bluuebunny/crossref_metadata_2025 huggingface dataset:
Arctic dipole anomaly and its contribution to sea ice export from the Arctic Ocean in the 20th century
Authors: Watanabe Eiji , Wang Jia , Sumi Akimasa , Hasumi Hiroyasu
Published: December 2006

The winter dipole anomaly (DA) in the Arctic atmosphere and its contribution to sea ice export are investigated by using a high‐resolution coupled global general circulation model. The spatial distributions of the first two leading EOF modes of winter mean sea level pressure (SLP) and geopotential height at 500 hPa north of 70°N obtained by the long‐term simulation (1900–2010) are highly similar to those derived from the National Center for Environmental Prediction and the National Center for the Atmospheric Research (NCEP/NCAR) reanalysis datasets (1948–2004). The first‐leading mode corresponds to the Arctic Oscillation (AO). The DA is defined as the second‐leading mode. The AO and DA account for 59% and 19% of the total variance, respectively. Composite spatial patterns of SLP, sea ice thickness and velocity in the extreme years when both the absolute values of principal component (PC1 and PC2) exceed 1.0 standard deviation indicate that the DA plays a great important role in sea ice export from the Arctic Ocean to the Greenland Sea due to its strong meridionality. Sea ice export is highly promoted (restricted) in the positive (negative) DA phase. The dependence of sea ice export on the DA is comparable to or rather larger than that on the AO.
Assessment of Gravity Recovery and Climate Experiment (GRACE) temporal signature over the upper Zambezi
Authors: Winsemius H. C. , Savenije H. H. G. , van de Giesen N. C. , van den Hurk B. J. J. M. , Zapreeva E. A. , Klees R.
Published: December 2006

The temporal signature of terrestrial storage changes inferred from the Gravity Recovery and Climate Experiment (GRACE) has been assessed by comparison with outputs from a calibrated hydrological model (lumped elementary watershed (LEW)) of the upper Zambezi and surroundings and an inspection of the within‐month ground track coverage of GRACE together with spatial‐temporal rainfall patterns. The comparison of the hydrological model with GRACE reveals temporal inconsistencies between both data sets. Because the LEW model has been calibrated and validated with independent data sources, we believe that this is a GRACE artifact. The within‐month ground track coverage shows an irregular orbit behavior which may well cause aliasing in the GRACE monthly deconvolutions. This aliasing is the most probable cause of observed temporal inconsistencies between GRACE and other data sets.
Neuropeptide Y modulates effects of bradykinin and prostaglandin E2 on trigeminal nociceptors via activation of the Y1 and Y2 receptors
Authors: Gibbs J L , Diogenes A , Hargreaves K M
Published: December 2006

Background and Purpose:

Although previous studies have demonstrated that neuropeptide Y (NPY) modulates nociceptors, the relative contributions of the Y1 and Y2 receptors are unknown. Therefore, we evaluated the effect of Y1 and Y2 receptor activation on nociceptors stimulated by bradykinin (BK) and prostaglandin E2 (PGE2).

Experimental approach:

Combined immunohistochemistry (IHC) with in situ hybridization (ISH) demonstrated that Y1‐ and Y2‐receptors are collocated with bradykinin 2 (B2)‐receptors in rat trigeminal ganglia (TG). The relative functions of the Y1 and Y2 receptors in modulating BK/PGE2‐evoked CGRP release and increased intracellular calcium levels in cultured TG neurons were evaluated.

Key results:

The Y1 and Y2 receptors are co‐expressed with B2 in TG neurons, suggesting the potential for direct NPY modulation of BK responses. Pretreatment with the Y1 agonist [Leu31,Pro34]‐NPY, inhibited BK/PGE2‐evoked CGRP release. Conversely, pretreatment with PYY(3‐36), a Y2 agonist, increased BK/PGE2 evoked CGRP release. Treatment with NPY evoked an overall inhibitory effect, although of lesser magnitude. Similarly, [Leu31,Pro34]‐NPY inhibited BK/PGE2‐evoked increases in intracellular calcium levels whereas PYY(3‐36) increased responses. NPY inhibition of BK/PGE2‐evoked release of CGRP was reversed by the Y1 receptor antagonist, BIBO3304, and higher concentrations of BIBO3304 significantly facilitated CGRP release. The Y2 receptor antagonist, BIIE0246, enhanced the inhibitory NPY effects.

Conclusions and implications:

These results demonstrate that NPY modulation of peptidergic neurons is due to net activation of inhibitory Y1 and excitatory Y2 receptor systems. The relative expression or activity of these opposing receptor systems may mediate dynamic responses to injury and pain.

British Journal of Pharmacology (2007) 150, 72–79. doi:10.1038/sj.bjp.0706967
Lack of selectivity of URB602 for 2‐oleoylglycerol compared to anandamide hydrolysis in vitro
Authors: Vandevoorde S , Jonsson K‐O , Labar G , Persson E , Lambert D M , Fowler C J
Published: December 2006

Background and purpose:

Two compounds, URB602 and URB754, have been reported in the literature to be selective inhibitors of monoacylglycerol lipase, although a recent study has questioned their ability to prevent 2‐arachidonoyl hydrolysis by brain homogenates and cerebellar membranes. In the present study, the ability of these compounds to inhibit monoacylglycerol lipase and fatty acid amide hydrolase has been reinvestigated.

