Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.abstract???
Amphibians are important vertebrates in toxicology often representing both aquatic and terrestrial forms within the life history of the same species. Of the thousands of species, only two have substantial genomics resources: the recently published genome of the Pipid, Xenopus (Silurana) tropicalis, and transcript information (and ongoing genome sequencing project) of Xenopus laevis. However, many more species representative of regional ecological niches and life strategies are used in toxicology worldwide. Since Xenopus species diverged from the most populous frog family, the Ranidae, ~200 million years ago, there are notable differences between them and the even more distant Caudates (salamanders) and Caecilians. These differences include genome size, gene composition, and extent of polyploidization. Application of toxicogenomics to amphibians requires the mobilization of resources and expertise to develop de novo sequence assemblies and analysis strategies for a broader range of amphibian species. The present mini-review will present the advances in toxicogenomics as pertains to amphibians with particular emphasis upon the development and use of genomic techniques (inclusive of transcriptomics, proteomics, and metabolomics) and the challenges inherent therein.
Figure 1. Cartoon depiction of RNA-seq results from the liver of premetamorphic Xenopus laevis and Rana catesbeiana tadpoles focusing upon arginine and proline metabolism including the urea cycle. Tadpoles were exposed to 10ânM 3,5,3â²-triiodothyronine (a thyroid hormone) or NaOH vehicle control for 48âh. The animals were treated and maintained in accordance with the guidelines of the Canadian Council on Animal Care. The liver transcriptomes were subjected to RNA-seq using 75 base HiSeq of paired end tagged (PET) libraries. The derived sequence information was assembled using the X. tropicalis genome as a scaffold and the contig identities were determined by a Blastx search against the X. tropicalis genome. The number of read counts (~400 million) was normalized between samples and the relative count frequencies of the indicated pathway components were compared based upon the X. tropicalis arginine and proline metabolism KEGG pathway (xtr00330; www.genome.jp/kegg). The results are depicted as a bipartite rectangle beside the name of the enzymes corresponding with measured transcripts in the RNA-seq experiment that were identified in the KEGG pathway. The left side represents the relative change in transcript abundance levels of Rana (R) and the right side mRNA levels of Xenopus (X) where red is increased, black is no change, and blue is decreased relative to control animals. Non-detected transcript is depicted by a crossed-out white box. Use of the X. tropicalis genome as an assembly scaffold had limited utility since X. laevis and R. catesbeiana sequences aligned imperfectly to the X. tropicalis genome with R. catesbeiana, not surprisingly, having the least benefit of alignment. Nevertheless, some transcript identities linked to count frequencies were positively confirmed and the data obtained for the urea cycle enzymes, for example, matched well with previous observations (Helbing et al., 1992; Xu et al., 1993; Iwase et al., 1995). This validates the method for transcripts that are identifiable and quantifiable in this way.
Baba,
Bisphenol A disrupts Notch signaling by inhibiting gamma-secretase activity and causes eye dysplasia of Xenopus laevis.
2009, Pubmed,
Xenbase
Baba,
Bisphenol A disrupts Notch signaling by inhibiting gamma-secretase activity and causes eye dysplasia of Xenopus laevis.
2009,
Pubmed
,
Xenbase
Bilesimo,
Specific histone lysine 4 methylation patterns define TR-binding capacity and differentiate direct T3 responses.
2011,
Pubmed
,
Xenbase
Domanski,
Analysis of the Rana catesbeiana tadpole tail fin proteome and phosphoproteome during T3-induced apoptosis: identification of a novel type I keratin.
2007,
Pubmed
Duarte-Guterman,
Regulation of thyroid hormone-, oestrogen- and androgen-related genes by triiodothyronine in the brain of Silurana tropicalis.
2010,
Pubmed
,
Xenbase
Eggert,
Sex determination: the amphibian models.
2004,
Pubmed
Gohin,
Comparative transcriptomic analysis of follicle-enclosed oocyte maturational and developmental competence acquisition in two non-mammalian vertebrates.
2010,
Pubmed
,
Xenbase
Gunderson,
Effect of low dose exposure to the herbicide atrazine and its metabolite on cytochrome P450 aromatase and steroidogenic factor-1 mRNA levels in the brain of premetamorphic bullfrog tadpoles (Rana catesbeiana).
2011,
Pubmed
Hayes,
The cause of global amphibian declines: a developmental endocrinologist's perspective.
2010,
Pubmed
Heimeier,
The xenoestrogen bisphenol A inhibits postembryonic vertebrate development by antagonizing gene regulation by thyroid hormone.
2009,
Pubmed
,
Xenbase
Helbing,
Peering into molecular mechanisms of action with frogSCOPE.
2010,
Pubmed
Helbing,
Sequential up-regulation of thyroid hormone beta receptor, ornithine transcarbamylase, and carbamyl phosphate synthetase mRNAs in the liver of Rana catesbeiana tadpoles during spontaneous and thyroid hormone-induced metamorphosis.
1992,
Pubmed
,
Xenbase
Helbing,
Identification of gene expression indicators for thyroid axis disruption in a Xenopus laevis metamorphosis screening assay. Part 1. Effects on the brain.
2007,
Pubmed
,
Xenbase
Hellsten,
The genome of the Western clawed frog Xenopus tropicalis.
