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Ping Yan

Publications and source records attributed to Ping Yan.

At least 19 recordsLinked to original sources
PubMed2025

The toxin-antitoxin system SavRS contributes to vancomycin resistance in vancomycin-intermediate Staphylococcus aureus by mediating cell wall thickening.

BACKGROUND: The emergence of vancomycin-intermediate Staphylococcus aureus (VISA) has significantly challenged the treatment of S. aureus infection. Toxin-antitoxin (TA) systems have been reported to mediate bacterial stress adaptation and virulence, but their role in vancomycin resistance remains elusive. This study investigated the vancomycin resistance mechanism regulated by the TA system SavRS in VISA. METHODS: savRS mutants in Mu50 and XN108 were generated via homologous recombination. To investigate the regulatory mechanism of vancomycin resistance mediated by savRS in VISA, phenotypic analyses including MICs, growth kinetics and cell wall thickness measurements were performed. Expression of cell wall synthesis-related genes was analysed using quantitative RT-PCR (RT-qPCR) and promoter-lacZ reporter assay. Electrophoretic mobility shift assay (EMSA) was performed to assess the binding of SavRS to the promoters of the cell wall synthesis-related genes. Pull-down assay identified an upstream regulatory element of savRS associated with vancomycin resistance. Quantitative assessment of bacterial burden in murine organ systems following vancomycin administration revealed the critical regulatory role of savRS in mediating vancomycin resistance in vivo. RESULTS: Compared with the WT, the savRS mutant exhibited enhanced vancomycin sensitivity, accelerated growth and reduced cell wall thickness. Correspondingly, RT-qPCR revealed marked down-regulation of the cell wall synthesis-related genes (glyS, dltA, scdA, pbp2, ddl). EMSA and promoter-lacZ reporter assay confirmed direct binding of SavRS to a conserved promoter motif, MGHYYTCCTCA. Pull-down assay identified UspA as an upstream regulator of SavRS, demonstrating that UspA directly controls savRS transcription and modulates VISA resistance. Mouse infection experiments showed that savRS promotes VISA to vancomycin resistance in vivo. CONCLUSIONS: SavRS critically regulates vancomycin resistance in VISA.

Cell Wall↗
PubMed2006

Matrix metalloproteinases expressed by astrocytes mediate extracellular amyloid-beta peptide catabolism.

It has been postulated that the development of amyloid plaques in Alzheimer's disease (AD) may result from an imbalance between the generation and clearance of the amyloid-beta peptide (Abeta). Although familial AD appears to be caused by Abeta overproduction, sporadic AD (the most prevalent form) may result from impairment in clearance. Recent evidence suggests that several proteases may contribute to the degradation of Abeta. Furthermore, astrocytes have recently been implicated as a potential cellular mediator of Abeta degradation. In this study, we examined the possibility that matrix metalloproteinases (MMPs), proteases known to be expressed and secreted by astrocytes, could play a role in extracellular Abeta degradation. We found that astrocytes surrounding amyloid plaques showed enhanced expression of MMP-2 and MMP-9 in aged amyloid precursor protein (APP)/presenilin 1 mice. Moreover, astrocyte-conditioned medium (ACM) degraded Abeta, lowering levels and producing several fragments after incubation with synthetic human Abeta(1-40) and Abeta(1-42). This activity was attenuated with specific inhibitors of MMP-2 and -9, as well as in ACM derived from mmp-2 or -9 knock-out (KO) mice. In vivo, significant increases in the steady-state levels of Abeta were found in the brains of mmp-2 and -9 KO mice compared with wild-type controls. Furthermore, pharmacological inhibition of the MMPs with N-[(2R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl]-L-tryptophan methylamide (GM 6001) increased brain interstitial fluid Abeta levels and elimination of half-life in APPsw mice. These results suggest that MMP-2 and -9 may contribute to extracellular brain Abeta clearance by promoting Abeta catabolism.

Amyloid beta-Peptides↗
PubMed2006

Unique contrast patterns from resonance-enhanced chiral SHG of cell membranes.