Experimental approach:

Homogenates and cell lines were incubated with test compounds and, thereafter, with either [3H]‐2‐oleoylglycerol or [3H]‐anandamide. Labelled reaction products were separated from substrate using chloroform: methanol extraction.

Key results:

In cytosolic fractions from rat brain, URB602 and URB754 inhibited the hydrolysis of 2‐oleoylglycerol with IC50 values of 25 and 48 μM, respectively. Anandamide hydrolysis by brain membranes was not sensitive to URB754, but was inhibited by URB602 (IC50 value 17 μM). Hydrolysis of 2‐oleoylglycerol by human recombinant monoacylglycerol lipase was sensitive to URB602, but not URB754. The lack of selectivity of URB602 for 2‐oleoylglycerol compared to anandamide hydrolysis was also observed for intact RBL2H3 basophilic leukaemia cells. C6 glioma expressed mRNA for monoacylglycerol lipase, and hydrolyzed 2‐oleoylglycerol in a manner sensitive to inhibition by methyl arachidonoyl fluorophosphonate but not URB754 or URB597. MC3T3‐E1 mouse osteoblastic cells, which did not express mRNA for monoacylglycerol lipase, hydrolyzed 2‐oleoylglycerol in the presence of URB597, but the hydrolysis was less sensitive to methyl arachidonoyl fluorophosphonate than for C6 cells.

Conclusions and implications:

The data demonstrate that the compounds URB602 and URB754 do not behave as selective and/or potent inhibitors of monoacylglycerol lipase.

British Journal of Pharmacology (2007) 150, 186–191. doi:10.1038/sj.bjp.0706971
Rectifying junction in a single ZnO vertical nanowire
Authors: Pradhan Basudev , Batabyal Sudip K. , Pal Amlan J.
Published: December 2006

The authors introduce dopants in vertically grown single crystalline ZnO nanowires in a controlled manner. A section of the nanowires is doped with aluminum as donor during crystal nucleation, resulting in n-n+ junction. Current-voltage characteristics of these single nanowire junctions via scanning tunneling microscopy and mercury-probe methods are asymmetric, displaying rectifying behavior. By inversing the junction during the growth or by introducing lithium as acceptor to form a n-p junction, the directionality of current flow in the nanowires becomes reversed. The single nanowire diode junctions are very stable in ambient condition and hence open up a new dimension in nanoelectronics.
Hole transport in p-type ZnO films grown by plasma-assisted molecular beam epitaxy
Authors: Sun J. W. , Lu Y. M. , Liu Y. C. , Shen D. Z. , Zhang Z. Z. , Li B. H. , Zhang J. Y. , Yao B. , Zhao D. X. , Fan X. W.
Published: December 2006

The hole transport properties of nitrogen doped p-type ZnO grown on c-plane sapphire (c-Al2O3) were investigated by temperature-dependent Hall-effect measurements. The experimental Hall mobility was found to be considerably lower than the calculated mobility including ionized impurity scattering, acoustic-mode deformation potential scattering, piezoelectric potential scattering, and polar optical phonon scattering. Atomic force microscopy and x-ray diffraction measurements demonstrated that p-type ZnO on c-Al2O3 consisted of two kinds of 30°-rotated domains surrounded by grain boundaries. Thus, taking the effect of inhomogeneous microstructure on the mobility into account, the calculated mobility agreed favorably with the experimental data. This agreement indicates that besides ionized impurity and acoustic deformation potential scattering at low temperatures and the polar optical phonon scattering at high temperatures, the effects of the inhomogeneous microstructure in p-type ZnO films play a more important role in determining the hole mobility.
Complementary analyses on the local polarity in lateral polarity-inverted GaN heterostructure on sapphire (0001) substrate
Authors: Katayama Ryuji , Kuge Yoshihiro , Onabe Kentaro , Matsushita Tomonori , Kondo Takashi
Published: December 2006

The fabrication of the lateral polarity-inverted GaN heterostructure on sapphire (0001) using a radio-frequency-plasma-enhanced molecular beam epitaxy is demonstrated. Its microscopic properties such as surface potentials, piezoelectric polarizations, and residual carrier densities were investigated by Kelvin force microscopy and micro-Raman scattering. The inversion from Ga polarity to N polarity in a specific domain and its higher crystal perfection had been unambiguously confirmed by these complementary analyses. The results were also fairly consistent with that of KOH etching, which suggests the applicability of these processes to the fabrication of photonic nanostructures.
Laser-activated surface-enhanced Raman scattering substrates capable of single molecule detection
Authors: Kalkan A. Kaan , Fonash Stephen J.
Published: December 2006

Surface-enhanced Raman scattering (SERS) substrates were obtained through silver reduction on and by nanostructured Si films. The absence of any chemical agents on the Ag nanoparticle surfaces allows analyte adsorption and SERS detection immediately with spotting. These SERS substrates have the further unique and useful attribute of being laser activated; i.e., laser impingement causes Ostwald ripening and formation of aggregates (e.g., dimers and trimers), which are essential for single molecule detection. Single molecule detection of fluorescein characterized with intermittent spectral fluctuations as well as a dramatic decrease in inhomogeneous Raman linewidth was demonstrated.
Methane clathrate: CH4 quantum rotor state dependent rattling potential
Authors: Prager M. , Press W.
Published: December 2006

