bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of sampling volume on the probability density function of steady state concentration
Authors: Schwede Ronnie L. , Cirpka Olaf A. , Nowak Wolfgang , Neuweiler Insa
Published: December 2008

In recent years, statistical theory has been used to compute the ensemble mean and variance of solute concentration in aquifer formations with second‐order stationary velocity fields. The merit of accurately estimating the mean and variance of concentration, however, remains unclear without knowing the shape of the probability density function (pdf). In a setup where a conservative solute is continuously injected into a domain, the concentration is bounded between zero and the concentration value in the injected solution. At small travel distances close to the fringe of the plume, an observation point may fall into the plume or outside, so that the statistical concentration distribution clusters at the two limiting values. Obviously, this results in non‐Gaussian pdf's of concentration. With increasing travel distance, the lateral plume boundaries are smoothed, resulting in increased probability of intermediate concentrations. Likewise, averaging the concentration in a larger sampling volume, as typically done in field measurements, leads to higher probabilities of intermediate concentrations. We present semianalytical results of concentration pdf's for measurements with point‐like or larger support volumes based on stochastic theory applied to stationary media. To this end, we employ a reversed auxiliary transport problem, in which we use analytical expressions for first and second central spatial lateral moments with an assumed Gaussian pdf for the uncertainty of the first lateral moment and Gauss‐like shapes in individual cross sections. The resulting concentration pdf can be reasonably fitted by beta distributions. The results are compared to Monte Carlo simulations of flow and steady state transport in 3‐D heterogeneous domains. In both methods the shape of the concentration pdf changes with distance to the contaminant source: Near the source, the distribution is multimodal, whereas it becomes a unimodal beta distribution far away from the contaminant source. The semianalytical and empirical pdf's differ slightly, which we contribute to the numerical artifacts in the Monte Carlo simulations but also to hard assumptions made in the semianalytical approach. Our results imply that geostatistical techniques for interpolation and other statistical inferences based on Gaussian distributions, such as kriging and cokriging, may be feasible only far away from the contaminant source. For calculations near the source, the beta‐like distribution of concentration should be accounted for.
Advances to G3
Authors: Anonymous
Published: December 2008

Geochemistry, Geophysics, Geosystems (G3), a joint publication of AGU and the Geochemical Society, publishes research papers that speak to a broad community interested in Earth processes that are best studied with interdisciplinary approaches. G3 publishes conventional papers but is especially interested in novel publication forms that take advantage of electronic formats, such as animations and readily reusable digitized data sets. G3's large number of submissions and subscriptions attests to how an interdisciplinary approach and electronic format benefit authors and readers.

In the past few months, G3 has undergone substantial improvements. These include several changes in the timeliness of publication, revised protocols for the publication of data sets, the appointment of new associate editors, an updated Web site, and improved access to articles. As the editors of G3, we are confident that these improvements will better serve AGU members.
Glacial Sedimentary Processes and Products
Authors: O'Cofaigh Colm
Published: December 2008

Research in the field of glacial sediments and sedimentary processes increasingly involves a range of different approaches including investigations of modern glacial processes, the paleoglacial record, and numerical ice sheet modeling. This diversity of approaches is reflected in this International Association of Sedimentologists special publication edited by Michael Hambrey et al., which stems from the 2005 “Conference on Glacial Sedimentary Processes and Products,” held at the University of Wales, Aberystwyth. Following a foreword about geologist Brian Harland (to whom the volume is dedicated) and the Neoproterozoic Snowball Earth theory, and an introduction by the editors, the book has four parts.

Part 1, “Glacier dynamics and sedimentation,” focuses on modern glacier and ice sheet processes. It includes three very diverse papers. A paper by Siegert et al. explores the possibility of hydrological links between Antarctic subglacial lakes and the consequences of rapid drainage events for subglacial erosion and deposition. This is followed by a paper (Midgley et al.) on moraine geomorphology and sedimentology in Svalbard, Norway, and a final paper (Rousselot et al.) on the description of a laboratory apparatus for investigating clast ploughing in sediments.
Carbon sequestration due to the abandonment of agriculture in the former USSR since 1990
Authors: Vuichard Nicolas , Ciais Philippe , Belelli Luca , Smith Pascale , Valentini Riccardo
Published: December 2008

The end of the Soviet Union and the collapse of its agricultural structures in the early 1990s has induced the abandonment of a large croplands area, which have been recovered by herbaceous plants. This widespread unintended and abrupt land use change took place over 200,000 km2, a large enough scale to impact the continental and global carbon budgets. The goal of this study is to estimate the net biome productivity (NBP) of the abandoned croplands and to assess the soil C storage dynamics due to recent land conversion. The soil C balance and its input (net primary productivity) and output (heterotrophic respiration) fluxes is simulated in a spatially explicit manner with the process‐driven natural vegetation/crop model Organizing Carbon and Hydrology in Dynamic Ecosystems‐Supra‐Thermal Ion Composion Spectrometer prescribed with successive area changes of abandoned croplands during the 1990s. We estimate that regional agricultural abandonment is responsible of a cumulated carbon sink over 1991–2000 of 373 gC m−2, or 64 TgC over the domain considered, which defines a mean annual C sink of 46.7 g C m−2 a−1. Agricultural practices during the former cultivation phase determine a legacy on the C sink following abandonment, which impacts by +37% to −25% according to the practice considered (no tillage, no fertilization, and export of some crop residues). We conclude that futures studies of this regional change in the C cycle should better consider management information in order to refine the NBP estimate.
Response of large‐scale ionospheric convection to substorm expansion onsets: A case study
Authors: Miyashita Y. , Hosokawa K. , Hori T. , Kamide Y. , Yukimatu A. S. , Fujimoto M. , Mukai T. , Machida S. , Sato N. , Saito Y. , Shinohara I. , Sigwarth J. B.
Published: December 2008

