bluuebunny/crossref_metadata_2025 huggingface dataset:
A case study of stratosphere to troposphere transport: The role of convective transport and the sensitivity to model resolution
Authors: Gray S. L.
Published: September 2003

The limitations of some commonly used model‐based methods of diagnosing extratropical cross‐tropopause transport in tropopause folding events are revealed by performing forecasts of a case study using the Met Office Unified Model including an idealized passive tracer. Evidence is presented that the transport which occurs in parameterized convection and turbulent mixing can lead to significant cross‐tropopause transport. Transport from the stratosphere to the troposphere by parameterized processes (across a potential vorticity defined tropopause zone) was found to be dominated by convective transport. Transport by parameterized processes accounted for a maximum of 38% of the tracer transported by both resolved and parameterized processes in a control forecast (integrated across the model domain); alternatively, transport by parameterized processes led to a maximum increase of 62% in the transported tracer above that transported by resolved processes only. The importance of these processes depends on the synoptic system under consideration and local effects can greatly exceed the domain average. These processes are neglected by methods of diagnosing cross‐tropopause transport based on trajectories calculated using the resolved scale winds or based on the nonconservation of potential vorticity. Estimates of transport are highly sensitive to model horizontal and vertical resolution and to the artificial diffusion required for model stability. The transported tracer was 78% greater at the end of the forecast in which most transport occurred compared with the forecast in which least transport occurred. Finally, transport by parameterized convection was found to be even more important when considering transport from the stratosphere to below 700 mb, a transport measure used in previous studies.
Geochemical modeling of dehydration and partial melting of subducting lithosphere: Toward a comprehensive understanding of high‐Mg andesite formation in the Setouchi volcanic belt, SW Japan
Authors: Tatsumi Yoshiyuki , Hanyu Takeshi
Published: September 2003

Possible mechanisms for the production of mantle‐derived, high‐Mg andesite magmas, including (1) partial melting of mantle wedge peridotite by addition of aqueous fluids from the subducting lithosphere and (2) partial melting of the subducting sediments and altered oceanic crust, and subsequent melt‐mantle interaction, were examined by geochemical formulation of dehydration, partial melting and melt‐solid reactions. The modeling results demonstrate that both mechanisms can reasonably explain the incompatible trace element characteristics of high‐Mg andesites in the Setouchi volcanic belt, SW Japan. However, simple hydrous melting of mantle wedge peridotite cannot account for the Sr‐Nd‐Pb‐Hf isotopic compositions of such andesites. By contrast, the latter mechanism, which is consistent with thermal structures beneath the Setouchi volcanic belt, can well reproduce the isotopic signature of those high‐Mg andesites.
A Study on Seismic Noise Variations at Colfiorito, Central Italy: Implications for the Use of H/V Spectral Ratios
Authors: Cara Fabrizio , Di Giulio Giuseppe , Rovelli Antonio
Published: September 2003

Seismic noise recorded by broad‐band stations in the middle of and around the Colfiorito plain is analyzed in the frequency band 0.1 to 10 Hz. Small daily variations in noise amplitude are found, on the order of 2 for f > 1 Hz. In contrast, long‐term amplitude variations due to weather conditions are significant throughout the analyzed frequency band; for f < 1 Hz, the amplitude increase can be as large as a factor of 50. In the low‐frequency band, horizontal components vary much more than the vertical at both firm and soft sites. However, these noise variations at low frequencies do not contaminate significantly the 0.9‐Hz peak of the H/V spectral ratio that fits the fundamental eigenfrequency of the sedimentary fill of the basin, resonating during earthquakes. Correlating the long‐term variations of noise with different meteorological parameters, we find that wind speed best matches the low‐frequency noise disturbances.
The use of ATSR active fire counts for estimating relative patterns of biomass burning – a study from the boreal forest region
Authors: Kasischke Eric S. , Hewson Jennifer H. , Stocks Brian , van der Werf Guido , Randerson James
Published: September 2003

Satellite fire products have the potential to construct inter‐annual time series of fire activity, but estimating area burned requires considering biases introduced by orbiting geometry, fire behavior, and the presence of clouds and smoke. Here we evaluated the performance of fire counts from the Advanced Thermal Scanning Radiometer (ATSR) for the boreal forest region using area burned information from other sources. We found ATSR detection rate varied between regions and different years, being higher during large fire years than during small fire years. The results show ATSR fire counts do not represent an unbiased sample of fire activity, and independent validation may be required prior to using this data set in studies of global emissions from biomass burning.
Limestones distinguished by magnetic hysteresis in three‐dimensional projections
Authors: Borradaile G. J. , Hamilton Tom
Published: September 2003

Magnetic hysteresis data determine the suitability of rocks for paleomagnetic work, provide clues to paleo‐environment and paleo‐climate and they may characterize depositional environments for limestones. However, the variables chosen for conventional two‐dimensional hysteresis plots, such as that of Day et al. [1977], are not always suitable to discriminate between samples. Distinguishing samples by their regression surfaces in 3D hysteresis space may be more successful in some cases [Borradaile and Lagroix, 2000] but a 2D projection with a less arbitrary viewing axis is preferable for routine reporting. We show that limestone samples are simply discriminated in a new 2D projection produced by projecting hysteresis data from three dimensions (x, y, z = Mr/Ms, Bcr, Bc) onto a plane containing the Mr/Ms axis. The orientation of the plane is controlled by its x‐axis that is defined by a suitably selected Bcr/Bc ratio, most often in the magnetite PSD range, 2< (Bcr/Bc) < 4.
Source model for the Mw 6.7, 23 October 2002, Nenana Mountain Earthquake (Alaska) from InSAR
Authors: Wright Tim J. , Lu Zhong , Wicks Chuck
Published: September 2003