Chirality can produce novel nonlinear optical effects that may form the basis for new imaging contrast agents. In this paper, we developed a new chiral chromophore 2, which is the dimer of a known voltage sensitive dye, monomer 1, with the chirality originating from the twisted orientation between two subunits. Racemic dimer and monomer 1 were used as the references to study the effect of chirality in SHG microscopy of live cells. All these dyes selectively stain the outer leaflets of cell membranes, producing strong resonance-enhanced SHG images. At the symmetric junction between two adherent cells, monomer or racemic dimer SHG is forbidden due to centrosymmetry, and indeed little SHG was observed (10 +/- 1% relative to nonjunction). When stained with the chiral dimer, the junction is no longer centrosymmetric and much stronger SHG was observed (39 +/- 4% relative to nonjunction). Plane polarized light produces highly polarized images of spherical cells stained with racemic dye, but for the chiral dye, the polarized pattern is largely eliminated by the chiral SHG emanating from the subresolution membrane convolutions.

Animals↗
PubMed2006

Antiviral interactions of an HCV polymerase inhibitor with an HCV protease inhibitor or interferon in vitro.

The combinations of Abbott Hepatitis C virus (HCV) polymerase A-782759 with either Boehringer Ingelheim HCV NS3 protease inhibitor BILN-2061 or interferon (IFN) displayed additive to synergistic relationships over a range of concentrations of two-drug combination. Treatment of HCV replicon with A-782759, IFN or BILN-2061 for about 16 days resulted in dramatic reductions in HCV RNA (5.1, 3.0 and 3.9 log10 RNA copies, respectively). However, none of the compounds tested alone lead to replicon RNA reduction to undetectable levels. Ongoing replication in the presence of A-782759 or BILN-2061 was associated with the appearance of resistant mutations M414T in NS5B and D168V in NS3, respectively. In contrast, a combination of A-782759 with BILN-2061 resulted in greater than 7 logs RNA reduction leading to undetectable replicon RNA after 16 days of treatment. Our findings suggest that a monotherapy with either drug alone is likely to result in development of resistant mutants. However, a combination therapy with polymerase inhibitor has the potential to improve the efficacy of IFN or a protease inhibitor alone in vivo, due to the lower likelihood of resistance development.

Antiviral Agents↗
PubMed2006

Matrix metalloproteinase-9 degrades amyloid-beta fibrils in vitro and compact plaques in situ.

The pathological hallmark of Alzheimer disease is the senile plaque principally composed of tightly aggregated amyloid-beta fibrils (fAbeta), which are thought to be resistant to degradation and clearance. In this study, we explored whether proteases capable of degrading soluble Abeta (sAbeta) could degrade fAbeta as well. We demonstrate that matrix metalloproteinase-9 (MMP-9) can degrade fAbeta and that this ability is not shared by other sAbeta-degrading enzymes examined, including endothelin-converting enzyme, insulin-degrading enzyme, and neprilysin. fAbeta was decreased in samples incubated with MMP-9 compared with other proteases, assessed using thioflavin-T. Furthermore, fAbeta breakdown with MMP-9 but not with other proteases was demonstrated by transmission electron microscopy. Proteolytic digests of purified fAbeta were analyzed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry to identify sites of Abeta that are cleaved during its degradation. Only MMP-9 digests contained fragments (Abeta(1-20) and Abeta(1-30)) from fAbeta(1-42) substrate; the corresponding cleavage sites are thought to be important for beta-pleated sheet formation. To determine whether MMP-9 can degrade plaques formed in vivo, fresh brain slices from aged APP/PS1 mice were incubated with proteases. MMP-9 digestion resulted in a decrease in thioflavin-S (ThS) staining. Consistent with a role for endogenous MMP-9 in this process in vivo, MMP-9 immunoreactivity was detected in astrocytes surrounding amyloid plaques in the brains of aged APP/PS1 and APPsw mice, and increased MMP activity was selectively observed in compact ThS-positive plaques. These findings suggest that MMP-9 can degrade fAbeta and may contribute to ongoing clearance of plaques from amyloid-laden brains.

