bluuebunny/crossref_metadata_2025 huggingface dataset:
Nitrous oxide emissions from sea animal colonies in the maritime Antarctic
Authors: Zhu Renbin , Liu Yashu , Xu Hua , Ma Jing , Zhao Sanping , Sun Liguang
Published: May 2008

Little is known about nitrous oxide (N2O) emissions from wild animal colonies. N2O fluxes were measured from a penguin colony on Ardley Island, a seal and skua colony on Fildes Peninsula in the maritime Antarctic using a static chamber technique. Mean fluxes from penguin, skua and seal colonies were 856, 132 and 189 μg N2O‐N m−2 h−1, respectively. The deposition of sea animal excreta controls spatial variations of N2O fluxes from the colonies. The highest fluxes (2559, 2836 and 2081 μg N2O‐N m−2 h−1 for penguin puddles, seal wallows and skua puddles, respectively) occurred during the freezing‐thawing period. Laboratory experiments showed that the freezing‐thawing cycle induced a flush of N2O from the soils sampled from the colonies and denitrification was the predominant process for the N2O source. We proposed that sea animal colonies represent the strong point sources of N2O in the maritime Antarctic.
Impact of terrestrial weather on the upper atmosphere
Authors: Fuller‐Rowell T. J. , Akmaev R. A. , Wu F. , Anghel A. , Maruyama N. , Anderson D. N. , Codrescu M. V. , Iredell M. , Moorthi S. , Juang H.‐M. , Hou Y.‐T. , Millward G.
Published: May 2008

A whole atmosphere model has been developed to demonstrate the impact of terrestrial weather on the upper atmosphere. The dynamical core is based on the NWS Global Forecast System model, which has been extended to cover altitudes from the ground to 600 km. The model includes the physical processes responsible for the stochastic nature of the lower atmosphere, which is a source of variability for the upper atmosphere. The upper levels include diffusive separation, wind induced transport of major species, and uses specific enthalpy as the dependent variable, to accommodate composition dependent gas constants and specific heats. A one‐year model simulation reveals planetary waves explicitly up to 100 km altitude. At higher altitude, multi‐day periodicities in the dynamics appear as a modulation of tidal amplitudes, particularly the migrating semi‐diurnal tide in the lower thermosphere dynamo region. The penetration of planetary wave periodicities from tropospheric weather into the upper atmosphere can explain terrestrial weather sources of variability in the thermospheric and ionospheric.
Velocity‐saturation relation for partially saturated rocks with fractal pore fluid distribution
Authors: Müller T. M. , Toms‐Stewart J. , Wenzlau F.
Published: May 2008

Reservoir rocks saturated with two immiscible fluids may exhibit considerable wave attenuation and dispersion due to wave‐induced fluid flow. Attenuation‐ and velocity‐saturation relations of P‐waves are developed for partially saturated porous media in which the fluid patches form random fractals on the mesoscopic scale. Depending on the fractal dimension of the pore fluid distribution the velocity‐saturation relation can vary between the exact Gassmann‐Wood and Gassmann‐Hill bounds. The results indicate that the fractal dimension is an additional measure that should be accounted for to consistently model effective acoustic properties of partially saturated rocks.
Cluster observations of O+ escape in the magnetotail due to shock compression effects during the initial phase of the magnetic storm on 17 August 2001
Authors: Echer E. , Korth A. , Zong Q.‐G. , Fraünz M. , Gonzalez W. D. , Guarnieri F. L. , Fu S. Y. , Reme H.
Published: May 2008

We study the O+ outflow into the magnetotail during the initial phase of the 17 August 2001 magnetic storm. Solar wind and magnetospheric data are used from instruments onboard ACE, WIND, and Cluster spacecraft. The interplanetary shock arrival at Earth caused a large compression of the magnetosphere. During this event, the Cluster spacecraft were crossing the plasma sheet boundary layer of the magnetotail. Thus this case study constitutes a unique opportunity to observe the magnetotail response to a shock driven storm with multiple S/C data. We observed a field aligned oxygen (O+) outflow in the plasma sheet boundary layer and a bidirectional O+ flux in the central plasma sheet. Using the Cluster multiple spacecraft data, we derived the O+ gradient and the escape rate into the magnetotail during the initial phase of the magnetic storm. We found an escape rate of 4.0 × 1024 O+ ions s−1 in the plasma sheet boundary layer of the magnetotail, which is about 20 times the O+ inflow into the ring current during an intense magnetic storm.
Cluster observations of electrostatic solitary waves near the Earth's bow shock
Authors: Hobara Y. , Walker S. N. , Balikhin M. , Pokhotelov O. A. , Gedalin M. , Krasnoselskikh V. , Hayakawa M. , André M. , Dunlop M. , Rème H. , Fazakerley A.
Published: May 2008

