Biomedical subjects

Yao Li

Publications and source records attributed to Yao Li.

At least 37 records · Page 2Linked to original sources

PubMed2005

[Impacts of donor and recipient's SNP of cytokine and cytokine receptor on early acute renal allograft rejection].

OBJECTIVE: To investigate the impact of donor and recipient's SNP of cytokine and cytokine receptor on early acute rejection after renal transplantation. METHODS: (1) 129 cases of cadaveric renal allograft recipients were divided into two groups according to the presence or absence of acute graft rejection. The distribution of 21 single nucleotide polymorphisms in cytokines and cytokine receptors gene were compared between two groups as well as latent factors affecting the development of acute rejection. (2) Based on the result of HLA-DR matching between donor and recipient, the recipients with AR were stratified into two conditions, 0-1 locus mismatched (0-1MM) and completely mismatched (2MM). By aids of SPSS 11.5 software, association analysis was assessed using Kruskal Wallis test, 2 x 2 or 2 x n contingency table, the Chi-square test. RESULTS: (1) Of 129 recipients of renal transplantation, 39 developed acute graft rejection (30.2%). (2) Compared with recipients without acute rejection, the number of HLA-DR mismatching was significantly higher in rejection group. (3) In rejection group and non-rejection group, the gene polymorphism distribution was significantly different. (4) 0-1MM group and 2MM group were various in the gene polymorphism distribution. CONCLUSIONS: In the whole, the susceptibility of acute rejection after renal transplantation may be predicted by the donor and recipient's SNP of cytokine and cytokine receptor.

Adult↗

PubMed2005

Failure of cAMP agonists to activate rescued deltaF508 CFTR in CFBE41o- airway epithelial monolayers.

The cystic fibrosis transmembrane conductance regulator (CFTR) is a cyclic AMP-regulated chloride channel. Mutations in the CFTR gene result in cystic fibrosis (CF). The most common mutation, deltaF508, results in endoplasmic reticulum-associated degradation (ERAD) of CFTR. DeltaF508 CFTR has been described as a temperature-sensitive mutation that can be rescued following growth at 27 degrees C. In order to study the processing and function of wild-type and rescued deltaF508 CFTR at the cell surface under non-polarized and polarized conditions, we developed stable cell lines expressing deltaF508 or wild-type CFTR. CFBE41o- is a human airway epithelial cell line capable of forming high resistance, polarized monolayers when cultured on permeable supports, while HeLa cells are normally grown under non-polarizing conditions. Immunoprecipitation, cell surface biotinylation, immunofluorescence, and functional assays confirmed the presence of deltaF508 CFTR at the cell surface in both cell lines after incubating the cells for 48 h at 27 degrees C. However, stimulators of wild-type CFTR such as forskolin, beta2-adrenergic or A2B-adenosine receptor agonists failed to activate rescued deltaF508 CFTR in CFBE41o- monolayers. Rescued deltaF508 CFTR could be stimulated with genistein independent of pretreatment with cAMP signalling agonists. Interestingly, rescued deltaF508 CFTR in HeLa cells could be efficiently stimulated with either forskolin or genistein to promote Cl- transport. These results indicate that deltaF508 CFTR, when rescued in CFBE41o- human airway epithelial cells, is poorly responsive to signalling pathways known to regulate wild-type CFTR. Furthermore, the differences in rescue and activation of deltaF508 CFTR in the two cell lines suggest that cell-type specific differences in deltaF508 CFTR processing are likely to complicate efforts to identify potentiators and/or correctors of the deltaF508 defect.

Adenosine Triphosphate↗

PubMed2005

Finding dominant sets in microarray data.

Clustering allows us to extract groups of genes that are tightly coexpressed from Microarray data. In this paper, a new method DSF_Clust is developed to find dominant sets (clusters). We have preformed DSF_Clust on several gene expression datasets and given the evaluation with some criteria. The results showed that this approach could cluster dominant sets of good quality compared to kmeans method. DSF_Clust deals with three issues that have bedeviled clustering, some dominant sets being statistically determined in a significance level, predefining cluster structure being not required, and the quality of a dominant set being ensured. We have also applied this approach to analyze published data of yeast cell cycle gene expression and found some biologically meaningful gene groups to be dug out. Furthermore, DSF_Clust is a potentially good tool to search for putative regulatory signals.

