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23 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3 [Next/Last]

Instruments / Technical Area	Publication Details	Published
B22-Multimode InfraRed imaging And Microspectroscopy	High resolution functional group mapping of fungi on a mineral surface Andrew Bray , Steeve Bonneville , Gianfelice Cinque , Mark Frogley , Katia Wehbe , Jacob Filik , A Duran , Achim Schmalenberger , Maria Romero-González , Liane G Benning Geochimica et Cosmochimica Acta	Aug 2010
B22-Multimode InfraRed imaging And Microspectroscopy	Biochemical characterization of single weathering hyphae of Paxillus involutus using CLSM and synchrotron-based µ-FTIR Achim Schmalenberger , Andrew Bray , Adele Duran , Jonathan Leake , Gianfelice Cinque , Mark Frogley , Jacob Filik , Jacek Pijanka , Steeve Bonneville , Liane G Benning , Maria Romero-González Goldschmidt 2011 Show Abstract ▼ Abstract: The mycelium of symbiotic ectomycorrhizal fungi (EM) increases nutrient uptake by the plants through fungal secretion of low molecular weight organic acids that can accelerate mineral dissolution. This EM weathering with pine trees plays a key role in nutrient mobilization processes and pedogenesis. Here we report first insights into the chemical variability of the weathering mycelium when studied on a micrometer scale using Confocal Laser Scanning Microscopy (CSLM) and synchrotron based micro Fourier Transform Infrared (μFTIR) spectroscopy. Pine seedlings ectomycorrhizal with Paxillus involutus were grown in microcosms containing wells with olivine, quartz, basalt, granite and limestone. CLSM analysis of EM hyphae with the molecular probe SNARF4F in contact with basalt and limestone revealed a pH below or at 4.6 while the pH of EM in contact with granite identified pH values that varied from pH 4.6 to 6.5 with variations observed within single cells. Chemical μFTIR maps of single hyphae at a resolution of 5x5 μm identified variabilities within the spatial distribution of lipids, amides and carbohydrates. Particular distinctions in intensities of carbohydrates and lipids were discovered on a single cell level. We conclude that mineralogy has a significant impact on the biochemistry of colonizing symbiotic EM mycelia, individual hyphae and cells. Earlier studies showed that exudation of oxalate is increased in the presence of basalt and limestone[1] and here we report the corresponding biochemical changes that take place on a single hypha scale.	Jul 2011
B22-Multimode InfraRed imaging And Microspectroscopy	Multimode InfraRed Imaging and Microspectroscopy (MIRIAM) beamline at Diamond Gianfelice Cinque , Mark Frogley , Katia Wehbe , Jacob Filik , Jacek Pijanka Synchrotron Radiation News 24 (5), 24 - 33 DOI: 10.1080/08940886.2011.618093 Show Abstract ▼ Abstract: InfraRed (IR) MicroSpectroscopy is a quantitative analytical and non-destructive technique that has undergone a renaissance since its coupling to synchrotron radiation (SR) [1]. The primary advantages of an SR IR source with respect to BlackBody (BB) are a wide broadband spectrum, high brightness/brilliance, intrinsic light polarization, and temporal pulse structure. SR IR spans a larger spectral distribution, also covering the far-IR (or THz region), and can be up to 1000 times brighter in the mid-IR than thermal sources. Fourier Transform IR (FTIR) interferometry has proven extremely effective for performing IR absorption spectroscopy, i.e. for quantifying optically active vibrational modes of molecular components. SR's high brightness benefits FTIR spectromicroscopy with a signal-to-noise ratio unreachable by other broadband sources at diffraction limited spatial resolution at the microscopic scale and in confocal geometry.	Sep 2011
B22-Multimode InfraRed imaging And Microspectroscopy	Electric field standing wave artefacts in FTIR micro-spectroscopy of biological materials Jacob Filik , Mark D. Frogley , Jacek K. Pijanka , Katia Wehbe , Gianfelice Cinque Analyst DOI: 10.1039/c2an15995c PMID: 22231204 Show Abstract ▼ Abstract: FTIR absorption micro-spectroscopy is a widely used, powerful technique for analysing biological materials. In principle it is a straightforward linear absorption spectroscopy, but it can be affected by artefacts that complicate the interpretation of the data. In this article, artefacts produced by the electric-field standing-wave (EFSW) in micro-reflection-absorption (transflection) spectroscopy are investigated. An EFSW is present at reflective metallic surfaces due to the interference of incident and reflected light. The period of this standing wave is dependent on the wavelength of the radiation and can produce non-linear changes in absorbance with increasing sample thickness (non-Beer–Lambert like behaviour). A protein micro-structure was produced as a simple experimental model for a biological cell and used to evaluate the differences between FTIR spectra collected in transmission and transflection. By varying the thickness of the protein samples, the relationship between the absorbance and sample thickness in transflection was determined, and shown to be consistent with optical interference due to the EFSW coupled with internal reflection from the sample top surface. FTIR spectral image data from MCF 7 breast adenocarcinoma cells was then analysed to determine the severity of the EFSW artefact in data from a real sample. The results from these measurements confirmed that the EFSW artefact has a profound effect on transflection spectra, and in this case the main spectral variations were related to the sample thickness rather than any biochemical differences.	Jan 2012
