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PubMed2000

Regulation of Pap phase variation. Lrp is sufficient for the establishment of the phase off pap DNA methylation pattern and repression of pap transcription in vitro.

The pyelonephritis-associated pili (pap) operon in Escherichia coli is regulated by an epigenetic mechanism involving the formation of specific DNA methylation patterns characteristic of transcriptionally active (phase ON) and inactive (phase OFF) cells. The formation of pap DNA methylation patterns in vivo was previously shown to require the leucine-responsive regulatory protein (Lrp) and DNA adenine methylase (Dam). To monitor the binding of Lrp to pap DNA, an in vitro methylation protection assay was developed. Binding of Lrp to a Dam target site proximal to the papBA promoter (designated GATC(prox)) blocked methylation of this site and specifically repressed transcription. The DNA methylation pattern and transcription state are identical to those observed in vivo in phase OFF cells. To determine if binding of Lrp at GATC(prox) was necessary for repression of papBA transcription, we analyzed a pap mutation (pap-13) that reduced the affinity of Lrp for the GATC(prox) region. Binding of Lrp to pap-13 DNA was shifted to a promoter distal Dam target site (designated GATC(dist)). Lrp blocked methylation of GATC(dist) in the pap-13 mutant, but did not repress papBA transcription. Together, these results show that binding of Lrp to the GATC(prox) region is sufficient for the establishment of the phase OFF DNA methylation pattern and repression of papBA transcription.

Bacterial Adhesion↗
PubMed1997

Modulation of phase I and phase II xenobiotic-metabolizing enzymes by selenium-enriched garlic in rats.

Previous research showed that treatment with selenium-enriched garlic (Se-garlic) was able to inhibit the initiation phase of mammary carcinogenesis in the dimethyl-benz[a]anthracene (DMBA) model in rats. The present study was designed to investigate the following parameters: 1) DMBA-DNA adduct formation in liver and mammary gland, 2) urinary excretion of DMBA metabolites, 3) phase I and phase II xenobiotic-metabolizing enzymes, and 4) tissue selenium levels as a function of Se-garlic supplementation. Prior feeding with an Se-garlic-containing diet (at 3 ppm Se) for two weeks resulted in a consistent reduction of all DMBA adducts in liver and mammary gland. This was accompanied by a 40% increase in urinary excretion of DMBA metabolites over a two-day period. Several liver P-450 enzymes were examined in rats fed a diet supplemented with 1, 2, or 3 ppm Se. Compared with controls receiving 0.1 ppm Se, no significant alteration in activity was detected with respect to P-450 1A1 (responsible for DMBA activation), 1A2, 2B1, 2E1, and 3A4. In contrast, glutathione S-transferase and uridine 5'-diphosphate-glucuronyltransferase activities were elevated to a maximum of 2- to 2.5-fold in liver and kidney. As expected, there was a dose-dependent elevation of selenium concentrations in liver, kidney, mammary gland, and plasma as a function of the level of Se-garlic supplementation. Our data seem to suggest that an increased detoxification of carcinogen via the phase II conjugating enzymes might represent a mechanism of tumor suppression by Se-garlic.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1982

Evidence that progression of cells into S-phase is not a prerequisite for recovery between split doses of U.V.-light in synchronized and plateau phase cultures of Ehrlich ascites tumour cells.

The ability of Ehrlich ascites tumour cells (EAT-cells) to perform split-dose recovery after U.V. exposure was studied with unfed plateau phase as well as with synchronized cells selected from exponentially growing cultures. The cells were kept in balanced salt solution which inhibited the progression of the cells through the cell cycle. The results indicated that split-dose recovery occurred in EAT-cells in all phases of the cell cycle and that progression of the cells into S-phase was not a prerequisite for this type of repair. The second-dose survival curves of G1- and S-phase cells showed, 24 hours after the first U.V. exposure, a shoulder width comparable to that of singly irradiated cells. Second-dose survival curves for G2-cells showed, after the same time interval, a shoulder width smaller than that for singly exposed cells, presumably due to some cell division. The recovery time constant (t50 between 4 and 8 hours) increased with increasing U.V. exposure.

