bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hamilton–Jacobi approach to photon wave mechanics: near‐field aspects
Authors: KELLER O. 
Published: February 2008

SummaryAfter having briefly reviewed the Hamilton–Jacobi theory of classical point‐particle mechanics, its extension to the quantum regime and the formal identity between the Hamilton–Jacobi equation for Hamilton's characteristic function and the eikonal equation of geometrical optics, an eikonal theory for free photons is established. The space‐time dynamics of the photon is described on the basis of the six‐component Riemann–Silberstein energy wave function. Form‐identical eikonal equations are obtained for the positive and negative helicity dynamics. Microscopic response theory is used to describe the linear photon–matter interaction. In the presence of matter the free‐photon concept is replaced by a quasi‐photon concept, and there is a quasi‐photon for each of the two helicity states. After having established integro–differential equations for the wave functions of the two quasi‐photons, the eikonal conditions for the quasi‐photons are determined. It appears that the eikonal condition contains complicated space integrals of the gradient of the eikonal over volumes of near‐field domain size. In these space integrals the dynamics of the electrons (matter particles) appears via transverse transition current densities between pairs of many‐body states. Generalized microscopic polarization and magnetization fields are introduced to establish the connection between the quasi‐photon and macroscopic eikonal theories.
Annular nanoantenna on fibre micro‐axicon
Authors: GROSJEAN T. , FAHYS A. , SUAREZ M. , CHARRAUT D. , SALUT R. , COURJON D. 
Published: February 2008

SummaryIn this paper, we propose to extend the concept of loop antenna to the optical domain. The aim is to develop a new generation of optical nanocollectors that are sensitive to specific electric or magnetic vectorial field components. For validating our approach, a preliminary one‐micron‐diameter gold nanoring is micromachined on the apex of a cone lens obtained from a tapered optical fibre. It is shown that such a nano‐object behaves as a nano‐antenna able to detect the longitudinal electric field from a Bessel beam in radial polarization and the longitudinal magnetic component from a Bessel beam in azimuthal polarization. In the latter case, the annular nano‐antenna exhibits the properties of an optical inductance.
Coupling efficiency of probes in emission‐mode scanning near‐field optical microscopy
Authors: ALVAREZ L. , XIAO M. 
Published: February 2008

SummaryIn scanning near‐field optical microscopy, a tapered fibre tip scans above the sample surface at nanometric distances. The fibre tip can be used either as a detector to receive the near‐field signal or as the light source to illuminate the sample or simultaneously for both purposes. When used as an emitter of light, the scanning near‐field optical microscopy is said to function in emission mode. In such emission mode, the light emitted by the probe interacts with the microscopic features on the sample surface, and the result of this interaction is focussed by means of a conventional microscope. In our present work, we concentrate on how the light is emitted from the fibre tip. The power emitted by the probe is critical because it is directly related to the power that reaches the detector and in turn to the resolution of the instrument. A typical probe is made of a tapered optical fibre coated with metal. For probes fabricated by etching, the taper angle is high and the radii of the core and cladding are constant. Thus, the probe can be crudely approximated by a circular aperture on top of a metal‐coated optical fibre end. It is interesting to study how the dielectric waveguide modes will couple into the metallic waveguide modes. In this work, a single mode excited in the dielectric waveguide is assumed, and calculations of the power transmitted through the aperture are carried out. A comparison between the power transmitted by different optical fibre modes and different optical fibre parameters is conducted, and the implications for the coupling efficiency of emission‐mode fibre tips are discussed.
The transcriptomics of life‐history trade‐offs in whitefish species pairs (Coregonussp.)
Authors: ST‐CYR J. , DEROME N. , BERNATCHEZ L. 
Published: February 2008

