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At least 487 records · Page 27Linked to original sources
PubMed1997

Antroduodenal manometry in children with no upper gastrointestinal symptoms.

BACKGROUND: The interpretation of antroduodenal manometry in children with gastrointestinal motility disorder has been limited by a paucity of data from normal children. The purpose of this study was to define antroduodenal manometry findings in children with no upper gastrointestinal symptoms. METHODS: We reviewed 260 consecutive antroduodenal manometries and selected 18 studies from subjects aged 2-12 years with no symptoms referable to a gastrointestinal motility disorder involving the stomach and/or the small bowel. RESULTS: During fasting, phase 3 of the migrating motor complex (MMC) was present in 14 of 18 children, and it was induced by erythromycin in 4 who failed to have a spontaneous phase 3. Phase 3 propagation velocity increased significantly with age. The cycle length between MMCs showed no age-dependent variation. Phase 3 occupied 3%; phase 1, 10%; and phase 2, 87% of the fasting recording time. CONCLUSIONS: Antroduodenal manometry findings in children with no upper gastrointestinal symptoms are similar to those in adults.

Adult↗
PubMed2005

Determination of curvature and twist by digital shearography and wavelet transforms.

A new technique based on digital shearography for determining the transient curvature and twist of a continuously deforming object from a series of speckle patterns is presented. The intensity variation of each pixel is analyzed along the time axis by using a complex Morlet wavelet transform. The absolute sign of the phase variation is determined by introduction of a temporal carrier when the speckle patterns are captured by a high-speed camera. A high-quality spatial distribution of the deflection derivative is extracted at any instant without the need for temporal or spatial phase unwrapping. The continuous Haar wavelet transform is subsequently processed as a differentiation operator to reconstruct the instantaneous curvature and twist of a continuously deforming object.

Journal Article↗
PubMedDate not supplied

Intragenic recombination leads to pilus antigenic variation in Neisseria gonorrhoeae.

The pilus of the bacterium Neisseria gonorrhoeae is a fimbriate surface structure which promotes attachment of the bacterium to host epithelial cells. Gonococcal pilus phase variation is characterized by a rapid on/off switch in which piliated (P+) cells throw off non-piliated (P-) variants and vice versa. Two regions of the gonococcal chromosome (pilE1 and pilE2) act as pilin expression loci, reminiscent of the MAT locus in the yeast Saccharomyces cerevisiae, while several other chromosomal regions contain silent (non-expressing) pilin sequences. Biochemical and antigenic diversity is seen in pili from a wide variety of clinical isolates. Pilins (pilus subunits) are composed of conserved N-terminal and variable C-terminal regions; the conserved region of gonococcal pilin is also found in pilins produced by widely disparate bacteria. We show here that the gonococcal pilin undergoes antigenic variation in vitro and in vivo. The protein consists of constant, semi-variable and hypervariable regions. This antigenic variation probably involves gene conversion of mini-cassettes of pilin information.

Amino Acid Sequence↗
PubMed2004

Ovarian cycle phase and same-sex mating behavior in Japanese macaque females.

The relationship of the ovarian cycle phase to same-sex mounting activity in adult female Japanese macaques (Macaca fuscata) was studied during the 1997/1998 mating season. Fecal samples were collected from eight female subjects two to three times per week and analyzed by enzyme immunoassay for fecal hormone levels. Hormone profiles of estrone (E1) and pregnanediol (PdG) were used to separate ovarian cycles into three phases: follicular, periovulatory, and luteal. Patterns of same-sex and heterosexual mounting behavior in the females were analyzed for phase variation during conceptive cycles. Same-sex mounting among female Japanese macaques occurred most frequently during the follicular and periovulatory phases of the cycle, and not at all during the luteal phase, paralleling the pattern found in heterosexual mounting behavior. These findings suggest a link between hormonal fluctuations and patterns of sexual mounting, regardless of whether the partner is of the same or opposite sex.