Animals↗
PubMed2001

Fuel spill identification using solid-phase extraction and solid-phase microextraction. 1. Aviation turbine fuels.

The water-soluble fraction of aviation jet fuels is examined using solid-phase extraction and solid-phase microextraction. Gas chromatographic profiles of solid-phase extracts and solid-phase microextracts of the water-soluble fraction of kerosene- and nonkerosene-based jet fuels reveal that each jet fuel possesses a unique profile. Pattern recognition analysis reveals fingerprint patterns within the data characteristic of fuel type. By using a novel genetic algorithm (GA) that emulates human pattern recognition through machine learning, it is possible to identify features characteristic of the chromatographic profile of each fuel class. The pattern recognition GA identifies a set of features that optimize the separation of the fuel classes in a plot of the two largest principal components of the data. Because principal components maximize variance, the bulk of the information encoded by the selected features is primarily about the differences between the fuel classes.

Journal Article↗
PubMed2001

Towards optimization of growth via nutrient supply phasing: nitrogen supply phasing increases broccoli (Brassica oleracea var. italica) growth and yield.

A greenhouse experiment on broccoli (Brassica oleracea var. italica, cvs Windsor and Arcadia) was carried out in order to demonstrate that supplying nitrogen (N) to meet the nitrogen demands of plant growth stages, through N phasing, improves plant growth and yield, as compared to fertilizing at the conventional, optimal, constant N rate. Two broccoli cultivars and two rates of starter nitrogen fertilizer (optimum, 250 mg l(-1) and sub-optimum, 150 mg l(-1)), were combined with three timings of fertigation change. Shifting N rate, at 60% and 75% of the market plant growth cycle significantly increased shoot dry weight and head fresh weight, compared to the constant-N rates treatments (controls). The highest yield and shoot dry weight were obtained when the N-rate was switched from the optimum level (250 mg l(-1)) to the sub-optimum level (150 mg l(-1)) at inflorescence initiation. The nitrogen-to-growth-stage-fitness effect was determined and partitioned into rate effect and phasing effect. The phasing effect was greatest, on both shoot dry weight and head fresh weight, at inflorescence initiation, and subsequently decreased until harvest time. None of the interactions was significant. The results demonstrated the superiority of nitrogen supply phasing over the conventional fixed-rate-supply method.

Brassica↗
PubMed2003

Broiler nonphytin phosphorus requirement in the finisher and withdrawal phases of a commercial four-phase feeding system.

Two experiments were conducted to determine the nonphytin phosphorus (nPP) requirement for broilers, based on broken line analysis, in the finisher (32 to 42 d) and withdrawal phases (42 to 49 d) of a four-phase feeding program. The determined nPP concentrations used were 0.15, 0.19, 0.26, and 0.31% in the finisher phase, experiment 1 (Exp 1), and 0.10, 0.13, 0.22, and 0.27% in the withdrawal phase, experiment 2 (Exp 2). The analyzed calcium levels in the diets were 0.69 +/- 0.02% and 0.72 +/- 0.05% in Exp 1 and 2, respectively. In Exp 2, an additional treatment was included in which birds were fed NRC-recommended (1994) nPP levels from hatch to 49 d. There were no differences (P>0.05) among dietary treatments in weight gain, feed intake, and feed efficiency in either experiment. In Exp 1, tibia ash weight of birds fed the diets containing 0.15% nPP was lower (P<0.05) than that of birds fed diets containing 0.19, 0.26, or 0.31% nPP. A requirement of 0.20 +/- 0.01% nPP was determined for male broilers weighing between 1,541 to 2,194 g and from 32 to 42 d of age based on broken line analysis of tibia ash weight response to different dietary nPP levels. In Exp 2, the nPP requirement of male broilers weighing between 2,396 g at 42 d and 3,076 g at 49 d, based on tibia ash weight, was 0.16 +/- 0.02% nPP.

