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Stuart MB, Davies M, Hobbs MJ, Pering TD, McGonigle AJS, Willmott JR. High-Resolution Hyperspectral Imaging Using Low-Cost Components: Application within Environmental Monitoring Scenarios. SENSORS 2022; 22:s22124652. [PMID: 35746433 PMCID: PMC9227882 DOI: 10.3390/s22124652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 01/04/2023]
Abstract
High-resolution hyperspectral imaging is becoming indispensable, enabling the precise detection of spectral variations across complex, spatially intricate targets. However, despite these significant benefits, currently available high-resolution set-ups are typically prohibitively expensive, significantly limiting their user base and accessibility. These limitations can have wider implications, limiting data collection opportunities, and therefore our knowledge, across a wide range of environments. In this article we introduce a low-cost alternative to the currently available instrumentation. This instrument provides hyperspectral datasets capable of resolving spectral variations in mm-scale targets, that cannot typically be resolved with many existing low-cost hyperspectral imaging alternatives. Instrument metrology is provided, and its efficacy is demonstrated within a mineralogy-based environmental monitoring application highlighting it as a valuable addition to the field of low-cost hyperspectral imaging.
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Affiliation(s)
- Mary B. Stuart
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 4DE, UK; (M.B.S.); (M.D.); (M.J.H.)
| | - Matthew Davies
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 4DE, UK; (M.B.S.); (M.D.); (M.J.H.)
| | - Matthew J. Hobbs
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 4DE, UK; (M.B.S.); (M.D.); (M.J.H.)
| | - Tom D. Pering
- Department of Geography, University of Sheffield, Sheffield S10 2TN, UK; (T.D.P.); (A.J.S.M.)
| | - Andrew J. S. McGonigle
- Department of Geography, University of Sheffield, Sheffield S10 2TN, UK; (T.D.P.); (A.J.S.M.)
| | - Jon R. Willmott
- Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield S1 4DE, UK; (M.B.S.); (M.D.); (M.J.H.)
- Correspondence:
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2
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Cohen SX, Webb SM, Gueriau P, Curis E, Bertrand L. Robust framework and software implementation for fast speciation mapping. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1049-1058. [PMID: 33566015 DOI: 10.1107/s1600577520005822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/27/2020] [Indexed: 06/12/2023]
Abstract
One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. Several authors have used different multivariate data processing strategies to establish speciation maps. In this manuscript, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. The algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.
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Affiliation(s)
- Serge X Cohen
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, IPANEMA, F-91192 Saint-Aubin, France
| | - Samuel M Webb
- Stanford Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Pierre Gueriau
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, IPANEMA, F-91192 Saint-Aubin, France
| | - Emmanuel Curis
- Laboratoire de Biomathématiques, EA 7537 - BioSTM, Faculté de Pharmacie de Paris - Université Paris Descartes, 4 Avenue de l'Observatoire, F-75006 Paris, France
| | - Loïc Bertrand
- Université Paris-Saclay, CNRS, Ministère de la Culture, UVSQ, IPANEMA, F-91192 Saint-Aubin, France
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3
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Hu H, Zhao J, Wang L, Shang L, Cui L, Gao Y, Li B, Li YF. Synchrotron-based techniques for studying the environmental health effects of heavy metals: Current status and future perspectives. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115721] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Ching DJ, Hidayetoğlu M, Biçer T, Gürsoy D. Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes. APPLIED OPTICS 2018; 57:8780-8789. [PMID: 30461860 DOI: 10.1364/ao.57.008780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/15/2018] [Indexed: 06/09/2023]
Abstract
We investigate the effects of angular diversity on image-reconstruction quality of scanning-probe x-ray tomography for both fly- and step-mode data collection. We propose probe-coverage maps as a tool for both visualizing and quantifying the distribution of probe interactions with the object. We show that data sampling with more angular diversity yields better tomographic image reconstruction as long as it does not come at the cost of not covering some voxels in the object. Therefore, for fly-mode data collection, rotation-as-fast-axis (RAFA) trajectories are superior to raster or other non-RAFA trajectories because they allow for the increasing of angular diversity without sacrificing spatial coverage uniformity. In contrast, for step-mode data collection and a fixed measurement budget, increasing angular diversity can come at the cost of not covering some voxels, and may not be desired. This study has implications for how scanning-probe microscopes should be collecting data in order to make the most of limited resources.
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5
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Localized zinc distribution in shark vertebrae suggests differential deposition during ontogeny and across vertebral structures. PLoS One 2018; 13:e0190927. [PMID: 29324879 PMCID: PMC5764331 DOI: 10.1371/journal.pone.0190927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/24/2017] [Indexed: 01/09/2023] Open
Abstract
The development of shark vertebrae and the possible drivers of inter- and intra-specific differences in vertebral structure are poorly understood. Shark vertebrae are used to examine life-history traits related to trophic ecology, movement patterns, and the management of fisheries; a better understanding of their development would be beneficial to many fields of research that rely on these calcified structures. This study used Scanning X-ray Fluorescence Microscopy to observe zinc distribution within vertebrae of ten shark species from five different orders. Zinc was mostly localised within the intermedialis and was generally detected at levels an order of magnitude lower in the corpus calcareum. In most species, zinc concentrations were higher pre-birth mark, indicating a high rate of pre-natal zinc deposition. These results suggest there are inter-specific differences in elemental deposition within vertebrae. Since the deposition of zinc is physiologically-driven, these differences suggest that the processes of growth and deposition are potentially different in the intermedialis and corpus calcareum, and that caution should be taken when extrapolating information such as annual growth bands from one structure to the other. Together these results suggest that the high inter-specific variation in vertebral zinc deposition and associated physiologies may explain the varying effectiveness of ageing methodologies applied to elasmobranch vertebrae.
