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PubMed1980

Sorogen elongation and side branching during fruiting body development in Polysphondylium pallidum.

We report a cinematographic analysis of culmination in fruiting bodies of Polysphondylium pallidum. During the final stages of aggregation, sorogen elongation is slow. An increase in the rate of sorogen elongation occurs when the growing stalk contacts the substratum, lifting the cell mass into the air. The elongation process slows and finally stops as differentation of the terminal spore mass occurs. During the rapid elongation phase, variations in the rate of elongation of the main cell mass are correlated with the process of side branching. Side-branch elongation resembles elongation of the main sorogen with the rate of elongation increasing as the side-branch stalk contacts the main stalk and slowing as spore differentiation occurs. The morphological events of branching have been studied in detail and models to explain this process are discussed.

Morphogenesis↗
PubMed1992

Role of fimbrial adhesins in the pathogenesis of Escherichia coli infections.

Escherichia coli strains are able to cause intestinal (enteritis, diarrhoeal diseases) and extraintestinal (urinary tract infections, sepsis, meningitis) infections. Most pathogenic E. coli strains produce specific fimbrial adhesins, which represent essential colonization factors: intestinal E. coli strains very often carry transferable plasmids with gene clusters specific for fimbrial adhesins, like K88 and K99, or colonization factor antigens (CFA) I and II. In contrast, the fimbrial gene clusters of extraintestinal E. coli strains, such as P, S, or F1C fimbriae, are located on the chromosomes. The fimbrial adhesin complexes consist of major and minor subunit proteins. Their binding specificity can generally be assayed in hemagglutination tests. In the case of fimbrial adhesins of intestinal E. coli strains, the major subunit proteins preferentially represent the hemagglutinating adhesins, whereas minor subunit proteins are the hemagglutinins of extraintestinal E. coli strains. Recently "alternative" adhesin proteins were identified, which have the capacity to bind to eukaryotic structures different from the receptors of the erythrocytes. Fimbrial adhesins are not constitutively expressed but are stringently regulated on the molecular level. Extraintestinal E. coli wild-type strains normally carry three or more fimbrial adhesin determinants, which have the capacity to influence the expression of one another (cross talk). Furthermore the fimbrial gene clusters undergo phase variation, which seems to be important for their contribution to pathogenesis of E. coli.

Animals↗
PubMed1991

Chaperone-assisted assembly and molecular architecture of adhesive pili.

The assembly of bacterial pili as exemplified here by P and type 1 pili of E. coli is a complex process involving specific molecular interactions between structural and chaperone proteins. The assembly process occurs postsecretionally, i.e. after the subunits are translocated across the cytoplasmic membrane. In a single cell, hundreds of thousands of interactive subunits are typically surface localized and assembled into pili. Periplasmic chaperones are generally required to bind to the interactive subunits and partition them into assembly-competent complexes. The binding of the chaperone to the subunits apparently protects the interactive surfaces and prevents them from aggregating at the wrong time and place within the cell. Pili are most likely assembled into linear polymers that package into right-handed helices after their translocation through specific outer-membrane channels. Each pilus filament is a quaternary assembly of the structural subunit and several minor subunits including the adhesin moiety. Although the assembly and organization of P and type 1 pili are very similar, there are some notable differences. For example, the P pilus adhesin is located exclusively at the tips of the pilus filament and forms part of a morphologically distinct structure. In contrast, the adhesion moiety of type 1 pili is inserted into the pilus filament at intervals, but only the adhesin molecule exposed at the pilus tip is functional. The variability in isoreceptor recognition amongst P pili has been solely ascribed to structural differences in the respective adhesin molecules, whereas in type 1 pili, variability in binding specificity has been attributed to the pilus filament that influences the conformation of the adhesin moiety. Less is known about the structure or assembly of type 4 pili, which are a unique class of pili expressed by several different species of gram-negative bacteria. The phase variation of the pilC assembly gene in N. gonorrheae to the off state results in the accumulation of unassembled subunits toxic to the cells. This process exerts a strong selection pressure on the cells that triggers alterations in the pilin structural gene. Thus, antigenic variation of pili in this organism may be regulated at the level of assembly. Finally, the concept of periplasmic chaperones in postsecretional assembly is most likely a general phenomenon in the biology of gram-negative bacteria. The investigations of pilus assembly will continue to provide insight into the details of how macromolecular assembly reactions are coordinated in the bacterial cell and how the regulation of assembly genes can profoundly affect biological processes.

Adhesins, Escherichia coli↗
PubMed1996

Molecular biology of mycoplasmas.

