1
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Neofytos DD, Gregersen SB, Andersen U, Corredig M. In situ single-droplet analysis of emulsified fat using confocal Raman microscopy: insights into crystal network formation within spatial resolution. SOFT MATTER 2024. [PMID: 38690673 DOI: 10.1039/d4sm00194j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Fat crystallization is one of the predominant factors influencing the structure and properties of fat-containing emulsions. In the present study, the role of emulsifiers on fat crystallization dynamics within droplet multiphase systems was evaluated via single-droplet analysis, taking advantage of the non-destructive properties of confocal Raman microscopy. Palm oil droplets dispersed in water were used as a model system, due to palm oil's well-known crystallization properties. Emulsion droplets of the same size were generated using two different emulsifiers (Whey Protein Isolate and Tween 60), at various concentrations. Fast and slow cooling treatments were applied to affect fat crystallisation and network formation as well as droplet morphology, and crystallization dynamics. Raman imaging analysis demonstrated that the chemical structure and concentration of the emulsifier significantly influenced both crystal nucleation within the droplets, as well as the spatial distribution and morphology of the fat crystal network. Additionally, analysis of the spectra of the crystallized phase provided essential information regarding the impact of the emulsifiers on the microstructure, degree of structural order, and structural arrangements of the fat crystal networks. Furthermore, by performing single droplet analysis during cooling it was possible to observe shape distortions in Tween 60 stabilized droplets, as a consequence of the formation of a three-dimensional network of fat crystals that strongly interacted with the interface. On the other hand, the droplets retained their shape when whey proteins were absorbed at the interface. Confocal Raman microscopy, in combination with polarized light microscopy, is, therefore, a well-suited tool for in situ, single-droplet analysis of emulsified oil systems, providing essential information about emulsified fat crystallization dynamics, contributing to better understanding and designing products with enhanced structure and function.
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Affiliation(s)
- Dionysios D Neofytos
- Department of Food Science, Aarhus University, Agro Food Park 48, 8200 Aarhus, Denmark.
| | | | - Ulf Andersen
- Arla Innovation Centre, Arla Foods, Agro Food Park 19, 8200 Aarhus, Denmark
| | - Milena Corredig
- Department of Food Science, Aarhus University, Agro Food Park 48, 8200 Aarhus, Denmark.
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2
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Akbali B, Boisdon C, Smith BL, Chaisrikhwun B, Wongravee K, Vilaivan T, Lima C, Huang CH, Chen TY, Goodacre R, Maher S. Focusing ion funnel-assisted ambient electrospray enables high-density and uniform deposition of non-spherical gold nanoparticles for highly sensitive surface-enhanced Raman scattering. Analyst 2023; 148:4677-4687. [PMID: 37697928 DOI: 10.1039/d3an01021j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Surface-enhanced Raman scattering (SERS) is a powerful technique for detecting trace amounts of analytes. However, the performance of SERS substrates depends on many variables including the enhancement factor, morphology, consistency, and interaction with target analytes. In this study, we investigated, for the first time, the use of electrospray deposition (ESD) combined with a novel ambient focusing DC ion funnel to deposit a high density of gold nanoparticles (AuNPs) to generate large-area, uniform substrates for highly sensitive SERS analysis. We found that the combination of ambient ion focusing with ESD facilitated high-density and intact deposition of non-spherical NPs. This also allowed us to take advantage of a polydisperse colloidal solution of AuNPs (consisting of nanospheres and nanorods), as confirmed by finite-difference time domain (FDTD) simulations. Our SERS substrate exhibited excellent capture capacity for model analyte molecules, namely 4-aminothiophenol (4-ATP) and Rhodamine 6G (R6G), with detection limits in the region of 10-11 M and a relative standard deviation of <6% over a large area (∼500 × 500 μm2). Additionally, we assessed the quantitative performance of our SERS substrate using the R6G probe molecule. The results demonstrated excellent linearity (R2 > 0.99) over a wide concentration range (10-4 M to 10-10 M) with a detection limit of 80 pM.
