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Common-path phase-shift interferometry surface plasmon resonance imaging system.

Surface plasmon resonance (SPR) and common-path phase-shift interferometry (PSI) techniques are integrated in a biosensing imaging system for measuring the two-dimensional spatial phase variation caused by biomolecular interactions on a sensing chip without the need for additional labeling. The common-path PSI technique has the advantage of long-term stability, even when it is subjected to external disturbances. Hence the system meets the requirements of the real-time kinetic studies involved in biomolecular interaction analysis. The proposed SPR-PSI imaging system demonstrates a detection limit of a 2 x 10(-7) refractive-index change, a long-term phase stability of 2.5 x 10(-4) pi rms for 4 h, and a spatial phase resolution of 10(-3) pi with a lateral resolution of 100 microm.

Biosensing Techniques↗

[Changes in the activity of antioxidizing enzymes during spermatogenesis].

A study was made of variation in the activity of the antioxidant defense system enzymes superoxide dismitase (SOD), glutathione peroxidase, (GP) and glutathione-S-transferase (GT) in the cells of mouse spermatogenic epithelium. The cells were fractionated in the gradient of human serum albumin using the STAPUT system. SOD activity was comparable to that in liver cells, that of GP was one order to magnitude lower, and that of GT one order of magnitude higher than in the liver. Differentiation of spermatogenic cells demonstrated phase variations in the activity of these enzymes, with a maximum seen at the stage of late pachytene spermatocytes. SOD, GP and GT activities were discovered to be reduced in postmeiotic cells (early spermatid fractions) by 2.8-3.5; 1.9-2.3 and 4.2-5.6 times, respectively. That reduction was followed by activation of the enzymes at the late stages of spermiogenesis.

Animals↗

Orientation-dependent enhancement by H-NS of the activity of the type 1 fimbrial phase switch promoter in Escherichia coli.

Phase variation of type 1 fimbriation in Escherichia coli is associated with the inversion of a 314-bp DNA element, positioned proximal to and upstream of fimA, which encodes the major type 1 fimbrial subunit. This DNA switch region contains a promoter that drives transcription of fimA only when the switch is in the ON orientation. Using chromosomal and plasmid-borne lacZ reporter cassettes, we show here how the global regulator H-NS affects the activity of the fimA promoter. In phase-locked reporter cassettes the activity of the fimA promoter was found to be enhanced in a hns-positive background, but only when the switch was in the ON orientation. Also, the number of fimbriae produced by a phase-locked ON strain was significantly higher in a hns-positive background. By means of competitive gel retardation and DNase I protection assays, H-NS binding to DNA segments adjacent to and within the phase switch region was demonstrated.

Bacterial Proteins↗

Novel lipopolysaccharide biosynthetic genes containing tetranucleotide repeats in Haemophilus influenzae, identification of a gene for adding O-acetyl groups.

Many of the genes for lipopolysaccharide (LPS) biosynthesis in Haemophilus influenzae are phase variable. The mechanism of this variable expression involves slippage of tetranucleotide repeats located within the reading frame of these genes. Based on this, we hypothesized that tetranucleotide repeat sequences might be used to identify as yet unrecognized LPS biosynthetic genes. Synthetic oligonucleotides (20 bases), representing all previously reported LPS-related tetranucleotide repeat sequences in H. influenzae, were used to probe a collection of 25 genetically and epidemiologically diverse strains of non-typeable H. influenzae. A novel gene identified through this strategy was a homologue of oafA, a putative O-antigen LPS acetylase of Salmonella typhimurium, that was present in all 25 non-typeable H. influenzae, 19 of which contained multiple copies of the tetranucleotide 5'-GCAA. Using lacZ fusions, we showed that these tetranucleotide repeats could mediate phase variation of this gene. Structural analysis of LPS showed that a major site of acetylation was the distal heptose (HepIII) of the LPS inner-core. An oafA deletion mutant showed absence of O-acetylation of HepIII. When compared with wild type, oafA mutants displayed increased susceptibility to complement-mediated killing by human serum, evidence that O-acetylation of LPS facilitates resistance to host immune clearance mechanisms. These results provide genetic and structural evidence that H. influenzae oafA is required for phase variable O-acetylation of LPS and functional evidence to support the role of O-acetylation of LPS in pathogenesis.