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6
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Dressler VL, Müller EI, Pozebon D. Bioimaging Metallomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1055:139-181. [DOI: 10.1007/978-3-319-90143-5_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Hare DJ, Jones MWM, Wimmer VC, Jenkins NL, de Jonge MD, Bush AI, McColl G. High-resolution complementary chemical imaging of bio-elements in Caenorhabditis elegans. Metallomics 2016; 8:156-60. [PMID: 26567696 DOI: 10.1039/c5mt00288e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Here, we present a sub-μm multimodal approach to image essential elements in Caenorhabditis elegans. A combination of chemical imaging technologies reveals total metal concentration, chemical state and the protein to which an element is associated. This application of distinct yet complementary chemical imaging techniques provided unique insight into essential and trace elements at the subcellular level.
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Affiliation(s)
- Dominic J Hare
- Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, New South Wales 2007, Australia and The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Michael W M Jones
- Australian Synchrotron, Clayton, Victoria 3168, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, 3086, Australia
| | - Verena C Wimmer
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nicole L Jenkins
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | | | - Ashley I Bush
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Gawain McColl
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia.
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Schaumlöffel D, Hutchinson R, Malherbe J, Coustumer PL, Gontier E, Isaure MP. Novel Methods for Bioimaging Including LA-ICP-MS, NanoSIMS, TEM/X-EDS, and SXRF. Metallomics 2016. [DOI: 10.1002/9783527694907.ch4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Dirk Schaumlöffel
- Université de Pau et des Pays de l'Adour, CNRS; Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM); UMR 5254 64000 Pau France
| | - Robert Hutchinson
- Electro Scientific Industries; 8 Avro Court, Ermine Business Park Huntingdon, Cambridge PE29 6XS UK
| | - Julien Malherbe
- Université de Pau et des Pays de l'Adour, CNRS; Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM); UMR 5254 64000 Pau France
| | - Philippe Le Coustumer
- Université de Bordeaux, UF Sciences de la Terre et Environnement; Allée G. Saint-Hillaire 33615 Pessac France
| | - Etienne Gontier
- Université de Bordeaux, Bordeaux Imaging Center; UMS 3420 CNRS - US4 INSERM, Pôle d'imagerie électronique; 146 rue Léo Saignat 33076 Bordeaux France
| | - Marie-Pierre Isaure
- Université de Pau et des Pays de l'Adour, CNRS; Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM); UMR 5254 64000 Pau France
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9
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Jin Q, Paunesku T, Lai B, Gleber SC, Chen SI, Finney L, Vine D, Vogt S, Woloschak G, Jacobsen C. Preserving elemental content in adherent mammalian cells for analysis by synchrotron-based x-ray fluorescence microscopy. J Microsc 2016; 265:81-93. [PMID: 27580164 PMCID: PMC5217071 DOI: 10.1111/jmi.12466] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/11/2016] [Accepted: 08/02/2016] [Indexed: 01/20/2023]
Abstract
Trace metals play important roles in biological function, and x-ray fluorescence microscopy (XFM) provides a way to quantitatively image their distribution within cells. The faithfulness of these measurements is dependent on proper sample preparation. Using mouse embryonic fibroblast NIH/3T3 cells as an example, we compare various approaches to the preparation of adherent mammalian cells for XFM imaging under ambient temperature. Direct side-by-side comparison shows that plunge-freezing-based cryoimmobilization provides more faithful preservation than conventional chemical fixation for most biologically important elements including P, S, Cl, K, Fe, Cu, Zn and possibly Ca in adherent mammalian cells. Although cells rinsed with fresh media had a great deal of extracellular background signal for Cl and Ca, this approach maintained cells at the best possible physiological status before rapid freezing and it does not interfere with XFM analysis of other elements. If chemical fixation has to be chosen, the combination of 3% paraformaldehyde and 1.5 % glutaraldehyde preserves S, Fe, Cu and Zn better than either fixative alone. When chemically fixed cells were subjected to a variety of dehydration processes, air drying was proved to be more suitable than other drying methods such as graded ethanol dehydration and freeze drying. This first detailed comparison for x-ray fluorescence microscopy shows how detailed quantitative conclusions can be affected by the choice of cell preparation method.
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Affiliation(s)
- Qiaoling Jin
- Department of Physics & Astronomy, Weinberg College of Arts and Sciences, Evanston, Illinois, U.S.A
| | - Tatjana Paunesku
- Department of Radiation Oncology, Northwestern University, Chicago, Illinois, U.S.A
| | - Barry Lai
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, U.S.A
| | | | - S I Chen
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, U.S.A
| | - Lydia Finney
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, U.S.A
| | - David Vine
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, U.S.A
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, U.S.A
| | - Gayle Woloschak
- Department of Radiation Oncology, Northwestern University, Chicago, Illinois, U.S.A
| | - Chris Jacobsen
- Department of Physics & Astronomy, Weinberg College of Arts and Sciences, Evanston, Illinois, U.S.A.,Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, U.S.A
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10
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De Brier N, Gomand SV, Donner E, Paterson D, Smolders E, Delcour JA, Lombi E. Element distribution and iron speciation in mature wheat grains (Triticum aestivum L.) using synchrotron X-ray fluorescence microscopy mapping and X-ray absorption near-edge structure (XANES) imaging. PLANT, CELL & ENVIRONMENT 2016; 39:1835-47. [PMID: 27038325 DOI: 10.1111/pce.12749] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 03/17/2016] [Accepted: 03/24/2016] [Indexed: 05/15/2023]
Abstract
Several studies have suggested that the majority of iron (Fe) and zinc (Zn) in wheat grains are associated with phytate, but a nuanced approach to unravel important tissue-level variation in element speciation within the grain is lacking. Here, we present spatially resolved Fe-speciation data obtained directly from different grain tissues using the newly developed synchrotron-based technique of X-ray absorption near-edge spectroscopy imaging, coupling this with high-definition μ-X-ray fluorescence microscopy to map the co-localization of essential elements. In the aleurone, phosphorus (P) is co-localized with Fe and Zn, and X-ray absorption near-edge structure imaging confirmed that Fe is chelated by phytate in this tissue layer. In the crease tissues, Zn is also positively related to P distribution, albeit less so than in the aleurone. Speciation analysis suggests that Fe is bound to nicotianamine rather than phytate in the nucellar projection, and that more complex Fe structures may also be present. In the embryo, high Zn concentrations are present in the root and shoot primordium, co-occurring with sulfur and presumably bound to thiol groups. Overall, Fe is mainly concentrated in the scutellum and co-localized with P. This high resolution imaging and speciation analysis reveals the complexity of the physiological processes responsible for element accumulation and bioaccessibility.