Animal Nutritional Physiological Phenomena↗
PubMed1992

Determination of fluconazole in human serum by solid-phase extraction and reversed-phase high-performance liquid chromatography.

A simple, rapid, and accurate reversed-phase octadecylsilyl high-performance liquid chromatographic method using solid-phase column extraction is described for measuring fluconazole in human serum. The column eluent was monitored by ultraviolet absorption at 210 nm. Fluconazole was extracted from diluted serum by adsorption on a small Bond-Elut C18 cartridge after the addition of UK48,134 as the internal standard and recovered by elution with methanol. The methanol was then evaporated to dryness and the residue reconstituted in 200 microliters of mobile phase and filtered prior to injecting an aliquot (50 microliters) onto an Adsorbosphere C18 column (4.6 x 250 mm, 5 microns particle size), using a mobile phase of 25 mM tris(hydroxymethyl)aminomethane-phosphate buffer (pH 7.0):acetonitrile (75:25, vol/vol). The retention times were 6.6 min for fluconazole and 9.0 min for the internal standard. The assay was precise, with inter- and intraassay coefficients of variation of less than or equal to 2.9% and less than or equal to 2.1%, respectively, and with good linearity (r = 1.000) in the range of 0.1 to 25 micrograms/ml. The duration of each analysis was 15 min and the minimum detectable serum concentration was 0.1 microgram/ml.

Administration, Oral↗
PubMed1997

The lag phase rather than the exponential-growth phase on glucose is associated with a higher cAMP level in wild-type and cAPK-attenuated strains of the yeast Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae several phenotypic properties controlled by cAMP-dependent protein kinase (cAPK) are indicative of high cAPK activity during growth on glucose and low activity during growth on non-fermentable carbon sources and in stationary phase. It has been a matter of debate whether the apparently higher activity of cAPK in cells growing on glucose is due to a higher cAMP level or to an alternative mechanism activating cAPK. The cAMP level during diauxic growth of yeast cells in cultures with different initial glucose levels and different initial cell densities has been reinvestigated and the previously reported twofold increase in cAMP during growth initiation has been confirmed. However, this increase was transient and entirely associated with the lag phase of growth. The initiation of exponential growth on glucose was associated with a decrease in the cAMP level and there was no correlation between this decrease in cAMP and the depletion of glucose in the medium. In mutants defective in feedback inhibition of cAMP synthesis, resuspension of exponential-phase glucose-grown cells in glucose medium caused an extended lag phase during which a huge, transient accumulation of cAMP occurred. The latter required the presence of glucose and nitrogen, but not phosphate or sulfate, and was not due to intracellular acidification, as shown by in vivo 31P-NMR spectroscopy. The initiation of exponential growth on glucose was also associated in this case with a decrease in cAMP rather than an increase. This behaviour was also observed in strains with attenuated catalytic subunit activity and lacking the regulatory subunit and even in strains without catalytic subunits of cAPK. This might indicate that other mechanisms are able to cause down-regulation of cAMP synthesis in a way mimicking feedback inhibition. Transfer of glucose-growing cells of wild-type or cAPK-attenuated strains to a nitrogen starvation medium resulted in an increase in the cAMP level rather than a decrease. The results indicate that the apparent changes in cAPK activity in vivo during diauxic growth on glucose and during nitrogen starvation cannot be explained on the basis of changes in the cAMP level.

Cyclic AMP↗
PubMed1997

Growth-phase-dependent transcriptional regulation of the pcm and surE genes required for stationary-phase survival of Escherichia coli.

