Biomedical subjects

Wei Zhao

Publications and source records attributed to Wei Zhao.

At least 55 records · Page 3Linked to original sources

PubMed2006

Retinoic acid receptor beta2 is epigenetically silenced either by DNA methylation or repressive histone modifications at the promoter in cervical cancer cells.

To elucidate the silencing mechanism of retinoic acid receptor beta2 (RAR beta2) in cervical carcinogenesis, we investigated RAR beta2 expression and the status of both DNA methylation and histone modifications at the promoter in cervical cancer cell lines. RAR beta2 was frequently repressed in cancer cell lines and in primary cancers of the cervix. Although the majority of RAR beta2-negative cancers had methylated promoter, RAR beta2 was repressed with hypomethylated promoter in a substantial fraction of the cancers. The RAR beta2-negative cells with hypomethylated promoters showed a repressive histone modification pattern at the promoter. RAR beta2 was reactivated by a histone deacetylase inhibitor, accompanied by formation of active histone modifications. The repressive modification was also observed in cells repressed with hypermethylated promoter, but RAR beta2 was reactivated only by DNA demethylating agent and not by histone deacetylase inhibitor. Our results suggest that RAR beta2 is silenced by either of the two key epigenetic pathways, DNA methylation or repressive histone modifications, depending on the individual cancer cells.

Base Sequence↗

PubMed2006

Effect of fluid resuscitation on ryanodine receptor in macaques with endotoxic shock.

OBJECTIVE: Our recent study demonstrated that sodium bicarbonate improved cardiac function in macaque models with early-phase endotoxic shock. In the present study, we investigated further the ryanodine receptor/calcium release-channel (RyR) and calcium pump after fluid resuscitation of macaques with early-phase endotoxic shock. METHODS: Twenty-four anaesthetised macaques were assigned to four groups. Nineteen animals were given an intravenous dose of 2.8 mgkg(-1) lipopolysaccharide (LPS). Sixty minutes after the LPS challenge, the animals were given (i) 5 mLkg(-1) normal saline (Ns group, n = 6), (ii) 5 mLkg(-1) of 5% sodium bicarbonate (Sb group, n = 6) or (iii) 5 mLkg(-1) of 3.5% hypertonic sodium chloride (Hs group, n = 7). The control group (Co group, n = 5) received 1 mLkg(-1) normal saline and then with 5 mLkg(-1) normal saline 60 min later. RESULTS: Endotoxin produced a reduction of the density of RyR but did not alter the affinity of RyR. Compared with normal saline, sodium bicarbonate or hypertonic saline induced a restoration of density of RyR but did not influence the affinity of RyR and the calcium pump. CONCLUSION: Up-regulation of RyR performance in myocardium following administration of sodium bicarbonate contributes to the improvement of cardiac function in macaques in the early phase of endotoxic shock.

Animals↗

PubMed2006

Cross-linked and chemically functionalized polymer supports by reactive reversal nanoimprint lithography.

A new format of polymer support having cross-linked polymeric micro- and nanoarrays has been fabricated via reactive reversal nanoimprint lithography. Reactive reversal nanoimprint lithography is a relatively simple method to imprint highly cross-linked and chemically tunable polymers. An array of chloromethyl-functionalized cross-linked polystyrene has been imprinted on hard (silicon) and soft (polymer) substrates, and a model esterification reaction is demonstrated. The imprints have been found to be relatively stable under both static and dynamic stability tests carried out in various organic solvents. The chemical functionality is evenly distributed over the imprinted array. This method of fabricating polymer supports offers a high degree of freedom in terms of the choice of chemical functionality, the types of polymer matrix, and the size of the polymer support. The functional polymer support has potential applications for chemical and biological assays.

Journal Article↗

PubMed2006

Neuronal SIRT1 activation as a novel mechanism underlying the prevention of Alzheimer disease amyloid neuropathology by calorie restriction.

