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Yan Wang

Publications and source records attributed to Yan Wang.

At least 73 records · Page 4Linked to original sources
PubMed2006

In situ bisulfite modification of membrane-immobilized DNA for multiple methylation analysis.

Increasing interest in DNA methylation has resulted in the recent development of array-based methods. However, these method require complex sample treatment processes, such as bisulfite modification in the liquid state of every sample. Here, we describe a microarray-based technology for interrogating DNA methylation status of multiple DNA samples at the same time, in which the DNA samples are first dotted on membranes and then treated with bisulfite directly. In this assay, plasmid pUC19 DNA is immobilized on nylon membranes and soaked in bisulfite reaction mixtures for 16h to convert unmethylated Cs to Us, and methylated Cs remain unchanged. The probes for detecting the methylation patterns of CpG sites are hybridized with the converted DNA dotted on the membranes, and the signals are revealed by chemiluminescence of DIG-labeled probes. The experiments show that this method can simplify the experimental processes and increase the efficiency of the bisulfite treatment. This new method could be used as a convenient tool for detecting the methylation status of multiple genes for a large number of samples in the future.

Clinical Laboratory Techniques↗
PubMed2006

Genome-wide functional analysis of human cell-cycle regulators.

Human cells have evolved complex signaling networks to coordinate the cell cycle. A detailed understanding of the global regulation of this fundamental process requires comprehensive identification of the genes and pathways involved in the various stages of cell-cycle progression. To this end, we report a genome-wide analysis of the human cell cycle, cell size, and proliferation by targeting >95% of the protein-coding genes in the human genome using small interfering RNAs (siRNAs). Analysis of >2 million images, acquired by quantitative fluorescence microscopy, showed that depletion of 1,152 genes strongly affected cell-cycle progression. These genes clustered into eight distinct phenotypic categories based on phase of arrest, nuclear area, and nuclear morphology. Phase-specific networks were built by interrogating knowledge-based and physical interaction databases with identified genes. Genome-wide analysis of cell-cycle regulators revealed a number of kinase, phosphatase, and proteolytic proteins and also suggests that processes thought to regulate G(1)-S phase progression like receptor-mediated signaling, nutrient status, and translation also play important roles in the regulation of G(2)/M phase transition. Moreover, 15 genes that are integral to TNF/NF-kappaB signaling were found to regulate G(2)/M, a previously unanticipated role for this pathway. These analyses provide systems-level insight into both known and novel genes as well as pathways that regulate cell-cycle progression, a number of which may provide new therapeutic approaches for the treatment of cancer.

Cell Cycle Proteins↗
PubMed2006

Common non-synonymous polymorphisms in the BRCA1 Associated RING Domain (BARD1) gene are associated with breast cancer susceptibility: a case-control analysis.

The BRCA1 Associated RING Domain (BARD1) gene has been identified as a high penetrance gene for breast cancer, whose germline and somatic mutations were reported in both non-BRCA1/2 hereditary site-specific and sporadic breast cancer cases. BARD1 plays a crucial role in tumor repression, along with its heterodimeric partner BRCA1. In the current study, we tested the hypothesis that common non-synonymous polymorphisms in BARD1 are associated with breast cancer susceptibility in a case-control study of 507 patients with incident breast cancer and 539 frequency-matched cancer-free controls in Chinese women. We genotyped all three common (minor allele frequency (MAF)>0.10) non-synonymous polymorphisms (Pro24Ser, Arg378Ser, and Val507Met) in BARD1. We found that the BARD1 Pro24Ser variant genotypes (24Pro/Ser and 24Ser/Ser) and Arg378Ser variant homozygote 378Ser/Ser were associated with a significantly decreased breast cancer risk, compared with their wild-type homozygotes, respectively. Furthermore, a significant locus-locus interaction was evident between Pro24Ser and Arg378Ser (P(int )= 0.032). Among the 378Ser variant allele carriers, the 24Pro/Pro wild-type homozygote was associated with a significantly increased breast cancer risk (adjusted OR=1.81, 95% CI=1.11-2.95), but the subjects having 24Pro/Ser or Ser/Ser variant genotypes had a significantly decreased risk (adjusted OR=0.74, 95% CI=0.56-0.99). In stratified analysis, this locus-locus interaction was more evident among subjects without family cancer history, those with positive estrogen receptor (ER) and individuals with negative progesterone receptor (PR). These findings indicate that the potentially functional polymorphisms Pro24Ser and Arg378Ser in BARD1 may jointly contribute to the susceptibility of breast cancer.

