Search PubMed⌕ Search

Biomedical subjects

Tao Li

Publications and source records attributed to Tao Li.

At least 127 records · Page 7Linked to original sources
PubMed2004

First-principles study of C adsorption, O adsorption, and CO dissociation on flat and stepped Ni surfaces.

The adsorption of atomic oxygen and carbon was studied with plane wave density functional theory on four Ni surfaces, Ni(110), Ni(111), Ni(210), and Ni(531). Various adsorption sites on these surfaces are examined in order to identify the most favorable adsorption site for each atomic species. The dependence of surface bonding on adsorbate coverage is also investigated. Adsorption energies and structural information are obtained and compared with existing experimental results for Ni(110) and Ni(111). In addition, activation barriers to CO dissociation have been determined on Ni(111) and Ni(531) by locating the transition states for these processes. Our results indicate that the binding energies of C are comparatively stronger on stepped surfaces than on flat surfaces, and the energy barriers associated with CO dissociation strongly favor reactions occurring near surface steps.

Journal Article↗
PubMed2004

IRAK1 serves as a novel regulator essential for lipopolysaccharide-induced interleukin-10 gene expression.

Being one of the key kinases downstream of Toll-like receptors, IRAK1 has initially thought to be responsible for NFkappaB activation. Yet IRAK1 knock-out mice still exhibit NFkappaB activation upon lipopolysaccharide (LPS) challenge, suggesting that IRAK1 may play other un-characterized function. In this report, we show that IRAK1 is mainly involved in Stat3 activation and subsequent interleukin-10 (IL-10) gene expression. Splenocytes from IRAK1-deficient mice fail to exhibit LPS-induced Stat3 serine phosphorylation and IL-10 gene expression yet still maintain normal IL-1beta gene expression upon LPS challenge. Mechanistically, we observe that IRAK1 modification upon LPS challenge leads to its modification, nuclear distribution, and interaction with Stat3. IRAK1 can directly use Stat3 as a substrate and cause Stat3 serine 727 phosphorylation. In addition, nuclear IRAK1 binds directly with IL-10 promoter in vivo upon LPS treatment. Atherosclerosis patients usually have elevated serum IL-10 levels. We document here that IRAK1 is constitutively modified and localized in the nucleus in the peripheral blood mononuclear cells from atherosclerosis patients. These observations reveal the mechanism for the novel role of IRAK1 in the complex Toll-like receptor signaling network and indicate that IRAK1 regulation may be intimately linked with the pathogenesis and/or resolution of atherosclerosis.

Animals↗
PubMed2004

Slow light in semiconductor quantum wells.

We demonstrate slow light via population oscillation in semiconductor quantum-well structures for the first time. A group velocity as low as 9600 m/s is inferred from the experimentally measured dispersive characteristics. The transparency window exhibits a bandwidth as large as 2 GHz.

Journal Article↗
PubMed2004

Association analysis of the DRD4 and COMT genes in methamphetamine abuse.

We analyzed two polymorphisms in genes encoding proteins of the dopamine system, the Val158Met polymorphism in the catechol-O-methyltransferase gene and the 120-bp VNTR polymorphism in the promoter of the dopamine D4 receptor gene for association with methamphetamine abuse. We used a case/control design with 416 methamphetamine abusing subjects and 435 normal controls. All subjects were Han Chinese from Taiwan. We found an excess of the high activity Val158 allele in the methamphetamine abuser group, consistent with several previous reports of association of this allele with drug abuse. The 120-bp VNTR polymorphism in the promoter of the dopamine D4 receptor gene itself did not show significant association with methamphetamine abuse. However, analysis of the 120-bp VNTR polymorphism and the exon 3 VNTR in the dopamine D4 receptor as a haplotype showed significant association with methamphetamine abuse, which gave an empirical P value 0.0034 for a heterogeneity model. Moreover, there were significant interactive effects between polymorphisms in the catechol-O-methyltransferase and dopamine D4 genes. The evidence of interaction between COMT 158 Val/Met and DRD4 48-bp VNTR polymorphisms (P = 0.0003, OR = 1.45, 95% CI: 1.148-1.77), and between COMT 158 Val/Met and DRD4 120 bp promoter polymorphisms (P = 0.01, OR = 1.10, 95% CI: 1.10-1.18) were significant but the latter was weak. We conclude that genetic variation in the dopamine system may encode an additive effect on risk of becoming a methamphetamine abuser.