Although mycoplasmas lack cell walls, they are in many respects similar to the gram-positive bacteria with which they share a common ancestor. The molecular biology of mycoplasmas is intriguing because the chromosome is uniquely small (< 600 kb in some species) and extremely A-T rich (as high as 75 mol% in some species). Perhaps to accommodate DNA with a lower G + C content, most mycoplasmas do not have the "universal" genetic code. In these species, TGA is not a stop codon; instead it encodes tryptophan at a frequency 10 times greater than TGG, the usual codon for this amino acid. Because of the presence of TGA codons, the translation of mycoplasmal proteins terminates prematurely when cloned genes are expressed in other eubacteria, such as Escherichia coli. Many mycoplasmas possess strikingly dynamic chromosomes in which high-frequency changes result from errors in DNA repair or replication and from highly active recombination systems. Often, high-frequency changes in the mycoplasmal chromosome are associated with antigenic and phase variation, which regulate the production of factors critical to disease pathogenesis.

Chromosomes, Bacterial↗
PubMedDate not supplied

In vivo micromechanical measurements of the organ of Corti in the basal cochlear turn.

Cochlear mechanical measurements of organ of Corti motion are generally accomplished in the apical or basal turn as in vivo or in vitro studies. In the apex it is possible to observe and measure tectorial membrane vibration as well as vibrations of structures such as the reticular lamina or the basilar membrane (BM). However, compared to the basal turn, cochlear amplification and nonlinearity are not strong in the apex. Basal turn studies have typically been limited to point location measurements of the BM but improved technology for laser interferometry is now making possible the spatial mapping of BM motion. The 'complexity' of BM motion in the radial direction (particularly the phase variation) is important to new models of cochlear wave amplification. In future work it may be possible to learn about vibration of structures within the organ of Corti.

Animals↗
PubMed2006

Distortion product otoacoustic emissions: a time domain analysis.

Distortion product otoacoustic emissions (DPOAEs) provide relatively easily accessible external information about internal properties of the inner ear. A primary result is that the detection of normal DPOAE components is a strong indicator of normal functioning of the cochlear mechanics. The details of amplitude and phase behavior of the DPOAEs, and the development over time (DPOAE delay) are not fully understood and subject of some debate. In this paper, I would like to emphasize the view that precise time domain experiments and time domain model analysis provide a superb tool, the power of which is generally underestimated. Results are presented from a model analysis in which the primary-tone phase variation technique introduced by Whitehead et al. was employed successfully.

Acoustic Stimulation↗
PubMed1997

Dissolution of mercury from dental amalgam at different pH values.

Dissolution of mercury from dental amalgam has been shown to be diminished by the formation of a tin oxide film on the surface of the mercury-rich gamma 1 phase (Marek, 1990b). Since tin oxides dissolve at low pH values (Deltombe et al., 1974), acidic conditions in the oral cavity may cause an increase in the mercury release. The purpose of this study was to determine the effect of acidity in the range of pH 1 to pH 8 on the rate of mercury dissolution in synthetic saliva from tin-free and tin-containing gamma 1 phase and two commercial dental amalgams. The tested hypothesis was that pH affects mercury dissolution only when a protective oxide film dissolves in an acidic environment. After exposures of the specimens for 2 hr or 24 hr in sealed glass bottles, the solutions were analyzed by flameless atomic absorption spectrophotometry for mercury and silver. The results have shown pH-independent mercury dissolution in the range of pH 3 to 8, and a much faster dissolution at pH 1. At all pH values, more mercury dissolved from the tin-free phase than from the tin-containing phase, and the rate of dissolution was lowest for the dental amalgams. The results were affected by the length of the test exposure. The pH independence in a wide range of pH values has been attributed to the atomic mechanism of mercury dissolution. The low rate of mercury dissolution from specimens containing tin has been explained by the formation of a barrier tin oxide film, which dissolved only at the lowest pH. Dissolution of silver at low pH values is believed to have accelerated dissolution of mercury from the tin-free gamma 1 phase. Variation of the dissolution rate with concentration of the dissolved species and kinetics of oxide film dissolution caused the effect of the exposure period.

Analysis of Variance↗
PubMed2006

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts.