Acetyltransferases↗

A conserved DNA sequence is required for efficient gonococcal pilin antigenic variation.

Antigenic variation of the Neisseria gonorrhoeae pilus occurs when a variant pilin sequence from a silent locus recombines into the expression locus by predominantly unidirectional, homologous recombination. At the 3' end of all pilin loci lies a conserved DNA sequence, called the Sma/Cla repeat, which has sequence similarity to several recombinase-binding sites, and therefore may be involved in pilin recombination. We have developed a novel reverse transcriptase/polymerase chain reaction (RT-PCR) assay for direct monitoring of pilin recombination, and both RT-PCR and phase variation were used to examine pilin recombination in a gonococcal strain that had had the pilE Sma/Cla repeat removed. Results from these experiments showed a decrease in pilin recombination when the Sma/Cla sequence was deleted from the expression locus, showing that a specialized site (Sma/Cla) is involved in efficient pilin recombination.

Antigenic Variation↗

Phenotypic switching of variable surface lipoproteins in Mycoplasma bovis involves high-frequency chromosomal rearrangements.

Mycoplasma bovis, an important pathogen of cattle, was recently shown to possess a family of phase- and size-variable membrane surface lipoprotein antigens (Vsps). These proteins spontaneously undergo noncoordinate phase variation between ON and OFF expression states, generating surface antigenic variation. In the present study, we show that the spontaneously high rate of Vsp phenotypic switching involves DNA rearrangements that occur at high frequency in the M. bovis chromosome. A 1.5-kb HindIII genomic fragment carrying the vspA gene from M. bovis PG45 was cloned and sequenced. The deduced VspA amino acid sequence revealed that 80% of the VspA molecule is composed of reiterated intragenic coding sequences, creating a periodic polypeptide structure. Four distinct internal regions of repetitive sequences in the form of in-tandem blocks extending from the N-terminal to the C-terminal portion of the Vsp product were identified. Southern blot analysis of phenotypically switched isogenic lineages representing ON or OFF phase states of Vsp products suggested that changes in the Vsp expression profile were associated with detectable changes at the DNA level. By using a synthetic oligonucleotide representing a sequence complementary to the repetitive vspA gene region as a probe, we could identify the vspA-bearing restriction fragment undergoing high-frequency reversible rearrangements during oscillating phase transition of vspA. The 1.5-kb HindIII fragment carrying the vspA gene (on state) rearranged and produced a 2.3-kb HindIII fragment (OFF state) and vice versa. Two newly discovered vsp genes (vspE and vspF) were localized on two HindIII fragments flanking the vsp gene upstream and downstream. Southern blot hybridization with vspE- and vspF-specific oligonucleotides as probes against genomic DNA of VspA phase variants showed that the organization and size of the fragments adjacent to the vspA gene remained unchanged during VspA ON-OFF switching. The mechanisms regulating the vsp genes are yet unknown; our findings suggest that a recombinative mechanism possibly involving DNA inversions, DNA insertion, or mobile genetic elements may play a role in generating the observed high-frequency DNA rearrangements.

Amino Acid Sequence↗

Evidence for a DNA inversion system in Bordetella pertussis.

The expression of virulence-associated genes in Bordetella pertussis can be lost in three ways: phase variation, antigenic modulation, or serotype conversion. The mechanism(s) of these alterations in gene expression is unclear. B. pertussis chromosomal DNA was probed with cloned pin genes from Escherichia coli and cloned hin genes from Salmonella typhimurium. DNA duplex melting temperature experiments indicated significant homology between B. Pertussis chromosomal DNA and both DNA inversion genes. Southern blots using the hin gene probe showed homology with a 15 kb EcoRI fragment of B. pertussis chromosomal DNA. We postulate here that B. pertussis contains a DNA inversion system which may be responsible for serotype conversion or virulence phase change in this organism.

Blotting, Southern↗

Expression of paragloboside-like lipooligosaccharides may be a necessary component of gonococcal pathogenesis in men.