Adult↗
PubMed2006

The catalytic subunit of the proteasome is engaged in the entire process of estrogen receptor-regulated transcription.

The ubiquitin-proteasome system plays an important role in a variety of cellular functions by means of its proteolytic activity. Interestingly, recent studies have indicated that the proteasome components are also integral parts of transcription complexes. In genome-wide screening for steroid receptor coactivator (SRC)-interacting proteins using yeast two-hybrid system, we found that the 20S proteasome beta subunit LMP2 (Low Molecular mass Polypeptide 2) interacts directly with the SRC coactivators. We showed that LMP2 is required for estrogen receptor (ER)-mediated gene transcription and for estrogen-stimulated cell cycle progression. We found that LMP2-associated proteasome is recruited to the entire sequence of ER target genes, implicating a role for the proteasome in both transcription initiation and elongation. We demonstrated that the recruitment of LMP2 by SRC coactivators is necessary for cyclic association of ER-regulated transcription complexes on ER targets. These results revealed a mechanism by which the proteasome machinery is recruited in ER-mediated gene transcription. Our experiments also provided evidence implicating SRC coactivators in gene transcription elongation.

Base Sequence↗
PubMed2006

Heterospectral two-dimensional correlation spectroscopy of mid-infrared and Fourier self-deconvolved near-infrared spectra of sugar solutions.

The mid- and near-infrared (mid-IR and NIR) spectra of aqueous solutions of glucose and fructose, fructose and galactose, and glucose and galactose were recorded and analyzed by heterospectral two-dimensional correlation spectroscopy (H2D-CS) to determine characteristic NIR wavelengths for each sugar. Fourier self-deconvolution (FSD) was applied to the NIR spectra prior to H2D-CS analysis to help resolve the strongly overlapping sugar absorptions. Examination of the H2D-CS data gave characteristic absorption wavelengths for glucose, fructose, and galactose. The wavelengths identified by H2D-CS were then used to develop multiple linear regression (MLR) calibrations for the quantitative analysis of mixtures of the three sugars in solution. This approach gave comparable results to MLR calibrations based on wavelengths selected by examination of the first- and second-derivative spectra of solutions of the individual sugars.

Fructose↗
PubMed2006

Inhibition of human tumor xenograft growth in nude mice by a conjugate of monoclonal antibody LA22 to epidermal growth factor receptor with anti-tumor antibiotics mitomycin C.

Anti-EGFR monoclonal antibodies LA22 and Erbitux bind to different epitopes of EGFR. The chemimmunoconjugates of MMC with LA22 or Erbitux were prepared, and in vitro cytotoxicity assays with A549 cells showed that LA22-MMC was much more potent than Erbitux or Erbitux-MMC. Viabilities of A549 cells treated with LA22-MMC, Erbitux or Erbitux-MMC were 35%, 94%, and 81%, respectively. Immunoscintigraphy of xenografts of human A431 and A549 cells in nude mice both showed that (125)I-labeled-LA22-MMC enriched in tumor sites prominently. Most importantly, in vivo assays showed LA22-MMC was significantly more effective than free drug MMC in the treatment of subcutaneous xenografts of human A431 cells in nude mice (83% inhibition for LA22-MMC and 30% for MMC). We concluded that LA22-MMC could be a very potent drug for treatment of solid tumors.

Animals↗
PubMed2006

First-principles theory of quantum well resonance in double barrier magnetic tunnel junctions.

Quantum well (QW) resonances in Fe(001)/MgO/Fe/MgO/Fe double barrier magnetic tunnel junctions are calculated from first principles. By including the Coulomb blockade energy due to the finite size islands of the middle Fe film, we confirm that the oscillatory differential resistance observed in a recent experiment [T. Nozaki, Phys. Rev. Lett. 96, 027208 (2006)10.1103/PhysRevLett.96.027208] originates from the QW resonances from the Delta1 band of the Fe majority-spin channel. The primary source of smearing at low temperatures is shown to be the variation of the Coulomb blockade energy.

Journal Article↗
PubMed2006

[A method to avoid the fixator failure by using pedicle screw combined vertebroplasty for spine fractures].