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Affiliation(s)
- Niels De Brier
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, B-3001, Belgium
| | - Sara V Gomand
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, B-3001, Belgium
| | - Erica Donner
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, South Australia, 5095, Australia
| | - David Paterson
- Australian Synchrotron, Clayton, Victoria, 3168, Australia
| | - Erik Smolders
- Division of Soil and Water Management, KU Leuven, Leuven, B-3001, Belgium
| | - Jan A Delcour
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, B-3001, Belgium
| | - Enzo Lombi
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, South Australia, 5095, Australia
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11
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Raoult V, Peddemors VM, Zahra D, Howell N, Howard DL, de Jonge MD, Williamson JE. Strontium mineralization of shark vertebrae. Sci Rep 2016; 6:29698. [PMID: 27424768 PMCID: PMC4947923 DOI: 10.1038/srep29698] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 06/22/2016] [Indexed: 12/02/2022] Open
Abstract
Determining the age of sharks using vertebral banding is a vital component of management, but the causes of banding are not fully understood. Traditional shark ageing is based on fish otolith ageing methods where growth bands are assumed to result from varied seasonal calcification rates. Here we investigate these assumptions by mapping elemental distribution within the growth bands of vertebrae from six species of sharks representing four different taxonomic orders using scanning x-ray fluorescence microscopy. Traditional visual growth bands, determined with light microscopy, were more closely correlated to strontium than calcium in all species tested. Elemental distributions suggest that vertebral strontium bands may be related to environmental variations in salinity. These results highlight the requirement for a better understanding of shark movements, and their influence on vertebral development, if confidence in age estimates is to be improved. Analysis of shark vertebrae using similar strontium-focused elemental techniques, once validated for a given species, may allow more successful estimations of age on individuals with few or no visible vertebral bands.
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Affiliation(s)
- Vincent Raoult
- Department of Biological Sciences, Macquarie University, Sydney NSW 2109, Australia
| | - Victor M Peddemors
- Fisheries NSW, Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman NSW 2088, Australia
| | - David Zahra
- ANSTO Life Sciences, Lucas Heights, NSW 2234, Australia
| | | | - Daryl L Howard
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Martin D de Jonge
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Jane E Williamson
- Department of Biological Sciences, Macquarie University, Sydney NSW 2109, Australia
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12
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Deng J, Vine DJ, Chen S, Nashed YSG, Jin Q, Peterka T, Vogt S, Jacobsen C. Advances and challenges in cryo ptychography at the Advanced Photon Source. AIP CONFERENCE PROCEEDINGS 2016; 1696:020030. [PMID: 27293302 PMCID: PMC4898057 DOI: 10.1063/1.4937524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ptychography has emerged as a nondestructive tool to quantitatively study extended samples at a high spatial resolution. In this manuscript, we report on recent developments from our team. We have combined cryo ptychography and fluorescence microscopy to provide simultaneous views of ultrastructure and elemental composition, we have developed multi-GPU parallel computation to speed up ptychographic reconstructions, and we have implemented fly-scan ptychography to allow for faster data acquisition. We conclude with a discussion of future challenges in high-resolution 3D ptychography.
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Affiliation(s)
- J Deng
- Applied Physics, Northwestern University, Evanston IL 60208, USA
| | - D J Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - S Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Y S G Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Q Jin
- Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - T Peterka
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - S Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - C Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Physics & Astronomy and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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13
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Hong YP, Chen S, Jacobsen C. A New Workflow for x-ray fluorescence tomography: MAPSToTomoPy. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9592. [PMID: 27103755 DOI: 10.1117/12.2194162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray fluorescence tomography involves the acquisition of a series of 2D x-ray fluorescence datasets between which a specimen is rotated. At the Advanced Photon Source at Argonne National Laboratory, the workflow at beamlines 2-ID-E and 21-ID-D (the Bionanoprobe, a cryogenic microscope system) has included the use of the program MAPS for obtaining elemental concentrations from 2D images, and the program TomoPy which was developed to include several tomographic reconstruction methods for x-ray transmission data. In the past, fluorescence projection images from an individual chemical element were hand-assembled into a 3D dataset for reconstruction using interactive tools such as ImageJ. We describe here the program MAPSToTomoPy, which provides a graphical user interface (GUI) to control a workflow between MAPS and TomoPy, with tools for visualizing the sinograms of projection image sequences from particular elements and to use these to help correct misalignments of the rotation axis. The program also provides an integrated output of the 3D distribution of the detected elements for subsequent 3D visualization packages.
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Affiliation(s)
- Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Argonne IL 60439-4837 USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Argonne IL 60439-4837 USA; Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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14
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Deng J, Vine DJ, Chen S, Nashed YSG, Peterka T, Ross R, Vogt S, Jacobsen C. Opportunities and limitations for combined fly-scan ptychography and fluorescence microscopy. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9592. [PMID: 27041790 DOI: 10.1117/12.2190749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray fluorescence offers unparalleled sensitivity for imaging the nanoscale distribution of trace elements in micrometer thick samples, while x-ray ptychography offers an approach to image light element containing structures at a resolution beyond that of the x-ray lens used. These methods can be used in combination, and in continuous scan mode for rapid data acquisition when using multiple probe mode reconstruction methods. We discuss here the opportunities and limitations of making use of additional information provided by ptychography to improve x-ray fluorescence images in two ways: by using position-error-correction algorithms to correct for scan distortions in fluorescence scans, and by considering the signal-to-noise limits on previously-demonstrated ptychographic probe deconvolution methods. This highlights the advantages of using a combined approach.