BACKGROUND: More than 12,000 simple sequence repeats (SSRs) have been identified in the genome of Burkholderia mallei ATCC 23344. As a demonstrated mechanism of phase variation in other pathogenic bacteria, these may function as mutable loci leading to altered protein expression or structure variation. To determine if such alterations are occurring in vivo, the genomes of various single-colony passaged B. mallei ATCC 23344 isolates, one from each source, were sequenced from culture, a mouse, a horse, and two isolates from a single human patient, and the sequence compared to the published B. mallei ATCC 23344 genome sequence. RESULTS: Forty-nine insertions and deletions (indels) were detected at SSRs in the five passaged strains, a majority of which (67.3%) were located within noncoding areas, suggesting that such regions are more tolerant of sequence alterations. Expression profiling of the two human passaged isolates compared to the strain before passage revealed alterations in the mRNA levels of multiple genes when grown in culture. CONCLUSION: These data support the notion that genome variability upon passage is a feature of B. mallei ATCC23344, and that within a host B. mallei generates a diverse population of clones that accumulate genome sequence variation at SSR and other loci.

Animals↗
PubMed2003

Diversity in coding tandem repeats in related Neisseria spp.

BACKGROUND: Tandem repeats contained within coding regions can mediate phase variation when the repeated units change the reading frame of the coding sequence in a copy number dependent manner. Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded. Three complete neisserial genomes were analyzed and compared to identify coding tandem repeats where the number of copies of the repeat will have some structural consequence for the protein. This is the first study to address coding tandem repeats that may affect protein structures using comparative genomics, combined with a population survey to investigate which show interstrain variability. RESULTS: A total of 28 genes were identified. Of these, 22 contain coding tandem repeats that vary in copy number between the three sequenced strains, three strain specific genes were included for investigation on the basis of having >90% identity between repeated units, and three genes with repeated elements of >250 bp were included although no length variations were seen in the genomes. Amplification, and sequencing of repeats showing altered copy number, of these 28 coding tandem repeat containing regions, from a set of largely unrelated strains, revealed further repeat length variation in several cases. CONCLUSION: Eighteen genes were identified which have variation in repeat copy number between strains of the same species, twelve of which show greater diversity in repeat copy number than is present in the sequenced genomes. In some cases, this may reflect a mechanism for the generation of antigenic variation, as previously described in other species. However, some of the genes identified encode proteins with cytoplasmic functions, including sugar metabolism, DNA repair, and protein production, in which repeat length variation may have other functions. Coding tandem repeats appear to represent a largely unexplored mechanism of generating diversity in the Neisseria spp.

Adhesins, Bacterial↗
PubMed2006

Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori.

BACKGROUND: Population structures are normally determined using genes under minimal functional selection. In this study we have assessed genes that are not always essential, show differences in alleles between strains, and are involved in the directly host-selectable phenotype of LPS biosynthesis. RESULTS: Eight complete LPS biosynthesis genes, seven of which are associated with phase variation in some or all strains of Helicobacter pylori, have been sequenced and their divergence analyzed. The differences observed indicate that recombination within these genes largely reflects exchange between strains within the population lineages previously determined on the basis of MLST using housekeeping genes. This indicates that the differences that are used for MLST are likely to broadly associate with genes under functional selection, and differences in strain behaviour. However, instances of exchange between the subpopulations were identified, including the hpAfrica2 subpopulation. Further, there were other differences in gene complements and the chromosomal location of genes indicative of greater diversity within the population than is revealed by the available genome sequences and comparative genome hybridization studies. CONCLUSION: These results indicate that the described population structure based upon MLST is broadly a good basis for studying the biology of H. pylori, but that individual alleles may not follow these associations. As a consequence, when working in unsequenced strains, it is necessary to carefully check the presence, sequence, and distribution of any individual gene of interest.

Alleles↗
PubMed1986

Regional hyperthermia for extensive pelvic tumours using an annular phased array applicator: a feasibility study.

Twenty patients with extensive pelvic tumours have been treated with radiotherapy and regional hyperthermia using an annular phased array applicator (APA). The majority of patients had bulky disease with a mean tumour volume of 206 cm3. In 63 of 67 attempted treatments heating was achieved, temperatures in excess of 42 degrees C being reached in the pelvis in 78%. Heat doses, however, were low, only 41% of treatments exceeding 5 min equivalent at 43 degrees C. Treatment was usually limited by acute toxicity and, although this was marked, it was of short duration and no long-term sequelae have been noted. With gain in operator experience, later treatments have achieved improved thermal doses. Response was difficult to assess but we have documented responses in six of 12 assessable patients. Palliation has been achieved in all patients with symptoms. Preliminary attempts to shift the region of maximum heating by phase variations in the APA output are promising, and this technique should improve the quality of treatments and reduce toxicity. The APA is thus capable of inducing pelvic regional hyperthermia, and a randomised controlled study is now planned to assess the value of pelvic hyperthermia as a treatment modality.

Adult↗
PubMed2002

Heterodyne measurements of laser light scattering by a turbulent phase screen.

