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Phase Variation (phase + variation)
Selected AbstractsPhase variable type III restriction-modification systems of host-adapted bacterial pathogensMOLECULAR MICROBIOLOGY, Issue 6 2007Kate L. Fox Summary Phase variation, the high-frequency on/off switching of gene expression, is a common feature of host-adapted bacterial pathogens. Restriction-modification (R-M) systems, which are ubiquitous among bacteria, are classically assigned the role of cellular defence against invasion of foreign DNA. These enzymes are not obvious candidates for phase variable expression, a characteristic usually associated with surface-expressed molecules subject to host immune selection. Despite this, numerous type III R-M systems in bacterial pathogens contain repetitive DNA motifs that suggest the potential for phase variation. Several roles have been proposed for phase variable R-M systems based on DNA restriction function. However, there is now evidence in several important human pathogens, including Haemophilus influenzae, Neisseria meningitidis and Neisseria gonorrhoeae, that these systems are ,phasevarions' (phasevariable regulons) controlling expression of multiple genes via a novel epigenetic mechanism. [source] High relative content of lysophospholipids of Helicobacter pylori mediates increased risk for ulcer diseaseFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2005Tone Tannaes Abstract Helicobacter pylori phospholipase A (OMPLA) degrades bacterial membrane phospholipids to lysophospholipids. High levels of lysophospholipids are associated with higher hemolytic activity, increased release of urease and vacA and better adherence to epithelial cells in vitro. The phospholipase A gene (pldA) displays phase variation due to a slippage in a homopolymeric tract. The aim of this study was to determine if the relative amount of lysophospholipids in the cell wall is associated with ulcer disease, and to further investigate the significance of pldA phase variation. H. pylori isolates of 40 patients were examined. The relative lysophospholipid content of each isolate was determined and the pldA gene was sequenced. The study indicated that H. pylori can regulate its OMPLA activity by phase variation in the pldA gene or by protein level regulation among phase variants in the pldA,ON' status. We found a significant difference between the relative amount of lysophospholipids of the ulcer group and the non-ulcer group (p= 0.022). When the lysophospholipid/phospholipid ratios were compared with outcome, the OR for ulcer disease was 9.0 (95% CI 1.6,49.4; p= 0.014). Isolates with a high OMPLA activity are significantly associated with patients with ulcer disease. [source] From grid cells to place cells: A mathematical modelHIPPOCAMPUS, Issue 12 2006Trygve Solstad Abstract Anatomical connectivity and recent neurophysiological results imply that grid cells in the medial entorhinal cortex are the principal cortical inputs to place cells in the hippocampus. The authors propose a model in which place fields of hippocampal pyramidal cells are formed by linear summation of appropriately weighted inputs from entorhinal grid cells. Single confined place fields could be formed by summing input from a modest number (10,50) of grid cells with relatively similar grid phases, diverse grid orientations, and a biologically plausible range of grid spacings. When the spatial phase variation in the grid-cell input was higher, multiple, and irregularly spaced firing fields were formed. These observations point to a number of possible constraints in the organization of functional connections between grid cells and place cells. © 2006 Wiley-Liss, Inc. [source] Spin-echo MRI using ,/2 and , hyperbolic secant pulses,MAGNETIC RESONANCE IN MEDICINE, Issue 1 2009Jang-Yeon Park Abstract Frequency-modulated (FM) pulses have practical advantages for spin-echo experiments, such as the ability to produce a broadband , rotation, with an inhomogeneous radiofrequency (RF) field. However, such use leads to a nonlinear phase of the transverse magnetization, which is why FM pulses like the hyperbolic secant (HS) pulse are not commonly used for multislice spin-echo magnetic resonance imaging (MRI). Here, a general theory and methods are described for conventional spin-echo imaging using a , HS pulse for refocusing. Phase profiles produced by the HS pulse are analytically described. The analysis is extended to yield the specific relationships between pulse parameters and gradients, which must be satisfied to compensate the nonlinear phase variation produced with a spin-echo sequence composed of ,/2 and , HS pulses (the ,/2 HS , , HS sequence). The latter offers advantages for multislice