Aging↗
PubMed2006

Fluorophore-assisted light inactivation of calmodulin involves singlet-oxygen mediated cross-linking and methionine oxidation.

Fluorophore-assisted light inactivation (FALI) permits the targeted inactivation of tagged proteins and, when used with cell-permeable multiuse affinity probes (MAPs), offers important advantages in identifying physiological function, because targeted protein inactivation is possible with spatial and temporal control. However, reliable applications of FALI, also known as chromophore-assisted light inactivation (CALI) with fluorescein derivatives, have been limited by lack of mechanistic information regarding target protein sensitivity. To permit the rational inactivation of targeted proteins, we have identified the oxidizing species and the susceptibility of specific amino acids to modification using the calcium regulatory protein calmodulin (CaM) that, like many essential proteins, regulates signal transduction through the reversible association with a large number of target proteins. Following the covalent and rigid attachment of 4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein (FlAsH) to helix A, we have identified light-dependent oxidative modifications of endogenous methionines to their corresponding methionine sulfoxides. Initial rates of methionine oxidation correlate with surface accessibility and are insensitive to the distance between the bound fluorophore and individual methionines, which vary between approximately 7 and 40 A. In addition, we observed a loss of histidines, as well as zero-length cross-linking with binding partners corresponding to the CaM-binding sites of smooth myosin light chain kinase and ryanodine receptor. Our results provide a rationale for proteomic screens using FALI to inhibit the function of many signaling proteins, which, like CaM, commonly present methionines at binding interfaces.

Amino Acid Sequence↗
PubMed2006

Towards pointwise motion tracking in echocardiographic image sequences--comparing the reliability of different features for speckle tracking.

In this paper, we studied the problem of feature-based motion tracking in echocardiographic image sequences. We described the relation between possible feature variations and different kinds of tissue motion using a linear convolution model. We also showed that motion-feature decorrelation (which means that the motion parameters estimated using feature tracking fail to represent the underlying tissue motion) compensation is an ill-posed inverse problem. Instead of finding a method that may provide better compensation results than previous approaches, we used an quantitative measure to compare the reliability of tracking features. Experiment results showed that the use of the reliability measure improved the robustness of displacement estimation. With the help of the reliability measure, we compared the performance of different features using simulations and phantom examples. While we noticed that the radio frequency (RF) signal outperforms the B-mode (BM) signal in the analysis of small deformation (e.g., less than 0.1% compression), we also found out that the BM signal works better than the RF signal in the analysis of large deformation (e.g., larger than 2% compression). The use of a band-passed filtered feature does not result in significant improvement in tracking.

Algorithms↗
PubMed2006

A cluster model for space-time disease counts.

Modelling disease clustering over space and time can be helpful in providing indications of possible exposures and planning corresponding public health practices. Though a considerable number of studies focus on modelling spatio-temporal patterns of disease, most of them do not directly model a spatio-temporal clustering structure and could be ineffective for detecting clusters. In this paper, we extend a purely spatial cluster model to accommodate space-time clustering. Inference is performed in a Bayesian framework using reversible jump Markov chain Monte Carlo. This idea is illustrated using data on female breast cancer mortality from Japan. A hierarchical parametric space-time model for mapping disease is used for comparison.

Adult↗
PubMed2006

The effects of sodium hypochlorite (5.25%), Chlorhexidine (2%), and Glyde File Prep on the bond strength of MTA-dentin.

The purpose of this study was to evaluate the effects of sodium hypochlorite (5.25%), chlorhexidine (2%), and Glyde File Prep on the bond strengths of MTA-dentin in vitro. Standardized dentin disks were prepared and the central hole in each disk was filled with mineral trioxide aggregate (MTA). The specimens were randomly divided into four groups to be immersed in saline, 5.25% NaOCl, 2% chlorhexidine, and Glyde File Prep for 2 hours. The bond strengths of MTA-dentin were measured with a material testing system (MTS) and the fractured surfaces on the root walls were observed by scanning electron microscopy. Compared with the control group, the bond strengths were significantly lower in Glyde File Prep group (p < 0.05) and there was no significant difference in the chlorhexidine group or in the NaOCl group (p > 0.05). This study suggested that Glyde File Prep could negatively affect the bond strengths of MTA-dentin.