Algorithms↗

PubMed2005

Meta-analysis of the association of CTLA-4 exon-1 +49A/G polymorphism with rheumatoid arthritis.

Rheumatoid arthritis (RA) is a common autoimmune disease. Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) is a highly suspected candidate gene for RA susceptibility. However, association studies on the polymorphism of CTLA-4 exon-1 +49A/G in RA have shown conflicting results. Therefore, we performed a meta-analysis to better assess the purported association. In order to look for ethnic effect, we performed subgroup meta-analysis in populations of European descent and Asian descent. Meta-regression analysis was also performed to explore the possible heterogeneity between the two subgroups. Ten studies (11 comparisons) with the CTLA-4 exon-1 +49A/G genotyping on 2,315 patients with RA and 2,536 controls were selected for our meta-analysis. Overall, the fixed-effects odds ratio (OR) for the G versus A allele was 1.11 (P=0.02, 95% confidence interval (CI) 1.02-1.21), with no between-study heterogeneity. Subgroup and meta-regression analysis according to the ethnicity (European or Asian) demonstrated different scenarios concerning the CTLA-4 exon-1 +49A/G polymorphism's role in RA susceptibility for the two different subgroups. No effect of G on susceptibility was seen in European descent (five comparisons; OR=1.04, P=0.30, 95% CI 0.95-1.19; no significant between-study heterogeneity). However, there is a significant association in Asian descent under both fixed [OR=1.21, 95% CI (1.06-1.39), P=0.005] and random-effect models [OR=1.19, 95% CI (1.01-1.42), P=0.04]. Meta-regression analysis also supports the heterogeneity between the two subgroups (P=0.082). We also explored the role of this polymorphism on RA risk under other various interested genetic contrasts. These results further support that this polymorphism could not be a risk factor for Europeans. Interestingly, we find that in Asians the G allele has a greater tendency to cause RA in a recessive genetic model. However, sensitivity analysis showed that the combined result of Asian populations was unstable. In conclusion, our meta-analysis results suggest that CTLA-4 exon-1 +49G allele would not be a risk factor for RA in Europeans but might play a role in RA susceptibility for Asians.

Alleles↗

PubMed2005

[Application of oligonucleotide array in single nucleotide polymorphism typing of cytokines and cytokine receptors].

OBJECTIVE: To develop an oligonucleotide array for single nucleotide polymorphism (SNP) typing of cytokines, such as tumor necrosis factor (TNF)-a, interleukin (IL)-10, tumor growth factor (TGF)-betal, IL-4, and IL-6, and their receptors and evaluate its function by direct sequencing. METHODS: According to relevant literature, SNP database of NCBI and SNP500 Cancer database of NCI, SNP loci and sequences of cytokines of clinical importance, TNF-a, IL-10, TGF-bl, IL-4 and IL-6, and matched cytokine receptors were chosen and 59 synthesized oligonucleotide probes were immobilized on a glass support, then the primer and Cy5-dCTP were used in multi-PCR, thus the products were labeled with Cy5. The labeled PCR products were hybridized with the probes in the array, and the signals were scanned by Scanner and then analyzed by Image software. Peripheral blood samples were collected from 80 healthy donors and 50 patients with uremia to isolate lymphocytes and DNA so as to undergo typing by this array, and the results were validated with direct sequencing. RESULTS: All the samples with PCR products except for 10 from uremia patients had been genotyped by cytokine array successfully. No diversity was found in genotyping for three times. Incorrect locus was not found with direct sequencing. CONCLUSION: With high specificity, sensitivity, repetitiveness, and throughout, and easy to manipulate, oligonucleotide array technique is an ideal molecular method for SNP genotyping of cytokine and cytokine receptor.

Cytokines↗

PubMed2005

cDNA microarray in isolation of novel differentially expressed genes related to human glioma and clone of a novel full-length gene.