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Affiliation(s)
- Baris Akbali
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK.
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Cedric Boisdon
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK.
| | - Barry L Smith
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK.
| | - Boonphop Chaisrikhwun
- Program in Petrochemistry and Polymer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanet Wongravee
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Cassio Lima
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Chen-Han Huang
- Department of Biomedical Engineering, National Central University, Zhongli 10608, Taiwan
| | - Tsan-Yao Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Royston Goodacre
- Centre for Metabolomics Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Simon Maher
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, Liverpool, L69 3GJ, UK.
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3
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Blake N, Gaifulina R, Griffin LD, Bell IM, Rodriguez-Justo M, Thomas GMH. Deep Learning Applied to Raman Spectroscopy for the Detection of Microsatellite Instability/MMR Deficient Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15061720. [PMID: 36980606 PMCID: PMC10046611 DOI: 10.3390/cancers15061720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Defective DNA mismatch repair is one pathogenic pathway to colorectal cancer. It is characterised by microsatellite instability which provides a molecular biomarker for its detection. Clinical guidelines for universal testing of this biomarker are not met due to resource limitations; thus, there is interest in developing novel methods for its detection. Raman spectroscopy (RS) is an analytical tool able to interrogate the molecular vibrations of a sample to provide a unique biochemical fingerprint. The resulting datasets are complex and high-dimensional, making them an ideal candidate for deep learning, though this may be limited by small sample sizes. This study investigates the potential of using RS to distinguish between normal, microsatellite stable (MSS) and microsatellite unstable (MSI-H) adenocarcinoma in human colorectal samples and whether deep learning provides any benefit to this end over traditional machine learning models. A 1D convolutional neural network (CNN) was developed to discriminate between healthy, MSI-H and MSS in human tissue and compared to a principal component analysis–linear discriminant analysis (PCA–LDA) and a support vector machine (SVM) model. A nested cross-validation strategy was used to train 30 samples, 10 from each group, with a total of 1490 Raman spectra. The CNN achieved a sensitivity and specificity of 83% and 45% compared to PCA–LDA, which achieved a sensitivity and specificity of 82% and 51%, respectively. These are competitive with existing guidelines, despite the low sample size, speaking to the molecular discriminative power of RS combined with deep learning. A number of biochemical antecedents responsible for this discrimination are also explored, with Raman peaks associated with nucleic acids and collagen being implicated.
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Affiliation(s)
- Nathan Blake
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Riana Gaifulina
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Lewis D. Griffin
- Department of Computer Science, University College London, London WC1E 6BT, UK
| | - Ian M. Bell
- Spectroscopy Products Division, Renishaw PLC, Wotton-under-Edge GL12 8JR, UK
| | - Manuel Rodriguez-Justo
- Department of Research Pathology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Geraint M. H. Thomas
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Correspondence: ; Tel.: +44-20-3549-5456
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4
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Thomas G, Fitzgerald ST, Gautam R, Chen F, Haugen E, Rasiah PK, Adams WR, Mahadevan-Jansen A. Enhanced characterization of breast cancer phenotypes using Raman micro-spectroscopy on stainless steel substrate. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1188-1205. [PMID: 36799369 DOI: 10.1039/d2ay01764d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Biochemical insights into varying breast cancer (BC) phenotypes can provide a fundamental understanding of BC pathogenesis, while identifying novel therapeutic targets. Raman spectroscopy (RS) can gauge these biochemical differences with high specificity. For routine RS, cells are traditionally seeded onto calcium fluoride (CaF2) substrates that are costly and fragile, limiting its widespread adoption. Stainless steel has been interrogated previously as a less expensive alternative to CaF2 substrates, while reporting increased Raman signal intensity than the latter. We sought to further investigate and compare the Raman signal quality measured from stainless steel versus CaF2 substrates by characterizing different BC phenotypes with altered human epidermal growth factor receptor 2 (HER2) expression. Raman spectra were obtained on stainless steel and CaF2 substrates for HER2 negative cells - MDA-MB-231, MDA-MB-468 and HER2 overexpressing cells - AU565, SKBr3. Upon analyzing signal-to-noise ratios (SNR), stainless steel provided a stronger Raman signal, improving SNR by 119% at 1450 cm-1 and 122% at 2925 cm-1 on average compared to the CaF2 substrate. Utilizing only 22% of laser power on sample relative to the CaF2 substrate, stainless steel still yielded improved spectral characterization over CaF2, achieving 96.0% versus 89.8% accuracy in BC phenotype discrimination and equivalent 100.0% accuracy in HER2 status classification. Spectral analysis further highlighted increased lipogenesis and altered metabolism in HER2 overexpressing cells, which was subsequently visualized with coherent anti-Stokes Raman scattering microscopy. Our findings demonstrate that stainless steel substrates deliver improved Raman signal and enhanced spectral characterization, underscoring its potential as a cost-effective alternative to CaF2 for non-invasively monitoring cellular biochemical dynamics in translational cancer research.
