bluuebunny/crossref_metadata_2025 huggingface dataset:
Changing behavior in the diurnal range of surface air temperatures over Mexico
Authors: Englehart Phil J. , Douglas Arthur V.
Published: January 2005

The diurnal range in surface temperatures (DTR = maximum − minimum temperature) has been widely used as one indicator of potential climate change. On hemispheric space scales DTR trends over about the last half‐century tend to be decreasing. This paper analyzes regional scale trends in DTR for Mexico (1940–2001). Our principal finding is that in recent decades (post‐1970) DTR trends over Mexico are positive as maximum temperatures are warming at a significantly higher rate than minimum temperatures. Regional land use and land cover changes (LCCs) are identified as potential forcing mechanisms responsible for at least part of the observed DTR behavior.
Coastal and global averaged sea level rise for 1950 to 2000
Authors: White Neil J. , Church John A. , Gregory Jonathan M.
Published: January 2005

We compare estimates of coastal and global averaged sea level for 1950 to 2000. During the 1990s and around 1970, we find coastal sea level is rising faster than the global average but that it rises slower than the global average during the late 1970s and late 1980s. The differences are largely a result of sampling the time‐varying geographical distribution of sea level rise along a coastline which is more convoluted in some regions than others. More rapid coastal rise corresponds to La Niña–like conditions in the tropical Pacific Ocean and a slower rate corresponds to El Niño–like conditions. Over the 51 year period, there is no significant difference in the rates of coastal and global averaged sea level rise, as found in climate model simulations of the 20th century. The best estimate of both global average and coastal sea level rise remains 1.8 ± 0.3 mm yr−1, as found in earlier studies.
Bayesian inference of plastosphere viscosities near the Kunlun Fault, northern Tibet
Authors: Hilley G. E. , Bürgmann R. , Zhang P.‐Z. , Molnar P.
Published: January 2005

Flow of the mid‐crust in the Tibetan Plateau may strongly influence the patterns of deformation and topography within this area. This flow requires the lower‐crust to have low viscosity and so quantifying this viscosity may be used to test the idea of channel flow. An application of Bayesian methods to geologic and geodetic data from north central Tibet yields lower‐crustal viscosities (assumed Newtonian) of 1 × 1019 Pa s and 2 × 1021 Pa s (95% bounds). The lower bound is larger than the value of 1016–1018 Pa s required by models of flow of the lower‐crust of Tibet, unless the entire lower crust participates in channel flow.
X‐ray bursts associated with leader steps in cloud‐to‐ground lightning
Authors: Dwyer J. R. , Rassoul H. K. , Al‐Dayeh M. , Caraway L. , Chrest A. , Wright B. , Kozak E. , Jerauld J. , Uman M. A. , Rakov V. A. , Jordan D. M. , Rambo K. J.
Published: January 2005

X‐ray and electric field measurements were made during five nearby negative natural lightning strikes in north central Florida during the summer of 2004. The observed X‐ray emission typically was detected ∼1 ms before the first return stroke, during the stepped‐leader phase, and had energies extending up to a few hundred keV. The X rays were produced in discrete, intense bursts emitted in coincidence with the formation of the leader steps, demonstrating unambiguously that the source of lightning X rays is closely related to the stepping process. The X‐ray emission from lightning stepped leaders is found to be remarkably similar to that from lightning dart leaders, suggesting that these different types of leaders share a common mechanism. The reported observations have important implications for understanding how runaway breakdown occurs and how lightning leaders propagate.
Arctic Ocean sea ice volume: What explains its recent depletion?
Authors: Rothrock D. A. , Zhang J.
Published: January 2005

Various observations and model results point to an arctic sea ice cover that was extraordinarily thin in the 1990s. This thin ice cover was caused by a strengthened cyclonic circulation of wind and ice and by unusual warmth of springtime air temperatures. Here modeled sea ice volume is decomposed into two components: first, a dynamic or wind‐forced response to interannually varying winds but a fixed annual cycle of air temperature and second, a thermally forced solution responding only to interannually varying temperatures. Over the 52‐year simulation from 1948 to 1999 these two components have a similar range and variance; the wind‐forced component has no substantial trend, but the temperature‐forced component has a significant downward trend of −3% per decade. Total ice volume shows a trend of −4% per decade. Export slightly exceeds production over the simulation. Annual export and production can differ from each other and from year to year by ±30%. This behavior seems to characterize an ice cover highly constrained by interannual variations in forcing and not in balance. The bulk (two thirds) of volume loss from the 1960s to the 1990s is a result of a striking thinning of undeformed ice. The remainder of the volume loss is due to thinning of ridged ice and reduced concentrations. The central Arctic Ocean and particularly the East Siberian Sea suffer the greatest losses (of up to 2 m); the ice north of the Canadian archipelago also thinned since the 1960s by ∼0.5 m.
Nighttime OClO in the winter Arctic vortex
Authors: Canty T. , Rivière E. D. , Salawitch R. J. , Berthet G. , Renard J.‐B. , Pfeilsticker K. , Dorf M. , Butz A. , Bösch H. , Stimpfle R. M. , Wilmouth D. M. , Richard E. C. , Fahey D. W. , Popp P. J. , Schoeberl M. R. , Lait L. R. , Bui T. P.
Published: January 2005