OBJECTIVE: To study a new implant material (carbonated hydroxyapatite, CHA) united pedicle screw to cure spine fracture. METHODS: Thirty-two cases of spine compressed fracture were used with pedicle screw fixator and vertebroplasty. Before operation, patients' vertebral body were compressed (46 + 21)% (20% approximately 70%) on average. In operation, broken vertebral body was reposition through pedicle screw technique, then used self-made syringe to inject CHA into anterior and central column of broken vertebral body through pedicle. And all of patients were not given any bone-graft. RESULTS: In 6 - 26 months followed-up, no immunologic rejection was found about hydroxyapatite, and no any broken of the screws and shafts was found, no loosing and other complications either. All the patients could move in 3 - 5 days after operation. The height of the broken vertebral body were reduced 97% compared with pre-operation. And CHA in vertebral body was degraded gradually, and at the same time it was replace by new bone in vertebral body. After operation, VAS score was 61 +/- 32, and there was significant difference compared with pre-operation. CONCLUSIONS: The pedicle screw fixation united vertebroplasty is an efficient way to prevent the failure of the treatment of spine fracture.

Adult↗
PubMed2006

Glucocorticoid up-regulates transforming growth factor-beta (TGF-beta) type II receptor and enhances TGF-beta signaling in human prostate cancer PC-3 cells.

Previous studies have shown that dexamethasone (Dex) induces the expression of TGF-beta1 in androgen-independent prostate cancer both in vitro and in vivo. However, it is not clear whether Dex has a direct effect on the expression of TGF-beta receptors. In this study, using the androgen-independent human prostate cancer cell line, PC-3 cells, we demonstrated that Dex increased the expression of TGF-beta receptor type II (TbetaRII), but not TGF-beta receptor type I (TbetaRI) in a time- and dose-dependent manner. The up-regulation of TbetaRII expression by Dex was mediated by glucocorticoid receptor and occurred at the transcriptional level. Dex also enhanced TGF-beta1 signaling and increased the expression of cyclin-dependent kinase inhibitors p15(INK4B) (p15) and p27(KIP1) (p27), which are the target genes of TGF-beta1 and have been identified as inducers of cell cycle arrest at the G1 checkpoint. The antiproliferative effect of Dex was partially blocked by anti-TbetaRII antibody, indicating that elevated TbetaRII and TGF-beta1 signaling were involved in the antiproliferative effect of Dex. Because the TGF-beta1 pathway could not fully explain the antiproliferative effect of Dex, we further examined the effects of Dex on the transcriptional activity of nuclear factor-kappaB (NF-kappaB) and the expression of IL-6 and found that Dex suppressed the transcriptional activity of NF-kappaB and IL-6 mRNA expression in PC-3 cells. These results demonstrated that glucocorticoid inhibited the proliferation of PC-3 cells not only through enhancing growth-inhibitory TGF-beta1 signaling, but also through suppressing transcriptional activities of NF-kappaB.

Cell Line, Tumor↗
PubMed2006

Co-transition absorption property of K2ZnCl4:Co2+ crystal.

Single-crystal K(2)ZnCl(4) doped with Co2+ has been grown successfully by use of the Czochralski technique. The absorption spectrum of the crystal was measured. The most intense line, centered at 650 nm, was associated with the transition (4)A(2)-->(4)T(1P), and a novel and important result that corporate transition (co-transition) between (4)A(2)-->(4)T(1F) and (4)A(2)-->(4)T(2) of Co2+ in the region of 1300-2400 nm was found and discussed. The mechanism that caused the phenomenon was explained by energy-level splitting theory. In the tetrahedral approximation, using the quantum and Tanaba-Sugano theories, Racah parameter B and crystal field parameter 10Dq were calculated. The optical energy gap, deduced to be 4.82 eV, was lower than that of pure K2ZnCl4.

Journal Article↗
PubMed2006

Mechanisms of and effect of coadsorption on water dissociation on an oxygen vacancy of the MgO(100) surface.