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Affiliation(s)
- Giju Thomas
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Sean T Fitzgerald
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Rekha Gautam
- Tyndall National Institute, Cork, T12 R5CP, Ireland
| | - Fuyao Chen
- Yale School of Medicine, Yale University, New Haven 06510, CT, USA
| | - Ezekiel Haugen
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Pratheepa Kumari Rasiah
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
| | - Wilson R Adams
- Department of Pharmacology, Vanderbilt University, Nashville 37232, TN, USA
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Vanderbilt University, Nashville 37235, TN, USA.
- Department of Biomedical Engineering, Vanderbilt University, Nashville 37235, TN, USA
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5
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Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R. Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME COMMUNICATIONS 2022; 2:52. [PMID: 37938730 PMCID: PMC9723565 DOI: 10.1038/s43705-022-00134-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 05/08/2023]
Abstract
Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.
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Affiliation(s)
- George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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6
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Gosling S, Calabrese D, Nallala J, Greenwood C, Pinder S, King L, Marks J, Pinto D, Lynch T, Lyburn ID, Hwang ES, Grand Challenge Precision Consortium, Rogers K, Stone N. A multi-modal exploration of heterogeneous physico-chemical properties of DCIS breast microcalcifications. Analyst 2022; 147:1641-1654. [PMID: 35311860 PMCID: PMC8997374 DOI: 10.1039/d1an01548f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ductal carcinoma in situ (DCIS) is frequently associated with breast calcification. This study combines multiple analytical techniques to investigate the heterogeneity of these calcifications at the micrometre scale. X-ray diffraction, scanning electron microscopy and Raman and Fourier-transform infrared spectroscopy were used to determine the physicochemical and crystallographic properties of type II breast calcifications located in formalin fixed paraffin embedded DCIS breast tissue samples. Multiple calcium phosphate phases were identified across the calcifications, distributed in different patterns. Hydroxyapatite was the dominant mineral, with magnesium whitlockite found at the calcification edge. Amorphous calcium phosphate and octacalcium phosphate were also identified close to the calcification edge at the apparent mineral/matrix barrier. Crystallographic features of hydroxyapatite also varied across the calcifications, with higher crystallinity centrally, and highest carbonate substitution at the calcification edge. Protein was also differentially distributed across the calcification and the surrounding soft tissue, with collagen and β-pleated protein features present to differing extents. Combination of analytical techniques in this study was essential to understand the heterogeneity of breast calcifications and how this may link crystallographic and physicochemical properties of calcifications to the surrounding tissue microenvironment.
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Affiliation(s)
- Sarah Gosling
- Cranfield Forensic Institute, Cranfield University, Shrivenham, UK.
| | | | | | | | - Sarah Pinder
- Division of Cancer Studies, King's College London, Guy's Hospital, London, UK
| | - Lorraine King
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Jeffrey Marks
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Thomas Lynch
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Iain D Lyburn
- Cranfield Forensic Institute, Cranfield University, Shrivenham, UK. .,Thirlestaine Breast Centre, Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, Gloucestershire, UK.,Cobalt Medical Charity, Cheltenham, UK
| | - E Shelley Hwang
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | | | - Keith Rogers
- Cranfield Forensic Institute, Cranfield University, Shrivenham, UK.
| | - Nicholas Stone
- School of Physics and Astronomy, University of Exeter, Exeter, UK.