Using a period of internal burst mode data from the Cluster Electric Field and Wave instrument a number of electrostatic solitary structures have been identified in the foot region of Earth's quasi‐perpendicular bow shock. The four individual probe potential measurements are utilized to investigate the fundamental characteristics of the solitary wave structures such as wave propagation vector, propagation velocity, scale‐size and potential amplitude. Two classes of waves are observed. Bipolar solitary waves typically propagate in the solar wind direction toward the shock but at a significant angle from the ambient magnetic field. Unipolar/tripolar solitary waves tend to propagate along the ambient magnetic field. The wave amplitude‐scale size relation is similar to that obtained for similar structures observed in the auroral zone. The structures lie in the theoretically allowed region in width‐amplitude space to be consistent with the BGK ion holes. Using a period of internal burst mode data from the Cluster Electric Field and Wave instrument a number of electrostatic solitary structures have been identified in the foot region of Earth's quasi‐perpendicular bow shock. The four individual probe potential measurements are utilized to investigate the fundamental characteristics of the solitary wave structures such as wave propagation vector, propagation velocity, scale‐size and potential amplitude. Two classes of waves are observed. Bipolar solitary waves typically propagate in the solar wind direction toward the shock but at a significant angle to the ambient magnetic field in contrast to most previous studies which assume parallel propagation to the ambient magnetic field. In contrast, unipolar/tripolar solitary waves tend to propagate along the ambient magnetic field. The wave amplitude‐scale size relation is similar to that obtained for structures observed in the auroral zone. The structures lie in the theoretically allowed region in width‐amplitude space to be consistent with the BGK (Bernstein‐Greene‐Kruskal) ion holes. The two classes of observed solitary waves may greatly influence the ambient plasma dynamics around the shock. The bipolar solitary waves do not exhibit a large net potential difference but may still play an important role in plasma thermalisation by particle scattering. Unipolar/tripolar solitary waves exhibit a remarkable net potential difference that may be responsible for the plasma energisation along the ambient magnetic field.
On the modification of tides in shallow water regions by wind effects
Authors: Jones J. Eric , Davies Alan M.
Published: May 2008

The influence of non‐linear effects upon tides in shallow coastal regions, due to the presence of a significant storm surge is examined using a two‐dimensional model of the west coast of Britain. The model has an unstructured grid, designed to have a high resolution mesh in the near coastal region of the eastern Irish Sea, the area chosen as the focus of this study. The influence of tide‐surge interaction upon the M2, M4 and M6 components of the tide, due to surges produced by steady uniform wind stresses is examined in detail. Calculations show that in deep regions the tide is unaffected by the surge. However, in shallow coastal regions there is significant modification of tidal elevations and currents. This arises because of changes in bottom stress, and the non‐linear interaction term in the hydrodynamic equations. In addition the locations of regions that “wet and dry” are changed during the tidal cycle due to the influence of the surge. This gives rise to significant spatial variations and changes in magnitude of the tide and its higher harmonics depending upon wind stress direction and water depth. These results explain why tidal energy remains in the surge residual in shallow water when it is computed by de‐tiding the total signal using a tide only calculation; an effect often found in observed surge residuals.
Finite element ocean circulation model based on triangular prismatic elements, with application in studying the effect of topography representation
Authors: Wang Q. , Danilov S. , Schröter J.
Published: May 2008

Topographic steering of waves and currents is one of the most important issues of the general ocean circulation. Its representation in ocean models depends on the spatial discretization, which heavily influences the ocean circulation even on the global scale. Models capable of working on unstructured grids allow to represent topography and coastlines continuously and to refine mesh locally. Finite Element Ocean circulation Model (FEOM) belongs to this class of ocean general circulation models. Its discretization is based on unstructured triangular meshes on the surface and prismatic elements in the volume. The model uses continuous linear representation for the horizontal velocity, surface elevation, temperature and salinity, and solves the standard set of hydrostatic primitive equations. The method to stabilize the numerical pressure modes and the implementation of hybrid vertical grids are discussed. The model supports hybrid vertical grids including z and σ grids and their combination within the same numerical kernel. A method for calculating pressure gradient forces is introduced to reduce pressure gradient errors on inclined computational surfaces. Its performance is assessed via numerical experiments. The influence of different vertical discretization is illustrated using a seamount configuration. The model is MPI parallelized and has the functionality required for ocean general circulation modeling. It can be used as an efficient and versatile numerical tool for regional and global oceanographic applications and climate studies.
Evaluation of ozone total column measurements by the Ozone Monitoring Instrument using a data assimilation system
Authors: Migliorini S. , Brugge R. , O'Neill A. , Dobber M. , Fioletov V. , Levelt P. , McPeters R.
Published: May 2008

