Biomedical subjects

Jing Wang

Publications and source records attributed to Jing Wang.

At least 73 records · Page 4Linked to original sources

PubMed2006

Molecular analysis of anoikis resistance in oral cavity squamous cell carcinoma.

Oral cavity squamous cell carcinoma (OSCC) is one of the leading causes of cancer deaths worldwide and most of these deaths result from local-regional recurrence and metastases. Evasion of apoptosis is an important hallmark of cancer development and progression, and previous studies have shown that evasion of anoikis, or detachment-induced apoptosis, correlates with a more aggressive phenotype of carcinoma cells in OSCC. To elucidate the cytogenetic and molecular characteristics of anoikis resistance, we generated several cell lines and clones that displayed this cellular phenotype. To test the hypothesis that chromosomal alterations may underlie this phenotypic transformation, we used karyotype analysis to observe changes in the chromosomal structure of anoikis-sensitive and anoikis-resistant cell lines. We further hypothesized that a unique pattern of gene expression was induced by cell-detachment of anoikis-resistant cell lines, and cDNA microarray analysis was performed using a panel of anoikis-resistant oral cancer cell lines grown under attached and detached growth conditions. We identified S100P, KLK6 and CTNNAL1 as genes whose expression levels were differentially regulated in the anoikis-resistant cell lines compared to the anoikis-sensitive cells under detached conditions. These results were verified using real-time RT-PCR. The anoikis-resistant phenotype of squamous cell carcinoma has a distinct genetic expression pattern that is marked by chromosomal alterations that may contribute to differential expression of genes involved in diverse cellular functions. Therapies targeting these potential mediators of anoikis resistance may prove to be beneficial in the treatment of metastatic squamous cell carcinoma.

Animals↗

PubMed2006

Grazing angle mirror-backed reflection (GMBR) for infrared analysis of monolayers on silicon.

An easy handling infrared measurement, grazing angle mirror-backed reflection (GMBR), has been established to analyze the silicon-based organic monolayer. Theoretical prediction gave the optimal configuration with p-polarized irradiation near a grazing angle 78.1 degrees of incidence. Experimental measurement of hydrogen-terminated, undecylenic acid (UA) and N-hydroxysuccinimide (NHS) functionalized silicon (111) surfaces showed good signal peaks and reproducibility.

Letter↗

PubMed2006

The orphan nuclear receptor Rev-erb alpha regulates circadian expression of plasminogen activator inhibitor type 1.

Plasminogen activator inhibitor type 1 (PAI-1) is a major physiologic regulator of the fibrinolytic system and has recently gained recognition as a modulator of inflammation and atherosclerosis. PAI-1 exhibits circadian rhythmicity in its expression, peaking in the early morning, which is associated with increased risk for cardiovascular events. However, the mechanisms that determine PAI-1 circadian rhythmicity remain poorly understood. We discovered that the orphan nuclear receptor Rev-erb alpha, a core component of the circadian loop, represses human PAI-1 gene expression through two Rev-erb alpha binding sites in the PAI-1 promoter. Mutations of these sites, as well as RNA interference targeting endogenous Rev-erb alpha and its corepressors, led to increased expression of the PAI-1 gene. Furthermore, glycogen synthase kinase 3beta (GSK3beta) contributes to pai-1 repression by phosphorylating and stabilizing Rev-erb alpha protein, which can be blocked by lithium. Interestingly, serum shock generated circadian oscillations in PAI-1 mRNA in NIH3T3 cells, suggesting that PAI-1 is a direct output gene of the circadian loop. Ectopic expression of a stabilized form of Rev-erb alpha that mimics GSK3beta phosphorylation dramatically dampened PAI-1 circadian oscillations. Thus, our results suggest that Rev-erb alpha is a major determinant of the circadian PAI-1 expression and a potential modulator of the morning susceptibility to myocardial infarction.

Animals↗

PubMed2006

Growth inhibition and induction of apoptosis and differentiation of tanshinone IIA in human glioma cells.