Animals↗
PubMed1993

The role of a repetitive DNA motif (5'-CAAT-3') in the variable expression of the Haemophilus influenzae lipopolysaccharide epitope alpha Gal(1-4)beta Gal.

Haemophilus influenzae lipopolysaccharide (LPS) contains structures, defined by monoclonal antibodies, which undergo phase variation. This investigation reports the nucleotide sequence of lic2A, which is required for the expression of at least three phase-variable LPS epitopes, one of which has the structure alpha Gal(1-4)beta Gal. lic2A contains multiple tandem repeats of the tetramer 5'-CAAT-3'. Previous studies have correlated changes in the number of 5'-CAAT-3' repeats with the phase-variable expression of the alpha Gal(1-4)beta Gal epitope. To obtain direct evidence for this, the 5'-CAAT-3' repeat region from lic2A was amplified directly from immunostained colonies and sequenced. This demonstrated that the variable expression of LPS epitopes, including alpha Gal(1-4)beta Gal, is in part directly dependent upon the number of copies of 5'-CAAT-3' within lic2A.

Amino Acid Sequence↗
PubMed1998

Simple sequence repeats in the Helicobacter pylori genome.

We describe an integrated system for the analysis of DNA sequence motifs within complete bacterial genome sequences. This system is based around ACeDB, a genome database with an integrated graphical user interface; we identify and display motifs in the context of genetic, sequence and bibliographic data. Tomb et aL (1997) previously reported the identification of contingency genes in Helicobacter pylori through their association with homopolymeric tracts and dinucleotide repeats. With this as a starting point, we validated the system by a search for this type of repeat and used the contextual information to assess the likelihood that they mediate phase variation in the associated open reading frames (ORFs). We found all of the repeats previously described, and identified 27 putative phase-variable genes (including 17 previously described). These could be divided into three groups: lipopolysaccharide (LPS) biosynthesis, cell-surface-associated proteins and DNA restriction/modification systems. Five of the putative genes did not have obvious homologues in any of the public domain sequence databases. The reading frame of some ORFs was disrupted by the presence of the repeats, including the alpha(1-2) fucosyltransferase gene, necessary for the synthesis of the Lewis Y epitope. An additional benefit of this approach is that the results of each search can be analysed further and compared with those from other genomes. This revealed that H. pylori has an unusually high frequency of homopurine:homopyrimidine repeats suggesting mechanistic biases that favour their presence and instability.

Base Sequence↗
PubMed1985

Virulence of Bordetella bronchiseptica in the porcine respiratory tract.

The virulence of Bordetella bronchiseptica in gnotobiotic piglets was studied by intranasal infection with 11 cultures derived from eight strains isolated from pigs (4), dogs (2), a human subject and a monkey. Six of the cultures contained organisms in phase I and five contained phenotypically different phase-III or -IV organisms. Of the phase-III and -IV cultures, four were derived from strains that had been isolated in phase I. Colonisation of the nasal cavity was investigated by counting bacteria in nasal swabs and washings. The toxigenicity of cell extracts from each strain and variant was determined by tests of lethality in mice or of cytopathogenicity in cell cultures. The results showed that two phase-I cultures from pigs colonised the nasal cavity and respiratory tract of gnotobiotic piglets better than did four phase-I cultures from other species. Phase-I organisms invariably produced capsules, fimbriae and mannose-resistant haemagglutination of guinea-pig erythrocytes. Four of five cultures in phases III and IV consisted of organisms that did not produce capsules, fimbriae or haemagglutination and colonised the nasal cavity poorly. Phase variation from I to III occurred in culture and in vivo, but variation from III to I occurred in vivo only and was accompanied by enhanced colonisation. Gnotobiotic piglets infected with porcine phase-I organisms exhibited atrophy of the nasal turbinate bones after 28 days; these organisms produced significantly more toxin than did bacteria in phase I from other species, or those in phases III and IV.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1982

Different sugar compositions of lipopolysaccharides isolated from phase I and pure phase II cells of Coxiella burnetii.