We show that a nighttime profile of OClO in the Arctic vortex during the winter of 2000 is overestimated, by nearly a factor of 2, using an isentropic trajectory model constrained by observed profiles of ClOx (ClO + 2 × ClOOCl) and BrO. Calculated abundances of nighttime OClO are shown to be sensitive to the abundance of BrOx (BrO + BrCl), details of the air parcel history during the most recent sunrise/sunset transitions, and the BrCl yield from the reaction BrO + ClO. Many uncertainties are considered, and the discrepancy between measured and modeled nighttime OClO appears to be robust. This discrepancy suggests that production of OClO occurs more slowly than implied by standard photochemistry. If the yield of BrCl from the reaction of BrO + ClO is increased from 7% (JPL 2002 value) to 11% (near the upper limit of the uncertainty), good agreement is found between measured and modeled nighttime OClO. This study highlights the importance of accurate knowledge of BrO + ClO reaction kinetics as well as air parcel trajectories for proper interpretation of nighttime OClO. These factors have a considerably smaller impact on the interpretation of OClO observations obtained during twilight (90° ≤ SZA ≤ 92°), when photolytic processes are still active.
Interlayer-related paramagnetic defects in stacks of ultrathin layers of SiOx, Al2O3, ZrO2, and HfO2 on (100)Si
Authors: Stesmans A. , Afanas’ev V. V.
Published: January 2005

An electron spin resonance (ESR) study has been carried out of the influence of postdeposition heating on stacks of (100)Si with nanometer-thick dielectric layers of SiOx and atomic-layer-deposited Al2O3, ZrO2, and HfO2. This reveals upon postdeposition oxidation (PDO) in the range 650–800°C the appearance of various SiO2-characteristic defects, including E′, EX, and a 95-G doublet, in different intensities with increasing anneal temperature, attesting to significant modification and∕or additional SiOx interlayer growth. The revealed defects enable probing of the quality of the interlayer on atomic level. In terms of the E′ criterion, it is found that the SiOx interlayer formed in (100)Si∕SiOx∕ZrO2 is drastically inferior to standard thermal (100)Si∕SiO2, exhibiting over one order of magnitude more O-deficiency (E′) centers. The (100)Si∕Al2O3 and (100)Si∕HfO2 systems appear more robust with better interlayer properties. Particularly in the (100)Si∕HfO2 structure, both the E′ and EX densities remain small (<1.6×1011cm−2) after PDO, which comes as one more favorable property for the application of HfO2 as an alternative gate dielectric. Yet, the Si∕Al2O3 entity exhibits the largest EX density, and there appears evidence for an additional Si∕dielectric interface defect. No obvious ESR-active defect inherent to the metal oxide layers could be detected.
Theory of bright-field scanning transmission electron microscopy for tomography
Authors: Levine Zachary H.
Published: January 2005

Radiation transport theory is applied to electron microscopy of samples composed of one or more materials. The theory, originally due to Goudsmit and Saunderson, assumes only elastic scattering and an amorphous medium dominated by atomic interactions. For samples composed of a single material, the theory yields reasonable parameter-free agreement with experimental data taken from the literature for the multiple scattering of 300-keV electrons through aluminum foils up to 25μm thick. For thin films, the theory gives a validity condition for Beer’s law. For thick films, a variant of Molière’s theory [V. G. Molière, Z. Naturforschg. 3a, 78 (1948)] of multiple scattering leads to a form for the bright-field signal for foils in the multiple-scattering regime. The signal varies as [tln(e1−2γt∕τ)]−1 where t is the path length of the beam, τ is the mean free path for elastic scattering, and γ is Euler’s constant. The Goudsmit–Saunderson solution interpolates numerically between these two limits. For samples with multiple materials, elemental sensitivity is developed through the angular dependence of the scattering. From the elastic scattering cross sections of the first 92 elements, a singular-value decomposition of a vector space spanned by the elastic scattering cross sections minus a delta function shows that there is a dominant common mode, with composition-dependent corrections of about 2%. A mathematically correct reconstruction procedure beyond 2% accuracy requires the acquisition of the bright-field signal as a function of the scattering angle. Tomographic reconstructions are carried out for three singular vectors of a sample problem with four elements Cr, Cu, Zr, and Te. The three reconstructions are presented jointly as a color image; all four elements are clearly identifiable throughout the image.
Schrödinger problems for surfaces of revolution—the finite cylinder as a test example
Authors: Gravesen Jens , Willatzen Morten , Lew Yan Voon L. C.
Published: January 2005

A set of ordinary differential equations is derived employing the method of differentiable forms so as to describe the quantum mechanics of a particle constrained to move on a general two-dimensional surface of revolution. Eigenvalues and eigenstates are calculated quasianalytically in the case of a finite cylinder (finite along the axis) and compared with the eigenvalues and eigenstates of a full three-dimensional Schrödinger problem corresponding to a hollow cylinder in the limit where the inner and outer radii approach each other. Good agreement between the two models is obtained for a relative difference less than 20% in inner and outer radii.
Uniqueness of the topological multivortex solution in the self-dual Chern–Simons theory
Authors: Choe Kwangseok
Published: January 2005

We establish a uniqueness result for the topological multivortex solution to the self-dual equations of the Abelian relativistic self-dual Chern–Simons–Higgs model. We prove that the topological multivortex solution is unique if the Chern–Simons coupling parameter κ>0 is sufficiently small. We also establish a uniqueness result for κ>0 sufficiently large.
Characteristics of constrained ferroelectricity in PbZrO3∕BaZrO3 superlattice films
Authors: Hung Cheng-Lung , Chueh Yu-Lun , Wu Tai-Bor , Chou Li-Jen
Published: January 2005

