Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “phase variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources
PubMed1999

Antigenic variation of the class I outer membrane protein in hyperendemic Neisseria meningitidis strains in the netherlands.

Since 1980, the number of cases of meningococcal disease caused by serogroup B isolates with the P1.4 serosubtype has greatly increased in The Netherlands. Screening for this serosubtype in the strain collection of The Netherlands Reference Laboratory for Bacterial Meningitis revealed that a low number of P1.4 strains had been present in the Dutch meningococcal population since 1965. Genotyping of P1.4 strains showed that one cluster of strains, the hyperendemic lineage III (D. A. Caugant et al., J. Infect. Dis. 162:867-874, 1990), is responsible for the increase since 1980. The diversity of the porA genes, which encode the P1 protein on which serosubtyping is based, was studied for genotypically different P1.4 strains and for lineage III strains expressing antigenically different P1 proteins. Sequence analysis showed that porA genes of genotypically distinct strains that express antigenically indistinguishable P1 proteins are identical only in the epitope-encoding region, suggesting that this region has spread through the meningococcal population via horizontal gene transfer. Analysis of porA genes of lineage III strains showed that both horizontal gene transfer and partial deletion of the epitope-encoding region may contribute to the different antigenic properties for P1 of these strains. Phase variation of expression of the porA gene seems to account for most nonreacting strains. These results show that serosubtyping may underestimate the rise of a hyperendemic clone.

Amino Acid Sequence↗
PubMed1993

A novel determinant (comA) essential for natural transformation competence in Neisseria gonorrhoeae and the effect of a comA defect on pilin variation.

A novel genetic determinant (comA) has been identified and found to be required for the transformation of piliated Neisseria gonorrhoeae. Mutants in comA of strain MS11 grow normally and are DNA-uptake proficient but blocked in the translocation of DNA into the cytoplasm. Here we show by site-specific mutagenesis and genetic complementation that only one of two open reading frames identified in comA is essential for competence: it encodes a protein (ComA) with a predicted size of 74 kDa. The comA gene maps upstream of the iga locus and is transcribed in the opposite orientation, probably under the control of a putative sigma 54-type promoter. While DNA probes specific for the N. gonorrhoeae iga locus reveal only a little cross-reactivity with commensal Neisseria species, the neighbouring comA gene appears to be present in most of them. ComA fusion proteins were obtained by in vitro translation. The synthesized gene products migrated atypically in SDS gels indicating its strong hydrophobicity. Several transmembrane alpha-helices were predicted from the amino acid sequence of ComA which, in the context of an observed sequence similarity with other inner membrane proteins, suggests a location for the protein in the inner membrane. Using piliated and non-piliated comA mutants the consequences of transformation deficiency on pilin phase variation were assessed. We show that the comA defect affects some but not all types of DNA rearrangements associated with pilE variation. The results are in agreement with previous observations supporting the notion that multiple recombination pathways contribute to the variability of pilE.

Amino Acid Sequence↗
PubMed2002

Identification of a second Listeria secA gene associated with protein secretion and the rough phenotype.

We describe the identification and characterization of a second secA gene in Listeria monocytogenes. This gene, termed secA2, is involved in smooth-rough phenotypic variation and secA2 expression contributes to bacterial virulence. Spontaneous rough (R-) variants of L. monocytogenes grow in chains and form rough colonies on solid media. A subset of R-variants, classified here as type I, also shows reduced secretion of an autolysin, p60. We find that disruptions and in frame deletions in secA2 confer phenotypes identical to those of spontaneous type I R-variants. Additionally, the secA2 genes from two spontaneous type I R-variants encoded truncated SecA2 proteins. Mutations were not found in the secA2 genes from the remaining five independent R-variants, four of which showed a distinct (type II) rough morphology and secreted wild-type levels of p60. Expression of an epitope-tagged SecA2 in the DeltasecA2 strain and a spontaneous R-variant restored normal cell septation and smooth colony morphology. These data suggest that mutations in both secA2 and other genes contribute to smooth-rough phase variation in L. monocytogenes. Expression of the full-length SecA2 also promotes secretion of p60 and a set of additional L. monocytogenes proteins. We hypothesize that SecA2-dependent protein secretion plays a role in the colonization of environmental and host surfaces.

Adenosine Triphosphatases↗
PubMed2003

Upstream short sequence repeats regulate expression of the alpha C protein of group B Streptococcus.