The 23 October 2002 Nenana Mountain Earthquake (Mw ∼ 6.7) occurred on the Denali Fault (Alaska), to the west of the Mw ∼ 7.9 Denali Earthquake that ruptured the same fault 11 days later. We used 6 interferograms, constructed using radar images from the Canadian Radarsat‐1 and European ERS‐2 satellites, to determine the coseismic surface deformation and a source model. Data were acquired on ascending and descending satellite passes, with incidence angles between 23 and 45 degrees, and time intervals of 72 days or less. Modeling the event as dislocations in an elastic half space suggests that there was nearly 0.9 m of right‐lateral strike‐slip motion at depth, on a near‐vertical fault, and that the maximum slip in the top 4 km of crust was less than 0.2 m. The Nenana Mountain Earthquake increased the Coulomb stress at the future hypocenter of the 3 November 2002, Denali Earthquake by 30–60 kPa.
30‐Year satellite record reveals contrasting Arctic and Antarctic decadal sea ice variability
Authors: Cavalieri D. J. , Parkinson C. L. , Vinnikov K. Y.
Published: September 2003

A 30‐year satellite record of sea ice extents derived mostly from satellite microwave radiometer observations reveals that the Arctic sea ice extent decreased by 0.30 ± 0.03 × 106 km2/10 yr from 1972 through 2002, but by 0.36 ± 0.05 × 106km2/10yr from 1979 through 2002, indicating an acceleration of 20% in the rate of decrease. In contrast, the Antarctic sea ice extent decreased dramatically over the period 1973–1977, then gradually increased. Over the full 30‐year period, the Antarctic ice extent decreased by 0.15 ± 0.08 × 106 km2/10 yr. The trend reversal is attributed to a large positive anomaly in Antarctic sea ice extent in the early 1970's, an anomaly that apparently began in the late 1960's, as observed in early visible and infrared satellite images.
Joint estimation of Martian 20 and rotation variations from simultaneous geodetic measurements: Numerical simulations of a Network Science Experiment
Authors: Duron J. , Rosenblatt P. , Yseboodt M. , Karatekin O. , Dehant V. , VanHoolst T. , Barriot J.‐P.
Published: September 2003

The Martian global‐scale CO2 seasonal cycle implies temporal variations in both the zonal gravity coefficients, such as 20, and in the rotation rate. To estimate the ability to detect simultaneously these two main geodetic signatures, a new approach based on a Network Science Experiment is investigated. We have numerically simulated the two types of Doppler signals involved, accurate orbiter tracking from the Earth and Martian lander tracking from the orbiter, by using a model of both the rotation variations and the seasonal variations of 20. Then, through a least square process, we have jointly adjusted the rotation and 20 parameters from an a priori knowledge. Our results show that it is possible to decorrelate 20 from all rotation parameters. We obtain an accurate adjustment of the 20 variations and a precision at the level of a few milliarcseconds for the estimation of the rotation rate variations.
Production of cosmogenic Be nuclei in the Earth's atmosphere by cosmic rays: Its dependence on solar modulation and the interstellar cosmic ray spectrum
Authors: Webber W. R. , Higbie P. R.
Published: September 2003

Recent work by McCracken [2001] shows that 10Be production rates by cosmic rays on the polar plateau are little affected by geomagnetic field changes in the last few hundred years. Also, the 10Be observed in ice cores on the polar plateau probably originated at high latitudes and precipitated to the Earth in about 1 year, according to McCracken. As a result of this assumption, ice core records of 10Be concentration extending back several hundred years, including the Maunder minimum, have the potential to study the solar modulation of cosmic rays on a time scale extending back several hundred years. These ice core records indicate that the 10Be concentration at the time of the Maunder minimum was ∼2.0 times what it was during recent sunspot minima in 1965 and 1976. We have examined 10Be production in the atmosphere using new data related to the interstellar cosmic ray spectrum and the effects of solar modulation as determined from Voyager spacecraft data in the outer heliosphere. We have used the FLUKA Monte Carlo program along with new cross‐section data to calculate the production of nucleons and 10Be nuclei in the atmosphere. These calculations show that 10Be temporal variations are sensitive indicators of low‐energy solar modulation. Our calculations of 10Be production are able to reproduce well the factor ∼1.5–2.0 change in 10Be observed in the ice core data as a result of the 11‐year solar modulation. We are also able to show that starting as recently as the sunspot minimum of 1954, the cosmic ray intensity at the Earth was higher than it was during more recent minima. The cosmic ray intensity during these minima time periods represents the residual modulation between the Earth and interstellar space. The 10Be measurements are consistant with the fact that given the interstellar cosmic ray spectrum used in this analysis, this residual modulation was small or zero at the time of the Maunder minimum.
Electric field measurements in the inner magnetosphere by Cluster EDI
Authors: Matsui H. , Quinn J. M. , Torbert R. B. , Jordanova V. K. , Baumjohann W. , Puhl‐Quinn P. A. , Paschmann G.
Published: September 2003

