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Ting Wang

Publications and source records attributed to Ting Wang.

90 records · Page 5Linked to original sources
PubMed2004

[The relationship between cytochrome P450, subfamily IIIA, polypeptide 5 gene and drug resistance in leukemia cell lines].

OBJECTIVE: To investigate if the transcription, expression and activities of cytochrome P450, subfamily IIIA, polypeptide 5 gene (CYP3A5) are correlated with drug resistance in leukemia cell lines. METHODS: Using RT-PCR, immunohistochemistry and reverse-phase high-performance liquid chromatography (HPLC) assay, CYP3A5 mRNA protein and activities in leukemia cell lines were detected. Daunorubicin (DNR) sensitivity profiles of leukemia cell lines were obtained with MTT assay. Cell cycle characteristics and apoptosis induced by DNR were observed with flow cytometry (FCM) analysis. RESULTS: K562, U937, HL-60, NB4 and Jurkat cells were chosen as experimental cell line panels. It was found that CYP3A5 mRNA were measured only in K562 and U937 cells. CYP3A4 and CYP3A7 were not detectable in each cell line. The five leukemia cell lines presented sensitivity to DNR (IC(50), mg/L) in an order as follows: NB4 (0.068 +/- 0.036) > Jurkat (0.076 +/- 0.013) > HL-60 (0.092 +/- 0.016) > K562 (0.148 +/- 0.041) > U937 (0.150 +/- 0.035). Interestingly, K562 and U937 cells (cell lines with CYP3A5 gene transcription) were more resistant to DNR as compared with the other three cell lines in a statistically significant way (P < 0.01). Furthermore, expression and activities of CYP3A5 gene and cell cycle characteristics were observed in K562 and NB4 cells, which represented cell lines with or without CYP3A5 gene transcription respectively. In comparison with NB4 cells, K562 cells expressed CYP3A5 protein and showed a statistically significant higher CYP3A5 activity (3.075 +/- 0.036) x 10(-3) versus (1.635 +/- 0.196) x 10(-3), P < 0.05. FCM analysis showed that S phase cell proportions were similar in K562 and NB4 cells. Incubation with DNR (1 mg/L) for 6 hours induced a remarkable apoptosis peak in NB4 cells, while such peak not occur in K562 cells (apoptosis cell percentage 18.4% and 0.8% respectively). CONCLUSION: Only CYP3A5 gene of CYP3A subfamily were detectable in leukemia cell lines, and its transcription, expression and activities were correlated with drug resistance in leukemia cell lines.

Antibiotics, Antineoplastic↗
PubMed2004

Effects of DNA methylation inhibitor on down-regulation of ribonuclease inhibitor expression in cancer cell lines.

BACKGROUND & OBJECTIVE: Human ribonuclease inhibitor (RI) could effectively block angiogenin-induced angiogenesis, and inhibit growth of transplant solid tumors in animals. However, its exact molecular mechanism of antitumor has not been totally ascertained. Many tumor suppressor genes occur loss of expression by aberrant methylation in promoter region. Demethylation, treated with methylation inhibitor 5-aza-2'-deoxycytidine (5-Aza-CdR),can restore the gene expression. To further explore functions of RI, and investigate relationship between RI and tumorigenesis, the study was designed to explore effects of 5-Aza-CdR on expression of RI in cancer cell lines. METHODS: Human breast cancer cell line MCF-7, human gastric cancer cell line BGC-823, human prostate cancer cell line DU-145, and human colon cancer cell line HT-29 were treated with 5-Aza-CdR. Expression of RI was analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR), Western blot, immunofluorescence, and immunocytochemistry. RESULTS: Expression of RI significantly elevated by 5-Aza-CdR at both mRNA and protein level in MCF-7, BGC-823, and DU-145 cells (P< 0.01). Compared with control cells, mRNA levels of RI in MCF-7, BGC-823, and DU-145 cells treated with 5-Aza-CdR were increased by percentages of 37.2%, 46.0%, and 32.4%, respectively; protein levels of RI were increased by percentages of 26.4%, 20.9%, and 24.4%, respectively; but no obvious change observed in HT-29 cells. CONCLUSION: RI gene may be involved in tumorigenesis of gastric, prostate, and breast cancer.

Azacitidine↗
PubMed2003

Combining phylogenetic data with co-regulated genes to identify regulatory motifs.