Tanshinone IIA is a derivative of phenanthrene-quinone isolated from Danshen, a widely used Chinese herbal medicine. It has antioxidant properties, cytotoxic activities against multiple human cancer cells, inducing apoptosis and differentiation of some human cancer cells. The purpose of this study is to confirm its anticancer activity on human glioma cells, and to elucidate mechanism of its activity. Human glioma cells were tested in vitro for cytotoxicity, colony formation inhibition, BrdU incorporation after treatment with tanshinone IIA. Its effect of apoptosis induction was detected through EB/AO staining, cell cycle analysis and the expressions of ADPRTL1 and CYP1A1 genes, the differentiation induction effect was investigated through morphology, mRNA and protein expressions of GFAP and nestin genes by RT-PCR and immunocytochemistry. Tanshinone IIA demonstrated a dose- and time-dependent inhibitory effect on cell growth, IC(50) was 100 ng/ml, and it significantly inhibited colony formation and BrdU incorporation of human glioma cells. After treatment with 25-100 ng/ml of tanshinone IIA, the apoptotic cells increased significantly (P < 0.01), the cells in G(0)/G(1) phase increased (P < 0.01), and decreased in S phase, ADPRTL1 and CYP1A1 mRNA expression increased 1-2 folds. The cells treated with 100 ng/ml tanshinone IIA demonstrated astrocytes or neuron-like morphology, GFAP mRNA and protein expressions increased, nestin mRNA and protein expressions decreased significantly. The findings in this study suggested that tanshinone IIA exhibited strong effects on growth inhibition and induction of apoptosis and differentiation in human glioma cells. It might serve as a novel promising differentiation-inducing and/or therapeutic agent for human gliomas, and need to be investigated further.

Abietanes↗

PubMed2006

The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella.

BACKGROUND: Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all lineages. RESULTS: For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames (ORFs), with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. CONCLUSION: These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.

DNA, Bacterial↗

PubMed2006

Determination of kinetic and equilibrium parameters of the batch adsorption of Ni(II) from aqueous solutions by Na-mordenite.

The potential to remove nickel(II) ions from aqueous solutions using Na-mordenite, a common zeolite mineral, was thoroughly investigated. The effects of relevant parameters solution pH, adsorbent dose, ionic strength, and temperature on nickel(II) adsorption capacity were examined. The sorption data followed the Langmuir, Freundlich, Langmuir-Freundlich and Dubinin-Radushkevich (D-R) isotherms. The maximum sorption capacity was found to be 5.324 mg/g at pH 6, initial concentration of 40 mg/L and temperature of 20 degrees C. Thermodynamic parameters, viz. changes in standard free energy (DeltaG degrees ), enthalpy (DeltaH degrees ) and entropy (DeltaS degrees ) have also been evaluated and the results show that the sorption process was spontaneous and endothermic in nature. Dynamics of the sorption process were studied and the values of rate constant of adsorption, rate constant of intraparticle diffusion were calculated. The activation energy (E(a)) was found to be 12.465 kJ/mol in the present study, indicating a chemical sorption process involving weak interactions between sorbent and sorbate. The sorption capacity increased with the increase of solution pH and the decrease of ionic strength and adsorbent dose. The nickel(II) ions sorption by the Na-mordenite is not completely attributable to ion exchange. Compared to the other adsorbents, the nickel(II) ions show a lower affinity towards the clay mineral adsorbents.

Aluminum Silicates↗

PubMed2006

Recruitment and activation of naive T cells in the islets by lymphotoxin beta receptor-dependent tertiary lymphoid structure.

The development of spontaneous insulin-dependent diabetes mellitus is preceded by the organization of tertiary lymphoid organ (TLO) in situ, but its role in the development of tissue destruction and the cytokines that control such structures have not been fully defined. We have now observed that TNF superfamily 14 (TNFSF14) is upregulated in aged nonobese diabetic (NOD) pancreas with the appearance of TLO. Blockade of TNFSF14 signaling caused a substantial reduction in the expression of lymphotoxin beta receptor (LTbetaR)-controlled migration factors within the islets and disrupts organization of tertiary structures, leading to prevention of diabetes. Consistently, enhancing LTbetaR signaling by transgenic expression of TNFSF14 in the islets of NOD mice rapidly promoted de novo formation of local TLO, resulting in diabetes, even in the absence of draining lymph nodes (LN). Thus, the TNFSF14-LTbetaR pathway appears to be critical in the development and maintenance of TLO for the onset of diabetes.

