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PubMedDate not supplied

Mood effects of alcohol and expectancies across the menstrual cycle.

To examine menstrual cycle phase variations in alcohol absorption and mood before and after drinking alcohol, 96 volunteers female heavy drinkers, unaware they were in a menstrual cycle study, were randomly assigned to 12 equal-sized groups with controls for the effects of alcohol, expectancy, and menstrual cycle phase. Alcohol subjects received sufficient alcohol to raise their blood alcohol level to .07 mg %. Mood, assessed with the Profile of Mood States, did not differ across menstrual cycle phases at baseline, failing to support the notion of menstrual phase-related moods. The only mood changes were a Beverage by Trials interaction on the Vigor and Confusion scales and a main effect for trials on the Tension-Anxiety and Vigor scales. Peak intoxication level did not differ across phases. The present findings of an absence of menstrual cycle phase-related differences in mood or alcohol absorption support social learning theory and suggest that phasic variations in mood are socially learned. They also suggest the need for systematic study of methodologic factors in this research area.

Absorption↗
PubMed2006

A novel phase-variable autotransporter serine protease, AusI, of Neisseria meningitidis.

The sequenced genomes of pathogenic Neisseria meningitidis strains contain up to eight genes putatively encoding autotransporters, which are secreted proteins implicated in virulence. Here, we have characterized one of these genes, designated ausI, which encodes an autotransporter of the serine protease family. It was found to be specific for N. meningitidis and present in 14 out of 20 isolates, although only six of them expressed the gene. We show that expression of the gene is subject to phase variation as a result of a variable number of cytosines in a poly-C tract in the coding region. The open reading frame went out-of-phase at the poly-C tract in seven strains that did not express AusI. In the eighth strain, the open reading frame remained in frame at the poly-C tract, but it was disrupted by a premature stop codon further downstream. In accordance with its assignment as an autotransporter, a secreted AusI passenger domain was released into the extracellular milieu. This release was influenced by another autotransporter, NalP, as different forms of AusI were produced in the presence or absence of NalP. In silico sequence analysis suggested several putative functions for AusI, which, however, could not be confirmed experimentally.

Blotting, Western↗
PubMed2005

Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals.

BACKGROUND: Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1). SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches -- most of which are irrelevant to the researcher. RESULTS: We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO) database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the yeast Pho4p binding sites, CACGTG and CACGTT. Also, a cross-species search is presented to illustrate how potential hidden correlations in genomic data can be quickly discerned. The findings in one species are used as a catalyst to discover something new in another species. These experiments also demonstrate that our system performs well while searching multiple genomes -- without the main memory constraints present in other systems. CONCLUSION: We present a time-efficient algorithm to locate small segments of DNA and concurrently to search the annotation data accompanying the sequence. Genome-wide searches for short sequences often return hundreds of hits. Our experiments show that subsequently searching the annotation data can refine and focus the results for the user. Our algorithms are also space-efficient in terms of main memory requirements. Source code is available upon request.

Algorithms↗
PubMed2002

Isolation of three new surface layer protein genes (slp) from Lactobacillus brevis ATCC 14869 and characterization of the change in their expression under aerated and anaerobic conditions.

Two new surface layer (S-layer) proteins (SlpB and SlpD) were characterized, and three slp genes (slpB, slpC, and slpD) were isolated, sequenced, and studied for their expression in Lactobacillus brevis neotype strain ATCC 14869. Under different growth conditions, L. brevis strain 14869 was found to form two colony types, smooth (S) and rough (R), and to express the S-layer proteins differently. Under aerobic conditions R-colony type cells produced SlpB and SlpD proteins, whereas under anaerobic conditions S-colony type cells synthesized essentially only SlpB. Anaerobic and aerated cultivations of ATCC 14869 cells in rich medium also resulted in S-layer protein patterns similar to those of the S- and R-colony type cells, respectively. Electron microscopy suggested the presence of only a single S-layer with an oblique structure on the cells of both colony forms. The slpB and slpC genes were located adjacent to each other, whereas the slpD gene was not closely linked to the slpB-slpC gene region. Northern analyses confirmed that both slpB and slpD formed a monocistronic transcription unit and were effectively expressed, but slpD expression was induced under aerated conditions. slpC was a silent gene under the growth conditions tested. The amino acid contents of all the L. brevis ATCC 14869 S-layer proteins were typical of S-layer proteins, whereas their sequence similarities with other S-layer proteins were negligible. The interspecies identity of the L. brevis S-layer proteins was mainly restricted to the N-terminal regions of those proteins. Furthermore, Northern analyses, expression of a PepI reporter protein under the control of the slpD promoter, and quantitative real-time PCR analysis of slpD expression under aerated and anaerobic conditions suggested that, in L. brevis ATCC 14869, the variation of S-layer protein content involves activation of transcription by a soluble factor rather than DNA rearrangements that are typical for most of the S-layer phase variation mechanisms known.