We report electric field measurements in the inner magnetosphere from the Electron Drift Instrument (EDI) on Cluster at distances of 4 < L < 10. The data used in this study span more than 1 year so that all local times are covered. Both components of the electric field perpendicular to the ambient magnetic field are mapped into the equatorial plane with the magnetic field model of Tsyganenko and Stern [1996]. Average values and standard deviations are sorted by the polarity of the BZ component of the interplanetary magnetic field (IMF). Average Kp values for both BZ polarities are 1.45 (BZ > 0) and 2.45 (BZ < 0). These electric fields are discussed in terms of their sources such as the ionospheric dynamo and the solar wind‐magnetosphere interaction. We also quantify the electric field as follows: the average shielding parameter γ [Volland, 1973; Stern, 1975] is ∼2, although the value for southward IMF is smaller than the value for northward IMF. The parameter γ is larger on the duskside than in the dawn sector. The average rate of sunward transport of magnetic flux, equivalent to the duskward electric field, is estimated as 0.32 mV/m for southward IMF. Finally, fluctuations tend to be larger than the DC component around the stagnation point, which could lead to outflow of plasmaspheric material.
Evolution of the magnetotail associated with substorm auroral breakups
Authors: Miyashita Y. , Machida S. , Liou K. , Mukai T. , Saito Y. , Hayakawa H. , Meng C.‐I. , Parks G. K.
Published: September 2003

We have statistically studied the three‐dimensional structure of evolution of the magnetotail associated with substorm expansion onsets. We selected 397 auroral breakups from Polar UVI data with a timing uncertainty of less than 2 min and then performed the two‐dimensional superposed epoch analysis using GEOTAIL data with 2 min resolution. We also performed the regional superposed epoch analysis with 1 min resolution using only the events for which we could determine the onset time with an uncertainty of less than 1 min. In particular, we found the simultaneous variations in the north‐south magnetic field, the duskward electric field, and the thermal flux immediately after onset around X ∼ −10RE and X ∼ −30RE, as well as the first total pressure decrease slightly (0–2 min) before onset around X ∼ −20RE. These results suggest that the merging of magnetic field lines or the magnetic reconnection first occurs around X ∼ −20RE in the premidnight tail at least 0–2 min before onset. Then, immediately after onset, the dipolarization occurs around X ∼ −10RE, which is simultaneous with substantial evolution of the plasmoid around X ∼ −30RE.
Recent warming in northwestern Ontario inferred from borehole temperature profiles
Authors: Gosselin Chantal , Mareschal Jean‐Claude
Published: September 2003

We have used the temperature depth profiles available in the region north and northwest of Lake Superior, in Ontario, Canada, to reconstruct the changes in ground surface temperature over the past 500 years. The 49 temperature depth profiles used were obtained for heat flow measurements and are part of two different data sets, one collected around 1980, the other one after 2000. We have discarded 16 of these profiles because of known nonclimatic perturbations (lakes, topography, clear signs of groundwater circulation). We have inverted the remaining 33 profiles to infer the variations in ground surface temperature. Individual and joint inversions consistently show a recent (150–200 years) warming (1–2 K) of the ground surface. This warming trend is similar to that inferred for northern Manitoba and Saskatchewan, to the northwest, and in eastern Ontario and Québec, to the southeast. However, there is no clear indication that a cold episode preceded the warming of the past 200 years in northwestern Ontario. The mean increase in ground surface temperature for all boreholes measured between 2000 and 2003 is 1.3 ± 0.8 K compared to 0.8 ± 0.6 K (σ) for the 1980 data. This difference suggests that the warming trend is persisting and might even have accelerated recently. Although the long‐term trend is climatic, part of the recent warming may be due to deforestation by the logging industry.
In‐canopy gradients, composition, sources, and optical properties of aerosol over the Amazon forest
Authors: Guyon Pascal , Graham Bim , Roberts Gregory C. , Mayol‐Bracero Olga L. , Maenhaut Willy , Artaxo Paulo , Andreae Meinrat O.
Published: September 2003

As part of the Large‐Scale Biosphere‐Atmosphere Experiment in Amazonia‐European Studies on Trace Gases and Atmospheric Chemistry (LBA‐EUSTACH), size‐fractionated aerosol samples were collected at a primary rain forest in the Brazilian Amazon during two field campaigns in April–May and September–October 1999. These two periods encompassed parts of the wet and dry seasons, respectively. Daytime‐nighttime‐segregated sampling was carried out at three different heights (above, within, and below canopy level) on a 54‐m meteorological tower at the forest site in order to better characterize the aerosol sources. The samples were analyzed for up to 19 trace elements by particle‐induced X‐ray emission analysis and for carbonaceous components by thermal‐optical analysis. Equivalent black carbon (BCe) and gravimetric analyses were also performed. The average mass concentrations for particles <2 μm diameter were 2.2 and 33.5 μg m−3for the wet and the dry seasons, respectively. The elements related to biomass burning and soil dust generally exhibited highest concentrations above the canopy and during daytime, while forest‐derived aerosol was more concentrated underneath the canopy and during nighttime. These variations can be largely attributed to daytime convective mixing and the formation of a shallow nocturnal boundary layer, along with the possibility of enhanced nighttime release of biogenic aerosol particles. Mass scattering (αs) and mass absorption efficiency (αa) data indicate that scattering was dominated by fine aerosol, while fine and coarse aerosol both contributed significantly to absorption during both seasons. The data also suggest that components other than elemental carbon were responsible for a substantial fraction of the absorption.
Explosive volcanism in the Tharsis region: Global evidence in the Martian geologic record
Authors: Hynek Brian M. , Phillips Roger J. , Arvidson Raymond E.
Published: September 2003

