Biomedical subjects

Yu Quan

Publications and source records attributed to Yu Quan.

6 recordsLinked to original sources

PubMed2006

GEPS: the Gene Expression Pattern Scanner.

Gene Expression Pattern Scanner (GEPS) is a web-based server to provide interactive pattern analysis of user-submitted microarray data for facilitating their further interpretation. Putative gene expression patterns such as correlated expression, similar expression and specific expression are determined globally and systematically using geometric comparison and correlation analysis methods. These patterns can be visualized via linear plot with quantitative measures. User-defined threshold value is allowed to customize the format of the pattern search results. For better understanding of gene expression, patterns derived from 329,205 non-redundant gene expression records from the GNF SymAltas and the Gene Expression Omnibus are also provided. These profiles cover 24,277 human genes in 79 tissues, 32,905 mouse genes in 61 tissues and 4201 rat genes in 44 tissues. GEPS is available at http://bioinf.xmu.edu.cn/software/geps/geps.php.

Animals↗

PubMed2005

Paraquat neurotoxicity is distinct from that of MPTP and rotenone.

Paraquat, MPTP, and rotenone reproduce features of Parkinson's disease (PD) in experimental animals. The exact mechanisms by which these compounds damage the dopamine system are not firmly established, but selective damage to dopamine neurons and inhibition of complex I are thought to be involved. We and others have previously documented that the toxic metabolite of MPTP, MPP+, is transported into dopamine neurons through the dopamine transporter (DAT), while rotenone is not transported by DAT. We have also demonstrated the requirement for complex I inhibition and oxidative damage in the dopaminergic neurodegeneration produced by rotenone. Based on structural similarity to MPP+, it has been proposed that paraquat exerts selective dopaminergic toxicity through transport by the DAT and subsequent inhibition of mitochondrial complex I. In this study we report that paraquat is neither a substrate nor inhibitor of DAT. We also demonstrate that in vivo exposure to MPTP and rotenone, but not paraquat, inhibits binding of 3H-dihydrorotenone to complex I in brain mitochondria. Rotenone and MPP+ were both effective inhibitors of complex I activity in isolated brain mitochondria, while paraquat exhibited weak inhibitory effects only at millimolar concentrations. These data indicate that, despite the apparent structural similarity to MPP+, paraquat exerts its deleterious effects on dopamine neurons in a manner that is unique from rotenone and MPTP.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗

PubMed2005

[Identification of signature amino acids in the env V3-V4 and flanking regions of human immunodeficiency virus type 1 predominant strains in China].

OBJECTIVE: To identify signature amino acids in the V3-V4 and flanking regions of the env gene from human immunodeficiency virus type 1 (HIV-1) predominant strains in China and to elucidate the role of these signature amino acids on epidemiologic tracking and the development of vaccine. METHODS: Fragments of the HIV-1 env gene were amplified by nested-PCR from the whole blood of HIV-1 infected individuals from 12 provinces in China. Then, the PCR products were directly sequenced by using ABI 377 DNA SEQUENCER. The sequences covering the env V3-V4 region of the strains were used for the analyses described here. Envelope sequence subtypes were assigned using BLAST (http://www.HIV-Web.lanl.gov). Phylogenetic analyses were performed using GCG and MEGA as well as signature amino acids were identified using VESPA. RESULTS: Subtype B' strains and two recombinants (B'/C and CRF01-AE) were discovered among 157 currently circulating strains in China. The most prevalent subtypes were B'/C (38.85%), followed by B' (34.40%), and CRF01-AE (26.75%). Phylogenetic tree analysis of env V3-V4 region showed that subtype B' strains were closely related to B.CN.RL42, while most of B'/C strains clustered with 97CN54A and 97CNGX6F, CRF01-AE strains clustered into two distinct subgroups, which were closely related to THCM240 and 97CNGX2F. Analysis of signature amino acids revealed that eight of positions were identified as conserved signature amino acid sites in the env V3-V4 and flanking regions of the subtype B' and B'/C strains and almost all signature amino acids were found in their reference strains. Interestingly, eleven signature amino acids were demonstrated in the same regions of the CRF01-AE strains, but nine out of 11 signature amino acid sites were distinct from the same positions of the reference strains 97CNGX2F and TH.CM240. It is noteworthy that these 9 signature amino acids were found in the strains from all of the selected provinces except those from Yunnan province. CONCLUSION: Analysis of the signature amino acids suggest that much of the current Chinese epidemics of subtype B' and B'/C strains are descended from a single introduction into China, while the epidemic caused by the CRF01-AE strain is caused by multiple introductions into China from Thailand. These results will contribute to the policy of AIDS prevention and control as well as the ongoing development of AIDS vaccine.

Adolescent↗

PubMed2004

[Distribution of recombinant human immunodeficiency virus type-1 CRF01_AE strains in China and its sequence variations in the env V3-C3 region].