Nicotinamide adenine dinucleotide (NAD)+-dependent sirtuins have been identified to be key regulators in the lifespan extending effects of calorie restriction (CR) in a number of species. In this study we report for the first time that promotion of the NAD+-dependent sirtuin, SIRT1-mediated deacetylase activity, may be a mechanism by which CR influences Alzheimer disease (AD)-type amyloid neuropathology. Most importantly, we report that the predicted attenuation of beta-amyloid content in the brain during CR can be reproduced in mouse neurons in vitro by manipulating cellular SIRT1 expression/activity through mechanisms involving the regulation of the serine/threonine Rho kinase ROCK1, known in part for its role in the inhibition of the non-amyloidogenic alpha-secretase processing of the amyloid precursor protein. Conversely, we found that the expression of constitutively active ROCK1 in vitro cultures significantly prevented SIRT1-mediated response, suggesting that alpha-secretase activity is required for SIRT1-mediated prevention of AD-type amyloid neuropathology. Consistently we found that the expression of exogenous human (h) SIRT1 in the brain of hSIRT1 transgenics also resulted in decreased ROCK1 expression and elevated alpha-secretase activity in vivo. These results demonstrate for the first time a role for SIRT1 activation in the brain as a novel mechanism through which CR may influence AD amyloid neuropathology. The study provides a potentially novel pharmacological strategy for AD prevention and/or treatment.

Alzheimer Disease↗

PubMed2006

Expression, purification, crystallization and preliminary X-ray characterization of the GRP carbohydrate-recognition domain from Homo sapiens.

Galectins are a family of animal lectins which share similar carbohydrate-recognition domains (CRDs) and an affinity for beta-galactosides. A novel human galectin-related protein named GRP (galectin-related protein; previously known as HSPC159) comprises only one conserved CRD with 38 additional N-terminal residues. The C-terminal fragment of human GRP (GRP-C; residues 38-172) containing the CRD has been expressed and purified. The protein was crystallized using the hanging-drop vapour-diffusion method from a solution containing 2% PEG 400 and 2M ammonium sulfate in 100 mM Tris-HCl buffer pH 7.5. Diffraction data were collected to a resolution limit of 2.0 angstroms at beamline 3W1A of Beijing Synchrotron Radiation Facility at 100 K. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 123.07, b = 96.67, c = 61.56 angstroms, beta = 118.72 degrees. The estimated Matthews coefficient was 2.6 angstroms3 Da(-1), corresponding to 51.8% solvent content.

Cloning, Molecular↗

PubMed2006

Capsaicin-induced inactivation of sensory neurons promotes a more aggressive gene expression phenotype in breast cancer cells.

Capsaicin-induced inactivation of sensory neurons has been reported to enhance metastasis of a murine breast cancer cell line, specifically enhancing myocardial metastases. Here we characterized changes in gene expression patterns in primary tumors which developed in capsaicin-treated vs. control mice. We identified a small cohort of genes (17) which all showed significant decreases in expression levels. All of the identified genes have been linked to cell growth, differentiation, and/or cancer progression. Three representative genes, Caspase-7 (an executor of apoptosis), ADAM-10 (A Disintegrin and Metalloprotease), and Elk-3 (a transcriptional repressor of the ternary factor subfamily of the Ets factors) were further investigated. All three showed dramatic downregulation at the protein level in primary tumors from capsaicin-treated animals compared with control (vehicle-treated) animals, and their expression was also lost in cell culture. Elk-3 and Caspase-7 were not expressed in vitro in cultured cell lines, suggesting that their expression was induced by the tumor microenvironment. Loss of Caspase-7 expression can be expected to result in loss of function of apoptotic pathways. At first glance, loss of ADAM-10 expression would be expected to result in decreased invasive capability, due to loss of matrix metalloprotease activity. However, just the opposite appears to be true. We found that ADAM-10 actually hydrolyzes Substance P. Specifically ADAM-10 produces the same growth-inhibitory products from Substance P (i.e., SP (1-7)) that Neprilysin does, so that loss of ADAM-10 expression actually results in loss of production of growth inhibitory peptides from Substance P. Similarly, ADAM-10 also efficiently hydrolyzes Calcitonin Gene-Related Peptide, which may act in concert with Substance P. Finally, overactivity of Ets transcriptional suppressor functions has been linked to inhibition of tumorigenesis (e.g., Erf and Mef), and in addition loss of Elk-3 expression might also be be linked to tumorigenesis via loss of its putative anti-inflammatory activities. There is anecdotal evidence in the literature to indicate that the rest of the down-regulated genes may also contribute to development of a more aggressive phenotype in this breast cancer model.