Group B streptococci (GBS) express a family of repeat-containing surface proteins, the prototype of which is the alpha C protein expressed in type Ia/C strain A909. We have isolated a series of mutant GBS strains by mouse-passage of A909 that do not produce normal levels of the alpha C protein. Polymerase chain reaction amplification and sequencing of the gene encoding the alpha C protein, bca, from four mutant strains revealed the presence of a full-length gene in each strain. However, Northern and RT-PCR analysis revealed greatly reduced levels of RNA encoding the alpha C protein. Sequence analysis of the mutant genes found the coding region unchanged from the wild-type gene in each case, but variation was observed in a specific locus located 110 bp upstream of the start codon. The presence of a 5-nucleotide repeat, AGATT, and a string of adenine residues mark this locus. Both deletion and expansion of the AGATT motif were associated with the complete null phenotype. Deletions in the string of adenine residues were associated with both a decreased-production phenotype and a complete null phenotype. Cloning of this upstream region into a green-fluorescent protein (GFP) reporter system in GBS demonstrated promoter activity that was completely abolished by changes in the pentanucleotide repeat or adenine string. Primer extension studies of the wild-type strain revealed one dominant and two minor transcription start sites. Primer extension studies of the null and low-expression mutant strains revealed that the dominant transcript is completely absent in each mutant. The short sequence repeat locus is located at position - 55 to - 78 relative to the start site of the dominant transcript. We have demonstrated in vitro phase variation in expression of the alpha C protein associated with variation at the pentanucleotide repeat locus. We conclude that this short sequence repeat motif is located upstream of the dominant promoter for the alpha C protein and represents a regulatory site for alpha C protein expression. This is the first evidence of transcriptional regulation by short-sequence repeats in a Gram-positive organism.

Animals↗
PubMed1998

Differential temperature modulation by H-NS of the fimB and fimE recombinase genes which control the orientation of the type 1 fimbrial phase switch.

Phase variation of type 1 fimbriation in Escherichia coli is associated with the inversion of a 314-bp DNA element. This DNA switch directs transcription of fimA, encoding the major type 1 fimbrial subunit, in the on orientation but not in the off orientation. Inversion of the DNA element requires either FimB (confers both on and off orientations) or FimE (confers off orientation). Here we show, by chromosomally located fimB- and fimE-lacZ cassettes in isogenic strain sets differing only in the hns locus, how the global regulator H-NS affects the expression of type 1 fimbriae. H-NS was found to downregulate fimB and fimE in a temperature-dependent manner which affected the genes inversely at 30 degrees C and 37 degrees C. By gel-retardation assays H-NS binding was demonstrated to the regions containing the fimB promoter and the fimE promoter, respectively. In vitro recombination analysis suggested no direct involvement of H-NS in the inversion of the phase switch. Rather than directly affecting the switching process per se, it appeared that the orientation of this element was affected by the differential temperature modulation of H-NS of the fimB and fimE genes. Taken together the results suggest that H-NS modulates expression of type 1 fimbriae in a way which seems to favor a fimbriate state at the mammalian body temperature.

Bacterial Proteins↗
PubMed1994

Circadian rhythms of paracetamol metabolism in healthy subjects; a preliminary report.

Paracetamol was used as a "probe" drug to study the circadian rhythms of metabolite ratios in man. Paracetamol was orally administered to six volunteers at different times of day, 0-8 h and 8-24 h urine samples being measured for sulphate and glucuronide formation. Results showed a wide interindividual variation in paracetamol metabolite excretion among the six subjects. However, when a 500 mg dose was administered, free paracetamol excretion was minimal when the dose was given at 12.00 h and maximal when given at 20.00 h for the 0-8 h collection period. Sulphate excretion rose slightly at night and decreased gradually during the day. Glucuronide excretion was greatest with drug administration at 16.00 h and least if paracetamol was ingested at 08.00 h. The 8-24 h profiles were roughly similar. At a higher dose (1500 mg), free paracetamol excretion showed a minimum from dosing at 20.00 h and a maximum from dosing at 24.00 h in both 0-8 h and 8-24 h collections, while the sulphate conjugate peaked for doses at 20.00 h and 8.00 h with collections at 0-8 h and 8-24 h respectively. The glucuronide conjugate was maximal for paracetamol administration at 16.00 h for both 0-8 h and 8-24 h collections. There appears to be a 12 hour phase variation in excretion; this may result from circadian rhythms in absorption and enzyme activities. These parameters may also affect metabolism at higher dose levels, so that the hepatotoxicity of paracetamol could vary with the time of dose.

Acetaminophen↗
PubMed1992

The amplitude of circadian FEV1 variation suitable for phase determination by cosinor analysis in stable asthmatic children.

