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PubMed2004

Genetics of capsule O-acetylation in serogroup C, W-135 and Y meningococci.

Capsular polysaccharides of serogroup C, W-135 and Y meningococci were previously reported to be O-acetylated at the sialic acid residues. There is evidence that O-acetylation affects the immunogenicity of polysaccharide vaccines. We identified genes indispensable for O-acetylation of serogroup C, W-135 and Y meningococci downstream of the capsule synthesis genes siaA-D. The genes were co-transcribed with the sia operon as shown by reverse transcription polymerase chain reaction analysis. The putative capsular polysaccharide O-acetyltransferases were designated OatC and OatWY. The protein OatWY of serogroups W-135 and Y showed sequence homologies to members of the NodL-LacA-CysE family of bacterial acetyltransferases, whereas no sequence homology with any known protein in the different databases was found for the serogroup C protein OatC. In serogroup W-135 and Y meningococci, several clonal lineages either lacked OatWY or OatWY was inactivated by insertion of IS1301. For serogroup C meningococci, we observed in vitro phase variation of O-acetylation, which resulted from slipped-strand mispairing in homopolymeric tracts. This finding explains the observation of naturally occurring de-O-acetylated serogroup C meningococci. Our report is the first description of sequences of sialic acid O-acetyltransferase genes that have not been cloned from either other bacterial or mammalian organisms.

Acetylation↗
PubMed1999

Structural analysis of the lipopolysaccharide oligosaccharide epitopes expressed by a capsule-deficient strain of Haemophilus influenzae Rd.

Structural elucidation of the lipopolysaccharide (LPS) of Haemophilus influenzae, strain Rd, a capsule-deficient type d strain, has been achieved by using high-field NMR techniques and electrospray ionization-mass spectrometry (ESI-MS) on delipidated LPS and core oligosaccharide samples. It was found that this organism expresses heterogeneous populations of LPS of which the oligosaccharide (OS) epitopes are subject to phase variation. ESI-MS of O-deacylated LPS revealed a series of related structures differing in the number of hexose residues linked to a conserved inner-core element, L-alpha-D-Hepp-(1-->2)-L-alpha-D-Hepp-(1-->3)-[beta-D-Glcp- (1-->4)-]- L-alpha-D-Hepp-(1-->5)-alpha-Kdo, and the degree of phosphorylation. The structures of the major LPS glycoforms containing three (two Glc and one Gal), four (two Glc and two Gal) and five (two Glc, two Gal and one GalNAc) hexoses were substituted by both phosphocholine (PCho) and phosphoethanolamine (PEtn) and were determined in detail. In the major glycoform, Hex3, a lactose unit, beta-D-Galp-(1-->4)-beta-D-Glcp, is attached at the O-2 position of the terminal heptose of the inner-core element. The Hex4 glycoform contains the PK epitope, alpha-D-Galp-(1-->4)-beta-D-Galp-(1-->4)-beta-D-Glcp while in the Hex5 glycoform, this OS is elongated by the addition of a terminal beta-D-GalpNAc residue, giving the P antigen, beta-D-GalpNAc-(1-->3)-alpha-D-Galp-(1-->4)-beta-D-Galp-(1-->4)-D-Glc p. The fully extended LPS glycoform (Hex5) has the following structure. [see text] The structural data provide the first definitive evidence demonstrating the expression of a globotetraose OS epitope, the P antigen, in LPS of H. influenzae. It is noteworthy that the molecular environment in which PCho units are found differs from that observed in an Rd- derived mutant strain (RM.118-28) [Risberg, A., Schweda, E. K. H. & Jansson, P-E. (1997) Eur. J. Biochem. 243, 701-707].

Carbohydrate Conformation↗
PubMed2001

Sensory changes during the ovulatory phase of the menstrual cycle in healthy women.