Adolescent↗
PubMed2004

Evidence for association between novel polymorphisms in the PRODH gene and schizophrenia in a Chinese population.

Haploinsufficiency for or mutation in at least one gene from the velocardiofacial syndrome (VCFS) region at chromosome 22q11 is implicated in psychosis. Linkage disequilibrium mapping of the region in patients identified a segment containing two genes, proline dehydrogenase (PRODH) and DGCR6, as candidates [Liu et al., 2002a] and by analysis of additional polymorphisms the PRODH gene was associated with schizophrenia in adult and early onset patients. In the present study we provide additional evidence in support of genetic association between PRODH and schizophrenia in a Chinese population. We analyzed the PRODH gene in a samples of schizophrenic patients and their families from Sichuan, SW China consisting of 528 family trios and sibling pairs. We genotyped six SNPs, PRODH*1195C-->T, PRODH*1482C-->T, PRODH*1483A-->G, PRODH*1766A-->G, PRODH*1852G-->A PRODH*1945T-->C, two of which (PRODH*1483A-->G and PRODH*1852G-->A) have not been previously reported. We found association with schizophrenia for two haplotypes consisting of PRODH*1945T-->C and PRODH*1852G-->A (Global P = 0.006), and PRODH*1852G-->A and PRODH*1766A-->G (Global P = 0.01) which include one of the newly identified markers. After six-fold Bonferroni correction for multiple testing the PRODH*1945T-C/PRODH*1852G-A haplotypes remained significant. This is a sub-haplotype of the PRODH haplotype previously associated with schizophrenia and it also maps to the 3' region of the gene, indicating that this is the region most likely to contain the underlying risk alleles. Overall this finding supports a role for the PRODH locus in schizophrenia.

Alleles↗
PubMed2004

Promoter-restricted histone code, not the differentially methylated DNA regions or antisense transcripts, marks the imprinting status of IGF2R in human and mouse.

Imprinting of the mouse Igf2r depends upon an intronic differentially methylated DNA region (DMR) and the presence of the Air antisense transcript. However, biallelic expression of mouse Igf2r in brain occurs despite the presence of Air, and biallelic expression of human IGF2R in peripheral tissues occurs despite the presence of an intronic DMR. We examined histone modifications throughout the mouse and human Igf2r/IGF2R using chromatin immuno-precipitation (ChIP) assays in combination with quantitative real time PCR. Methylation of Lys4 and Lys9 of histone H3 in the promoter regions marks the active and silenced alleles, respectively. We measured di- and tri-methyl Lys4 and Lys9 across the Igf2r and Air promoters. While both di- and tri-methyl Lys4 marked the active Igf2r and the active Air allele, tri-methyl Lys9, but not di-methyl Lys9, marked the suppressed Air allele. We show here that enrichment of parental allele-specific histone modifications in the promoter region, rather than the presence of DNA methylation or antisense transcription, correctly identifies the tissue- and species- specific imprinting status of Igf2r/IGF2R. We discuss these findings in light of recent progress in identifying specific components of the epigenetic marks in imprinted genes.

Acetylation↗
PubMed2004

Expression of subtypes of somatostatin receptors in hepatic stellate cells.