On 15 July 2004, the Ozone Monitoring Instrument (OMI) on board the EOS Aura mission was launched. One of OMI's priorities is to continue the record of high spatial resolution ozone total column measurements provided by the various Total Ozone Mapping Spectrometer (TOMS) instruments since 1978. To this end, it is essential to estimate the errors affecting OMI ozone total column measurements and to see whether the actual accuracy is consistent with estimated values before launch. In this paper, data assimilation techniques are used to create a large comparison data set composed of ozone analyses resulting from assimilation of standard meteorological observations and ozone retrievals (independent of OMI measurements) into a numerical weather prediction model. This data set provides excellent global coverage and temporal resolution, not limited by the spatial and temporal distribution of other satellite or ground based information. The accuracy of the analyses is evaluated against ozone total column retrievals from Brewer measurements, while the assimilated ozone data set is compared to ozone predictions made using the ECMWF model, to check for the presence of bias. The OMI ozone column measurements considered here are obtained with the TOMS‐V8 total ozone algorithm and denoted as OMTO3 columns. They are compared with simulated OMI ozone columns, i.e., the quantities that the TOMS‐V8 algorithm would retrieve in the case when the atmospheric ozone profile at a specific location and time is equal to the one prescribed by the analysis. In this way, the comparison is statistically robust even when data acquired during a relatively short temporal interval or over a relatively small geographical area only is considered. A discussion of relevant error sources (including systematic components), vertical resolution, and contributions from prior information is provided. Special attention is given to determining the importance of representativeness errors. Our results show a solar zenith angle (SZA) dependence of the bias between measured and simulated OMI columns. This is believed to be due to moderate nonlinearity of the observation forward model and its effects on our definition of simulated OMI columns at high SZA. In view of these findings the final results of the intercomparison methodology used in this paper are obtained from OMI ozone columns retrieved using the basic implementation of the TOMS‐V8 algorithm applied to measurements taken at SZA not exceeding 70°. Intercomparison results between measured and simulated OMI ozone columns at SZA less than 70° show a relative bias of −3.2 ± 3.1% and a root‐mean‐square error of 4.5 ± 1.5%. The resulting bias is consistent with available estimates of the bias of OMTO3 columns with respect to SBUV/2 between 60°S and 60°N, as well as with respect to global Dobson data and Brewer measurements between 30°N and 60°N.
Integration of the variable infiltration capacity model soil hydrology scheme into the community land model
Authors: Wang Aihui , Li Kaiyuan Y. , Lettenmaier Dennis P.
Published: May 2008

Enhancements to the soil hydrology scheme in the NCAR Community Land Model version 3 (CLM3) are described, which are intended to improve the ability of CLM to represent land surface hydrologic processes. Specifically, the CLM3 soil hydrology scheme has been replaced with the scheme used in the Variable Infiltration Capacity model (VIC). While the modified model incorporates VIC soil hydrology, the original model structure in CLM3 is unchanged in most other respects, such as the representation of vegetation and its controls on surface energy exchanges. The modified version of CLM3 makes direct use of VIC soil parameters that have been developed for off‐line regional, continental, and global simulations. The performance of the new model and CLM3 are evaluated through a comparison with observations at three flux tower sites: ABRACOS, a pasture clearing in the Brazilian rain forest, HAPEX‐MOBILHY, a midlatitude agricultural site in France, and Valdai, a midlatitude grassland in Russia, as well as two large river basins (Arkansas‐Red and Colorado in the United States). Overall, the results show that the merged model better reproduces observed soil hydrological variability, in particular, the seasonal evolution and amplitude of soil moisture, as compared to CLM3. The river basin simulations show that in the merged model, total runoff is generally less than in CLM3 and better agrees with observations. Owing to the interaction of runoff and soil moisture, the simulation of total evapotranspiration (or latent heat) is also improved in the merged model.
EAKF‐CMAQ: Introduction and evaluation of a data assimilation for CMAQ based on the ensemble adjustment Kalman filter
Authors: Zubrow Alexis , Chen Li , Kotamarthi V. R.
Published: May 2008

A new approach is presented for data assimilation using the ensemble adjustment Kalman filter (EAKF) technique for surface measurements of carbon monoxide in a single tracer version of the community air quality model. An implementation of the EAKF known as the Data Assimilation Research Testbed at the National Center for Atmospheric Research was used for developing the model. Three different sets of numerical experiments were performed to test the effectiveness of the procedure and the range of key parameters used in implementing the procedure. The model domain includes much of the northeastern United States. The first two numerical experiments use idealized measurements derived from defined model runs, and the last test uses measurements of carbon monoxide from approximately 220 Air Quality System monitoring sites over the northeastern United States, maintained by the U.S. Environmental Protection Agency. In each case, the proposed method provided better results than the method without data assimilation.
Formation of secondary organic aerosol from irradiated α‐pinene/toluene/NOx mixtures and the effect of isoprene and sulfur dioxide
Authors: Jaoui Mohammed , Edney Edward O. , Kleindienst Tadeusz E. , Lewandowski Michael , Offenberg John H. , Surratt Jason D. , Seinfeld John H.
Published: May 2008

Secondary organic aerosol (SOA) was generated by irradiating a series of α‐pinene/toluene/NOx mixtures in the absence and presence of isoprene or sulfur dioxide. The purpose of the experiment was to evaluate the extent to which chemical perturbations to this base‐case (α‐pinene/toluene) mixture led to changes in the gas‐phase chemistry which strongly influences mass and composition of SOA and secondary organic carbon (SOC) formed. The chemical composition was examined by gas chromatography‐mass spectrometry (GC‐MS) and laser desorption ionization‐mass spectrometry (LDI‐MS). The results showed that the addition of isoprene to the base‐case mixture significantly lowered the amount of toluene reacted, and thereby lowered the amount SOC produced. Simultaneous measurement of the organic NOy showed that reactions of isoprene effectively sequester NO2 by producing gas‐phase organic nitrates. The addition of SO2 to the base‐case mixture, while having little effect on the gas‐phase chemistry, formed sulfuric acid which led to a modest enhancement of the SOC through acid‐catalyzed or sulfur‐incorporating reactions of α‐pinene. The contribution of each hydrocarbon to the composition of the SOA was estimated using an organic tracer method. SOC from the tracer technique tended to underpredict the measured SOC, although the underprediction was especially pronounced with SO2 present. A comparison of the chromatographic results from samples of the irradiation of the α‐pinene/toluene/isoprene/NOx/SO2 mixture and ambient PM2.5 showed the presence of two unique peaks that were associated with reactions of isoprene and SO2.
Spectral induced polarization and electrodic potential monitoring of microbially mediated iron sulfide transformations
Authors: Personna Yves Robert , Ntarlagiannis Dimitrios , Slater Lee , Yee Nathan , O'Brien Michael , Hubbard Susan
Published: May 2008

