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At least 667 records · Page 37Linked to original sources
PubMed2002

Numerical characterization of high harmonic attosecond pulses.

A numerical simulation of attosecond harmonic pulse generation in a three-dimensional field-ionizing gas is presented. Calculated harmonic efficiencies quantitatively reproduce experimental findings. This allows a quantitative characterization of attosecond pulse generation revealing information currently not accessible by experiment. The rapid phase variation and spatiotemporal distortions of harmonics are smaller than anticipated, allowing focusing of 30-nm, 750-as pulses to intensities in excess of 10(13) W/cm(2). Feasibility of such pulses brings novel applications such as extreme ultraviolet nonlinear optics and attosecond pump probe spectroscopy within reach.

Journal Article↗
PubMed2006

Order-chaos-order transitions in electrosprays: the electrified dripping faucet.

Electrosprays have diverse applications including protein analysis, electrospinning, and nanoencapsulation for drug delivery. We show that a variety of electrospray regimes exhibit fundamental analogy with the nonlinear dynamics of a dripping faucet. The applied voltage in electrosprays results in additional period doublings and temporal order-chaos-order transitions. Attractors in the return maps show logarithmic self-similarity in time, suggesting self-similar capillary waves on the meniscus. The bifurcations in ejection time can be explained by phase variations between capillary waves and pinch-off conditions and by ejection mode changes due to contact angle variations.

Journal Article↗
PubMed2006

Sweeping from the superfluid to the Mott phase in the Bose-Hubbard model.

We study the sweep through the quantum phase transition from the superfluid to the Mott state for the Bose-Hubbard model with a time-dependent tunneling rate J(t). In the experimentally relevant case of exponential decay J(t) proportional variant e -gamma t, an adapted mean-field expansion for large fillings n yields a scaling solution for the fluctuations. This enables us to analytically calculate the evolution of the number and phase variations (on-site) and correlations (off-site) for slow (gamma< >mu) sweeps, where mu is the chemical potential. Finally, we derive the dynamical decay of the off-diagonal long-range order as well as the temporal shrinkage of the superfluid fraction in a persistent ring-current setup.

Journal Article↗
PubMed1999

A low-complexity intracardiac electrogram compression algorithm.

Implantable cardioverter defibrillators (ICD's) detect, diagnose and treat the potentially fatal heart arrhythmias known as bradycardia, ventricular tachycardia (VT), and ventricular fibrillation (VF) in cases where these arrhythmias are resistant to surgical and drug-based treatments by direct sensing and electrical stimulation of the heart muscle. Since the ICD is implanted, power consumption, reliability, and size are severe design constraints. This paper targets the problems associated with increasing the signal recording capabilities of an ICD. A data-compression algorithm is described which has been optimized for low power consumption and high reliability implementation. Reliance on a patients morphology or that of a population of patients is avoided by adapting to the intracardiac electrogram (ICEG) amplitude and phase variations and by using adaptive scalar quantization. The algorithm is compared to alternative compression algorithms which are also patient independent using a subset of VT arrhythmias from a data base of 146 patients. At low distortion the algorithm is closest to the Shannon lower bound achieving an average of 3.5 b/sample at 5% root mean square distortion for a 250-Hz sample rate. At higher distortion vector quantization and Karhunen-Loeve Transform approaches are superior but at the cost of considerable additional computational complexity.

Algorithms↗
PubMed1988

Recombination among protein II genes of Neisseria gonorrhoeae generates new coding sequences and increases structural variability in the protein II family.

Expression of Neisseria gonorrhoeae Protein II (P.II) is subject to phase variation and antigenic variation. The P.II proteins made by one strain possess both unique and conserved antigenic determinants. To study the mechanism of antigenic variation, we cloned several P.II genes, using as probes a panel of monoclonal antibodies (MAbs) specific for unique determinants. The DNA sequences of three P.II genes showed that they shared a conserved framework, with two short hypervariable (HV) regions being responsible for most of the differences among them. We demonstrated that unique epitopes recognized by the MAbs were at least partially encoded by one of the HV regions. Moreover, we found that reassortment of the two HV regions among P.II genes occurs, generating increased structural and antigenic variability in the P.II protein family.

Antigens, Bacterial↗
PubMed1988

Three copies of a single protein II-encoding sequence in the genome of Neisseria gonorrhoeae JS3: evidence for gene conversion and gene duplication.