A global equatorial set of layered deposits on Mars has been reexamined with Mars Global Surveyor data. The stratigraphy, morphology, and erosional characteristics of units separated by thousands of kilometers are remarkably similar to each other and consistent with a widespread, episodic, subaerial source of fine‐grained material. This study is the first to propose a genetic link between many units that have traditionally been considered on a local or regional level, including the Medusae Fossae Formation, Valles Marineris interior deposits, chaotic terrain, Terra Meridiani, and Arabia materials. Mapping relationships suggest that all of these units are post‐Noachian in age and formation may have continued until the recent past. Thinning of deposits with increasing distance from the Tharsis rise suggests that much of these materials may be volcanic ash flows and air fall from explosive eruptions in the Tharsis region, analogous to those produced by terrestrial plinian eruptions. Contemporary Martian winds would preferentially transport ash from an eruption plume near Tharsis east or west along the equator depending on the season. Erosion has removed much of the original volcanic ash, and only isolated layered stacks remain, sometimes in topographic depressions that inhibit erosion. Modeling indicates that widespread dispersion of ash after an eruption is easily attainable in present or past atmospheric conditions, consistent with the hypothesis that the far‐reaching deposits may be composed of ash from past explosive eruptions in the vicinity of Tharsis.
On observing the compositional variability of the surface of Venus using nightside near‐infrared thermal radiation
Authors: Hashimoto George L. , Sugita Seiji
Published: September 2003

There are several windows in the near‐infrared wavelength range (∼1 μm), in which thermal radiation emitted from the planetary surface penetrates through the thick Venus atmosphere and clouds. In this study we develop an improved method to estimate the surface emissivity on the basis of near‐infrared thermal emission from the nightside Venus, which is observed through these windows. A simple radiative transfer model demonstrates that multiple reflection of thermal radiation between the atmosphere (including clouds) and the solid surface has a significant influence on the observed radiance under the condition of Venus, where reflectivity of overlying atmosphere and clouds is high. Thus it is necessary to take the effect of the reflection by the planetary surface into account in order to estimate accurately the variation in the surface emissivity on the basis of near‐infrared observation of Venus. The net effect of multiple reflection of surface thermal radiation between the atmosphere and the surface is to significantly reduce the spatial contrast in thermal radiation due to surface compositional variation. The model calculation demonstrates that despite this effect, detection of granitic rocks on the Venus surface using near‐infrared windows is feasible. Since granitic and basaltic rocks have dramatically different 1 μm emissivities, granitic rocks are distinguishable from basaltic rocks by ground‐based telescopic observation. A Venus orbiter that measures both the near‐infrared thermal radiation and the surface altitude with great accuracy will provide us with a reliable surface emissivity map of Venus, which is a very valuable tool to detect granitic (i.e., Earth‐like continental) rocks on Venus.
Cloud‐tracked winds for the first Mars Global Surveyor mapping year
Authors: Wang Huiqun , Ingersoll Andrew P.
Published: September 2003

We have measured winds using cloud motion in consecutive Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) wide‐angle global map swaths taken during the first mapping year (Ls 135°–360°–111°). We present a total of ∼11,200 wind vectors collected in the north polar region during Ls 135°–195° (late summer/early fall) and Ls 20°–55° (mid spring) and in the south polar region during Ls 337°–10° (late summer/early fall). For cases with good coverage, we also present the derived mean zonal and meridional winds and the associated eddies. The speed of the zonal winds in 60°N–70°N increases at ∼0.6 m/s/°Ls in late northern summer, and that in 60°S–70°S increases at a rate of ∼0.7 m/s/°Ls in late southern summer. The latitudinal distribution of zonal wind within 50°N–75°N from mid northern summer to early northern fall indicates that winds at higher latitudes are generally weaker than those at lower latitudes, but the rate of increase with time is faster at higher latitudes. There is a cyclonic gyre in the 90°W–0°–30°E sector in the north polar region. There are large‐scale waves in the weekly mean meridional wind and in the biweekly mean eddy momentum flux and eddy kinetic energy fields in the north polar region from mid to late summer. The cloud‐tracked winds in the north are generally consistent with winds calculated by general circulation model at the water condensation level derived from MGS Thermal Emission Spectrometer (TES) observations but appear stronger than the gradient winds derived from TES assuming no flow at the surface.
Multifaceted nature of hydrogeologic scaling and its interpretation
Authors: Neuman Shlomo P. , Di Federico Vittorio
Published: September 2003