This study compared the pain sensitivity in healthy women at the abdomen and lower back (presumed referral areas of menstrual pain), thigh and arm (control areas), in the menstrual, ovulatory, luteal and premenstrual phases of confirmed ovulatory cycles, with that of males. The pressure pain threshold (PPT) and pinch pain threshold (PiPT) was determined by an electronic pressure algometer, heat pain threshold (HPT) by a contact thermode and tactile threshold (TT) with von Frey hairs. The abdominal PPT was significantly lower in females in all menstrual phases as compared to the control sites ( p<0.0007). The abdominal and lower back HPT was significantly lower in females in all menstrual phases compared with control areas, and to the sites in males ( p<0.002). The TT was significantly reduced in females compared with males ( p< 0.013). There was no difference in the PiPT between females and males. In males, the HPT, PPT and TT were not different within any site. During the ovulatory phase, the HPT was significantly reduced at the abdomen and the PPT at the back compared with the menstrual, luteal and premenstrual phases (p<0.0002). There were no within-menstrual phase variations in the PiPT and TT at any site, or for the HPT and PPT at the control areas. The reduced thresholds in menstruating women may be due to the presence of latent uterine algogenic stimuli, and the increased levels of oestrogen and leuteinizing hormone at ovulation may enhance nociception by acting both at the peripheral and central level, resulting in the hypersensitivity changes at the abdomen and lower back areas.

Abdominal Pain↗
PubMed2000

Haemophilus influenzae in chronic bronchitis.

Colonization of the adult respiratory tract with nontypable Haemophilus influenzae is a dynamic process with new strains being acquired and replacing old strains periodically. The organism is a common cause of exacerbations of chronic bronchitis based on 3 lines of evidence: quantitative culture of the lower airways obtained by protected specimen brush, antibiotic trials, and serological studies. Nontypable H. influenzae expresses multiple adhesin molecules that mediate adherence to the respiratory tract mucosa. Recent studies have established that the bacterium penetrates the mucosal surface and survives intracellularly and in the interstitium of the submucosa. The organism shows a remarkable degree of antigenic diversity on its surface, including phase variation of lipooligosaccharide, antigenic heterogeneity of surface proteins, point mutations in genes encoding surface proteins and horizontal transfer of genes. These strategies facilitate evasion of the human immune response. Substantial progress has been made in identifying vaccine antigens to prevent infections caused by nontypable H. influenzae.

Adult↗
PubMed2004

Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella.

Extensive population-level genetic variability at the Salmonella rfb locus, which encodes enzymes responsible for synthesis of the O-antigen polysaccharide, is thought to have arisen through frequency-dependent selection (FDS) by means of exposure of this pathogen to host immune systems. The FDS hypothesis works well for pathogens such as Haemophilus influenzae and Neisseria meningitis, which alter the composition of their O-antigens during the course of bloodborne infections. In contrast, Salmonella remains resident in epithelial cells or macrophages during infection and does not have phase variability in its O-antigen. More importantly, Salmonella shows host-serovar specificity, whereby strains bearing certain O-antigens cause disease primarily in specific hosts; this behavior is inconsistent with FDS providing selection for the origin or maintenance of extensive polymorphism at the rfb locus. Alternatively, selective pressure may originate from the host intestinal environment itself, wherein diversifying selection mediated by protozoan predation allows for the continued existence of Salmonella able to avoid consumption by host-specific protozoa. This selective pressure would result in high population-level diversity at the Salmonella rfb locus without phase variation. We show here that intestinal protozoa recognize antigenically diverse Salmonella with different efficiencies and demonstrate that differences solely in the O-antigen are sufficient to allow for prey discrimination. Combined with observations of the differential distributions of both serotypes of bacterial species and their protozoan predators among environments, our data provides a framework for the evolution of high genetic diversity at the rfb locus and host-specific pathogenicity in Salmonella.

Animals↗
PubMed2004

Metastability of Helicobacter pylori bab adhesin genes and dynamics in Lewis b antigen binding.