Aerobiosis↗
PubMed2005

Spectral-domain optical coherence phase microscopy for quantitative phase-contrast imaging.

We describe a novel microscopy technique for quantitative phase-contrast imaging of a transparent specimen. The technique is based on depth-resolved phase information provided by common path spectral-domain optical coherence tomography and can measure minute phase variations caused by changes in refractive index and thickness inside the specimen. We demonstrate subnanometer level path-length sensitivity and present images obtained on reflection from a known phase object and human epithelial cheek cells.

Cells, Cultured↗
PubMed2002

Anti-Vel reactivity diminished by adsorption with rabbit RBC stroma.

BACKGROUND: An anti-Vel, nearly missed in antibody identification studies, and the effect of a commercially available rabbit RBC stroma (RESt, Immucor) adsorptions on eight anti-Vel sera are reported. Anti-Vel is an antibody to an antigen of high prevalence. CASE REPORT: A 48-year-old woman with chronic vaginal bleeding presented with a Hct of 14.7 percent. The transfusion service was not informed of her history of anti-Vel when she was transferred from another institution. Studies performed on an emergency request for transfusion were interpreted as a cold autoantibody as adsorption with a commercial source of RESt eliminated the reactivity. Stored anti-Vel sera were tested by titration studies before and after adsorption with commercial RESt. RESULTS: Serum from the index case did not react after adsorption with RESt at the transfusion service. Studies with the stored anti-Vel indicated antibody adsorption with four of four samples at immediate spin (IS) and room temperature (RT) phases, four of eight samples at 37 degrees C in albumin (ALB) phase, and four of eight samples at ALB-IgG-AGT phase. Variations in antibody reactivity were observed in the samples tested, but RESt adsorption diminished antibody reactivity in most samples. All eight stored sera demonstrated some reactivity in at least one phase after adsorption with RESt. CONCLUSION: Anti-Vel was completely or partially adsorbed by RESt. Caution should be used when interpreting cold agglutinins with this method. The manufacturer warns that uncommon alloantibodies may be adsorbed.

ABO Blood-Group System↗
PubMed2006

Surface plasmon interferometric microscopy for three-dimensional imaging of dynamic processes.

A method, which we named surface plasmon interferometric microscopy, for real-time displaying of the dynamic evolution of the refractive index (RI) of a sample in three-dimensions is demonstrated experimentally. The Fourier fringe analysis technique is employed to get the phase variations of the samples by demodulating the interference patterns captured by a CCD camera, and the 3D RI distribution can be obtained through numerical interpolation from the relation between the phase and the RI of the samples. Our method may provide an interesting way to monitor fast dynamics of physical, biological, and chemical processes in real time.

Fourier Analysis↗
PubMed1986

Surface proteins of Bordetella pertussis: comparison of virulent and avirulent strains and effects of phenotypic modulation.

The surface proteins of several Bordetella strains and their modulated derivatives were examined by surface radioiodination, cell fractionation, and Western blotting. A surface protein with a high Mr, missing in a mutant lacking the filamentous hemagglutinin, was identified in virulent Bordetella pertussis and Bordetella parapertussis cells and was absent in avirulent B. pertussis strains. The electrophoretic profiles of lipopolysaccharide and the 40,000-Mr anion-selective porin were not determinants which correlated with phase variation or phenotypic modulation. At least three envelope proteins (91,000, 32,000, and 30,000 molecular weight) were found only in virulent B. pertussis strains and were absent or diminished in the avirulent phase and most phenotypically modulated strains. Two transposon-induced mutants unable to produce hemolysin, dermonecrotic toxin, pertussis toxin, and filamentous hemagglutinin also lacked these three envelope proteins, confirming that virulence-associated envelope proteins were genetically regulated with other virulence-associated traits.