BACKGROUND: This investigation was undertaken to obtain differentially expressed genes related to human glioma using cDNA microarray and the characterization of one novel full-length gene. METHODS: Total RNA was extracted from human glioma tissues and normal brain tissues, and mRNA was used to make probes. After hybridization and washing, the results were scanned using a computer system. The gene named 681F05 clone was an expressed gene to human glioma through four-time hybridization and scanning. Subsequently northern blot analysis was performed by northern blot, 5'RACE and bioinformatics. RESULTS: Fifteen differentially expressed genes to human glioma were obtained through four-time hybridization and scanning. Northern blot analysis confirmed that 681F05 clone was low-expressed in human brain tissues and over-expressed in human glioma tissues. The analysis of BLASTn and BLASTx showed that 681F05 clone is two cDNA clones encoding two novel proteins that are highly identified to the cyclophilin isoform 10 of C. Elgans, respectively. Sequence analysis revealed the two cDNA clones are two different splicing variants of a novel cycophilin-like gene (PPIL3a and PPIL3b). CONCLUSIONS: cDNA microarray technology can be successfully used to identify differentially expressed genes. The novel full-length gene of human PPIL3 may be correlated with the formation of human glioma.

Amino Acid Sequence↗

PubMed2005

Analysis of the factors affecting the accuracy of detection for single base alterations by oligonucleotide microarray.

The oligonucleotide microarray, a high-throughput polymorphism detection technology, holds great promise for the characterization of complex genetic variance. To achieve greater sensitivity and specificity for it to be an effective platform technology we present results and discuss some of the factors influencing signal intensities and single-mismatch discrimination in array-based mutation/SNP detection. Probes with a series of concentrations were spotted onto the slide in order to find the optimal concentration with the identifiable satisfying signals and the stable ratios between matched and mismatched probes. It was found that under our experimental conditions, when the initial probe concentration is higher than the maximum immobilization capability of the slide (7.5 microM), the hybridization signal will be saturated and the ratio between matched and mismatched probes will be more stable than at a lower probe concentration. Considering the cost of probes and the systematic stability, a constant spotting concentration of 10 microM was selected. The stability of different types of mismatched oligo-DNA duplexes on the glass surface was also confirmed. The results show that the order of stability of mismatched oligo-DNA duplexes on a glass surface is in general agreement with previous reports conducted using liquid and polyacrylamide gel pads. This suggests that the influence of the mismatched base pair on the stability of the duplex in a solid hybridization system is similar to that in the solution hybridization environment.

Nucleic Acid Heteroduplexes↗

PubMed2005

[A pilot study of spectrum of gene expression of acute leukemia].

OBJECTIVE: To investigate the gene expression of acute leukemia so as to study the pathogenesis of leukemia. METHODS: Five ml of bone marrow was collected from 22 patients with leukemia, 15 males and 7 females, aged 15-86, 17 with acute myelocytic leukemia, 4 with acute lymphocytic leukemia, and 1 with AHL. Mononuclear cells were isolated. Total RNA was extracted and mRNA was purified. DNA microarray technique with 12 848 genes was used to analyze the gene expression profiles. RESULTS: The predicted 45 genes were enormously expressed in 21 patients with acute leukemia, which were consistent with the ALL and AML classification standards reported by Golub and others. 7 genes which were overexpressed in multiple-resistant cell line K562-n/VCR were also overexpressed in 6 cases of refractory acute leukemia. Further analysis showed that 31 genes were upregulated in AML (M(4)-M(6)) and ALL but downregulated in AML (M(1)-M(3)). CONCLUSION: This results support the standard Golub has put forward. The reason that adult patients with ALL and subtypes of AML (M(4)-M(6)) have poorer prognosis in comparison with AMLM(1)-M(3) is attributed to alterations in gene expression. Primary drug resistance may be the major characteristics of refractory leukemia. Analysis of gene expression profile in acute leukemia is significant for classification and prognosis.

Adolescent↗

PubMed2005

[Apolipoprotein B is associated with metabolic syndrome in Chinese pedigrees with familial hyperlipidemia].