The dissociation mechanism of a water molecule at an oxygen vacancy on the MgO(100) surface was studied by using the embedded cluster method at the DFT/B3 LYP level, while the energetic information was refined by using the IMOMO method at the CCSD level. We found that a water molecule initially adsorbs on one of the magnesium ions surrounding the vacancy site with a binding energy of 15.98 kcal mol(-1). It then can dissociate on the MgO(100) surface along two possible dissociation pathways. One pathway produces a hydroxyl group bonded to the original magnesium with a proton filling the vacancy via a transition state with a barrier of 4.67 kcal mol(-1) relative to the adsorbed water configuration. The other pathway yields two hydroxy groups; the hydroxy group originally belonging to the water molecule fills the vacancy, while the hydrogen atom binds with the surface oxygen to form the other hydroxy group. Hydrogen atoms of these hydroxy groups can recombine to form a hydrogen molecule and the surface is healed. Although the barrier (14.09 kcal mol(-1)) of the rate-controlling step of the latter pathway is higher than that of the former one, the energies of all of its stationary points are lower than that of the separated reactants (H(2)O+cluster). The effects of water coadsorption are modeled by placing an additional water molecule near the active center, which suggests that the more coadsorbed water molecules further stabilize the hydroxy species and prevent the hydrogen molecule formation through the latter pathway. The results support the photoemission spectral evidence of water dissociation on the defective MgO(100) surface at low water coverage.

Adsorption↗
PubMed2006

Identification of novel proteins associated with both alpha-synuclein and DJ-1.

The molecular mechanisms leading to neurodegeneration in Parkinson disease (PD) remain elusive, although many lines of evidence have indicated that alpha-synuclein and DJ-1, two critical proteins in PD pathogenesis, interact with each other functionally. The investigation on whether alpha-synuclein directly interacts with DJ-1 has been controversial. In the current study, we analyzed proteins associated with alpha-synuclein and/or DJ-1 with a robust proteomics technique called stable isotope labeling by amino acids in cell culture (SILAC) in dopaminergic MES cells exposed to rotenone versus controls. We identified 324 and 306 proteins in the alpha-synuclein- and DJ-1-associated protein complexes, respectively. Among alpha-synuclein-associated proteins, 141 proteins displayed significant changes in the relative abundance (increase or decrease) after rotenone treatment; among DJ-1-associated proteins, 119 proteins displayed significant changes in the relative abundance after rotenone treatment. Although no direct interaction was observed between alpha-synuclein and DJ-1, whether analyzed by affinity purification followed by mass spectrometry or subsequent direct co-immunoprecipitation, 144 proteins were seen in association with both alpha-synuclein and DJ-1. Of those, 114 proteins displayed significant changes in the relative abundance in the complexes associated with alpha-synuclein, DJ-1, or both after rotenone treatment. A subset of these proteins (mortalin, nucleolin, grp94, calnexin, and clathrin) was further validated for their association with both alpha-synuclein and DJ-1 using confocal microscopy, Western blot, and/or immunoprecipitation. Thus, we not only confirmed that there was no direct interaction between alpha-synuclein and DJ-1 but also, for the first time, report these five novel proteins to be associating with both alpha-synuclein and DJ-1. Further characterization of these docking proteins will likely shed more light on the mechanisms by which DJ-1 modulates the function of alpha-synuclein, and vice versa, in the setting of PD.

Animals↗
PubMed2006

[Safety and efficacy of resection of hemivertebrae by posterior approach in treatment of thoracolumbar kyphoscoliosis in adolescents].

OBJECTIVE: To investigate the safety and efficacy of resection of hemivertebrae by posterior approach in treatment of thoracolumbar kyphoscoliosis in adolescents. METHODS: twenty-eight patients of kyphoscoliosis, 19 male and 9 female, aged 12 approximately 16, 12 cases with the hemivertebra located in T(12), 10 cases in L(1), and 6 cases in T(11), and with a mean angle of 75 degrees in kyphosis and 48 degrees in scoliosis by the Cobb measurement, underwent resection of the hemivertebrae via the posterior approach and were followed up for 3.5 years. RESULTS: The mean surgical time was 3.7 hours and the average blood loss was 900 ml. Intercostal neuralgia occurred in one patient and relieved automatically without treatment. Hemothorax and pneumothorax were found in two cases during the operation and were healed after 1 week. Solid fusion was obtained in all the patients. The Cobb measurement was 19 degrees in kyphosis and 14 degrees in scoliosis on average at the final follow-up. No neurological deficit and infection was noted in the late stage. Clinically, no spinal imbalance or trunk shift was observed in all patients. CONCLUSION: Resection of hemivertebrae via posterior approach is safe and effective in the treatment of thoracolumbar kyphoscoliosis in adolescents.