Stimulated sulfate‐reduction is a bioremediation technique utilized for the sequestration of heavy metals in the subsurface. We performed laboratory column experiments to investigate the geoelectrical response of iron sulfide transformations by Desulfovibrio vulgaris. Two geoelectrical methods, (1) spectral induced polarization (SIP), and (2) electrodic potential measurements, were investigated. Aqueous geochemistry (sulfate, lactate, sulfide, and acetate), observations of precipitates (identified from electron microscopy as iron sulfide), and electrodic potentials on bisulfide ion (HS−) sensitive silver‐silver chloride (Ag‐AgCl) electrodes (∼−630 mV) were diagnostic of induced transitions between anaerobic iron sulfide forming conditions and aerobic conditions promoting iron sulfide dissolution. The SIP data showed ∼10 mrad anomalies during iron sulfide mineralization accompanying microbial activity under an anaerobic transition. These anomalies disappeared during iron sulfide dissolution under the subsequent aerobic transition. SIP model parameters based on a Cole‐Cole relaxation model of the polarization at the mineral‐fluid interface were converted to (1) estimated biomineral surface area to pore volume (Sp), and (2) an equivalent polarizable sphere diameter (d) controlling the relaxation time. The temporal variation in these model parameters is consistent with filling and emptying of pores by iron sulfide biofilms, as the system transitions between anaerobic (pore filling) and aerobic (pore emptying) conditions. The results suggest that combined SIP and electrodic potential measurements might be used to monitor spatiotemporal variability in microbial iron sulfide transformations in the field.
Mixing at the interface between two fluids in aquifer well upconing steady flow
Authors: Paster A. , Dagan G.
Published: May 2008

Because of transverse pore‐scale dispersion, a mixing layer develops along the interface between a lighter fluid (fresh water) that flows toward a well or sink above a heavier fluid (seawater) in a steady axisymmetric configuration. The Peclet number characterizing mixing, Pe = L/αT, where L is the aquifer thickness and αT is transverse dispersivity, is generally much larger than unity. The existence of a narrow transition zone calls for a boundary layer solution, which is obtained by the following steps: (1) the potential flow solution of the upper fluid above a sharp interface is assumed to be known; (2) the equations are reformulated with the potential and Stokes stream function of this flow serving as independent variables; (3) boundary layer approximate equations are formulated in terms of these variables; and (4) simple analytical solutions are obtained by von Kármán integral method. Approximate solutions are presented for a few configurations: a confined aquifer of constant thickness, a phreatic aquifer with constant recharge, and a point sink above the interface in an unbounded domain. In each case the thickness of the boundary layer and the salinity of the pumped water are determined analytically or by quadratures. The results are illustrated for a few particular cases.
Climate Change Assessment for the Baltic Sea Basin
Authors: Reckermann Marcus , Von Storch Hans , Isemer Hans‐Jörg
Published: May 2008

The Fourth Assessment Report of the Intergovernmental Panel on Climate Change [IPCC, 2007] has had a big impact on the public perception and acknowledgment of global climate change. However, regional climate change assessments are urgently needed to complement the big picture with regional results and scenarios of higher resolution, which local decision makers and stakeholders can use [Visbeck, 2008; von Storch and Meinke, 2008].

An outstanding example of a regional assessment is the BALTEX (Baltic Sea Experiment) Assessment of Climate Change for the Baltic Sea Basin (BACC; http://www.baltex‐research.eu/BACC/), which was compiled by a consortium of 84 scientists from 13 countries around the Baltic Sea [BACC Author Team, 2008]. The assessment covers various disciplines related to climate research and related impacts.
What Motivates Member Donations to the Union?
Authors: Austin James A. , Grove Timothy L.
Published: May 2008

In the fall of 2007, the AGU Development Board commissioned the development staff to survey the approximately 1200 AGU supporting members to learn why these members give $100 to AGU each year—many give much more—to fund activities in education, public affairs, public information, the sections, and the focus groups. (A recent list of supporting members was published in Eos, 88(49), 544–545, 2007.) With supporting membership having more than doubled since 2003, the development staff and the Development Board wanted to find out more about the individual motivations underlying this trend. We also were trying to identify new incentives for members to support the Union's special projects and programs.
Ostracodology—Linking Bio‐ and Geosciences: Proceedings of the 15th International Symposium on Ostracoda, Berlin, 2005
Authors: Cronin Thomas M.
Published: May 2008