AIM: To elucidate the mechanism by which somatostatin and its analogue exert the influence on liver fibrosis, and to investigate the mRNA expression of somatostatin receptors subtypes (SSTRs) and the distribution of somatostatin analogue octreotide in rat hepatic stellate cells (HSCs). METHODS: HSCs were isolated from Sprague Dawley (SD) rats by in situ perfusion and density gradient centrifugation. After several passages, the mRNA expression of 5 subtypes of SSTRs were assessed by reverse transcription-polymerase chain reaction (RT-PCR). HSCs were planted on coverslip and co-cultured with octreotide tagged by FITC. Then the distribution of FITC fluorescence was observed under laser scanning confocal microscope (LSCM) in 12-24 h. RESULTS: There were mRNA expression of SSTR2, SSTR3 and SSTR5 but not SSTR1 and SSTR4 in SD rat HSCs. The mRNA expression level of SSTR2 was significantly higher than that of other subtypes (P<0.01). FITC fluorescence of octreotide was clearly observed on the surface and in the cytoplasm, but not in the nuclei of HSCs under LSCM. CONCLUSION: The effect exerted by somatostatin and its analogues on HSCs may mainly depend on the expression of SSTR2, SSTR3 and SSTR5. Octreotide can perfectly combine with HSCs, and thereby exerts its biological activity on regulating the characters of active HSCs. This provides a potential prevention and management against liver fibrosis.

Animals↗
PubMed2004

mRNA expression profiling reveals a role of Helicobacter pylori vacuolating toxin in escaping host defense.

AIM: To study the immune response of host to Helicobacter pylori VacA. METHODS: The monocyte/macrophage-like U937 cells were infected with Helicobacter pylori vacA-positive strain NCTC 11638 or isogenic vacA-negative mutant. Differentially expressed genes were identified at 2, 6, 10, and 24 h post-infection by cDNA microarray. Differential expressions of some genes were confirmed by Northern blot. RESULTS: More than 100 genes altered their mRNA expression at different time points respectively, many of which were identified to be related to immune evasion. CONCLUSION: VacA is a crucial element for H pylori to escape from host immune defense by means of differentially regulating the expression of some related genes. These genes, previously known or unknown to be involved in the mechanism of immune evasion, deserve further investigation to unearth much more information complicated in the immune response.

Bacterial Proteins↗
PubMed2004

Augmentation of chemotherapy-induced cytokine production by expression of the platelet-activating factor receptor in a human epithelial carcinoma cell line.

In addition to their known cytotoxic effects, chemotherapeutic agents can trigger cytokine production in tumor cells. Moreover, many chemotherapeutic agents are potent pro-oxidative stressors. Although the lipid mediator platelet-activating factor (PAF) is synthesized in response to oxidative stress, and many epidermal carcinomas express PAF receptors (PAF-R) linked to cytokine production, it is not known whether PAF is involved in chemotherapeutic agent-induced cytokine production. These studies examined the role of the PAF system in chemotherapy-mediated cytokine production using a model system created by retroviral-mediated transduction of the PAF-R-negative human epidermal carcinoma cell line KB with the human PAF-R. The presence of the PAF-R in KB cells resulted in augmentation of the production of cytokines IL-8 and TNF-alpha induced by the chemotherapeutic agents etoposide and mitomycin C. These effects were specific for the PAF-R, as expression of the G protein-coupled receptor for fMLP did not affect chemotherapeutic agent-induced cytokine production. Moreover, ablation of the native PAF-R in the epithelial cell line HaCaT using an inducible antisense PAF-R strategy inhibited etoposide-induced cytokine production. Oxidative stress and the transcription factor NF-kappaB were found to be involved in this augmentative effect, because it was mimicked by the oxidant tert-butyl-hydroperoxide, which was blocked both by antioxidants and by inhibition of the NFkappaB pathway using a super-repressor IkappaBM mutant. These studies provide evidence for a novel pathway by which the epidermal PAF-R can augment chemotherapy-induced cytokine production through an NF-kappaB-dependent process.

Adjuvants, Immunologic↗
PubMed2004

[The effect of somatostatin analogue on expression of connective tissue growth factor gene of rat hepatic stellate cells].