Heterogeneity among Helicobacter pylori strains in gastric epithelial adherence is postulated to contribute to pathogen fitness in the physiologically diverse human population. H. pylori adherence to ABO and Lewis b (Leb) blood group antigens in the human stomach is mediated by the blood group antigen-binding adhesin BabA. Approximately 70% of Swedish and U.S. H. pylori clinical isolates exhibit Leb binding, but here we show that the babA gene is present in each of 10 Leb-nonbinding strains. Fluorescence microscopy identified occasional bacterial cells with a Leb-binding phenotype in populations of Leb-nonbinding strains. Thus, nonbinding seemed to be a metastable phenotype. To model metastable transition into the virulence-associated Leb-binding mode, Leb-binding clones were isolated from nonadherent strains by panning with Leb-magnetic beads and characterized. Strain 17875 has two babA genes, babA1 (silent) and babA2 (expressed). We found that a babA2-cam derivative of strain 17875 regained Leb binding by recombination of the formerly silent babA1 gene into the expressed and partially homologous babB locus. The chimeric BabB/A adhesin binds Leb with an affinity similar to that of wild-type BabA adhesin, but its expression level was lower and was subject to phase variation through slipped-strand mispairing. Equivalent results were obtained with strain NCTC11638. We propose that adhesin metastability and heterogeneity contributes to bacterial fitness and results in some clones having potential for periodic activation and deactivation of virulence appropriate for intensity of the host response to infection.

Adhesins, Bacterial↗
PubMed2004

Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12.

Bacterial-host attachment by means of bacterial adhesins is a key step in host colonization. Phase variation (reversible on-off switching) of the type 1 fimbrial adhesin of Escherichia coli involves a DNA inversion catalyzed by FimB (switching in either direction) or FimE (mainly on-to-off switching). fimB is separated from the divergent yjhATS operon by a large (1.4 kbp) intergenic region. Short ( approximately 28 bp) cis-active elements (regions 1 and 2) close to yjhA stimulate fimB expression and are required for sialic acid (Neu(5)Ac) sensitivity of its expression [El-Labany, S., Sohanpal, B. K., Lahooti, M., Akerman, R. & Blomfield, I. C. (2003) Mol. Microbiol. 49, 1109-1118]. Here, we show that whereas NanR, a sialic acid-response regulator, binds to region 1, NagC, a GlcNAc-6P-responsive protein, binds to region 2 instead. The NanR- and NagC-binding sites lie adjacent to deoxyadenosine methylase (Dam) methylation sites (5'-GATC) that are protected from modification, and the two regulators are shown to be required for methylation protection at regions 1 and 2, respectively. Mutations in nanR and nagC diminish fimB expression, and both fimB expression and FimB recombination are inhibited by GlcNAc (3- and >35-fold, respectively). Sialic acid catabolism generates GlcNAc-6-P, and whereas GlcNAc disrupts methylation protection by NagC alone, Neu(5)Ac inhibits the protection mediated by both NanR and NagC as expected. Type 1 fimbriae are proinflammatory, and host defenses enhance the release of both Neu(5)Ac and GlcNAc by a variety of mechanisms. Inhibition of type 1 fimbriation by these amino sugars may thus help balance the interaction between E. coli and its hosts.

Acetylglucosamine↗
PubMed1980

Analysis of the nucleotide sequence of an invertible controlling element.

The nucleotide sequence of the inversion region responsible for flagellar phase variation in Salmonella was determined. The inversion region is 995 base pairs (bp) in length and is bounded by a 14-bp inverted repeat sequence. A homologous recombination event between the 14-bp inverted repeat sequences would result in the inversion of the DNA segment between them. Sequence homologies with other systems suggest that the 14-bp inverted repeat sequences may have some general significance as sites for specific recombinational events. The gene which specifies H2 flagellin synthesis begins 16 bp outsie the inversion region. Within the inversion region, an open translational frame exists which could encode a low molecualr weight polypeptide (190 amino acids).

Amino Acid Sequence↗
PubMed1984

Two-dimensional S1 nuclease heteroduplex mapping: detection of rearrangements in bacterial genomes.