MOTIVATION: Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Two categories of algorithms have been developed to identify common motifs from a set of DNA sequences. The first can be called a 'multiple genes, single species' approach. It proposes that a degenerate motif is embedded in some or all of the otherwise unrelated input sequences and tries to describe a consensus motif and identify its occurrences. It is often used for co-regulated genes identified through experimental approaches. The second approach can be called 'single gene, multiple species'. It requires orthologous input sequences and tries to identify unusually well conserved regions by phylogenetic footprinting. Both approaches perform well, but each has some limitations. It is tempting to combine the knowledge of co-regulation among different genes and conservation among orthologous genes to improve our ability to identify motifs. RESULTS: Based on the Consensus algorithm previously established by our group, we introduce a new algorithm called PhyloCon (Phylogenetic Consensus) that takes into account both conservation among orthologous genes and co-regulation of genes within a species. This algorithm first aligns conserved regions of orthologous sequences into multiple sequence alignments, or profiles, then compares profiles representing non-orthologous sequences. Motifs emerge as common regions in these profiles. Here we present a novel statistic to compare profiles of DNA sequences and a greedy approach to search for common subprofiles. We demonstrate that PhyloCon performs well on both synthetic and biological data. AVAILABILITY: Software available upon request from the authors. http://ural.wustl.edu/softwares.html

Algorithms↗
PubMed2003

Using nitrile-derivatized amino acids as infrared probes of local environment.

It is well-known that the C=N stretching vibration in acetonitrile is sensitive to solvent. Therefore, we proposed in this contribution to use this vibrational mode to report local environment of a particular amino acid in proteins or local environmental changes upon binding or folding. We have studied the solvent-induced frequency shift of two nitrile-derivatized amino acids, which are, AlaCN and PheCN, in H(2)O and tetrahydrofuran (THF), respectively. Here, THF was used to approximate a protein's hydrophobic interior because of its low dielectric constant. As expected, the C=N stretching vibrations of both AlaCN and PheCN shift as much as approximately 10 cm(-1) toward higher frequency when THF was replaced with H2O, indicative of the sensitivity of this vibration to solvation. To further test the utility of nitrile-derivatized amino acids as probes of the environment within a peptide, we have studied the binding between calmodulin (CaM) and a peptide from the CaM binding domain of skeletal muscle myosin light chain kinase (MLCK(579-595)), which contains a single PheCN. MLCK(579-595) binds to CaM in a helical conformation. When the PheCN was substituted on the polar side of the helix, which was partially exposed to water, the C=N stretching vibration is similar to that of PheCN in water. In constrast, when PheCN is introduced at a site that becomes buried in the interior of the protein, the C=N stretch is similar to that of PheCN in THF. Together, these results suggest that the C=N stretching vibration of nitrile-derivatized amino acids can indeed be used as local internal environmental markers, especially for protein conformational studies.

Alanine↗
PubMed2003

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation.

The suitability of three implicit solvent models for flexible protein-protein docking by procedures using molecular dynamics simulation is investigated. The three models are (i) the generalized Born (GB) model implemented in the program AMBER6.0; (ii) a distance-dependent dielectric (DDD) model; and (iii) a surface area-dependent model that we have parameterized and call the NPSA model. This is a distance-dependent dielectric model modified by neutralizing the ionizable side-chains and adding a surface area-dependent solvation term. These solvent models were first tested in molecular dynamics simulations at 300 K of the native structures of barnase, barstar, segment B1 of protein G, and three WW domains. These protein structures display a range of secondary structure contents and stabilities. Then, to investigate the performance of the implicit solvent models in protein docking, molecular dynamics simulations of barnase/barstar complexation, as well as PIN1 WW domain/peptide complexation, were conducted, starting from separated unbound structures. The simulations show that the NPSA model has significant advantages over the DDD and GB models in maintaining the native structures of the proteins and providing more accurate docked complexes.

Bacterial Proteins↗
PubMed2003

DSMM: a Database of Simulated Molecular Motions.

We describe a Database of Simulated Molecular Motions (DSMM). This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch.de/mcm/database/dsmm.

Computer Graphics↗
PubMed2003

[Study of CYP3A5 in drug resistance mechanisms in acute leukemia].