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7
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Święch D, Palumbo G, Piergies N, Pięta E, Szkudlarek A, Paluszkiewicz C. Spectroscopic Investigations of 316L Stainless Steel under Simulated Inflammatory Conditions for Implant Applications: The Effect of Tryptophan as Corrosion Inhibitor/Hydrophobicity Marker. COATINGS 2021; 11:1097. [DOI: 10.3390/coatings11091097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
In this paper, the conformational changes of tryptophan (Trp) on the corroded 316 L stainless steel (SS) surface obtained under controlled simulated inflammatory conditions have been studied by Raman (RS) and Fourier-transform infrared (FT-IR) spectroscopy methods. The corrosion behavior and protective efficiency of the investigated samples were performed using the potentiodynamic polarization (PDP) technique in phosphate-buffered saline (PBS) solution acidified to pH 3.0 at 37 °C in the presence and absence of 10−2 M Trp, with different immersion times (2 h and 24 h). The amino acid is adsorbed onto the corroded SS surface mainly through the lone electron pair of the nitrogen atom of the indole ring, which adopts a more/less tilted orientation, and the protonated amine group. The visible differences in the intensity of the Fermi doublet upon adsorption of Trp onto the corroded SS surface, which is a sensitive marker of the local environment, suggested that a stronger hydrophobic environment is observed. This may result in an improvement of the corrosion resistance, after 2 h than 24 h of exposure time. The electrochemical results confirm this statement—the inhibition efficiency of Trp, acting as a mixed-type inhibitor, is made drastically higher after a short period of immersion.
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Affiliation(s)
- Dominika Święch
- Faculty of Foundry Engineering, AGH University of Science and Technology, al. Mickiewicza 30, PL-30059 Krakow, Poland
| | - Gaetano Palumbo
- Faculty of Foundry Engineering, AGH University of Science and Technology, al. Mickiewicza 30, PL-30059 Krakow, Poland
| | - Natalia Piergies
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Ewa Pięta
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Aleksandra Szkudlarek
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, al. Mickiewicza 30, PL-30059 Krakow, Poland
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8
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Osei EB, Paniushkina L, Wilhelm K, Popp J, Nazarenko I, Krafft C. Surface-Enhanced Raman Spectroscopy to Characterize Different Fractions of Extracellular Vesicles from Control and Prostate Cancer Patients. Biomedicines 2021; 9:biomedicines9050580. [PMID: 34065470 PMCID: PMC8161280 DOI: 10.3390/biomedicines9050580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Extracellular vesicles (EVs) are membrane-enclosed structures ranging in size from about 60 to 800 nm that are released by the cells into the extracellular space; they have attracted interest as easily available biomarkers for cancer diagnostics. In this study, EVs from plasma of control and prostate cancer patients were fractionated by differential centrifugation at 5000× g, 12,000× g and 120,000× g. The remaining supernatants were purified by ultrafiltration to produce EV-depleted free-circulating (fc) fractions. Spontaneous Raman and surface-enhanced Raman spectroscopy (SERS) at 785 nm excitation using silver nanoparticles (AgNPs) were employed as label-free techniques to collect fingerprint spectra and identify the fractions that best discriminate between control and cancer patients. SERS spectra from 10 µL droplets showed an enhanced Raman signature of EV-enriched fractions that were much more intense for cancer patients than controls. The Raman spectra of dehydrated pellets of EV-enriched fractions without AgNPs were dominated by spectral contributions of proteins and showed variations in S-S stretch, tryptophan and protein secondary structure bands between control and cancer fractions. We conclude that the AgNPs-mediated SERS effect strongly enhances Raman bands in EV-enriched fractions, and the fractions, EV12 and EV120 provide the best separation of cancer and control patients by Raman and SERS spectra.