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Affiliation(s)
- Junjing Deng
- Applied Physics, Northwestern University, Evanston, IL 60208, USA
| | - David J Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Youssef S G Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Tom Peterka
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Rob Ross
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Chris Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA; Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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15
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Gürsoy D, Biçer T, Lanzirotti A, Newville MG, De Carlo F. Hyperspectral image reconstruction for x-ray fluorescence tomography. OPTICS EXPRESS 2015; 23:9014-23. [PMID: 25968737 DOI: 10.1364/oe.23.009014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A penalized maximum-likelihood estimation is proposed to perform hyperspectral (spatio-spectral) image reconstruction for X-ray fluorescence tomography. The approach minimizes a Poisson-based negative log-likelihood of the observed photon counts, and uses a penalty term that has the effect of encouraging local continuity of model parameter estimates in both spatial and spectral dimensions simultaneously. The performance of the reconstruction method is demonstrated with experimental data acquired from a seed of arabidopsis thaliana collected at the 13-ID-E microprobe beamline at the Advanced Photon Source. The resulting element distribution estimates with the proposed approach show significantly better reconstruction quality than the conventional analytical inversion approaches, and allows for a high data compression factor which can reduce data acquisition times remarkably. In particular, this technique provides the capability to tomographically reconstruct full energy dispersive spectra without compromising reconstruction artifacts that impact the interpretation of results.
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16
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Deng J, Nashed YSG, Chen S, Phillips NW, Peterka T, Ross R, Vogt S, Jacobsen C, Vine DJ. Continuous motion scan ptychography: characterization for increased speed in coherent x-ray imaging. OPTICS EXPRESS 2015; 23:5438-51. [PMID: 25836777 PMCID: PMC4394751 DOI: 10.1364/oe.23.005438] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/07/2015] [Accepted: 01/12/2015] [Indexed: 05/18/2023]
Abstract
Ptychography is a coherent diffraction imaging (CDI) method for extended objects in which diffraction patterns are acquired sequentially from overlapping coherent illumination spots. The object's complex transmission function can be reconstructed from those diffraction patterns at a spatial resolution limited only by the scattering strength of the object and the detector geometry. Most experiments to date have positioned the illumination spots on the sample using a move-settle-measure sequence in which the move and settle steps can take longer to complete than the measure step. We describe here the use of a continuous "fly-scan" mode for ptychographic data collection in which the sample is moved continuously, so that the experiment resembles one of integrating the diffraction patterns from multiple probe positions. This allows one to use multiple probe mode reconstruction methods to obtain an image of the object and also of the illumination function. We show in simulations, and in x-ray imaging experiments, some of the characteristics of fly-scan ptychography, including a factor of 25 reduction in the data acquisition time. This approach will become increasingly important as brighter x-ray sources are developed, such as diffraction limited storage rings.
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Affiliation(s)
- Junjing Deng
- Applied Physics Program, Northwestern University, Evanston, IL 60208,
USA
| | - Youssef S. G. Nashed
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Nicholas W. Phillips
- Australian Research Council, Centre of Excellence for Advanced Molecular Imaging, La Trobe University, VIC 3086,
Australia
- CSIRO Manufacturing Flagship, Parkville, Victoria 3052,
Australia
| | - Tom Peterka
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Rob Ross
- Mathematics and Computing Science Division, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
| | - Chris Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
- Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208,
USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208,
USA
| | - David J. Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439,
USA
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Dimmock MR, de Jonge MD, Howard DL, James SA, Kirkham R, Paganin DM, Paterson DJ, Ruben G, Ryan CG, Brown JMC. Validation of a Geant4 model of the X-ray fluorescence microprobe at the Australian Synchrotron. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:354-365. [PMID: 25723937 DOI: 10.1107/s1600577515000223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
A Geant4 Monte Carlo simulation of the X-ray fluorescence microprobe (XFM) end-station at the Australian Synchrotron has been developed. The simulation is required for optimization of the scan configuration and reconstruction algorithms. As part of the simulation process, a Gaussian beam model was developed. Experimental validation of this simulation has tested the efficacy for use of the low-energy physics models in Geant4 for this synchrotron-based technique. The observed spectral distributions calculated in the 384 pixel Maia detector, positioned in the standard back-scatter configuration, were compared with those obtained from experiments performed at three incident X-ray beam energies: 18.5, 11.0 and 6.8 keV. The reduced χ-squared (\chi^{2}_{\rm{red}}) was calculated for the scatter and fluorescence regions of the spectra and demonstrates that the simulations successfully reproduce the scatter distributions. Discrepancies were shown to occur in the multiple-scatter tail of the Compton continuum. The model was shown to be particularly sensitive to the impurities present in the beryllium window of the Maia detector and their concentrations were optimized to improve the \chi^{2}_{\rm{red}} parametrization in the low-energy fluorescence regions of the spectra.
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Affiliation(s)
- Matthew Richard Dimmock
- Department of Medical Imaging and Radiation Sciences, Monash University, Clayton, VIC 3800, Australia
| | | | - Daryl Lloyd Howard
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | | | | | | | | | - Gary Ruben
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
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18
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Hare DJ, New EJ, de Jonge MD, McColl G. Imaging metals in biology: balancing sensitivity, selectivity and spatial resolution. Chem Soc Rev 2015; 44:5941-58. [DOI: 10.1039/c5cs00055f] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A Tutorial Review to aid in designing the most comprehensive metal imaging experiments for biological samples.