An Artificially layered perovskite composed of antiferroelectric PbZrO3 and paraelectric BaZrO3 (BZO) was fabricated on LaNiO3∕Pt∕Ti∕SiO2∕Si substrates at 475 °C by radio-frequency magnetron sputtering. It had an (001)-oriented superlattice structure with an average composition of (Pb0.75Ba0.25)ZrO3 (PBZ). X-ray diffraction, cross-sectional transmission electron microscopy, and a depth profile of a secondary-ion mass spectrometer confirmed the formation of superlattice structure with designed composition modulation. Ferroelectricity was induced in the superlattice films, and the ferroelectric as well as the dielectric properties were enhanced with reducing the stacking periodicity. The remanent polarization Pr and coercive field Ec were found linearly dependent on the applied voltage but independent of the measurement temperature up to 100 °C. The retention loss of superlattice films was small and significantly less than that of (Pb1−xBax)ZrO3 (PBZ) solid-solution films either at room temperature or 100 °C. The dielectric constant of the superlattice films was also found insensitive to temperature up to 175 °C, but not for the PBZ solid-solution film, which exhibited a clear dielectric maximum at the Curie temperature of 125 °C. Moreover, a significant suppression of leakage current down to 10−8–10−9A∕cm2 was obtained in the superlattice films constructed with the wide-bandgap sublayer of BZO.
Recombination-induced athermal migration of hydrogen and deuterium in SiC
Authors: Koshka Yaroslav , Krishnan Bharat
Published: January 2005

The phenomenon of recombination-induced formation of hydrogen-defect complexes in epitaxial silicon carbide (SiC) was further investigated on p-type samples treated in deuterium plasma. Qualitatively similar effects were observed for hydrogen and deuterium. The formation of hydrogen-related (deuterium-related) defects would depend on the temperature of the sample during plasma treatment, with lower process temperatures causing only incorporation of hydrogen (deuterium) near the surface without any significant formation of electrically or optically active hydrogen-related or deuterium-related defects in the epilayer. Higher process temperatures normally produced more efficient formation of new centers, including passivation of acceptors in SiC. In all cases, prolonged excitation of the hydrogenated (deuterated) samples with above-bandgap light at reduced temperatures caused recombination-induced formation of a few different defect centers. A confirmation of the long-range athermal migration of hydrogen from the surface into the bulk of the sample was obtained. It has been established that it is the recombination-induced migration of hydrogen that is responsible for the formation of hydrogen-related defect centers under optical excitation.
High-temperature carrier transport and thermoelectric properties of heavily La- or Nb-doped SrTiO3 single crystals
Authors: Ohta Shingo , Nomura Takashi , Ohta Hiromichi , Koumoto Kunihito
Published: January 2005

Electron and thermal transport properties, i.e., electrical conductivity, carrier concentration, Hall mobility, Seebeck coefficient, thermal conductivity, of heavily La- or Nb-doped SrTiO3 (STO) bulk single crystals were measured at high temperatures, (300–1050K) to clarify the influence of doping upon the thermoelectric performance of STO. The temperature dependence of Hall mobility and Seebeck coefficient changed at ∼750K in all samples because the dominant mechanism for carrier scattering changed with increasing temperature from coupled scattering by polar optical phonons and acoustic phonons to mere acoustic phonon scattering. The density-of-states effective mass of Nb-doped STO, which was estimated from the carrier concentration and Seebeck coefficient, was larger than that of La-doped STO. Thermal conductivity of the samples, which was similar to that of undoped STO single crystal, decreased proportionally to T−1, indicating that the phonon conduction takes place predominantly and the electronic contribution to thermal conductivity is negligible.
The nonmevalonate pathway supports both monoterpene and sesquiterpene formation in snapdragon flowers
Authors: Dudareva Natalia , Andersson Susanna , Orlova Irina , Gatto Nathalie , Reichelt Michael , Rhodes David , Boland Wilhelm , Gershenzon Jonathan
Published: January 2005

Terpenoids, the largest class of plant secondary metabolites, play essential roles in both plant and human life. In higher plants, the five-carbon building blocks of all terpenoids, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate, are derived from two independent pathways localized in different cellular compartments. The methylerythritol phosphate (MEP or nonmevalonate) pathway, localized in the plastids, is thought to provide IPP and dimethylallyl diphosphate for hemiterpene, monoterpene, and diterpene biosynthesis, whereas the cytosol-localized mevalonate pathway provides C
5
units for sesquiterpene biosynthesis. Stable isotope-labeled, pathway-specific precursors (1-deoxy-[5,5-
2
H
2
]-
d
-xylulose and [2,2-
2
H
2
]-mevalolactone) were supplied to cut snapdragon flowers, which emit both monoterpenes and the sesquiterpene, nerolidol. We show that only one of the two pathways, the plastid-localized MEP pathway, is active in the formation of volatile terpenes. The MEP pathway provides IPP precursors for both plastidial monoterpene and cytosolic sesquiterpene biosynthesis in the epidermis of snapdragon petals. The trafficking of IPP occurs unidirectionally from the plastids to cytosol. The MEP pathway operates in a rhythmic manner controlled by the circadian clock, which determines the rhythmicity of terpenoid emission.
Stargazin is an AMPA receptor auxiliary subunit
Authors: Vandenberghe Wim , Nicoll Roger A. , Bredt David S.
Published: January 2005

AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors mediate fast excitatory synaptic transmission in brain and underlie aspects of synaptic plasticity. Numerous AMPA receptor-binding proteins have been implicated in AMPA receptor trafficking and anchoring. However, the relative contributions of these proteins to the composition of native AMPA receptor complexes in brain remain uncertain. Here, we use blue native gel electrophoresis to analyze the composition of native AMPA receptor complexes in cerebellar extracts. We identify two receptor populations: a functional form that contains the transmembrane AMPA receptor-regulatory protein stargazin and an apo-form that lacks stargazin. Limited proteolysis confirms assembly of stargazin with a large proportion of native AMPA receptors. In contrast, other AMPA receptor-interacting proteins, such as synapse-associated protein 97, glutamate receptor-interacting protein 1, protein kinase Cα binding protein,N-ethylmaleimide-sensitive fusion protein, AP2, and protein 4.1N, do not show significant association with AMPA receptor complexes on native gels. These data identify stargazin as an auxiliary subunit for a neurotransmitter-gated ion channel.
A-kinase-interacting protein localizes protein kinase A in the nucleus
Authors: Sastri Mira , Barraclough David M. , Carmichael Peter T. , Taylor Susan S.
Published: January 2005

The genetic variability and covalent modifications associated with the amino terminus of the protein kinase A (PKA) catalytic (C) subunit suggest that it may contribute to protein–protein interactions and/or localization. By using a yeast two-hybrid screen, we identified a PKA-interacting protein (AKIP1) that binds to the amino terminus (residues 1–39) of the C subunit of PKA. The interaction was localized to the A helix (residues 14–39) of the C subunit and to the carboxyl terminus of AKIP1. AKIP1 thus defines the amino-terminal A helix of PKA as a protein interaction motif. In normal breast (Hs 578 Bst) and HeLa cells, AKIP1 is present in the nucleus as speckles. A nuclear localization signal (Arg-14 and Arg-15) was identified. Upon stimulation with forskolin, HeLa cells expressing AKIP1 accumulated higher levels of the endogenous C subunit in the nucleus. Deletion of the carboxyl terminus of AKIP1 or overexpression of residues 1–39 of the C subunit abolished nuclear localization of the activated endogenous C subunit. Thus, AKIP1 describes a PKA-interacting protein that can contribute to localization by a mechanism that is distinct from A-kinase anchoring proteins that interact with the regulatory subunits.
Phylogeny determined by protein domain content
Authors: Yang Song , Doolittle Russell F. , Bourne Philip E.
Published: January 2005

A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides the 174 taxa into Archaea, Bacteria, and Eukarya and satisfactorily sorts most of the major groups within these superkingdoms. The most challenging problem involved 119 Bacteria, many of which have reduced genomes. When a weighting factor was used that takes account of difference in genome size (number of considered folds), small-genome taxa were mostly grouped with their full-sized counterparts. Although not every organism appears exactly at its classical phylogenetic position in these trees, the agreement appears comparable with the efforts of others by using sophisticated sequence analysis and/or combinations of gene content and gene order. During the course of the study, it emerged that there is a core set of ≈50 folds that is found in all 174 genomes and a single fold diagnostic of all Archaea.
Glycogen synthase kinase-3 is an endogenous inhibitor of Snail transcription
Authors: Bachelder Robin E. , Yoon Sang-Oh , Franci Clara , de Herreros Antonio García , Mercurio Arthur M.
Published: January 2005

We report that the activity of glycogen synthase kinase-3 (GSK-3) is necessary for the maintenance of the epithelial architecture. Pharmacological inhibition of its activity or reducing its expression using small interfering RNAs in normal breast and skin epithelial cells results in a reduction of E-cadherin expression and a more mesenchymal morphology, both of which are features associated with an epithelial–mesenchymal transition (EMT). Importantly, GSK-3 inhibition also stimulates the transcription of Snail, a repressor of E-cadherin and an inducer of the EMT. We identify NFκB as a transcription factor inhibited by GSK-3 in epithelial cells that is relevant for Snail expression. These findings indicate that epithelial cells must sustain activation of a specific kinase to impede a mesenchymal transition.
TACI and BAFF-R mediate isotype switching in B cells
Authors: Castigli Emanuela , Wilson Stephen A. , Scott Sumi , Dedeoglu Fatma , Xu Shengli , Lam Kong-Peng , Bram Richard J. , Jabara Haifa , Geha Raif S.
Published: January 2005

The tumor necrosis factor family members BAFF and APRIL induce Ig isotype switching in human B cells. We analyzed the ability of BAFF and APRIL to induce isotype switching in murine B cells to IgG1, IgA, and IgE. APRIL and BAFF each engage two receptors, transmembrane activator and calcium-modulator and cytophilin ligand interactor (TACI) and B cell maturation antigen (BCMA), on B cells. In addition, BAFF engages a third receptor on B cells, BAFF-R. To determine the role of these receptors in isotype switching, we examined B cells from mice deficient in TACI, BCMA, and BAFF-R. The results obtained indicate that both TACI and BAFF-R are able to transduce signals that result in isotype switching.
Spred-1 negatively regulates allergen-induced airway eosinophilia and hyperresponsiveness
Authors: Inoue Hiromasa , Kato Reiko , Fukuyama Satoru , Nonami Atsushi , Taniguchi Kouji , Matsumoto Koichiro , Nakano Takako , Tsuda Miyuki , Matsumura Mikiko , Kubo Masato , Ishikawa Fumihiko , Moon Byoung-gon , Takatsu Kiyoshi , Nakanishi Yoichi , Yoshimura Akihiko
Published: January 2005