OBJECTIVE: To investigate if CYP3A5 is involved in drug resistances mechanisms of acute leukemia. METHODS: By using RT-PCR, immunohistochemistry and MTT assay, CYP3A5 mRNA and protein were detected in leukemia cell lines and acute leukemia patients, meanwhile transcriptional regulation of CYP3A5 induced by daunorubicin was observed. A pcDNA3-CYP3A5 reconstituted plasmid and its stably transfected cell line HL-60/CYP3A5 were both established. RESULTS: CYP3A5 mRNA was detected in K562 and U937 cells, whose IC(50) values of daunorubicin were 2.1-fold higher than those of NB4 and HL-60 cells. Bone marrow CYP3A5 positive blast cell percentage at the time of diagnosis in primary drug resistance group (17.2%) was significantly higher than that of continuous complete remission (CCR) group (0.4%) and secondary drug resistance group (5.4%). In their first complete remission of the early relapsed group, the positive rate had been 23.9% as compared with that of CCR group (1.3%). Daunorubicin increased CYP3A5 mRNA level in K562/A02 and activated its transcription in HL-60/ADR. HL-60/CYP3A5 cell was significantly resistant to daunorubicin and vincristine than HL-60 cells did (3.0 and 4.0 times, respectively). CONCLUSION: CYP3A5 expressed in leukemia cells may cause in situ metabolization of many kinds of anticancer drugs, thus led to drug resistance.

Cytochrome P-450 CYP3A↗
PubMed2003

[Simultaneous determination of ammonium thiocyanate and its isomeride by dual wavelength multiplication subtractive spectrophotometry].

A method was purposed for simultaneous determination of ammonium thiocyanate and its isomeride thiourea by dual wavelength multiplication subtractive spectrophotometry. The approach was based on the measurement of the absorbance of both standard solutions and mixture samples at 216 and 236 nm. The concentration of ammonium thiocyanate and thiourea was obtained through the calculation of balancing coefficient and slope. The method was successfully applied to the determination of ammonium thiocyanate and thiourea, which existed in isomerization reaction. A comparison was also made with the dual wavelength method and reversed ion-pair chromamotography, and the dual wavelength multiplication subtractive spectrophotometry offered the advantages of simple, rapid and accurate determination.

Isomerism↗
PubMed2003

[Analysis on the SARS-CoV genome of PUMC01 isolate].

OBJECTIVE: To perform variation and phylogenetics analysis on the SARS-CoV genome sequence (PUMC01) isolated in the Peking Union Medical College Hospital. METHODS: The cDNA library of SARS-CoV (PUMC01 isolate) was constructed by means of random-priming strategy. Random selected plasmid was sequenced and the genome sequence of SARS-CoV-PUMC01 was assembled by conventional methods (The Genebank Accession No. of SARS-CoV-PUMC01 is AY350750). The variation and phylogenetics analysis were performed by comparing the PUMC01 sequence with other SARS-CoV isolates. RESULTS: Ten variation sites were found by comparing PUMC01 isolate with Tor2 and Urbani isolates. In phylogenetic analysis of 18 SARS-CoV isolates, two classes were observed and there is different differential time between these two classes and the different isolates in each class. CONCLUSIONS: The evidence of phylogenetic analysis of different SARS-CoV isolates from different region is instructive for understanding the clinical relations between the different isolates and the transmission chain of SARS-CoV.

Amino Acid Sequence↗
PubMed2003

[cDNAs cloning of SARS-CoV PUMC2 viral genome].

OBJECTIVE: To get the cDNA clones which cover the whole genome of SARS-CoV PUMC2 strain. METHODS: Using the SARS-CoV PUMC2 strain genomic RNA as the template, the cDNA fragments were amplified by RT-PCR, the PCR products were further purified and ligated into the pGEM-T vector, and all the clones obtained were sequenced. RESULTS: The cDNA clones which cover the whole genome of SARS-CoV PUMC2 strain were obtained. CONCLUSIONS: These cDNAs can be provided for the function study of SARS-CoV proteins and the construction of full-length infectious cDNA clone of SARS-CoV.

Amino Acid Sequence↗
PubMed2002

Groups of p53 target genes involved in specific p53 downstream effects cluster into different classes of DNA binding sites.