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Affiliation(s)
- Eric Boateng Osei
- Leibniz Institute of Photonic Technology, Member of Research Alliance “Health Technologies“, Albert-Einstein-Straße 9, 07745 Jena, Germany; (E.B.O.); (J.P.)
- Institute of Physical Chemistry and Abbe School of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Liliia Paniushkina
- Medical Center University Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; (L.P.); (I.N.)
| | - Konrad Wilhelm
- Center for Surgery, Medical Center, Department of Urology, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany;
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Member of Research Alliance “Health Technologies“, Albert-Einstein-Straße 9, 07745 Jena, Germany; (E.B.O.); (J.P.)
- Institute of Physical Chemistry and Abbe School of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Irina Nazarenko
- Medical Center University Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; (L.P.); (I.N.)
- German Cancer Consortium, Partner Site Freiburg and German Cancer Research Center (DKFZ), Hugstetter Str. 55, 79106 Freiburg, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology, Member of Research Alliance “Health Technologies“, Albert-Einstein-Straße 9, 07745 Jena, Germany; (E.B.O.); (J.P.)
- Correspondence: ; Tel.: +49-3641-206306
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9
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Gaifulina R, Caruana DJ, Oukrif D, Guppy NJ, Culley S, Brown R, Bell I, Rodriguez-Justo M, Lau K, Thomas GMH. Rapid and complete paraffin removal from human tissue sections delivers enhanced Raman spectroscopic and histopathological analysis. Analyst 2020; 145:1499-1510. [PMID: 31894759 PMCID: PMC7677988 DOI: 10.1039/c9an01030k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/14/2019] [Indexed: 12/29/2022]
Abstract
Incomplete removal of paraffin and organic contaminants from tissues processed for diagnostic histology has been a profound barrier to the introduction of Raman spectroscopic techniques into clinical practice. We report a route to rapid and complete paraffin removal from a range of formalin-fixed paraffin embedded tissues using super mirror stainless steel slides. The method is equally effective on a range of human and animal tissues, performs equally well with archived and new samples and is compatible with standard pathology lab procedures. We describe a general enhancement of the Raman scatter and enhanced staining with antibodies used in immunohistochemistry for clinical diagnosis. We conclude that these novel slide substrates have the power to improve diagnosis through anatomical pathology by facilitating the simultaneous combination of improved, more sensitive immunohistochemical staining and simplified, more reliable Raman spectroscopic imaging, analysis and signal processing.
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Affiliation(s)
- Riana Gaifulina
- Department of Cell and Developmental Biology
, University College London
,
UK
.
; Tel: +44 (0)20 7679 6098
- Department of Chemistry
, University College London
,
UK
| | | | - Dahmane Oukrif
- Research Department of Pathology
, University College London
,
UK
| | - Naomi J. Guppy
- UCL Advanced Diagnostics
, University College Hospital
,
UK
| | - Siân Culley
- Department of Cell and Developmental Biology
, University College London
,
UK
.
; Tel: +44 (0)20 7679 6098
- MRC Laboratory for Molecular Cell Biology
, University College London
,
UK
| | - Robert Brown
- Spectroscopy Products Division
,
Renishaw plc
, UK
.
| | - Ian Bell
- Spectroscopy Products Division
,
Renishaw plc
, UK
.
| | - Manuel Rodriguez-Justo
- Department of Gastrointestinal Pathology
, University College Hospital and Department of Research Pathology/Cancer Institute
,
UCL
, UK
| | - Katherine Lau
- Spectroscopy Products Division
,
Renishaw plc
, UK
.
| | - Geraint M. H. Thomas
- Department of Cell and Developmental Biology
, University College London
,
UK
.