In methane hydrate the dominant peak in the density of states above 3meV represents a rattling mode of the guest molecule CH4 in the large ice cages. This mode shifts from 6.7meV at T=4.5K to T=30K to 7.14meV with conversion of CH4 guest molecules into the tunneling ground state. The less symmetric angular density distribution ΨΨ* in the excited rotational state compared to the ground state allows the methane to fit better in the orientation dependent cage potential surface. This leads to a larger average distance to the cage-forming molecules with a weaker potential and a reduced rattling energy. A two state single particle model with characteristic rattling energies of 5.20meV for pure T-methane and 7.3meV for pure A-methane weighted by the population factors can fit the data.
Molecular dynamics simulation of the polymer electrolyte poly(ethylene oxide)/LiClO4. II. Dynamical properties
Authors: Siqueira Leonardo J. A. , Ribeiro Mauro C. C.
Published: December 2006

The dynamical properties of the polymer electrolyte poly(ethylene oxide) (PEO)∕LiClO4 have been investigated by molecular dynamics simulations. The effect of changing salt concentration and temperature was evaluated on several time correlation functions. Ionic displacements projected on different directions reveal anisotropy in short-time (rattling) and long-time (diffusive) dynamics of Li+ cations. It is shown that ionic mobility is coupled to the segmental motion of the polymeric chain. Structural relaxation is probed by the intermediate scattering function F(k,t) at several wave vectors. Good agreement was found between calculated and experimental F(k,t) for pure PEO. A remarkable slowing down of polymer relaxation is observed upon addition of the salt. The ionic conductivity estimated by the Nernst-Einstein equation is approximately ten times higher than the actual conductivity calculated by the time correlation function of charge current.
Thermal annealing-induced enhancement of the field-effect mobility of regioregular poly(3-hexylthiophene) films
Authors: Cho Shinuk , Lee Kwanghee , Yuen Jonathan , Wang Guangming , Moses Daniel , Heeger Alan J. , Surin Mathieu , Lazzaroni Roberto
Published: December 2006

Polymer field-effect transistors with a field-effect mobility of μ≈0.3cm2s−1V−1 have been demonstrated using regioregular poly(3-hexylthiophene) (rr-P3HT). Devices were fabricated by dip coating the semiconducting polymer followed by annealing at 150°C for 10min. The heat annealed devices exhibit an increased field-effect mobility compared with the as-prepared devices. Morphology studies and analysis of the channel resistance demonstrate that the annealing process increases the crystallinity of rr-P3HT and improves the contact between the electrodes and the P3HT films, thereby increasing the field-effect mobility of the films.
Interface characterization and carrier transportation in metal/HfO2/silicon structure
Authors: Chiu Fu-Chien
Published: December 2006

Metal-oxide-semiconductor capacitors incorporating HfO2 dielectrics were fabricated and investigated. In this work, the structural and electrical characterizations were performed at the interfaces of HfO2∕Si and Al∕HfO2, respectively. The physical analyses reveal that an interfacial layer of Hf-silicate between 700°C-annealed HfO2 and Si was formed. The dominant conduction mechanisms of the Al∕HfO2∕p-Si structure are the Schottky emission at high temperatures (≳465K) and low electric fields (≲2.2MV∕cm) and the Fowler-Nordheim tunneling at low temperature (77K) and high electric fields (≳2.6MV∕cm), respectively. The electron effective mass in HfO2 and the barrier height at the Al∕HfO2 interface are evaluated using both the intercept of the Schottky plot and the slope of the Fowler-Nordheim plot. Therefore, the barrier height at the Al∕HfO2 interface was determined to be about 0.94eV. The electron effective masses in HfO2 are 0.4m0 and 0.09m0 for the effective oxide thickness (EOT)=6nm and EOT=3.15nm, respectively.
Fabrication of probe-typed carbon nanotube point emitters
Authors: Jung Seung Il , Choi Jai Seong , Shim Hyung Cheoul , Kim Soohyun , Jo Sung Ho , Lee Cheol Jin
Published: December 2006

Probe-typed carbon nanotube (CNT) point emitter was fabricated by attaching single-walled CNT (SWCNT) and double-walled CNT (DWCNT) bundles onto the atomic force microscope tip using dielectrophoresis method. The field emission current from SWCNT point emitter was 4.9μA at 750V, which is corresponding to the emission current density of at least 1.2×103A∕cm2. The Fowler-Nordheim plots for the SWCNT and DWCNT point emitters revealed that the SWCNT bundle consists of more individual SWCNTs than DWCNT bundle and, as a result, the field emission performance of the SWCNT point emitter is better than the DWCNT point emitter. It is suggested that the probe-typed CNT point emitters can be used for microwave amplifiers and high-resolution electron-beam instruments.
A polymorphism in the norepinephrine transporter gene alters promoter activity and is associated with attention-deficit hyperactivity disorder
Authors: Kim Chun-Hyung , Hahn Maureen K. , Joung Yoosook , Anderson Susan L. , Steele Angela H. , Mazei-Robinson Michelle S. , Gizer Ian , Teicher Martin H. , Cohen Bruce M. , Robertson David , Waldman Irwin D. , Blakely Randy D. , Kim Kwang-Soo
Published: December 2006

