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 433 records · Page 24Linked to original sources
PubMed1996

Quantification of trabecular structure in the distal femur using magnetic resonance phase imaging.

A new approach for quantifying trabecular bone tissue using the phase images of a simple gradient-echo sequence is presented. The proposed method is based on the hypothesis that the differences in susceptibility between bone and bone marrow cause magnetic field (i.e., precession phase) variations between the image voxels. Phase images of the distal femur were obtained in vivo and characterised with the use of the phase variance. Computer simulations and experimental results indicate that the distribution of the phases varies with echo time and image resolution, as expected. Keeping these fixed, however, the phase variance is found to strongly reflect variations in trabecular structure.

Adult↗
PubMed2006

Identification of the functional initiation codons of a phase-variable gene of Haemophilus influenzae, lic2A, with the potential for differential expression.

Simple sequence repeats located within reading frames mediate phase-variable ON/OFF switches in gene expression by generating frameshifts. Multiple translation initiation codons in different reading frames are found upstream of most Haemophilus influenzae tetranucleotide repeat tracts, raising the possibility of multiple active reading frames and more than two levels of gene expression for these loci. Phase variation between three levels of gene expression (strong, weak, and none) was observed when lic2A was fused to a lacZ reporter gene. The lic2A 5' CAAT repeat tract is preceded by four 5' ATG codons (x, y, z1, and z2) in two reading frames. Each of these initiation codons was inactivated by site-directed mutagenesis. Strong expression from frame 1 was associated with x but not y. Weak expression from frame 2 was mainly dependent on the z2 codon, and there was no expression from frame 3. Using monoclonal antibodies specific for a digalactoside epitope of lipopolysaccharide whose synthesis requires Lic2A, two levels (strong and undetectable) of antibody reactivity were detected, suggesting that weak expression of lic2A is not discernible at the phenotypic level. Inactivation of the x initiation codon resulted in loss of strong expression of the digalactoside epitope and elevated killing by human serum. The failure to detect more than two phenotypes for lic2A, despite clear evidence of weak expression from the z1/z2 initiation codons, leaves open the question of whether or not multiple initiation codons are associated with more complex patterns of phenotypic variation rather than classical phase-variable switching between two phenotypes.

Amino Acid Sequence↗
PubMed1993

Differential protein expression and surface presentation generate high-frequency antigenic variation in Mycoplasma fermentans.

Mycoplasma fermentans, a wall-less prokaryote, is currently under investigation as a potential human pathogen. Recently, several surface lipoproteins have been shown to vary in expression between M. fermentans strains. Using specific antibodies to these lipoproteins, we investigated the extent and nature of antigenic variation within this species. Immunoscreening of type strain PG18 agar-grown colonies revealed marked heterogeneity in expression of distinct surface lipoproteins. Subsequent isolation and propagation of clonal isolates established isogenic lineages which displayed high-frequency (10(-2) to 10(-5) per generation) antigenic phase variation. [35S]cysteine-labeled protein profiles and Western immunoblots of phase-variant clones showed that several distinct integral membrane proteins undergo noncoordinate variation in expression. In addition to differential expression of epitope-bearing lipoproteins, differential accessibility of epitopes to antibodies was also documented as a mechanism generating surface phenotypic variation. Examination of one strain-variant antigen showed high-frequency phase variation to underlie previously observed antigenic differences between strains of this species. Thus, M. fermentans has a complex system capable of creating rapid changes in surface mosaics. This may profoundly affect mycoplasma-host interactions and may limit the methods by which populations of M. fermentans may be studied in vivo.

Antibodies, Monoclonal↗
PubMed1991

Variation in suicide occurrence by time of day, day of the week, month, and lunar phase.