To elucidate the criterion for amplitude of circadian FEV1 variation suitable for phase analysis, six FEV1 measurements within a day were made on 346 days in 125 stable asthmatic children aged 8 to 12 years. Since coefficient of variation (CV) of FEV1 within a day in nonasthmatic children in our laboratory is less than 5 percent, circadian FEV1 variations were divided into CV greater than or equal to 5 percent and CV less than 5 percent groups. Forty-two (12 percent) variations with significant fit of cosinor rhythm were CV greater than or equal to 5 percent. Troughs in 32 (76 percent) variations of the 42 were distributed between 12 PM and 6 AM, and the deviation was highly significant against a uniform distribution (p less than 0.001). This was consistent with nocturnal asthma. Thirty-five (10 percent) variations with significant fit of cosinor rhythm were CV less than 5 percent. Troughs in 12 (34 percent) variations of the 35 were distributed between 12 PM and 6 AM, and the deviation from a uniform distribution was nonsignificant. These suggest that 5 percent or more of CV of FEV1 may be clinically suitable for analysis of circadian FEV1 variation.

Asthma↗
PubMed1991

In situ expression and localization of Neisseria gonorrhoeae opacity proteins in infected epithelial cells: apparent role of Opa proteins in cellular invasion.

During natural infection, gonococcal opacity proteins (Opa) undergo rapid phase variation, but how this phenomenon contributes to the virulence of the bacteria is not well understood. In the present immunomorphological study we examined the actual Opa status of individual gonococci during various stages of gonococcal infection of Chang epithelial cells, by probing ultrathin sections of infected specimens with Opa-specific monoclonal antibodies. Our results demonstrate a heterogeneous Opa expression during the initial interaction of the bacteria, but an almost 100% expression of one of the probed Opas during their secondary attachment and entry into the host cells, suggesting a role for distinct Opas in cellular penetration. The association between Opa expression, tight attachment, and bacterial invasion into the host cells could be confirmed with isogenic variants that expressed different Opa proteins. Once inside the epithelial cells, both morphologically intact, Opa positive and morphologically disintegrated, Opa negative bacteria were observed. The loss of Opa immunoreactivity in intracellular gonococci could not be related to the presence of a particular Opa protein, but could be mimicked by incubating the organisms with extracts of sonicated uninfected epithelial cells, suggesting that it was caused by host cell proteolytic activity. Taken together, our data suggest that Opa phase transitions confer a functional adaptation of the bacteria enabling host cell penetration.

Antigens, Bacterial↗
PubMed2002

Immunologic and genetic characterization of lipooligosaccharide variants in a Neisseria meningitidis serogroup C strain.

Neisseria meningitidis shows great variation in expression of structurally different lipooligosaccharides (LOS) on its cell surface. To better understand the LOS diversity that may occur within an individual strain, a group C wild-type strain, BB305-Tr4, and two stable isogenic LOS variants, Tr5 and Tr7, were selected for this study. SDS-PAGE analysis showed a size reduction of Tr5 and Tr7 LOS compared to that of Tr4. Immunoblotting showed that parental Tr4 LOS reacted with L1, L2 and L3,7 antibodies, variant Tr5 LOS with L1 and L6 antibodies, while Tr7 LOS was non-typeable. Genetic analysis showed that the gene organization at the lgt-1 locus in the three strains was lgtZ,C,A,B,H4 in Tr4, lgtZ,C,A,H4 in Tr5 and lgtZ,C,A,H9 in Tr7. The genetic differences in the three strains were consistent with their phenotypic changes. Sequence comparison revealed two independent recombination events. The first was the recombination of repeated DNA fragments in the flanking regions to delete lgtB in Tr5. The second was the recombination of a fragment of two genes, lgtB and lgtH4, to create an inactive lgtH9 allele with a mosaic structure in Tr7. These findings suggest that besides phase variation, homologous recombination can contribute to the genetic diversity of the lgt locus and to the generation of LOS variation in N. meningitidis.

Base Sequence↗
PubMed2001

Acute and convalescent changes in plasma homocysteine concentrations in acute coronary syndromes.