To learn how lipooligosaccharide (LOS) phase variations affect pathogenesis, we studied two male volunteers who were challenged intraurethrally with Neisseria gonorrhoeae that make a single LOS of 3,600 daltons and sequentially followed LOS expression by gonococci as urethritis developed. LOS variation occurred in vivo. Signs and symptoms of gonorrhea began with the appearance of variants making 4,700-dalton LOS that are immunochemically similar to glycosphingolipids of human hematopoietic cells (Mandrell, R.E., J.M. Griffiss, and B.A. Macher. 1989. J. Exp. Med. 168:107) and that have acceptors for sialic acid. A variant that appeared at the onset of leukorrhoea was shed by 34/36 men with naturally acquired gonorrhea at the time they sought medical attention; the other two shed the variant associated with dysuria. None shed the challenge variant. These data show that in vivo phase shifts to higher molecular mass LOS that mimic human cell membrane glycolipids are associated with the development of gonococcal leukorrhea.

Carbohydrate Sequence↗

[Factors intervening in the variations of in vitro adhesion power of enterotoxinogenic colibacillus (ETEC) to human enterocytes].

Human enterotoxigenic Escherichia coli adhere to the brush border of human enterocytes. The mean number of bacteria adhering to one enterocyte (adhesion index) varied from 0.5 to 3.1 when the strains produce adhesins. Different factors related to enterocytes and to bacteria are involved in this variability. The number of bacteria which adhered to enterocytes issued from the same donor varied from from 0 to 12. Moreover the proportion of enterocytes on which several bacteria sticked did not exceed 20%. This variability might be due to the disparity in the maturation of the enterocytes. On the other hand, whatever the adhesion factors considered, the adhesion index varied according to the donors. ETEC strains did not express adhesion when bacteria were grown in a liquid medium but this capacity could be restored after transfer on solid medium. This phenomenon seemed like a phase-variation and appeared to be linked to a 4 to 6 kilobases (kb) plasmid. On the other hand, when the bacteria were grown on agar medium (CFA-agar or Mueller-Hinton agar) two phenotypes of colonies could be observed: large colonies (LC) which were composed of non-adhesive bacteria and small colonies (SC) which were composed of a majority of adhesive bacteria; when the number of subcultures was not too great, a majority of colonies presented the small colonies phenotype. The plasmid content analysis showed the segregation of a high molecular weight plasmid DNA (approximately 100 kb) for the bacteria issued from large colonies phenotype.

Age Factors↗

Design and realization of the microwave cavity in the PTB caesium atomic fountain clock CSF1.

At the Physikalisch-Technische Bundesanstalt (PTB), the caesium atomic fountain clock CSF1 was developed. One key element of it is its microwave cavity, which was designed to have a low transversal phase variation across the cavity opening. This usually is achieved by using a cylindrical cavity with a TE011 field mode, having a high intrinsic quality factor, and by feeding the cavity symmetrically via two apertures at opposite position in the cavity wall. In contrast to other solutions, the CSF1 cavity is tightly coupled to the microwave feeds (Qload approximately 2000). Therefore, detuning of the cavity resonance frequency has a reduced impact on the microwave field amplitude in the cavity compared to the case of weak coupling. Thus, a temperature stabilization of the cavity can be avoided. The extent to which the tight coupling may have an impact on the transversal phase distribution was studied. This question was solved analytically for a simplified cavity model. The results were applied to define the coupling geometry of the CSF1 cylindrical cavity in such a manner that the transversal phase distribution should become minimized. The key parameter is the electric length of the waveguides that constitute the junction to the coupling apertures. The theoretical studies are presented in some detail, and steps of the practical realization of the cavity are described.

Cesium↗

Unique regulation of SclB - a novel collagen-like surface protein of Streptococcus pyogenes.