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Affiliation(s)
- Dominic J. Hare
- Elemental Bio-imaging Facility
- University of Technology Sydney
- Broadway
- Australia
- The Florey Institute of Neuroscience and Mental Health
| | | | | | - Gawain McColl
- The Florey Institute of Neuroscience and Mental Health
- The University of Melbourne
- Parkville
- Australia
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19
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Shi WQ, Yuan LY, Wang CZ, Wang L, Mei L, Xiao CL, Zhang L, Li ZJ, Zhao YL, Chai ZF. Exploring actinide materials through synchrotron radiation techniques. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7807-7848. [PMID: 25169914 DOI: 10.1002/adma.201304323] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 04/24/2014] [Indexed: 06/03/2023]
Abstract
Synchrotron radiation (SR) based techniques have been utilized with increasing frequency in the past decade to explore the brilliant and challenging sciences of actinide-based materials. This trend is partially driven by the basic needs for multi-scale actinide speciation and bonding information and also the realistic needs for nuclear energy research. In this review, recent research progresses on actinide related materials by means of various SR techniques were selectively highlighted and summarized, with the emphasis on X-ray absorption spectroscopy, X-ray diffraction and scattering spectroscopy, which are powerful tools to characterize actinide materials. In addition, advanced SR techniques for exploring future advanced nuclear fuel cycles dealing with actinides are illustrated as well.
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Affiliation(s)
- Wei-Qun Shi
- Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Institute of High Enegy Physics, Chinese Academy of Sciences, Beijing, 100049, China
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20
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Gleber SC, Wojcik M, Liu J, Roehrig C, Cummings M, Vila-Comamala J, Li K, Lai B, Shu D, Vogt S. Fresnel zone plate stacking in the intermediate field for high efficiency focusing in the hard X-ray regime. OPTICS EXPRESS 2014; 22:28142-28153. [PMID: 25402054 DOI: 10.1364/oe.22.028142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Focusing efficiency of Fresnel zone plates (FZPs) for X-rays depends on zone height, while the achievable spatial resolution depends on the width of the finest zones. FZPs with optimal efficiency and sub-100-nm spatial resolution require high aspect ratio structures which are difficult to fabricate with current technology especially for the hard X-ray regime. A possible solution is to stack several zone plates. To increase the number of FZPs within one stack, we first demonstrate intermediate-field stacking and apply this method by stacks of up to five FZPs with adjusted diameters. Approaching the respective optimum zone height, we maximized efficiencies for high resolution focusing at three different energies, 10, 11.8, and 25 keV.
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21
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Calcium micro-depositions in jugular truncular venous malformations revealed by Synchrotron-based XRF imaging. Sci Rep 2014; 4:6540. [PMID: 25286775 PMCID: PMC4187013 DOI: 10.1038/srep06540] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/09/2014] [Indexed: 12/25/2022] Open
Abstract
It has been recently demonstrated that the internal jugular vein may exhibit abnormalities classified as truncular venous malformations (TVMs). The investigation of possible morphological and biochemical anomalies at jugular tissue level could help to better understand the link between brain venous drainage and neurodegenerative disorders, recently found associated with jugular TVMs. To this end we performed sequential X-ray Fluorescence (XRF) analyses on jugular tissue samples from two TVM patients and two control subjects, using complementary energies at three different synchrotrons. This investigation, coupled with conventional histological analyses, revealed anomalous micro-formations in the pathological tissues and allowed the determination of their elemental composition. Rapid XRF analyses on large tissue areas at 12.74 keV showed an increased Ca presence in the pathological samples, mainly localized in tunica adventitia microvessels. Investigations at lower energy demonstrated that the high Ca level corresponded to micro-calcifications, also containing P and Mg. We suggest that advanced synchrotron XRF micro-spectroscopy is an important analytical tool in revealing biochemical changes, which cannot be accessed by conventional investigations. Further research on a larger number of samples is needed to understand the pathogenic significance of Ca micro-depositions detected on the intramural vessels of vein walls affected by TVMs.
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22
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de Jonge MD, Ryan CG, Jacobsen CJ. X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1031-47. [PMID: 25177992 PMCID: PMC4151681 DOI: 10.1107/s160057751401621x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/11/2014] [Indexed: 05/22/2023]
Abstract
X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer.
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Affiliation(s)
- Martin D. de Jonge
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Christopher G. Ryan
- CSIRO Earth Science and Research Engineering, Clayton, Victoria 3168, Australia
| | - Chris J. Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Department of Physics, Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
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23
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Hirose A, Kobayashi NI, Tanoi K, Nakanishi TM. A microautoradiographic method for fresh-frozen sections to reveal the distribution of radionuclides at the cellular level in plants. PLANT & CELL PHYSIOLOGY 2014; 55:1194-1202. [PMID: 24747953 DOI: 10.1093/pcp/pcu056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microautoradiography (MAR) is a conventional imaging method based on the daguerreotype. The technique is used to visualize the distribution of radionuclide-labeled compounds within a tissue section. However, application of the classical MAR method to plant tissue sections is associated with several difficulties. In this study, we report an MAR method applicable to fresh-frozen plant sections. Our method had two features: (i) the sample was kept frozen from plant tissue collection to radioisotope detection, making it possible to fix solutes without solvent exchange; and (ii) 1.2 µm thick polyphenylene sulfide film was inserted between the fresh-frozen plant section and the photosensitive nuclear emulsion to separate the section from the emulsion before autoradiography was conducted, which significantly improved the quality of the section until microscopic detection, the quality of the MAR image and the success rate. Then, the passage of cadmium (Cd) through vegetative rice stem tissue after 24 h of (109)Cd absorption was described for the first time using the MAR method. MAR clearly revealed the distribution of (109)Cd at the tissue level with high resolution. The (109)Cd concentration in phloem cells was found to be particularly high, whereas the xylem cells contained only small amounts of (109)Cd. The MAR method was also applicable for detecting (109)Cd and [(33)P]phosphate in roots. The MAR method developed here is expected to provide distribution images for a variety of compounds and ions in plant tissue.
