Computational protocol: Gain-of-Function Alleles in Caenorhabditis elegans Nuclear Hormone Receptor nhr-49 Are Functionally Distinct

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Protocol publication

[…] Predictions of nematode NHR-49 orthologs were from WormBase WS248 and/or a BLASTP search with NHR-49 isoform C. Full-length sequences for these NHR-49 orthologs were downloaded from UniProt (http://www.uniprot.org/). Sequence alignments were performed using ClustalW (http://www.genome.jp/tools/clustalw/). 9aaTAD motifs were detected using the online prediction tool (http://www.med.muni.cz/9aaTAD/index.php) [,]. We selected the “most stringent pattern” option to identify 9aaTAD motifs in NHR-49 isoform C. NLS prediction was performed with cNLS Mapper (http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi) []. [...] For microscopy, worms were transferred onto 2% (w/v) agarose pads, which contained NaN3. We captured images on a CoolSnap HQ camera (Photometrics) attached to a Zeiss Axioplan 2 compound microscope, and used MetaMorph Imaging Software with Autoquant 3D digital deconvolution for image acquisition. […]

Pipeline specifications

Software tools MetaMorph, AutoQuant
Application Conventional fluorescence microscopy
Organisms Caenorhabditis elegans
Diseases Hyperlipoproteinemia Type II