Antibodies, Monoclonal↗
PubMed1997

A novel regulatory mechanism for a novel phase-variable outer membrane protein of Escherichia coli.

Antigen 43 (Ag43) is a prominent hetero-oligomeric protein complex in the outer membrane of Escherichia coli. It is composed of two subunits. alpha 43 (M(r) 60, 000) and beta 43 (M(r) 53, 000) in 1:1 stoichiometry. alpha 43 is surface expressed, extends beyond the O-side chains of smooth lipopolysaccharide and is bound to the cell surface through an interaction with beta 43, itself an integral outer membrane protein, alpha 43 shows limited sequence homology with some enterobacterial adhesins. Expression of Ag43 is subject to reversible phase variation, the rates of variation from the Ag43+ve to Ag43-ve states in liquid minimal medium being approximately 2.2 x 10(-3), the corresponding rates from Ag43-ve to Ag43+ve states being approximately 1 x 10(-3). Phase switching of genes encoding Ag43 are transcriptionally regulated by DNA methylation (deoxyadenosine methylase [dam] mutants being "locked OFF") and by OxyR (oxyR mutants being "locked ON"). It is proposed that OxyR acts as a repressor of Ag43 transcription by binding to unmethylated GATC sites in the regulatory region of the gene. Sequencing and mapping has identified Ag43 as the likely product of the metastable flu gene first described in 1980 by Diderichsen and responsible for colony form variation in E. coli.

Amino Acid Sequence↗
PubMed1990

Variation in expression of class 1 and class 5 outer membrane proteins during nasopharyngeal carriage of Neisseria meningitidis.

Accidental nasopharyngeal colonization of a laboratory worker by a human disease isolate of Neisseria meningitidis allowed us to examine the variation in expression of outer membrane components and the host humoral response over time. There were quantitative differences in class 1 outer membrane protein expression in nasopharyngeal isolates obtained at different times. Isolates also showed phase variation of all four class 5 outer membrane proteins produced by the colonizing strain. After colonization, we detected new host serum immunoglobulin G antibodies directed against class 1, class 5, and H.8 outer membrane proteins.

Bacterial Outer Membrane Proteins↗
PubMed2006

Third-harmonic generation in air by use of femtosecond radiation in tight-focusing conditions.

Third-harmonic generation (THG) in air in tight-focusing conditions is presented. Variation of the pulse duration supplied optimal conditions for THG by femtosecond pulses that varied in the range 110-1300 fs. We show that this third-harmonic generation was caused by Kerr-induced phase variations of fundamental and harmonic beams. Various characteristics (laser intensity, focusing conditions, pulse duration, air pressure, etc.) of THG in air were analyzed to optimize this process. The THG conversion efficiency of 795 nm, 300 fs radiation was 1 x 10(-3). The harmonic radiation did not show considerable disruption of its spectral and spatial distribution in tight focusing conditions for intensities as high as 5 x 10(14) W cm(-2).

Journal Article↗
PubMed2006

Phase-aberration correction with a 3-D ultrasound scanner: feasibility study.

We tested the feasibility of using adaptive imaging, namely phase-aberration correction, with two-dimensional (2-D) arrays and real-time, 3-D ultrasound. Because of the high spatial frequency content of aberrators, 2-D arrays, which generally have smaller pitch and thus higher spatial sampling frequency, and 3-D imaging show potential to improve the performance of adaptive imaging. Phase-correction algorithms improve image quality by compensating for tissue-induced errors in beamforming. Using the illustrative example of transcranial ultrasound, we have evaluated our ability to perform adaptive imaging with a real-time, 3-D scanner. We have used a polymer casting of a human temporal bone, root-mean-square (RMS) phase variation of 45.0 ns, full-width-half-maximum (FWHM) correlation length of 3.35 mm, and an electronic aberrator, 100 ns RMS, 3.76 mm correlation, with tissue phantoms as illustrative examples of near-field, phase-screen aberrators. Using the multilag, least-squares, cross-correlation method, we have shown the ability of 3-D adaptive imaging to increase anechoic cyst identification, image brightness, contrast-to-speckle ratio (CSR), and, in 3-D color Doppler experiments, the ability to visualize flow. For a physical aberrator skull casting we saw CSR increase by 13% from 1.01 to 1.14, while the number of detectable cysts increased from 4.3 to 7.7.

Algorithms↗
PubMed2003

Expression and localization of vascular endothelial growth factor and its receptors in pig corpora lutea during the oestrous cycle.