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Affiliation(s)
- Atsushi Hirose
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Natsuko I Kobayashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Tomoko M Nakanishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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24
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Ryan CG, Siddons DP, Kirkham R, Li ZY, de Jonge MD, Paterson DJ, Kuczewski A, Howard DL, Dunn PA, Falkenberg G, Boesenberg U, De Geronimo G, Fisher LA, Halfpenny A, Lintern MJ, Lombi E, Dyl KA, Jensen M, Moorhead GF, Cleverley JS, Hough RM, Godel B, Barnes SJ, James SA, Spiers KM, Alfeld M, Wellenreuther G, Vukmanovic Z, Borg S. Maia X-ray fluorescence imaging: Capturing detail in complex natural samples. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/499/1/012002] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Siddons DP, Kirkham R, Ryan CG, De Geronimo G, Dragone A, Kuczewski AJ, Li ZY, Carini GA, Pinelli D, Beuttenmuller R, Elliott D, Pfeffer M, Tyson TA, Moorhead GF, Dunn PA. Maia X-ray Microprobe Detector Array System. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/499/1/012001] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Gräfe M, Donner E, Collins RN, Lombi E. Speciation of metal(loid)s in environmental samples by X-ray absorption spectroscopy: a critical review. Anal Chim Acta 2014; 822:1-22. [PMID: 24725743 DOI: 10.1016/j.aca.2014.02.044] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 02/12/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
Element specificity is one of the key factors underlying the widespread use and acceptance of X-ray absorption spectroscopy (XAS) as a research tool in the environmental and geo-sciences. Independent of physical state (solid, liquid, gas), XAS analyses of metal(loid)s in complex environmental matrices over the past two decades have provided important information about speciation at environmentally relevant interfaces (e.g. solid-liquid) as well as in different media: plant tissues, rhizosphere, soils, sediments, ores, mineral process tailings, etc. Limited sample preparation requirements, the concomitant ability to preserve original physical and chemical states, and independence from crystallinity add to the advantages of using XAS in environmental investigations. Interpretations of XAS data are founded on sound physical and statistical models that can be applied to spectra of reference materials and mixed phases, respectively. For spectra collected directly from environmental matrices, abstract factor analysis and linear combination fitting provide the means to ascertain chemical, bonding, and crystalline states, and to extract quantitative information about their distribution within the data set. Through advances in optics, detectors, and data processing, X-ray fluorescence microprobes capable of focusing X-rays to micro- and nano-meter size have become competitive research venues for resolving the complexity of environmental samples at their inherent scale. The application of μ-XANES imaging, a new combinatorial approach of X-ray fluorescence spectrometry and XANES spectroscopy at the micron scale, is one of the latest technological advances allowing for lateral resolution of chemical states over wide areas due to vastly improved data processing and detector technology.
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Affiliation(s)
- Markus Gräfe
- Division of Process Science and Engineering, Commonwealth Scientific Industrial Research Organisation, Australian Minerals Research Centre, 7 Conlon Street, Waterford, WA 6152, Australia.
| | - Erica Donner
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes, SA 5095, Australia; CRC-CARE, P.O. Box 486, Salisbury, SA 5106, Australia
| | - Richard N Collins
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Enzo Lombi
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes, SA 5095, Australia
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27
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Zhao FJ, Moore KL, Lombi E, Zhu YG. Imaging element distribution and speciation in plant cells. TRENDS IN PLANT SCIENCE 2014; 19:183-92. [PMID: 24394523 DOI: 10.1016/j.tplants.2013.12.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 05/08/2023]
Abstract
To maintain cellular homeostasis, concentrations, chemical speciation, and localization of mineral nutrients and toxic trace elements need to be regulated. Imaging the cellular and subcellular localization of elements and measuring their in situ chemical speciation are challenging tasks that can be undertaken using synchrotron-based techniques, such as X-ray fluorescence and X-ray absorption spectrometry, and mass spectrometry-based techniques, such as secondary ion mass spectrometry and laser-ablation inductively coupled plasma mass spectrometry. We review the advantages and limitations of these techniques, and discuss examples of their applications, which have revealed highly heterogeneous distribution patterns of elements in different cell types, often varying in chemical speciation. Combining these techniques with molecular genetic approaches can unravel functions of genes involved in element homeostasis.
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Affiliation(s)
- Fang-Jie Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - Katie L Moore
- Department of Materials, University of Oxford, Oxford OX1 3PH, UK
| | - Enzo Lombi
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, Mawson Lakes, South Australia SA-5095, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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28
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Hong YP, Gleber SC, O’Halloran TV, Que EL, Bleher R, Vogt S, Woodruff TK, Jacobsen C. Alignment of low-dose X-ray fluorescence tomography images using differential phase contrast. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:229-34. [PMID: 24365941 PMCID: PMC3874022 DOI: 10.1107/s1600577513029512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/25/2013] [Indexed: 05/09/2023]
Abstract
X-ray fluorescence nanotomography provides unprecedented sensitivity for studies of trace metal distributions in whole biological cells. Dose fractionation, in which one acquires very low dose individual projections and then obtains high statistics reconstructions as signal from a voxel is brought together (Hegerl & Hoppe, 1976), requires accurate alignment of these individual projections so as to correct for rotation stage runout. It is shown here that differential phase contrast at 10.2 keV beam energy offers the potential for accurate cross-correlation alignment of successive projections, by demonstrating that successive low dose, 3 ms per pixel, images acquired at the same specimen position and rotation angle have a narrower and smoother cross-correlation function (1.5 pixels FWHM at 300 nm pixel size) than that obtained from zinc fluorescence images (25 pixels FWHM). The differential phase contrast alignment resolution is thus well below the 700 nm × 500 nm beam spot size used in this demonstration, so that dose fractionation should be possible for reduced-dose, more rapidly acquired, fluorescence nanotomography experiments.