OBJECTIVE: To investigate the prevalence of metabolic syndrome (MS) as well as the potential predictors in families with familial combined hyperlipidemia (FCHL), familial hypertriglyceridemia (FHTG), familial hypercholesterolemia (FH) and normolipidemic families in China. METHODS: The prevalence of MS was identified among 70 different families with 560 individuals aged > or = 20, including 43 FCHL families with 379 individuals, 3 FHTG families with 30 individuals, 16 FH families with 102 individuals and 8 normolipidemic families with 49 individuals. Diagnosis of MS was based on the modified criteria of National Cholesterol Education Program, US, substituting body mass index for waist circumference. Multivariate logistic regression was used to analyze the association between MS and different pedigrees. RESULTS: MS was identified in 60.7% of the FCHL patients and 71.4% of the FHTG patients. The prevalence of MS in the family members was 36.7% for the FCHL families, 33.3% for the FHTG families, 17.6% for the FH families, and 16.3% for the normolipidemic families, with an odds ratio (OR) of 2.97 (95% CI 1.29 to 7.07) in the FCHL families compared with in the normolipidemic families. Multivariate logistic regression showed an association between apolipoprotein (apo) B and MS with an OR of 1.05 (1.03 to 1.07) in the FCHL families, an OR of 1.26 (1.03 to 1.55) in the FHTG families, and an OR of 1.07 (1.01 to 1.12) in the FH families, independent of variables such as age, gender, apoA1, and LDL cholesterol, but showed no association in the normolipidemic families (P >0.05). Similarly, apo A1 provided an OR of 0.95 (0.94 to 0.97) in the FCHL families and an OR of 0.94 (0.90 to 0.99) in the FH families, but neither in the FHTG families nor in the normolipidemic families (both P >0.05). CONCLUSION: Apo B may be regarded as a relevant factor in the assessment of MS in FCHL, FHTG and FH families in Chinese. However, this finding needs to be verified by prospective studies in diverse ethnicities and warrants additional studies to elucidate the possible mechanisms linking apoB to MS.

Adult↗

PubMed2005

cDNA microarray analysis of differential gene expression in Candida albicans biofilm exposed to farnesol.

Candida albicans biofilms are structured microbial communities with high levels of drug resistance. Farnesol, a quorum-sensing molecule that inhibits hyphal formation in C. albicans, has been found to prevent biofilm formation by C. albicans. There is limited information, however, about the molecular mechanism of farnesol against biofilm formation. We used cDNA microarray analysis to identify the changes in the gene expression profile of a C. albicans biofilm inhibited by farnesol. Confocal scanning laser microscopy was used to visualize and confirm normal and farnesol-inhibited biofilms. A total of 274 genes were identified as responsive, with 104 genes up-regulated and 170 genes down-regulated. Independent reverse transcription-PCR analysis was used to confirm the important changes detected by microarray analysis. In addition to hyphal formation-associated genes (e.g., TUP1, CRK1, and PDE2), a number of other genes with roles related to drug resistance (e.g., FCR1 and PDR16), cell wall maintenance (e.g., CHT2 and CHT3), and iron transport (e.g., FTR2) were responsive, as were several genes encoding heat shock proteins (e.g., HSP70, HSP90, HSP104, CaMSI3, and SSA2). Further study of these differentially regulated genes is warranted to evaluate how they may be involved in C. albicans biofilm formation. Consistent with the down-regulation of the cell surface hydrophobicity-associated gene (CSH1), the water-hydrocarbon two-phase assay showed a decrease in cell surface hydrophobicity in the farnesol-treated group compared to that in the control group. Our data provide new insight into the molecular mechanism of farnesol against C. albicans biofilm formation.

Biofilms↗

PubMed2005

Study on the dynamic behavior of a DNA microarray.

A theoretical dynamic kinetic model was derived and a series of experiments were carried out using low-density microarrays in various concentrations of spotting probe ([P]) and labeling target ([T]). It has been shown that target and probe determined the signal intensity together. At a certain range of DNA concentration, the signal intensity was in proportion to spotting [P]. At the higher DNA concentrations, there was a decrease in hybridization signal intensity, especially in cDNA microarrays. Since the DNA microarray was constructed on a solid surface, steric hindrance, which is induced by the solid surface and the high [P], decreased the probe immobilization efficiency, leading to a decrease of the immobilized probe density. The decreased hybridization efficiency also caused the compression in signal intensity when the target increased. Nevertheless, the intensity ratio of Cy5 to Cy3 was not compressed within a microarray in the two-color system. The ratio of Cy5/Cy3 is only determined by the ratio of two targets and independent of the density and the types of probe. Therefore, the two-color fluorescent strategy is more reasonable and reliable in detection of differential gene expression. All these results indicate that the DNA microarray can be used to detect differently expressed genes, though it cannot be used to detect the absolute mRNA abundance.