AbstractDespite the progress achieved in elucidating the ecological mechanisms of adaptive radiation, there has been little focus on documenting the extent of adaptive differentiation in physiological functions during this process. Moreover, a thorough understanding of the genomic basis underlying phenotypic adaptive divergence is still in its infancy. One important evolutionary process for which causal genetic mechanisms are largely unknown pertains to life‐history trade‐offs. We analysed patterns of gene transcription in liver tissue of sympatric dwarf and normal whitefish from two natural lakes, as well as from populations reared in controlled environments, using a 16 006‐gene cDNA microarray in order to: (i) document the extent of physiological adaptive divergence between sympatric dwarf and normal species pairs, and (ii) explore the molecular mechanisms of differential life history trade‐offs between growth and survival potentially involved in their adaptive divergence. In the two natural lakes, 6.45% of significantly transcribed genes showed regulation either in parallel fashion (2.39%) or in different directions (4.06%). Among genes showing parallelism in regulation patterns, we observed a higher proportion of over‐expressed genes in dwarf relative to normal whitefish (70.6%). Patterns observed in controlled conditions were also generally congruent with those observed in natural populations. Dwarf whitefish consistently showed significant over‐expression of genes potentially associated with survival through enhanced activity (energy metabolism, iron homeostasis, lipid metabolism, detoxification), whereas more genes associated with growth (protein synthesis, cell cycle, cell growth) were generally down‐regulated in dwarf relative to normal whitefish. Overall, parallelism in patterns of gene transcription, as well as patterns of interindividual variation across controlled and natural environments, provide strong indirect evidence for the role of selection in the evolution of differential regulation of genes involving a vast array of potentially adaptive physiological processes between dwarf and normal whitefish. Our results also provide a first mechanistic, genomic basis for the observed trade‐off in life‐history traits distinguishing dwarf and normal whitefish species pairs, wherein enhanced survival via more active swimming, necessary for increased foraging and predator avoidance, engages energetic costs that translate into slower growth rate and reduced fecundity in dwarf relative to normal whitefish.
YcbX and yiiM, two novel determinants for resistance of Escherichia coli to N‐hydroxylated base analogues
Authors: Kozmin Stanislav G. , Leroy Prune , Pavlov Youri I. , Schaaper Roel M. 
Published: February 2008

SummaryWe have shown previously that lack of molybdenum cofactor (MoCo) in Escherichia coli leads to hypersensitivity to the mutagenic and toxic effects of N‐hydroxylated base analogues, such as 6‐N‐hydroxylaminopurine (HAP). However, the nature of the MoCo‐dependent mechanism is unknown, as inactivation of all known and putative E. coli molybdoenzymes does not produce any sensitivity. Presently, we report on the isolation and characterization of two novel HAP‐hypersensitive mutants carrying defects in the ycbX or yiiM open reading frames. Genetic analysis suggests that the two genes operate within the MoCo‐dependent pathway. In the absence of the ycbX‐ and yiiM‐dependent pathways, biotin sulfoxide reductase plays also a role in the detoxification pathway. YcbX and YiiM are hypothetical members of the MOSC protein superfamily, which contain the C‐terminal domain (MOSC) of the eukaryotic MoCo sulphurases. However, deletion of ycbX or yiiM did not affect the activity of human xanthine dehydrogenase expressed in E. coli, suggesting that the role of YcbX and YiiM proteins is not related to MoCo sulphuration. Instead, YcbX and YiiM may represent novel MoCo‐dependent enzymatic activities. We also demonstrate that the MoCo/YcbX/YiiM‐dependent detoxification of HAP proceeds by reduction to adenine.
Post‐initiation control by the initiation factor sigma
Authors: Artsimovitch Irina 
Published: February 2008

SummaryBacterial core RNA polymerase can initiate transcription at promoters only if guided by a σ subunit that directs the core enzyme to a subset of σ‐specific promoters. Specific and stable interactions between the promoter DNA elements and σ are required for efficient promoter recognition. At the same time, persistent σ‐DNA contacts can hinder RNA polymerase escape from a promoter or halt the enzyme downstream from the transcription start site, thereby reducing transcription of the affected genes. This microcommentary reviews recent data arguing that σ‐dependent stalled transcription complexes form frequently in vivo, where they likely play important and diverse regulatory roles.
Structural and mutational analysis of the cell division protein FtsQ
Authors: Van Den Ent Fusinita , Vinkenvleugel Thessa M. F. , Ind Alice , West Philip , Veprintsev Dmitry , Nanninga Nanne , Den Blaauwen Tanneke , Löwe Jan 
Published: February 2008