Slipped-strand mispairing at sites containing so-called coding repeats (CRs) can lead to phase variation of surface proteins in Gram-negative bacteria. This mechanism, believed to contribute to virulence, has so far not been identified in a Gram-positive bacterium. In the genome of the Gram-positive human pathogen Streptococcus pyogenes, we identified pentanucleotide CRs within a putative signal sequence of an open reading frame (ORF) encoding a novel collagen-like surface protein, denoted SclB. In 12 S. pyogenes strains, the number of CRs in the sclB gene varied from three to 19, rendering the start codon in frame with the downstream ORF in four strains and out of frame in eight strains. A protein reacting with anti-SclB antibodies could only be solubilized from three strains, all containing an intact sclB gene. Variations in the number of CRs were observed within strains of the same M serotype and occurred during growth of S. pyogenes in fresh human blood, but not in medium. The SclB protein has a hypervariable N-terminal part, a collagen-like central part and a typical cell wall sorting sequence containing the LPXTGX motif. SclB is related to the collagen-like SclA and is, like SclA, involved in the adhesion of S. pyogenes bacteria to human cells. However, the Mga protein, known to upregulate sclA and several additional genes encoding virulence factors of S. pyogenes, downregulates sclB transcription. This observation and the potential of SclB to phase vary by slipped-strand mispairing emphasize the unique regulation of this novel S. pyogenes surface protein.

Amino Acid Sequence↗

Critical coagulation concentration for a suspension of cation-absorptive biocolloids.

Critical coagulation concentration (CCC) of a biocolloidal suspension is investigated theoretically by taking into account the influences of cationic absorption in particulate membrane phase, variation in dielectric constant, size of charged species and nonuniform distribution of fixed membrane groups. Here, an increase in both valence and effective radius of the original functional group (OFG) via absorption of electrolyte cation(s) is especially considered. The simulated results indicate that stronger membrane electricity yields a larger electrostatic repulsion and a higher potential energy, which generates a higher CCC. A lower CCC can be resulted from a larger (1) cation-functional group complex (CFGC) for a fixed difference between the radius of CFGC and that of OFG, Delta, (2) number of OFG(s) involved in the formation of a CFGC, (3) Delta for a positively charged CFGC, (4) dielectric constant of main membrane phase, in general, (5) membrane thickness for a constant amount of space-average functional groups, and (6) effective radius of anions. CCC decreases with the following parameters: (1) Delta for a negatively charged CFGC, (2) equilibrium constant of the reaction of cationic absorption, (3) nonuniform feature index of fixed groups, and (4) effective radius of cations.

Absorption↗

Histoplasma variation and adaptive strategies for parasitism: new perspectives on histoplasmosis.

This review summarizes the biology of Histoplasma capsulatum in relation to a wide variety of corresponding pathologies in histoplasmosis. Features of these disease syndromes can be explained in part by natural variations within the fungal population and adaptations made by individual organisms to specific environments. H. capsulatum grows as mycelia and conidia in the soil; once inhaled, the organism undergoes a dramatic morphological and physiological conversion to a yeast form. The yeasts proliferate within the phagolysosomes of macrophages, using a variety of specific strategies for intracellular survival. Even avirulent strains or variants are able to avoid being killed by macrophages and instead establish inapparent or persistent infections. The ingested avirulent organisms assume enlarged shapes similar in appearance to those seen in histological sections of tissues from patients with histoplasmosis. Respiratory tract epithelial cells also appear to play a role in persistence: within them yeasts undergo phenotypic switching akin to the phase variation observed in other pathogens. This particular change involves the loss or modification of cell wall alpha-(1,3)-glucan, which is also correlated with the spontaneous appearance of avirulent variants. The repertoire of adaptive responses and natural variations within this species probably evolved from the need to adjust to a wide range of dynamic environments. In combination with the immune status of the host, these characteristics of H. capsulatum appear to influence the epidemiology, extent, and persistence of histoplasmosis.

Animals↗

Managing variability in the summary and comparison of gait data.