Previous studies suggest that suicide occurrence varies by month and day of the week, but not by lunar phase. Variation by time of day has never before been adequately examined; to our knowledge, all previous studies have failed to obtain time-of-death information for a large percentage of cases. We examined suicide occurrence among residents of Sacramento County, CA, during the period from 1925 to 1983. Data were abstracted from coroner's autopsy and investigative reports. In contrast to previous studies, data on time of death were available for a large percentage of cases. 4,190 suicide deaths were identified during the study period. Suicide occurrence varied substantially by time of day; for both sexes and for ages under 65 years, the fewest suicide deaths occurred during the early morning hours, from 0401 to 0800. For recent years of the study, suicides occurred most frequently on Monday for both males and females and for most age groups. Variation by month followed no consistent pattern by gender, age, years of the study, or combinations of these factors. Contrary to popular belief, suicide occurrence did not vary by lunar phase.

California↗
PubMed2002

Growth phase influences complement resistance of Bordetella pertussis.

The BrkA protein of Bordetella pertussis inhibits killing by the antibody-dependent classical pathway of complement; however, susceptibility to complement can be highly variable. Log-phase bacteria grown in Stainer-Scholte (SS) broth plated on Bordet-Gengou (BG) agar were about 500 times more sensitive to killing by complement than stationary-phase SS-BG cultures. While always more susceptible to complement than the wild-type strain, a BrkA mutant displayed a similar growth phase variation in susceptibility to complement. Growth phase susceptibility to complement was also observed for a mutant constitutive for Bvg activation of BrkA, suggesting that modulation of virulence factor expression was not responsible for sensitivity to complement. Susceptibility was not due to differential antigenic expression, since serum adsorbed with complement-resistant, stationary-phase SS-BG cultures lacked bactericidal activity against B. pertussis harvested at all times during the growth cycle. These results suggest that log-phase susceptibility to complement is not due to variable expression of BrkA or antigenic differences and may be an inherent property of rapidly growing cultures. Implications for vaccine development are discussed.

Antigenic Variation↗
PubMed1993

Individual, phase, and weekly variations in daily cycles of wrist activity in freeliving humans.

Wrist activity was monitored in 17 college students for 11-15 days each. Records of individuals had distinctive patterns, like fingerprints. The subjects all exhibited daily cycles in their activity with activity during the daytime and with period lengths close to 24 h. There was individual variation in average phase (onset 5.3 h, offset 4.5 h, acrophase 6.1 h). Individual subjects all showed 7-day oscillations in their activity patterns associated with the weekly work-leisure schedules. During the leisure weekends, the subjects as a group had a 2.1-h delay in onset, a 1.5-h delay in acrophase, and a 0.8-h shortening in alpha.

Adult↗
PubMed1988

Molecular cloning of the wild-type phoM operon in Escherichia coli K-12.

A metastable bacterial alkaline phosphatase (Bap) phenotype is seen in phoR mutants, which alternately express a Bap-constitutive or -negative phenotype. The alteration is affected by mutations in the phoM region near 0 min. By molecular cloning of the wild-type phoM operon onto a multicopy plasmid and recombining onto the plasmid the pho-510 mutation that abolishes variation, the phoM operon, rather than some nearby gene, was shown to control variation. Complementation tests indicated that the wild-type phoM allele is dominant to the pho-510 mutation when both are in single copy, but whichever allele is present in higher copy appears as dominant when multicopy plasmids are examined. The alternating phenotypic variation of BAP synthesis was not seen in phoR+ cells with multicopy wild-type phoM plasmids, thus showing that the variation is associated with phoM-dependent Bap expression. The alternation acted at the level of phoA transcription; it was also recA independent. BAP clonal variation is phenotypically similar to Salmonella phase variation, which is controlled by a DNA rearrangement. No evidence was found for a DNA change near the phoM operon that might be responsible for the variable Bap phenotype.

Alkaline Phosphatase↗
PubMed1996

Circadian variation of human acute phase response.