The norepinephrine transporter critically regulates both neurotransmission and homeostasis of norepinephrine in the nervous system. In this study, we report a previously uncharacterized and common A/T polymorphism at −3081 upstream of the transcription initiation site of the human norepinephrine transporter gene [solute carrier family 6, member 2 (
SLC6A2
)]. Using both homologous and heterologous promoter-reporter constructs, we found that the −3081(T) allele significantly decreases promoter function compared with the A allele. Interestingly, this T allele creates a new palindromic E2-box motif that interacts with Slug and Scratch, neural-expressed transcriptional repressors binding to the E2-box motif. We also found that both Slug and Scratch repress the
SLC6A2
promoter activity only when it contains the T allele. Finally, we observed a significant association between the −3081(A/T) polymorphism and attention-deficit hyperactivity disorder (ADHD), suggesting that anomalous transcription factor-based repression of
SLC6A2
may increase risk for the development of attention-deficit hyperactivity disorder and other neuropsychiatric diseases.
Solution structure and dynamics of the complex between cytochromecand cytochromecperoxidase determined by paramagnetic NMR
Authors: Volkov Alexander N. , Worrall Jonathan A. R. , Holtzmann Elodie , Ubbink Marcellus
Published: December 2006

The physiological complex of yeast cytochromecperoxidase andiso-1-cytochromecis a paradigm for biological electron transfer. Using paramagnetic NMR spectroscopy, we have determined the conformation of the protein complex in solution, which is shown to be very similar to that observed in the crystal structure [Pelletier H, Kraut J (1992)Science258:1748–1755]. Our results support the view that this transient electron transfer complex is dynamic. The solution structure represents the dominant protein–protein orientation, which, according to our estimates, is occupied for >70% of the lifetime of the complex, with the rest of the time spent in the dynamic encounter state. Based on the observed paramagnetic effects, we have delineated the conformational space sampled by the protein molecules during the dynamic part of the interaction, providing experimental support for the theoretical predictions of the classical Brownian dynamics study [Northrup SH, Boles JO, Reynolds JCL (1988)Science241:67–70]. Our findings corroborate the dynamic behavior of this complex and offer an insight into the mechanism of the protein complex formation in solution.
Release of autoinhibition converts ESCRT-III components into potent inhibitors of HIV-1 budding
Authors: Zamborlini Alessia , Usami Yoshiko , Radoshitzky Sheli R. , Popova Elena , Palu Giorgio , Göttlinger Heinrich
Published: December 2006

The endosomal sorting complex ESCRT-III, which is formed by the structurally related CHMP proteins, is engaged by HIV-1 to promote viral budding. Here we show that progressive truncations into the C-terminal acidic domains of CHMP proteins trigger an increasingly robust anti-HIV budding activity. Together with biochemical evidence for specific intramolecular interactions between the basic and acidic halves of CHMP3 and CHMP4B, these results suggest that the acidic domains are autoinhibitory. The acidic half of CHMP3 also interacts with the endosome-associated ubiquitin isopeptidase AMSH, and the coexpression of AMSH or its CHMP3-binding domain converts wild-type CHMP3 into a potent inhibitor of HIV-1 release. Point mutations in CHMP3 that prevent binding to AMSH abrogate this effect, suggesting that binding to AMSH relieves the autoinhibition of CHMP3. Collectively, our results indicate that CHMP proteins are regulated through an autoinhibitory switch mechanism that allows tight control of ESCRT-III assembly.
A statistical approach to close packing of elastic rods and to DNA packaging in viral capsids
Authors: Katzav E. , Adda-Bedia M. , Boudaoud A.
Published: December 2006

We propose a statistical approach for studying the close packing of elastic rods. This phenomenon belongs to the class of problems of confinement of low dimensional objects, such as DNA packaging in viral capsids. The method developed is based on Edwards' approach, which was successfully applied to polymer physics and to granular matter. We show that the confinement induces a configurational phase transition from a disordered (isotropic) phase to an ordered (nematic) phase. In each phase, we derive the pressure exerted by the rod (DNA) on the container (capsid) and the force necessary to inject (eject) the rod into (out of) the container. Finally, we discuss the relevance of the present results with respect to physical and biological problems. Regarding DNA packaging in viral capsids, these results establish the existence of ordered configurations, a hypothesis upon which previous calculations were built. They also show that such ordering can result from simple mechanical constraints.
Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables
Authors: Zapala Matthew A. , Schork Nicholas J.
Published: December 2006

A fundamental step in the analysis of gene expression and other high-dimensional genomic data is the calculation of the similarity or distance between pairs of individual samples in a study. If one has collected
N
total samples and assayed the expression level of
G
genes on those samples, then an
N
×
N
similarity matrix can be formed that reflects the correlation or similarity of the samples with respect to the expression values over the
G
genes. This matrix can then be examined for patterns via standard data reduction and cluster analysis techniques. We consider an alternative to conventional data reduction and cluster analyses of similarity matrices that is rooted in traditional linear models. This analysis method allows predictor variables collected on the samples to be related to variation in the pairwise similarity/distance values reflected in the matrix. The proposed multivariate method avoids the need for reducing the dimensions of a similarity matrix, can be used to assess relationships between the genes used to construct the matrix and additional information collected on the samples under study, and can be used to analyze individual genes or groups of genes identified in different ways. The technique can be used with any high-dimensional assay or data type and is ideally suited for testing subsets of genes defined by their participation in a biochemical pathway or other
a priori
grouping. We showcase the methodology using three published gene expression data sets.
Modernism vs Urban Renaissance: Negotiating Post-war Heritage in English City Centres
Authors: While Aidan
Published: December 2006