ADAM Proteins↗

PubMed2006

Nanocrystalline diamond modified gold electrode for glucose biosensing.

Boron-doped diamond has drawn much attention in electrochemical sensors. However there are few reports on non-doped diamond because of its weak conductivity. Here, we reported a glucose biosensor based on electrochemical pretreatment of non-doped nanocrystalline diamond (N-NCD) modified gold electrode for the selective detection of glucose. N-NCD was coated on gold electrode and glucose oxidase (GOx) was immobilized onto the surfaces of N-NCD by forming amide linkages between enzyme amine residues and carboxylic acid groups on N-NCD. The anodic pretreatment of N-NCD modified electrode not only promoted the electron transfer rate in the N-NCD thin film, but also resulted in a dramatic improvement in the reduction of the dissolved oxygen. This performance could be used to detect glucose at negative potential through monitoring the current change of oxygen reduction. The biosensor effectively performs a selective electrochemical analysis of glucose in the presence of common interferents, such as ascorbic acid (AA), acetaminophen (AP) and uric acid (UA). A wide linear calibration range from 10 microM to 15 mM and a low detection limit of 5 microM were achieved for the detection of glucose.

Biosensing Techniques↗

PubMed2006

Two-photon photoemission spectroscopy study of 1,3-butadiene on Cu(111): electronic structures and excitation mechanism.

The characteristics of 1,3-butadiene (C(4)H(6)) adsorbed on Cu(111) were investigated with temperature-programmed desorption (TPD) and two-photon photoemission spectroscopy (2PPE). Dosed at 90 K, the work function drops by 0.4 eV and TPD provides no evidence for dissociation, but there are four coverage-dependent local maxima located at 195, 135, 121, and 115 K. From the 2PPE spectra, three unoccupied electronic states of the C(4)H(6)-Cu(111) system were identified: the LUMO (pi(1)*, 2a(u)), LUMO + 1 (pi(2)*, 2b(g)), and LUMO + 2 (sigma*, 7b(u)), lying 1.3, 3.4, and 4.8 eV above the Fermi level, respectively. Although the excitation mechanisms for the LUMO and LUMO + 1 are substrate mediated, the excitation of the LUMO + 2 is attributed to intramolecular excitation.

Journal Article↗

PubMed2006

The impact of missing and erroneous genotypes on tagging SNP selection and power of subsequent association tests.

OBJECTIVE: Single nucleotide polymorphisms (SNPs) serve as effective markers for localizing disease susceptibility genes, but current genotyping technologies are inadequate for genotyping all available SNP markers in a typical linkage/association study. Much attention has recently been paid to methods for selecting the minimal informative subset of SNPs in identifying haplotypes, but there has been little investigation of the effect of missing or erroneous genotypes on the performance of these SNP selection algorithms and subsequent association tests using the selected tagging SNPs. The purpose of this study is to explore the effect of missing genotype or genotyping error on tagging SNP selection and subsequent single marker and haplotype association tests using the selected tagging SNPs. METHODS: Through two sets of simulations, we evaluated the performance of three tagging SNP selection programs in the presence of missing or erroneous genotypes: Clayton's diversity based program htstep, Carlson's linkage disequilibrium (LD) based program ldSelect, and Stram's coefficient of determination based program tagsnp.exe. RESULTS: When randomly selected known loci were relabeled as 'missing', we found that the average number of tagging SNPs selected by all three algorithms changed very little and the power of subsequent single marker and haplotype association tests using the selected tagging SNPs remained close to the power of these tests in the absence of missing genotype. When random genotyping errors were introduced, we found that the average number of tagging SNPs selected by all three algorithms increased. In data sets simulated according to the haplotype frequecies in the CYP19 region, Stram's program had larger increase than Carlson's and Clayton's programs. In data sets simulated under the coalescent model, Carlson's program had the largest increase and Clayton's program had the smallest increase. In both sets of simulations, with the presence of genotyping errors, the power of the haplotype tests from all three programs decreased quickly, but there was not much reduction in power of the single marker tests. CONCLUSIONS: Missing genotypes do not seem to have much impact on tagging SNP selection and subsequent single marker and haplotype association tests. In contrast, genotyping errors could have severe impact on tagging SNP selection and haplotype tests, but not on single marker tests.

