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Pipeline publication

[…] erase and β-galactosidase activity, as previously described (). Luciferase activity is reported as fold activation relative to the vehicle control (0.5% DMSO) and normalized for β-galactosidase activity. Each combination of receptor and ligand was run in triplicate at three doses and repeated whenever the coefficient of variance exceeded 0.15. Positive control ligands were assigned based on previously published data or empirically determined upon cloning of the novel orthologs. We also ran a negative control consisting of vector lacking an NR1I2 LBD for each ligand to ensure luciferase activity was not promoted via LBD-independent pathways., Novel sequences were checked for similarity using blastn and blastp () and submitted to GenBank (). We used ClustalX () to align deduced amino acid LBD sequences and create an identity matrix. A neighbor-joining phylogenetic tree was constructed using the PHYLIP computer program () using NR1I3 as a closely related outgroup., Comparison of NR1I2 ortholog LBD sequences () revealed a relatively high degree of similarity among mammalian orthologs compared to nonmammals. Human SXR amino acid residues that line the LBD and interact with various ligands (shaded) have been characterized by X-ray crystallography (; , ). The corresponding residues appear to be highly conserved within mammals or are typically represented by functionally similar amino acid substitutions such as nonpolar valine, leucine, and methionine, or polar serine and threonine. Notable exceptions include the substitution of serine for leucine at position 105 in rodents and leucine o […]

Pipeline specifications

Software tools BLASTN, BLASTP, Clustal W, PHYLIP
Organisms Homo sapiens