SummaryBacterial cytokinesis requires the divisome, a complex of proteins that co‐ordinates the invagination of the cytoplasmic membrane, inward growth of the peptidoglycan layer and the outer membrane. Assembly of the cell division proteins is tightly regulated and the order of appearance at the future division site is well organized. FtsQ is a highly conserved component of the divisome among bacteria that have a cell wall, where it plays a central role in the assembly of early and late cell division proteins. Here, we describe the crystal structure of the major, periplasmic domain of FtsQ from Escherichia coli and Yersinia enterocolitica. The crystal structure reveals two domains; the α‐domain has a striking similarity to polypeptide transport‐associated (POTRA) domains and the C‐terminal β‐domain forms an extended β‐sheet overlaid by two, slightly curved α‐helices. Mutagenesis experiments demonstrate that two functions of FtsQ, localization and recruitment, occur in two separate domains. Proteins that localize FtsQ need the second β‐strand of the POTRA domain and those that are recruited by FtsQ, like FtsL/FtsB, require the surface formed by the tip of the last α‐helix and the two C‐terminal β‐strands. Both domains act together to accomplish the role of FtsQ in linking upstream and downstream cell division proteins within the divisome.
Esterification of cholesterol by a type III secretion effector during intracellular Salmonella infection
Authors: Nawabi Parwez , Catron Drew M. , Haldar Kasturi 
Published: February 2008

SummarySurvival of Salmonella typhimurium within a vacuole in host cells depends on secreted virulence factors encoded by the Salmonella pathogenicity island 2 (SPI‐2). High levels of cholesterol are detected at the Salmonella‐containing vacuole (SCV). Here we show that the SPI‐2 effector SseJ esterifies cholesterol in vitro, in cells and during infection. Intracellular infections with wild‐type as compared with ΔsseJ bacteria led to higher levels of cholesterol ester production in HeLa cells and RAW macrophages and were shown to increase levels of lipid droplets (structures enriched in cholesterol esters). Ectopic expression of SseJ reduced cholesterol levels in cellular membranes and antagonized a major membrane activity of a second bacterial effector known to be important to the stability of the SCV. Previous studies in mouse models of infection have established a virulence defect in ΔsseJ bacteria and have suggested a role for SseJ in regulating SCV dynamics. Our data indicating the molecular activity of SseJ suggest that cholesterol and its esterification at the SCV are functionally important for intracellular bacterial survival.
The ATP‐binding cassette transporter–encoding gene CgSNQ2 is contributing to the CgPDR1‐dependent azole resistance of Candida glabrata
Authors: Torelli Riccardo , Posteraro Brunella , Ferrari Sélène , La Sorda Marilena , Fadda Giovanni , Sanglard Dominique , Sanguinetti Maurizio 
Published: February 2008

SummaryOur previous investigation on Candida glabrata azole‐resistant isolates identified two isolates with unaltered expression of CgCDR1/CgCDR2, but with upregulation of another ATP‐binding cassette transporter, CgSNQ2, which is a gene highly similar to ScSNQ2 from Saccharomyces cerevisiae. One of the two isolates (BPY55) was used here to elucidate this phenomenon. Disruption of CgSNQ2 in BPY55 decreased azole resistance, whereas reintroduction of the gene in a CgSNQ2 deletion mutant fully reversed this effect. Expression of CgSNQ2 in a S. cerevisiae strain lacking PDR5 mediated not only resistance to azoles but also to 4‐nitroquinoline N‐oxide, which is a ScSNQ2‐specific substrate. A putative gain‐of‐function mutation, P822L, was identified in CgPDR1 from BPY55. Disruption of CgPDR1 in BPY55 conferred enhanced azole susceptibility and eliminated CgSNQ2 expression, whereas introduction of the mutated allele in a susceptible strain where CgPDR1 had been disrupted conferred azole resistance and CgSNQ2 upregulation, indicating that CgSNQ2 was controlled by CgPDR1. Finally, CgSNQ2 was shown to be involved in the in vivo response to fluconazole. Together, our data first demonstrate that CgSNQ2 contributes to the development of CgPDR1‐dependent azole resistance in C. glabrata. The overlapping in function and regulation between CgSNQ2 and ScSNQ2 further highlight the relationship between S. cerevisiae and C. glabrata.
The tryptophan aminotransferase Tam1 catalyses the single biosynthetic step for tryptophan‐dependent pigment synthesis in Ustilago maydis
Authors: Zuther Katja , Mayser Peter , Hettwer Ursula , Wu Wenying , Spiteller Peter , Kindler Bernhard L. J. , Karlovsky Petr , Basse Christoph W. , Schirawski Jan 
Published: February 2008