The compositions of lipopolysaccharides I and II, isolated from Coxiella burnetii phase I and pure phase II cells, respectively, showed drastic and clear-cut differences. Lipopolysaccharide II exhibited a comparatively simple composition. It contained, in addition to glucosamine (from lipid A) and a 2-keto-3-deoxyoctulosonic acid-related, thiobarbituric acid-positive substance, only two aldoses in high amounts, namely D-mannose and D-glycero-D-mannoheptose. Lipopolysaccharide I contained the same components, but it also contained at least eight other constituents including neutral sugars, e.g., an unusual branched sugar (3-C-methyl-6-deoxy-hexose) and unusual aminohexoses. Some components were characterized by a very high retention time in gas-liquid chromatography. The similarity of the phase variation in C. burnetii to the well-known smooth-to-rough mutation found in Enterobacteriaceae is discussed. Cells of phase I correspond to enterobacterial smooth forms, whereas cells of phase II might be compared to the rough forms.

Amino Sugars↗
PubMed2003

Type 1 fimbriae of Salmonella enterica serovar Typhimurium bind to enterocytes and contribute to colonization of swine in vivo.

Salmonella enterica serovar Typhimurium strain 798 is a clinical isolate from a pig and is known to be able to cause persistent, asymptomatic infections. This strain also is known to exist in two phenotypes (adhesive and nonadhesive to enterocytes) and can switch between the two phenotypes at a rate consistent with phase variation. Cells in the adhesive phenotype are more readily phagocytosed by leukocytes than nonadhesive cells. Once in a leukocyte, adhesive-phase cells survive while nonadhesive-phase cells die. In the present study, nonadhesive mutants were obtained with the transposon TnphoA. A nonadhesive mutant was selected for study and was shown by electron microscopy not to produce fimbriae. The gene encoding the adhesin was cloned and sequenced. Based on its sequence, the adhesin was shown to be FimA, the major subunit of type 1 fimbriae. The nonadhesive mutant was attenuated in its ability to colonize both mouse and pig intestines, but remained capable of systemic spread in mice. The nonadhesive mutant was phagocytosed to the same extent as parental cells in the adhesive phase and then survived intracellularly. These results demonstrated that type 1 fimbriae were important for attachment to enterocytes and promoted intestinal colonization. However, they were not important in promoting phagocytosis or intracellular survival.

Animals↗
PubMed2000

Age effect on phase relations between respiratory oscillations of the RR interval and systolic pressure.

Spectral analysis may allow the evaluation of (baroreflex) gain and phase between the RR interval and systolic pressure oscillations synchronous with respiration but, unlike baroreflex gain, the determinants of phase are not completely understood. We evaluated the correlates of spectral phase in 92 healthy subjects (44 men) aged 10-80 years. To do so, the cardiorespiratory signals during paced breathing at 16 breaths/min were continuously recorded and analyzed. In addition, respiratory sinus arrhythmia and baroreflex gain (two indices of cardiac vagal activity) and phase were calculated by using an autoregressive spectral technique. At univariate analysis, the phase correlated with age (r = 0.48, P < 0.001), the RR interval (r = 0.32, P < 0.01), respiratory sinus arrhythmia (r = -0.3, P < 0.01), baroreflex gain (r = -0.29, P < 0.01), and body mass index (r = 0.25, P < 0.05). At multivariate analysis, age was the most important physiological correlate of phase, accounting for 23% of interindividual phase variation. Cardiac vagal activity measures (which were higher in women than men) and the RR interval were also significant independent correlates of phase. We conclude that in addition to the RR interval and cardiac vagal activity, age has a significant impact on the phase relationship between respiratory related oscillations of the RR interval and systolic blood pressure. This spectral measure may contain additional information concerning the mechanisms that influence cardiovascular rhythms.

Adolescent↗
PubMed2002

Incorporation of N-acetylneuraminic acid into Haemophilus somnus lipooligosaccharide (LOS): enhancement of resistance to serum and reduction of LOS antibody binding.