OBJECTIVE: To investigate the effect of somatostatin analogue-octreotide (OCT) on expression of connective tissue growth factor (CTGF) gene of murine hepatic stellate cells (HSCs) in vitro. METHODS: HSCs separated from Sprague Dawley rats by in situ perfusion and Nycodenz gradient were divided into 5 groups. HSCs in 4 out of 5 groups were co-cultured with octreotide at different dosages, and the remaining group served as control. The expression of CTGF and TGF-beta mRNA were assessed by reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: OCT down-regulates the expression of CTGF and TGF-beta mRNA in HSCs. The effect is increased with a dose dependent manner. CONCLUSIONS: OCT could exert the inhibitory effect on HSCs by down-regulating the expression of CTGF and TGF-beta. This provides a potential for the prevention and management of hepatic fibrosis.

Animals↗
PubMed2004

Nickel(II) and cobalt(II) complexes of hydroxyl-substituted triazamacrocyclic ligand as potential antitumor agents.

The stability constants for the formation of nickel(II) and cobalt(II) complexes of the ligand [1,4,7]triazecan-9-ol (L) were presented. Antitumor activity of two complexes was reported. Nuclei of [NiL]-stimulated BEL-7402 cells clearly exhibited condensation and break down into chromatin clumps typical of apoptosis. Also it exhibited perturbation effects to cell cycle, and optimal induction of apoptosis was found by Flow-Cytometric analysis. But CoL complex did not exhibit introduction effects to BEL-7402 cells apoptosis; and could not perturb cell cycle. NiL and CuL complexes could cleave supercoiled DNA (pBR 322 DNA) to nicked and linear DNA, and DNA of cells treated with NiL or CuL complex was obviously damaged; while CoL complex only could cleave supercoiled DNA (pBR 322 DNA) to nicked DNA, and DNA of cells treated with CoL complex had no significant difference with control.

Antineoplastic Agents↗
PubMed2004

A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression.

This paper studies the problem of building multiclass classifiers for tissue classification based on gene expression. The recent development of microarray technologies has enabled biologists to quantify gene expression of tens of thousands of genes in a single experiment. Biologists have begun collecting gene expression for a large number of samples. One of the urgent issues in the use of microarray data is to develop methods for characterizing samples based on their gene expression. The most basic step in the research direction is binary sample classification, which has been studied extensively over the past few years. This paper investigates the next step-multiclass classification of samples based on gene expression. The characteristics of expression data (e.g. large number of genes with small sample size) makes the classification problem more challenging. The process of building multiclass classifiers is divided into two components: (i) selection of the features (i.e. genes) to be used for training and testing and (ii) selection of the classification method. This paper compares various feature selection methods as well as various state-of-the-art classification methods on various multiclass gene expression datasets. Our study indicates that multiclass classification problem is much more difficult than the binary one for the gene expression datasets. The difficulty lies in the fact that the data are of high dimensionality and that the sample size is small. The classification accuracy appears to degrade very rapidly as the number of classes increases. In particular, the accuracy was very low regardless of the choices of the methods for large-class datasets (e.g. NCI60 and GCM). While increasing the number of samples is a plausible solution to the problem of accuracy degradation, it is important to develop algorithms that are able to analyze effectively multiple-class expression data for these special datasets.

Algorithms↗
PubMed2004

Thermodynamic profiling of conformationally constrained cyclic ligands for the PDZ domain.

Inspired by structure-based design and tailored for combinatorial preparation, a series of novel cyclic peptides has been developed to yield binding ligands for the third PDZ domain (PDZ3) of PSD-95. These side chain-side chain bridged peptides permit the systematic expansion or contraction of ring size, which is intended to maximize the conformational diversity of the ensemble. Isothermal titration calorimetry (ITC) was used to measure the dissociation constants (K(d)) and associated thermodynamic binding parameters.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Activating and silencing histone modifications form independent allelic switch regions in the imprinted Gnas gene.