SummaryTryptophan is a precursor for many biologically active secondary metabolites. We have investigated the origin of indole pigments first described in the pityriasis versicolor‐associated fungus Malassezia furfur. Some of the identified indole pigments have properties potentially explaining characteristics of the disease. As M. furfur is not amenable to genetic manipulation, we used Ustilago maydis to investigate the pathway leading to pigment production from tryptophan. We show by high‐performance liquid chromatography, mass spectrometry and nuclear magnetic resonance analysis that the compounds produced by U. maydis include those putatively involved in the etiology of pityriasis versicolor. Using a reverse genetics approach, we demonstrate that the tryptophan aminotransferase Tam1 catalyses pigment biosynthesis by conversion of tryptophan into indolepyruvate. A forward genetics approach led to the identification of mutants incapable of producing the pigments. These mutants were affected in the sir1 gene, presumably encoding a sulphite reductase. In vitro experiments with purified Tam1 showed that 2‐oxo 4‐methylthio butanoate serves as a substrate linking tryptophan deamination to sulphur metabolism. We provide the first direct evidence that these indole pigments form spontaneously from indolepyruvate and tryptophan without any enzymatic activity. This suggests that compounds with a proposed function in M. furfur‐associated disease consist of indolepyruvate‐derived spontaneously generated metabolic by‐products.
Delineation of the recombination sites necessary for integration of pathogenicity islands II and III into the Escherichia coli 536 chromosome
Authors: Wilde Caroline , Mazel Didier , Hochhut Bianca , Middendorf Barbara , Le Roux Frédérique , Carniel Elisabeth , Dobrindt Ulrich , Hacker Jörg 
Published: February 2008

SummaryIn uropathogenic Escherichia coli strain 536, six pathogenicity islands (PAIs) encode key virulence factors. All PAIs except PAI IV536 are flanked by direct repeats and four of them encode integrases responsible for their chromosomal excision. To study recombination sites used for the integration by PAI II536 and III536 integrases, we measured site‐specific recombination between the chromosomal integration site attB, and the PAI‐specific attachment site attP. We show that PAI III536 IntB, but not IntA, mediates PAI III536 integration. Studies of integrative recombination sites of both PAIs show that, when using a large cognate attP site (839 bp for PAI II536 and 268 bp for PAI III536), PAI II536 and III536 attB sites could be reduced to 16 bp and 20 bp, respectively, without affecting recombination. Further reduction to 14 bp for PAI II536 and 13 bp for PAI III536 diminished recombination efficiency. Surprisingly, attP sites could also be reduced to 14 bp (PAI II536) and 20 bp (PAI III536). The integration host factor (IHF) and the DNA‐bending HU protein do not influence PAI II536 recombination, but IHF enhances PAI‐III536 excision and negatively affects its integration. These data suggest that PAI intasomes differ from those of lambda and P4 integrase paradigms.
Patterns of chromosomal fragmentation due to uracil‐DNA incorporation reveal a novel mechanism of replication‐dependent double‐stranded breaks
Authors: Kouzminova Elena A. , Kuzminov Andrei 
Published: February 2008

SummaryThere is growing evidence that spontaneous chromosomal fragmentation, one of the main contributors to genetic instability, is intimately linked to DNA replication. In particular, we proposed before that uracil incorporation in DNA triggers chromosomal fragmentation due to replication fork collapse at uracil‐excision intermediates. We tested predictions of this model at the chromosomal level in the dut mutants of Escherichia coli, by determining the relationship between DNA replication and patterns of fragmentation in defined chromosomal segments. Here we show that the uracil‐DNA‐triggered chromosomal fragmentation: (i) has a gradient that parallels the replication gradient, (ii) shows polarity within defined segments pointing towards replication origins and (iii) reorganizes to match induced replication gradients, confirming its dynamic pattern. Unexpectedly, these fragmentation patterns not only support the replication fork collapse model, but also reveal another mechanism of the replication‐dependent chromosomal fragmentation triggered by uracil excision.
Abnormal IFN‐γ‐dependent immunoproteasome modulation by Trypanosoma cruzi‐infected macrophages
Authors: BERGERON M. , BLANCHETTE J. , ROULEAU P. , OLIVIER M. 
Published: February 2008