We report experiments in which a fiber-coupled heterodyne laser system operating at a wavelength of 1.5 microm is used to measure the phase fluctuations induced on a laser beam by passage through a thin layer of turbulent air and subsequent propagation through free space. We investigate the statistical properties and power spectra of the phase and its rate of change, in addition to the intensity statistics. We find that the power spectrum of the rate of change of phase has a simple negative exponential form. We discuss our results in the context of the problem of detection of phase variations over an extended turbulent atmospheric path.

Journal Article↗
PubMed2003

Visualization of phase objects by use of a differentiation filter.

For the visualization of phase objects by use of a differentiation filter, the phase variation is changed into the intensity variation by differentiation, and then the differentiated image is integrated. In the method used in practice, the differentiated image has been recorded on a film, and then integrated by use of a filter. In this paper, however, the image differentiated by means of a filter is entered into a computer using a CCD camera and then integrated. As a result, the method provides rapid on-line processing. We have performed computer simulations and a detailed analysis of the differentiation filter and also provide the experimental results of three-dimensional image visualization.

Journal Article↗
PubMed2005

Code counting of optical fringes: methodology and realization.

A new optical fringe-counting method that entails coding interference fringes is proposed. This method features not only the implementation of reliable bidirectional optical fringe counting but also the accurate counting of oscillating optical fringes. Its main merit is the achievement of a higher phase resolution, lambda/16 (lambda, wavelength), as opposed to lambda/8 of earlier fringe-counting methods. The robustness of fringe-code counting with regard to relative phase variations in the sine and cosine interference signals constitutes another merit of this method. The principle and realization circuit of the fringe-code-counting method are described in detail, and the experimental results with a resolution of lambda/16 are presented to show the feasibility of this method.

Journal Article↗
PubMed2005

Grating projection system for surface contour measurement.

A grating projection system is a low-cost surface contour measurement technique that can be applied to a wide range of applications. There has been a resurgence of interest in the technique in recent years because of developments in computer hardware and image processing algorithms. We describe a method that projects a phase-shifted grating through a lens on an object surface. The deformed grating image on the object surface is captured by a CCD camera for subsequent analysis. Phase variation is achieved by a linear translation stage on which the grating is mounted. We compare the experimental results with the test results using a mechanical stylus method.

Journal Article↗
PubMed2005

Surface profiling of a transparent object by use of phase-shifting Talbot interferometry.

Talbot interferometry is used to study the surface profile of a transparent object. Periodic patterns are produced by illuminating a grating with a collimated laser beam. The object is placed on the self-image plane of the grating. The deformed grating image, which interferes with another grating, results in the Talbot interferometric fringes. The fringe pattern is recorded on a CCD camera for subsequent analysis, and the phase variation is achieved by a linear translation stage. In this application two specimens are tested to demonstrate the validity of the method; one is a transparent object with a spherical shape with a height of less than 350 microm, and the other is a transparent object with an uneven surface of 50-microm average height. The experimental results are compared with the test results obtained with the mechanical stylus method.

Journal Article↗
PubMed2006

Stress-mapping sensors for high-power adaptive micro-optics.

Continuous deformable membrane mirrors are becoming more attractive for use in adaptive optics because they cause no diffraction in the reflected beam and ensure smooth and continuous phase variations across the mirrors. However, when such mirrors are used to correct a high-power incident wave front, the absorption in the coatings causes the temperature of the membrane to increase, thereby creating in-plane thermal stress due to the rigidly clamped boundaries. We present a technique to measure thermal stress in such nondeforming membrane structures. The directional stress and temperature effects are simultaneously measured and decoupled in micromachined membrane mirrors by using a group of three ion-implanted silicon resistors with different orientations. In stress measurements made with incident power, the sensors measure changes in compressive thermal stress to within 80-90 kPa.

Journal Article↗
PubMed2007

Coherence estimation in synthetic aperture radar data based on speckle noise modeling.

In the past we proposed a multidimensional speckle noise model to which we now include systematic phase variation effects. This extension makes it possible to define what is believed to be a novel coherence model able to identify the different sources of bias when coherence is estimated on multidimensional synthetic radar aperture (SAR) data. On the one hand, low coherence biases are basically due to the complex additive speckle noise component of the Hermitian product of two SAR images. On the other hand, the availability of the coherence model permits us to quantify the bias due to topography when multilook filtering is considered, permitting us to establish the conditions upon which information may be estimated independently of topography. Based on the coherence model, two coherence estimation approaches, aiming to reduce the different biases, are proposed. Results with simulated and experimental polarimetric and interferometric SAR data illustrate and validate both, the coherence model and the coherence estimation algorithms.

Journal Article↗