; Tel: +44 (0)20 7679 6098
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10
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Direct growth of MWCNTs on stainless steel by V-type flame: mechanism of carbon nanotube growth induced by surface reconstruction. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00721-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Improving Sensitivity in Raman Imaging for Thin Layered and Powdered Food Analysis Utilizing a Reflection Mirror. SENSORS 2019; 19:s19122698. [PMID: 31208026 PMCID: PMC6631819 DOI: 10.3390/s19122698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/24/2022]
Abstract
Raman imaging has been proven to be a powerful analytical technique for the characterization and visualization of chemical components in a range of products, particularly in the food and pharmaceutical industries. The conventional backscattering Raman imaging technique for the spatial analysis of a deep layer suffers from the presence of intense fluorescent and Raman signals originating from the surface layer which mask the weaker subsurface signals. Here, we demonstrated the application of a new reflection amplifying method using a background mirror as a sample holder to increase the Raman signals from a deep layer. The approach is conceptually demonstrated on enhancing the Raman signals from the subsurface layer. Results show that when bilayer samples are scanned on a reflection mirror, the average signals increase 1.62 times for the intense band at 476 cm−1 of starch powder, and average increases of 2.04 times (for the band at 672 cm−1) for a subsurface layer of high Raman sensitive melamine powder under a 1 mm thick teflon sheet. The method was then applied successfully to detect noninvasively the presence of small polystyrene pieces buried under a 2 mm thick layer of food powder (a case of powdered food adulteration) which otherwise are inaccessible to conventional backscattering Raman imaging. In addition, the increase in the Raman signal to noise ratio when measuring samples on a mirror is an important feature in many applications where high-throughput imaging is of interest. This concept is also applicable in an analogous manner to other disciplines, such as pharmaceutical where the Raman signals from deeper zones are typically, substantially diluted due to the interference from the surface layer.
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12
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Abstract
Abstract
Micro Raman spectroscopy has been applied very early in environmental analytics. However, until now the field of application is quite limited. The main reasons for the low acceptance are high cost of the method and the low throughput. New developments in technology lead to cheaper instrumentation. Automation of Raman microscopy of particles might be a solution for a higher throughput and a broader application in environmental analytics. A more detailed analysis of aerosols and microplastic is good examples that could benefit from this development.
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Jaafreh S, Valler O, Kreyenschmidt J, Günther K, Kaul P. In vitro discrimination and classification of Microbial Flora of Poultry using two dispersive Raman spectrometers (microscope and Portable Fiber-Optic systems) in tandem with chemometric analysis. Talanta 2019; 202:411-425. [PMID: 31171202 DOI: 10.1016/j.talanta.2019.04.082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023]
Abstract
Discrimination and classification of eight strains related to meat spoilage and pathogenic microorganisms commonly found in poultry meat were successfully carried out using two dispersive Raman spectrometers (Microscope and Portable Fiber-Optic systems) in combination with chemometric methods. Principal components analysis (PCA) and multi-class support vector machines (MC-SVM) were applied to develop discrimination and classification models. These models were certified using validation data sets which were successfully assigned to the correct bacterial species and even to the right strain. The discrimination of bacteria down to the strain level was performed for the pre-processed spectral data using a 3-stage model based on PCA. The spectral features and differences among the species on which the discrimination was based were clarified through PCA loadings. In MC-SVM the pre-processed spectral data was subjected to PCA and utilized to build a classification model. When using the first two components, the accuracy of the MC-SVM model was 97.64% and 93.23% for the validation data collected by the Raman Microscope and the Portable Fiber-Optic Raman system, respectively. The accuracy reached 100% for the validation data by using the first eight and ten PC's from the data collected by Raman Microscope and by Portable Fiber-Optic Raman system, respectively. The results reflect the strong discriminative power and the high performance of the developed models, the suitability of the pre-processing method used in this study and that the low accuracy of the Portable Fiber-Optic Raman system does not adversely affect the discriminative power of the developed models.