The tumor suppressor protein p53, once activated, can cause either cell cycle arrest or apoptosis through transactivation of target genes with p53 DNA binding sites (DBS). To investigate the role of p53 DBS in the regulation of this profound, yet poorly understood decision of life versus death, we systematically studied all known and potential p53 DBS. We analysed the DBS separated from surrounding promoter regions in yeast and mammalian assays with and without DNA damage. p53 efficiently utilized the DBS of MDM2 and of genes connected to cell cycle arrest, DNA repair and the death receptor pathway of apoptosis. However, p53 was unable to utilize two-thirds of the isolated DBS, a subset that included almost all DBS of apoptosis-related genes. Neither ASPP2, a p53-interacting protein reported to specifically stimulate p53 transcriptional activity on apoptosis-related promoters, nor DNA damage resulted in p53 utilization of isolated DBS of apoptosis-related genes. Thus, a major regulation of p53 activity occurs at the level of p53 DBS themselves by posing additional requirements for the successful utilization of apoptosis-related DBS.

Apoptosis↗
PubMed2002

Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics.

The periplasmic oligopeptide binding component (OppA) of the oligopeptide permease found in Gram-negative bacteria acts as a receptor for peptide transport across the cell membrane and is a potential target for antibacterial drug design. OppA exhibits broad specificity, binding to diverse peptides of 2-5 amino acid residues length. Crystallographic and calorimetric measurements have been carried out by Tame et al. of the binding of 28 peptides of sequence K-X-K to OppA, where X is a natural or nonnatural amino acid. Despite this extensive experimental characterization, a clear relationship between structural and thermodynamic parameters could not be readily identified, with a complicating factor being the observation of varying numbers of water molecules at the binding interface in the different complexes. Consequently, we have applied COMparative BINding Energy (COMBINE) analysis to derive quantitative structure-activity relationships (QSARs) for these 28 OppA-tripeptide complexes. This is the first application of COMBINE analysis to predict binding enthalpies and entropies, and predictive QSAR models were obtained for these quantities as well as for binding free energies. These QSAR models highlight several protein residues and bound water molecules in the binding site, as well as the electrostatic desolvation energies of the protein and the peptides, as responsible for most of the differences in binding thermodynamics between the peptides studied. The QSAR models aid rationalization of the determinants of binding affinity of the OppA:peptide complexes and provide guides for further ligand design. This study also points to the general applicability of COMBINE analysis to estimating thermodynamic parameters for protein-peptide complexes.

Bacterial Proteins↗
PubMed2002

Both tissue inhibitors of metalloproteinases-1 (TIMP-1) and TIMP-2 activate Ras but through different pathways.

Tissue inhibitors of metalloproteinases-1 (TIMP-1) and TIMP-2 have growth-stimulating activity for a wide range of cell types. Ras, which comprises a family of three members, i.e, Ha-Ras, Ki-Ras, and H-Ras, is known to participate in growth control in all its facets, including cell proliferation, transformation, differentiation, and apoptosis. In this study, we tested the hypothesis that Ras might be involved in the cell growth-promoting activity of TIMPs. Using MG-63 human osteosarcoma cells, we demonstrated that both TIMP-1 and TIMP-2 caused an increase in the Ras-GTP level in a dose-dependent manner. Our previous results indicated that TIMP-1 activity is mediated through the tyrosine kinase (TYK)/mitogen-activated protein kinase (MAPK) pathway. Here, we demonstrated that Ras activation by TIMP-1 was inhibited by a specific TYK inhibitor, herbimycin A, suggesting that the TYK/MAPK signaling pathway was involved in Ras activation by TIMP-1. However, the activation of Ras by TIMP-2 was inhibited by an inhibitor specific for cyclic AMP-dependent protein kinase (PKA), H89, suggesting the involvement of the PKA-mediated pathway. Furthermore, TIMP-2 promoted the formation of a complex between Ras-GTP and phosphoinositide 3-kinase.

Benzoquinones↗
PubMed2002

The ClC-3 chloride channel promotes acidification of lysosomes in CHO-K1 and Huh-7 cells.

ClC-3 is a voltage-gated Cl- channel that is highly conserved and widely expressed, although its function, localization, and properties remain a matter of considerable debate. In this study, we have shown that heterologous expression of ClC-3 in either Chinese hamster ovary (CHO-K1) or human hepatoma (Huh-7) cells results in the formation of large, acidic vesicular structures within cells. Vesicle formation is prevented by bafilomycin, an inhibitor of the vacuolar ATPase, and is not induced by an E224A mutant of ClC-3 with altered channel activity. This demonstrates that vesicle formation requires both proton pumping and Cl- channel activity. Manipulation of the intracellular Cl- concentration demonstrated that the ClC-3-associated vesicles shrink and swell consistent with a highly Cl--permeable membrane. The ClC-3 vesicles were identified as lysosomes based on their colocalization with the lysosome-associated proteins lamp-1, lamp-2, and cathepsin D and on their failure to colocalize with fluorescently labeled endosomes. We conclude that ClC-3 is an intracellular channel that conducts Cl- when it is present in intracellular vesicles. Its overexpression results in its appearance in enlarged lysosome-like structures where it contributes to acidification by charge neutralization.