Variability in quantitative gait data arises from many potential sources, including natural temporal dynamics of neuromotor control, pathologies of the neurological or musculoskeletal systems, the effects of aging, as well as variations in the external environment, assistive devices, instrumentation or data collection methodologies. In light of this variability, unidimensional, cycle-based gait variables such as stride period should be viewed as random variables and prototypical single-cycle kinematic or kinetic curves ought to be considered as random functions of time. Within this framework, we exemplify some practical solutions to a number of commonly encountered analytical challenges in dealing with gait variability. On the topic of univariate gait variables, robust estimation is proposed as a means of coping with contaminated gait data, and the summary of non-normally distributed gait data is demonstrated by way of empirical examples. On the summary of gait curves, we discuss methods to manage undesirable phase variation and non-robust spread estimates. To overcome the limitations of conventional comparisons among curve landmarks or parameters, we propose as a viable alternative, the combination of curve registration, robust estimation, and formal statistical testing of curves as coherent units. On the basis of these discussions, we provide heuristic guidelines for the summary of gait variables and the comparison of gait curves.

Journal Article↗

Molecular characterization of the Mycoplasma gallisepticum pvpA gene which encodes a putative variable cytadhesin protein.

A putative cytadhesin-related protein (PvpA) undergoing variation in its expression was identified in the avian pathogen Mycoplasma gallisepticum. The pvpA gene was cloned, expressed in Escherichia coli, and sequenced. It exhibits 54 and 52% homology with the P30 and P32 cytadhesin proteins of the human pathogens Mycoplasma pneumoniae and Mycoplasma genitalium, respectively. In addition, 50% homology was found with the MGC2 cytadhesin of M. gallisepticum and 49% homology was found with a stretch of 205 amino acids of the cytadherence accessory protein HMW3 of M. pneumoniae. The PvpA molecule possesses a proline-rich carboxy-terminal region (28%) containing two identical directly repeated sequences of 52 amino acids and a tetrapeptide motif (Pro-Arg-Pro-X) which is repeated 14 times. Genetic analysis of several clonal isolates representing different expression states of the PvpA product ruled out chromosomal rearrangement as the mechanism for PvpA phase variation. The molecular basis of PvpA variation was revealed in a short tract of repeated GAA codons, encoding five successive glutamate resides, located in the N-terminal region and subject to frequent mutation generating an in-frame UAA stop codon. Size variation of the PvpA protein was observed among M. gallisepticum strains, ranging from 48 to 55 kDa and caused by several types of deletions occurring at the PvpA C-terminal end and within the two directly repeated sequences. By immunoelectron microscopy, the PvpA protein was localized on the mycoplasma cell surface, in particular on the terminal tip structure. Collectively, these findings suggest that PvpA is a newly identified variable surface cytadhesin protein of M. gallisepticum.

Adhesins, Bacterial↗

O-antigen structural variation: mechanisms and possible roles in animal/plant-microbe interactions.

Current data from bacterial pathogens of animals and from bacterial symbionts of plants support some of the more general proposed functions for lipopolysaccharides (LPS) and underline the importance of LPS structural versatility and adaptability. Most of the structural heterogeneity of LPS molecules is found in the O-antigen polysaccharide. In this review, the role and mechanisms of this striking flexibility in molecular structure of the O-antigen in bacterial pathogens and symbionts are illustrated by some recent findings. The variation in O-antigen that gives rise to an enormous structural diversity of O-antigens lies in the sugar composition and the linkages between monosaccharides. The chemical composition and structure of the O-antigen is strain-specific (interstrain LPS heterogeneity) but can also vary within one bacterial strain (intrastrain LPS heterogeneity). Both LPS heterogeneities can be achieved through variations at different levels. First of all, O-polysaccharides can be modified non-stoichiometrically with sugar moieties, such as glucosyl and fucosyl residues. The addition of non-carbohydrate substituents, i.e. acetyl or methyl groups, to the O-antigen can also occur with regularity, but in most cases these modifications are again non-stoichiometric. Understanding LPS structural variation in bacterial pathogens is important because several studies have indicated that the composition or size of the O-antigen might be a reliable indicator of virulence potential and that these important features often differ within the same bacterial strain. In general, O-antigen modifications seem to play an important role at several (at least two) stages of the infection process, including the colonization (adherence) step and the ability to bypass or overcome host defense mechanisms. There are many reports of modifications of O-antigen in bacterial pathogens, resulting either from altered gene expression, from lysogenic conversion or from lateral gene transfer followed by recombination. In most cases, the mechanisms underlying these changes have not been resolved. However, in recent studies some progress in understanding has been made. Changes in O-antigen structure mediated by lateral gene transfer, O-antigen conversion and phase variation, including fucosylation, glucosylation, acetylation and changes in O-antigen size, will be discussed. In addition to the observed LPS heterogeneity in bacterial pathogens, the structure of LPS is also altered in bacterial symbionts in response to signals from the plant during symbiosis. It appears to be part of a molecular communication between bacterium and host plant. Experiments ex planta suggest that the bacterium in the rhizosphere prepares its LPS for its roles in symbiosis by refining the LPS structure in response to seed and root compounds and the lower pH at the root surface. Moreover, modifications in LPS induced by conditions associated with infection are another indication that specific structures are important. Also during the differentiation from bacterium to bacteroid, the LPS of Rhizobium undergoes changes in the composition of the O-antigen, presumably in response to the change of environment. Recent findings suggest that, during symbiotic bacteroid development, reduced oxygen tension induces structural modifications in LPS that cause a switch from predominantly hydrophilic to predominantly hydrophobic molecular forms. However, the genetic mechanisms by which the LPS epitope changes are regulated remain unclear. Finally, the possible roles of O-antigen variations in symbiosis will be discussed.