Expression and localization of mRNAs for vascular endothelial growth factor (VEGF), VEGF receptor 1 (Flt) and VEGF receptor 2 (KDR) (VEGFR-1 and VEGFR-2, respectively) were investigated in pig corpora lutea. Northern blot analysis of total RNA indicated hybridization of pig VEGF, VEGFR-1 and VEGFR-2 cDNA probes to mRNA transcripts of approximately 3.9, 7.0 and 5.0 kb, respectively. The expression of mRNAs for VEGF and its receptors during the luteal phase (days 4, 7, 10, 13 and 15 after the onset of oestrus) were assessed by northern blot analysis, and hybridization signals were normalized to expression of pig 18S rRNA. Relative hybridization signals of expression of VEGF mRNA appeared to be constant; however, expression of VEGFR-1 mRNA was low on day 4, increased on day 7, and was higher on days 10, 13 and 15 (P<0.05, compared with day 4). In contrast, no changes in expression of mRNA for VEGFR-2 were evident on days 4-13, but a decrease was detected (P<0.05) at day 15. In situ hybridization revealed that VEGF mRNA was localized predominantly in large luteal cells, whereas both VEGFR-1 and VEGFR-2 were localized to small cells. These data indicate that the VEGF system may be involved in the regulation of luteal vasculature throughout the lifespan of the corpus luteum. Although the expression of VEGF mRNA was unchanged during the luteal phase, variations in the expression of VEGFR-1 and VEGFR-2 mRNAs indicate that differential regulation of expression of the VEGF receptors may play a role in the control of VEGF-mediated vascular growth at different phases of development and maturation of the pig corpus luteum.

Animals↗
PubMed1998

Motion artifacts reduction in DWI using navigator echoes: a robust and simple correction scheme.

NMR signal phase variation caused by macroscopic motion of an object during application of the diffusion gradient is a well-known effect in diffusion-weighted imaging (DWI) using the standard pulsed gradient spin-echo sequence (PGSE). This phase error causes severe ghost artifacts in the output image when phase encoding techniques, such as two dimensional Fourier transform (2DFT) imaging, are used. One possible way to eliminate the motion effects is the navigator echo technique. The method is based on estimating the phase error from the navigator echo and using it for the correction of the image echo. The phase errors (zero and first order) for the phase correction of the image echo are usually evaluated from the navigator echo after Fourier transform (FT) in the readout direction, correcting for both translation and rotation. We present here a simple algorithm which enables evaluation and correction in the time domain of phase errors induced by motion. This approach has the advantage of improved correction of motional artifacts and minimized sensitivity to noise and inaccurate setting up of the experiment.

Algorithms↗
PubMed1995

Major membrane proteins and lipoproteins as highly variable immunogenic surface components and strain-specific antigenic markers of Mycoplasma arthritidis.

Surface antigenic variation was investigated in Mycoplasma arthritidis, an agent that produces chronic arthritis in rats which shares several features with many mycoplasma-induced diseases and thus defines a well-characterized model system. Hyperimmune rabbit antisera (anti-ISR1, anti-PG6, anti-H606 and anti-158p10) to whole M. arthritidis organisms were used as immunological probes in Western immunoblots of four M. arthritidis prototype strains (ISR1, PG6, H606 and D263) and five rat-passaged substrains (ISR1p1, ISR1p7, ISR1p8, 158p10 and D263p1). Several prominent antigens were identified that varied in expression. By Triton X-114 phase fractionation and treatment of whole cells with trypsin and carboxypeptidase Y, these strain-variant antigens were shown to be integral membrane proteins with C-termini and portions of the polypeptide chains oriented outside the membrane. Western blot immunoscreening of a large number of randomly selected clonal isolates and well-established clonal lineages from stock cultures of M. arthritidis ISR1p7, 158p10, PG6 and H606 revealed an expanded repertoire of variant membrane proteins whose expression was subject to independent, reversible phase variation. Colony immunoblots of these clonal populations with a hyperimmune rabbit antiserum to a gel-purified variant membrane protein (P36) showed that this phase switching occurred at a high frequency (10(-4) to 10(-2) per generation). Detailed immunological and biochemical characterization of the phase-variant membrane proteins demonstrated that they are: (i) antigenically related or distinct; (ii) apparently specific to particular strain populations; (iii) proteins or lipoproteins; (iv) major immunogens of M. arthritidis, recognized by serum antibodies from convalescent rat; and (v) able to undergo variation in expression during in vivo passage. Thus, M. arthritidis possesses a complex system capable of creating large repertoires of cell surface phenotypes which may affect the multiple interactions of this organism with its host and dictate its potential as a successful infectious agent and pathogen.