B22-Multimode InfraRed imaging And Microspectroscopy	Morphological analysis of vibrational hyperspectral imaging data Jacob Filik , Abigail V. Rutter , Josep Sulé-Suso , Gianfelice Cinque Analyst 137 (24) DOI: 10.1039/c2an35914f PMID: 23001149 Show Abstract ▼ Abstract: This study demonstrates the use of standard morphological image processing techniques to reduce the hyperspectral image data of samples, containing discrete particles or domains, to a single average spectrum per particle. The processing is automated and successful even when the particles are in contact. Focal Plane Array, Fourier transform infrared (FTIR) absorbance images of biological cells are used as an example dataset. The large number of spectra in the image (?40 000) can be intelligently averaged to ?100 mean spectra, approximately one per cell, greatly simplifying further analysis. As well as reducing the data, the morphological analysis provides useful information, such as the size of each cell, and allows every spectrum associated with each cell to be identified and analysed independently of the full dataset. Using these methods, combined with principal components analysis, consistent spectral differences are found between the spectra of the whole cells and a cell region approximately corresponding to the nucleus. These spectral differences compare well with previous IR measurements on whole CALU-1 cells and their isolated nuclei, but with a simpler sample preparation. The algorithm created to analyse the CALU-1 cells has been applied to a second cell line (NL20), which has a very different growth morphology, to demonstrate that this processing method is applicable to varied samples with little or no modification.	Jan 2012
B22-Multimode InfraRed imaging And Microspectroscopy	Optical standing wave artifacts in reflection-absorption FTIR microspectroscopy of biological materials. Jacob Filik , Mark Frogley , Jacek Pijanka , Katia Wehbe , Gianfelice Cinque 6th Workshop on Infrared Spectroscopy and Microscopy with Accelerator-Based Sources (WIRMS11) DOI: 10.1088/1742-6596/359/1/012006 Open Access Show Abstract ▼ Abstract: Reflection-absorption spectra obtained with an infrared microscope should yield the same absorption coefficients as direct micro-transmission measurements as long as the correct effective sample thickness is used, but in practice, severe optical artifacts can complicate the spectra. Using deposited protein gel fdms as a homogenous model for biological cell-like samples, we demonstrate the effect of standing-wave interference of the IR beam at the reflective substrate surface which dramatically and systematically alters the absorbance intensity across the spectrum as a function of sample thickness. To explain the observed spectral artifacts, we simulate the optical standing-wave for the focussed IR beam, and insert the parameters into an existing standing-wave absorption theory. By introducing an additional term to the theory representing a component of the standing-wave resonant with the film thickness, the data are accurately reproduced, and the relative band intensities can be corrected to the direct transmission values. This approach may be generally applicable in reflection-absorption experiments to obtain reliable absorbance spectra of homogenous samples even when the sample thickness is larger than the IR wavelength.	May 2012
B22-Multimode InfraRed imaging And Microspectroscopy	Isolating stem cells in the inter-follicular epidermis employing synchrotron radiation-based Fourier-transform infrared microspectroscopy and focal plane array imaging Imran Patel , Wesley Harrison , Jemma G. Kerns , Jacob Filik , Katia Wehbe , Paul L. Carmichael , Andrew D. Scott , Mike P. Philpott , Mark D. Frogley , Gianfelice Cinque , Francis L. Martin Analytical And Bioanalytical Chemistry 404, 1745 - 1758 DOI: 10.1007/s00216-012-6314-y Show Abstract ▼ Abstract: Normal function and physiology of the epidermis is maintained by the regenerative capacity of this tissue via adult stem cells (SCs). However, definitive identifying markers for SCs remain elusive. Infrared (IR) spectroscopy exploits the ability of cellular biomolecules to absorb in the mid-IR region (λ = 2.5–25 μm), detecting vibrational transitions of chemical bonds. In this study, we exploited the cell’s inherent biochemical composition to discriminate SCs of the inter-follicular skin epidermis based on IR-derived markers. Paraffin-embedded samples of human scalp skin (n = 4) were obtained, and 10-μm thick sections were mounted for IR spectroscopy. Samples were interrogated in transmission mode using synchrotron radiation-based Fourier-transform IR (FTIR) microspectroscopy (15 × 15 μm) and also imaged employing globar-source FTIR focal plane array (FPA) imaging (5.4 × 5.4 μm). Dependent on the location of derived spectra, wavenumber–absorbance/intensity relationships were examined using unsupervised principal component analysis. This approach showed clear separation and spectral differences dependent on cell type. Spectral biomarkers concurrently associated with segregation of SCs, transit-amplifying cells and terminally-differentiated cells of epidermis were primarily PO2− vibrational modes (1,225 and 1,080 cm−1), related to DNA conformational alterations. FPA imaging coupled with hierarchical cluster analysis also indicated the presence of specific basal layer cells potentially originating from the follicular bulge, suggested by co-clustering of spectra. This study highlights PO2− vibrational modes as potential putative SC markers.	Oct 2012