We have studied the response of large‐scale ionospheric convection to substorm expansion onsets on the basis of two weak substorms of 1 May 2001, during which a large part of the dawn cell of the two‐cell ionospheric convection pattern was monitored by the SuperDARN radars. Ionospheric convection began to enhance first in a localized region of the equatorward part of the dawn cell ∼2 minutes before the expansion onsets of both substorms and then enhanced in the entire dawn cell successively. The enhanced convection persisted throughout their expansion phase, possibly even near the footprint of a plasma sheet region without fast flows observed by Geotail. These observations suggest that ionospheric convection begins to enhance just before substorm expansion onset and then enhances in the entire cell, possibly regardless of the presence of fast earthward flows in the corresponding plasma sheet region of the magnetotail. The global enhancement of ionospheric convection is consistent with that of magnetotail convection, which also begins just before onset.
Measurements and modeling of Δ17O of nitrate in snowpits from Summit, Greenland
Authors: Kunasek S. A. , Alexander B. , Steig E. J. , Hastings M. G. , Gleason D. J. , Jarvis J. C.
Published: December 2008

We quantify controls on seasonal changes of the oxygen isotope anomaly of nitrate (Δ17O(NO3−), wherein Δ17O ≈ δ17O − (0.52 × δ18O)) in snow at Summit, Greenland, in an effort to enable quantitative reconstructions of paleoatmospheric oxidant concentrations from ice core Δ17O(NO3−). Measurements of Δ17O(NO3−) from a snowpit at Summit are compared to calculations from an atmospheric chemical box model. Measured values of Δ17O(NO3−) covering three seasonal cycles (January–December 2000, July 2003–March 2006) range from 22.4‰ in summertime to 33.7‰ in wintertime, while model results show a larger range (18.9–31.5‰). Agreement between observed and modeled results is excellent for winter, when O3 oxidation of nitrogen oxides dominates nitrate production (winter averages agree within 0.3‰). The 2–7‰ discrepancy between summertime box model results and measurements of Δ17O(NO3−) may result from several influences not accounted for by our box model, including nonzero Δ17O of OH over polar regions, stratospheric influence on surface O3 at Summit, participation of BrO in nitrate production, and tropospheric transport of nitrate. A box model sensitivity study shows that annual mean Δ17O(NO3−) is most sensitive to changes in the ratio of [O3]/([HO2] + [RO2]) in summer.
Trends and interdecadal changes of weather predictability during 1950s–1990s
Authors: Ding Ruiqiang , Li Jianping , Ha Kyung‐Ja
Published: December 2008

To study the atmospheric predictability from the view of nonlinear error growth dynamics, a new approach using the nonlinear local Lyapunov exponent (NLLE) is introduced by the authors recently. In this paper, the trends and interdecadal changes of weather predictability limit (WPL) during 1950s–1990s are investigated by employing the NLLE approach. The results show that there exist significant trend changes for WPL over most of the globe. At three different pressure levels in the troposphere (850, 500, and 200 hPa), spatial distribution patterns of linear trend coefficients of WPL are similar. Significant decreasing trends in WPL could be found in the most regions of the northern midlatitudes and Africa, while significant increasing trends in WPL lie in the most regions of the tropical Pacific and southern mid‐high latitudes. In the lower stratosphere (50 hPa), the WPL in the whole tropics all shows significant increasing trends, while it displays significant decreasing trends in the most regions of the Antarctic and northern mid‐high latitudes. By examining the temporal variations of WPL in detail, we find that the interdecadal changes of WPL in most regions at different levels mainly happen in the 1970s, which is consistent with the significant climate shift occurring in the late 1970s. Trends and interdecadal changes of WPL are found to be well related to those of atmospheric persistence, which in turn are linked to the changes of atmospheric internal dynamics. Further analysis indicates that the changes of atmospheric static stability due to global warming might be one of main causes responsible for the trends and interdecadal changes of atmospheric persistence and predictability in the southern and northern mid‐high latitudes. The increased sea surface temperature (SST) variability exerts a stronger external forcing on the tropical Pacific atmosphere that tends to enhance the persistence of tropical Pacific atmosphere. This process appears to be responsible for the increase of atmospheric predictability and persistence in the tropical Pacific since the late 1970s.
SHARAD radar sounding of the Vastitas Borealis Formation in Amazonis Planitia
Authors: Campbell Bruce , Carter Lynn , Phillips Roger , Plaut Jeffrey , Putzig Nathaniel , Safaeinili Ali , Seu Roberto , Biccari Daniela , Egan Anthony , Orosei Roberto
Published: December 2008