Algorithms↗

PubMed2006

The controlling effect of pH on oxidation of Cr(III) by manganese oxide minerals.

Oxidation of Cr(III) by three types of manganese oxide minerals (birnessite I, birnessite II, and todorokite) and effects of pH were investigated by chemical analysis, equilibrium redox, X-ray diffraction (XRD), and transmission electron microscopy. The effects of pH in the reaction systems on the oxidation of Cr(III) were similar among the three manganese oxide minerals. As pH increased from pH 2.0, the amount of Cr(III) oxidized by the tested manganese oxide minerals first increased, and then peaked at pH 3.0-3.5. While pH continually increased from 3.0 to 3.5, the amount of Cr(III) oxidized by the manganese oxide minerals sharply decreased. Until pH was higher than 5.0-5.5, the Cr(III) oxidation amounts changed to a small extent or kept stable. pH influenced the oxidation of Cr(III) mainly by altering the redox potential in the system, i.e., the concentration of H+, the species of Cr(III), and their distributions in the system. However, the surface charge of the manganese oxide minerals, subjected to the pH in the system, was not found to greatly influence the extent of the oxidation. When pH was below 5.0, oxidation of Cr(III) by the manganese oxide minerals was (or tended to be) an equilibrium reaction and was controlled thermodynamically. When pH was above 5.0-5.5, Cr(OH)3 precipitate was produced in the system and pH had little effect on the oxidation content of Cr(III).

Journal Article↗

PubMed2006

Panzea: a database and resource for molecular and functional diversity in the maize genome.

Serving as a community resource, Panzea (http://www.panzea.org) is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one single-nucleotide polymorphism every approximately 100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize-teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.

Chromosome Mapping↗

PubMed2006

Gramene: a bird's eye view of cereal genomes.

Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication.

Arabidopsis↗

PubMed2006

Identification of radiation-induced cross-linking between thymine and tryptophan by electrospray ionization-mass spectrometry.

Upon exposure to ionizing radiation, DNA undergoes a variety of modifications including the production of a covalent bond between the nucleobase thymine and aromatic amino acids. In this work, electrospray ionization-mass spectrometry(ESI-MS) was used to identify the gamma radiation-induced covalent cross-linking of model peptides (sequence YPPW and pYPPW) with the nucleobase thymine. Tandem electrospray ionization-mass spectrometry (ESI-MSn) was employed to investigate the cross-linking sites. The results showed that irrespective of whether tyrosine was phosphorylated or not, the nucleobase thymine was cross-linked with the tryptophan residue. Possible cross-linking mechanisms are proposed by investigating the related mass peaks.

Cross-Linking Reagents↗

PubMed2006

Providers' HIV prevention discussions with HIV-seropositive injection drug users.

Public health agencies have recommended incorporating HIV prevention counseling into the medical care of persons living with HIV/AIDS. Injection drug users (IDUs) especially need HIV risk-reduction counseling because of their high risk for HIV transmission through both sexual and injection behaviors. The objective of this study was to assess the prevalence of, and patient factors associated with, the delivery of HIV prevention messages to HIV-seropositive IDUs in primary care settings. A majority of participants reported having an HIV prevention discussion with their provider during their most recent primary care visit. Factors significantly associated with report of such discussion were being Hispanic or non-Hispanic Black; high school education or less; and better perception of engagement with provider. Medical providers should provide prevention messages to all HIV-seropositive IDUs, regardless of demographic factors. Effective HIV prevention interventions in primary care settings, including interventions to improve patient-provider communication, are needed for HIV-seropositive IDUs.

Adult↗

PubMed2006

Breast ultrasound image enhancement using fuzzy logic.