Aluminum Compounds↗
PubMed2006

Screening and evaluation of human single-chain fragment variable antibody against hepatitis B virus surface antigen.

BACKGROUND: Phage display technology has become a vital tool in studies aimed at identifying molecules binding to a specific target. It enables the rapid generation and selection of high affinity, fully human antibody product candidates to essentially any disease target appropriate for antibody therapy. In this study, we prepared the recombinant single-chain fragment variable (ScFv) antibody to hepatitis B virus surface antigen (HBsAg) by the phage display technology for obtaining a virus-targeting mediator. METHODS: mRNA was isolated from B-lymphocytes from a healthy volunteer and converted into cDNA. The fragment variables of heavy and light chain were amplified separately and assembled into ScFv DNA with a specially constructed DNA linker by polymerase chain reaction. The ScFv DNA was ligated into the phagmid vector pCANTAB5E and the ligated sample was transformed into competent E.coli TG1. The transformed cells were infected with M13K07 helper phage to form a human recombinant phage antibody library. The volume and recombinant rate of the library were evaluated by bacterial colony count and restriction analysis. After two rounds of panning with HBsAg, the phage clones displaying ScFv of the antibody were selected by enzyme-linked immunosorbant assay (ELISA) from the enriched phage clones. The antigen binding affinity of the positive clone was detected by competition ELISA. HB2151 E.coli was transfected with the positive phage clone demonstrated by competition ELISA for production of a soluble form of the anti-HBsAg ScFv. ELISA assay was used to detect the antigen binding affinity of the soluble anti-HBsAg ScFv. Finally, the relative molecular mass of soluble anti-HBsAg ScFv was measured by SDS-PAGE. RESULTS: The variable heavy (VH) and variable light (VL) and ScFv DNAs were about 340 bp, 320 bp and 750 bp, respectively. The volume of the library was up to 2 x 10(6) and 8 of 10 random clones were recombinants. Two phage clones could strongly compete with the original HBsAb for binding to HBsAg. Within 2 strong positive phage clones, the soluble anti-HBsAg ScFv from one clone was found to have the binding activity with HBsAg. SDS-PAGE showed that the relative molecular weight of soluble anti-HBsAg ScFv was 32 kDa. CONCLUSION: The anti-HBsAg ScFv successfully produced by phage antibody technology may be useful for broadening the scope of application of the antibody.

Antibodies, Monoclonal↗
PubMed2005

Theoretical models and analytic expressions for buildup time of pulsed confocal unstable optical parametric oscillators with uniform or Gaussian reflectivity mirrors.

A theoretical model and a simplified analytic expression are developed to describe the buildup time of a pulsed confocal unstable optical parametric oscillator (OPO) with a uniform-reflectivity mirror (URM) or a Gaussian-reflectivity mirror (GRM). Two analytic expressions have been demonstrated to correspond to theoretical models with a sufficient degree of accuracy. The effects of a variety of cavity and pump parameters on the buildup time of an OPO were investigated and analyzed. It was found that a GRM unstable OPO generally exhibits a shorter buildup time than the corresponding URM unstable OPO with equally effective output coupling.

Journal Article↗
PubMed2005

Ultrafast spectroscopy of the solvent dependence of electron transfer in a perylenebisimide dimer.

We investigate the photoinduced intramolecular electron-transfer (IET) behavior of a perylenebisimide dimer in a variety of solvents using femtosecond transient absorption spectroscopy. Overlapping photoinduced absorptions and stimulated emission give rise to complicated traces, but they are well fit with a simple kinetic model. IET rates were found to depend heavily on solvent dielectric constant. Good quantitative agreement with rates derived from fluorescence quantum yield and time-resolved fluorescence measurements was found for forward electron transfer and charge recombination rates.