Redevelopment and growth regimes are often eager to remove the physical remnants of post-war modernism. Largely unloved, and ofter out-of-step with current design principles, the 1950s/60s cityscape is fast disappearing as urban leaders seek to remodel and reimage the built environment. In some places, however, the push to redevelop and reclad the modernist legacy is coming up against increasing demands for the preservation of 'modern landmarks'. Certainly in England, the decision to extend statutory protection to the post-war era has resulted in a series of conservation conflicts over the meaning and value of modernist structures. Taking the contested rehabilitation of modernism as a starting-point, this article explores potential tensions and complementarities between the politics of redevelopment and that of post-war preservation. Empirically, the article is grounded on the experience of two English city centres (Coventry and Plymouth) with historically significant, but challenging, relics of 1950s/60s modernist architecture and post-was planning. The article offers insights into the (multiscaled) politics of urban preservation and the renegotiation of modernist meaning in the city.
The Decentralising Metropolis: Economic Diversity and Commuting in the US Suburbs
Authors: Lee Shin , Seo Jong Gook , Webster Chris
Published: December 2006

This paper investigates historical changes in economic structure and the spatial distribution of jobs and commuting patterns during a period of consolidating suburban decentralisation in US cities. The analysis of selected US metropolitan areas is based on data drawn from the 1980 and 1990 PUMS (public use microdata samples). First, the paper compares changes in employment composition between regions and between two geographical subdivisions in each of the metropolitan areas: the suburb and the central city. A diversity index is then measured for suburbs and central cities and an intertemporal comparison is made. Finally, changes in travel characteristics are discussed and analysed by industrial sector and geographical sub-division. The analysis shows a strong growth of suburban cities compared with central cities in each region, increased urbanisation economies in suburban cities and the dominance of suburb-to-suburb commuting. The historical pattern gives urban analysts and planners in Europe and elsewhere much to think about: in particular, the self-reinforcing nature of suburban agglomeration economies, the influence of growing suburban employment centres on commute patterns, the growth of centre-to-suburb commutes and the dominance of suburb-to-suburb commutes; and the ability of cities to reshape themselves as individual firms and households adopt strategies that lower the costs of transacting labour, services and all manner of commodities.
Phosphoregulation of Cbk1 is critical for RAM network control of transcription and morphogenesis
Authors: Jansen Jaclyn M. , Barry Margaret F. , Yoo Charles K. , Weiss Eric L.
Published: December 2006

The budding yeast regulation of Ace2 and morphogenesis (RAM) network integrates cell fate determination and morphogenesis. Its disruption impairs polarized growth and causes mislocalization of the transcription factor Ace2, resulting in failure of daughter cell–specific transcription required for cell separation. We find that phosphoregulation of the conserved AGC family kinase Cbk1 is critical for RAM network function. Intramolecular autophosphorylation of the enzyme's activation loop is critical for kinase activity but is only partially required for cell separation and polarized growth. In marked contrast, phosphorylation of a C-terminal hydrophobic motif is required for Cbk1 function in vivo but not for its kinase activity, suggesting a previously unappreciated level of control for this family of kinases. Phosphorylation of the C-terminal site is regulated over the cell cycle and requires the transcription factor Ace2 as well as all RAM network components. Therefore, Ace2 is not only a downstream target of Cbk1 but also reinforces activation of its upstream regulator.
A Boy With Proximal Weakness and Cardiomyopathy
Authors: Mitchell Christopher W , Bertorini Tulio E , Shadle Mariallan
Published: December 2006

Educational Objectives:

1) To present an adolescent patient with proximal weakness and cardiomyopathy and discuss the differential diagnosis. 2) To appreciate cardiac involvement in a subset of myopathic disorders.

Key Questions:

1) What is the differential diagnosis for an adolescent with proximal muscle weakness and cardiomyopathy? 2) What is the diagnostic workup for this patient? 3) What is the management of a patient with this disorder?
Mechanical deformation model of the western United States instantaneous strain-rate field
Authors: Pollitz Fred F. , Vergnolle Mathilde
Published: December 2006

We present a relationship between the long-term fault slip rates and instantaneous velocities as measured by Global Positioning System (GPS) or other geodetic measurements over a short time span. The main elements are the secularly increasing forces imposed by the bounding Pacific and Juan de Fuca (JdF) plates on the North American plate, viscoelastic relaxation following selected large earthquakes occurring on faults that are locked during their respective interseismic periods, and steady slip along creeping portions of faults in the context of a thin-plate system. In detail, the physical model allows separate treatments of faults with known geometry and slip history, faults with incomplete characterization (i.e. fault geometry but not necessarily slip history is available), creeping faults, and dislocation sources distributed between the faults. We model the western United States strain-rate field, derived from 746 GPS velocity vectors, in order to test the importance of the relaxation from historic events and characterize the tectonic forces imposed by the bounding Pacific and JdF plates. Relaxation following major earthquakes (Mγ 8.0) strongly shapes the present strain-rate field over most of the plate boundary zone. Equally important are lateral shear transmitted across the Pacific–North America plate boundary along ∼1000 km of the continental shelf, downdip forces distributed along the Cascadia subduction interface, and distributed slip in the lower lithosphere. Post-earthquake relaxation and tectonic forcing, combined with distributed deep slip, constructively interfere near the western margin of the plate boundary zone, producing locally large strain accumulation along the San Andreas fault (SAF) system. However, they destructively interfere further into the plate interior, resulting in smaller and more variable strain accumulation patterns in the eastern part of the plate boundary zone. Much of the right-lateral strain accumulation along the SAF system is systematically underpredicted by models which account only for relaxation from known large earthquakes. This strongly suggests that in addition to viscoelastic-cycle effects, steady deep slip in the lower lithosphere is needed to explain the observed strain-rate field.
Stress transfer relations among the earthquakes that occurred in Kerman province, southern Iran since 1981
Authors: Nalbant Suleyman S. , Steacy Sandy , McCloskey John
Published: December 2006