Haemophilus somnus isolates from cases of thrombotic meningoencephalitis, pneumonia, and other disease sites are capable of undergoing a high rate of phase variation in the oligosaccharide component of their lipooligosaccharides (LOS). In contrast, the LOS of commensal strains isolated from the normal reproductive tract phase vary little or not at all. In addition, the LOS of H. somnus shares conserved epitopes with LOS from Neisseria gonorrhoeae, Haemophilus influenzae, and other species that can incorporate sialic acid into their LOS. We now report that growth of disease isolates of H. somnus with CMP-N-acetylneuraminic acid (CMP-NeuAc) or NeuAc added to the medium resulted in incorporation of NeuAc into the LOS. However, NeuAc was not incorporated into the LOS of commensal isolates and one disease isolate following growth in medium containing CMP-NeuAc or NeuAc. Sialylated LOS was detected by an increase in the molecular size or an increase in the amount of the largest-molecular-size LOS electrophoretic bands, which disappeared following treatment with neuraminidase. Sialylated LOS could also be detected by reactivity with Limax flavus agglutinin lectin, which is specific for sialylated species, by dot blot assay; this reactivity was also reversed by neuraminidase treatment. H. somnus strain 2336 LOS was found to contain some sialic acid when grown in medium lacking CMP-NeuAc or NeuAc, although supplementation enhanced NeuAc incorporation. In contrast strain 738, an LOS phase variant of strain 2336, was less extensively sialylated when the growth medium was supplemented with CMP-NeuAc or NeuAc, as determined by electrophoretic profiles and electrospray mass spectrometry. The sialyltransferase of H. somnus strain 738 was confirmed to preferentially sialylate the Gal(beta)-(1-3)-GlcNAc component of the lacto-N-tetraose structure by capillary electrophoresis assay. Enhanced sialylation of the strain 2336 LOS inhibited the binding of monoclonal antibodies to LOS by enzyme immunoassay and Western blotting. Furthermore, sialylation of the LOS enhanced the resistance of H. somnus to the bactericidal action of antiserum to LOS. Sialylation and increased resistance to killing by normal serum also occurred in a deletion mutant that was deficient in the terminal Gal-GlcNAc disaccharide. LOS sialylation may therefore be an important virulence mechanism to protect H. somnus against the host immune system.

Animals↗
PubMed2001

Analysis of phase-specific gene expression at the single-cell level in the white-opaque switching system of Candida albicans.

The opportunistic fungal pathogen Candida albicans can switch spontaneously and reversibly between different cell forms, a capacity that may enhance adaptation to different host niches and evasion of host defense mechanisms. Phenotypic switching has been studied intensively for the white-opaque switching system of strain WO-1. To facilitate the molecular analysis of phenotypic switching, we have constructed homozygous ura3 mutants from strain WO-1 by targeted gene deletion. The two URA3 alleles were sequentially inactivated using the MPA(R)-flipping strategy, which is based on the selection of integrative transformants carrying a mycophenolic acid (MPA) resistance marker that is subsequently deleted again by site-specific, FLP-mediated recombination. To investigate a possible cell type-independent switching in the expression of individual phase-specific genes, two different reporter genes that allowed the analysis of gene expression at the single-cell level were integrated into the genome, using URA3 as a selection marker. Fluorescence microscopic analysis of cells in which a GFP reporter gene was placed under the control of phase-specific promoters demonstrated that the opaque-phase-specific SAP1 gene was detectably expressed only in opaque cells and that the white-phase-specific WH11 gene was detectably expressed only in white cells. When MPA(R) was used as a reporter gene, it conferred an MPA-resistant phenotype on opaque but not white cells in strains expressing it from the SAP1 promoter, which was monitored at the level of single cells by a significantly enlarged size of the corresponding colonies on MPA-containing indicator plates. Similarly, white but not opaque cells became MPA resistant when MPA(R) was placed under the control of the WH11 promoter. The analysis of these reporter strains showed that cell type-independent phase variation in the expression of the SAP1 and WH11 genes did not occur at a detectable frequency. The expression of these phase-specific genes of C. albicans in vitro, therefore, is tightly linked to the cell type.