Base Sequence↗

PubMed2005

[Effects of comprehensive interventions in community on smoking, chronic bronchitis, and asthma in rural areas of Beijing].

OBJECTIVE: To study the effects of comprehensive interventions in community on smoking, chronic bronchitis, and asthma in rural areas of Beijing. METHODS: Twenty-three villages in rural areas of Beijing were randomly divided into interventional (13 villages) and control villages (10 villages) in 1992. Comprehensive interventions including education of former-smokers and improvement of living environment were carried out in the interventional villages, and none was done in the control villages. In April 2000, surveys on smoking, chronic bronchitis, and asthma were carried out among 34,436 participants aged 15 or more in the interventional and control villages. During the same period, knowledge on prevention from chronic obstructive pulmonary diseases (COPD), living environments, and smoking were assessed among 1658 high-risk individuals of COPD at baseline and following-up period. RESULTS: The scores of knowledge and improvement on living environments in the interventional villages were significantly higher than those in control villages (P < 0.001). The decrease rate of smoking and current smoking rate in the interventional villages were significantly higher than in the control villages (0.4% vs -0.8%, P < 0.001; 2.4% vs 1.3%, P < 0.001) in men, while not different in women (P > 0.05). Among never smokers at baseline, the accumulated incidence of smoking among people aged 15 to 24 from 1993 to 2000 was significantly lower in the interventional villages than in the control villages in men (18.9% vs 23.7%, P = 0.005) and in women (0% vs 0.7%, P = 0.005). Daily cigarettes smoked by smokers in the interventional villages were less than in control villages in both men (14.8 +/- 7.0 vs 17.2 +/- 8.2 cigs daily, P < 0.001) and women (12.8 +/- 6.9 vs 13.4 +/- 7.2 cigs daily, P = 0.088). The increase of prevalence of chronic bronchitis in the interventional villages was less than in the control villages (men: 0.9% vs 1.3%, P = 0.012; women: 0.1% vs 0.3%, P = 0.003). After the age factor is adjusted, odds ratio (OR) for accumulated incidence of chronic bronchitis from 1993 to 2000 in the interventional villages were 0.80 (95%CI: 0.60-1.07) for men, 0.76 (95%CI: 0.45-1.28) in women. The OR for asthma was not significant in both men and women. CONCLUSIONS: Comprehensive interventions in community may improve knowledge of COPD prevention and living environments, decrease the smoking rate, cigarettes smoked per day, and incidence of chronic bronchitis, but have no significant effects on asthma.

Adolescent↗

PubMed2005

[Spectrum of gene expression of a multi-drug resistant leukemia cell line with high tumorigenicity in nude mice].

OBJECTIVE: To investigate the mechanism of multi-drug resistance of K562-n/VCR cell line with both bcr-abl and mdr-1 expressions by clustering analysis of differential gene expression profiles. METHODS: By DNA microarray technique, genes differentially expressed by K562-n/VCR and K562-n cell lines were identified and analyzed. RESULTS: DNA microarray analysis of K562-n/VCR and K562-n cells was repeated three times and revealed 58 genes significantly differentially expressed among 12,800 genes arrayed. All but one was up-regulated in K562-n/VCR cells. The only gene down-regulated was a-myb. The up-regulated genes were MDR-associated genes, oncogenes, cytoskeleton, protein kinases and phosphatases, apoptotic and antiapoptotic factors, metabolism, transcriptional regulators associated with stress response, cell cycle checkpoint control, and genes for signal transduction proteins. CONCLUSION: These results indicate that, besides MDR-associated genes, other known and unknown genes may also be involved in the mechanism of multi-drug resistance.

Animals↗

PubMed2005

[Reactivity of the limestone in wet flue gas desulfurization].