Acetone↗
PubMed2005

Self-organized perylene diimide nanofibers.

A propeller-shaped perylene diimide trimer was synthesized and a simple evaporation method was used for the self-organization of trimer molecules into fluorescent nanofibers. The sizes of these fibers-from 4 to 150 nm in diameter-were measured by atomic force microscopy and can be controlled by adjusting the concentration of the initial solution. The aspect ratios (length/height) are around 500. The plane of the trimer was determined by polarized scanning confocal microscopy to be perpendicular to the axis of the fibers, in agreement with molecular mechanics calculations. UV/vis and NMR spectroscopies were used to monitor concentration-dependent pi-pi stacking in solution. Single-fiber fluorescence imaging and spectroscopy were performed using a total internal reflection fluorescence microscope equipped with a digital color camera and imaging CCD spectrometer. Strongly red-shifted fluorescence from these fibers indicates a high degree of electronic delocalization, and breaking up this delocalization by photobleaching blue-shifts the emission toward that of an isolated noninteracting molecule. The delocalization along these nanofibers and the ability to study the electronic structure using fluorescence make them potentially useful in nanoscale devices, such as field effect transistors and photoconductors.

Imides↗
PubMed2005

Molecular switch based on a biologically important redox reaction.

Building on our earlier report of a single-molecule probe, we show how biologically important redox centers, nicotinamide and quinone, incorporated into a fluorophore-spacer-receptor molecular structure, form redox active molecular switches, with the photoinduced electron-transfer behavior of each depending on the oxidation state of the receptor subunit. The switch based on nicotinamide (3/6) is strongly fluorescent in its oxidized state (Phi(F) approximately 1.0) but nonfluorescent in the reduced state (Phi(F) < 0.001) due to electron transfer from the reduced nicotinamide to the photoexcited fluorophore. The fluorescence can be reversibly switched off and on chemically by successive reduction with NaBH(3)CN and oxidation with tetrachlorobenzoquinone and switched electrochemically over 10 cycles without significant degradation. A similar switch based on quinonimine turned out to be nonfluorescent in both reduced and oxidized states: in addition to a similar quenching mechanism in the reduced state, quenching also occurs in the oxidized state, due to electron transfer from the fluorophore to the receptor. Ab initio quantum chemical calculations of orbital energy levels were used to corroborate these quenching mechanisms. Calculations predicted photoinduced electron transfer to be energetically favorable in all cases where quenching was observed and unfavorable in all cases where it was not. Application of the perylene analogue as a biosensor has also been demonstrated by coupling the switch to the catalytic pathway of yeast alcohol dehydrogenase, a common NADH/NAD(+)-utilizing enzyme.

Alcohol Dehydrogenase↗
PubMed2005

A boundary element-based approach to analysis of LV deformation.

Quantification of left ventricular (LV) deformation from 3D image sequences (4D data) is important for the assessment of myocardial viability, which can have important clinical implications. To date, feature information from either Magnetic Resonance, computed tomographic or echocardiographic image data has been assembled with the help of different interpolative models to estimate LV deformation. These models typically are designed to be computationally efficient (e.g. regularizing strategies using B-splines) or more physically realistic (e.g. finite element approximations to biomechanical models), but rarely incorporate both notions. In this paper, we combine an approach to the extraction and matching of image-derived point features based on local shape properties with a boundary element model. This overall scheme is intended to be both computationally efficient and physically realistic. In order to illustrate this, we compute strains using our method on canine 4D MR image sequences and compare the results to those found from a B-spline-based method (termed extended free-form deformation (EFFD)) and a method based on finite elements (FEM). All results are compared to displacements found using implanted markers, taken to be agold standard.

Algorithms↗
PubMed2005

[Effect of cadmium on estrogen receptor from rat uterus in vitro.].

