Unknown,Transcriptomics,Genomics,Proteomics

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Potential of the hepatic transcriptome expression profile of the striped seabream (Lithognathus mormyrus) as an environmental biomarker

ABSTRACT: The potential of an hepatic transcriptome expression profile, evaluated in a sentinel feral fish, to serve as an environmental biomarker was examined. Gene expression profiles of individuals of Lithognathus mormyrus were examined using a cDNA microarray and were correlated to the set of environmental exposure conditions at their site and date of collection. The clusters of individual gene expression profiles were reasonably related to the fish samples and several sample-specific clusters of genes, designated gene signatures of the sample, were determined. The relationship between transcriptome expression and the fish samples indicated a potential for their utilization as an environmental biomarker. Ten fish were sampled at each of two sites (Dor, Israel and Haifa, Israel) each of two years (2007 and 2008) for a total of 40 fish. All fish were hybridized to a common reference RNA population using a dye-swap design. Hence, each fish was hybridized twice vs. the reference RNA. The reference RNA was an equalized pool of the RNAs from all 10 fish comprising sample D7.

ORGANISM(S): Lithognathus mormyrus

SUBMITTER: M Auslander

PROVIDER: E-GEOD-22629 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Potential of the hepatic transcriptome expression profile of the striped seabream (Lithognathus mormyrus) as an environmental biomarker.

Yudkovski Yana Y Ramšak Andreja A Ausland Meirav M Tom Moshe M

Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals 20100916 7

The potential of the hepatic transcriptome expression profile evaluated in a sentinel feral fish to serve as an environmental biomarker was examined. Expression profiles of Lithognathus mormyrus individuals were exhibited using cDNA microarray and were related to the set of exposure conditions at their sites and dates of collection. Expression profiles of individual fish were reasonably clustered according to the fish samples. In addition, several sample-specific gene clusters were determined, d ...[more]

PMID: 20846022

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Project description:Deciduous and permanent human teeth represent a model system to study ageing of mesenchymal populations. Aging is tightly connected to self-renewal and proliferation and thus, mapping potential molecular differences in these characteristics between populations constitutes an important task. Specifically designed microarray panels were used. We have detected a number of molecules that were differentially expressed in dental pulp mesenchyme from deciduous and permanent teeth extracted from young children and adults, respectively. Among the differentially regulated genes HMGA2, a stem cell-associated marker, stood out as a remarkable example with a robust expression in deciduous pulp cells. In addition to this, we discovered that several proliferation-related genes, including CDC2A and CDK4, were up-regulated in deciduous pulp cells, while matrix genes COL1A1, fibronectin and several signaling molecules, such as VEGF, FGFr-1 and IGFr-1 were up-regulated in the pulp cells from permanent teeth. Taken together, our data suggest that deciduous pulp cells are more robust in self- renewal and proliferation, whereas adult dental pulp cells are more capable of signaling and matrix synthesis. The deciduous teeth were collected from 3-12-year-old children (N=8), whereas the permanent teeth were collected from adults, 19-52 years of age (N=8). The tooth was mechanically separated into two halves to remove all soft tissue in the pulp. The pulp tissue was digested and the dissociated cells were passed through cell strainer and plated with culture medium. The cells were then passaged at 90% confluency to a 10 cm dish for expansion. RNA was extracted from passage one cells with the Qiagen RNeasy Mini Kit. Microarray analysis was performed using PIQORTM Stem Cell Microarray chip (Miltenyi Biotech), which is comprised of 942 relevant genes for stem/progenitor cells and key genes for cell differentiation, to identify gene sets that are differentially expressed between cells in the deciduous and adult teeth. A total of 1 μg RNA for each sample was used for amplification and further analysis with the PIQORTM stem cell microarray chip (Miltenyi Biotec), followed by detection with a laser scanner (Agilent Technologies). In total, 8 comparisons were performed with dataset consisting of two microarrays, each containing a total of 11 slides with signal intensities within the R/Bioconductor statistical framework. The Linear Model for Microarray Data package (Limma) was used to pre-process the raw data, perform quality controls and estimate statistical significance. Expression intensities were background-corrected using a convolution of normal and exponential distributions with an offset of 50, which were then normalized within every slide using loess normalization. We analyzed the red and green channels separately using the mixed model method and different groups were quantile-normalized separately. The correlation was computed between the two channels for the same spot. Differentially expressed genes were identified by computing the contrasts, fitting to a linear model, performing the hypothesis tests, and correcting for multiple testing by performing the false discovery rate using the Benjamini-Hochberg correction.

Dataset Information

Potential of the hepatic transcriptome expression profile of the striped seabream (Lithognathus mormyrus) as an environmental biomarker

Publications

Potential of the hepatic transcriptome expression profile of the striped seabream (Lithognathus mormyrus) as an environmental biomarker.

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