Circadian variation of temperature, both normal and febrile, is a well known fact. Mediators of fever are also regulators of acute phase response and are associated with stimulation of pituitary hormone production related with defervescence and with a circadian pattern of secretion. Acute phase response may consequently have circadian variations in its components. Measurements of temperature, erythrocyte sedimentation rate, complete blood cell count, serum cortisol and fibrinogen were made at 7:00, 15:00, and 23:00 h during two consecutive days in 35 patients with fever and acute infection, 15 patients with clinically active ankylosing spondylitis without fever and 10 healthy volunteers. Temperature curves showed statistically significant circadian rhythms, with higher values at night and lower ones during early morning. Erythrocyte sedimentation rate, leukocyte count and fibrinogen also showed statistically significant circadian rhythms, but with higher values at 15:00 h. Serum cortisol also showed statistically significant circadian rhythmicity but with a higher rhythm adjusted mean (MESOR), and a 100 degrees (6 h) phase shift in patients with fever, as compared to patients with ankylosing spondylitis and healthy controls. In conclusion, components of acute phase response, including fever, have circadian rhythmicity, but asynchronically. Differences between fever and ankylosing spondylitis can be due to the intensity of acute phase response stimulation.

Acute-Phase Reaction↗
PubMed2005

The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes.

Several host-adapted bacterial pathogens contain methyltransferases associated with type III restriction-modification (R-M) systems that are subject to reversible, high-frequency on/off switching of expression (phase variation). To investigate the role of phase-variable expression of R-M systems, we made a mutant strain lacking the methyltransferase (mod) associated with a type III R-M system of Haemophilus influenzae and analyzed its phenotype. By microarray analysis, we identified a number of genes that were either up- or down-regulated in the mod mutant strain. This system reports the coordinated random switching of a set of genes in a bacterial pathogen and may represent a widely used mechanism.

Bacterial Proteins↗
PubMed1999

Relationship between cell surface carbohydrates and intrastrain variation on opsonophagocytosis of Streptococcus pneumoniae.

Streptococcus pneumoniae undergoes spontaneous phase variation between a transparent and an opaque colony phenotype, the latter being more virulent in a murine model of sepsis. Opaque pneumococci have previously been shown to express lower amounts of C polysaccharide (cell wall teichoic acid) and in this study were shown to have a higher content of capsular polysaccharide by immunoelectron microscopy. This report then examined the relationship between expression of these two cell surface carbohydrate structures and their relative contribution to the increased virulence of opaque variants. Comparison of genetically related strains showed that the differential content of capsular polysaccharide did not affect the amount of teichoic acid as measured by a capture enzyme-linked immunosorbent assay (ELISA). In contrast, when the teichoic acid structure was altered by replacing choline in the growth medium with structural analogs, the quantity of capsular polysaccharide as measured by a capture ELISA was decreased, demonstrating a linkage in the expression of the two surface carbohydrate structures. A standardized assay was used to assess the relative contribution of cell surface carbohydrates to opsonophagocytosis. The opaque variants required 1.2- to 30-fold more immune human serum to achieve 50% opsonophagocytic killing than did related transparent variants (types 6B and 9V). The opsonophagocytic titer was proportional to the quantity of capsular polysaccharide rather than teichoic acid. The major factor in binding of the opsonin, C-reactive protein (CRP), was also the amount of capsular polysaccharide rather than the teichoic acid ligand. Only for the transparent variant (type 6B), which bound more CRP, was there enhanced opsonophagocytic killing in the presence of this serum protein. Increased expression of capsular polysaccharide, therefore, appeared to be the major factor in the decreased opsonophagocytic killing of opaque pneumococci.

Animals↗
PubMed2006

Complex amplitude correlation for compensation of large in-plane motion in digital speckle pattern interferometry.

The use of complex amplitude correlation to compensate for large in-plane motion in digital speckle pattern interferometry is investigated. The result is compared with experiments where digital speckle photography (DSP) is used for compensation. An advantage of using complex amplitude correlation instead of intensity correlation (as in DSP) is that the phase change describing the deformation is retrieved directly from the correlation peak, and there is no need to compensate for the large movement and then use the interferometric algorithms. A discovered drawback of this method is that the correlation values drop quickly if a phase gradient larger than pi is present in the subimages used for cross correlation. This means that, for the complex amplitude correlation to be used, the size of the subimages must be well chosen or a third parämeter in the cross-correlation algorithm that compensates for the phase variation is needed. Correlation values and wrapped phase maps from the two techniques (intensity and complex amplitude correlation) are presented.