We explore the possible stress triggering relationship of the M≥ 6.4 earthquakes that occurred in Kerman Province, southern Iran since 1981. We calculated stress changes due to both coseismic sudden movement in the upper crust and the time-dependent viscous relaxation of the lower crust and/or upper mantle following the event. Four events of M≥ 6.4 occurred between 1981 and 2005, on and close to the Gowk fault, show a clear Coulomb stress load to failure relationship. The 2003 M= 6.5 Bam earthquake, however, which occurred approximately 95 km SW of the closest Gowk event, shows a very weak stress relation to preceding earthquakes. The coseismic static stress change at the hypocentre of the Bam earthquake is quite small (∼0.006 bars). The time-dependent post-seismic stress change could be 26 times larger or 7 times lower than that of coseismic static stress alone depending on the choice of viscoelastic crustal model and the effective coefficient of friction. Given the uncertainties in the viscoelastic earth models and the effective coefficient of friction, we cannot confidently conclude that the 2003 Bam event was brought closer to failure through coseismic or post-seismic stress loading. Interestingly, the southern Gowk segment with a similar strike to that of the Bam fault, experienced a stress load of up to 8.3 bars between 1981 and 2003, and is yet to have a damaging earthquake.
Isolated lymphoid follicle maturation induces the development of follicular dendritic cells
Authors: Glaysher Bridget R. , Mabbott Neil A.
Published: December 2006

Isolated lymphoid follicles (ILFs) are recently identified lymphoid structures in the small intestine with features similar to Peyer's patches (PPs). Using immunohistochemistry we characterized the composition of ILFs in the small intestines of immunocompetent mice and of mice that lacked PPs as a result of either genetic deficiency of lymphotoxin or temporary in utero lymphotoxin‐β receptor‐signalling blockade. We showed that although both immature and mature ILFs were present in the intestines of immunocompetent mice, PP‐deficiency induced a significantly greater number of mature ILFs. We found that in addition to B‐lymphocyte‐containing germinal centres, mature ILFs also possessed large networks of follicular dendritic cells (FDCs). These features were not detected within immature ILFs. Indeed, the presence of FDCs could be used to reliably distinguish ILF maturity. Further analysis revealed that the area occupied by the FDCs within mature ILFs was substantial. The total area occupied by FDCs in all the mature ILFs in mice lacking PPs was equivalent to the total area occupied by FDCs in all the PPs and the few mature ILFs in immunocompetent mice. Based on these data we reasoned that in the absence of PPs, mature ILFs are important inductive sites for intestinal immune responses. Indeed, in mice that lacked PPs, ILF maturation coincided with a restoration of faecal immunoglobulin A levels to values that were comparable to those found in immunocompetent mice. Taken together, these data imply that the induction of germinal centres and FDC networks within mature ILFs in response to PP deficiency provides an important compensatory mechanism.
Cryptic behaviours, inverse genetic landscapes, and spatial avoidance of inbreeding in the Pacific jumping mouse
Authors: VIGNIERI SACHA N.
Published: December 2006

Although the behaviour of individuals is known to impact the genetic make‐up of a population, observed behavioural patterns do not always correspond to patterns of genetic structure. In particular, philopatric or dispersal‐limited species often display lower‐than‐expected values of relatedness or inbreeding suggestive of the presence of cryptic migration, dispersal, or mating behaviours. I used a combination of microsatellite and mark–recapture data to test for the influence of such behaviours in a dispersal‐limited species, the Pacific jumping mouse, within a semi‐isolated population over three seasons. Despite short dispersal distances and a low rate of first generation migrants, heterozygosities were high and inbreeding values were low. Dispersal was male‐biased; interestingly however, this pattern was only present when dispersal was considered to include movement away from paternal home range. Not unexpectedly, males were polygynous; notably, some females were also found to be polyandrous, selecting multiple neighbouring mates for their single annual litter. Patterns of genetic structure were consistent with these more inconspicuous behavioural patterns. Females were more closely related than males and isolation by distance was present only in females. Furthermore, detailed genetic landscapes revealed the existence of strong, significant negative correlations, with areas of low genetic distance among females overlapping spatially with areas of high genetic distance among males. These results support the hypothesis that the detected cryptic components of dispersal and mating behaviour are reducing the likelihood of inbreeding in this population through paternally driven spatial mixing of male genotypes and polyandry of females.
Phylogeography and population history of the crab‐eating fox (Cerdocyon thous)
Authors: TCHAICKA LIGIA , EIZIRIK EDUARDO , DE OLIVEIRA TADEU G. , CÂNDIDO JOSÉ FLÁVIO , FREITAS THALES R. O.
Published: December 2006

