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Zebrafish mutants calamity and catastrophe define critical pathways of gene-nutrient interactions in developmental copper metabolism.

PLoS genetics | Nov 14, 2008

Nutrient availability is an important environmental variable during development that has significant effects on the metabolism, health, and viability of an organism. To understand these interactions for the nutrient copper, we used a chemical genetic screen for zebrafish mutants sensitive to developmental copper deficiency. In this screen, we isolated two mutants that define subtleties of copper metabolism. The first contains a viable hypomorphic allele of atp7a and results in a loss of pigmentation when exposed to mild nutritional copper deficiency. This mutant displays incompletely penetrant skeletal defects affected by developmental copper availability. The second carries an inactivating mutation in the vacuolar ATPase that causes punctate melanocytes and embryonic lethality. This mutant, catastrophe, is sensitive to copper deprivation revealing overlap between ion metabolic pathways. Together, the two mutants illustrate the utility of chemical genetic screens in zebrafish to elucidate the interaction of nutrient availability and genetic polymorphisms in cellular metabolism.

Pubmed ID: 19008952 RIS Download

Mesh terms: Adenosine Triphosphatases | Alleles | Animals | Cells, Cultured | Copper | Embryo, Nonmammalian | Humans | Melanosomes | Menkes Kinky Hair Syndrome | Mutation | Phenotype | Protein Transport | Zebrafish | Zebrafish Proteins

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SoftBerry

A software resource for genomic resource. SoftBerry focuses on computational methods of high throughput biomedical data analysis such as software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNA detection, and selection of disease specific SNP subsets.

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Ensembl

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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Sanger: Danio rerio Sequencing Project

In February 2001 the Sanger Institute started sequencing the genome of the zebrafish (Danio rerio). To obtain the genome sequence we map and sequence clones from BAC libraries. The finished clones are manually annotated and accessible in Vega. To provide additional data whilst the above project is ongoing, we also generate integrated whole genome assemblies by filling in the yet existent gaps between clone contigs with whole genome shotgun sequence. These assemblies are then automatically annotated and accessible in Ensembl.

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