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Affiliation(s)
- Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Correspondence e-mail:
| | - Sophie-Charlotte Gleber
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Thomas V. O’Halloran
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Emily L. Que
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Reiner Bleher
- Department of Materials Science and Engineering, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Teresa K. Woodruff
- Department of Obstetrics and Gynecology, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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29
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Wang P, Menzies NW, Lombi E, McKenna BA, de Jonge MD, Donner E, Blamey FPC, Ryan CG, Paterson DJ, Howard DL, James SA, Kopittke PM. Quantitative determination of metal and metalloid spatial distribution in hydrated and fresh roots of cowpea using synchrotron-based X-ray fluorescence microscopy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 463-464:131-139. [PMID: 23792255 DOI: 10.1016/j.scitotenv.2013.05.091] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
Many metals and metalloids, jointly termed metal(loid)s, are toxic to plants even at low levels. This has limited the study of their uptake, distribution, and modes of action in plant roots grown at physiologically relevant concentrations. Synchrotron-based X-ray fluorescence microscopy was used to examine metal(loid)s in hydrated cowpea (Vigna unguiculata L.) roots exposed to Zn(II), Ni(II), Mn(II), Cu(II), Hg(II), Se(IV), Se(VI), As(III), or As(V). Development of a mathematical model enabled in situ quantitative determination of their distribution in root tissues. The binding strength of metals influenced the extent of their movement through the root cylinder, which influenced the toxic effects exerted-metals (e.g. Cu, Hg) that bind more strongly to hard ligands had high concentrations in the rhizodermis and caused this tissue to rupture, while other metals (e.g. Ni, Zn) moved further into the root cylinder and did not cause ruptures. When longitudinal distributions were examined, the highest Se concentration in roots exposed to Se(VI) was in the more proximal root tissues, suggesting that Se(VI) is readily loaded into the stele. This contrasted with other metal(loid)s (e.g. Mn, As), which accumulated in the apex. These differences in metal(loid) spatial distribution provide valuable quantitative data on metal(loid) physiology, including uptake, transport, and toxicity in plant roots.
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Affiliation(s)
- Peng Wang
- The University of Queensland, School of Agriculture and Food Sciences, St. Lucia, Queensland, 4072, Australia.
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31
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Medjoubi K, Leclercq N, Langlois F, Buteau A, Lé S, Poirier S, Mercère P, Sforna MC, Kewish CM, Somogyi A. Development of fast, simultaneous and multi-technique scanning hard X-ray microscopy at Synchrotron Soleil. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:293-299. [PMID: 23412486 DOI: 10.1107/s0909049512052119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/31/2012] [Indexed: 06/01/2023]
Abstract
A distributed fast-acquisition system for synchronized multi-technique experiments is presented, in which the collection of metadata and the asynchronous merging of large data volumes from multiple detectors are managed as part of the data collection process. This fast continuous scanning scheme, named FLYSCAN, enables measurement of microscopy data on a timescale of milliseconds per pixel. Proof-of-principle multi-technique experiments, namely scanning X-ray fluorescence spectrometry combined with absorption, differential phase contrast and dark-field imaging, have been performed on biological and geological samples.
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Affiliation(s)
- Kadda Medjoubi
- Synchrotron Soleil, Saint-Aubin, Gif sur Yvette, France.
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32
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Donner E, de Jonge MD, Kopittke PM, Lombi E. Mapping element distributions in plant tissues using synchrotron X-ray fluorescence techniques. Methods Mol Biol 2013; 953:143-159. [PMID: 23073881 DOI: 10.1007/978-1-62703-152-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Synchrotron-based X-ray fluorescence (XRF) is allowing substantial advances in several disciplines of plant science by allowing the in situ examination of elements within plant tissues. Continual improvements in detector speed, sensitivity, and resolution are increasing the diversity of questions that can be addressed using this technique, including the in situ analysis of elements (such as nutrients or toxicants) within fresh and hydrated tissues. Here, we describe the general principles for designing and conducting experiments for the examination of elemental distributions in plant material using micro-XRF.
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Affiliation(s)
- Erica Donner
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Adelaide, SA, Australia
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33
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Alessi DS, Uster B, Borca CN, Grolimund D, Bernier-Latmani R. Beam-induced oxidation of monomeric U(IV) species. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:197-199. [PMID: 23254675 DOI: 10.1107/s0909049512041763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 10/05/2012] [Indexed: 06/01/2023]
Abstract
Uranium L(III)-edge X-ray absorption spectroscopy is often used to probe the oxidation state and coordination of uranium in environmental samples, and micrometre-sized beams can be used to spatially map the distribution of uranium relative to other elements. Here a variety of uranium-containing environmental samples are analyzed at both microbeam and larger beam sizes to determine whether reoxidation of U(IV) occurred. Monomeric U(IV), a recently discovered product of U(VI) reduction by microbes and certain iron-bearing minerals at uranium-contaminated field sites, was found to be reoxidized during microbeam (3 µm × 2 µm) analysis of biomass and sediments containing the species but not at larger beam sizes. Thus, care must be taken when using X-ray microprobes to analyze samples containing monomeric U(IV).
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Affiliation(s)
- Daniel S Alessi
- Environmental Microbiology Laboratory, Ecole Polytechnique, Fédérale de Lausanne, Switzerland.
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Majumdar S, Peralta-Videa JR, Castillo-Michel H, Hong J, Rico CM, Gardea-Torresdey JL. Applications of synchrotron μ-XRF to study the distribution of biologically important elements in different environmental matrices: A review. Anal Chim Acta 2012; 755:1-16. [DOI: 10.1016/j.aca.2012.09.050] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 09/24/2012] [Accepted: 09/30/2012] [Indexed: 10/27/2022]
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Kempson IM, Chien CC, Chung CY, Hwu Y, Paterson D, de Jonge MD, Howard DL. Fate of intravenously administered gold nanoparticles in hair follicles: follicular delivery, pharmacokinetic interpretation, and excretion. Adv Healthc Mater 2012. [PMID: 23184825 DOI: 10.1002/adhm.201200101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Gold nanoparticles (GNPs) are intravenously administered to mice. Deposition at the pilosebacious unit and whiskers is visualized with X-ray fluorescence after 30 minutes and 14 days. After 30 minutes the dermal papilla, bulge region, and root sheath all contain NPs. GNPs are driven externally out from follicles, counteractive to transfollicular delivery. After 14 days, gold bands in hairs reflect pharmacokinetic profiles indicating blood concentration kinetics. Elimination rate constants infer half-lives from 3 hairs from an individual mouse within reasonable agreement (6.08, 7.15, and 8.66 hours). 3D reconstruction of NP distributions with confocal microscopy identifies aggregates within the medullary canal. Intermittent NP deposition continues randomly over the two week period demonstrating prolonged NP mobility in vivo. NPs are still retained at the hair bulb after 14 days. The observations further account for the excretory mechanisms of NPs and their behavior in the pilosebacous unit, and demonstrate monitoring pharmacokinetic behavior in individual animals.