Geology is ubiquitously heterogeneous, exhibiting both discrete and continuous spatial variations on a multiplicity of scales. It is therefore natural to expect that hydrogeologic and other geophysical variables would do likewise. We present evidence that hydrogeologic variables exhibit isotropic and directional dependencies on scales of measurement (data support), observation (extent of phenomena such as a dispersing plume), sampling window (domain of investigation), spatial correlation (structural coherence), and spatial resolution (descriptive detail). We then show that it is possible to interpret these multiple scale dependencies within a unified theoretical framework. This and similar theoretical frameworks may be applicable to a wider range of geophysical scale issues.
Direct measurement of Gag–Gag interaction during retrovirus assembly with FRET and fluorescence correlation spectroscopy
Authors: Larson Daniel R. , Ma Yu May , Vogt Volker M. , Webb Watt W.
Published: September 2003

During retrovirus assembly, the polyprotein Gag directs protein multimerization, membrane binding, and RNA packaging. It is unknown whether assembly initiates through Gag–Gag interactions in the cytosol or at the plasma membrane. We used two fluorescence techniques—two-photon fluorescence resonance energy transfer and fluorescence correlation spectroscopy—to examine Rous sarcoma virus Gag–Gag and –membrane interactions in living cells. Both techniques provide strong evidence for interactions between Gag proteins in the cytoplasm. Fluorescence correlation spectroscopy measurements of mobility suggest that Gag is present in large cytosolic complexes, but these complexes are not entirely composed of Gag. Deletion of the nucleocapsid domain abolishes Gag interactions and membrane targeting. Deletion of the membrane-binding domain leads to enhanced cytosolic interactions. These results indicate that Gag–Gag interactions occur in the cytosol, are mediated by nucleocapsid domain, and are necessary for membrane targeting and budding. These methods also have general applicability to in vivo studies of protein–protein and –membrane interactions involved in the formation of complex macromolecular structures.
Stored elastic energy powers the 60-μm extension of the Limulus polyphemus sperm actin bundle
Authors: Shin Jennifer H. , Mahadevan L. , Waller Guillermina S. , Langsetmo Knut , Matsudaira Paul
Published: September 2003

During the 5 s of the acrosome reaction of Limulus polyphemus sperm, a 60-μm-long bundle of scruin-decorated actin filaments straightens from a coiled conformation and extends from the cell. To identify the motive force for this movement, we examined the possible sources of chemical and mechanical energy and show that the coil releases ∼10−13 J of stored mechanical strain energy, whereas chemical energy derived from calcium binding is ∼10−15 J. These measurements indicate that the coiled actin bundle extends by a spring-based mechanism, which is distinctly different from the better known polymerization or myosin-driven processes, and that calcium initiates but does not power the reaction.
Bloom syndrome cells undergo p53-dependent apoptosis and delayed assembly of BRCA1 and NBS1 repair complexes at stalled replication forks
Authors: Davalos Albert R. , Campisi Judith
Published: September 2003

Bloom syndrome (BS) is a hereditary disorder characterized by pre- and postnatal growth retardation, genomic instability, and cancer. BLM, the gene defective in BS, encodes a DNA helicase thought to participate in genomic maintenance. We show that BS human fibroblasts undergo extensive apoptosis after DNA damage specifically when DNA replication forks are stalled. Damage during S, but not G1, caused BLM to rapidly form foci with γH2AX at replication forks that develop DNA breaks. These BLM foci recruited BRCA1 and NBS1. Damaged BS cells formed BRCA1/NBS1 foci with markedly delayed kinetics. Helicase-defective BLM showed dominant-negative activity with respect to apoptosis, but not BRCA1/NBS1 recruitment, suggesting catalytic and structural roles for BLM. Strikingly, inactivation of p53 prevented the death of damaged BS cells and delayed recruitment of BRCA1/NBS1. These findings suggest that BLM is an early responder to damaged replication forks. Moreover, p53 eliminates cells that rapidly assemble BRCA1/NBS1 without BLM, suggesting that BLM is essential for timely BRCA1/NBS1 function.
EphA kinase activation regulates HGF-induced epithelial branching morphogenesis
Authors: Miao Hui , Nickel Christian H. , Cantley Lloyd G. , Bruggeman Leslie A. , Bennardo Laura N. , Wang Bingcheng
Published: September 2003

Eph kinases and their ephrin ligands are widely expressed in epithelial cells in vitro and in vivo. Our results show that activation of endogenous EphA kinases in Madin-Darby canine kidney (MDCK) cells negatively regulates hepatocyte growth factor/scatter factor (HGF)–induced branching morphogenesis in collagen gel. Cotreatment with HGF and ephrin-A1 reduced sprouting of cell protrusions, an early step in branching morphogenesis. Moreover, addition of ephrin-A1 after HGF stimulation resulted in collapse and retraction of preexisting cell protrusions. In a newly developed assay that simulates the localized interactions between Ephs and ephrins in vivo, immobilized ephrin-A1 suppressed HGF-induced MDCK cell scattering. Ephrin-A1 inhibited basal ERK1/2 mitogen-activated protein kinase activity; however, the ephrin-A1 effect on cell protrusion was independent of the mitogen-activated protein kinase pathway. Ephrin-A1 suppressed HGF-induced activation of Rac1 and p21-activated kinase, whereas RhoA activation was retained, leading to the preservation of stress fibers. Moreover, dominant-negative RhoA or inhibitor of Rho-associated kinase (Y27632) substantially negated the inhibitory effects of ephrin-A1. These data suggest that interfering with c-Met signaling to Rho GTPases represents a major mechanism by which EphA kinase activation inhibits HGF-induced MDCK branching morphogenesis.
RhoA/ROCK regulation of neuritogenesis via profilin IIa–mediated control of actin stability
Authors: Da Silva Jorge Santos , Medina Miguel , Zuliani Cecilia , Di Nardo Alessia , Witke Walter , Dotti Carlos G.
Published: September 2003