Gonococci express a family of related outer membrane proteins designated protein II (P.II). These surface proteins are subject to both phase variation and antigenic variation. The P.II gene repertoire of Neisseria gonorrhoeae strain JS3 was found to consist of at least ten genes, eight of which were cloned. Sequence analysis and DNA hybridization studies revealed that one particular P.II-encoding sequence is present in three distinct, but almost identical, copies in the JS3 genome. These genes encode the P.II protein that was previously identified as P.IIc. Comparison of their sequences shows that the multiple copies of this P.IIc-encoding gene might have been generated by both gene conversion and gene duplication.

Amino Acid Sequence↗
PubMed1991

H-DNA formation by the coding repeat elements of neisserial opa genes.

The coding repeat region of opa genes from Neisseria gonorrhoeae and Neisseria meningitidis determines the expression state of their respective genes through high-frequency addition of deletion of pentanucleotide coding repeat units (CRs; CTTCT). In vitro analyses of cloned opa gene CR regions using single-strand specific nucleases, oligonucleotide protection experiments, and modifications of non-B-DNA residues indicate that the regions form structures resembling H-DNA under acidic conditions in the presence of negative supercoiling. The purine/pyrimidine strand bias and H-palindromic nature of the repeat region are consistent with sequence requirements for H-DNA formation. Sequences flanking the repeat elements are required to form the H-DNA structure in vitro as judged by the pattern of exposed non-B-DNA residues in CR sequences synthesized as oligonucleotides to form beta-galactosidase::CR translational fusions. The fusions phase vary by addition and deletion of CR elements and the rate of phase variation increases upon induction of the fusion genes. The opa gene CR region is the first reported bacterial H-DNA structure and is unique in that it lies within the coding sequence for the gene.

Amino Acid Sequence↗
PubMed1992

Evidence for global regulatory control of pilus expression in Escherichia coli by Lrp and DNA methylation: model building based on analysis of pap.

Pyelonephritis-associated pilus (Pap) expression is regulated by a phase variation control mechanism involving PapB, Papl, catabolite activator protein (CAP), leucine-responsive regulatory protein (Lrp) and deoxyadenosine methylase (Dam). Lrp and Papl bind to a specific non-methylated pap regulatory DNA region containing the sequence 'GATC' and facilitate the formation of an active transcriptional complex. Evidence indicates that binding of Lrp and Papl to this region inhibits methylation of the GATC site by Dam. However, if this GATC site is first methylated by Dam, binding of Lrp and Papl is inhibited. These events lead to the formation of two different pap methylation states characteristic of active (ON) and inactive (OFF) pap transcription states. The fae (K88), daa (F1845) and sfa (S) pilus operons share conserved 'GATC-box' domains with pap and may be subject to a similar regulatory control mechanism involving Lrp and DNA methylation.

Bacterial Proteins↗
PubMed1994

Generalized transposon shuttle mutagenesis in Neisseria gonorrhoeae: a method for isolating epithelial cell invasion-defective mutants.

One requirement for the invasion of, and tight adherence to, human epithelial cells by Neisseria gonorrhoeae is the synthesis of distinct opacity (Opa) outer membrane proteins, encoded by a family of phase-variable chromosomal genes. However, cloning and surface expression of invasion-promoting Opas in Escherichia coli is not sufficient for the efficient invasion of epithelial cells: additional factors besides Opa may be involved in this process. Using the phoA mini-transposon TnMax4, a library of gonococcal mutants affected in the expression of genes encoding exported proteins was generated through shuttle mutagenesis. Of a total of 608 PhoA+ plasmid clones identified in E. coli E145 approximately 40% were used successfully in transforming N. gonorrhoeae and in activating the corresponding chromosomal genes. Gonococci producing the invasion-promoting Opa50 served as the genetic background to identify 51 mutants unable to enter Chang human epithelial cells. We expect some of these mutations affect the interaction of N. gonorrhoeae with epithelial cells directly, while other mutants may carry defects in general house-keeping, secretory and/or regulatory determinants. In some mutants the loss of invasiveness appears to be due to a negative dominant effect of the PhoA+ fusions produced in these mutants. Some of the identified genes display a phase-variation phenomenon in E. coli and several genes are found in multiple copies in N. gonorrhoeae and/or present only in pathogenic Neisseria species.

Biological Transport↗
PubMed1994

The site-specific recombination system regulating expression of the type 1 fimbrial subunit gene of Escherichia coli is sensitive to changes in DNA supercoiling.