OBJECTIVE: To characterize CRF01_AE strains of recombinant human immunodeficiency virus type-1 (HIV-1) found in the Second National Molecular Epidemiology Study on HIV in China and to analyze its sequence variation in the env V3-C3 region during the First National Molecular Epidemiology Study (NMES1, 1996 - 1998) to the Second National Molecular Epidemiology Study (NMES2, 2001 - 2002). METHODS: DNA was extracted from peripheal blood mononuclear cells of the subjects with HIV infection. The env C2-V4 region of HIV-1 was amplified with nested polymerase chain reaction (n-PCR). PCR products were directly sequenced using ABI 377 DNA sequencer, then the gene-based phylogenetic tree was constructed and its variation of amino acids was analyzed with GCG software. RESULTS: Totally, 169 strains of recombinant HIV-1 CRF01_AE were identified from blood samples collected from different high risk groups in 17 of 31 provinces, municipalities and autonomous regions all over China by the end of 2002. Although sexual transmission still dominated during NMES1 (62.2%, 23/37) and NMES2 (55.3%, 73/132), prevalence of HIV-1 CRF01_AE in intravenous drug users (IDUs) increased to 41.6% (57/137) during NMES2 from 27% (10/37) during NMES1. Phylogenetic tree analysis showed that HIV-1 CRF01_AE strains prevalent in IDUs during NMES2 did not cluster with those prevalent in the subjects infected by sexual transmission during NMES2 and those in IDUs during NMES1. The amino acid residues of V3 region of HIV-1 CRF01_AE in IDUs were relatively conservative, but the sixth, eighth, ninth, tenth, twelfth, fifteenth, sixteenth amino acid residues of C3 region displayed regular changes. CONCLUSIONS: HIV-1 CRF01_AE strain has been introduced into inland provinces from southeastern coast areas and southwestern border areas, with an increasing prevalence in IDUs. The sequence of env V3-C3 region of recombinant HIV-1 CRF01_AE strains prevalent in IDUs during NMES2 was obviously different from that during NMES1, suggesting that HIV-1 CRF01_AE strains prevalent in IDUs during NMES2 might come from a new source and have a potential to spread.

Amino Acid Sequence↗

PubMed2004

[Prevalence of drug resistance mutations among antiretroviral drug-naive HIV-1-infected patients in China].

OBJECTIVE: To collect background information on drug-resistant HIV-1 strains in various regions before the start of nation-wide antiretroviral therapy in China. METHODS: Twenty percent of the 2,000 blood samples from antiretroviral therapy naive patients collected for the 2nd national HIV molecular epidemiology survey (NHMES) in 2002 were randomly sampled for this study. The entire protease gene and 20-230 amino acids of the reverse transcriptase gene were amplified by PCR from provirus DNA and sequenced. The results were analyzed with HIV db-Drug Resistance Algorithm and genotypic resistance mutations were determined to particular anti-HIV drugs. RESULTS: Totally 164 protease gene sequences and 138 reverse transcriptase gene sequences were obtained from patients; 0.61% of 164 sequences displayed primary resistance mutations in the protease gene, whereas 99.39% carried 1 or more secondary mutations. Genotypic resistance to at least one nucleoside reverse transcriptase inhibitors (NRTI) was present in 5.80%,and resistance to at least one non-nucleo side reverse transcriptase inhibitors (NNRTI) was present in 1.45% of samples. CONCLUSION: The prevalence of genotypic drug resistance is very low in drug-naive HIV infected patients from 21 provinces of China tested in this study. Laboratories participated in the NHMES have organized a network to provide drug resistance monitoring service in the current nation-wide antiviral treatment program in China.

Anti-HIV Agents↗

PubMed2003

[Study on the evolutionary pressure on the env gene of the human immunodeficiency virus type 1 CRF01-AE strains circulating in China].

OBJECTIVE: To identify variations in the env gene of human immunodeficiency virus type 1 (HIV-1) subtype CRF01-AE strains circulating in China and to elucidate the potential relationship between genetic variation and evolutionary pressure. METHODS: Fragments of the HIV-1 env gene were amplified by nested-polymerase chain reaction (n-PCR) from the whole blood of HIV-1 infected individuals from four provinces in Southeast China (Guangdong, Hunan, Jiangsu and Jiangxi). The PCR products were then directly sequenced by ABI 377 DNA sequencers. The sequences covering the env V3-V4 region of 34 HIV-1 subtype CRF01-AE strains were selected to analyse phylogenetic trees and amino acid mutations. The accumulation of synonymous (Ks) and antonymous (Ka) substitutions as well as Ks/Ka ratios were calculated using DIVERGE. RESULTS: Phylogenetic trees showed that the 34 HIV-1 subtype CRF01-AE strains from China clustered with the Chinese AE reference strain (AE.97CNGX2F), as well as with the reference strains from Thailand (AE.CM240 and AE.93TH253). The amino acid sequences of the env V4 and C3 regions in the samples were highly variable, compared with those of V3 and V3-downstream regions. The V3 loop central motif in the majority (87.5%) of the strains was GPGQ. The majority of strains did not contain positively charged amino acids at positions 306 and 320 in V3 loop. The N-linked glycosylation sites in the V3-V4 region and flanking regions in these strains were relatively conserved. Analysis of the entire region showed that the mean Ks values were significantly higher than that of the Ka values (P < 0.001), with the Ks/Ka significantly higher than 1.0 (P < 0.001). In contrast, the Ks/Ka ratio in the V4 region was significantly lower than 1.0 (P < 0.01). CONCLUSIONS: Our study indicated that the majority of HIV-1 subtype CRF01-AE strains circulating in China were highly homogeneous. The amino acid sequences of the V4 and C3 regions were significantly more variable than those of the V3 loop. Our analysis also suggested that the phenotype of nearly all strains was likely to be non-syncytium inducing (NSI). Finally, the variation found in the V3-V4 sequence was significantly influenced by functional constraints as opposed to positive selective pressure, while the variability of the lone V4 region was strongly related to positive selective pressure.

Adult↗