The crab‐eating fox is a medium‐sized Neotropical canid with generalist habits and a broad distribution in South America. We have investigated its genetic diversity, population structure and demographic history across most of its geographic range by analysing 512 base pairs (bp) of the mitochondrial DNA (mtDNA) control region, 615 bp of the mtDNA cytochrome b gene and 1573 total nucleotides from three different nuclear fragments. MtDNA data revealed a strong phylogeographic partition between northeastern Brazil and other portions of the species’ distribution, with complete separation between southern and northern components of the Atlantic Forest. We estimated that the two groups diverged from each other c. 400 000–600 000 years ago, and have had contrasting population histories. A recent demographic expansion was inferred for the southern group, while northern populations seem to have had a longer history of large population size. Nuclear sequence data did not support this north–south pattern of subdivision, likely due at least in part to secondary male‐mediated historical gene flow, inferred from multilocus coalescent‐based analyses. We have compared the inferred phylogeographic patterns to those observed for other Neotropical vertebrates, and report evidence for a major north–south demographic discontinuity that seems to have marked the history of the Atlantic Forest biota.
The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium
Authors: Sittka Alexandra , Pfeiffer Verena , Tedin Karsten , Vogel Jörg
Published: December 2006

The RNA chaperone, Hfq, plays a diverse role in bacterial physiology beyond its original role as a host factor required for replication of Qβ RNA bacteriophage. In this study, we show that Hfq is involved in the expression and secretion of virulence factors in the facultative intracellular pathogen, Salmonella typhimurium. A Salmonella hfq deletion strain is highly attenuated in mice after both oral and intraperitoneal infection, and shows a severe defect in invasion of epithelial cells and a growth defect in both epithelial cells and macrophages in vitro. Surprisingly, we find that these phenotypes are largely independent of the previously reported requirement of Hfq for expression of the stationary phase sigma factor, RpoS. Our results implicate Hfq as a key regulator of multiple aspects of virulence including regulation of motility and outer membrane protein (OmpD) expression in addition to invasion and intracellular growth. These pleiotropic effects are suggested to involve a network of regulatory small non‐coding RNAs, placing Hfq at the centre of post‐transcriptional regulation of virulence gene expression in Salmonella. In addition, the hfq mutation appears to cause a chronic activation of the RpoE‐mediated envelope stress response which is likely due to a misregulation of membrane protein expression.
Mutations in transmembrane domains 1, 4 and 9 of thePlasmodium falciparumchloroquine resistance transporter alter susceptibility to chloroquine, quinine and quinidine
Authors: Cooper Roland A. , Lane Kristin D. , Deng Bingbing , Mu Jianbing , Patel Jigar J. , Wellems Thomas E. , Su Xinzhuan , Ferdig Michael T.
Published: December 2006

Mutations in thePlasmodium falciparumchloroquine (CQ) resistance transporter (PfCRT) can result in verapamil‐reversible CQ resistance and altered susceptibility to other antimalarials. PfCRT contains 10 membrane‐spanning domains and is found in the digestive vacuole (DV) membrane of intraerythrocytic parasites. The mechanism by which PfCRT mediates CQ resistance is unclear although it is associated with decreased accumulation of drug within the DV. On the permissive background of theP. falciparum106/1K76parasite line, we used single‐step drug selection to generate isogenic clones containing uniquepfcrtpoint mutations that resulted in amino acid changes in PfCRT transmembrane domains 1 (C72R, K76N, K76I and K76T) and 9 (Q352K, Q352R). The resulting changes of charge and hydropathy affected quantitative CQ susceptibility and accumulation as well as the stereospecific responses to quinine and quinidine. These results, together with a previously described S163R mutation in transmembrane domain 4, indicate that transmembrane segments 1, 4 and 9 of PfCRT provide important structural components of a substrate recognition and translocation domain. Charge‐affecting mutations within these segments may affect the ability of PfCRT to bind different quinoline drugs and determine their net accumulation in the DV.
A fail‐safe system for the ribosome under zinc‐limiting conditions inBacillus subtilis
Authors: Natori Yousuke , Nanamiya Hideaki , Akanuma Genki , Kosono Saori , Kudo Toshiaki , Ochi Kozo , Kawamura Fujio
Published: December 2006

As zinc is an essential trace metal ion for all living cells, cells elaborate a variety of strategies to cope with zinc starvation. InBacillus subtilis, genes encoding ribosomal proteins L31 and S14 are duplicated into two types: one type contains a zinc‐binding motif (RpmE or RpsN), whereas the other does not (YtiA or YhzA). We have previously shown that displacement of RpmE (L31) by YtiA from already assembled ribosomes is controlled by zinc, and this replacement could contribute to zinc mobilization under zinc‐limiting conditions. We propose here that the switch between the two types of S14 has a different significance.rpsNis indispensable for growth and depletion of RpsN results in defective 30S subunits. YhzA can functionally replace RpsN to allow continued ribosome assembly under zinc‐limiting conditions. Unlike YtiA, YhzA appeared in the ribosome at a slower rate consistent with incorporation into newly synthesized, rather than pre‐existing ribosomes. These results raise the possibility that YhzA is involved in a fail‐safe system for thede novosynthesis of ribosomes under zinc‐limiting conditions.
NifX and NifEN exchange NifB cofactor and the VK‐cluster, a newly isolated intermediate of the iron‐molybdenum cofactor biosynthetic pathway
Authors: Hernandez Jose A. , Igarashi Robert Y. , Soboh Basem , Curatti Leonardo , Dean Dennis R. , Ludden Paul W. , Rubio Luis M.
Published: December 2006