Activation and suppression of gene transcription is tightly controlled by epigenetic modifications. The imprinted Gnas1 gene region contains closely juxtaposed maternally expressed (Nesp) and paternally expressed (Nespas, Gnasxl, Exon 1A) transcripts, providing a unique opportunity to study how epigenetic modifications change in nucleosomes from active to silenced promoters. Using 30 polymorphic sites across the Gnas1 gene region in (C57BL/6JxMus spretus) F(1) mice and chromatin immunoprecipitation (ChIP) assays we identified two allelic switch regions (ASRs) that mark boundaries of epigenetic information. We show that activating signals (histone acetylation and methylation of H3 Lys4) and silencing signals (histone methylation of H3 Lys9 and DNA methylation) segregate independently across the ASRs and suggest that these ASRs allow the transcriptional elongation to proceed through the silenced domain of nearby imprinted promoters. We discuss these findings in light of recent progress in the conceptualization of nucleosome remodeling during transcriptional elongation and in the development of histone code.

Alleles↗
PubMed2004

Identification of the gene for vitamin K epoxide reductase.

Vitamin K epoxide reductase (VKOR) is the target of warfarin, the most widely prescribed anticoagulant for thromboembolic disorders. Although estimated to prevent twenty strokes per induced bleeding episode, warfarin is under-used because of the difficulty of controlling dosage and the fear of inducing bleeding. Although identified in 1974 (ref. 2), the enzyme has yet to be purified or its gene identified. A positional cloning approach has become possible after the mapping of warfarin resistance to rat chromosome 1 (ref. 3) and of vitamin K-dependent protein deficiencies to the syntenic region of human chromosome 16 (ref. 4). Localization of VKOR to 190 genes within human chromosome 16p12-q21 narrowed the search to 13 genes encoding candidate transmembrane proteins, and we used short interfering RNA (siRNA) pools against individual genes to test their ability to inhibit VKOR activity in human cells. Here, we report the identification of the gene for VKOR based on specific inhibition of VKOR activity by a single siRNA pool. We confirmed that MGC11276 messenger RNA encodes VKOR through its expression in insect cells and sensitivity to warfarin. The expressed enzyme is 163 amino acids long, with at least one transmembrane domain. Identification of the VKOR gene extends our understanding of blood clotting, and should facilitate development of new anticoagulant drugs.

Animals↗
PubMed2004

Systematic comparison of the fidelity of aRNA, mRNA and T-RNA on gene expression profiling using cDNA microarray.

In cDNA microarray technology, there are three main reverse transcription based RNA labeling methods, using total RNA (T-RNA), mRNA, and amplified antisense RNA (aRNA), respectively. However, despite the common use of the three types of RNAs, limited data are available regarding their differences and concordances. In this report, we compared the three methods through two sets of self-comparison experiments using the same RNA sample in all cases. Within each method, duplicate hybridizations are highly reproducible with low biases, which are randomly produced. When combining different RNAs within a single array, correlation coefficients between the two channels are rather low, while the discrepancies are persistent. Furthermore, the fidelity of aRNA and mRNA microarrays in the expression profile study shows no significant difference with standard T-RNA based labeling methods. These results suggest that some RNA abundance are selectively changed during aRNA amplification/mRNA purification processes, but it will not affect the gene expression ratio of the two samples if the same type RNA are used. Therefore all three types of RNAs can be used in expression profiling analysis as long as the test and reference samples are generated by identical method within single study.

Carcinoma, Hepatocellular↗
PubMed2004

Possible association between Cys311Ser polymorphism of paraoxonase 2 gene and late-onset Alzheimer's disease in Chinese.

The common polymorphism at codon 311 (C311S) of paraoxonase 2 gene (PON2) was investigated in 165 patients with sporadic late-onset Alzheimer's disease (LOAD) and 174 controls in Chinese. The PON2*C allele frequency was significantly increased in the patients as compared with controls. However, no significant difference was observed after stratification of apolipoprotein E (ApoE) epsilon4 allele. These results suggested that the PON2 polymorphism might be a risk factor for LOAD independent of ApoE epsilon4 status in Chinese.

Aged↗