Neuritogenesis, the first step of neuronal differentiation, takes place as nascent neurites bud from the immediate postmitotic neuronal soma. Little is known about the mechanisms underlying the dramatic morphological changes that characterize this event. Here, we show that RhoA activity plays a decisive role during neuritogenesis of cultured hippocampal neurons by recruiting and activating its specific kinase ROCK, which, in turn, complexes with profilin IIa. We establish that this previously uncharacterized brain-specific actin-binding protein controls neurite sprouting by modifying actin stability, a function regulated by ROCK-mediated phosphorylation. Furthermore, we determine that this novel cascade is switched on or off by physiological stimuli. We propose that RhoA/ROCK/PIIa-mediated regulation of actin stability, shown to be essential for neuritogenesis, may constitute a central mechanism throughout neuronal differentiation.
Compartmentalization of integrin α6β4 signaling in lipid rafts
Authors: Gagnoux-Palacios Laurent , Dans Michael , van't Hof Wouter , Mariotti Agnese , Pepe Angela , Meneguzzi Guerrino , Resh Marilyn D. , Giancotti Filippo G.
Published: September 2003

Integrin α6β4 signaling proceeds through Src family kinase (SFK)–mediated phosphorylation of the cytoplasmic tail of β4, recruitment of Shc, and activation of Ras and phosphoinositide-3 kinase. Upon cessation of signaling, α6β4 mediates assembly of hemidesmosomes. Here, we report that part of α6β4 is incorporated in lipid rafts. Metabolic labeling in combination with mutagenesis indicates that one or more cysteine in the membrane-proximal segment of β4 tail is palmitoylated. Mutation of these cysteines suppresses incorporation of α6β4 in lipid rafts, but does not affect α6β4-mediated adhesion or assembly of hemidesmosomes. The fraction of α6β4 localized to rafts associates with a palmitoylated SFK, whereas the remainder does not. Ligation of palmitoylation-defective α6β4 does not activate SFK signaling to extracellular signal–regulated kinase and fails to promote keratinocyte proliferation in response to EGF. Thus, compartmentalization in lipid rafts is necessary to couple the α6β4 integrin to a palmitoylated SFK and promote EGF-dependent mitogenesis.
Functional interaction of chloroplast SRP/FtsY with the ALB3 translocase in thylakoids
Authors: Moore Misty , Goforth Robyn L. , Mori Hiroki , Henry Ralph
Published: September 2003

Integration of thylakoid proteins by the chloroplast signal recognition particle (cpSRP) posttranslational transport pathway requires the cpSRP, an SRP receptor homologue (cpFtsY), and the membrane protein ALB3. Similarly, Escherichia coli uses an SRP and FtsY to cotranslationally target membrane proteins to the SecYEG translocase, which contains an ALB3 homologue, YidC. In neither system are the interactions between soluble and membrane components well understood. We show that complexes containing cpSRP, cpFtsY, and ALB3 can be precipitated using affinity tags on cpSRP or cpFtsY. Stabilization of this complex with GMP-PNP specifically blocks subsequent integration of substrate (light harvesting chl a/b-binding protein [LHCP]), indicating that the complex occupies functional ALB3 translocation sites. Surprisingly, neither substrate nor cpSRP43, a component of cpSRP, was necessary to form a complex with ALB3. Complexes also contained cpSecY, but its removal did not inhibit ALB3 function. Furthermore, antibody bound to ALB3 prevented ALB3 association with cpSRP and cpFtsY and inhibited LHCP integration suggesting that a complex containing cpSRP, cpFtsY, and ALB3 must form for proper LHCP integration.
Uncovering multiple axonal targeting pathways in hippocampal neurons
Authors: Wisco Dolora , Anderson Eric D. , Chang Michael C. , Norden Caren , Boiko Tatiana , Fölsch Heike , Winckler Bettina
Published: September 2003

Neuronal polarity is, at least in part, mediated by the differential sorting of membrane proteins to distinct domains, such as axons and somata/dendrites. We investigated the pathways underlying the subcellular targeting of NgCAM, a cell adhesion molecule residing on the axonal plasma membrane. Following transport of NgCAM kinetically, surprisingly we observed a transient appearance of NgCAM on the somatodendritic plasma membrane. Down-regulation of endocytosis resulted in loss of axonal accumulation of NgCAM, indicating that the axonal localization of NgCAM was dependent on endocytosis. Our data suggest the existence of a dendrite-to-axon transcytotic pathway to achieve axonal accumulation. NgCAM mutants with a point mutation in a crucial cytoplasmic tail motif (YRSL) are unable to access the transcytotic route. Instead, they were found to travel to the axon on a direct route. Therefore, our results suggest that multiple distinct pathways operate in hippocampal neurons to achieve axonal accumulation of membrane proteins.
Maintaining epithelial integrity
Authors: Röper Katja , Brown Nicholas H.
Published: September 2003