B22-Multimode InfraRed imaging And Microspectroscopy	The effect of optical substrates on micro-FTIR analysis of single mammalian cells Katia Wehbe , Jacob Filik , Mark Frogley , Gianfelice Cinque Analytical And Bioanalytical Chemistry DOI: 10.1007/s00216-012-6521-6 PMID: 23151654 Open Access Show Abstract ▼ Abstract: The study of individual cells with infrared (IR) microspectroscopy often requires living cells to be cultured directly onto a suitable substrate. The surface effect of the specific substrates on the cell growth—viability and associated biochemistry—as well as on the IR analysis—spectral interference and optical artifacts—is all too often ignored. Using the IR beamline, MIRIAM (Diamond Light Source, UK), we show the importance of the substrate used for IR absorption spectroscopy by analyzing two different cell lines cultured on a range of seven optical substrates in both transmission and reflection modes. First, cell viability measurements are made to determine the preferable substrates for normal cell growth. Successively, synchrotron radiation IR microspectroscopy is performed on the two cell lines to determine any genuine biochemically induced changes or optical effect in the spectra due to the different substrates. Multivariate analysis of spectral data is applied on each cell line to visualize the spectral changes. The results confirm the advantage of transmission measurements over reflection due to the absence of a strong optical standing wave artifact which amplifies the absorbance spectrum in the high wavenumber regions with respect to low wavenumbers in the mid-IR range. The transmission spectra reveal interference from a more subtle but significant optical artifact related to the reflection losses of the different substrate materials. This means that, for comparative studies of cell biochemistry by IR microspectroscopy, it is crucial that all samples are measured on the same substrate type.	Nov 2012
	Study of gemcitabine-sensitive/resistant cancer cells by cell cloning and synchrotron FTIR microspectroscopy Abigail Rutter , Muhammad Siddique , Jacob Filik , Christophe Sandt , Paul Dumas , Gianfelice Cinque , Dhruvananda Sockalingum , Ying Yang , Josep Sule-Suso Cytometry Part A DOI: 10.1002/cyto.a.22488 Show Abstract ▼ Abstract: Over the last few years, significant scientific insight on the effects of chemotherapy drugs at cellular level using synchrotron-based FTIR (S-FTIR) microspectroscopy has been obtained. The work carried out so far has identified spectral differences in cancer cells before and after the addition of drugs. However, this had to account for the following issues. First, chemotherapy agents cause both chemical and morphological changes in cells, the latter being responsible for changes in the spectral profile not correlated with biochemical characteristics. Second, as the work has been carried out in mixed populations of cells (resistant and sensitive), it is important to distinguish the spectral differences which are due to sensitivity/resistance to those due to cell morphology and/or cell mixture. Here, we successfully cloned resistant and sensitive lung cancer cells to a chemotherapy drug. This allowed us to study a more uniform population and, more important, allowed us to study sensitive and resistant cells prior to the addition of the drug with S-FTIR microscopy. Principal component analysis (PCA) did not detect major differences in resistant cells prior to and after adding the drug. However, PCA separated sensitive cells prior to and after the addition of the drug. This would indicate that the spectral differences between cells prior to and after adding a drug might reside on those more or less sensitive cells that have been able to remain alive when they were collected to be studied with S-FTIR microspectroscopy. This is a proof of concept and a feasibility study showing a methodology that opens a new way to identify the effects of drugs on more homogeneous cell populations using vibrational spectroscopy	May 2014
B18-Core EXAFS I18-Microfocus Spectroscopy	Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT S. W. T. Price , K. Ignatyev , K. Geraki , M. Basham , J. Filik , N. T. Vo , P. T. Witte , A. M. Beale , J. F. W. Mosselmans Physical Chemistry Chemical Physics DOI: 10.1039/C4CP04488F PMID: 25407850 Diamond Proposal Number(s): [4939] Show Abstract ▼ Abstract: The physicochemical state of a catalyst is a key factor in determining both activity and selectivity; however these materials are often not structurally or compositionally homogeneous. Here we report on the 3-dimensional imaging of an industrial catalyst, Mo- promoted colloidal Pt supported on carbon. The distribution of both the active Pt species and Mo promoter have been mapped over a single particle of catalyst using microfocus X-ray Fluorescence computed tomography. X-ray absorption near edge spectroscopy (XANES) and extended X-ray absorption fine structure revealed a mixed local coordination environment, including the presence of both metallic Pt clusters and Pt chloride species, but also no direct interaction between the catalyst and Mo promoter. We also report on the benefits of scanning μ-XANES computed tomography for chemical imaging, allowing for 2- and 3-dimensional mapping of the local electronic and geometric environment, in this instance for both the Pt catalyst and Mo promoter throughout the catalyst particle.	Nov 2014

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