldrich Jeffrey R. , Meyerdirk Dale E. , Lapointe Stephen L.
Published: June 2004

Two compounds that together constitute the female sex pheromone of the pink hibiscus mealybug (PHM),
Maconellicoccus hirsutus
, were isolated, identified, and synthesized. They are (
R
)-2-isopropenyl-5-methyl-4-hexenyl (
S
)-2-methylbutanoate [common name is (
R
)-lavandulyl (
S
)-2-methylbutanoate] and [(
R
)-2,2-dimethyl-3-(1-methylethylidene)cyclobutyl]methyl (
S
)-2-methylbutanoate [which we refer to as (
R
)-maconelliyl (
S
)-2-methylbutanoate]. Maconelliol is an unusual cyclobutanoid monoterpene, and its structure has been established by enantioselective synthesis from precursors of known structure and configuration. A 1:5 synthetic mixture of the two
RS
esters (1 μg per rubber septum) proved to be a potent attractant of males in field bioassays. The pheromone component, maconelliyl 2-methylbutanoate, represents a heretofore undescribed natural product.
Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA
Authors: Jiang Xunqing , Belasco Joel G.
Published: June 2004

RNase E is an endonuclease that plays a central role in RNA processing and degradation in
Escherichia coli
. Like its
E. coli
homolog RNase G, RNase E shows a marked preference for cleaving RNAs that bear a monophosphate, rather than a triphosphate or hydroxyl, at the 5′ end. To investigate the mechanism by which 5′-terminal phosphorylation can influence distant cleavage events, we have developed fluorogenic RNA substrates that allow the activity of RNase E and RNase G to be quantified much more accurately and easily than before. Kinetic analysis of the cleavage of these substrates by RNase E and RNase G has revealed that 5′ monophosphorylation accelerates the reaction not by improving substrate binding, but rather by enhancing the catalytic potency of these ribonucleases. Furthermore, the presence of a 5′ monophosphate can increase the specificity of cleavage site selection within an RNA. Although monomeric forms of RNase E and RNase G can cut RNA, the ability of these enzymes to discriminate between RNA substrates on the basis of their 5′ phosphorylation state requires the formation of protein multimers. Among the molecular mechanisms that could account for these properties are those in which 5′-end binding by one enzyme subunit induces a protein structural change that accelerates RNA cleavage by another subunit.
Rat adult stem cells (marrow stromal cells) engraft and differentiate in chick embryos without evidence of cell fusion
Authors: Pochampally Radhika R. , Neville Brian T. , Schwarz Emily J. , Li Marilyn M. , Prockop Darwin J.
Published: June 2004

Cell fusion was recently reported to account for the plasticity of adult stem cells
in vivo
. Adult stem cells, referred to as mesenchymal stem cells or marrow stromal cells, from rat marrow, were infused into 1.5- to 2-day-old chick embryos. After 4 days, the rat cells had expanded 1.3- to 33-fold in one-third of surviving embryos. The cells engrafted into many tissues, and no multinuclear cells were detected. The most common site of engraftment was the heart, apparently because the cells were infused just above the dorsal aorta. Some of the cells in the heart expressed cardiotin, and α-heavy-chain myosin. GFP
+
cells reisolated from the embryos had a rat karyotype. Therefore, the cells engrafted and partially differentiated without evidence of cell fusion.
TorI, a response regulator inhibitor of phage origin inEscherichia coli
Authors: Ansaldi Mireille , Théraulaz Laurence , Méjean Vincent
Published: June 2004

ThetorIgene has been identified by using a genetic multicopy approach as a negative regulator of thetorCADoperon that encodes the trimethylamineN-oxide reductase respiratory system inEscherichia coli. The negative effect was due to a previously unidentified small ORF (66 aa) of phage origin that we calledtorIforTor inhibition. Overexpression oftorIled to an 8-fold decrease of thetorCADoperon transcription. This operon is positively regulated, in the presence of trimethylamineN-oxide, by a four-step phosphorelay involving the TorS sensor and the TorR response regulator. Epistatic experiments showed that TorI acts downstream of TorS and needs the presence of TorR.In vitroexperiments showed that it is neither a TorR phosphatase nor a histidine kinase inhibitor and that it binds to the effector domain of TorR. Unexpectedly, TorI did not impede TorR DNA binding, and we propose that it may prevent RNA polymerase recruitment to thetorCpromoter. This study thus reveals a previously uncharacterized class of response regulator inhibitors.
Synaptotagmin IV regulates glial glutamate release
Authors: Zhang Qi , Fukuda Mitsunori , Van Bockstaele Elisabeth , Pascual Olivier , Haydon Philip G.
Published: June 2004