Animal Population Groups↗

The organic surface of 5145 Pholus: constraints set by scattering theory.

No known body in the Solar System has a spectrum redder than that of object 5145 Pholus. We use Hapke scattering theory and optical constants measured in this laboratory to examine the ability of mixtures of a number of organic solids and ices to reproduce the observed spectrum and phase variation. The primary materials considered are poly-HCN, kerogen, Murchison organic extract, Titan tholin, ice tholin, and water ice. In a computer grid search of over 10 million models, we find an intraparticle mixture of 15% Titan tholin, 10% poly-HCN, and 75% water ice with 10-micrometers particles to provide an excellent fit. Replacing water ice with ammonia ice improves the fits significantly while using a pure hydrocarbon tholin, Tholin alpha, instead of Titan tholin makes only modest improvements. All acceptable fits require Titan tholin or some comparable material to provide the steep slope in the visible, and poly-HCN or some comparable material to provide strong absorption in the near-infrared. A pure Titan tholin surface with 16-micrometers particles, as well as all acceptable Pholus models, fit the present spectrophotometric data for the transplutonian object 1992 QB1. The feasibility of gas-phase chemistry to generate material like Titan tholin on such small objects is examined. An irradiated transient atmosphere arising from sublimating ices may generate at most a few centimeters of tholin over the lifetime of the Solar System, but this is insignificant compared to the expected lag deposit of primordial contaminants left behind by the sublimating ice. Irradiation of subsurface N2/CH4 or NH3/CH4 ice by cosmic rays may generate approximately 20 cm of tholin in the upper 10 m of regolith in the same time scale but the identity of this tholin to its gas-phase equivalent has not been demonstrated.

Ammonia↗

Clonal variation in Xenorhabdus nematophila virulence and suppression of Manduca sexta immunity.

Virulence of the insect pathogen Xenorhabdus nematophila is attributed in part to its ability to suppress immunity. For example, X. nematophila suppresses transcripts encoding several antimicrobial proteins, even in the presence of Salmonella enterica, an inducer of these transcripts. We show here that virulence and immune suppression phenotypes can be lost in a subpopulation of X. nematophila. Cells that have undergone 'virulence modulation' (vmo) have attenuated virulence and fail to suppress antimicrobial transcript levels, haemocyte aggregation and nodulation in Manduca sexta insects. When plated on certain media, vmo cells have a higher proportion of translucent (versus opaque) colonies compared with non-vmo cells. Like vmo strains, translucent colony isolates are defective in virulence and immune suppression. The X. nematophila genome encodes two 'opacity' genes with similarity to the Ail/PagC/Rck family of outer membrane proteins involved in adherence, invasion and serum resistance. Quantitative polymerase chain reaction analysis shows that RNA levels of one of these opacity genes, opaB, are higher in opaque relative to translucent colonies. We propose that in X. nematophila opaB may be one of several factors involved in immune suppression during infection, and expression of these factors can be co-ordinately eliminated in a subpopulation, possibly through a phase variation mechanism.

Animals↗