On the basis of the analysis of chemical components of the natural limestones from different deposits in China, the pore structures of the typical limestones, with the different CaCO3 content, were examined. The reactivity of the limestones was investigated by sulfuric acid titration and gas-liquid absorption methods. The research results showed that the specific surface area of the natural limestones studied in this work was about 1.8 m2/g. It was seen that the pH of the limestone slurry rapidly decreased and then back up when the sulfuric acid was added. The higher the CaCO3 content was, or the smaller the particle size was, the larger the pH back-up rate was, and similarly the faster the SO2 concentration of the reactor outlet increased. The Reactivity of the limestone obtained by the sulfuric acid titration had the same features as that obtained by the gas liquid absorption. Compared with the specific surface area, the CaCO3 content had more effect on the reactivity of the limestones. The particle size of the limestones had a significant effect on the reactivity when the particle size was relatively large, that is less than 300-360 mesh, vice versa.

Air Pollution↗

PubMed2005

[Design of the mobile clinical information system based on PDA].

This paper is based upon a certain hospital's Mobile Clinical Information System. It discusses the design of the system in detail from three aspects: its function, its framework and the selection of its software and hardware. Finally some discussions are made for its improvement and perfection. PDA (personal digital assistant), clinical information, wireless network

Hospital Information Systems↗

PubMed2004

Quadruple-wavelength actively mode-locked fiber laser with polarization-controlled wavelength switching.

An actively mode-locked fiber laser with two overlapping cavities is proposed and successfully demonstrated to generate switchable quadruple-wavelength picosecond pulses. The wavelengths are specified by two Bragg gratings in polarization-maintaining and absorption-reducing fiber. By simple adjustment of two polarization controllers, the proposed laser can be made to operate at quadruple wavelength or to switch between wavelengths at room temperature. For wavelength switching, four single-wavelength, six dual-wavelength, and four triple-wavelength operations were performed without changing the repetition rate of the output pulses.

Journal Article↗

PubMed2004

Comparison of hybridization behavior between double and single strands of targets and the application of asymmetric PCR targets in cDNA microarray.

Double stranded targets on the cDNA microarray contain representatives of both the coding and noncoding strands, which will introduce hybridization competition with probes. Here, the effect of double and single strands of targets on the signal intensity and the ratios of Cy5/Cy3 within the same slide were compared. The results show that single stranded targets can increase the hybridization efficiency without changing the Cy5/Cy3 ratio. Based on these results, a new strategy was established by generating cDNA targets with asymmetric PCR, instead of conventional PCR, to increase the sensitivity of the cDNA microarray. Furthermore, the feasibility of this approach was validated. The results indicate that the cDNA microarray system based on asymmetric PCR is more sensitive, with no decrease in the reliability and reproducibility as compared with that based on conventional symmetric PCR.

Carbocyanines↗

PubMed2004

Gene expression profiles in an hepatitis B virus transfected hepatoblastoma cell line and differentially regulated gene expression by interferon-alpha.

AIM: To study interactions between hepatitis B virus (HBV) and interferon-alpha in liver- derived cells. METHODS: mRNAs were separately isolated from an HBV-transfected cell line (HepG(2)2.2.15) and its parental cell line (HepG(2)) pre- and post-interferon-alpha (IFN-alpha) treatment at 6, 24 and 48 h, followed by hybridization with a cDNA microarray filter dotted with 14 000 human genes. After hybridization and scanning of the arrays, the data were analyzed using ArrayGauge software. The microarray data were further verified by Northern blot analysis. RESULTS: Compared to HepG(2) cells, 14 genes with known functions were down-regulated 3 to 12- magnitudes, while 7 genes were up-regulated 3-13 magnitudes in HepG(2)2.2.15 cells prior to IFN-alpha treatment. After interferon-alpha treatment, the expression of four genes (vascular endothelial growth factor, tyrosine phosphate 1E, serine protein with IGF-binding motif and one gene of clathrin light chain) in HepG(2)2.2.15 were up-regulated, while one gene encoding a GTP-binding protein, two genes of interferon-induced kinases and two proto-oncogenes were further down- regulated. Interestingly, under IFN-alpha treatment, a number of differentially regulated genes were new ESTs or genes with unknown functions. CONCLUSION: The up-regulated genes in HepG(2)2.2.15 cell line suggested that under IFN-alpha treatment, these repressed cellular genes in HBV infected hepatocytes could be partially restored, while the down- regulated genes were most likely the cellular genes which could not be restored under interferon treatment. These down-regulated genes identified by microarray analysis could serve as new targets for anti-HBV drug development or for novel therapies.

Antiviral Agents↗