A method of two-dimensional S1 nuclease heteroduplex mapping was developed to detect gene rearrangements and repeated sequences in total bacterial chromosomes. To detect DNA rearrangements between two variant bacterial strains, total chromosomal DNA preparations from the two strains are digested with four-base-recognizing restriction enzymes, mixed together, denatured, renatured, and separated on first-dimension polyacrylamide slab gels. Gel strips are cut out and soaked in a buffer containing S1 nuclease, which diffuses into the strips and digests the DNA fragments at single-stranded regions. The digested DNA is then electrophoresed in a second dimension perpendicular to the first dimension. DNA heteroduplexes that were digested by the S1 nuclease are resolved as distinct spots below a bright unresolved band of homoduplex. This report describes testing of this method on a model system consisting of two nearly isogeneic strains of Escherichia coli, and the application of this method in detecting DNA rearrangements associated with phase variation in Myxococcus xanthus.

Chromosome Mapping↗
PubMed1996

DNA repeats identify novel virulence genes in Haemophilus influenzae.

The whole genome sequence (1.83 Mbp) of Haemophilus influenzae strain Rd was searched to identify tandem oligonucleotide repeat sequences. Loss or gain of one or more nucleotide repeats through a recombination-independent slippage mechanism is known to mediate phase variation of surface molecules of pathogenic bacteria, including H. influenzae. This facilitates evasion of host defenses and adaptation to the varying microenvironments of the host. We reasoned that iterative nucleotides could identify novel genes relevant to microbe-host interactions. Our search of the Rd genome sequence identified 9 novel loci with multiple (range 6-36, mean 22) tandem tetranucleotide repeats. All were found to be located within putative open reading frames and included homologues of hemoglobin-binding proteins of Neisseria, a glycosyltransferase (lgtC gene product) of Neisseria, and an adhesin of Yersinia. These tetranucleotide repeat sequences were also shown to be present in two other epidemiologically different H. influenzae type b strains, although the number and distribution of repeats was different. Further characterization of the lgtC gene showed that it was involved in phenotypic switching of a lipopolysaccharide epitope and that this variable expression was associated with changes in the number of tetranucleotide repeats. Mutation of lgtC resulted in attenuated virulence of H. influenzae in an infant rat model of invasive infection. These data indicate the rapidity, economy, and completeness with which whole genome sequences can be used to investigate the biology of pathogenic bacteria.

Animals↗
PubMed2004

Haemophilus somnus virulence factors and resistance to host immunity.

Haemophilus somnus ('Histophilus somni) is a Gram-negative bacterium and opportunistic pathogen associated with multisystemic diseases of bovines. Some strains of H. somnus are relatively avirulent, but are biochemically and antigenically similar to the virulent strains. Several virulence factors have been identified in H. somnus, of which lipo-oligosaccharide phase variation, induction of apoptosis, intraphagocytic survival and immunoglobulin Fc binding proteins have been well studied. The sequencing of the genomes of two strains of H. somnus has facilitated the identification of genes responsible for distinctive attributes within this species and related bacteria. The genetic characterization of this bacterium will enhance our understanding of H. somnus virulence factors and facilitate the development of new and improved vaccines. This review presents an overview of H. somnus virulence factors, their role in resistance to host defenses and pathogenesis, and the host immune response to this bacterium. Current areas of investigation in the post-genomic era and recent insights into new pathogenic mechanisms are also discussed.

Animals↗
PubMed1987

Flow cytometric analysis of the effects of 0.4 MeV fission neutrons on mouse spermatogenesis.

