title: Feathers as a source of RNA for genomic studies in avian species.
abstract: Dioxins and dioxin-like chemicals (DLCs) cause a suite of adverse effects in terrestrial species. Most of the adverse effects occur subsequent to binding to the aryl hydrocarbon receptor. Avian species vary in their sensitivity to the effects of DLCs and current research indicates that this is mediated by variations in the amino acid sequence within the ligand binding domain (LBD) of the aryl hydrocarbon receptor 1 (AHR1). Eighty-eight avian species have been classified into three broad categories of sensitivity, based on the amino acid variations within the AHR1 LBD: sensitive type 1 (Ile324_Ser380), moderately sensitive type 2 (Ile324_Ala380), and relatively insensitive type 3 (Val324_Ala380). Risk assessment of avian species can be complicated due to the variability in sensitivity among species. A predictive tool for selecting the priority species at a given site would have broad implications for the risk assessment community. We present a method for AHR1 genotyping using plucked feathers as a source of RNA. The method is extremely robust, requires minimal sample processing and handling, and eliminates the need for blood sampling or tissue collection from the species of interest. Using this method we were able to determine the amino acid sequence of the AHR LBD of three avian species: the chicken, the herring gull, and the zebra finch, and to categorize them based on the identity of amino acids at key sites within the LBD.
authors.affiliation: Environment Canada, National Wildlife Research Centre, Carleton University, 1125 Colonel By Drive, Raven Road, Ottawa, ON, K1A 0H3, Canada, Stephanie.Jones@ec.gc.ca.
authors.forename: Stephanie P
authors.initials: SP
authors.lastname: Jones
authors.forename: Sean W
authors.initials: SW
authors.lastname: Kennedy
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001717:Birds / Q000235:genetics*; D046091:Charadriiformes; D002645:Chickens; D004147:Dioxins / Q000633:toxicity; D005241:Feathers / Q000737:chemistry*; D046369:Finches; D060005:Genotyping Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D011309:Preservation, Biological; D054730:Protein Interaction Domains and Motifs; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification; D018336:Receptors, Aryl Hydrocarbon / Q000235:genetics*
chemical_list: D004147:Dioxins; D018336:Receptors, Aryl Hydrocarbon; D012313:RNA