BACKGROUND: Raised plasma homocysteine is a risk factor for coronary artery disease. Patients with myocardial infarction or unstable angina show greater activation of coagulation, greater troponin release, and a worse outcome. OBJECTIVE: To examine variations in plasma homocysteine concentration in relation to C reactive protein (CRP) in patients presenting with acute coronary syndromes. METHODS: Consecutive patients presenting with acute myocardial infarction (22) and unstable angina pectoris (12) were studied. Plasma samples were obtained on admission (before clinical intervention), on days 2, 7, and 28, and again six months after admission. Plasma homocysteine, assayed by high performance liquid chromatography, and CRP were both determined at the same time points. Changes were assessed by analysis of variance. RESULTS: CRP concentrations showed a classical rise on day 2, followed by a gradual decline to normal values taken at six months from admission in both myocardial infarction (p < 0.0001) and unstable angina (p = 0.02). Homocysteine concentrations in myocardial infarction (median, 25th to 75th interquartile range) were: 11.9 (10.7 to 12.6), 11.5 (9.1 to 13.4), 12.1 (11.4 to 14.1), 12.4 (11.1 to 14.4), and 12.1 (11.2 to 14.0) micromol/l, for days 1, 2, 7, 28, and 180, respectively (p = 0.02). Significant differences were observed only between day 2 and day 7 (p < 0.05). The final homocysteine measurement was not different from the admission level. Homocysteine concentrations in unstable angina did not differ between admission and convalescence (12.5 (9.1 to 14.5) micromol/l and 12.3 (7.7 to 14.9) micromol/l, respectively). CONCLUSIONS: Plasma homocysteine concentrations are minimally influenced by acute phase variations with reliable measurements obtained on admission in patients with myocardial infarction and unstable angina.

Acute Disease↗
PubMed1999

Flow distortion and signal loss in spiral imaging.

The effect of in-plane motion on the point spread function (velocity PSF) in spiral imaging is studied experimentally and derived mathematically and is shown to consist of a smoothed, trailing edge and fringes around the leading edge. The velocity PSF remains largely in phase with the static PSF, consistent with the absence of signal loss by motion-related phase shifts in central k space. However, single-shot spiral imaging gives no clear improvement in complex and turbulent flow signal uniformity compared with echo-planar imaging with early, central k-space acquisition, which requires explanation given the spiral's earlier coverage of central k space. Alternate leading-edge fringes of the spiral's velocity PSF are in antiphase to the source, and cancellation may occur when these overlap other in-phase signals. Phase variations toward peripheral k space in turbulent flow also cause distortion. It is concluded that spiral imaging may lose complex and turbulent flow signals because of complex PSF distortion.

Algorithms↗
PubMed2006

From grid cells to place cells: a mathematical model.

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.

Animals↗
PubMed1992

Sequence-specific interaction of the Salmonella Hin recombinase in both major and minor grooves of DNA.

The Hin recombinase of Salmonella catalyzes a site-specific recombination event which leads to flagellar phase variation. Starting with a fully symmetrical recombination site, hixC, a set of 40 recombination sites which vary by pairs of single base substitutions was constructed. This set was incorporated into the Salmonella-specific bacteriophage P22 based challenge phage selection and used to define the DNA sequence determinants for the binding of Hin to DNA in vivo. The critical sequence-specific contacts between a Hin monomer and a 13 bp hix half-site are at two T:A base pairs in the major groove of the DNA which are separated by one base pair, and two consecutive A:T contacts in the minor groove. The base substitutions in the major groove recognition portion which were defective in binding Hin still retained residual binding capability in vivo, while the base pair substitutions affecting the minor groove recognition region lost all in vivo binding. Using in vitro binding assays, Hin was found to bind to hix symmetrical sites with A:T base pairs or I:C base pairs in the minor groove recognition sequences, but not to G:C base pairs. In separate in vitro binding assays, Hin was equally defective in binding to either a G:C or a I:C contact in a major groove recognition sequence. Results from in vitro binding assays to hix sites in which 3-deazaadenine was substituted for adenine are consistent with Hin making a specific contact to either the N3 of adenine or O2 of thymine in the minor groove within the hix recombination site on each symmetric half-site. These results taken with the results of previous studies on the DNA binding domain of Hin suggest a sequence-specific minor groove DNA binding motif.

Base Sequence↗
PubMed1993

Variable opacity (Opa) outer membrane proteins account for the cell tropisms displayed by Neisseria gonorrhoeae for human leukocytes and epithelial cells.