Acids↗
PubMed2002

[Effect of tetrandrine and droloxifene on the reversion of drug resistance of K562/A02 cell line and induction of apoptosis].

OBJECTIVE: To study the reversal effect of tetrandrine (Tet) and droloxifene (Drol) on multidrug resistant cell line K562/A02 and apoptosis induction. METHODS: The cytotoxicity of daunorubicin (DNR) was assayed by MTT method. The effects of Tet and DRL, alone or combined were detected through the apoptosis of K562/A02 by agarose gel electrophoresis. RESULTS: The cytotoxicity of DNR to K562/A02 was enhanced by 0.62 microg/ml Tet or 1.94 microg/ml Drol with IC(50) 7.28 +/- 2.06 microg/ml, 7.58 +/- 3.44 microg/ml, giving a reversal effect of 2.94 and 2.82. But IC(50) of combined Tet and Drol was 1.66 +/- 0.41 microg/ml with the reversal effect markedly increased to 12.9. Neither 0.62 microg/ml Tet nor 1.94 microg/ml Drol could induce apoptosis of K562/A02 cells. CONCLUSION: Multidrug resistance (MDR) can be partially reversed by Tet or Drol, of which the combination shows a great synergistic reversal effect. The mechanism of Tet and Drol reversing multidrug resistance is not correlated with the apoptosis of K562/A02 cells.

Alkaloids↗
PubMed2002

Procedures for congenital choledochal cysts and curative effect analysis in adults.

OBJECTIVE: To evaluate the procedures and timing of operation as well as long-term postoperative effect of congenital choledochal cysts (CCC) in adults. METHODS: The procedures and timing of operation, effective rate, re-operation rate and incidence of carcinoma after operation for 70 adult patients with CCC from January 1980 to June 1999 were analyzed retrospectively. RESULTS: The re-operation rate of external drainage was 86% (6/7). The effective rate of internal drainage was significantly lower than that of cyst resection (3/10 vs 45/49, chi2=20.94, P<0.001). The re-operation rate and incidence of carcinoma of internal drainage were higher than those of cyst resection (5/10 vs 3/49, chi2=13.64, P<0.001 and 3/10 vs 3/49, chi2=5.18, P<0.025). The reoperation rate of emergency surgery was higher than that of selective operation (8/10 vs 6/56, chi2=24.37, P<0.001). CONCLUSIONS: External drainage should be the first-aid measure and the therapy of choice on emergency basis. Internal drainage should never be attempted. Cyst resection with Roux-en-Y hepaticojejunostomy is recommended as the treatment of choice in selective operation.

Adenocarcinoma↗
PubMedDate not supplied

Boosting: an ensemble learning tool for compound classification and QSAR modeling.

A classification and regression tool, J. H. Friedman's Stochastic Gradient Boosting (SGB), is applied to predicting a compound's quantitative or categorical biological activity based on a quantitative description of the compound's molecular structure. Stochastic Gradient Boosting is a procedure for building a sequence of models, for instance regression trees (as in this paper), whose outputs are combined to form a predicted quantity, either an estimate of the biological activity, or a class label to which a molecule belongs. In particular, the SGB procedure builds a model in a stage-wise manner by fitting each tree to the gradient of a loss function: e.g., squared error for regression and binomial log-likelihood for classification. The values of the gradient are computed for each sample in the training set, but only a random sample of these gradients is used at each stage. (Friedman showed that the well-known boosting algorithm, AdaBoost of Freund and Schapire, could be considered as a particular case of SGB.) The SGB method is used to analyze 10 cheminformatics data sets, most of which are publicly available. The results show that SGB's performance is comparable to that of Random Forest, another ensemble learning method, and are generally competitive with or superior to those of other QSAR methods. The use of SGB's variable importance with partial dependence plots for model interpretation is also illustrated.

ATP Binding Cassette Transporter, Subfamily B, Mem↗