Ionomics

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Ionomics is the measurement of the total elemental composition of an organism to address biological problems.[1][2] Questions within physiology, ecology, evolution, and many other fields can be investigated using ionomics, often coupled with bioinformatics and other genetic tools.[3][4][5][6][7] Observing an organism's ionome is a powerful approach to the functional analysis of its genes and the gene networks. Information about the physiological state of an organism can also be revealed indirectly through its ionome, for example iron deficiency in a plant can be identified by looking at a number of other elements, rather than iron itself.[8] A more typical example is in a blood test, where a number of conditions involving nutrition or disease may be inferred from testing this single tissue for sodium, potassium, iron, chlorine, zinc, magnesium, calcium and copper.[9]

In practice, the total elemental composition of an organism is rarely determined. The number and type of elements measured are limited by the available instrumentation, the assumed value of the element in question, and the added cost of measuring each additional element. Also, a single tissue may be measured instead of the entire organism, as in the example given above of a blood test, or in the case of plants, the sampling of just the leaves or seeds. These are simply issues of practicality.[8]

Various techniques may be fruitfully used to measure elemental composition. Among the best are Inductively-Coupled Plasma Optical Emission Spectroscopy (ICP-OES), Inductively-Coupled Plasma Mass Spectrometry (ICP-MS), X-Ray Fluorescence (XRF), synchrotron-based microXRF,[10] and Neutron activation analysis (NAA). This latter technique has been applied to perform ionomics in the study of breast cancer,[11][12] colorectal cancer[13] and brain cancer.[14] High-throughput ionomic phenotyping has created the need for data management systems to collect, organize and share the collected data with researchers worldwide.[15]

References[edit]

  1. ^ Lahner B, Gong J, Mahmoudian M, Smith EL, Abid KB, Rogers EE, Guerinot ML, Harper JF, Ward JM, McIntyre L, Schroeder JI, Salt DE (2003) Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana. Nat Biotechnol 21: 1215-1221.[1]
  2. ^ Salt DE (2004) Update on ionomics. Plant Physiology 136: 2451-2456
  3. ^ Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, Harper JF (2005). Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol 6:R77.[2]
  4. ^ Robinson AB, Pauling L (1974) Techniques of orthomolecular diagnosis. Clin Chem 20: 961-965.[3]
  5. ^ Rus A, Baxter I, Muthukumar B, Gustin J, Lahner B, Yakubova E and Salt DE (2006) Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. PLoS Genet 2(12): e210.[4]
  6. ^ Baxter I, Muthukumar B, Park HC, Buchner P, Lahner B, Danku J, Zhao K, Lee J, Hawkesford MJ, Guerinot ML, Salt DE (2008) Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana is Controlled By a Mitochondrial Molybdenum Transporter (MOT1). PLoS Genet 4(2): e1000004.[5]
  7. ^ Watanabe T, Broadley MR, Jansen S, White PJ, Takada J, Satake K, Takamatsu T, Tuah SJ, Osaki M (2007) Evolutionary control of leaf element composition in plants. New Physiol 174: 516-523.[6]
  8. ^ a b Baxter, I (2009) Ionomics: studying the social network of mineral nutrients.Curr Opin Plant Biol;12(3):381-6.[7]
  9. ^ Brody, Tom. Nutritional Biochemistry. San Diego: Academic Press, 1998.
  10. ^ Young LW, Westcott ND, Attenkofer K, Reaney MJ (2006). A high-throughput determination of metal concentrations in whole intact Arabidopsis thalianaseeds using synchrotron-based X-ray fluorescence spectroscopy. J Synchrotron Radiat 13: 304-313.[8]
  11. ^ Garg AN, Singh V, Weginwar RG, Sagdeo VN (1994). An elemental correlation study in cancerous and normal breast tissue with successive clinical stages by neutron activation analysis. Biol Trace Elem Res 46: 185-202.
  12. ^ Ng KH, Ong SH, Bradley DA, Looi LM (1997). Discriminant analysis of normal and malignant breast tissue based upon INAA investigation of elemental concentration. Appl Radiat Isot 48: 105-109.2&_cdi=5296&_user=29441&_orig=search&_coverDate=01%2F31%2F1997&_sk=999519998&view=c&wchp=dGLbVzW-zSkWz&md5=4518026bdf3dd2556b557736207f4291&ie=/sdarticle.pdf
  13. ^ Shenberg C, Feldstein H, Cornelis R, Mees L, Versieck J, Vanballenberghe L, Cafmeyer J, Maenhaut W (1995). Br, Rb, Zn, Fe, Se and K in blood of colorectal patients by INAA and PIXE. J Trace Elem Med Biol 9: 193-199.
  14. ^ Andrási E, Suhajda M, Sáray I, Bezúr L, Ernyei L, Réffy A (1993). Concentration of elements in human brain: glioblastoma multiforme. Sci Total Environ 139-140: 399-402.
  15. ^ Baxter I, Ouzzani M, Orcun S, Kennedy B, Jandhyala SS, Salt DE (2007) Purdue Ionomics Information Management System (PIIMS): An integrated functional genomics platform. Plant Physiol 143: 600-611.[9]

External links[edit]

The ionomicshub (iHUB) is a collaborative international network for ionomics [10]