T helper 2 cytokines, including interleukin (IL)-4, IL-5, and IL-13, play a critical role in allergic asthma. These cytokines transmit signals through the Janus kinase/signal transducer and activator of transcription (STAT) and the Ras–extracellular signal-regulated kinase (ERK) signaling pathways. Although the suppressor of cytokine signaling (SOCS) family proteins have been shown to regulate the STAT pathway, the mechanism regulating the ERK pathway has not been clarified. The Sprouty-related Ena/VASP homology 1–domain-containing protein (Spred)-1 has recently been identified as a negative regulator of growth factor–mediated, Ras-dependent ERK activation. Here, using Spred-1–deficient mice, we demonstrated that Spred-1 negatively regulates allergen-induced airway eosinophilia and hyperresponsiveness, without affecting helper T cell differentiation. Biochemical assays indicate that Spred-1 suppresses IL-5–dependent cell proliferation and ERK activation. These data indicate that Spred-1 negatively controls eosinophil numbers and functions by modulating IL-5 signaling in allergic asthma.
Synergy of IL-21 and IL-15 in regulating CD8+ T cell expansion and function
Authors: Zeng Rong , Spolski Rosanne , Finkelstein Steven E. , Oh SangKon , Kovanen Panu E. , Hinrichs Christian S. , Pise-Masison Cynthia A. , Radonovich Michael F. , Brady John N. , Restifo Nicholas P. , Berzofsky Jay A. , Leonard Warren J.
Published: January 2005

Interleukin (IL)-21 is the most recently recognized of the cytokines that share the common cytokine receptor γ chain (γc), which is mutated in humans with X-linked severe combined immunodeficiency. We now report that IL-21 synergistically acts with IL-15 to potently promote the proliferation of both memory (CD44high) and naive (CD44low) phenotype CD8+ T cells and augment interferon-γ production in vitro. IL-21 also cooperated, albeit more weakly, with IL-7, but not with IL-2. Correspondingly, the expansion and cytotoxicity of CD8+ T cells were impaired in IL-21R−/− mice. Moreover, in vivo administration of IL-21 in combination with IL-15 boosted antigen-specific CD8+ T cell numbers and resulted in a cooperative effect on tumor regression, with apparent cures of large, established B16 melanomas. Thus, our studies reveal that IL-21 potently regulates CD8+ T cell expansion and effector function, primarily in a synergistic context with IL-15.
Conversion of CD4+ CD25− cells into CD4+ CD25+ regulatory T cells in vivo requires B7 costimulation, but not the thymus
Authors: Liang Shuang , Alard Pascale , Zhao Yuan , Parnell Sarah , Clark Sherry L. , Kosiewicz Michele M.
Published: January 2005

The CD4+ CD25+ regulatory T cells play a critical role in controlling autoimmunity, but little is known about their development and maintenance. In this study, we investigated whether CD4+ CD25− cells can convert to CD4+ CD25+ regulatory T cells in vivo under natural conditions. CD4+ CD25− cells from CD45.1+ mice were sorted and transferred into congenic CD45.2+ mice. Converted CD4+ CD25+ cells could be detected in lymphoid organs as early as 1 wk after transfer and by 6 wk after transfer, 5–12% of transferred CD4+ cells expressed CD25. Converted CD4+ CD25+ cells themselves failed to proliferate after stimulation, but could suppress proliferation of responder cells in vitro, and also expressed high levels of Foxp3 mRNA. In addition, CD4+ CD25− cells transferred into thymectomized congenic mice converted to CD4+ CD25+ cells that also suppressed responder cell proliferation in vitro, and expressed high levels of Foxp3 mRNA. Finally, CD4+ CD25− cells transferred into B7−/− mice failed to convert into CD4+ CD25+ cells that exhibit the regulatory phenotype. These data indicate that CD4+ CD25− cells convert into CD4+ CD25+ regulatory T cells spontaneously in vivo and suggest that this conversion process could contribute significantly to the maintenance of the peripheral CD4+ CD25+ regulatory T cell population.
Do developing B cells need antigen?
Authors: Weill Jean-Claude , Reynaud Claude-Agnès
Published: January 2005

Just as potentially useful T cells are positively selected by MHC–peptide complexes in the thymus, it has been proposed that self or commensal bacterial epitopes might select B cell populations with the capacity to recognize polysaccharide or protein structures on pathogens. Recent studies indicate that the repertoire of B cells entering the periphery is not shaped by specific stimuli, but that mature B cell subsets may be under different selective pressures.
Changes of the phagosomal elemental concentrations by Mycobacterium tuberculosis Mramp
Authors: Wagner Dirk , Maser Jörg , Moric Ivana , Boechat Neio , Vogt Stefan , Gicquel Brigitte , Lai Barry , Reyrat Jean-Marc , Bermudez Luiz
Published: January 2005