We have studied the effect of altering the in vivo level of DNA supercoiling on the phase-variable expression of the Escherichia coli fimA gene. Transcription from the fimA promoter was unaffected by changes in DNA supercoiling whether caused by the introduction of a topA::Tn10 mutation or by inhibition of DNA gyrase with the antibiotic novobiocin. However, inversion of the fimA promoter fragment was altered in response to perturbation of DNA supercoiling. Specifically, inactivation of topA reduced the rate of promoter fragment inversion in both the ON-to-OFF and the OFF-to-ON directions. This effect correlated with the loss of functional topA and not with the global level of DNA supercoiling. Inhibition of DNA gyrase introduced a bias in favour of the OFF-to-ON inversion; the ON-to-OFF inversion was affected only slightly. Changes in expression of fimB, the gene coding for the recombinase that catalyses fimA promoter fragment inversion in the strains used in this study, did not correlate with effects on fimA phase variation: we found that transcription of fimB was inhibited by loss of functional topA and was enhanced by inhibition of DNA gyrase in a manner that correlated well with the global level of in vivo DNA supercoiling. A model is presented to account for the effects of lost topoisomerase function on fimA gene expression.

Bacterial Proteins↗
PubMed2005

Contact with host cells induces a DNA repair system in pathogenic Neisseriae.

DNA repair systems play a major role in maintaining the integrity of bacterial genomes. Neisseria meningitidis, a human pathogen capable of colonizing the human nasopharynx, possesses numerous DNA repair genes but lacks inducible DNA repair systems such as the SOS response, present in most bacteria species. We recently identified a set of genes upregulated by contact with host cells. An open reading frame having high homology with the small subunit of Escherichia coli exonuclease VII (xseB) belongs to this regulon. The increased sensitivity of a mutant in this coding sequence to UV irradiation, alkylating agent and nalidixic acid demonstrates the participation of this gene in meningococcal DNA repair. In addition, the upregulation of the transcription of this open reading frame upon interaction of N. meningitidis with host cells increased not only the bacterial ability to repair its DNA but also the rate of phase variation by frameshifting. Together these data demonstrate that N. meningitidis possesses an inducible DNA repair system that might be used by the bacteria to adapt to its niches when it is colonizing a new host.

Bacterial Proteins↗
PubMed2005

Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-gamma-dl-glutamic acid production and biofilm formation.

Biofilms are communities of microbial cells that are encased in a self-produced, polymeric matrix and are adherent to a surface. For several species of bacteria, an enhanced ability to form biofilms has been linked with an increased capability to produce exopolymers. To identify exopolymers of Bacillus subtilis that can contribute to biofilm formation, we transferred the genetic determinants that control exopolymer production from a wild, exopolymer-positive strain to a domesticated, exopolymer-negative strain. Mapping these genetic determinants led to the identification of gamma-poly-dl-glutamic acid (gamma-PGA) as an exopolymer that increases biofilm formation, possibly through enhancing cell-surface interactions. Production of gamma-PGA by Bacillus subtilis was known to be dependent on the two-component regulator ComPA; this study highlighted the additional dependence on the DegS-DegU, DegQ and SwrA regulator proteins. The inability of the domestic strain of B. subtilis to produce gamma-PGA was mapped to two base pairs; a single base pair change in the promoter region of degQ and a single base pair insertion in the coding region of swrA. Introduction of alleles of degQ and swrA from the wild strain into the domestic strain was sufficient to allow gamma-PGA production. In addition to controlling gamma-PGA production, ComPA and DegSU were also shown to activate biofilm formation through an as yet undefined pathway. The identification of these regulators as affecting gamma-PGA production and biofilm formation suggests that these processes are regulated by osmolarity, high cell density and phase variation.

Alleles↗
PubMed2005

Carbohydrate composition of meningococcal lipopolysaccharide modulates the interaction of Neisseria meningitidis with human dendritic cells.

Meningococcal lipopolysaccharide (LPS) is of crucial importance for the pathogenesis of invasive infection. We show that sialylation and elongation of the alpha-chain effectively shields viable unencapsulated Neisseria meningitidis from recognition by human dendritic cells (DC). In contrast, beta- and gamma- chain of the LPS carbohydrate moiety play only a minor role in the interaction with DC. The protective function of the LPS for the bacteria can be counteracted in vivo by phase variation of the lgtA gene encoding LPS glycosyltransferase A. Capsule expression protects N. meningitidis efficiently from recognition and phagocytosis by DC independent of the LPS structure. Despite the significant impact of LPS composition on the adhesion and phagocytosis of N. meningitidis no differences were found in terms of cytokine levels secreted by DC for IL1-beta, IL-6, IL-8, TNF-alpha, IFN-gamma and GM-CSF. However, significantly lower levels of the regulatory mediator IL-10 were induced by encapsulated strains in comparison to isogenic unencapsulated derivatives. IL-10 secretion was shown to depend on phagocytosis because poly alpha-2,8 sialic acid did not influence IL-10 secretion. The use of truncated LPS isoforms in vaccine preparations can therefore not only result in attenuation but also in more efficient targeting of DC.