Animals↗

PubMed2006

Reduced NMDA receptor tyrosine phosphorylation in PTPalpha-deficient mouse synaptosomes is accompanied by inhibition of four src family kinases and Pyk2: an upstream role for PTPalpha in NMDA receptor regulation.

Mice lacking protein tyrosine phosphatase alpha (PTPalpha) exhibited defects in NMDA receptor (NMDAR)-associated processes such as learning and memory, hippocampal neuron migration, and CA1 hippocampal long-term potentiation (LTP). In vivo molecular effectors linking PTPalpha and the NMDAR have not been reported. Thus the involvement of PTPalpha as an upstream regulator of NMDAR tyrosine phosphorylation was investigated in synaptosomes of wild-type and PTPalpha-null mice. Tyrosine phosphorylation of the NMDAR NR2A and NR2B subunits was reduced upon PTPalpha ablation, indicating a positive effect of this phosphatase on NMDAR phosphorylation via intermediate molecules. The NMDAR is a substrate of src family tyrosine kinases, and reduced activity of src, fyn, yes and lck, but not lyn, was apparent in the absence of PTPalpha. In addition, autophosphorylation of proline-rich tyrosine kinase 2 (Pyk2), a tyrosine kinase linked to NMDAR signaling, was also reduced in PTPalpha-deficient synaptosomes. Altered protein tyrosine phosphorylation was not accompanied by altered expression of the NMDAR or the above tyrosine kinases at any stage of PTPalpha-null mouse development examined. In a human embryonic kidney (HEK) 293 cell expression system, PTPalpha enhanced fyn-mediated NR2A and NR2B tyrosine phosphorylation by several-fold. Together, these findings provide evidence that aberrant NMDAR-associated functions in PTPalpha-null mice are due to impaired NMDAR tyrosine phosphorylation resulting from the reduced activity of probably more than one of the src family kinases src, fyn, yes and lck. Defective NMDAR activity in these mice may also be linked to the loss of PTPalpha as an upstream regulator of Pyk2.

Animals↗

PubMed2006

Vacuum ultraviolet photoionization mass spectrometric study of ethylenediamine.

The photoionization and dissociative photoionizations of ethylenediamine have been studied both experimentally and theoretically. In experiments, photoionization efficiency spectra for ions NH(2)CHCH(3)(+), NH(2)CH=CH(2)(+), CH(2)NH(2)(+), NH(3)(+), NH(2)CH(2)CHNH(2)(+) and NH(2)CH(2)CH(2)NH(2)(+) have been obtained. In addition, the energetics of the dissociative photoionization is investigated with ab initio Gaussian-3 (G3) calculations. The computational results are useful in analyzing the dissociation channels near the ionization thresholds. With the help of the G3 results, the dissociation channels for the formation of the aforementioned fragment ions have been established.

Journal Article↗

PubMed2006

Electron attachment-induced DNA single strand breaks: C3'-O3' sigma-bond breaking of pyrimidine nucleotides predominates.

A detailed understanding of DNA strand breaks induced by low energy electrons (LEE) is of crucial importance for the advancement of many areas of molecular biology and medicine. To elucidate the mechanism of DNA strand breaks by LEEs, theoretical investigations of the electron attachment-induced C3'-O3' sigma-bond breaking of the pyrimidine nucleotides have been performed. Calculations of 2'-deoxycytidine-3'-monophosphate and 2'-deoxythymidine-3'-monophosphate in their protonated form (denoted as 3'-dCMPH and 3'-dTMPH) have been carried out with the reliably calibrated B3LYP/DZP++ theoretical approach. Our results demonstrate that the transfer of the negative charge from the pi*-orbital of the radical anion of pyrimidines to the DNA backbone does not pass through the N1-glycosidic bond. Instead, the migration of the excessive negative charge through the atomic orbital overlap between the C6 of pyrimidine and the C3' of ribose most likely represents a pathway that subsequently leads to the strand breaks. The proposed mechanism of the LEE-induced single strand breaks in DNA assumes that the formation of the base-centered radical anions is the first step in this process. Subsequently, these electronically stable radical anions may undergo either C-O bond breaking or N-glycosidic bond rupture. The present investigation of 3'-dCMPH and 3'-dTMPH yields an energy barrier of 6.2-7.1 kcal/mol for the C3'-O3' sigma-bond cleavage. This is much lower than the energy barriers required for the C5'-O5' sigma-bond and the N1-glycosidic bond break. Therefore, we conclude that the C3'-O3' sigma-bond rupture dominates the LEE-induced single strand breaks of DNA.