SUMMARY Proteasomes are the main producers of Ag loaded onto MHC class I molecules. Following IFN‐γ stimulation however, the constitutive subunits of the proteasome are replaced by the immunosubunits low molecular weight protein 2 (LMP2), multicatalytic endopeptidase complex‐like 1 and low molecular weight protein 7 (LMP7), which generally heighten the immunogenecity of proteasome generated epitopes. Given that Trypanosoma cruzi, the aetiological agent of Chagas’ disease, elicits a Thelper1 response from its host if the infection is to be contained, the aim of this study was to verify whether this parasite modulates J774 and B10R mouse macrophage (ΜΦ) immunoproteasome subunit and MHC class I expressions and, if so, identify the mechanism(s) responsible for that modulation. Results show that T. cruzi infection of mouse ΜΦ reduces IFN‐γ‐mediated immunoproteasome synthesis, along with MHC class I mRNA synthesis and cell surface expression. The infection by T. cruzi induces the release of reactive oxygen species (ROS) from ΜΦ, and those ROS significantly inhibit protein tyrosine phosphatase activity, thereby leading to the activation of the SAPK/JNK signalling pathway, which is responsible for the observed IFN‐γ‐mediated immunoproteasome synthesis and MHC class I down‐regulation. To our knowledge, this is the first report that specifically identifies a mechanism by which a pathogen achieves immunoproteasome down‐modulation.
Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites inArabidopsisrosettes to a progressive decrease of temperature in the non‐freezing range
Authors: USADEL BJÖRN , BLÄSING OLIVER E. , GIBON YVES , POREE FABIEN , HÖHNE MELANIE , GÜNTER MANUELA , TRETHEWEY RICHARD , KAMLAGE BEATE , POORTER HENDRIK , STITT MARK 
Published: February 2008

ABSTRACTThis paper characterizes the transcriptional and metabolic response of a chilling‐tolerant species to an increasingly large decrease of the temperature.ArabidopsisCol‐0 was grown at 20 °C and transferred to 17, 14, 12, 10 or 8 °C for 6 and 78 h, before harvesting the rosette and profiling >22 000 transcripts, >20 enzyme activities and >80 metabolites. Most parameters showed a qualitatively similar response across the entire temperature range, with the amplitude increasing as the temperature decreased. Transcripts typically showed large changes after 6 h, which were often damped by 78 h. Genes were induced for sucrose, proline, raffinose, tocopherol and polyamine synthesis, phenylpropanoid and flavonoid metabolism, fermentation, non‐phosphorylating mitochondrial electron transport, RNA processing, and protein synthesis, targeting and folding. Genes were repressed for carbonic anhydrases, vacuolar invertase, and ethylene and jasmonic acid signalling. While some enzyme activities and metabolites changed rapidly, most changed slowly. After 6 h, there was an accumulation of phosphorylated intermediates, a shift of partitioning towards sucrose, and a perturbation of glycine decarboxylation and nitrogen metabolism. By 78 h, there was an increase of the overall protein content and many enzyme activities, a general increase of carbohydrates, organic and amino acids, and an increase of many stress‐responsive metabolites including raffinose, proline, tocopherol and polyamines. When the responses of transcripts and metabolism were compared, there was little agreement after 6 h, but considerable agreement after 78 h. Comparison with the published studies indicated that much, but not all, of the response was orchestrated by the CBF programme. Overall, our results showed that transcription and metabolism responded in a continuous manner across a wide range of temperatures. The general increase of enzyme activities and metabolites emphasized the positive and compensatory nature of this response.
An Association Analysis Between a Silent C558T Polymorphism at the Pig Vascular Cell Adhesion Molecule 1 Locus and Sow Reproduction and Piglet Survivability Traits
Authors: Ramirez O , Tomàs A , Casellas J , Blanch M , Noguera JL , Amills M 
Published: February 2008

ContentsThe vascular cell adhesion molecule 1 (VCAM1) has a strong influence on embryonic development and on the formation of the umbilical cord and placenta. These developmental processes are crucial to ensure the success of pregnancy. In this work, we have identified two T306A and C558T single nucleotide polymorphisms (SNP) at exons 2 and 3 of the pig VCAM1 locus, respectively. The T306A substitution involves a non conservative Asn to Lys replacement at amino acid position 102, whereas the C558T polymorphism is synonymous. An in silico prediction of the consequences of the Asn102→Lys102 mutation with the PolyPhen software revealed that it is not deleterious. The T306A SNP segregated in the Iberian, Piétrain, Duroc, Large White and Landrace breeds as well as in European wild boars. The C558T SNP also segregated and most of commercial standard breeds. The genotyping of the C558T SNP in an Iberian × Meishan intercross allowed to find a suggestive association (Bonferroni threshold, p < 0.004) between C558T genotype and time the newborn piglet needs to reach the udder (p = 0.013) as well as a significant one with time to make the first ingestion of colostrum (p = 0.003). The biological basis of these associations remains unclear and they should be interpreted with caution.