Response of rainbow trout transcriptome to model chemical contaminants

Koskinen, Heikki; Pehkonen, Petri; Vehniäinen, Eeva-Riikka; Krasnov, Aleksei; Rexroad, Caird E.; Afanasyev, Sergey; Mölsä, Hannu; Oikari, Aimo

doi:10.1016/j.bbrc.2004.06.024

Cited by 122 publications

(81 citation statements)

References 13 publications

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“…Another study in rainbow trout fry reported similar gene expression profiles in response to high doses of four different toxicants ( -naphthoflavone ( NF), Cd, CCl4, and pyrene). They suggested this could represent nonspecific toxic effects at high doses (13). Because of poor annotation of D. magna genes, it is difficult to discern the role of the differentially expressed genes at the NOEC.…”

Section: Resultsmentioning

confidence: 99%

Gene Expression Profiling in Daphnia magna Part I: Concentration-Dependent Profiles Provide Support for the No Observed Transcriptional Effect Level

Poynton

Loguinov

Varshavsky

et al. 2008

Environ. Sci. Technol.

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Ecotoxicogenomic approaches to environmental monitoring provide holistic information, offer insight into modes of action, and help to assess the causal agents and potential toxicity of effluents beyond the traditional end points of death and reproduction. Recent investigations of toxicant exposure indicate dose-dependent changes are a key issue in interpreting genomic studies. Additionally, there is interest in developing methods to integrate gene expression studies in environmental monitoring and regulation, and the No Observed Transcriptional Effect Level (NOTEL) has been proposed as a means for screening effluents and unknown chemicals for toxicity. However, computational methods to determine the NOTEL have yet to be established. Therefore, we examined effects on gene expression in Daphnia magna following exposure to Cu, Cd, and Zn over a range of concentrations including a tolerated, a sublethal, and a nearly acutely toxic concentration. Each concentration produced a distinct gene expression profile. We observed differential expression of a very few genes at tolerated concentrations that were distinct from the expression profiles observed at concentrations associated with toxicity. These results suggest that gene expression analysis may offer a strategy for distinguishing toxic and nontoxic concentrations of metals in the environment and provide support for a NOTEL for metal exposure in D. magna. Mechanistic insights could be inferred from the concentration-dependent gene expression profiles including metal specific effects on disparate metabolic processes such as digestion, immune response, development and reproduction, and less specific stress responses at higher concentrations.

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Section: Resultsmentioning

confidence: 99%

Gene Expression Profiling in Daphnia magna Part I: Concentration-Dependent Profiles Provide Support for the No Observed Transcriptional Effect Level

Poynton

Loguinov

Varshavsky

et al. 2008

Environ. Sci. Technol.

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“…A number of teleost fish-specific microarray chips have been developed for research in nutrition (34), toxicology (38,40), immunology (13,14,41,46,47,62), pathology (27,48,63), physiology (30,35,39,67,78), reproduction (80,81), and development (45,67,76). We have utilized genomics resources developed by the Genomic Research on Atlantic Article published online before print.…”

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confidence: 99%

Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salarL.): a role for tumor suppressor p53 in AGD pathogenesis?

Morrison

Cooper

Koop

et al. 2006

Physiological Genomics

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Neoparamoeba spp. are amphizoic amoebae with the capacity to colonize the gills of some marine fish, causing AGD. Here, the gill tissue transcriptome response of Atlantic salmon ( Salmo salar L.) to AGD is described. Tanks housing Atlantic salmon were inoculated with Neoparamoeba spp. and fish sampled at time points up to 8 days postinoculation (pi.). Gill tissues were taken from AGD-affected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-unaffected fish. A total of 206 genes, representing 190 unique transcripts, were reproducibly identified as up- or downregulated in response to Neoparamoeba spp. infection. Informative transcripts having GO biological process identifiers were grouped according to function. Although a number of genes were placed into each category, no distinct patterns were observed. One Atlantic salmon cDNA that was upregulated in infected gill relative to noninfected gill at 114 and 189 h pi. showed significant identity with the Xenopus, mouse, and human anterior gradient-2 (AG-2) homologs. Two Atlantic salmon AG-2 mRNA transcripts, designated asAG-2/1 and asAG-2/2, were cloned, sequenced, and shown to be predominantly expressed in the gill, intestine, and brain of a healthy fish. In AGD-affected fish, differential asAG-2 expression was confirmed in samples used for microarray analyses as well as in AGD-affected gill tissue taken from fish in an independent experiment. The asAG-2 upregulation was restricted to AGD lesions relative to unaffected tissue from the same gill arch, while p53 tumor suppressor protein mRNA was concurrently downregulated in AGD lesions. Differential expression of p53-regulated transcripts, proliferating cell nuclear antigen and growth arrest and DNA damage-inducible gene-45β (GADD45β) in AGD lesions, suggests a role for p53 in AGD pathogenesis. Thus AGD may represent a novel model for comparative analysis of p53 and p53-regulated pathways.

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“…These are all personalized microarrays. Furthermore, Panicker et al (2004) Microarray have also been used to explore the response of rainbow trout transcriptome to chemical contaminants (Koskinen et al, 2004), toxicogenomic profiling of hepatic tumour promoters (Tilton et al, 2006), and gene expression in atrophying muscle (Salem et al, 2006). The application of DNA microarray in fish biology and aquaculture could have immense significance through discovery of novel genes, their expression profiles and response to various environmental stimulations at genome level.…”

Section: Array Based Platformsmentioning

confidence: 99%

Untitled

Hakim¹

2017

GenAqua

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Although aquaculture management becomes challenging because of overuse, pollution and human activities reduced resources and genetic variations, current developments in molecular technology and genome programs have created an enormous evidence to be used for the genetic advancement of aquaculture. Over the past decade, using molecular markers showed polymorphism at the DNA level and played rising role in aquaculture. The utility of DNA markers has certified the hastiness in the exploration of fish germplasm. Various molecular markers present and their differences in principles, methodologies and applications still need careful consideration in selecting more useful marker for the successful management of aquaculture. In addition to the basic principles, necessities, pros and cons of various markers, this review also discusses their usage in different aspects of aquaculture; we provide an overview of the potential of various techniques of functional genomics like expressed sequence tags (EST), microarrays and RNA sequencing in aquaculture.

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Response of rainbow trout transcriptome to model chemical contaminants

Cited by 122 publications

References 13 publications

Gene Expression Profiling in Daphnia magna Part I: Concentration-Dependent Profiles Provide Support for the No Observed Transcriptional Effect Level

Gene Expression Profiling in Daphnia magna Part I: Concentration-Dependent Profiles Provide Support for the No Observed Transcriptional Effect Level

Transcriptome profiling the gills of amoebic gill disease (AGD)-affected Atlantic salmon (Salmo salarL.): a role for tumor suppressor p53 in AGD pathogenesis?

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