Two neighbouring genes, surE and pcm, at 59 min on the Escherichia coli chromosome are both required for stationary-phase survival. Operon fusions of the putative promoter regions in front of surE (P2) or pcm (P3) with the lacZ reporter gene were constructed to study the transcriptional regulation of pcm and surE. Both promoter regions were able to activate beta-galactosidase activity in a growth-phase-dependent way in either rich or minimal medium. Induction from both promoters reached the highest level in late stationary phase and was independent of the rpoS/katF gene. Spent medium from early as well as late stationary-phase cultures could induce the expression of either promoter even after dialysis or boiling. A high cell density could induce the promoters more rapidly but not to a greater extent. It is proposed that the induction might be correlated with the decline in growth rate of the cells. The induction patterns of either P2 or P3 were very similar. pcm can thus be transcribed from both the P2 and P3 promoters that are regulated in similar ways.

Acid Phosphatase↗
PubMed2000

Phase separation and shape deformation of two-phase membranes

Within a coupled-field Ginzburg-Landau model we study analytically phase separation and accompanying shape deformation on a two-phase elastic membrane in simple geometries such as cylinders, spheres, and tori. Using an exact periodic domain wall solution we solve for the shape and phase separating field, and estimate the degree of deformation of the membrane. The results are pertinent to preferential phase separation in regions of differing curvature on a variety of vesicles.

Journal Article↗
PubMed2000

Collective phase slips and phase synchronizations in coupled oscillator systems

Phase synchronization dynamics in coupled limit cycles with distributed natural frequencies are explored. A synchronization tree from free oscillations to local clustering and global phase locking is found. A desynchronization-induced transition to chaos is shown. Near the onset of various phase synchronization points, a simultaneous quantized stick-slip feature of the phases of oscillators is observed on the desynchronization side and heuristically interpreted in terms of a heteroclinic path instability.

Journal Article↗
PubMed2003

Stochastic phase resetting of two coupled phase oscillators stimulated at different times.

A model of two coupled phase oscillators is presented, where the oscillators are subject to random forces and are stimulated at different times. Transient phase dynamics, synchronization, and desynchronization, which are stimulus locked (i.e., tightly time locked to a repetitively administered stimulus), are investigated. Complex coordinated responses, in terms of a noise-induced switching across trials between qualitatively different responses, may occur when the two oscillators are reset close to an unstable fixed point of their relative phases. This can be achieved with an appropriately chosen delay between the two stimuli. The switching of the responses shows up as a coordinated cross-trial (CT) response clustering of the oscillators, where the two oscillators produce two different pairs of responses. By varying noise amplitude and coupling strength we observe a stochastic resonance and a coupling-mediated resonance of the CT response clustering, respectively. The presented data analysis method makes it possible to detect such processes in numerical and experimental signals. Its time resolution is enormous, since it is only restricted by the time resolution of the preprocessing necessary for extracting the phases from experimental data. In contrast, standard data analysis tools applied across trials relative to stimulus onset, such as CT averaging (where an ensemble of poststimulus responses is simply averaged), CT standard deviation, and CT cross correlation, fail in detecting complex coordinated responses and lead to severe misinterpretations and artifacts. The consequences for the analysis of evoked responses in medicine and neuroscience are significant and are discussed in detail.

Animals↗
PubMed2004

Phase diagram of van der Waals-like phase separation in a driven granular gas.

Equations of granular hydrostatics are used to compute the phase diagram of the recently discovered van der Waals-like phase separation in a driven granular gas. The model two-dimensional system consists of smooth hard disks in a rectangular box, colliding inelastically with each other and driven by a "thermal" wall at zero gravity. The spinodal line and the critical point of the phase separation are determined. Close to the critical point, the spinodal and binodal (coexistence) lines are determined analytically. Effects of the finite size of the confining box in the direction parallel to the thermal wall are investigated. These include suppression of the phase separation by heat conduction in the lateral direction and a change from supercritical to subcritical bifurcation.