Amazonis Planitia has undergone alternating episodes of sedimentary and volcanic infilling, forming an interleaved sequence with an upper surface that is very smooth at the kilometer scale. Earlier work interprets the near‐surface materials as either young, rough lava flows or ice‐rich sediment layers, overlying a basement comprising the Vastitas Borealis Formation and earlier Hesperian plains. Sounding radar profiles across Amazonis Planitia from the Shallow Radar (SHARAD) instrument on the Mars Reconnaissance Orbiter reveal a subsurface dielectric interface that increases in depth toward the north along most orbital tracks. The maximum depth of detection is 100–170 m, depending upon the real dielectric permittivity of the materials, but the interface may persist at greater depth to the north if the reflected energy is attenuated below the SHARAD noise floor. The dielectric horizon likely marks the boundary between sedimentary material of the Vastitas Borealis Formation and underlying Hesperian volcanic plains. The SHARAD‐detected interface follows the surface topography across at least one of the large wrinkle ridges in north central Amazonis Planitia. This conformality suggests that Vastitas Borealis sediments, at least in this region, were emplaced prior to compressional tectonic deformation. The change in radar echo strength with time delay is consistent with a loss tangent of 0.005–0.012 for the column of material between the surface and the reflector. These values are consistent with dry, moderate‐density sediments or the lower end of the range of values measured for basalts. While a component of distributed ice in a higher‐loss matrix cannot be ruled out, we do not find evidence for a dielectric horizon within the Vastitas Borealis Formation that might suggest an abrupt change from an upper dry layer to an ice‐rich lower deposit.
Morphology and texture of particles along the Spirit rover traverse from sol 450 to sol 745
Authors: Yingst R. A. , Crumpler L. , Farrand W. H. , Li R. , Cabrol N. A. , Neakrase L. D.
Published: December 2008

We quantified and classified the shape, roundness, size, and texture of 935 loose surface particles along the Spirit rover traverse from sols 450–745 to assess origin, transport, and other alteration mechanisms that altered particles during and after formation. Variation in particle morphologic parameters along traverse is consistent with crossing mapped geologic unit boundaries. Texture is divided into four types: vesicular, smooth and flat‐faceted, rough and flat‐faceted, and very rough. Sphericity and roundness are intermediate and low, respectively, comparable to particles moved by high‐energy transport or to crushed particles. This indicates intermittent, high‐energy emplacement or modification of a single lithology, rather than systematic, continuous low‐energy abrasion or wear over time. Comparison with particle morphology at other Mars landing sites is consistent with the hypothesis that no secondary systematic transport or wide‐scale chemical alteration was active at a significant enough level to alter macromorphology. In particular, particle morphology at the Mars Pathfinder site shows stronger evidence of abrasion than along the Spirit traverse, suggesting Mars Pathfinder particles have undergone abrasion processes that particles in this study area have not. Additionally, morphology indices have correlation coefficients near zero, indicating that a fluvial transport mechanism is likely not responsible for morphology. Morphology and texture are instead related to origin and composition rather than subsequent modification. Morphology and texture support a volcanic origin, possibly without modification, but most likely altered primarily by ballistic impact, implying that the Spirit landing site and traverse may be utilized in the future as a standard site for characterization of impact‐derived morphology.
Induced magnetosphere and its outer boundary at Venus
Authors: Zhang T. L. , Delva M. , Baumjohann W. , Volwerk M. , Russell C. T. , Wei H. Y. , Wang C. , Balikhin M. , Barabash S. , Auster H.‐U. , Kudela K.
Published: December 2008

The induced magnetosphere at Venus consists of regions near the planet and its wake for which the magnetic pressure dominates all other pressure contributions. Initial Venus Express measurements indicate a well‐defined outer boundary, the magnetopause, of the induced magnetosphere. This magnetopause acts as an obstacle to deflect the solar wind. Across this boundary, the magnetic field exhibits abrupt directional changes and pronounced draping. In this paper, we examine the structure of the magnetopause using Venus Express magnetic measurements. We find that the magnetopause is a directional discontinuity resembling either a tangential or a rotational discontinuity depending on the interplanetary magnetic field orientation.
Impact of deep plowing on groundwater recharge in a semiarid region: Case study, High Plains, Texas
Authors: Scanlon B. R. , Reedy R. C. , Baumhardt R. L. , Strassberg G.
Published: December 2008