The Short stop (Shot/Kakapo) spectraplakin is a giant cytoskeletal protein, which exists in multiple isoforms with characteristics of both spectrin and plakin superfamilies. Previously characterized Shot isoforms are similar to spectrin and dystrophin, with an actin-binding domain followed by spectrin repeats. We describe a new large exon within the shot locus, which encodes a series of plakin repeats similar to the COOH terminus of plakins such as plectin and BPAG1e. We find that the plakin repeats are inserted between the actin-binding domain and spectrin repeats, generating isoforms as large as 8,846 residues, which could span 400 nm. These novel isoforms localized to adherens junctions of embryonic and follicular epithelia. Loss of Shot within the follicle epithelium leads to double layering and accumulation of actin and ZO-1 in between, and a reduction of Armadillo and Discs lost within, mutant cells, indicative of a disruption of adherens junction integrity. Thus, we identify a new role for spectraplakins in mediating cell–cell adhesion.
Molecular Coupling between Voltage Sensor and Pore Opening in the Arabidopsis Inward Rectifier K+ Channel KAT1
Authors: Latorre Ramon , Olcese Riccardo , Basso Claudia , Gonzalez Carlos , Muñoz Fabian , Cosmelli Diego , Alvarez Osvaldo
Published: September 2003

Animal and plant voltage-gated ion channels share a common architecture. They are made up of four subunits and the positive charges on helical S4 segments of the protein in animal K+ channels are the main voltage-sensing elements. The KAT1 channel cloned from Arabidopsis thaliana, despite its structural similarity to animal outward rectifier K+ channels is, however, an inward rectifier. Here we detected KAT1-gating currents due to the existence of an intrinsic voltage sensor in this channel. The measured gating currents evoked in response to hyperpolarizing voltage steps consist of a very fast (τ = 318 ± 34 μs at −180 mV) and a slower component (4.5 ± 0.5 ms at −180 mV) representing charge moved when most channels are closed. The observed gating currents precede in time the ionic currents and they are measurable at voltages (less than or equal to −60) at which the channel open probability is negligible (≈10−4). These two observations, together with the fact that there is a delay in the onset of the ionic currents, indicate that gating charge transits between several closed states before the KAT1 channel opens. To gain insight into the molecular mechanisms that give rise to the gating currents and lead to channel opening, we probed external accessibility of S4 domain residues to methanethiosulfonate-ethyltrimethylammonium (MTSET) in both closed and open cysteine-substituted KAT1 channels. The results demonstrate that the putative voltage–sensing charges of S4 move inward when the KAT1 channels open.
Asymmetric Temporal Properties in the Receptive Field of Retinal Transient Amacrine Cells
Authors: Djupsund Kaj , Furukawa Tetsuo , Yasui Syozo , Yamada Masahiro
Published: September 2003

The speed of signal conduction is a factor determining the temporal properties of individual neurons and neuronal networks. We observed very different conduction velocities within the receptive field of fast-type On-Off transient amacrine cells in carp retina cells, which are tightly coupled to each other via gap junctions. The fastest speeds were found in the dorsal area of the receptive fields, on average five times faster than those detected within the ventral area. The asymmetry was similar in the On- and Off-part of the responses, thus being independent of the pathway, pointing to the existence of a functional mechanism within the recorded cells themselves. Nonetheless, the spatial decay of the graded-voltage photoresponse within the receptive field was found to be symmetrical, with the amplitude center of the receptive field being displaced to the faster side from the minimum-latency location. A sample of the orientation of varicosity-laden polyaxons in neurobiotin-injected cells supported the model, revealing that ∼75% of these processes were directed dorsally from the origin cells. Based on these results, we modeled the velocity asymmetry and the displacement of amplitude center by adding a contribution of an asymmetric polyaxonal inhibition to the network. Due to the asymmetry in the conduction velocity, the time delay of a light response is proposed to depend on the origin of the photostimulus movement, a potentially important mechanism underlying direction selectivity within the inner retina.
The Mitochondrial Barriers Segregate Agonist-induced Calcium-dependent Functions in Human Airway Epithelia
Authors: Ribeiro Carla M. Pedrosa , Paradiso Anthony M. , Livraghi Alessandra , Boucher Richard C.
Published: September 2003

In airway epithelia, purinergic receptor (P2Y2-R) stimulation of intracellular calcium (Ca2+i)–regulated ion transport is restricted to the membrane domain ipsilateral to receptor activation, implying compartmentalization of Ca2+i signaling. Because mitochondria can spatially restrict cellular Ca2+i signals, immunocytochemical, electron microscopic, and fluorescent studies of mitochondria localization were performed in human airway epithelia. Although concentrated at the apical domain, mitochondria were found distributed at both the apical and the basolateral poles and in close association with the endoplasmic reticulum. The role of mitochondria in locally restricting P2Y2-R–induced Ca2+i signals was investigated by measuring changes in mitochondrial Ca2+ (Ca2+m) in human airway epithelial monolayers. P2Y2-R activation induced Ca2+m accumulation in mitochondria confined to the domain ipsilateral to P2Y2-R stimulation, which was blocked by mitochondrial uncoupling with 1 μM CCCP and 2.5 μg/ml oligomycin. The role of mitochondria in restricting the cellular cross-talk between basolateral P2Y2-R–dependent Ca2+i mobilization and apical membrane Ca2+-activated Cl− secretion was investigated in studies simultaneously measuring Ca2+i and Cl− secretion in cystic fibrosis human airway epithelial monolayers. Activation of basolateral P2Y2-Rs produced similar increases in Ca2+i in monolayers without and with pretreatment with uncouplers, whereas Ca2+i-activated Cl− secretion was only efficiently triggered in mitochondria-uncoupled conditions. We conclude that (a) mitochondria function as a Ca2+i-buffering system in airway epithelia, compartmentalizing Ca2+i-dependent functions to the membrane ipsilateral to receptor stimulation; and (b) the mitochondria provide structural barriers that protect the airway epithelia against nonspecific activation of Ca2+i-modulated functions associated with Ca2+i signals emanating from the apical or the basolateral membrane domains.
On asymptotic behavior of solutions of the Dirichlet problem in half-space for linear and quasi-linear elliptic equations
Authors: Denisov Vasily , Muravnik Andrey
Published: September 2003