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Metallomics in environmental and health related research: Current status and perspectives. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5496-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Kopittke PM, de Jonge MD, Menzies NW, Wang P, Donner E, McKenna BA, Paterson D, Howard DL, Lombi E. Examination of the distribution of arsenic in hydrated and fresh cowpea roots using two- and three-dimensional techniques. PLANT PHYSIOLOGY 2012; 159:1149-58. [PMID: 22635118 PMCID: PMC3387701 DOI: 10.1104/pp.112.197277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/21/2012] [Indexed: 05/02/2023]
Abstract
Arsenic (As) is considered to be the environmental contaminant of greatest concern due to its potential accumulation in the food chain and in humans. Using novel synchrotron-based x-ray fluorescence techniques (including sequential computed tomography), short-term solution culture studies were used to examine the spatial distribution of As in hydrated and fresh roots of cowpea (Vigna unguiculata 'Red Caloona') seedlings exposed to 4 or 20 µm arsenate [As(V)] or 4 or 20 µm arsenite. For plants exposed to As(V), the highest concentrations were observed internally at the root apex (meristem), with As also accumulating in the root border cells and at the endodermis. When exposed to arsenite, the endodermis was again a site of accumulation, although no As was observed in border cells. For As(V), subsequent transfer of seedlings to an As-free solution resulted in a decrease in tissue As concentrations, but growth did not improve. These data suggest that, under our experimental conditions, the accumulation of As causes permanent damage to the meristem. In addition, we suggest that root border cells possibly contribute to the plant's ability to tolerate excess As(V) by accumulating high levels of As and limiting its movement into the root.
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Affiliation(s)
- Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
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Donner E, Punshon T, Guerinot ML, Lombi E. Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology. Anal Bioanal Chem 2012; 402:3287-98. [PMID: 22200921 PMCID: PMC3913160 DOI: 10.1007/s00216-011-5624-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/25/2011] [Accepted: 11/28/2011] [Indexed: 02/03/2023]
Abstract
Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus for phytoremediation, crop biofortification and food security research. Recent advances in X-ray focussing optics and fluorescence detection have greatly improved the potential to use synchrotron techniques in plant science research. With use of methods such as micro X-ray fluorescence mapping, micro computed tomography and micro X-ray absorption near edge spectroscopy, metal(loids) can be imaged in vivo in hydrated plant tissues at submicron resolution, and laterally resolved metal(loid) speciation can also be determined under physiologically relevant conditions. This article focuses on the benefits of combining molecular biology and synchrotron-based techniques. By using molecular techniques to probe the location of gene expression and protein production in combination with laterally resolved synchrotron techniques, one can effectively and efficiently assign functional information to specific genes. A review of the state of the art in this field is presented, together with examples as to how synchrotron-based methods can be combined with molecular techniques to facilitate functional characterisation of genes in planta. The article concludes with a summary of the technical challenges still remaining for synchrotron-based hard X-ray plant science research, particularly those relating to subcellular level research.
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Affiliation(s)
- Erica Donner
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Building X, Mawson Lakes Campus, Mawson Lakes, SA 5095, Australia.
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Bohic S, Cotte M, Salomé M, Fayard B, Kuehbacher M, Cloetens P, Martinez-Criado G, Tucoulou R, Susini J. Biomedical applications of the ESRF synchrotron-based microspectroscopy platform. J Struct Biol 2012; 177:248-58. [DOI: 10.1016/j.jsb.2011.12.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/30/2023]
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A review of recent developments in the speciation and location of arsenic and selenium in rice grain. Anal Bioanal Chem 2011; 402:3275-86. [PMID: 22159463 DOI: 10.1007/s00216-011-5579-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/10/2011] [Accepted: 11/14/2011] [Indexed: 10/14/2022]
Abstract
Rice is a staple food yet is a significant dietary source of inorganic arsenic, a class 1, nonthreshold carcinogen. Establishing the location and speciation of arsenic within the edible rice grain is essential for understanding the risk and for developing effective strategies to reduce grain arsenic concentrations. Conversely, selenium is an essential micronutrient and up to 1 billion people worldwide are selenium-deficient. Several studies have suggested that selenium supplementation can reduce the risk of some cancers, generating substantial interest in biofortifying rice. Knowledge of selenium location and speciation is important, because the anti-cancer effects of selenium depend on its speciation. Germanic acid is an arsenite/silicic acid analogue, and location of germanium may help elucidate the mechanisms of arsenite transport into grain. This review summarises recent discoveries in the location and speciation of arsenic, germanium, and selenium in rice grain using state-of-the-art mass spectrometry and synchrotron techniques, and illustrates both the importance of high-sensitivity and high-resolution techniques and the advantages of combining techniques in an integrated quantitative and spatial approach.
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Moore KL, Lombi E, Zhao FJ, Grovenor CRM. Elemental imaging at the nanoscale: NanoSIMS and complementary techniques for element localisation in plants. Anal Bioanal Chem 2011; 402:3263-73. [DOI: 10.1007/s00216-011-5484-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/28/2011] [Accepted: 10/06/2011] [Indexed: 12/14/2022]
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Lombi E, de Jonge MD, Donner E, Kopittke PM, Howard DL, Kirkham R, Ryan CG, Paterson D. Fast x-ray fluorescence microtomography of hydrated biological samples. PLoS One 2011; 6:e20626. [PMID: 21674049 PMCID: PMC3107226 DOI: 10.1371/journal.pone.0020626] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/05/2011] [Indexed: 11/18/2022] Open
Abstract
Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples.
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Affiliation(s)
- Enzo Lombi
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, South Australia, Australia.
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