Aspartic Acid Endopeptidases↗
PubMed2003

Cell-cycle-dependent three-dimensional redistribution of nuclear proteins, P 120, pKi-67, and SC 35 splicing factor, in the presence of the topoisomerase I inhibitor camptothecin.

Topoisomerase I (Topo I) is mostly known for its role in DNA relaxation, which is required for duplication and transcription. Topo I acts as a protein kinase mainly directed to the mRNA splicing factor SC35. Camptothecin is one of the specific Topo I inhibitors and is effective on the two functions of the enzyme. In this study we demonstrated that treatment of KB cells with camptothecin for only 30 min induced the 3D reorganization and redistribution of three proteins involved in the nucleus machinery, P 120, pKi-67, and SC 35, and this occurred in a cell cycle-dependent manner. Our data were obtained from confocal microscopic studies after immunolabeling, 3D reconstruction, and measurement of the nuclear components volumes. In the presence of camptothecin, P 120, which occupied the nucleolar volume, lost its reticulation and pKi-67 was redistributed within the nucleoplasm and even into the cytoplasm. Finally, for SC 35 the fusion of its dots into bigger volumes was observed specifically during the G1 phase. Variations of volumes were also observed for the nucleolus and for the nucleus. These results pointed out that, depending on the cell cycle phase, Topo I functions were selective toward the three different proteins.

Camptothecin↗
PubMed1991

Pure absorption-mode spectra from Bayesian maximum entropy analysis of ion cyclotron resonance time-domain signals.

Fourier transform ion cyclotron resonance (FT/ICR) mass spectra are normally reported in the (phase-independent) magnitude-mode format. In principle, the absorption-mode format offers spectral resolution enhanced by a factor ranging from square root of 3 to 2 over the corresponding magnitude-mode spectrum obtained by discrete FT of the same unapodized time-domain data. However, an absorption-mode display is generally unsuitable in practice because of the auxiliary spectral peaks (Gibbs oscillations) resulting from the relatively long time delay between excitation and detection. Although the resulting large phase variation (up to 100 pi rad or more across the Nyquist spectral bandwidth) can be corrected exactly for a continuous time-domain signal, phase correction of a discrete time-domain signal results in Gibbs oscillations even for a perfectly phased absorption-mode spectrum. In this paper, we show that a Bayesian "maximum-entropy" analysis of simulated and experimental ion cyclotron resonance time-domain noisy signals can recover a precisely phased absorption-mode frequency-domain spectrum that is devoid of Gibbs oscillations, is less sensitive to noise, and offers improved mass accuracy over that obtained from a conventional magnitude-mode discrete fast Fourier transform (FFT) spectrum.

Fourier Analysis↗
PubMed1995

Influence of Osmolarity on Phase Shift in Photorhabdus luminescens.

The influence of osmolarity and other environmental factors like low oxygen levels, light, extreme pH values, and temperatures on phase variation of Photorhabdus luminescens, the symbiotic bacterium of entomopathogenic nematodes of the genus Heterorhabditis, was investigated. Only subculturing in low-osmolarity medium triggered a phase shift to secondary phase reliably.

Journal Article↗
PubMed2003

The role of pilin glycan in neisserial pathogenesis.

