Biomedical subjects

Yunxia Zhu

Publications and source records attributed to Yunxia Zhu.

6 recordsLinked to original sources

PubMed2006

Co-culture with fat cells induces cellular insulin resistance in primary hepatocytes.

Obesity is highly correlated with systemic insulin resistance. To assess the effect of fat cell on the development of hepatic insulin resistance, an in vitro system was developed in which primary hepatocytes were kept in co-culture with 3T3-L1 cells, then insulin signaling and glycogen production were subsequently analyzed in hepatocytes. The results showed that insulin-induced tyrosine phosphorylation of insulin receptor substrate (IRS)-2 was significantly blocked. Insulin-regulated activation of Akt kinase and glucose production in the hepatocytes were also reduced after co-culture. On the other hand, addition of TNF-alpha or IL-6 neutralizing antibodies to the supernatant of co-culture recovered both IRS-2 phosphorylation and Akt activation. In conclusion, fat cells may induce insulin resistance in liver cells, and this process appears to be mediated by TNF-alpha and IL-6. Our data present first the direct evidence of interaction for insulin signaling event between the adipocytes and hepatocytes.

3T3-L1 Cells↗

PubMed2006

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.

Animals↗

PubMed2004

[Molecular epidemiologic investigation of infertile male's semen infected by Gardnerella vaginalis].

OBJECTIVE: To investigate the status of the semen of the infertility patients infected by Gardnerella vaginalis (Gv). METHODS: Semen samples from 373 clinic patients of infertility and vaginal samples from 63 positive patients' wives were collected from April 2002 to May 2003. And the samples were tested by nested polymerase chain reaction (nPCR). RESULTS: The positive rate of the infertile males' semen infected by Gv was 44.2%, while that of the postive patients' wives was 87.3%. CONCLUSION: The positive rate of the infertile male's semen infected by Gv is high and Gv can be spread by sexual intercourse.

Adult↗

PubMed2003

Controlling integration specificity of a yeast retrotransposon.

Retrotransposons and retroviruses integrate nonrandomly into eukaryotic genomes. For the yeast retrotransposon Ty5, integration preferentially occurs within domains of heterochromatin. Targeting to these locations is determined by interactions between an amino acid sequence motif at the C terminus of Ty5 integrase (IN) called the targeting domain, and the heterochromatin protein Sir4p. Here we show that new Ty5 integration hot spots are created when Sir4p is tethered to ectopic DNA sites. Targeting to sites of tethered Sir4p is abrogated by single amino acid substitutions in either IN or Sir4p that prevent their interaction. Ty5 target specificity can be altered by replacing the IN-targeting domain with other peptide motifs that interact with known protein partners. Integration occurs at high efficiency and in close proximity to DNA sites where the protein partners are tethered. These findings define a mechanism by which retrotransposons shape their host genomes and suggest ways in which retroviral integration can be controlled.

Bacterial Proteins↗

PubMed2003

Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.

Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced when the sequences they contain are integrated with such biological information as genomic location, gene function, gene expression and phenotypic variation. We present the analysis and results of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse Genome Informatics (MGI) database.

Animals↗

PubMed2003

Connecting sequence and biology in the laboratory mouse.

The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrate these data with the ever-expanding knowledge about the roles of genes and gene products in biological processes, and how to provide useful views to the scientific community. Public resources, such as the National Center for Biotechnology Information (NCBI; http://www.ncbi.nih.gov), and model organism databases, such as the Mouse Genome Informatics database (MGI; http://www.informatics.jax.org), maintain the primary data and provide connections between sequence and biology. In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data now available for the laboratory mouse. In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink.

Animals↗