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Affiliation(s)
- Sawsan Jaafreh
- Institute of Safety and Security Research, Bonn-Rhein-Sieg University of Applied Sciences, Von Liebig-Straße 20, 53359 Rheinbach, Germany.
| | - Ole Valler
- Rhine-Waal University of Applied Sciences, Marie-Curie-Straße 1, 47533 Kleve, Germany
| | | | - Klaus Günther
- Institute of Nutritional and Food Sciences, Food Chemistry, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany; Institute of Bio- and Geosciences (IBG-2), Research Centre Jülich, 52425 Jülich, Germany
| | - Peter Kaul
- Institute of Safety and Security Research, Bonn-Rhein-Sieg University of Applied Sciences, Von Liebig-Straße 20, 53359 Rheinbach, Germany
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Livermore LJ, Isabelle M, Bell IM, Scott C, Walsby-Tickle J, Gannon J, Plaha P, Vallance C, Ansorge O. Rapid intraoperative molecular genetic classification of gliomas using Raman spectroscopy. Neurooncol Adv 2019; 1:vdz008. [PMID: 31608327 PMCID: PMC6777649 DOI: 10.1093/noajnl/vdz008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The molecular genetic classification of gliomas, particularly the identification of isocitrate dehydrogenase (IDH) mutations, is critical for clinical and surgical decision-making. Raman spectroscopy probes the unique molecular vibrations of a sample to accurately characterize its molecular composition. No sample processing is required allowing for rapid analysis of tissue. The aim of this study was to evaluate the ability of Raman spectroscopy to rapidly identify the common molecular genetic subtypes of diffuse glioma in the neurosurgical setting using fresh biopsy tissue. In addition, classification models were built using cryosections, formalin-fixed paraffin-embedded (FFPE) sections and LN-18 (IDH-mutated and wild-type parental cell) glioma cell lines. METHODS Fresh tissue, straight from neurosurgical theatres, underwent Raman analysis and classification into astrocytoma, IDH-wild-type; astrocytoma, IDH-mutant; or oligodendroglioma. The genetic subtype was confirmed on a parallel section using immunohistochemistry and targeted genetic sequencing. RESULTS Fresh tissue samples from 62 patients were collected (36 astrocytoma, IDH-wild-type; 21 astrocytoma, IDH-mutated; 5 oligodendroglioma). A principal component analysis fed linear discriminant analysis classification model demonstrated 79%-94% sensitivity and 90%-100% specificity for predicting the 3 glioma genetic subtypes. For the prediction of IDH mutation alone, the model gave 91% sensitivity and 95% specificity. Seventy-nine cryosections, 120 FFPE samples, and LN18 cells were also successfully classified. Meantime for Raman data collection was 9.5 min in the fresh tissue samples, with the process from intraoperative biopsy to genetic classification taking under 15 min. CONCLUSION These data demonstrate that Raman spectroscopy can be used for the rapid, intraoperative, classification of gliomas into common genetic subtypes.
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Affiliation(s)
- Laurent James Livermore
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, UK
| | | | - Ian Mac Bell
- Renishaw plc., Spectroscopy Products Division, UK
| | - Connor Scott
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, UK
| | | | - Joan Gannon
- Department of Chemistry, University of Oxford, UK
| | - Puneet Plaha
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, UK
| | | | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, UK
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15
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Liquid Biopsies in Lung Cancer: Four Emerging Technologies and Potential Clinical Applications. Cancers (Basel) 2019; 11:cancers11030331. [PMID: 30866571 PMCID: PMC6468998 DOI: 10.3390/cancers11030331] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/28/2019] [Indexed: 12/27/2022] Open
Abstract
Background: Liquid biopsies offer a promising alternative to tissue samples, providing non-invasive diagnostic approaches or serial monitoring of disease evolution. However, certain challenges remain, and the full potential of liquid biopsies has yet to be reached. Here we report several methodological approaches to interrogate liquid biopsies using circulating tumour cell (CTC) enumeration and characterisation, transcriptomics, Raman spectroscopy, and copy number instability (CNI) scores using blood samples of lung cancer (LC) patients. Methods: We choose LC; since it still is the most common cause of cancer-related mortality worldwide, and therefore there is a need for development of new non-invasive diagnostic/prognostic technologies. Changes in gene expression were assessed using RNA-seq, and in CTCs using ImageStream, an imaging flow-cytometer. CNI scores, from paired tissue/ctDNA were also explored. Raman spectroscopy was used to provide chemical fingerprints of plasma samples. Results: CTCs were detected in all LC patients (n = 10). We observed a significant increase in CTC levels in LC patients (n = 10) compared to controls (n = 21). A similar CNI was noted in the tissue and plasma of 2 patients, where higher CNI scores corresponded with poorer outcome. Significant changes in Raman spectra (carotenoid concentrations) were noted in LC patients (n = 20) compared to controls (n = 10). RNA-seq revealed differential expression of 21 genes between LC cases and controls in both LC tissue and blood samples. Conclusions: Liquid biopsies can potentially provide a more comprehensive picture of the disease compared to a single tissue biopsy. CTC enumeration is feasible and sensitive for LC patients. Molecular profiling of CTCs is also possible from total blood. CNI scores and Raman spectra require further investigation. Further work is being undertaken to explore these methods of detection in a larger LC cohort.