(C57Bl/Cne X C3H/Cne)F1 male mice were irradiated with single acute doses of 0.4 MeV neutrons ranging from 0.05 to 2 Gy, and testis cell suspensions were prepared for cytometric analysis of the DNA content 2-70 days after irradiation. Various cell subpopulations could be identified in the control histogram including mature and immature spermatids, diploid spermatogonia and spermatocytes, tetraploid cells and cells in the S-phase. Variations in the relative proportions of different cell types were detected at each dose and time, reflecting lethal damage induced on specific spermatogenetic stages. The reduction of the number of elongated spermatids 28 days after irradiation was shown to be a particularly sensitive parameter for the cytometrical assessment of the radiosensitivity of differentiating gonia. A D0 value of 0.13 Gy was calculated and compared with data obtained after X-irradiation, using the same experimental protocol. In the latter case a biphasic curve was obtained over the dose range from 0.25 to 10 Gy, possibly reflecting the existence of some cell population heterogeneity. RBE values were estimated at different neutron doses relative to the radiosensitive component of the X-ray curve, and ranged from 3.3 to 4, in agreement with data in the literature. Genotoxic effects were monitored 7 days after irradiation by a dose-dependent increase of the coefficient of variation (CV) values of the round spermatid peak, reflecting the induction of numerical and structural chromosome aberrations, and 14 or 21 days after irradiation by the detection of diploid elongated spermatids, probably arising from a radiation-induced complete failure of the first or second meiotic division.

Animals↗
PubMed1996

Conservation of the lipooligosaccharide synthesis locus lgt among strains of Neisseria gonorrhoeae: requirement for lgtE in synthesis of the 2C7 epitope and of the beta chain of strain 15253.

The present study was undertaken to examine the extent to which the lgt locus varies among strains of gonococci. This locus encodes five glycosyl transferases involved in the synthesis of the lipooligosaccharide (LOS) of Neisseria gonorrhoeae. We examined seven gonococcal strains and found that the structure of the lgt locus is conserved among six of these strains. The locus is strikingly altered in strain 15253. This is one of the few strains where extensive structural analysis of its LOS is available, and therefore, we defined the altered lgt locus and focused on the reactivity of mAB 2C7. We found that strain 15253 contains only two lgt genes, lgtA and lgtE. As in F62, lgtA encodes a GlcNAc transferase and is subject to phase variation. In addition, by analysis of deletion mutants, we found that lgtE, which encodes a galactosyl transferase that is required for elongating the alpha-chain, is also necessary for completing the beta chain.

Blotting, Southern↗
PubMed2004

Helicobacter pylori modulates the T helper cell 1/T helper cell 2 balance through phase-variable interaction between lipopolysaccharide and DC-SIGN.

The human gastric pathogen Helicobacter pylori spontaneously switches lipopolysaccharide (LPS) Lewis (Le) antigens on and off (phase-variable expression), but the biological significance of this is unclear. Here, we report that Le+ H. pylori variants are able to bind to the C-type lectin DC-SIGN and present on gastric dendritic cells (DCs), and demonstrate that this interaction blocks T helper cell (Th)1 development. In contrast, Le- variants escape binding to DCs and induce a strong Th1 cell response. In addition, in gastric biopsies challenged ex vivo with Le+ variants that bind DC-SIGN, interleukin 6 production is decreased, indicative of increased immune suppression. Our data indicate a role for LPS phase variation and Le antigen expression by H. pylori in suppressing immune responses through DC-SIGN.

Cell Adhesion Molecules↗
PubMed2006

Helicobacter pylori HopH (OipA) and bacterial pathogenicity: genetic and functional genomic analysis of hopH gene polymorphisms.

BACKGROUND: Expression of the Helicobacter pylori outer membrane protein HopH is regulated by phase variation within a CT dinucleotide repeat motif of the hopH gene. METHODS: To investigate the importance of HopH for bacterial pathogenicity, we performed a detailed functional genomic and population-based genetic characterization of this contingency locus. RESULTS: Sequencing of hopH in H. pylori strains from 58 patients revealed that the hopH "on" genotype is linked to bacterial virulence determinants, such as the vacAs1, vacAm1, babA2, and, most strongly, cagA genotypes. hopH mutagenesis resulted in reduced bacterial adherence to gastric epithelia in vitro. Complementation of hopH in trans restored the adherence properties of hopH mutants. Although HopH has been previously linked to proinflammatory epithelial signaling, hopH mutagenesis did not alter epithelial interleukin-8 secretion in vitro. Comparative epithelial gene-expression profiling by cDNA microarrays revealed no significant differences between the wild-type-specific and hopH mutant-specific transcriptomes. By contrast, a large set of genes was differentially regulated in a cag pathogenicity island-dependent manner. CONCLUSION: An in-frame hopH gene may be linked to gastroduodenal diseases because of its association with other virulence factors or increased bacterial adherence and colonization. The strong linkage with cagA indicates that HopH may contribute to the fitness of cagA-positive strains in vivo.

