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, chemometrics [3] and other genetic tools. [4] [5] [6] [7] [8] 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. [9] 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. [10]

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 [11] or seeds. These are simply issues of practicality. [9]

Various techniques may be fruitfully used to measure elemental composition. Among the best are Inductively-Coupled Plasma Optical Emission Spectroscopy (ICP-OES), [3] Inductively-Coupled Plasma Mass Spectrometry (ICP-MS), X-Ray Fluorescence (XRF), synchrotron-based microXRF, [12] and Neutron activation analysis (NAA). This latter technique has been applied to perform ionomics in the study of breast cancer, [13] [14] colorectal cancer [15] and brain cancer. [16] High-throughput ionomic phenotyping has created the need for data management systems to collect, organize and share the collected data with researchers worldwide. [17]

Related Research Articles

<i>Arabidopsis</i> Genus of flowering plants

Arabidopsis (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress, one of the model organisms used for studying plant biology and the first plant to have its entire genome sequenced. Changes in thale cress are easily observed, making it a very useful model.

<i>Arabidopsis thaliana</i> Model plant species in the family Brassicaceae

Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. A. thaliana is considered a weed; it is found along the shoulders of roads and in disturbed land.

<span class="mw-page-title-main">Root</span> Basal organ of a vascular plant

In vascular plants, the roots are the organs of a plant that are modified to provide anchorage for the plant and take in water and nutrients into the plant body, which allows plants to grow taller and faster. They are most often below the surface of the soil, but roots can also be aerial or aerating, that is, growing up above the ground or especially above water.

<span class="mw-page-title-main">Mineral (nutrient)</span> Chemical element required as an essential nutrient by organisms to perform life functions

In the context of nutrition, a mineral is a chemical element required as an essential nutrient by organisms to perform functions necessary for life. However, the four major structural elements in the human body by weight, are usually not included in lists of major nutrient minerals. These four elements compose about 96% of the weight of the human body, and major minerals (macrominerals) and minor minerals compose the remainder.

<span class="mw-page-title-main">Plant nutrition</span> Study of the chemical elements and compounds necessary for normal plant life

Plant nutrition is the study of the chemical elements and compounds necessary for plant growth and reproduction, plant metabolism and their external supply. In its absence the plant is unable to complete a normal life cycle, or that the element is part of some essential plant constituent or metabolite. This is in accordance with Justus von Liebig’s law of the minimum. The total essential plant nutrients include seventeen different elements: carbon, oxygen and hydrogen which are absorbed from the air, whereas other nutrients including nitrogen are typically obtained from the soil.

Gold fingerprinting is a method of identifying an item made of gold based on the impurities or trace elements it contains.

<span class="mw-page-title-main">Ecological stoichiometry</span>

Ecological stoichiometry considers how the balance of energy and elements influences living systems. Similar to chemical stoichiometry, ecological stoichiometry is founded on constraints of mass balance as they apply to organisms and their interactions in ecosystems. Specifically, how does the balance of energy and elements affect and how is this balance affected by organisms and their interactions. Concepts of ecological stoichiometry have a long history in ecology with early references to the constraints of mass balance made by Liebig, Lotka, and Redfield. These earlier concepts have been extended to explicitly link the elemental physiology of organisms to their food web interactions and ecosystem function.

<i>Hyaloperonospora parasitica</i> Species of plant pathogen

Hyaloperonospora parasitica is an oomycete from the family Peronosporaceae. It has been considered for a long time to cause downy mildew of a variety of species within the Brassicaceae, on which the disease can cause economically important damage by killing seedlings or affecting the quality of produce intended for freezing. Hyaloperonospora parasitica causes downy mildew on a wide range of many different plants. It belongs to the Kingdom Chromista, the phylum Oomycota, and the family Peronosporaceae. The former name for H. parasitica was Peronospora parasitica until it was reclassified and put in the genus Hyaloperonospora. It is an especially vicious disease on crops of the family Brassicaceae. It is most famous for being a model pathogen of Arabidopsis thaliana which is a model organism used for experimental purposes. Accordingly, the former Hyaloperonospora parasitica has been split into a large number of species. For instance, the taxonomically correct name of the parasite of the well-known model organism Arabidopsis thaliana is Hyaloperonospora arabidopsidis, not H. parasitica, whereas the pathogen of Brassica has to be called Hyaloperonospora brassicae.

<span class="mw-page-title-main">Adenylosuccinate synthase</span> Enzyme

In molecular biology, adenylosuccinate synthase is an enzyme that plays an important role in purine biosynthesis, by catalysing the guanosine triphosphate (GTP)-dependent conversion of inosine monophosphate (IMP) and aspartic acid to guanosine diphosphate (GDP), phosphate and N(6)-(1,2-dicarboxyethyl)-AMP. Adenylosuccinate synthetase has been characterised from various sources ranging from Escherichia coli to vertebrate tissues. In vertebrates, two isozymes are present: one involved in purine biosynthesis and the other in the purine nucleotide cycle.

mir-172 microRNA precursor family

The mir-172 microRNA is thought to target mRNAs coding for APETALA2-like transcription factors. It has been verified experimentally in the model plant, Arabidopsis thaliana. The mature sequence is excised from the 3' arm of the hairpin.

The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family of proteins commonly found in the plant kingdom. They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding for them.