Pathogenic mycobacteria survive within phagosomes which are thought to represent a nutrient-restricted environment. Divalent cation transporters of the Nramp family in phagosomes and mycobacteria (Mramp) may compete for metals that are crucial for bacterial survival. The elemental concentrations in phagosomes of macrophages infected with wild-typeMycobacterium tuberculosis(M. tuberculosisstrain H37Rv) and aM. tuberculosis Mrampknockout mutant (Mramp-KO), derived from a clinical isolate isogenic to the strain MT103, were compared. Time points of 1 and 24 h after infection of mouse peritoneal macrophages (bcgS) were compared in both cases. Increased concentrations of P, Ni and Zn and reduced Cl concentration in Mramp-KO after 1 h of infection were observed, compared toM. tuberculosisvacuoles. After 24 h of infection, significant differences in the P, Cl and Zn concentrations were still present. The Mramp-KO phagosome showed a significant increase of P, Ca, Mn, Fe and Zn concentrations between 1 and 24 h after infection, while the concentrations of K and Ni decreased. In theM. tuberculosisvacuole, the Fe concentration showed a similar increase, while the Cl concentration decreased. The fact that the concentration of several divalent cations increased in the Mramp-KO strain suggests that Mramp may have no impact on the import of these divalent cations into the mycobacterium, but may function as a cation efflux pump. The concordant increase of Fe concentrations withinM. tuberculosis, as well as within the Mramp-KO vacuoles, implies that Mramp, in contrast to siderophores, might not be important for the attraction of Fe and its retention in phagosomes of unstimulated macrophages.
DNA-binding activity of LndI protein and temporal expression of the gene that upregulates landomycin E production in Streptomyces globisporus 1912
Authors: Rebets Yu. , Ostash B. , Luzhetskyy A. , Kushnir S. , Fukuhara M. , Bechthold A. , Nashimoto M. , Nakamura T. , Fedorenko V.
Published: January 2005

The gene lndI is involved in the pathway-specific positive regulation of biosynthesis of the antitumour polyketide landomycin E in Streptomyces globisporus 1912. LndI was overexpressed in Escherichia coli as a protein C-terminally fused to the intein-chitin-binding-domain tag and purified in a one-step column procedure. Results of in vivo LndI titration, DNA gel mobility-shift assays and promoter-probing experiments indicate that LndI is an autoregulatory DNA-binding protein that binds to its own gene promoter and to the promoter of the structural gene lndE. Enhanced green fluorescent protein was used as a reporter to study the temporal and spatial pattern of lndI transcription. Expression of lndI started before cells entered mid-exponential phase and peak expression coincided with maximal accumulation of landomycin E and biomass. In solid-phase analysis, lndI expression was evident in substrate mycelia but was absent from aerial hyphae and spores.
The formation of cyclopropane fatty acids in Salmonella enterica serovar Typhimurium
Authors: Kim Bae Hoon , Kim Seungki , Kim Hyeon Guk , Lee Jin , Lee In Soo , Park Yong Keun
Published: January 2005

The formation of cyclopropane fatty acid (CFA) and its role in the acid shock response inSalmonella entericaserovar Typhimurium (S. typhimurium) was investigated. Data obtained by GC/MS demonstrated that the CFA level inS. typhimuriumincreased upon its entry to the stationary phase, as in other bacteria. Thecfagene encoding CFA synthase was cloned, and mutants of thecfagene were constructed by allelic exchange. Acfamutant could not produce CFA and was sensitive to low pH. Introduction of a functionalcfagene into acfamutant cell made the mutant convert all unsaturated fatty acids to CFAs and partially restored resistance to low pH. Interestingly, the alternative sigma factor RpoS, which was induced during the stationary phase, affected the production of C19CFA but not C17CFA. Western blotting analysis showed that the increase in expression of CFA synthase at early stationary phase was due to the alternative sigma factor RpoS.
Acetaminophen toxicity and resistance in the yeast Saccharomyces cerevisiae
Authors: Srikanth Chittur V. , Chakraborti Asit K. , Bachhawat Anand K.
Published: January 2005

Acetaminophen (paracetamol), one of the most widely used analgesics, is toxic under conditions of overdose or in certain disease conditions, but the mechanism of acetaminophen toxicity is still not entirely understood. To obtain fresh insights into acetaminophen toxicity, this phenomenon was investigated in yeast. Acetaminophen was found to be toxic to yeast cells, withergmutants displaying hypersensitivity. Yeast cells grown in the presence of acetaminophen were found to accumulate intracellular acetaminophen, but no metabolic products of acetaminophen could be detected in these extracts. The toxicity response did not lead to an oxidative stress response, although it did involve Yap1p. The cytochrome P450 enzymes of yeast, Erg5p and Erg11p, did not appear to participate in this process, unlike the mammalian systems. Furthermore, we could not establish a central role for glutathione depletion or the cellular glutathione redox status in acetaminophen toxicity, suggesting differences from mammalian systems in the pathways causing toxicity. Investigations of the resistance mechanisms revealed that deletion of the glutathione-conjugate pumps Ycf1p (a target of Yap1p) and Bpt1p, surprisingly, led to acetaminophen resistance, while overexpression of the multidrug resistance pumps Snq2p and Flr1p (also targets of Yap1p) led to acetaminophen resistance. The Yap1p-dependent resistance to acetaminophen required a functional Pdr1p or Pdr3p protein, but not a functional Yrr1p. In contrast, resistance mediated by Pdr1p/Pdr3p did not require a functional Yap1p, and revealed a distinct hierarchy in the resistance to acetaminophen.
Modelling protection from antimicrobial agents in biofilms through the formation of persister cells
Authors: Roberts Mark E. , Stewart Philip S.
Published: January 2005