Carbon↗

PubMed2006

The Arabidopsis ascorbate peroxidase 3 is a peroxisomal membrane-bound antioxidant enzyme and is dispensable for Arabidopsis growth and development.

Ascorbate peroxidase (APX) exists as several isoforms that are found in various compartments in plant cells. The cytosolic and chloroplast APXs appear to play important roles in antioxidation metabolism in plant cells, yet the function of peroxisomal APX is not well studied. In this study, the localization of a putative peroxisomal membrane-bound ascorbate peroxidase, APX3 from Arabidopsis, was confirmed by studying the green fluorescent protein (GFP)-APX3 fusion protein in transgenic plants. GFP-APX3 was found to co-localize with a reporter protein that was targeted to peroxisomes by the peroxisomal targeting signal 1. The function of APX3 in Arabidopsis was investigated by analysing an APX3 knockout mutant under normal and several stress conditions. It was found that loss of function in APX3 does not affect Arabidopsis growth and development, suggesting that APX3 may not be an important antioxidant enzyme in Arabidopsis, at least under the conditions that were tested, or the function of APX3 could be compensated by other antioxidant enzymes in plant cells.

Amino Acid Sequence↗

PubMed2006

Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9.

Leukaemias and other cancers possess a rare population of cells capable of the limitless self-renewal necessary for cancer initiation and maintenance. Eradication of these cancer stem cells is probably a critical part of any successful anti-cancer therapy, and may explain why conventional cancer therapies are often effective in reducing tumour burden, but are only rarely curative. Given that both normal and cancer stem cells are capable of self-renewal, the extent to which cancer stem cells resemble normal tissue stem cells is a critical issue if targeted therapies are to be developed. However, it remains unclear whether cancer stem cells must be phenotypically similar to normal tissue stem cells or whether they can retain the identity of committed progenitors. Here we show that leukaemia stem cells (LSC) can maintain the global identity of the progenitor from which they arose while activating a limited stem-cell- or self-renewal-associated programme. We isolated LSC from leukaemias initiated in committed granulocyte macrophage progenitors through introduction of the MLL-AF9 fusion protein encoded by the t(9;11)(p22;q23). The LSC were capable of transferring leukaemia to secondary recipient mice when only four cells were transferred, and possessed an immunophenotype and global gene expression profile very similar to that of normal granulocyte macrophage progenitors. However, a subset of genes highly expressed in normal haematopoietic stem cells was re-activated in LSC. LSC can thus be generated from committed progenitors without widespread reprogramming of gene expression, and a leukaemia self-renewal-associated signature is activated in the process. Our findings define progression from normal progenitor to cancer stem cell, and suggest that targeting a self-renewal programme expressed in an abnormal context may be possible.

Animals↗

PubMed2006

Enlargement of gold nanoparticles on the surface of a self-assembled monolayer modified electrode: a mode in biosensor design.

Gold nanoparticle (Au-NP) seeds were adsorbed onto the surface of a self-assembled monolayer (SAM)-modified electrode. With the treatment of this modified electrode by Au-NPs growth solution containing different concentrations of H2O2 or cholesterol along with cholesterol oxidase (ChOx), the Au-NP seeds on the electrode surface were enlarged in varying degrees. As a result, the peak currents in corresponding cyclic voltammograms were inversely proportional to the concentration of H2O2 or cholesterol. ChOx was also further modified onto the surface of Au/SAM/Au-NP electrode to prepare Au/SAM/Au-NP/ChOx electrode. Using the enzyme-modified electrode to detect cholesterol, which also utilized the enlargement of the NPs, an extraordinary low detection limit of 5 x 10(-9) M was achieved and two linear dependence ranges of 7.5 x 10(-8)-1 x 10(-6) and 1 x 10(-6)-5 x 10(-5) M were obtained. Consequently, new kinds of H2O2 and cholesterol biosensors could be fabricated.

Biosensing Techniques↗

PubMed2006

Molecular basis of the recognition process: hydrogen-bonding patterns in the guanine primary recognition site of ribonuclease T1.