Journal Article↗
PubMed2004

Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant.

Reversible phase variation between the rugose and smooth colony variants is predicted to be important for the survival of Vibrio cholerae in natural aquatic habitats. Microarray expression profiling studies of the rugose and smooth variants of the same strain led to the identification of 124 differentially regulated genes. Further expression profiling experiments showed how these genes are regulated by the VpsR and HapR transcription factors, which, respectively, positively and negatively regulate production of VPS(El Tor), a rugose-associated extracellular polysaccharide. The study of mutants of rpoN and rpoS demonstrated the effects of these alternative sigma factors on phase variation-specific gene expression. Bioinformatics analysis of these expression data shows that 'rugosity' and 'smoothness' are determined by a complex hierarchy of positive and negative regulators, which also affect the biofilm, surface hydrophobicity and motility phenotypes of the organism.

Adaptation, Physiological↗
PubMed1985

Lipopolysaccharide variation in Coxiella burnetti: intrastrain heterogeneity in structure and antigenicity.

We isolated lipopolysaccharides (LPSs) from phase variants of Coxiella burnetii Nine Mile and compared the isolated LPS and C. burnetii cells by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting. The LPSs were found to be the predominant component which varied structurally and antigenically between virulent phase I and avirulent phase II. A comparison of techniques historically used to extract the phase I antigenic component revealed that the aqueous phase of phenol-water, trichloroacetic acid, and dimethyl sulfoxide extractions of phase I C. burnettii cells all contained phase I LPS, although the efficiency and specificity of extraction varied. Our studies provide additional evidence that phase variation in C. burnetii is analogous to the smooth-to-rough LPS variation of gram-negative enteric bacteria, with phase I LPS being equivalent to smooth LPS and phase II being equivalent to rough LPS. In addition, we identified a variant with a third LPS chemotype with appears to have a structural complexity intermediate to phase I and II LPSs. All three C. burnetii LPS contain a 2-keto-3-deoxyoctulosonic acid-like substance, heptose, and gel Limulus amoebocyte lysates in subnanogram amounts. The C. burnetii LPSs were nontoxic to chicken embryos at doses of over 80 micrograms per embryo, in contrast to Salmonella typhimurium smooth- and rough-type LPSs, which were toxic in nanogram amounts.

Bacterial Proteins↗
PubMed1993

Paradoxical effect of pilus expression on binding of antibodies by Haemophilus influenzae.

Haemophilus influenzae type b (Hib) pili are surface proteins that are associated with the ability of Hib to attach to human epithelial cells. Like pilus expression of other bacteria, expression of Hib pili undergoes phase variation. We observed that Hib in the piliated phase (Hib p+) bound monoclonal antibodies directed against six conserved, surface-exposed, nonpilus Hib outer membrane epitopes to a greater extent than Hib in the nonpiliated phase (Hib p-). However, after extended incubation, p+ and p- cells bound these antibodies in a similar fashion. The differential in nonpilus antibody binding to p+ and p- Hib was not related to the presence of the type b capsule. In addition, Hib p+ organisms whose pilin gene was insertionally inactivated and did not produce pili and Hib in the nonpiliated phase bound the nonpilus Hib antibodies similarly. Hib p+ and p- organisms did not differ in their binding of anti-type b capsule antibody, and the binding was specific for the epitopes recognized by the antibodies. In complement-dependent bactericidal assays, the nonpilus antibodies killed Hib p+ more effectively than Hib p-. The increased binding to, and killing of, Hib p+ by a variety of nonpilus antibodies may be important for host defense against invasive Hib.

Animals↗
PubMed2000

flhDC, the flagellar master operon of Xenorhabdus nematophilus: requirement for motility, lipolysis, extracellular hemolysis, and full virulence in insects.