We study the Dirichlet problem in half-space for the equation

Δ
u
+
g
(
u
)

|

∇
u

|

2

=
0
,

{\Delta u+g(u)|\nabla u|^2=0,}

where

g
g

is continuous or has a power singularity (in the latter case positive solutions are considered). The results presented give necessary and sufficient conditions for the existence of (pointwise or uniform) limit of the solution as

y
→
∞
,

y\to \infty ,

where

y
y

denotes the spatial variable, orthogonal to the hyperplane of boundary-value data. These conditions are given in terms of integral means of the boundary-value function.
Predicting gene function in Saccharomyces cerevisiae
Authors: Clare A. , King R. D.
Published: October 2003

Motivation: S.cerevisiae is one of the most important model organisms, and has has been the focus of over a century of study. In spite of these efforts, 40% of its open reading frames (ORFs) remain classified as having unknown function (MIPS: Munich Information Center for Protein Sequences). We wished to make predictions for the function of these ORFs using data mining, as we have previously successfully done for the genomes of M.tuberculosis and E.coli. Applying this approach to the larger and eukaryotic S.cerevisiae genome involves modifying the machine learning and data mining algorithms, as this is a larger organism with more data available, and a more challenging functional classification.

Results: Novel extensions to the machine learning and data mining algorithms have been devised in order to deal with the challenges. Accurate rules have been learned and predictions have been made for many of the ORFs whose function is currently unknown. The rules are informative, agree with known biology and allow for scientific discovery.

Availability: All predictions are freely available from http://www.genepredictions.org, all datasets used in this study are freely available from http://www.aber.ac.uk/compsci/Research/bio/dss/yeastdataand software for relational data mining is available from http://www.aber.ac.uk/compsci/Research/bio/dss/polyfarm.

Key words: yeast, S.cerevisiae, DMP, prediction, functional genomics, scientific discovery

Contact: afc@aber.ac.uk

*To whom correspondence should be addressed.
A novel approach to fold recognition using sequence-derived
properties from sets of structurally similar local fragments of
proteins
Authors: Hvidsten Torgeir R. , Kryshtafovych Andriy , Komorowski Jan , Fidelis Krzysztof
Published: October 2003

Comparative modeling methods can consistently produce reliable structural models for protein sequences with more than 25% sequence identity to proteins with known structure. However, there is a good chance that also sequences with lower sequence identity have their structural components represented in structural databases. To this end, we present a novel fragment-based method using sets of structurally similar local fragments of proteins. The approach differs from other fragment-based methods that use only single backbone fragments. Instead, we use a library of groups containing sets of sequence fragments with geometrically similar local structures and extract sequence related properties to assign these specific geometrical conformations to target sequences. We test the ability of the approach to recognize correct SCOP folds for 273 sequences from the 49 most popular folds. 49% of these sequences have the correct fold as their top prediction, while 82% have the correct fold in one of the top five predictions. Moreover, the approach shows no performance reduction on a subset of sequence targets with less than 10% sequence identity to any protein used to build the library.

Contact: janko@lcb.uu.se

*To whom correspondence shoudl be addressed.
Modeling sequencing errors by combining Hidden Markov models
Authors: Lottaz C. , Iseli C. , Jongeneel C. V. , Bucher P.
Published: October 2003

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.

Keywords: coding region prediction, sequencing errors, expressed sequence tags, hidden Markov models.

Contact: Claudio.Lottaz@molgen.mpg.de

*To whom correspondence should be addressed. Current address: Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin (Germany)
Finding subtle motifs by branching from sample strings
Authors: Price Alkes , Ramabhadran Sriram , Pevzner Pavel A.
Published: October 2003

Many motif finding algorithms apply local search techniques to a set of seeds. For example, GibbsDNA (Lawrence et al.. 1993, Science , 262, 208–214) applies Gibbs sampling to random seeds, and MEME (Bailey and Elkan, 1994, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (ISMB-94) , 28–36) applies the EM algorithm to selected sample strings , i.e. substrings of the sample. In the case of subtle motifs, recent benchmarking efforts show that both random seeds and selected sample strings may never get close to the globally optimal motif. We propose a new approach which searches motif space by branching from sample strings, and implement this idea in both pattern-based and profile-based settings. Our PatternBranching and ProfileBranching algorithms achieve favorable results relative to other motif finding algorithms.

Availability: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Contact: aprice@cs.ucsd.edu

*To whom correspondence should be addressed.