If you want to know about the “paradox of sex” or why a tiny crustacean prefers spinach over brussels sprouts, then read this book. Ostracodes are a class of small crustaceans of 33,000 known living and extinct species and many more yet to be described. They are notable for their application to paleoclimatology and paleoenvironmental reconstruction—as described by J. Holmes and A. Chivas in the 2002 AGU Geophysical Monograph Series volume 131. In addition, they can make the evolutionary claim to the oldest proven male animal, a 435‐million‐year‐old Silurian fossil from England called Colymbosathon ecplecticos (D. J. Siveter et al., Science, 302, 1749–1751, 2003).
Solomon Islands Tsunami, One Year Later
Authors: McAdoo Brian G. , Fritz Hermann , Jackson Kelly L. , Kalligeris Nikos , Kruger Jens , Bonte‐Grapentin Michael , Moore Andrew L. , Rafiau Wilson B. , Billy Douglas , Tiano Braddley
Published: May 2008

The geologic and economic effects of the 2 April 2007 Solomon Islands earthquake and tsunami are distinctly visible a little more than a year after the event. Coral reef colonies that were sheared off and uplifted are slowly recovering, and many new earthquake‐triggered landslides remain mobile. Large volumes of sediment created by the earthquake and mobilized by the tsunami have been flushed from the lagoons between the reef and shoreline into deeper water, although significant quantities remain on land. Sediment from the lagoons covers piles of shattered coral that the tsunami moved from the lagoons to the base of channels in the barrier reef. These shattered corals have a higher chance of preservation as paleotsunami deposits than the material deposited on land.
Ocean Color Reveals Increased Blooms in Various Parts of the World
Authors: Kahru Mati , Mitchell B. Greg
Published: May 2008

The magnitude of phytoplankton blooms has increased significantly in many areas of the world during the past 11 years, as shown in data from ocean color sensors on board satellites. These areas with increased blooms are likely to be environmentally stressed and undergoing undesirable environmental changes such as a higher frequency of harmful algal blooms and oxygen depletion in bottom layers of oceans, estuaries, and lakes. These changes can disrupt traditional fisheries and recreational use in many coastal areas.

An algal bloom is a rapid increase in the concentration of phytoplankton algae that occurs when conditions turn favorable for algal growth. A typical example of a bloom is the phytoplankton spring bloom. Algal blooms are natural phenomena that remove dissolved carbon and nutrients. In addition, they produce new biomass that supports higher trophic levels including fish and fisheries. However, the blooms also lead to excessive turbidity, oxygen depletion in the bottom layers, and the possible death of fish, benthic animals, and bottom vegetation.
Pembroke J. Hart (1929–2008)
Authors: Malone Thomas F.
Published: May 2008

Pembroke J. Hart, who received AGU's Edward A. Flinn III Award in 2006 for “unselfish cooperation in research” after many years of facilitating, coordinating, and implementing international collaboration in geophysics, died 10 February after a short illness. He was 79.
Ohtani Receives 2007 N. L. Bowen Award
Authors: Karato Shun‐Ichiro , Ohtani Eiji
Published: May 2008

It is my pleasure to present Eiji Ohtani, one of the recipients of the N. L. Bowen Award of the American Geophysical Union.

Eiji Ohtani is indisputably the most prominent leader in the experimental studies of properties of Earth materials, particularly the melting relationships and the properties of melts under high pressures and temperatures. Eiji started his brilliant career in Mineo Kumazawa's lab at Nagoya University in the early 1970s. Mineo Kumazawa is one of the pioneers of large‐volume high‐pressure devices (others include Naoto Kawai and Syun‐iti Akimoto), and Eiji played a major role as a young student in establishing new techniques of high‐pressure and high‐temperature experiments using a large‐volume apparatus. His reputation was established already in the early 1980s based on his seminal papers on the melting of fayalite and forsterite under high pressures (to 20 gigapascals).
The Arctic and Antarctic: Two Faces of Climate Change
Authors: Overland James , Turner John , Francis Jennifer , Gillett Nathan , Marshall Gareth , Tjernström Michael
Published: May 2008

Although both the Arctic and Antarctic are subject to a similar annual cycle of solar radiation and the same increasing greenhouse gas concentrations, over the previous two decades the two regions have experienced dramatically different changes in sea ice extent, temperature, and other climatic indicators. While these differing responses suggest a paradox, they are largely consistent with known climate dynamics. This conclusion was drawn by scientists participating in the Second Workshop on Recent High Latitude Climate Change, in Seattle, Wash., in October 2007, against the dramatic backdrop of major Arctic sea ice reductions 1 month earlier [World Climate Research Programme, 2007].
Mapping Geomagnetic Field Variations with Unmanned Airborne Vehicles
Authors: Gee Jeffrey S. , Cande Steven C. , Kent Dennis V. , Partner Richard , Heckman Kate
Published: May 2008

Unmanned airborne vehicles (UAVs) are increasingly being used for a variety of commercial and research applications. The small (wingspan ∼3 meters), fully autonomous aircraft are well suited for use in remote areas or dangerous settings. UAVs that are launched and recovered on land are being used for atmospheric chemistry and surface imaging studies and for aeromagnetic surveys [Curry et al., 2004; Ramanathan et al., 2007; Funaki et al., 2007]. We report here on the first deployment of UAVs launched from a marine research vessel. The UAVs mapped fluctuations in the magnetic field in a remote area of the southwestern Pacific Ocean.
The Meeting of the Americas
Authors: Bates John , Fucugauchi Jaime Urrutia
Published: May 2008

