title: Construction and characterization of Japanese medaka (Oryzias latipes) hepatic cDNA library and its implementation to biomarker screening in aquatic toxicology.
abstract: To strengthen the toxicogenomic study, we constructed a library of hepatic cDNA from Japanese medaka under influence of specific chemical mediated stress responses. Gene expression profile analysis of the cDNA microarrays followed by real time RT-PCR assay were conducted to screen particular biomarkers for 17-beta estradiol (E2), nonylphenol (NP) and 2-chlorophenol (2CP). Information of 1509 high-quality ESTs including 260 new ESTs was added onto GenBank and dbEST. The ESTs were clustered and assembled into 159 contigs and 372 singletons. Among them, 128 contigs and 163 singletons (54.8%) were functionally characterized and 13 UniESTs (2.5%) were hypothetical proteins. Ontology analysis resulting in 282 UniESTs which involved with 2102 GOs and 93 sequences associated with 116 enzyme codes. For each test chemical, two specific biomarkers were selected from the gene expression profiling of microarrays. The expression patterns of the marker genes in real time PCR analysis were consistent with the regulated gene expression patterns in microarrays. The tentative biomarkers showed unique gene expression patterns depending on chemical concentration(s) and exposure duration in real time RT-PCR analysis. The analysis accomplished of the hepatic cDNA library and its information added to genetic and genomic resources could be sufficiently valuable specifically for aquatic toxicity studies.
authors.affiliation: College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Chi Hoa
authors.initials: CH
authors.lastname: Pham
authors.forename: Kyung Seo
authors.initials: KS
authors.lastname: Park
authors.forename: Byoung Chan
authors.initials: BC
authors.lastname: Kim
authors.forename: Han Na
authors.initials: HN
authors.lastname: Kim
authors.forename: Man Bock
authors.initials: MB
authors.lastname: Gu
mesh_terms: D000818:Animals; D001483:Base Sequence; D015415:Biomarkers; D002733:Chlorophenols / Q000633:toxicity; D004305:Dose-Response Relationship, Drug; D054750:Ecotoxicology / Q000379:methods*; D004958:Estradiol / Q000633:toxicity; D020869:Gene Expression Profiling; D015723:Gene Library; D008099:Liver; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D009990:Oryzias / Q000235:genetics*; D010636:Phenols / Q000633:toxicity; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059467:Transcriptome / Q000187:drug effects*; D014874:Water Pollutants, Chemical / Q000633:toxicity*
chemical_list: D015415:Biomarkers; D002733:Chlorophenols; D010636:Phenols; D014874:Water Pollutants, Chemical; D004958:Estradiol; C025256:nonylphenol; C030683:2-chlorophenol