Bacterial Capsules↗
PubMed1998

Identification of two genes, cpsX and cpsY, with putative regulatory function on capsule expression in group B streptococci.

Two divergently transcribed open reading frames: cpsX and cpsY separated by a common regulatory region was identified upstream of the cpsA-D genes involved in polysaccharide capsule biosynthesis in group B streptococci (GBS). We suggest that these genes are involved in the regulation of capsule expression in GBS, since the CpsX protein shares sequence similarities with LytR of Bacillus subtilis, an attenuator of transcription while CpsY has similarity to a wide variety of members of the LysR family of transcriptional regulators. No deletions, insertions, DNA rearrangements, or apparent differences were discovered in the postulated regulatory genes when the gene region was compared in GBS with different capsule phenotypes. Thus, other yet unidentified gene loci may control capsule phase variation in GBS.

Amino Acid Sequence↗
PubMed1994

Localization of promoters in the fim gene cluster and the effect of H-NS on the transcription of fimB and fimE.

The expression of type 1 fimbriae in Escherichia coli undergoes phase variation in which individual bacteria switch between a fimbriated and non-fimbriated state. The transition from one state to the other is caused by inversion of a DNA segment containing the promoter for the fimA gene. The orientation of the invertible segment is controlled by two proteins, FimB and FimE, which mediate an on/off and off only orientation of the segment, respectively. In this study we have mapped the 5' termini of the fimB, fimE and fimA transcripts. Furthermore, we show that expression of fimB and fimE is strongly influenced by the H-NS nucleoid protein.

Bacterial Outer Membrane Proteins↗
PubMed1998

Engineering the luxCDABE genes from Photorhabdus luminescens to provide a bioluminescent reporter for constitutive and promoter probe plasmids and mini-Tn5 constructs.

The luxCDABE operon of Photorhabdus luminescens has been cloned and engineered as an easily mobilisable cassette flanked by sites for commonly used restriction enzymes. Constitutive and promoter probe plasmids utilising the P. luminescens luxCDABE have been constructed using a number of compatible replicons and antibiotic markers. Complementary to these plasmids, a range of promoterless and constitutive luxCDABE mini-Tn5 derivatives has been constructed. The potential of coupling mini-Tn5 luxCDABE promoter probe transposons with automated luminometry and photometry to screen for mutants that exhibit growth phase variation in gene expression is demonstrated.

Cloning, Molecular↗
PubMed2000

On the relationships between the fixed-f1, fixed-f2, and fixed-ratio phase derivatives of the 2f1-f2 distortion product otoacoustic emission.

For primary frequency ratios, f2/f1, in the range 1.1-1.3, the fixed-f1 ("f2-sweep") phase derivative of the 2f1-f2 distortion product otoacoustic emission (DPOAE) is larger than the fixed-f2("f1-sweep") one. It has been proposed by some researchers that part or all of the difference between these delays may be attributed to the so-called cochlear filter "build-up" or response time in the DPOAE generation region around the f2 tonotopic site. The analysis of an approximate theoretical expression for the DPOAE signal [Talmadge et al., J. Acoust. Soc. Am. 104, 1517-1543 (1998)] shows that the contributions to the phase derivatives associated with the cochlear filter response is small. It is also shown that the difference between the phase derivatives can be qualitatively accounted for by assuming the approximate scale invariance of cochlear mechanics. The effects of DPOAE fine structure on the phase derivative are also explored, and it is found that the interpretation of the phase derivative in terms of the phase variation of a single DPOAE component can be quite problematic.

Humans↗
PubMed2001

Second-harmonic generation in sound beams reflected from, and transmitted through, immersed elastic solids.

Second-harmonic generation in sound beams reflected from and transmitted through thick isotropic elastic solids is investigated experimentally. Measurements of diffraction patterns are compared with a theoretical model based on integral solutions for harmonic generation in sound beams. The solutions are connected by classical linear theory for reflection and transmission at fluid-solid interfaces. Nonspecular phenomena associated with rapid phase variations near critical angles are accurately described. The principal restriction is that the solid is sufficiently thick that internal reflections may be ignored.

Journal Article↗