2010,
Pubmed
,
Xenbase
Hinther,
C-fin: a cultured frog tadpole tail fin biopsy approach for detection of thyroid hormone-disrupting chemicals.
2010,
Pubmed
Howe,
Toxicity of glyphosate-based pesticides to four North American frog species.
2004,
Pubmed
Iwase,
Cloning of cDNAs encoding argininosuccinate lyase and arginase from Rana catesbeiana liver and regulation of their mRNAs during spontaneous and thyroid hormone-induced metamorphosis.
1995,
Pubmed
Katsu,
Molecular cloning of estrogen receptor alpha (ERalpha; ESR1) of the Japanese giant salamander, Andrias japonicus.
2006,
Pubmed
,
Xenbase
Ko,
Female-enriched expression of ERalpha during gonad differentiation of the urodele amphibian Pleurodeles waltl.
2008,
Pubmed
Langlois,
Expression profiles of reproduction- and thyroid hormone-related transcripts in the brains of chemically-induced intersex frogs.
2011,
Pubmed
,
Xenbase
Langlois,
Low levels of the herbicide atrazine alter sex ratios and reduce metamorphic success in Rana pipiens tadpoles raised in outdoor mesocosms.
2010,
Pubmed
Martin,
Next-generation transcriptome assembly.
2011,
Pubmed
Massari,
Aromatase mRNA expression in the brain of adult Xenopus laevis exposed to Lambro river water and endocrine disrupting compounds.
2010,
Pubmed
,
Xenbase
Mitsui,
Development of metamorphosis assay using Silurana tropicalis for the detection of thyroid system-disrupting chemicals.
2006,
Pubmed
,
Xenbase
Mortensen,
Thyroid hormone-dependent gene expression as a biomarker of short-term 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE) exposure in European common frog (Rana temporaria) tadpoles.
2006,
Pubmed
Oka,
Application of metamorphosis assay to a native Japanese amphibian species, Rana rugosa, for assessing effects of thyroid system affecting chemicals.
2009,
Pubmed
,
Xenbase
Oka,
Effect of atrazine on metamorphosis and sexual differentiation in Xenopus laevis.
2008,
Pubmed
,
Xenbase
Oppenheimer,
Evolving concepts of thyroid hormone action.
1999,
Pubmed
Park,
Effects of nonylphenol on early embryonic development, pigmentation and 3,5,3'-triiodothyronine-induced metamorphosis in Bombina orientalis (Amphibia: Anura).
2010,
Pubmed
,
Xenbase
Qin,
Thyroid disruption by technical decabromodiphenyl ether (DE-83R) at low concentrations in Xenopus laevis.
2010,
Pubmed
,
Xenbase
Relyea,
The toxicity of Roundup Original Max to 13 species of larval amphibians.
2009,
Pubmed
Rossi,
Effects of TCDD on spermatogenesis related factor-2 (SRF-2): gene expression in Xenopus.
2009,
Pubmed
,
Xenbase
Searcy,
Thyroid hormone-dependent development in Xenopus laevis: a sensitive screen of thyroid hormone signaling disruption by municipal wastewater treatment plant effluent.
2012,
Pubmed
,
Xenbase
Serrano,
In vivo assessment and potential diagnosis of xenobiotics that perturb the thyroid pathway: Proteomic analysis of Xenopus laevis brain tissue following exposure to model T4 inhibitors.
2010,
Pubmed
,
Xenbase
Suda,
Up-regulation of FSHR expression during gonadal sex determination in the frog Rana rugosa.
2011,
Pubmed
Sumida,
Sequencing and analysis of the internal transcribed spacers (ITSs) and coding regions in the EcoR I fragment of the ribosomal DNA of the Japanese pond frog Rana nigromaculata.
2004,
Pubmed
,
Xenbase
Tietge,
Early temporal effects of three thyroid hormone synthesis inhibitors in Xenopus laevis.
2010,
Pubmed
,
Xenbase
Urbatzka,
Expression profiles of LHbeta, FSHbeta and their gonadal receptor mRNAs during sexual differentiation of Xenopus laevis tadpoles.
2010,
Pubmed
,
Xenbase
Veldhoen,
Use of heterologous cDNA arrays and organ culture in the detection of thyroid hormone-dependent responses in a sentinel frog, Rana catesbeiana.
2006,
Pubmed
Veldhoen,
The bactericidal agent triclosan modulates thyroid hormone-associated gene expression and disrupts postembryonic anuran development.
2006,
Pubmed
,
Xenbase
Veldhoen,
Exposure to tetrabromobisphenol-A alters TH-associated gene expression and tadpole metamorphosis in the Pacific tree frog Pseudacris regilla.
2006,
Pubmed
Xu,
Developmental and hormonal regulation of the Xenopus liver-type arginase gene.
1993,
Pubmed
,
Xenbase
Zaya,
Exposure to atrazine affects the expression of key genes in metabolic pathways integral to energy homeostasis in Xenopus laevis tadpoles.
2011,
Pubmed
,
Xenbase
Zhang,
Evaluation of gene expression endpoints in the context of a Xenopus laevis metamorphosis-based bioassay to detect thyroid hormone disruptors.
2006,
Pubmed
,
Xenbase
Zimmermann,
An aryl hydrocarbon receptor repressor from Xenopus laevis: function, expression, and role in dioxin responsiveness during frog development.
2008,
Pubmed
,
Xenbase