Animals↗
PubMed2000

A homologue of the recombination-dependent growth gene, rdgC, is involved in gonococcal pilin antigenic variation.

Neisseria gonorrhoeae pilin undergoes high-frequency changes in primary amino acid sequence that aid in the avoidance of the host immune response and alter pilus expression. The pilin amino acid changes reflect nucleotide changes in the expressed gene, pilE, which result from nonreciprocal recombination reactions with numerous silent loci, pilS. A series of mini-transposon insertions affecting pilin antigenic variation were localized to three genes in one region of the Gc chromosome. Mutational analysis with complementation showed that a Gc gene with sequence similarity to the Escherichia coli rdgC gene is involved in pilus-dependent colony phase variation and in pilin antigenic variation. Furthermore, we show that the Gc rdgC homologue is transcriptionally linked in an operon with a gene encoding a predicted GTPase. The inability to disrupt expression of this gene suggests it is an essential gene (engA, essential neisserial GTPase). While some of the transposon mutations in rdgC and insertions in the 5'-untranslated portion of engA showed a growth defect, all transposon insertions investigated conferred an aberrant cellular morphology. Complementation analysis showed that the growth deficiencies are due to the interruption of RdgC expression and not that of EngA. The requirement of RdgC for efficient pilin variation suggests a role for this protein in specialized DNA recombination reactions.

Amino Acid Sequence↗
PubMed1994

[Structural analysis of the chromatin loop in human chromosome by immunoelectron microscopy].

Synchronized human lymphocytes were exposed to 5-bromo-2'-deoxyuridine (BrdU) for incorporation in the late S-phase. The substituted chromosome bands were detected immunohistochemically by monoclonal anti-BrdU antibodies with the protein A-gold complex. The bands composed of many chromatin loop clusters were examined by electron microscopy without trypsin treatment. These banding patterns corresponded to the G-band by immunostaining. Chromatin loops were stretched around the chromosome, revealing the structure of coiled chromosome with trypsin treatment. The stretched loops were observed in the whole S-phase without treatment of trypsin but were not seen in the late S-phase. Variations in the degree of stretching were correlated with the duration of the BrdU treatment and the period of trypsin treatment. These results indicate that the trypsin treatment is essential to chromatin loops for their stretching in late S-phase and that the chromosome band is composed of numerous chromatin loops.

Antibodies, Monoclonal↗
PubMed2003

Variable lipoprotein genes of Mycoplasma agalactiae are activated in vivo by promoter addition via site-specific DNA inversions.

Mycoplasma agalactiae, the etiological agent of contagious agalactia of small ruminants, has a family of related genes (avg genes) which encode surface lipoprotein antigens that undergo phase variation. A series of 13 M. agalactiae clonal isolates, obtained from one chronically infected animal over a period of 7 months, were found to undergo major rearrangement events within the avg genomic locus. We show that these rearrangements regulate the phase-variable expression of individual avg genes. Northern blot analysis and reverse transcription-PCR showed that only one avg gene is transcribed, while the other avg genes are transcriptionally silent. Sequence analysis and primer extension experiments with two M. agalactiae clonal isolates showed that a specific 182-bp avg 5' upstream region (avg-B(2)) that is present as a single chromosomal copy serves as an active promoter and exhibits a high level of homology with the vsp promoter of the bovine pathogen Mycoplasma bovis. PCR analysis showed that each avg gene is associated with the avg-B(2) promoter in a subpopulation of cells that is present in each subclone. Multiple sequence-specific sites for DNA recombination (vis-like), which are presumably recognized by site-specific recombinase, were identified within the conserved avg 5' upstream regions of all avg genes and were found to be identical to the recombination sites of the M. bovis vsp locus. In addition, a gene encoding a member of the integrase family of tyrosine site-specific recombinases was identified adjacent to the variable avg locus. The molecular genetic basis for avg phase-variable expression appears to be mediated by site-specific DNA inversions occurring in vivo that allow activation of a silent avg gene by promoter addition. A model for the control of avg genes is proposed.

Animals↗