Groundwater recharge is critical in semiarid regions where aquifers are currently being mined for intensive irrigation. Land use management related to agriculture can be used to control partitioning of water near the land surface and to potentially manage water resources. The purpose of this study was to quantify impacts of deep plowing in rainfed (nonirrigated) agriculture in a semiarid region on groundwater recharge, which had not been previously evaluated. Deep (0.7 m) plowing was conducted once in 1971 to remove low‐permeability soil layers (0.15–0.70 m deep) in Pullman clay loam (20,000 km2 area) in a bench terrace system in the semiarid High Plains in Texas (USA). Deep plowing was followed by conventional tillage. Boreholes were drilled in deep plowed cropland (three boreholes) and also beneath conventionally tilled cropland (four) and natural ecosystems (three) to provide baseline controls. Soil samples were analyzed for water content, chloride concentrations, and matric potentials to quantify subsurface water movement. Bulges of chloride that accumulated beneath natural ecosystems during the past 9,000–14,000 years (Holocene period) provided a marker to quantify time‐integrated response of subsurface drainage to hydrologic forcing in deep‐plowed cropland. Displacement of chloride bulges to depths of 10.7, 12.3, and 13.7 m beneath deep‐plowed cropland indicate minimum drainage rates of 58, 60, and 81 mm/a, whereas drainage beneath conventionally tilled cropland ranged from 0 (nonterraced) to 9 and 14 mm/a (bench terraced). Deep plowing slightly increased crop yield during wet years by reducing waterlogging. If deep plowing were applied to 10% of the Pullman soils, it could increase regional volumetric recharge by 0.1 km3/a, which is similar to the current regional volumetric recharge. Low‐permeability soil layers are widespread in cropland areas globally, and deep plowing could greatly enhance groundwater recharge in such areas, which is critical in semiarid regions where recharge is negligible.
Geophysical imaging of watershed subsurface patterns and prediction of soil texture and water holding capacity
Authors: Abdu H. , Robinson D. A. , Seyfried M. , Jones S. B.
Published: December 2008

The spatial distribution of subsurface soil textural properties across the landscape is an important control on the hydrological and ecological function of a watershed. Traditional methods of mapping soils involving subjective assignment of soil boundaries are inadequate for studies requiring a quantitative assessment of the landscape and its subsurface connectivity and storage capacity. Geophysical methods such as electromagnetic induction (EMI) provide the possibility of obtaining high‐resolution images across a landscape to identify subtle changes in subsurface soil patterns. In this work we show how EMI can be used to image the subsurface of a ∼38 ha watershed. We present an imaging approach using kriging to interpolate and sequential Gaussian simulation to estimate the uncertainty in the maps. We also explore the idea of difference ECamapping to try to exploit changes in soil moisture to identify more hydrologically active locations. In addition, we use a digital elevation model to identify flow paths and compare these with the ECameasurement as a function of distance. Finally, we perform a more traditional calibration of ECawith clay percentage across the watershed and determine soil water holding capacity (SWHC). The values of SWHC range from 0.07 to 0.22 m3m−3across the watershed, which contrast with the uniform value of 0.13 derived from the traditional soil survey maps. Additional work is needed to appropriately interpret and incorporate EMI data into hydrological studies; however, we argue that there is considerable merit in identifying subsurface soil patterns from these geophysical images.
Intra‐meander hyporheic flow in alluvial rivers
Authors: Revelli Roberto , Boano Fulvio , Camporeale Carlo , Ridolfi Luca
Published: December 2008

Several geomorphological fluvial features are able to induce hyporheic exchange between the rivers and the alluvial sediments. However, while the small‐scale exchange induced by bed forms has been thoroughly investigated, the role of the larger features remains poorly understood. Here, we focus on the hyporheic flows driven by the channel sinuosity in the intrameander zone. A physically based model is adopted to simulate the morphodynamic evolution of three different meandering rivers, from the first stages of the meander evolution until the incipient meander cutoff. For each stage, the sinuosity‐driven intrameander hyporheic flow is computed. In this way, the hyporheic flow field, the fluxes exchanged with the river, and the residence times are described during the whole meander evolution. The main result concerns the existence of a remarkable zonation induced by the flow field in the intrameander zone. The more the meander evolves, the more the zonation becomes pronounced, and the probability distribution of the residence times shows a bimodal shape with an intermediate power law behavior. Some general rules governing the typical timescales of the intrameander hyporheic flow and the mean exchanged flux are also deduced.
NF‐κB p52:RelB heterodimer recognizes two classes of κB sites with two distinct modes
Authors: Fusco Amanda J , Huang De‐Bin , Miller Dustyn , Wang Vivien Ya‐Fan , Vu Don , Ghosh Gourisankar
Published: December 2008

The X‐ray structure of the nuclear factor‐κB (NF‐κB) p52:RelB:κB DNA complex reveals a new recognition feature not previously seen in other NF‐κB:κB DNA complexes. Arg 125 of RelB is in contact with an additional DNA base pair. Surprisingly, the p52:RelB R125A mutant heterodimer shows defects both in DNA binding and in transcriptional activity only to a subclass of κB sites. We found that the Arg 125‐sensitive κB sites contain more contiguous and centrally located A:T base pairs than do the insensitive sites. A protein‐induced kink observed in this complex, which used an AT‐rich κB site, might allow the DNA contact by Arg 125; such a kink might not be possible in complexes with non‐AT‐rich κB sites. Furthermore, we show that the p52:RelB heterodimer binds to a broader spectrum of κB sites when compared with the p50:RelA heterodimer. We suggest that the p52:RelB heterodimer is more adaptable to complement sequence and structural variations in κB sites when compared with other NF‐κB dimers.
Rng3, a member of the UCS family of myosin co‐chaperones, associates with myosin heavy chains cotranslationally
Authors: Amorim Maria J , Mata Juan
Published: December 2008