A mathematical model of biofilm dynamics was used to investigate the protection from antimicrobial killing that could be afforded to micro-organisms in biofilms based on a mechanism of ‘persister’ cell or phenotypic variant formation. The persister state is a hypothetical, highly protected state adopted by a small fraction of the cells in a biofilm. Persisters were assumed to be generated at a fixed rate, independent of the presence of substrate or antimicrobial agent. Cells were assumed to revert from the persister state when exposed to the growth substrate. Persister cells were assumed to be incapable of growth. The model predicted that persister cells increased in numbers in the biofilm, even though they were unable to grow, accumulating in regions of substrate limitation. In these regions, normal cells failed to grow, but did slowly convert to the persister state. Calculations of persister formation in planktonic cultures predicted that persisters would be present in low numbers in growing cultures, but should accumulate under conditions of slow growth, e.g. very low dilution rates in continuous culture or stationary phase in batch culture. When antibiotic treatment was simulated, bacteria near the biofilm surface were killed, but persisters in the depth of the biofilm were poorly killed. After antibiotic treatment ceased, surviving persister cells quickly reverted and allowed the biofilm to regrow. This modelling study provides motivation for further investigation of the hypothetical persister cell state as an explanation for biofilm resistance to antimicrobial agents.
Campylobacter jejuni gene expression in response to iron limitation and the role of Fur
Authors: Holmes Kathryn , Mulholland Francis , Pearson Bruce M. , Pin Carmen , McNicholl-Kennedy Johanna , Ketley Julian M. , Wells Jerry M.
Published: January 2005

Campylobacter jejuni is a zoonotic pathogen and the most common cause of bacterial foodborne diarrhoeal illness worldwide. To establish intestinal colonization prior to either a commensal or pathogenic interaction with the host, C. jejuni will encounter iron-limited niches where there is likely to be intense competition from the host and normal microbiota for iron. To gain a better understanding of iron homeostasis and the role of ferric uptake regulator (Fur) in iron acquisition in C. jejuni, a proteomic and transcriptome analysis of wild-type and fur mutant strains in iron-rich and iron-limited growth conditions was carried out. All of the proposed iron-transport systems for haemin, ferric iron and enterochelin, as well as the putative iron-transport genes p19, Cj1658, Cj0177, Cj0178 and cfrA, were expressed at higher levels in the wild-type strain under iron limitation and in the fur mutant in iron-rich conditions, suggesting that they were regulated by Fur. Genes encoding a previously uncharacterized ABC transport system (Cj1660–Cj1663) also appeared to be Fur regulated, supporting a role for these genes in iron uptake. Several promoters containing consensus Fur boxes that were identified in a previous bioinformatics search appeared not to be regulated by iron or Fur, indicating that the Fur box consensus needs experimental refinement. Binding of purified Fur to the promoters upstream of the p19, CfrA and CeuB operons was verified using an electrophoretic mobility shift assay (EMSA). These results also implicated Fur as having a role in the regulation of several genes, including fumarate hydratase, that showed decreased expression in response to iron limitation. The known PerR promoters were also derepressed in the C. jejuni Fur mutant, suggesting that they might be co-regulated in response to iron and peroxide stress. These results provide new insights into the effects of iron on metabolism and oxidative stress response as well as the regulatory role of Fur.
Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits
Authors: Gordon David M. , Stern Steven E. , Collignon Peter J.
Published: January 2005

Escherichia coliwere isolated from the faeces of 266 individuals living in the Canberra region of Australia. The isolates were characterized for their ECOR group membership (A, B1, B2 or D) and for the presence of 29 virulence-associated traits. Overall, 19·5 % of the strains were members of group A, 12·4 % B1, 45·1 % B2 and 22·9 % D. The frequency with which strains belonging to the four ECOR groups were observed varied with the age and sex of the hosts from which they were isolated. In males, the probability of isolating A or D strains increased with host age, whilst the probability of detecting a group B2 strain declined. In females, the probability of recovering A or B2 strains increased with increasing host age and there was a concomitant decline in the likelihood of isolating B1 or D strains. Of the 29 virulence-associated traits examined, 24 were detected in more than one strain. The likelihood of detecting most traits varied with a strain's ECOR membership, with the exception ofafa/draBC,astA,cvaC,eaeA,issandiutA, for which there was no statistically significant evidence of an association with ECOR group. The frequency with whichfimH,iha,eaeA,iroN,hlyD,iss,ompTand K1 were detected in a strain depended on the age or sex of the host from which the strain was isolated. In group B2 strains many of the virulence traits were non-randomly associated, with some co-occurring in a strain less often than expected by chance, whilst others were co-associated. In 17 cases, the extent to which two virulence traits were co-associated was found to depend on host sex and age. The results of this study suggest that the morphological, physiological and dietary differences that occur among human individuals of different sex or age may influence the distribution ofE. coligenotypes.
Characterization of the cleavage site and function of resulting cleavage fragments after limited proteolysis of Clostridium difficile toxin B (TcdB) by host cells
Authors: Rupnik Maja , Pabst Stefan , Rupnik Marjan , von Eichel-Streiber Christoph , Urlaub Henning , Söling Hans-Dieter
Published: January 2005

Clostridium difficiletoxin B (TcdB) is a single-stranded protein consisting of a C-terminal domain responsible for binding to the host cell membrane, a middle part involved in internalization, and the N-terminal catalytic (toxic) part. This study shows that TcdB is processed by a single proteolytic step which cleaves TcdB10463between Leu543and Gly544and the naturally occurring variant TcdB8864between Leu544and Gly545. The cleavage occurs at neutral pH and is catalysed by a pepstatin-sensitive protease localized in the cytoplasm and on the cytoplasmic face of intracellular membranes. The smaller N-terminal cleavage products [63 121 Da (TcdB10463) and 62 761 Da (TcdB8864)] harbour the cytotoxic and glucosyltransferase activities of the toxins. When microinjected into cultured Chinese hamster lung fibroblasts, the N-terminal cleavage fragment shows full cytotoxic activity shortly after injection whereas the holotoxin initially exhibits a very low activity which, however, increases with time. Twenty minutes after the start of internalization of TcdB, the larger cleavage products [206 609 Da (TcdB10463) and 206 245 Da (TcdB8864)] are found exclusively in a membrane fraction, whereas the N-terminal cleavage products appear mainly in the cytosol and associated with the membrane. This is in line with a proposed model according to which the longer, C-terminal, part of these toxins forms a channel allowing for the translocation of the toxic N-terminal part, which is subsequently cleaved off at the cytoplasmic face of an intracellular compartment, most likely endosomes.
Aminopeptidases and dipeptidyl-peptidases secreted by the dermatophyte Trichophyton rubrum
Authors: Monod Michel , Léchenne Barbara , Jousson Olivier , Grand Daniela , Zaugg Christophe , Stöcklin Reto , Grouzmann Eric
Published: January 2005