OBJECTIVE: To investigate the effect of cadmium (Cd) on estrogen receptor and to assess its endocrine disrupting action. METHODS: The estrogen receptor rich supernatant was prepared from the ovariectomized Sprague-Dawley rats. The effects of cadmium on estrogen binding were performed using a sing-dose ligand-binding assay. Extract from uterus were treated with various concentrations of cadmium (0, 10(-3), 10(-5) or 10(-7) mol/L) for various pre-incubation time (0, 30, 60, 90 min) by means of orthogonal experimental design with orthogonal layout of L16(4(5)) (the experiment was repeated for 5 times). In addition to the radioinert competitor, each assay included a zero tube and a DES standard curve for quality control purpose. Data for cadmium and the DES standard curve were plotted as percent [3H]-E2 bound versus log (molar concentration), and the IC50 for cadmium was determined. The RBA for cadmium was calculated by dividing the IC50 of DES in terms of the IC50 of cadmium. RESULTS: Cadmium could not block the binding of estradiol to the receptor because hormone binding did not change with increasing cadmium concentration or increasing preincubation time. The results showed that the binding of [3H]-estradiol to uterine cytosols was not significant (P > 0.05). The Bmax (its unit is pmol/mg protein) of various concentrations of cadmium (0, 10(-3), 10(-5) or 10(-7) mol/L) for pre-incubating 0 min is 203.15 +/- 75.16, 203.41 +/- 22.78, 220.82 +/- 45.35, 209.10 +/- 49.66 respectively; The Bmax of them for pre-incubating 30 min is 215.67 +/- 92.97, 139.79 +/- 53.78, 205.27 +/- 23.60, 172.63 +/- 55.09 respectively. The Bmax of them for pre-incubating 60 min is 197.11 +/- 50.68, 203.24 +/- 66.33, 183.92 +/- 31.89, 183.33 +/- 32.70, respectively. The Bmax of them for pre-incubating 90 min is 229.69 +/- 76.88, 175.70 +/- 70.28, 164.26 +/- 24.46, 150.78 +/- 65.97 respectively. Mean IC50 for cadmium is 10(-4) - 10(-3) M. If the affinities of DES binding to estrogen receptors was taken to be 100%, the relative binding affinities of cadmium was 10(-6) - 10(-7). The results indicated that cadmium had only a very poor affinity with estrogen receptor. CONCLUSION: In vitro assay cadmium did not have distinct disrupting effect on binding of estradiol to estrogen receptors from rat uterine.

Animals↗
PubMed2005

[Relationship between millimeter wave irradiation in pregnant mice and c-Fos protein expression in hippocampus and learning and memory functions in their offsprings].

OBJECTIVE: To determine the threshold of millimeter wave irradiation for fetal injury in mice and the mechanism of decrease of learning and memory function in their offsprings and to verify whether the millimeter wave has the non-thermal effect. METHODS: Pregnant mice were irradiated by millimeter wave with frequencies of 37.4, 42.2, 53.0 and 60.0 GHz at power densities of 1, 3, 5, 8 mW/cm(2) for two hours daily from the 6th to 15th day of their gestation. Learning and memory functions of their offsprings were tested by a Y-type electric maze. c-Fos protein expression level in hippocampus of their offsprings was determined with immunohistochemistry 0, 30, 60, 90 and 120 minutes after the offsprings were trained respectively. RESULTS: The minimal power density of millimeter wave for the decrease in learning and memory function and decrease of c-Fos protein expression level in hippocampus of their offsprings caused by 37.4, 42.2 GHz and 53.0, 60.0 GHz was 5 and 3 mW/cm(2). Severity of injury for learning and memory in offsprings caused by irradiation increased with the power density of millimeter wave. The millimeter wave did not cause increase of the body temperature of the pregnant mice. CONCLUSION: The threshold of millimeter wave with 37.4, 42.2 GHz, and 53.0, 60.0 GHz causing fetal injury in mice is 5 and 3 mW/cm(2) respectively. The decrease in learning and memory functions in offspring mice is related with decrease of c-Fos protein expression level in hippocampus. Millimeter wave has the non-thermal effects.

Animals↗