The production of functional myosin heavy chains in many eukaryotic organisms requires the function of proteins containing UCS domains (UNC‐45/CRO1/She4), which bind to the myosin head domain and stimulate its folding. UCS proteins are essential for myosin‐related functions such as muscle formation, RNA localization and cytokinesis. Here, we show that the Schizosaccharomyces pombe UCS protein Rng3 associates with polysomes, suggesting that UCS proteins might assist myosin folding cotranslationally. To identify Rng3 cotranslational targets systematically, we purified Rng3‐associated RNAs and used DNA microarrays to identify the transcripts. Rng3 copurified with only seven transcripts (around 0.1% of S. pombe genes), including all five messenger RNAs encoding myosin heavy chains. These results suggest that every myosin heavy chain in S. pombe is a cotranslational target of Rng3. Furthermore, our data suggest that microarray‐based approaches allow the genome‐wide identification of cotranslational chaperone targets, and thus pave the way for the dissection of translation‐linked chaperone networks.
Ca2+ oscillations at fertilization in mammals
Authors: Halet G. , Marangos P. , FitzHarris G. , Carroll J.
Published: December 2008

The mouse egg provided the first direct measurement of Ca2+ oscillations in any cell type. These sperm-induced Ca2+ oscillations occur at a relatively low frequency, and can be detected up to 18–20 h after sperm–egg fusion. The Ca2+ oscillations consist of two series of transients; the first lasts about 4 h, from metaphase II until interphase of the first cell cycle, and the second lasts the duration of the first mitotic division. This cell-cycle-regulated aspect to the pattern of Ca2+ signalling at fertilization is reflected in the role of the Ca2+ transients in stimulating exit from metaphase arrest. Recent developments have started to shed light on the mechanism initiating Ca2+ oscillations at fertilization, on how the frequency of the oscillations is set, and on what determines their temporal pattern.
Generation and modulation of cytosolic Ca2+ signals in pancreatic acinar cells: techniques and mechanisms
Authors: Dolman N.J. , Tepikin A.V. , Petersen O.H.
Published: December 2008

Calcium is a ubiquitous signalling molecule, known to control a vast array of cellular processes. In order to retain stimulus fidelity, the cell encodes the increases in intracellular calcium in the form of oscillations that are regulated both temporally and spatially. Here, we review recent work, using the pancreatic acinar cell as a model system, on the mechanisms employed to generate and modulate cytosolic Ca2+ signals, and the technical advances that have made these studies possible.
Agonist-induced calcium and oxidative stress responses in endothelial cells
Authors: Wilkinson Jenny A. , Jacob Ron
Published: December 2008

[Ca2+]i (cytosolic [Ca2+]) and OS (oxidative stress) were measured simultaneously in calf pulmonary artery endothelial cells using fura-2 and carboxy-2´,7´-dichlorodihydrofluorescein. ATP stimulated a [Ca2+]i increase that was followed a few seconds later by an increase in OS. Pre-exposure to 5 μM H2O2 potentiated these responses to ATP. Elevating or removing extracellular Ca2+ increased or reduced the [Ca2+]i response to ATP and caused parallel changes in the OS response, suggesting that this response was a consequence of the [Ca2+]i response. Inhibition of mitochondria with rotenone or antimycin A affected the responses but not in a manner that allowed a simple interpretation of the role of mitochondria. These data show an initimate connection between [Ca2+]i and OS that can be modulated by low levels of exogenously applied OS, allowing the possibility of positive feedback.
The Ras binary switch: an ideal processor for decoding complex Ca2+ signals?
Authors: Walker S.A. , Lockyer P.J. , Cullen P.J.
Published: December 2008

Activation of cell-surface receptors often leads to changes in intracellular calcium concentration ([Ca2+]i). Receptor-generated calcium transients are often seen as repetitive spikes of elevated intracellular calcium concentration ([Ca2+]i), whose frequency varies according to the amplitude of the receptor stimuli. This suggests a requirement for molecular decoders, capable of interpreting such complex calcium signals into the correct physiological response. Ras proteins are binary molecular switches controlling a plethora of cellular responses. Whether Ras is in its active GTP-bound, or inactive GDP-bound, form is determined by the activity of guanine nucleotide exchange factors (GEFs) and GTPase-activating protein (GAPs). Calcium-regulated GEFs and GAPs have been identified, some with an exquisite sensitivity to [Ca2+]i, implicating a potential role of complex calcium signals in regulating Ras.
X-ray crystallographic studies of protein–ligand interactions
Authors: Palmer R.A. , Niwa H.
Published: December 2008

X-ray crystallography enables details of covalent and non-covalent interactions to be analysed quantitatively in three dimensions, thus providing the basis for the understanding of binding of ligands to proteins as well as modes of action such as cell-surface binding. This article is concerned with current methods employed for the X-ray analysis of protein structures complexed with ligands. It deals mainly with ‘what can be done’ in current research, rather than providing details of ‘how to do it’. In recent years significant advances have been made in a variety of techniques: growing protein crystals from very small samples by scanning a wide range of conditions; X-ray intensity data collection and measurement through the use of charge-coupled devices and high-intensity, versatile synchrotron sources; cryo-crystallography which both stabilizes the crystals and provides improved data; methods for analysing and interpreting the structures, dependent, at least in part, on both structural and sequence databases; and improvements in hardware and software. To illustrate the type of results achievable two examples involving protein–sugar interactions are discussed: (i) SNAII (the lectin Sambucus nigra agglutinin-II from elder) N-terminal sugar-binding site where terminal sugar units in a glycosylation chain from a symmetry-related molecule bind and (ii) MLI (mistletoe lectin I) C-terminal sugar-binding site with lactose.
Protein–ligand and protein–protein interactions studied by electrospray ionization and mass spectrometry
Authors: Burkitt W.I. , Derrick P.J. , Lafitte D. , Bronstein I.
Published: December 2008