The pilus of pathogenic Neisseria is a polymer composed mainly of the glycoprotein, pilin. Recent investigations significantly enhanced characterization of pilin glycan (Pg) from N. gonorrhoeae (gonococcus, GC) and N. meningitidis (meningococcus, MC). Several pilin glycosylation genes were discovered recently from these bacteria and some of these genes transfer sugars previously unknown to be present in neisserial pili. Due to these findings, glycans of GC and MC pilin are now considered more complex. Furthermore, various Pg can be expressed by different strains and variants of GC, as well as MC. Intra-species variation of Pg between different groups of GC or MC can partly be due to polymorphisms of glycosylation genes. In pilus of pathogenic Neisseria, alternative glycoforms are also produced due to phase-variation (Pv) of pilin glycosylation genes. Most remarkably, the pgtA (pilin glycosyl transferase A) gene of GC can either posses or lack the ability of Pv. Many GC strains carry the phase-variable (Pv+) pgtA, whereas others carry the allele lacking Pv (Pv-). Mostly, the GC isolates from disseminated gonococcal infection (DGI) carry Pv+ pgtA but organisms from uncomplicated gonorrhea (UG) contain the Pv- allele. This data suggests that Pv of pgtA facilitates DGI, whereas constitutive expression of the Pv- pgtA may promote UG. Additional implications of Pg in various physiological and pathogenic mechanisms of Neisseria can also be envisaged based on various recent data.

Amino Acid Sequence↗
PubMed2004

The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori.

Phase variation is a common mechanism used by pathogenic bacteria to generate intra-strain diversity that is important in niche adaptation and is strongly associated with virulence determinants. Previous analyses of the complete sequences of the Helicobacter pylori strains 26695 and J99 have identified 36 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Here a comparative analysis of the two genomes is reported and an updated and expanded list of 46 candidate phase-variable genes in H. pylori is described. These have been systematically investigated by PCR and sequencing for the presence of the genes, and the presence and variability in length of the repeats in strains 26695 and J99 and in a collection of unrelated H. pylori strains representative of the main global subdivisions recently suggested. This provides supportive evidence for the phase variability of 30 of the 46 candidates. Other differences in this subset of genes were observed (i) in the repeats, which can be present or absent among the strains, or stabilized in different strains and (ii) in the gene-complements of the strains. Differences between genes were not consistently correlated with the geographic population distribution of the strains. This study extends and provides new evidence for variation of this type in H. pylori, and of the high degree of diversity of the repertoire of genes which display phase-variable switching within individual strains.

Animals↗
PubMed2006

Phased array ghost elimination.

Parallel imaging may be applied to cancel ghosts caused by a variety of distortion mechanisms, including distortions such as off-resonance or local flow, which are space variant. Phased array combining coefficients may be calculated that null ghost artifacts at known locations based on a constrained optimization, which optimizes SNR subject to the nulling constraint. The resultant phased array ghost elimination (PAGE) technique is similar to the method known as sensitivity encoding (SENSE) used for accelerated imaging; however, in this formulation is applied to full field-of-view (FOV) images. The phased array method for ghost elimination may result in greater flexibility in designing acquisition strategies. For example, in multi-shot EPI applications ghosts are typically mitigated by the use of an interleaved phase encode acquisition order. An alternative strategy is to use a sequential, non-interleaved phase encode order and cancel the resultant ghosts using PAGE parallel imaging. Cancellation of ghosts by means of phased array processing makes sequential, non-interleaved phase encode acquisition order practical, and permits a reduction in repetition time, TR, by eliminating the need for echo-shifting. Sequential, non-interleaved phase encode order has benefits of reduced distortion due to off-resonance, in-plane flow and EPI delay misalignment. Furthermore, the use of EPI with PAGE has inherent fat-water separation and has been used to provide off-resonance correction using a technique referred to as lipid elimination with an echo-shifting N/2-ghost acquisition (LEENA), and may further generalized using the multi-point Dixon method. Other applications of PAGE include cancelling ghosts which arise due to amplitude or phase variation during the approach to steady state. Parallel imaging requires estimates of the complex coil sensitivities. In vivo estimates may be derived by temporally varying the phase encode ordering to obtain a full k-space dataset in a scheme similar to the autocalibrating TSENSE method. This scheme is a generalization of the UNFOLD method used for removing aliasing in undersampled acquisitions. The more general scheme may be used to modulate each EPI ghost image to a separate temporal frequency as described in this paper.

Algorithms↗