Xenorhabdus is a major insect pathogen symbiotically associated with nematodes of the family Steinernematidae. This motile bacterium displays swarming behavior on suitable media, but a spontaneous loss of motility is observed as part of a phenomenon designated phase variation which involves the loss of stationary-phase products active as antibiotics and potential virulence factors. To investigate the role of one of the transcriptional activators of flagellar genes, FlhDC, in motility and virulence, the Xenorhabdus nematophilus flhDC locus was identified by functional complementation of an Escherichia coli flhD null mutant and DNA sequencing. Construction of X. nematophilus flhD null mutants confirmed that the flhDC operon controls flagellin expression but also revealed that lipolytic and extracellular hemolysin activity is flhDC dependent. We also showed that the flhD null mutant displayed a slightly attenuated virulence phenotype in Spodoptera littoralis compared to that of the wild-type strain. Thus, these data indicated that motility, lipase, hemolysin, or unknown functions controlled by the flhDC operon are involved in the infectious process in insects. Our investigation expands the view of the flagellar regulon as a checkpoint coupled to a major network involving bacterial physiological aspects as well as motility.

Animals↗
PubMed2004

Pathogenic consequences of Neisseria gonorrhoeae pilin glycan variation.

A Neisseria gonorrhoeae (gonococcus, GC) pilin glycosylation gene, pgtA, can either possess or lack phase-variation ability. Many GC, particularly the disseminated strains, carry a phase-variable pgtA. However, other GC, predominantly the uncomplicated gonorrhea isolates, carry a pgtA lacking phase-variability. These and other results suggest GC pilin glycan's pathogenic involvement.

Bacterial Proteins↗
PubMedDate not supplied

FETAX interlaboratory validation study: phase III--Part 1 testing.

The Frog Embryo Teratogenesis Assay-Xenopus (FETAX) is a 96-h whole embryo developmental toxicity screening assay that can be used in ecotoxicology and in detecting mammalian developmental toxicants when an in vitro metabolic activation system is employed. A standardized American Society for Testing and Materials (ASTM) guide for the conduct of FETAX has been published, along with a companion atlas that aids in embryo staging and identifying malformations. As part of the ASTM process, a three-phase interlaboratory validation study was undertaken to evaluate the repeatability and reliability of FETAX. Seven different participants collaborated in the study. In Phase I, FETAX proved to be more repeatable and reliable than many bioassays. However, some excessive variation was observed in a few laboratories. An initial lack of assay experience by some technicians caused variation. Phase II showed far less intra- and interlaboratory variability than Phase I. Non-teratogens showed the most consistent results, while more variability was observed for the two teratogens tested. Interlaboratory coefficient of variation values for all endpoints ranged from 7.3 to 54.7. Phase III--Part 1, using coded samples and test concentration ranges selected by each laboratory, showed results similar to Phase I. Analysis of the causes of variation suggested that some technicians judged some embryos to be malformed while others consistently judged similar embryos as normal. Concentration ranges tested by some of the laboratories varied greatly and a new protocol for selecting concentrations for initial testing was written to reduce variation from this source. Testing to date suggests that FETAX is as repeatable and reliable as other standard bioassays.

Aminopropionitrile↗
PubMed2005

Ion-pair mediated transport of small model peptides in liquid phase micro extraction under acidic conditions.

This paper discusses the behaviour of five small model peptides in a three phase (aqueous donor-organic-aqueous acceptor) liquid phase micro extraction system in relation to their physico-chemical properties (charge, hydrophobicity). It is proved that for all peptides transport over the organic phase is mediated by aliphatic sulphonic acids. Heptane-1-sulphonic acid gave the best overall recoveries. It appeared that peptides with hydrophobic properties (IPI) and a high number of positive charges (KYK) show good recoveries and are enriched in the acceptor phase. Variation in the pH (1.6-4.4) of the donor phase shows that there are peptide-dependent optimal pH-values for their recovery. Increasing pH in the acceptor phase shows that in most cases the recovery decreases due to decreased ion-pair mediated membrane transport. For KYK the partition between the organic phase and the aqueous acceptor-phase is also driven by the solubility in the aqueous acceptor phase. Increase of the ion strength of the acceptor phase did not affect the recovery of the peptides. Except for KYK, which showed decreased recovery when the ion strength increased. Another finding is that delocalisation of positive charge causes bad recovery, probably due to incomplete ion-pair-peptide complex formation.

Acids↗