The nature of secreted aminopeptidases inTrichophyton rubrumwas investigated by using a reverse genetic approach.T. rubrumgenomic and cDNA libraries were screened withAspergillusspp. andSaccharomyces cerevisiaeaminopeptidase genes as the probes. Two leucine aminopeptidases, ruLap1 and ruLap2, and two dipeptidyl-peptidases, ruDppIV and ruDppV, were characterized and compared to orthologues secreted byAspergillus fumigatususing a recombinant protein fromPichia pastoris. RuLap1 is a 33 kDa nonglycosylated protein, while ruLap2 is a 58–65 kDa glycoprotein. The hydrolytic activity of ruLap1, ruLap2 andA. fumigatusorthologues showed various preferences for different aminoacyl-7-amido-4-methylcoumarin substrates, and various sensitivities to inhibitors and cations. ruDppIV and ruDppV showed similar activities toA. fumigatusorthologues. In addition to endopeptidases, the four aminopeptidases ruLap1, ruLap2, ruDppIV and ruDppV were produced byT. rubrumin a medium containing keratin as the sole nitrogen source. Synergism between endo- and exopeptidases is likely to be essential for dermatophyte virulence, since these fungi grow only in keratinized tissues.
Respiratory gene clusters of Metallosphaera sedula – differential expression and transcriptional organization
Authors: Kappler Ulrike , Sly Lindsay I. , McEwan Alastair G.
Published: January 2005

Metallosphaera sedulais a thermoacidophilic Crenarchaeon which is capable of leaching metals from sulfidic ores. The authors have investigated the presence and expression of genes encoding respiratory complexes in this organism when grown heterotrophically or chemolithotrophically on either sulfur or pyrite. The presence of three gene clusters, encoding two terminal oxidase complexes, the quinol oxidase SoxABCD and the SoxM oxidase supercomplex, and a gene cluster encoding a high-potential cytochromeband components of abc1complex analogue (cbsBA–soxL2Ngene cluster) was established. Expression studies showed that thesoxMgene was expressed to high levels during heterotrophic growth ofM. sedulaon yeast extract, while thesoxABCDmRNA was most abundant in cells grown on sulfur. Reduced-minus-oxidized difference spectra of cell membranes showed cytochrome-related peaks that correspond to published spectra ofSulfolobus-type terminal oxidase complexes. In pyrite-grown cells, expression levels of the two monitored oxidase gene clusters were reduced by a factor of 10–12 relative to maximal expression levels, although spectra of membranes clearly contained oxidase-associated haems, suggesting the presence of additional gene clusters encoding terminal oxidases inM. sedula. Pyrite- and sulfur-grown cells contained high levels of thecbsAtranscript, which encodes a membrane-bound cytochromebwith a possible role in iron oxidation or chemolithotrophy. ThecbsAgene is not co-transcribed with thesoxL2Ngenes, and therefore does not appear to be an integral part of thisbc1complex analogue. The data show for the first time the differential expression of theSulfolobus-type terminal oxidase gene clusters in a Crenarchaeon in response to changing growth modes.
A unique nine-gene comY operon in Streptococcus mutans
Authors: Merritt Justin , Qi Fengxia , Shi Wenyuan
Published: January 2005

Many Gram-positive and Gram-negative bacteria possess natural competence mechanisms for DNA capture and internalization. In Bacillus subtilis, natural competence is absolutely dependent upon the presence of a seven-gene operon known as the comG operon (comGA–G). In species of Streptococcus, this function has been described for a four-gene operon (comYA–D in Streptococcus gordonii and cglA–D in Streptococcus pneumoniae). In this study, a nine-orf operon (named comYA–I) required for natural competence in Streptococcus mutans was identified and characterized. Orf analysis of this operon indicates that the first four Orfs (ComYA–D) share strong homology with ComYA–D of S. gordonii and CglA–D of S. pneumoniae, the fifth to seventh Orfs (ComYE–G) match conserved hypothetical proteins from various species of Streptococcus with ComYF possessing a predicted ComGF domain, the eighth Orf (ComYH) shows a strong homology to numerous DNA methyltransferases from restriction/modification systems, and the ninth Orf (ComYI) is homologous to acetate kinase (AckA). RT-PCR analysis of the orf junctions confirmed that all nine orfs were present in a single transcript, while real-time RT-PCR analysis demonstrated that these orfs were expressed at a level very similar to that of the first orf in the operon. Mutations were constructed in all nine putative orfs. The first seven genes (comYA–G) were found to be essential for natural competence, while comYH and comYI had reduced and normal natural competence ability, respectively. Analyses of S. mutans comY–luciferase reporter fusions indicated that comY expression is growth-phase dependent, with maximal expression at an OD600 of about 0·2, while mutations in ciaH, comC and luxS reduced the level of comY expression. In addition, comY operon expression appears to be correlated with natural competence ability.