Electrospray ionization has made possible the transference of non-covalently bound complexes from solution phase to high vacuum. In the process, a complex acquires a net charge and becomes amenable to measurement by MS. FTICR (Fourier-transform ion cyclotron resonance) MS allows these ions to be measured with sufficiently high resolution for the isotopomers of complexes of small proteins to be resolved from each other (true for complexes up to about 100 kDa for the most powerful FTICR instruments), which is of crucial significance in the interpretation of spectra. Results are presented for members of the S100 family of proteins, demonstrating how non-covalently bound complexes can be distinguished unambiguously from covalently bound species. Consideration relevant both to determination of binding constants in solution from the gas-phase results and to the elucidation of protein folding and unfolding in solution are discussed. The caveats inherent to the basic approach of using electrospray and MS to characterize protein complexes are weighed and evaluated.
Scanning FCS, a novel method for three-dimensional particle tracking
Authors: Levi V. , Ruan Q. , Kis-Petikova K. , Gratton E.
Published: December 2008

We describe a novel method to track fluorescent particles in three dimensions with nanometre precision and millisecond time resolution. In this method, we use our two-photon excitation microscope. The galvomotor-driven x–y scanning mirrors allow the laser beam to move repetitively in a circular path with a radius of half the width of the point spread function of the laser. When the fluorescent particle is located within the scanning radius of the laser, the precise position of the particle in the x–x plane can be determined by its fluorescence intensity distribution along the circular scanning path. A z-nanopositioner on the objective was used to change the laser focus at two planes (half width of the point spread function apart). The difference of the fluorescence intensity in the two planes is used to calculate the z-position of the fluorescent particle. The laser beam is allowed to scan multiple circular orbits before it is moved to the other plane, thus improving the signal to noise ratio. With a fast feedback mechanism, the position of the laser beam is directed to the centre of the fluorescent particle, thus allowing us to track a particle in three dimensions. In this contribution we describe some calibration experiments performed to test the three-dimensional tracking capability of our system over a large range.
Interprotein interactions are responsible for the confined diffusion of a G-protein-coupled receptor at the cell surface
Authors: Daumas F. , Destainville N. , Millot C. , Lopez A. , Dean D. , Salomé L.
Published: December 2008

The monitoring of the movements of membrane proteins (or lipids) by single-particle tracking enables one to obtain reliable insights into the complex dynamic organization of the plasma membrane constituents. Using this technique, we investigated the diffusional behaviour of a G-protein-coupled receptor. The trajectories of the receptors revealed a diffusion mode combining a short-term rapid confined diffusion with a long-term slow diffusion. A detailed statistical analysis shows that the receptors have a diffusion confined to a domain which itself diffuses, the confinement being due to long-range attractive inter-protein interactions. The existing models of the dynamic organization of the cell membrane cannot explain our results. We propose a theoretical Brownian model of interacting proteins that is consistent with the experimental observations and accounts for the variations found as a function of the domain size of the short-term and long-term diffusion coefficients.
The development of chromatography for the characterization of protein interactions: a personal perspective
Authors: Winzor D.J.
Published: December 2008

This article reviews the progress of a personal endeavour to develop chromatography as a quantitative procedure for the determination of reaction stoichiometries and equilibrium constants governing protein interactions. As well as affording insight into an aspect of chromatography with which many protein chemists are unfamiliar, it shows the way in which minor adaptations of conventional chromatographic practices have rendered the technique one of the most powerful methods available for the characterization of interactions. That pathway towards quantification is followed from the introduction of frontal gel filtration for the study of protein self-association to the characterization of ligand binding by the biosensor variant of quantitative affinity chromatography.
Mucoadhesive interactions
Authors: Harding S.E.
Published: December 2008

The adhesive properties of certain types of biopolymer can be used to increase the residence time of orally or nasally administered drugs. A fuller understanding of the molecular processes underpinning such ‘mucoadhesive’ phenomena will help in the optimal design of delivery systems. The interactions involved are, however, less well defined compared with those often encountered in protein-recognition phenomena: mucoadhesive interaction products can be very large and polydisperse, so to probe them we need to adopt a different strategy to those used by protein biochemists. Reviewed herein is some of the recent work at physiological or near-physiological solution conditions involving molecular hydrodynamics – with analytical ultracentrifugation and SEC-MALLs (size-exclusion chromatography coupled to multi-angle laser light scattering) as the cornerstones – reinforced by viscometry and the imaging probes of electron microscopy and atomic force microscopy. These clearly demonstrate the mucoadhesive properties of both an unusual cationic protein [Deacon, Davis, Waite and Harding (1998) Biochemistry 37, 14108–14112] and more significantly chitosan polysaccharides of varying degrees of charge/acetylation as a function of solution conditions, and are providing the platform for the construction of stable formulations.
Time-resolved stimulated emission depletion in two-photon excited states
Authors: Bain A.J. , Marsh R.J. , Armoogum D.A. , Mongin O. , Porrès L. , Blanchard-Desce M.
Published: December 2008