spin-echo MRI, including excellent slice-selection and partial compensation for RF inhomogeneity. Furthermore, it can be implemented with a shorter echo time and lower power deposition than a previously described method using a pair of , HS pulses. Magn Reson Med 61:175,187, 2009. © 2008 Wiley-Liss, Inc. [source] LeuX tRNA-dependent and -independent mechanisms of Escherichia coli pathogenesis in acute cystitisMOLECULAR MICROBIOLOGY, Issue 1 2008Thomas J. Hannan Summary Uropathogenic Escherichia coli (UPEC) contain multiple horizontally acquired pathogenicity-associated islands (PAI) implicated in the pathogenesis of urinary tract infection. In a murine model of cystitis, type 1 pili-mediated bladder epithelial invasion and intracellular proliferation are key events associated with UPEC virulence. In this study, we examined the mechanisms by which a conserved PAI contributes to UPEC pathogenesis in acute cystitis. In the human UPEC strain UTI89, spontaneous excision of PAI IIUTI89 disrupts the adjacent leuX tRNA locus. Loss of wild-type leuX -encoded tRNA5Leu significantly delayed, but did not eliminate, FimB recombinase-mediated phase variation of type 1 pili. FimX, an additional FimB-like, leuX -independent recombinase, was also found to mediate type 1 pili phase variation. However, whereas FimX activity is relatively slow in vitro, it is rapid in vivo as a non-piliated strain lacking the other fim recombinases rapidly expressed type 1 pili upon experimental infection. Finally, we found that disruption of leuX, but not loss of PAI IIUTI89 genes, reduced bladder epithelial invasion and intracellular proliferation, independent of type 1 piliation. These findings indicate that the predominant mechanism for preservation of PAI IIUTI89 during the establishment of acute cystitis is maintenance of wild-type leuX, and not PAI IIUTI89 gene content. [source] Phase variable type III restriction-modification systems of host-adapted bacterial pathogensMOLECULAR MICROBIOLOGY, Issue 6 2007Kate L. Fox Summary Phase variation, the high-frequency on/off switching of gene expression, is a common feature of host-adapted bacterial pathogens. Restriction-modification (R-M) systems, which are ubiquitous among bacteria, are classically assigned the role of cellular defence against invasion of foreign DNA. These enzymes are not obvious candidates for phase variable expression, a characteristic usually associated with surface-expressed molecules subject to host immune selection. Despite this, numerous type III R-M systems in bacterial pathogens contain repetitive DNA motifs that suggest the potential for phase variation. Several roles have been proposed for phase variable R-M systems based on DNA restriction function. However, there is now evidence in several important human pathogens, including Haemophilus influenzae, Neisseria meningitidis and Neisseria gonorrhoeae, that these systems are ,phasevarions' (phasevariable regulons) controlling expression of multiple genes via a novel epigenetic mechanism. [source] Identification of a gene (lpt-3) required for the addition of phosphoethanolamine to the lipopolysaccharide inner core of Neisseria meningitidis and its role in mediating susceptibility to bactericidal killing and opsonophagocytosisMOLECULAR MICROBIOLOGY, Issue 4 2002Fiona G. Mackinnon Summary We have identified a gene, lpt-3, that is required for the addition of phosphoethanolamine to the 3-position (PEtn-3) on the , -chain heptose (HepII) of the inner core lipopolysaccharide (LPS) of Neisseria meningitidis (Nm). The presence of this PEtn-3 substituent is characteristic of the LPS of a majority (, 70%) of hypervirulent Nm strains, irrespective of capsular serogroup, and is required for the binding of a previously described monoclonal antibody (mAb B5) to a surface-accessible epitope. All strains of Nm that have PEtn-3 possess the lpt-3 gene. In some lpt-3 -containing strains, the 3-position on HepII is preferentially substituted by glucose instead of PEtn, the result of lgtG phase variation mediated by slippage of a homopolymeric tract of cytidines. Inactivation of lpt-3 resulted in loss of PEtn-3, lack of reactivity with mAb B5 and conferred relative resistance to bactericidal killing and opsonophagocytosis by mAb B5 in vitro. Thus, the identification of lpt-3 has facilitated rigorous genetic, structural and immunobiological definition of an immunodominant epitope that is a candidate immunogen for inclusion in an LPS-based vaccine to protect against invasive meningococcal disease. [source] Curve registration by local regressionTHE CANADIAN JOURNAL OF STATISTICS, Issue 1 2000A. Kneip Abstract Functional data analysis involves the extension of familiar statistical procedures such as principal-components