The AGU Joint Assembly, previously known as the Spring Meeting, has formally adopted the designation “The Meeting of the Americas.” This designation reflects the objective of the Joint Assembly to promote cooperative efforts among Earth and science societies in the Americas. To achieve this objective, future Joint Assembly locations will rotate among different cities in the United States, Canada, and Latin America; the Program Committee includes representatives from throughout the Americas; and the meetings will be convened jointly with scientific societies throughout the Americas.
The Rb/E2F pathway and Ras activation regulate RecQ helicase gene expression
Authors: Liu Yongqing , El-Naggar Shahenda , Clem Brian , Chesney Jason , Dean Douglas C.
Published: May 2008

Disruption of the Rb (retinoblastoma protein)/E2F cell-cycle pathway and Ras activation are two of the most frequent events in cancer, and both of these mutations place oncogenic stress on cells to increase DNA replication. In the present study, we demonstrate that these mutations have an additive effect on induction of members of the RecQ DNA helicase family. RecQ activity is important for genomic stability, initiation of DNA replication and telomere maintenance, and mutation of the BLM (Bloom's syndrome gene), WRN (Werner's syndrome gene) or RECQL4 (Rothmund–Thomson syndrome gene) family members leads to premature aging syndromes characterized by genetic instability and telomere loss. RecQ family members are frequently overexpressed in cancers, and overexpression of BLM has been shown to cause telomere elongation. Concomitant with induction of RecQ genes in response to Rb family mutation and Ras activation, we show an increase in the number of telomeric repeats. We suggest that this induction of RecQ genes in response to common oncogenic mutations may explain the up-regulation of the genes seen in cancers, and it may provide a means for transformed cells to respond to an increased demand for DNA replication.
The role of the diphthamide-containing loop within eukaryotic elongation factor 2 in ADP-ribosylation by Pseudomonas aeruginosa exotoxin A
Authors: Zhang Yong , Liu Suya , Lajoie Gilles , Merrill A. Rod
Published: May 2008

eEF2 (eukaryotic elongation factor 2) contains a post-translationally modified histidine residue, known as diphthamide, which is the specific ADP-ribosylation target of diphtheria toxin, cholix toxin and Pseudomonas aeruginosa exotoxin A. Site-directed mutagenesis was conducted on residues within the diphthamide-containing loop (Leu693–Gly703) of eEF2 by replacement with alanine. The purified yeast eEF2 mutant proteins were then investigated to determine the role of this loop region in ADP-ribose acceptor activity of elongation factor 2 as catalysed by exotoxin A. A number of single alanine substitutions in the diphthamide-containing loop caused a significant reduction in the eEF2 ADP-ribose acceptor activities, including two strictly conserved residues, His694 and Asp696. Analysis by MS revealed that all of these mutant proteins lacked the 2′-modification on the His699 residue and that eEF2 is acetylated at Lys509. Furthermore, it was revealed that the imidazole ring of Diph699 (diphthamide at position 699) still functions as an ADP-ribose acceptor (albeit poorly), even without the diphthamide modification on the His699. Therefore, this diphthamide-containing loop plays an important role in the ADP-ribosylation of eEF2 catalysed by toxin and also for modification of His699 by the endogenous diphthamide modification machinery.
Sphingomyelin synthases regulate production of diacylglycerol at the Golgi
Authors: Villani Maristella , Subathra Marimuthu , Im Yeong-Bin , Choi Young , Signorelli Paola , Del Poeta Maurizio , Luberto Chiara
Published: May 2008

SMS [SM (sphingomyelin) synthase] is a class of enzymes that produces SM by transferring a phosphocholine moiety on to ceramide. PC (phosphatidylcholine) is believed to be the phosphocholine donor of the reaction with consequent production of DAG (diacylglycerol), an important bioactive lipid. In the present study, by modulating SMS1 and SMS2 expression, the role of these enzymes on the elusive regulation of DAG was investigated. Because we found that modulation of SMS1 or SMS2 did not affect total levels of endogenous DAG in resting cells, whereas they produce DAG in vitro, the possibility that SMSs could modulate subcellular pools of DAG, once acute activation of the enzymes is triggered, was investigated. Stimulation of SM synthesis was induced by either treatment with short-chain ceramide analogues or by increasing endogenous ceramide at the plasma membrane, and a fluorescently labelled conventional C1 domain [from PKC (protein kinase C)] enhanced in its DAG binding activity was used to probe subcellular pools of DAG in the cell. With this approach, we found, using confocal microscopy and subcellular fractionation, that modulation of SMS1 and, to a lesser extent, SMS2 affected the formation of DAG at the Golgi apparatus. Similarly, down-regulation of SMS1 and SMS2 reduced the localization of the DAG-binding protein PKD (protein kinase D) to the Golgi. These results provide direct evidence that both enzymes are capable of regulating the formation of DAG in cells, that this pool of DAG is biologically active, and for the first time directly implicate SMS1 and SMS2 as regulators of DAG-binding proteins in the Golgi apparatus.
Cholesterol binding is a prerequisite for the activity of the steroidogenic acute regulatory protein (StAR)
Authors: Roostaee Alireza , Barbar Élie , LeHoux Jean-Guy , Lavigne Pierre
Published: May 2008