<span class="mw-page-title-main">Ethylene-responsive element binding protein</span> Protein family

Ethylene-responsive element binding protein(EREBP) is a homeobox gene from Arabidopsis thaliana and other plants which encodes a transcription factor. EREBP is responsible in part for mediating the response in plants to the plant hormone ethylene.

Micro x-ray fluorescence (µXRF) is an elemental analysis technique that relies on the same principles as x-ray fluorescence (XRF). Synchrotron X-rays may be used to provide elemental imaging with biological samples. The spatial resolution diameter of micro x-ray fluorescence is many orders of magnitude smaller than that of conventional XRF. While a smaller excitation spot can be achieved by restricting x-ray beam using a pinhole aperture, this method blocks much of the x-ray flux which has an adverse effect on the sensitivity of trace elemental analysis. Two types of x-ray optics, polycapillary and doubly curved crystal focusing optics, are able to create small focal spots of just a few micrometers in diameter. By using x-ray optics, the irradiation of the focal spot is much more intense and allows for enhanced trace element analysis and better resolution of small features. Micro x-ray fluorescence using x-ray optics has been used in applications such as forensics, small feature evaluations, elemental mapping, mineralogy, electronics, multi-layered coating analysis, micro-contamination detection, film and plating thickness, biology and environment.

<span class="mw-page-title-main">Plant genetics</span> Study of genes and heredity in plants

Plant genetics is the study of genes, genetic variation, and heredity specifically in plants. It is generally considered a field of biology and botany, but intersects frequently with many other life sciences and is strongly linked with the study of information systems. Plant genetics is similar in many ways to animal genetics but differs in a few key areas.

<span class="mw-page-title-main">UVR8</span>

UV-B resistance 8 (UVR8) also known as ultraviolet-B receptor UVR8 is an UV-B – sensing protein found in plants and possibly other sources. It is responsible for sensing ultraviolet light in the range 280-315 nm and initiating the plant stress response. It is most sensitive at 285nm, near the lower limit of UVB. UVR8 was first identified as a crucial mediator of a plant's response to UV-B in Arabidopsis thaliana containing a mutation in this protein. This plant was found to have a hypersensitivity to UV-B which damages DNA. UVR8 is thought to be a unique photoreceptor as it doesn't contain a prosthetic chromophore but its light-sensing ability is intrinsic to the molecule. Tryptophan (Trp) residue 285 has been suggested to act the UV-B sensor, while other Trp residues have been also seen to be involved although in-vivo data suggests that Trp285 and Trp233 are most important.

Dennis Robert Hoagland was an American chemist and plant scientist working in the fields of plant nutrition, agricultural chemistry, and physiology. He was Professor of Plant Nutrition at the University of California at Berkeley from 1927 until his death in 1949. Hoagland is commonly known for discovering the active transport of nutrients in plants, using innovative model systems under controlled experimental conditions, such as solution culture. He and his associates formulated an artificial, complete inorganic nutrient medium, universally known as Hoagland solution, that is still widely used for culturing plants hydroponically.

Arabidopsis thaliana is a first class model organism and the single most important species for fundamental research in plant molecular genetics.

CLE peptides are a group of peptides found in plants that are involved with cell signaling. Production is controlled by the CLE genes. Upon binding to a CLE peptide receptor in another cell, a chain reaction of events occurs, which can lead to various physiological and developmental processes. This signaling pathway is conserved in diverse land plants.

The P-type plasma membrane H+
-ATPase is found in plants and fungi. For the gastric H+
/K+
 ATPase, see Hydrogen potassium ATPase.

<span class="mw-page-title-main">SEM-XRF</span> X-ray sources for SEM

SEM-XRF is an established technical term for adding a X-ray generator to a Scanning Electron Microscope (SEM). Technological progress in the fields of small-spot low-power X-ray tubes and of polycapillary X-ray optics has enabled the development of compact micro-focus X-ray sources that can be attached to a SEM equipped for energy-dispersive X-ray spectroscopy.

References

  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.
  2. ↑ Salt DE (2004) Update on ionomics. Plant Physiology 136: 2451-2456
  3. 1 2 Cotrim, GS; Silva, DM; Graça, JP; Oliveira Junior, A; Castro, C; Zocolo, GJ; Lannes, LS; Hoffmann-Campo, CB (2023). "Glycine max (L.) Merr. (Soybean) metabolome responses to potassium availability". Phytochemistry. 205: 113472. doi:10.1016/j.phytochem.2022.113472. ISSN   0031-9422. PMID   36270412. S2CID   253027906.
  4. ↑ 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.
  5. ↑ Robinson AB, Pauling L (1974) Techniques of orthomolecular diagnosis. Clin Chem 20: 961-965.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. 1 2 Baxter, I (2009) Ionomics: studying the social network of mineral nutrients.Curr Opin Plant Biol;12(3):381-6.
  10. ↑ Brody, Tom. Nutritional Biochemistry. San Diego: Academic Press, 1998.
  11. ↑ Pillon, Y., Petit, D., Gady, C., Soubrand, M., Joussein, E., & Saladin, G. (2019). Ionomics suggests niche differences between sympatric heathers (Ericaceae). Plant and soil, 434(1-2), 481-489.https://doi.org/10.1007/s11104-018-3870-8
  12. ↑ 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.[ permanent dead link ]
  13. ↑ 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.
  14. ↑ 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
  15. ↑ 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.
  16. ↑ 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.
  17. ↑ 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.

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