analysis, linear modelling and canonical correlation analysis to data where the raw observation is a function x, (t). An essential preliminary to a functional data analysis is often the registration or alignment of salient curve features by suitable monotone transformations hi(t). In effect, this conceptualizes variation among functions as being composed of two aspects: phase and amplitude. Registration aims to remove phase variation as a preliminary to statistical analyses of amplitude variation. A local nonlinear regression technique is described for identifying the smooth monotone transformations hi, and is illustrated by analyses of simulated and actual data. L'analyse de données se présentant sous la forme de fonctions x,(t) repose sur la généralisation d'outils statistiques familiers tels que l'analyse en composantes principales, les modèles linéaires et l'analyse des corrélations canoniques. L'étalonnage des caractéristiques saillantes des courbes à l'aide de transformations monotones hi(t) constitue souvent un préiequis essentiel au traitement statistique de telles données. II découle d'une décomposition en deux parties de la variation entre les fonctions observées: une phase et une amplitude. L'étalonnage vise à éliminer la première de ces deux sources de variation, ce qui permet de concentrer ensuite l'analyse sur la seconde. Les auteurs décrivent ici une technique de régression non linéaire locale facilitant l'identification de transformations monotones lisses hi appropriées. Leur propos est illustré à l'aide de données réelles et simulées. [source] Operator-oriented CRS interpolationGEOPHYSICAL PROSPECTING, Issue 6 2009German Hoecht ABSTRACT In common-reflection-surface imaging the reflection arrival time field is parameterized by operators that are of higher dimension or order than in conventional methods. Using the common-reflection-surface approach locally in the unmigrated prestack data domain opens a potential for trace regularization and interpolation. In most data interpolation methods based on local coherency estimation, a single operator is designed for a target sample and the output amplitude is defined as a weighted average along the operator. This approach may fail in presence of interfering events or strong amplitude and phase variations. In this paper we introduce an alternative scheme in which there is no need for an operator to be defined at the target sample itself. Instead, the amplitude at a target sample is constructed from multiple operators estimated at different positions. In this case one operator may contribute to the construction of several target samples. Vice versa, a target sample might receive contributions from different operators. Operators are determined on a grid which can be sparser than the output grid. This allows to dramatically decrease the computational costs. In addition, the use of multiple operators for a single target sample stabilizes the interpolation results and implicitly allows several contributions in case of interfering events. Due to the considerable computational expense, common-reflection-surface interpolation is limited to work in subsets of the prestack data. We present the general workflow of a common-reflection-surface-based regularization/interpolation for 3D data volumes. This workflow has been applied to an OBC common-receiver volume and binned common-offset subsets of a 3D marine data set. The impact of a common-reflection-surface regularization is demonstrated by means of a subsequent time migration. In comparison to the time migrations of the original and DMO-interpolated data, the results show particular improvements in view of the continuity of reflections events. This gain is confirmed by an automatic picking of a horizon in the stacked time migrations. [source] Review of generative models for the narrowband land mobile satellite propagation channelINTERNATIONAL JOURNAL OF SATELLITE COMMUNICATIONS AND NETWORKING, Issue 4 2008F. P. Fontan Abstract The land mobile satellite (LMS) propagation channel is frequently described using statistical models. These models usually make different assumptions regarding the behavior of the direct signal, the diffuse multipath component and the shadowing effects. This paper analyzes the theoretical formulation and implementation of time-series synthesizers based on three typical statistical models: Loo, Corazza,Vatalaro and Suzuki, describing their similarities and differences. The discussion is not limited to the amplitude of the complex envelope but also to the phase variations and Doppler spectra. Finally, guidelines are also provided for comparing model parameters supplied by different authors. Copyright © 2008 John Wiley & Sons, Ltd. [source] | |||||||||||||