Journal Article↗
PubMed2005

Phase diagrams in the lattice restricted primitive model: from order-disorder to gas-liquid phase transition.

The phase behavior of the lattice restricted primitive model (RPM) for ionic systems with additional short-range nearest neighbor (NN) repulsive interactions has been studied by grand canonical Monte Carlo simulations. We obtain a rich phase behavior as the NN strength is varied. In particular, the phase diagram is very similar to that of the continuum RPM for high NN strength. Specifically, we have found both gas-liquid phase separation, with associated Ising critical point, and a first-order liquid-solid transition. We discuss how the line of continuous order-disorder transitions present for the low NN strength changes into continuum-space behavior as one increases the NN strength and compare our findings with recent theoretical results by Ciach and Stell [Phys. Rev. Lett. 91, 060601 (2003)].

Journal Article↗
PubMed2006

Distinct layered structure with density modulation in solid phase formed from B2 phase of banana molecules.

A unique two-dimensional (2D) long-range structure has been observed in a low-temperature phase X1 for a banana molecule having bromine atom substituted on the central core using synchrotron radiation (SR) x-ray scattering measurements. The X1 phase is formed from the B2 phase with the SmC(A)P(A) structure upon cooling and then shows multiple reflections around the first layer line, which are interpreted as a peculiar frustrated structure with long-range layer modulation order. Furthermore, the observation of a well-defined (100) reflection with a spacing of 171A means that there is the electron density modulation along the layers. By coupling these reflections, a 2D lattice with a=173 A, c=53.4A, and beta=81.1 degrees, is determined where the a axis is parallel to the original layer of the phase. This unique structure with modulation can be interpreted as an undulated layer structure and suggested to be the result from deformation with polarization splay defects periodically occurring along the layer. The angle, beta=81.1 degrees, between a and c axes indicates that the position of splay defects in one layer is staggered from that in the neighboring layer. In other words, the splay defect lines run in a direction tilted by roughly 80 degrees with respect to the a axis.

Journal Article↗
PubMed2002

First-order phase transition and phase coexistence in a spin-glass model.

We study the mean-field static solution of the Blume-Emery-Griffiths-Capel model with quenched disorder, an Ising-spin lattice gas with random magnetic interaction. The thermodynamics is worked out in the full replica symmetry breaking scheme. The model exhibits a high temperature/low density paramagnetic phase. As temperature decreases or density increases, a phase transition to a full replica symmetry breaking spin-glass phase occurs. The nature of the transition can be either of the second order or, at temperature below a given critical value, of the first order in the Ehrenfest sense, with a discontinuous jump of the order parameter, a latent heat, and coexistence of phases.

Journal Article↗
PubMed2005

Spin-orbit coupling-induced magnetic phase in the d-density-wave phase of La(2-x)Ba(x)CuO4 superconductors.

We study the effects of spin-orbit coupling in the d-density wave (DDW) phase. In the low-temperature orthorhombic phase of La(2-x)Ba(x)CuO4, we find that spin-orbit coupling induces ferromagnetic moments in the DDW phase, which are polarized along the [110] direction with a considerable magnitude. This effect does not exist in the superconducting phase. On the other hand, if the d-density wave order does not exist at zero field, a magnetic field along the [110] direction always induces such a staggered orbital current. We discuss experimental constraints on the DDW states in light of our theoretical predictions.

Journal Article↗
PubMed2006

Bistable phase locking of a nonlinear optical cavity via rocking: Transmuting vortices into phase patterns.

We report the experimental observation of the conversion of a phase-invariant nonlinear system into a bistable phase-locked one via rocking [G. J. de Valcárcel and K. Staliunas, Phys. Rev. E 67, 026604 (2003)10.1103/PhysRevE.67.026604]. This conversion results in vortices of the phase-invariant system being replaced by phase patterns such as domain walls. A model for the experimental device, a photorefractive oscillator, is given that reproduces the observed behavior.

Journal Article↗