Calcium-binding synaptotagmins (Syts) are membrane proteins that are conserved from nematode to human. Fifteen Syts (Syts I–XV) have been identified in mammalian species. Syt I has been well studied and is a candidate for the Ca
2+
-sensor that triggers evoked exocytosis underlying fast synaptic transmission. Whereas the functions of the other Syts are unclear, Syt IV is of particular interest because it is rapidly up-regulated after chronic depolarization or seizures, and because null mutations exhibit deficits in fine motor coordination and hippocampus-dependent memory. Screening Syts I–XIII, which are enriched in brain, we find that Syt IV is located in processes of astroglia
in situ
. Reduction of Syt IV in astrocytes by RNA interference decreases Ca
2+
-dependent glutamate release, a gliotransmission pathway that regulates synaptic transmission. Mutants of the C2B domain, the only putative Ca
2+
-binding domain in Syt IV, act in a dominant-negative fashion over Ca
2+
-regulated glial glutamate release, but not gliotransmission induced by changes in osmolarity. Because we find that Syt IV is expressed predominantly by astrocytes and is not in the presynaptic terminals of the hippocampus, and because Syt IV knockout mice exhibit hippocampal-based memory deficits, our data raise the intriguing possibility that Syt IV-mediated gliotransmission contributes to hippocampal-based memory.
Dynamical basis of intentions and expectations in a simple neuronal network
Authors: Proekt Alex , Brezina Vladimir , Weiss Klaudiusz R.
Published: June 2004

Selection of behavioral responses to external stimuli is strongly influenced by internal states, such as intentions and expectations. These internal states are often attributed to higher-order brain functions. Yet here we show that even in the simple feeding network of
Aplysia
, external stimuli do not directly specify which motor output is expressed; instead, the motor output is specified by the state of the network at the moment of stimulation. The history-dependence of this network state manifests itself in the same way as do intentions and expectations in the behavior of higher animals. Remarkably, we find that activity-dependent plasticity of a synapse within the network itself, rather than some higher-order network, mediates one important aspect of the change in the network state. Through this mechanism, changes in the network state become an automatic consequence of the generation of behavior. Altogether, our findings suggest that intentions and expectations may emerge within behavior-generating networks themselves from the plasticity of the very processes that generate the behavior.
Phospholipase Dα1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and regulates abscisic acid signaling
Authors: Zhang Wenhua , Qin Chunbo , Zhao Jian , Wang Xuemin
Published: June 2004

Phospholipase D (PLD) and protein phosphatase 2C (PP2C) both play a role in mediating plant responses to abscisic acid (ABA). In this article, we show that PLDα1 and its product, phosphatidic acid (PA), regulate a PP2C, ABI1, which is a negative regulator of ABA responses in
Arabidopsis
. Leaves from a T-DNA insertional mutant of
PLD
α
1
and
PLD
α
1
-antisense plants lose more water than do wild-type plants. The stomatal closure of
PLD
α
1
-null leaves is insensitive to ABA but is promoted by PA. ABA treatment promotes an increase in PA from phosphatidylcholine in wild type but not in
PLD
α
1
-null cells. PLDα1-derived PA binds to ABI1; the PA–ABI1 binding is demonstrated by coprecipitating PA with ABI1 from plant cells, measuring binding of PA from vesicles to ABI1, and assaying ABI1 bound to PA immobilized on a filter. Deletion and site-specific mutational analyses show that arginine 73 in ABI1 is essential for PA–ABI1 binding. PA binding decreases the phosphatase activity of ABI1. The lack of ABA-induced production of PA in
PLD
α
1
-null cells results in a decrease in the association of ABI1 with the plasma membrane in response to ABA. These results indicate that PA produced by PLDα1 inhibits the function of the negative regulator ABI1, thus promoting ABA signaling. The identification of ABI1 as a direct target of the lipid messenger PA provides a functional link between the two families of important signaling enzymes, PLD and PP2C.
Evidence for large methane releases to the atmosphere from deep-sea gas-hydrate dissociation during the last glacial episode
Authors: de Garidel-Thoron Thibault , Beaufort Luc , Bassinot Franck , Henry Pierre
Published: June 2004

Past atmospheric methane-concentration oscillations recorded in polar ice cores vary together with rapid global climatic changes during the last glacial episode. In the “clathrate gun hypothesis,” massive releases of deep-sea methane from marine gas-hydrate dissociation led to these well known, global, abrupt warmings in the past. If evidence for such releases in the water column exists, however, the mechanism and eventual transfer to the atmosphere has not yet been documented clearly. Here we describe a high-resolution marine-sediment record of stable carbon isotopic changes from the Papua Gulf, off Papua New Guinea, which exhibits two extremely depleted excursions (down to -9‰) at ≈39,000 and ≈55,000 years. Morphological, isotopic, and trace metal evidence dismisses authigenic calcite as the main source of depleted carbon. Massive methane release associated with deep-sea gas-hydrate dissociation is the most likely cause for such large depletions of δ
13
C. The absence of a δ
13
C gradient in the water column during these events implies that the methane rose through the entire water column, reaching the sea–air interface and thus the atmosphere. Foraminiferal δ
18
O composition suggests that the rise of the methane in the water column created an upwelling flow. These inferred emission events suggest that during the last glacial episode, this process was likely widespread, including tropical regions. Thus, the release of methane from the ocean floor into the atmosphere cannot be dismissed as a strong positive feedback in climate dynamics processes.