title: Methodological approaches for using synchrotron X-ray fluorescence (SXRF) imaging as a tool in ionomics: examples from Arabidopsis thaliana.
abstract: Here we present approaches for using multi-elemental imaging (specifically synchrotron X-ray fluorescence microscopy, SXRF) in ionomics, with examples using the model plant Arabidopsis thaliana. The complexity of each approach depends on the amount of a priori information available for the gene and/or phenotype being studied. Three approaches are outlined, which apply to experimental situations where a gene of interest has been identified but has an unknown phenotype (phenotyping), an unidentified gene is associated with a known phenotype (gene cloning) and finally, a screening approach, where both gene and phenotype are unknown. These approaches make use of open-access, online databases with which plant molecular genetics researchers working in the model plant Arabidopsis will be familiar, in particular the Ionomics Hub and online transcriptomic databases such as the Arabidopsis eFP browser. The approaches and examples we describe are based on the assumption that altering the expression of ion transporters can result in changes in elemental distribution. We provide methodological details on using elemental imaging to aid or accelerate gene functional characterization by narrowing down the search for candidate genes to the tissues in which elemental distributions are altered. We use synchrotron X-ray microprobes as a technique of choice, which can now be used to image all parts of an Arabidopsis plant in a hydrated state. We present elemental images of leaves, stem, root, siliques and germinating hypocotyls.
authors.affiliation: Dartmouth College, Department of Biological Sciences, Life Science Center, 78 College Street, Hanover, NH 03755.
authors.forename: Tracy
authors.initials: T
authors.lastname: Punshon
authors.affiliation: Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Porto Alegre, Brasil.
authors.forename: Felipe Klein
authors.initials: FK
authors.lastname: Ricachenevsky
authors.affiliation: Dartmouth College, Department of Biological Sciences, Life Science Center, 78 College Street, Hanover, NH 03755.
authors.forename: Maria
authors.initials: M
authors.lastname: Hindt
authors.affiliation: Dartmouth College, Department of Biological Sciences, Life Science Center, 78 College Street, Hanover, NH 03755.
authors.forename: Amanda L
authors.initials: AL
authors.lastname: Socha
authors.affiliation: Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du général Zimmer, 67084 Strasbourg Cedex, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Zuber
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D005838:Genotype; D008670:Metals / Q000378:metabolism*; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000235:genetics / Q000378:metabolism*; D013052:Spectrometry, X-Ray Emission / Q000379:methods*; D017356:Synchrotrons
chemical_list: D029681:Arabidopsis Proteins; D008670:Metals
references.citation: Plant Physiol. 2006 Aug;141(4):1544-54
references.pmid: 16766666
references.citation: Annu Rev Plant Biol. 2008;59:709-33
references.pmid: 18251712
references.citation: J Biol Chem. 2008 Mar 28;283(13):8374-83
references.pmid: 18203721
references.citation: New Phytol. 2009 Nov;184(3):581-595
references.pmid: 19761446
references.citation: Nature. 2008 May 15;453(7193):391-5
references.pmid: 18425111
references.citation: New Phytol. 2007;174(1):39-45
references.pmid: 17335495
references.citation: Trends Plant Sci. 2012 Jan;17(1):47-55
references.pmid: 22093370
references.citation: J Nutr. 2006 Apr;136(4):1064-7
references.pmid: 16549478
references.citation: Plant Cell. 2009 Oct;21(10):3326-38
references.pmid: 19861554
references.citation: Anal Bioanal Chem. 2012 Apr;402(10):3287-98