A new approach to time-resolved fluorescence spectroscopy based on stimulated emission depletion (STED) of two-photon excited states is presented. Combined with time-resolved detection, STED can circumvent orientational averaging constraints and spontaneous emission selection rules inherent in all conventional techniques. Applications of STED to the study of molecular probe dynamics are presented, together with studies of STED dynamics in a new push–push two-photon chromophore.
The extended postprandial phase in diabetes
Authors: Owens D.
Published: December 2008

Atherosclerosis is a major complication of diabetes, yet the reason for this remains obscure. Mechanisms of plaque formation are discussed and, in particular, metabolic alterations in the postprandial phase in diabetes are examined. A major metabolic effect of insulin deficiency is a failure to suppress non-esterified fatty acids. The importance of non-esterified fatty acids in the formation of the lipoproteins is discussed, as well as the effects of non-esterified fatty acids on insulin secretion and glucose transport, since the hallmark of Type II diabetes is insulin resistance. The genesis of large triacylglycerol-rich lipoproteins is examined and, in particular, the formation of the intestinally derived chylomicron particle is discussed in some depth with reference to microsomal triacylglycerol transfer protein and apolipoprotein B48, the structural protein for the intestinally derived lipoproteins. The role of microsomal triacylglycerol transfer protein polymorphisms is mentioned. The final section of this review examines alterations to the low-density lipoprotein particle that are found in patients with diabetes and the mechanisms that create an atherogenic low-density lipoprotein particle in diabetes. In conclusion, the lipoprotein cascade is severely disrupted in diabetes, with a major abnormality being found in the metabolism of non-esterified fatty acids. It appears that, at each level of disruption of the normal pathway, the alterations that have been described have the potential to accelerate cholesterol deposition in the plaque and to cause plaque disruption, explaining in part the increased cardiovascular disease found in diabetes.
Postprandial lipaemia in familial combined hyperlipidaemia
Authors: Castro Cabezas M.
Published: December 2008

FCHL (familial combined hyperlipidaemia) is the most frequent inherited disorder of lipid metabolism leading to premature atherosclerosis. The usual phenotype in FCHL is elevated fasting plasma triacylglycerols, low HDL (high-density lipoprotein)-cholesterol concentrations and elevated plasma apolipoprotein B concentrations. The metabolic basis for this phenotype is hepatic overproduction of VLDL (very-low-density lipoprotein), which is only partly linked to the insulin resistance associated with FCHL. At this stage the molecular basis for this VLDL overproduction is not known, but emerging evidence points to a disturbed trapping of peripheral fatty acids, resulting in enhanced hepatic flux of NEFA [non-esterified (‘free’) fatty acids]. Postprandial hyperlipidaemia with accumulation of lipoprotein remnants and NEFA have been implicated in the development of atherosclerosis in this disorder. It has been proposed that, by VLDL overproduction, fasting hypertriglyceridaemia may lead to ‘overflow’ of the catabolic cascade for triacylglycerol-rich particles, thereby explaining the delayed catabolism of remnants in FCHL. Delayed clearance of remnants of VLDL and chylomicrons leads to enhanced interaction of these highly atherogenic particles with the endothelium, and enhanced trans-endothelial migration of the particles, resulting in a chronic inflammatory response that is the initiation of the atherosclerotic lesion. In this process, activated leucocytes (either directly by the remnants or indirectly by released NEFA) play an important role by adherence to the endothelium and migration into the subendothelial space, where the uptake of atherogenic remnants results in a vicious cycle of activation of endothelium, leucocytes and production of cytokines.
Isolating excitonic Raman coherence in semiconductors using two-dimensional correlation spectroscopy
Authors: Yang Lijun , Zhang Tianhao , Bristow Alan D. , Cundiff Steven T. , Mukamel Shaul
Published: December 2008

We present the experimental and simulation results of two-dimensional optical coherent correlation spectroscopy signals along the phase-matching direction kI=−k1+k2+k3 projected on the two-dimensional (2D) (Ω3,Ω2) plane corresponding to the second and third delay periods. Overlapping Raman coherences in the conventional (Ω3,Ω1) 2D projection may now be clearly resolved. The linewidths of the heavy-hole (HH) and light-hole (LH) excitonic Raman coherence peaks are obtained. Further insights on the higher-order (beyond time-dependent Hartree–Fock) correlation effects among mixed (HH and LH) two excitons can be gained by using a cocircular pulse polarization configuration.
Correlating exchange bias with magnetic anisotropy in ion-beam bombarded NiFe/Mn-oxide bilayers
Authors: Lin K.-W , Guo J.-Y. , Chen T.-J. , Ouyang H. , Vass E. , van Lierop J.
Published: December 2008