Steroidogenesis depends on the delivery of cholesterol from the outer to the inner mitochondrial membrane by StAR (steroidogenic acute regulatory protein). However, the mechanism by which StAR binds to cholesterol and its importance in cholesterol transport are under debate. According to our proposed molecular model, StAR possesses a hydrophobic cavity, which can accommodate one cholesterol molecule. In the bound form, cholesterol interacts with hydrophobic side-chains located in the C-terminal α-helix 4, thereby favouring the folding of this helix. To verify this model experimentally, we have characterized the in vitro activity, overall structure, thermodynamic stability and cholesterol-binding affinity of StAR lacking the N-terminal 62 amino acid residues (termed N-62 StAR). This mature form is biologically active and has a well-defined tertiary structure. Addition of cholesterol to N-62 StAR led to an increase in the α-helical content and T° (melting temperature), indicating the formation of a stable complex. However, the mutation F267Q, which is located in the C-terminal helix interface lining the cholesterol-binding site, reduced the biological activity of StAR. Furthermore, the cholesterol-induced thermodynamic stability and the binding capacity of StAR were significantly diminished in the F267Q mutant. Titration of StAR with cholesterol yielded a 1:1 complex with an apparent KD of 3×10−8. These results support our model and indicate that StAR can readily bind to cholesterol with an apparent affinity that commensurates with monomeric cholesterol solubility in water. The proper function of the C-terminal α-helix is essential for the binding process.
The tyrosine phosphatase CD148 interacts with the p85 regulatory subunit of phosphoinositide 3-kinase
Authors: Tsuboi Nobuo , Utsunomiya Tadahiko , Roberts Richard L. , Ito Hideyuki , Takahashi Keiko , Noda Masaharu , Takahashi Takamune
Published: May 2008

CD148 is a transmembrane tyrosine phosphatase that has been implicated in the regulation of cell growth and transformation. However, the signalling mechanisms of CD148 are incompletely understood. To identify the specific intracellular molecules involved in CD148 signalling, we carried out a modified yeast two-hybrid screening assay. Using the substrate-trapping mutant form of CD148 (CD148 D/A) as bait, we recovered the p85 regulatory subunit of PI3K (phosphoinositide 3-kinase). CD148 D/A, but not catalytically active CD148, interacted with p85 in a phosphorylation-dependent manner in vitro and in intact cells. Growth factor receptor and PI3K activity were also trapped by CD148 D/A via p85 from pervanadate-treated cell lysates. CD148 prominently and specifically dephosphorylated p85 in vitro. Co-expression of CD148 reduced p85 phosphorylation induced by active Src, and attenuated the increases in PI3K activity, yet CD148 did not alter the basal PI3K activity. Finally, CD148 knock-down by siRNA (short interfering RNA) increased PI3K activity on serum stimulation. Taken together, these results demonstrate that CD148 may interact with and dephosphorylate p85 when it is phosphorylated and modulate the magnitude of PI3K activity.
In vivo quantitative relationship between plastid division proteins FtsZ1 and FtsZ2 and identification of ARC6 and ARC3 in a native FtsZ complex
Authors: Mcandrew Rosemary S. , Olson Bradley J. S. C. , Kadirjan-Kalbach Deena K. , Chi-Ham Cecilia L. , Vitha Stanislav , Froehlich John E. , Osteryoung Katherine W.
Published: May 2008

FtsZ1 and FtsZ2 are phylogenetically distinct homologues of the tubulin-like bacterial cell division protein FtsZ that play major roles in the initiation and progression of plastid division in plant cells. Both proteins are components of a mid-plastid ring, the Z-ring, which functions as a contractile ring on the stromal surface of the chloroplast IEM (inner envelope membrane). FtsZ1 and FtsZ2 have been shown to interact, but their in vivo biochemical properties are largely unknown. To gain insight into the in vivo biochemical relationship between FtsZ1 and FtsZ2, in the present study we investigated their molecular levels in wild-type Arabidopsis thaliana plants and endogenous interactions in Arabidopsis and pea. Quantitative immunoblotting and morphometric analysis showed that the average total FtsZ concentration in chloroplasts of 3-week-old Arabidopsis plants is comparable with that in Escherichia coli. FtsZ levels declined as plants matured, but the molar ratio between FtsZ1 and FtsZ2 remained constant at approx. 1:2, suggesting that this stoichiometry is regulated and functionally important. Density-gradient centrifugation, native gel electrophoresis, gel filtration and co-immunoprecipitation experiments showed that a portion of the FtsZ1 and FtsZ2 in Arabidopsis and pea chloroplasts is stably associated in a complex of ∼200–245 kDa. This complex also contains the FtsZ2-interacting protein ARC6 (accumulation and replicatioin of chloroplasts 6), an IEM protein, and analysis of density-gradient fractions suggests the presence of the FtsZ1-interacting protein ARC3. Based on the mid-plastid localization of ARC6 and ARC3 and their postulated roles in promoting and inhibiting chloroplast FtsZ polymer formation respectively, we hypothesize that the FtsZ1–FtsZ2–ARC3–ARC6 complex represents an unpolymerized IEM-associated pool of FtsZ that contributes to the dynamic regulation of Z-ring assembly and remodelling at the plastid division site in vivo.
Membrane pore formation by pentraxin proteins from Limulus, the American horseshoe crab
Authors: Harrington John M. , Chou Hui-Ting , Gutsmann Thomas , Gelhaus Christoph , Stahlberg Henning , Leippe Matthias , Armstrong Peter B.
Published: May 2008