references.pmid: 22200921
references.citation: PLoS Genet. 2008 Feb 29;4(2):e1000004
references.pmid: 18454190
references.citation: Nat Protoc. 2006;1(2):824-7
references.pmid: 17406313
references.citation: Plant Cell. 2006 May;18(5):1121-33
references.pmid: 16531494
references.citation: Annu Rev Plant Biol. 2010;61:517-34
references.pmid: 20192749
references.citation: PLoS Genet. 2012 Sep;8(9):e1002923
references.pmid: 22969436
references.citation: Mol Plant. 2009 Jul;2(4):803-822
references.pmid: 19626137
references.citation: Plant Cell. 2004 May;16(5):1327-39
references.pmid: 15100400
references.citation: Plant Cell. 2009 Jul;21(7):2133-42
references.pmid: 19574435
references.citation: Environ Sci Technol. 2005 Aug 1;39(15):5531-40
references.pmid: 16124284
references.citation: Proc Nutr Soc. 2006 May;65(2):169-81
references.pmid: 16672078
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references.pmid: 11752295
references.citation: Plant Cell Environ. 2012 Feb;35(2):334-46
references.pmid: 21486307
references.citation: J Comput Chem. 2004 Oct;25(13):1605-12
references.pmid: 15264254
references.citation: PLoS One. 2011;6(6):e20626
references.pmid: 21674049
references.citation: Plant J. 2008 Nov;56(3):483-92
references.pmid: 18643981
references.citation: Plant Cell. 2011 Jan;23(1):240-57
references.pmid: 21258004
references.citation: J Am Chem Soc. 2011 Jun 8;133(22):8606-16
references.pmid: 21563821
references.citation: Nutr Clin Pract. 2010 Dec;25(6):603-12
references.pmid: 21139124
references.citation: Annu Rev Nutr. 2009;29:401-21
references.pmid: 19400753
references.citation: Plant Physiol. 2012 Jan;158(1):352-62
references.pmid: 22086421
references.citation: Plant Physiol. 2005 Apr;137(4):1228-35
references.pmid: 15824285
references.citation: Plant Physiol. 2010 Apr;152(4):1986-99
references.pmid: 20181755
references.citation: Curr Opin Plant Biol. 2011 Jun;14(3):252-9
references.pmid: 21531166
references.citation: Plant Physiol. 2006 Jul;141(3):1021-34
references.pmid: 16731580
references.citation: PLoS One. 2011;6(9):e24476
references.pmid: 21915334
references.citation: Nat Biotechnol. 2007 Aug;25(8):930-7
references.pmid: 17676037
references.citation: New Phytol. 2012 Mar;193(4):859-66
references.pmid: 22403822
references.citation: PLoS Genet. 2005 Jul;1(1):109-18
references.pmid: 16103920
references.citation: EMBO J. 2005 Dec 7;24(23):4041-51
references.pmid: 16270029
references.citation: J Exp Bot. 2000 Oct;51(351):1635-45
references.pmid: 11053452
references.citation: J Cell Biochem. 2006 Dec 15;99(6):1489-502
references.pmid: 17006954
references.citation: Science. 2006 Nov 24;314(5803):1295-8
references.pmid: 17082420
references.citation: Plant Physiol. 2000 Sep;124(1):125-33
references.pmid: 10982428
references.citation: Plant Mol Biol. 1999 May;40(1):37-44
references.pmid: 10394943
references.citation: Nature. 2011 Aug 28;477(7365):419-23
references.pmid: 21874022
references.citation: Plant Cell. 2003 May;15(5):1131-42
references.pmid: 12724539
references.citation: Plant Signal Behav. 2010 Jan;5(1):56-7
references.pmid: 20592810
references.citation: Environ Sci Technol. 2003 Jan 15;37(2):229-34
references.pmid: 12564892
references.citation: New Phytol. 2011 May;190(3):583-94
references.pmid: 21261624
references.citation: Plant Sci. 2011 Apr;180(4):562-74
references.pmid: 21421405
references.citation: Nat Rev Genet. 2003 Jan;4(1):29-38
references.pmid: 12509751
references.citation: Curr Opin Plant Biol. 2009 Jun;12(3):373-80
references.pmid: 19473871
references.citation: Trends Plant Sci. 2005 Dec;10(12):586-93
references.pmid: 16271501
references.citation: Adv Bioinformatics. 2008;2008:420747
references.pmid: 19956698
references.citation: Plant Physiol. 2007 Feb;143(2):600-11
references.pmid: 17189337