The iron‐molybdenum cofactor of nitrogenase (FeMo‐co) is synthesized in a multistep process catalysed by several Nif proteins and is finally inserted into a pre‐synthesized apo‐dinitrogenase to generate mature dinitrogenase protein. The NifEN complex serves as scaffold for some steps of this synthesis, while NifX belongs to a family of small proteins that bind either FeMo‐co precursors or FeMo‐co during cofactor synthesis. In this work, the binding of FeMo‐co precursors and their transfer between purified Azotobacter vinelandii NifX and NifEN proteins was studied to shed light on the role of NifX on FeMo‐co synthesis. Purified NifX binds NifB cofactor (NifB‐co), a precursor to FeMo‐co, with high affinity and is able to transfer it to the NifEN complex. In addition, NifEN and NifX exchange another [Fe‐S] cluster that serves as a FeMo‐co precursor, and we have designated it as the VK‐cluster. In contrast to NifB‐co, the VK‐cluster is electronic paramagnetic resonance (EPR)‐active in the reduced and the oxidized states. The NifX/VK‐cluster complex is unable to support in vitro FeMo‐co synthesis in the absence of NifEN because further processing of the VK‐cluster into FeMo‐co requires the simultaneous activities of NifEN and NifH. Our in vitro studies suggest that the role of NifX in vivo is to serve as transient reservoir of FeMo‐co precursors and thus help control their flux during FeMo‐co synthesis.
The major chemotaxis gene cluster of Rhizobium leguminosarum bv. viciae is essential for competitive nodulation
Authors: Miller Lance D. , Yost Christopher K. , Hynes Michael F. , Alexandre Gladys
Published: December 2006

Rhizobium leguminosarum biovar viciae strain 3841 is a motile alpha‐proteobacterium that can establish a nitrogen‐fixing symbiosis within the roots of pea plants. In order to determine the contribution of chemotaxis to the lifestyle of R. leguminosarum, we have characterized the function of two chemotaxis gene clusters (che1 and che2) in controlling motility behaviour. We have found that both chemotaxis gene clusters modulate the motility swimming bias of R. leguminosarum cells and that the che1 cluster is the major pathway controlling swimming bias and chemotaxis. The che2 cluster also contributes to swimming bias, but has a minor effect on chemotaxis. Using competitive nodulation assays, we have demonstrated that a functional che1 cluster, but not the che2 cluster, promotes competitive nodulation of the peas. This finding implies that the environmental cue(s) triggering chemotaxis of R. leguminosarum bv. viciae cells towards the roots of pea and facilitating colonization are likely to be processed through the che1 cluster despite the contribution of both che clusters to swimming behaviour. A phylogenetic analysis of the distribution of che1 and che2 orthologues in the alpha‐proteobacteria together with our results allow us to propose that che1 homologues are major controllers of chemotaxis and host association in the Rhizobiaceae.
Equal rates of repair of DNA photoproducts in transcribed and non‐transcribed strands in Sulfolobus solfataricus
Authors: Dorazi Robert , Götz Dorothee , Munro Stacey , Bernander Rolf , White Malcolm F.
Published: December 2006

The nucleotide excision repair (NER) pathway removes bulky lesions such as photoproducts from DNA. In both bacteria and eukarya, lesions located in transcribed strands are repaired significantly faster than those located in non‐transcribed strands due to damage signalling by stalled RNA polymerase molecules: a phenomenon known as transcription‐coupled repair (TCR). TCR requires a mechanism for coupling the detection of stalled RNA polymerase molecules to the NER pathway, provided in bacteria by the Mfd protein. In the third domain of life, archaea, the pathway of NER is not well defined, there are no Mfd homologues and the existence of TCR has not been investigated. In this report we looked at rates of removal of photoproducts in three different operons of the crenarchaeon Sulfolobus solfataricus following UV irradiation. We found no evidence for significantly faster repair in the transcribed strands of these three operons. The rate of global genome repair in S. solfataricus is relatively rapid, and this may obviate the requirement for a specialized TCR pathway. Significantly faster repair kinetics were observed in the presence of visible light, consistent with the presence of a gene for photolyase in the genome of S. solfataricus.
Tryptophanase in sRNA control of the Escherichia coli cell cycle
Authors: Chattoraj Dhruba K.
Published: December 2006

The field of gene regulation underwent a major revolution with the discovery of small non‐coding RNAs (sRNAs) and the various roles they play in organisms from bacteria to man. Escherichia coli has more than 60 sRNAs that are transcribed primarily from intergenic regions. They usually target the leader region of mRNAs and prevent their translation. Protein targets are relatively rare. In this issue of Molecular Microbiology, Chant and Summers provide an example of a totally unexpected protein target. They show that dimers of plasmid ColE1 make an sRNA that interacts directly with the enzyme tryptophanase and enhances its affinity for its substrate, tryptophan. A breakdown product, indole, then arrests cell division until the dimers are resolved to monomers. The monomerization helps to prevent plasmid loss. Targeting a catabolic enzyme to buy time for recombination is an amazing example of adaptation, which illustrates the power of a selfish element (a plasmid in this case) to exploit the host cell machinery to its advantage.