Adhesins, Bacterial↗
PubMed1978

RF magnetic field penetration, phase shift and power dissipation in biological tissue: implications for NMR imaging.

The magnetic field penetration, phase shift and power deposition in planar and cylindrical models of biological tissue exposed to a sinusoidal time-dependent magnetic field have been investigated theoretically over the frequency range 1 to 100 MHz. The results are based on measurements of the relative permittivity and resistivity dispersions of a variety of freshly excised rat tissue at 37 and 25 degrees C, and are analysed in terms of their implications for human body nuclear magnetic resonance (NMR) imaging. The results indicate that at NMR operating frequencies much greater than about 30 MHz, magnetic field amplitude and phase variations experienced by the nuclei may cause serious distortions in an image of a human torso. The maximum power deposition envisaged during an NMR imaging experiment on a human torso is likely to be comparable to existing long-term safe exposure levels, and will depend ultimately on the imaging technique and NMR frequency employed.

Animals↗
PubMed1989

Measurement of the frequency response and common-mode gain of neonatal respiratory pressure and flow measurement systems. Part 1: Apparatus.

It is necessary, especially in neonatal work, for investigators to measure accurately the frequency response and common mode gain of respiratory pressure and flow transducers in air and other gas mixtures. Many of the systems designed for this task have been incompletely analysed and have unknown frequency responses themselves. We analyse aspects of systems employed previously and show that substantial amplitude and phase errors may have occurred. We describe a plethysmograph-based system which operates in any available gas mixture. A mathematical model of the acoustic microphone used as reference transducer, the microphone preamplifier, and the thermal behaviour of the plethysmograph, is developed to quantify the frequency response of the system. Maximum deviation from a perfect response is less than 1% in amplitude and 1 degree in phase for both pressure and flow measurements over the range 1-100 Hz. Measurements using a pressure transducer mounted on the tip of a catheter indicate that the error due to amplitude and phase variation in the plethysmograph is less than 0.1 dB and 0.4 degrees at 100 Hz.

Humans↗
PubMed2026

TPMM: three-component posterior mixture model enables robust inverton detection in low-depth metagenomes and suggests potential viral invertons.

SUMMARY: Bacterial phase variation enables reversible, locus-specific phenotypic switching, often driven by DNA inversion (invertons). To identify these events, researchers commonly rely on sequencing reads that provide orientation-specific support. Metagenomic sequencing, which captures total genetic material independent of cultivation, offers a powerful platform for the comprehensive study of invertons. However, computational inverton calling from metagenomic data is difficult at low sequencing depth: hard read-support cutoffs can miss true events, while sequence-only predictors lack read-backed interpretability and uncertainty quantification. To address this, we present TPMM, a three-component posterior mixture model for inverton calling in metagenomic data. TPMM explicitly incorporates sequencing depth to formulate inverton detection as a probabilistic mixture problem. Starting from candidates flanked by inverted repeats, the model classifies the candidates into noise, low-probability, or high-probability inversion signals using read evidence. Finally, TPMM assigns posterior probabilities as soft labels and applies cumulative Bayesian False Discovery Rate control to robustly identify true invertons. On two real gut metagenomic datasets, TPMM agrees well with PhaseFinder at high depth but recovers substantially more invertons under systematic downsampling, demonstrating superior performance in sparse-data regimes. We further examine potential reversible inversion elements in viral genomes and provide supporting analyses, suggesting a broader scope for inversion-mediated regulation. AVAILABILITY: The source code of TPMM is available via: https://github.com/KennyxxD/TPMM.

Metagenomics↗