Opacity proteins (Opa) of Neisseria gonorrhoeae, a family of variant outer membrane proteins implicated in pathogenesis, are subject to phase variation. In strain MS11, 11 different opa gene alleles have been identified, the expression of which can be turned on and off independently. Using a reverse genetic approach, we demonstrate that a single Opa protein variant of strain MS11, Opa50, enables gonococci to invade epithelial cells. The remaining variant Opa proteins show no, or very little, specificity for epithelial cells but instead confer interaction with human polymorphonuclear neutrophils (PMNs). Thus, depending on the opa allele expressed, gonococci are capable of invading epithelial cells or of interacting with human leukocytes. The respective properties of Opa proteins are maintained independent of the gonococcal strain; thus, the specificity for epithelial cells or leukocytes is intrinsic to Opa proteins. Significant homology exists in the surface exposed variable regions of two invasion supporting Opa proteins from independent strains. Efficient epithelial cell invasion is favoured by high level Opa production, however, a 10-fold reduction still allows significant invasion by gonococci. In contrast, recombinant Escherichia coli expressing Opa proteins adhered or invaded poorly under similar experimental conditions, thus indicating that additional factors besides Opa are required in the Opa-mediated interaction with human cells.

Amino Acid Sequence↗
PubMed2002

Breath-hold three-dimensional true-FISP imaging of coronary arteries using asymmetric sampling.

PURPOSE: To evaluate the feasibility of using asymmetric sampling in a three-dimensional, magnetization-prepared, segmented true-FISP (fast imaging with steady-state precession) sequence in order to reduce the sensitivity to resonance offsets, while simultaneously improving imaging speed. MATERIALS AND METHODS: Asymmetric sampling reduces the repetition time, leading to reduced resonance offset effects and improved resolution in a fixed imaging time. However, it introduces additional phase terms due to blood flow, which can cause image artifacts. Computer simulations were performed to study the off-resonance and flow effects of asymmetric sampling in true-FISP. Coronary artery imaging was performed in healthy volunteers. RESULTS: Simulations and volunteer studies show that image artifacts due to flow-induced phase variations may be acceptable at low velocities. Volunteer studies demonstrate that relatively high-resolution coronary artery images can then be acquired within a single breath-hold with segmented three-dimensional true-FISP imaging using data asymmetry in the readout direction. CONCLUSION: Asymmetric sampling is a useful modification to true-FISP for reducing the off-resonance artifacts and improving imaging speed when the flow velocities are small.

Adult↗
PubMedDate not supplied

Phase-constrained data extrapolation method for reduction of truncation artifacts.

The authors present an improvement to a sigma-filter extrapolation method for the reconstruction of magnetic resonance (MR) images from symmetric discrete Fourier data. By making use of the phase information in the image data, the proposed method can overcome the data inconsistency problem of the original method for handling MR image data with large phase variations, such as those obtained in gradient-echo pulse sequences. Reconstruction results show that its performance is comparable with that of the modified complex sigma-filter method proposed previously to handle the inconsistency problem. However, the new approach has the advantage of reducing computation time by a factor of two with use of a sigma filter applied to real instead of complex images. It is expected that this method will be more practical for use in clinical MR imaging systems.

Algorithms↗
PubMed2003

Radial alternating TE sequence for faster fat suppression.

This study describes a steady-state sequence that uses a radial k-space trajectory and alternating echo times (TEs) between even and odd k-space views. The sequence generated a single data set that was used to reconstruct images with inherent fat suppression. This fat suppression results from the fat phase variation in alternate echoes giving rise to cancellation in the central portion of k-space. This new fat-suppression method provides inherent fat suppression in half the acquisition time relative to the radial two-point Dixon method. The improvement in k-space sampling efficiency is demonstrated in phantom and clinical images, and through measured point-spread functions (PSFs). As a result, the radial alternating TE sequence offers improved temporal resolution over a radial version of the two-point Dixon sequence by requiring fewer total projections to obtain the same effective resolution in water-based tissues.

Adipose Tissue↗
PubMed1996

Fast interleaved echo-planar imaging with navigator: high resolution anatomic and functional images at 4 Tesla.

Echo-planar imaging (EPI) is sensitive to magnetic field inhomogeneities, which lead to signal loss and geometric distortions of the image. Magnetic field inhomogeneities induced by susceptibility differences, as encountered in the human body, increase with the magnetic field strength, thus, complicating implementation of high resolution EPI techniques on high magnetic field systems. These problems were overcome by using a fast multishot high resolution EPI method that uses variable flip angles, center-out k-space sampling, and navigator echoes. This approach maximizes signal-to-noise ratio, reduces flow artifacts, and permits correction of intersegment amplitude and phase variations, providing high spatial and temporal resolution. This scheme can be implemented with a single magnetization preparation for contrast that precedes the segments. The utility of this ultrafast segmented EPI technique with navigator is demonstrated for anatomic and functional imaging studies on the human brain at 4 T.

Artifacts↗