Adolescent↗
PubMed2006

Prediction of pi-turns in proteins using PSI-BLAST profiles and secondary structure information.

Due to the structural and functional importance of tight turns, some methods have been proposed to predict gamma-turns, beta-turns, and alpha-turns in proteins. In the past, studies of pi-turns were made, but not a single prediction approach has been developed so far. It will be useful to develop a method for identifying pi-turns in a protein sequence. In this paper, the support vector machine (SVM) method has been introduced to predict pi-turns from the amino acid sequence. The training and testing of this approach is performed with a newly collected data set of 640 non-homologous protein chains containing 1931 pi-turns. Different sequence encoding schemes have been explored in order to investigate their effects on the prediction performance. With multiple sequence alignment and predicted secondary structure, the final SVM model yields a Matthews correlation coefficient (MCC) of 0.556 by a 7-fold cross-validation. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/piturn/.

Amino Acid Sequence↗
PubMed2006

Drug susceptibilities of yeast cells are affected when expressing mutant Candida albicans drug resistance protein.

In the present study, wild-type and mutant Candida drug resistance protein 1 (Cdr1p) was expressed in Saccharomyces cerevisiae and phenotype alterations were observed in order to understand the importance of Cdr1p in azole resistance. Cdr1p was subjected to site-directed mutagenesis resulting in an alteration (W629L) to transmembrane segment 4 (TMS4). The susceptibilities to azole antifungal drugs of yeast cells as well as passive efflux of Rhodamine 6G were measured. The mutant strain showed greater sensitivity to azole antifungal drugs than the strain with the wild-type plasmid (AD-CDR1) as well as reduced efflux of Rhodamine 6G. Taken together, these phenotypic alterations of yeast cells were caused by the mutation in TMS4 of Cdr1p, which suggests that TMS4 plays a major role in azole antifungal drug efflux and is an azole antifungal drug-binding site.

Amino Acid Sequence↗
PubMed2006

An evaluation on the efficacy and safety of amlexanox oral adhesive tablets in the treatment of recurrent minor aphthous ulceration in a Chinese cohort: a randomized, double-blind, vehicle-controlled, unparallel multicenter clinical trial.

OBJECTIVE: The objectives of this study were to clinically determine the topical efficacy and safety of amlexanox oral adhesive tablets in the treatment of recurrent minor aphthous ulcerations (MiRAU) in a Chinese cohort. STUDY DESIGN: A randomized, double-blind, vehicle-controlled, unparallel multicenter clinical trial was carried out. The tablets were applied by subjects themselves 4 times a day for 5 days. Four parameters (pain scale, size change, degree of erythema and exudation, and efficacy index) were recorded both before (baseline) and during the trial (on the morning of days 4 and 6). RESULTS: There were 104 and 108 subjects who fulfilled the trial in the amlexanox group and the vehicle-control group, respectively. Group differences for all parameters but degree of erythema and exudation of day 4 were statistically significant both for the day 4 visit and the day 6 visit (P < .05). No systemic side effects were reported. CONCLUSIONS: Amlexanox oral adhesive tablets are effective and safe in reducing aphthous ulcer pain and lesion size, as well as erythema and exudation in this Chinese cohort.

Adhesives↗
PubMed2006

Interleukin-10 inhibits HIV-1 LTR-directed gene expression in human macrophages through the induction of cyclin T1 proteolysis.

Regulation of HIV-1 replication in human monocytes/macrophages occurs at multiple levels including transcription of the proviral genome, which depends on virally encoded Tat protein. Interleukin-10 (IL-10), an anti-inflammatory cytokine which is up-regulated during disease progression of AIDS, has been reported to suppress HIV-1 replication in macrophages at a post-entry stage of the virus life cycle. Our previous studies have demonstrated that Tat function is regulated during the differentiation of monocyte-derived macrophages (MDMs) in a manner that correlates with the early induction and subsequent shut-off of its cellular cofactor cyclin T1. Here, we report that IL-10 down-regulates cyclin T1 expression through the induction of proteasome-mediated proteolysis in human macrophages. Using a reporter virus that is deficient in Tat function, we also demonstrate that IL-10 inhibits HIV-1 gene expression in a Tat-dependent manner. Together, these results suggest that the down-regulation of cyclin T1, and consequently Tat function, contributes to the suppressive effect of IL-10 on HIV-1 replication in human macrophages.

Base Sequence↗