Investigation of the intrinsic H-bonding pattern of the guanine complex with a sizable segment (from Asn43 to Glu46) of the primary recognition site (PRS) in RNase T1 at the B3LYP/6-311G(d,p) level of theory enables the electronic density characteristics of the H-bonding patterns of the guanine-PRS complexes to be identified. The perfect H-bonding pattern in the guanine recognition site is achieved through the guanine complex interactions with the large segment of the PRS. Two significant short H-bonds, O epsilon 1...HN1 and O epsilon 2...HN2, have been identified. The similar short H-bond distances found in the anionic GC- base pair and in this study suggest that the short hydrogen-bond distances may be characteristic of the multiple H-bonded anionic nucleobases. The H-bonding energy distribution, the geometric analysis of the H-bonding pattern, and the electron structure characteristics of the H-bonds in the guanine PRS of RNase T1 all suggest that the O epsilon 1...HN1 and O epsilon 2...HN2 side-chain H-bonds dominate the binding at the guanine recognition site of RNase T1. Also, the geometry evidence, the electron structure characteristics, and the properties of the bond critical points of the H-bonds reveal that the side-chain H-bonding and the main-chain H-bonding are mutually intensifying. Thus the positive cooperativity between Asn43 to Tyr45 and Glu46 is proposed.

Binding Sites↗

PubMed2006

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a.

BACKGROUND: Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been sequenced, revealing dynamic and diverse features. To investigate the intra-species diversity of S. flexneri genomes further, we have sequenced the complete genome of S. flexneri 5b strain 8401 (abbreviated Sf8401) and compared it with S. flexneri 2a (Sf301). RESULTS: The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of Sf301, mainly because the former lacks the SHI-1 pathogenicity island (PAI). Compared with Sf301, there are 6 inversions and one translocation in Sf8401, which are probably mediated by insertion sequences (IS). There are clear differences in the known PAIs between these two genomes. The bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from Sf8401 but a specific related protein is found next to the pheV locus. SHI-2 is involved in one intra-replichore inversion near the origin of replication, which may change the expression of iut/iuc genes. Moreover, genes related to the glycine-betaine biosynthesis pathway are present only in Sf8401 among the known Shigella genomes. CONCLUSION: Our data show that the two S. flexneri genomes are very similar, which suggests a high level of structural and functional conservation between the two serotypes. The differences reflect different selection pressures during evolution. The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O was integrated and the serotypes diverged. SHI-1 was subsequently deleted from the S. flexneri 5b genome by recombination, but stabilized in the S. flexneri 2a genome. These events may have contributed to the differences in pathogenicity and epidemicity between the two serotypes of S. flexneri.

Chromosome Aberrations↗

PubMed2006

Extract echo signal in HFR imaging system.

Ultrasonic high frame rate (HFR) method was developed by Jianyu Lu in 1997. This method constructs images in frequency domain; the spectrum of space domain objects is calculated based on the spectrum of echo signals, and the image is obtained by using IFFT (inverse fast Fourier transform). Because of this imaging process, the echo signal from each individual scatterer cannot be obtained directly. In this paper, we present a method, which can pick up the echo signal of every scatterer in HFR imaging method. Computer simulation has been performed to verify our method. With the new method we have developed, many other imaging methods, such as Doppler blood flow and elastic imaging, can be easily combined with HFR method to give more information of the imaged objects.

Algorithms↗

PubMed2006

WEGO: a web tool for plotting GO annotations.

Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at http://wego.genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@genomics.org.cn.

Genes↗

PubMed2006

PQN and DQN: algorithms for expression microarrays.

An ideal expression algorithm should be able to tell truly different expression levels with small false positive errors and be robust to assay changes. We propose two algorithms. PQN is the non-central trimmed mean of perfect match intensities with quantile normalization. DQN is the non-central trimmed mean of differences between perfect match and mismatch intensities with quantile normalization. The quantiles for normalization can be either empirical or theoretical. When array types and/or assay change in a study, the normalization to common quantiles at the probe set level is essential. We compared DQN, PQN, RMA, GCRMA, DCHIP, PLIER and MAS5 for the Affymetrix Latin square data and our data of two sets of experiments using the same bone marrow but different types of microarrays and different assay. We found the computation for AUC of ROC at affycomp.biostat.jhsph.edu can be improved.

Algorithms↗