The exchange bias field dependence on the Mn-oxide and its microstructure in NiFe/Mn-oxide bilayers was investigated. Transmission electron microscopy results have shown that the bilayer bottom consisted of either α-Mn, rocksalt MnO, or a composite of tetragonal Mn3O4+MnO, depending on the ratio of O2/Ar used during dual ion-beam deposition. Magnetometry results at 5 K indicate that the exchange bias field (Hex∼−300 Oe) is largest in a NiFe/Mn (0%O2/Ar) bilayer. The MnO formation by in situ Mn oxidation results in a decrease in Hex in a NiFe/Mn-oxide (21%O2/Ar) bilayer. In contrast, a further increase in the O2/Ar ratio during deposition results in larger Hex and Hc. This is attributed to the oxidation of MnO into a harder ferrimagnet, Mn3O4. Our results indicate that the antiferromagnetic Mn enabled stronger coupling with NiFe than MnO. In addition, we find that the MnO–Mn3O4 coupling dominates the exchange bias effects at high oxygen concentrations.
Room temperature ferromagnetism in Sn1−xVxO2 films prepared by sol-gel method
Authors: Zhang Li , Ge Shihui , Zuo Yalu , Zhou Xueyun , Xiao Yuhua , Yan Shiming , Han Xiufeng , Wen Zhenchao
Published: December 2008

The structure and magnetic properties of Sn1−xVxO2 (x=0.02–0.22) thin films fabricated on Si (111) substrate using a sol-gel method and spin coating technique have been investigated. All the samples have pure rutile polycrystalline structure and exhibit room temperature ferromagnetism. The magnetic moment per V reaches 2.92μB for the Sn0.98V0.02O2 film and drops rapidly as V content is increased. X-ray photoelectron spectroscopy study reveals that vanadium is in V4+ chemical state. Various annealing treatments were performed to explore the origin of the ferromagnetism. It is found that the ferromagnetism of Sn0.98V0.02O2 film disappears after annealing in a rich-oxygen atmosphere and occurs again after annealing in a low vacuum condition. Furthermore, an annealing in Sn vapor leads to the decrease in ferromagnetism. These results confirm that the oxygen vacancies play a critical role in introducing ferromagnetism of Sn1−xVxO2 films; therefore, the origin of the ferromagnetism in our samples can be understood in the framework of the bound magnetic polaron model.
On the surface of glasses
Authors: Stevenson Jacob D. , Wolynes Peter G.
Published: December 2008

Dynamics near the surface of glasses is generally much faster than in the bulk. Neglecting static perturbations of structure at the surface, we use random first order transition (RFOT) theory to show the free energy barrier for activated motion near a free surface should be half that of the bulk at the same temperature. The increased mobility allows the surface layers to descend much further on the energy landscape than the bulk ordinarily does. The simplified RFOT calculation, however, predicts a limiting value for the configurational entropy a vapor deposited glass may reach as a function of deposition rate. We sketch how mode coupling effects extend the excess free surface mobility into the bulk so that the glass transition temperature is measurably perturbed at depths greater than the naive length scale of dynamic cooperativity.
Constructing diabatic states from adiabatic states: Extending generalized Mulliken–Hush to multiple charge centers with Boys localization
Authors: Subotnik Joseph E. , Yeganeh Sina , Cave Robert J. , Ratner Mark A.
Published: December 2008

This article shows that, although Boys localization is usually applied to single-electron orbitals, the Boys method itself can be applied to many electron molecular states. For the two-state charge-transfer problem, we show analytically that Boys localization yields the same charge-localized diabatic states as those found by generalized Mulliken–Hush theory. We suggest that for future work in electron transfer, where systems have more than two charge centers, one may benefit by using a variant of Boys localization to construct diabatic potential energy surfaces and extract electronic coupling matrix elements. We discuss two chemical examples of Boys localization and propose a generalization of the Boys algorithm for creating diabatic states with localized spin density that should be useful for Dexter triplet-triplet energy transfer.
Viscous and inviscid flows generated by wall-normal injection into a cylindrical cavity with a headwall
Authors: Kurdyumov Vadim N.
Published: December 2008

An analysis of viscous and inviscid steady flows in a cylindrical cavity of a circular cross section with a headwall is presented. The flow is induced by wall-normal injection from both the sidewall and the headwall which includes the zeroth tangential velocity at the injecting boundaries. It is shown that in the inviscid limit the functional vorticity-stream function relation is essentially nonlinear and singular becoming linear far downstream.
Linearized model Fokker–Planck collision operators for gyrokinetic simulations. I. Theory
Authors: Abel I. G. , Barnes M. , Cowley S. C. , Dorland W. , Schekochihin A. A.
Published: December 2008

A new analytically and numerically manageable model collision operator is developed specifically for turbulence simulations. The like-particle collision operator includes both pitch-angle scattering and energy diffusion and satisfies the physical constraints required for collision operators: it conserves particles, momentum, and energy, obeys Boltzmann’s H-theorem (collisions cannot decrease entropy), vanishes on a Maxwellian, and efficiently dissipates small-scale structure in the velocity space. The process of transforming this collision operator into the gyroaveraged form for use in gyrokinetic simulations is detailed. The gyroaveraged model operator is shown to have more suitable behavior at small scales in phase space than previously suggested models. Model operators for electron-ion and ion-electron collisions are also presented.