Breast cancer is still a serious disease in the world. Early detection is very essential for breast cancer prevention and diagnosis. Breast ultrasound (US) imaging has been proven to be a valuable adjunct to mammography in the detection and classification of breast lesions. Because of the fuzzy and noisy nature of the US images and the low contrast between the breast cancer and tissue, it is difficult to provide an accurate and effective diagnosis. This paper presents a novel algorithm based on fuzzy logic that uses both the global and local information and has the ability to enhance the fine details of the US images while avoiding noise amplification and overenhancement. We normalize the images and then fuzzify the normalized images based on the maximum entropy principle. Edge and textural information are extracted to describe the lesion features and the scattering phenomenon of US images and the contrast ratio measuring the degree of enhancement is computed and modified. The defuzzification process is used to obtain the enhanced US images. To demonstrate the performance of the proposed approach, the algorithm was tested on 86 breast US images. Experimental results confirm that the proposed method can effectively enhance the details of the breast lesions without overenhancement or underenhancement.

Algorithms↗

PubMed2006

Hypocrellin D, a cytotoxic fungal pigment from fruiting bodies of the ascomycete Shiraia bambusicola.

A fungal pigment, hypocrellin D (1), together with three known perylenequinone derivatives hypocrellin A (2), B (3) and C (4), was isolated from the fruiting bodies of Shiraia bambusicola. Its structure was elucidated on the basis of spectral data including 2D NMR experiments. Hypocrellin D (1) significantly inhibited the growth of tumor cell lines Bel-7721, A-549 and Anip-973 with IC50 values of 1.8, 8.8, 38.4 microg/ml, respectively.

Antibiotics, Antineoplastic↗

PubMed2006

Gene array expression profiling in acne lesions reveals marked upregulation of genes involved in inflammation and matrix remodeling.

The pathogenesis of acne has been linked to multiple factors such as increased sebum production, inflammation, follicular hyperkeratinization, and the action of Propionibacterium acnes within the follicle. In an attempt to understand the specific genes involved in inflammatory acne, we performed gene expression profiling in acne patients. Skin biopsies were obtained from an inflammatory papule and from normal skin in six patients with acne. Biopsies were also taken from normal skin of six subjects without acne. Gene array expression profiling was conducted using Affymetrix HG-U133A 2.0 arrays comparing lesional to nonlesional skin in acne patients and comparing nonlesional skin from acne patients to skin from normal subjects. Within the acne patients, 211 genes are upregulated in lesional skin compared to nonlesional skin. A significant proportion of these genes are involved in pathways that regulate inflammation and extracellular matrix remodeling, and they include matrix metalloproteinases 1 and 3, IL-8, human beta-defensin 4, and granzyme B. These data indicate a prominent role of matrix metalloproteinases, inflammatory cytokines, and antimicrobial peptides in acne lesions. These studies are the first describing the comprehensive changes in gene expression in inflammatory acne lesions and are valuable in identifying potential therapeutic targets in inflammatory acne.

Acne Vulgaris↗

PubMed2006

Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III tau subunit.

To investigate the possible role of accessory subunits of Escherichia coli DNA polymerase III holoenzyme (HE) in determining chromosomal replication fidelity, we have investigated the role of the dnaX gene. This gene encodes both the tau and gamma subunits of HE, which play a central role in the organization and functioning of HE at the replication fork. We find that a classical, temperature-sensitive dnaX allele, dnaX36, displays a pronounced mutator effect, characterized by an unusual specificity: preferential enhancement of transversions and -1 frameshifts. The latter occur predominantly at non-run sequences. The dnaX36 defect does not affect the gamma subunit, but produces a tau subunit carrying a missense substitution (E601K) in its C-terminal domain (domain V) that is involved in interaction with the Pol III alpha subunit. A search for new mutators in the dnaX region of the chromosome yielded six additional dnaX mutators, all carrying a specific tau subunit defect. The new mutators displayed phenotypes similar to dnaX36: strong enhancement of transversions and frameshifts and only weak enhancement for transitions. The combined findings suggest that the tau subunit of HE plays an important role in determining the fidelity of the chromosomal replication, specifically in the avoidance of transversions and frameshift mutations.

Alleles↗