The pentraxins are a family of highly conserved plasma proteins of metazoans known to function in immune defence. The canonical members, C-reactive protein and serum amyloid P component, have been identified in arthropods and humans. Mammalian pentraxins are known to bind lipid bilayers, and a pentraxin representative from the American horseshoe crab, Limulus polyphemus, binds and permeabilizes mammalian erythrocytes. Both activities are Ca2+-dependent. Utilizing model liposomes and planar lipid bilayers, in the present study we have investigated the membrane-active properties of the three pentraxin representatives from Limulus and show that all of the Limulus pentraxins permeabilize lipid bilayers. Mechanistically, Limulus C-reactive protein forms transmembrane pores in asymmetric planar lipid bilayers that mimic the outer membrane of Gram-negative bacteria and exhibits a Ca2+-independent form of membrane binding that may be sufficient for pore formation.
Kinetic, thermodynamic and X-ray structural insights into the interaction of melatonin and analogues with quinone reductase 2
Authors: Calamini Barbara , Santarsiero Bernard D. , Boutin Jean A. , Mesecar Andrew D.
Published: May 2008

Melatonin exerts its biological effects through at least two transmembrane G-protein-coupled receptors, MT1 and MT2, and a lower-affinity cytosolic binding site, designated MT3. MT3 has recently been identified as QR2 (quinone reductase 2) (EC 1.10.99.2) which is of significance since it links the antioxidant effects of melatonin to a mechanism of action. Initially, QR2 was believed to function analogously to QR1 in protecting cells from highly reactive quinones. However, recent studies indicate that QR2 may actually transform certain quinone substrates into more highly reactive compounds capable of causing cellular damage. Therefore it is hypothesized that inhibition of QR2 in certain cases may lead to protection of cells against these highly reactive species. Since melatonin is known to inhibit QR2 activity, but its binding site and mode of inhibition are not known, we determined the mechanism of inhibition of QR2 by melatonin and a series of melatonin and 5-hydroxytryptamine (serotonin) analogues, and we determined the X-ray structures of melatonin and 2-iodomelatonin in complex with QR2 to between 1.5 and 1.8 Å (1 Å=0.1 nm) resolution. Finally, the thermodynamic binding constants for melatonin and 2-iodomelatonin were determined by ITC (isothermal titration calorimetry). The kinetic results indicate that melatonin is a competitive inhibitor against N-methyldihydronicotinamide (Ki=7.2 μM) and uncompetitive against menadione (Ki=92 μM), and the X-ray structures shows that melatonin binds in multiple orientations within the active sites of the QR2 dimer as opposed to an allosteric site. These results provide new insights into the binding mechanisms of melatonin and analogues to QR2.
Monitoring conformational changes during the catalytic cycle of OpuAA, the ATPase subunit of the ABC transporter OpuA from Bacillus subtilis
Authors: Horn Carsten , Jenewein Stefan , Tschapek Britta , Bouschen Werner , Metzger Sabine , Bremer Erhard , Schmitt Lutz
Published: May 2008

The ABC transporter (ATP-binding-cassette transporter) OpuA is one of five membrane transport systems in Bacillus subtilis that mediate osmoprotection by importing compatible solutes. Just like all bacterial and archaeal ABC transporters that catalyse the import of substrates, OpuA (where Opu is osmoprotectant uptake) is composed of an ATPase subunit (OpuAA), a transmembrane subunit (OpuAB) and an extracellular substrate-binding protein (OpuAC). In contrast with many well-known ABC-ATPases, OpuAA is composed not only of a catalytic and a helical domain but also of an accessory domain located at its C-terminus. The paradigm of such an architecture is MalK, the ABC-ATPase of the maltose importer of Escherichia coli, for which detailed structural and functional information is available. In the present study, we have applied solution FRET (Förster resonance energy transfer) techniques using two single cysteine mutants to obtain initial structural information on the architecture of the OpuAA dimer in solution. Analysing our results in detail and comparing them with the existing MalK structures revealed that the catalytic and helical domains adopted an arrangement similar to those of MalK, whereas profound differences in the three-dimensional orientation of the accessory domain, which contains two CBS (cystathionine β-synthetase) domains, were observed. These results shed new light on the role of this accessory domain present in a certain subset of ABC-ATPase in the fine-tuning of three-dimensional structure and biological function.
Stimuli-dependent cleavage of Dicer during apoptosis
Authors: Matskevich Alexey A. , Moelling Karin
Published: May 2008

miRNAs (microRNAs) play important roles in diverse physiological processes, including stress response, apoptosis and carcinogenesis. Even though the role of individual miRNAs has been demonstrated, expression of proteins involved in miRNA production in response to acute stress or harmful agents has not been extensively investigated. Here, we have studied the role of Dicer, one of the central proteins of the miRNA processing machinery during apoptosis, and show that down-regulation of Dicer results in accelerated apoptosis of HeLa cells, triggered by TNFα (tumour necrosis factor α). We have also investigated the integrity of Dicer, and provide evidence that Dicer is a target for caspases during apoptosis. The cleavage of Dicer is stimulidependent and more pronounced when apoptosis is induced by PKC (protein kinase C) inhibitors, and can also be observed in HIV-1-infected cells at late stages of infection. Thus the apoptotic machinery may regulate the miRNA pathway by affecting individual proteins, such as Dicer.