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16
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Ito H, Uragami N, Miyazaki T, Yokoyama N, Inoue H. Raman spectroscopic evaluation of human serum using metal plate and 785- and 1064-nm excitation lasers. PLoS One 2019; 14:e0211986. [PMID: 30768643 PMCID: PMC6377121 DOI: 10.1371/journal.pone.0211986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
In this study, we utilized a stainless steel (SUS304) plate for measuring the Raman scattering spectra of body fluid samples. Using this stainless steel plate, we recorded the Raman scattering spectra of 99.5% ethanol and human serum samples by performing irradiation with 785- and 1064-nm lasers. Raman scattering spectra with intensities equal to or greater than those reported previously were obtained. In addition, the Raman scattering spectra acquired using the 1064-nm laser were less influenced by autofluorescence than those obtained via use of the shorter-wavelength laser. Moreover, the shapes of the spectra did not show any dependence on integration time, and denaturation of the samples was minimal. Our method, based on 1064-nm laser and the stainless steel plate, provides performance equal to or better than the methods reported thus far for the measurement of Raman scattering spectra from liquid samples. This method can be employed to rapidly evaluate the components of serum in liquid form without using surface-enhanced Raman scattering.
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Affiliation(s)
- Hiroaki Ito
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Toyosu, Koto-ku, Tokyo, Japan
- * E-mail:
| | - Naoyuki Uragami
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Toyosu, Koto-ku, Tokyo, Japan
| | - Tomokazu Miyazaki
- Research Planning Department, JSR Corporation, Higashi-Sinbashi, Minato-ku, Tokyo, Japan
| | - Noboru Yokoyama
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Toyosu, Koto-ku, Tokyo, Japan
| | - Haruhiro Inoue
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Toyosu, Koto-ku, Tokyo, Japan
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17
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18
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Lewis AT, Gaifulina R, Guppy NJ, Isabelle M, Dorney J, Lloyd GR, Rodriguez-Justo M, Kendall C, Stone N, Thomas GM. Developing Raman spectroscopy as a diagnostic tool for label-free antigen detection. JOURNAL OF BIOPHOTONICS 2018; 11:e201700028. [PMID: 28700142 DOI: 10.1002/jbio.201700028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 05/31/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
For several decades, a multitude of studies have documented the ability of Raman spectroscopy (RS) to differentiate between tissue types and identify pathological changes to tissues in a range of diseases. Furthermore, spectroscopists have illustrated that the technique is capable of detecting disease-specific alterations to tissue before morphological changes become apparent to the pathologist. This study draws comparisons between the information that is obtainable using RS alongside immunohistochemistry (IHC), since histological examination is the current GOLD standard for diagnosing a wide range of diseases. Here, Raman spectral maps were generated using formalin-fixed, paraffin-embedded colonic tissue sections from healthy patients and spectral signatures from principal components analysis (PCA) were compared with several IHC markers to confirm the validity of their localizations. PCA loadings identified a number of signatures that could be assigned to muscle, DNA and mucin glycoproteins and their distributions were confirmed with antibodies raised against anti-Desmin, anti-Ki67 and anti-MUC2, respectively. The comparison confirms that there is excellent correlation between RS and the IHC markers used, demonstrating that the technique is capable of detecting compositional changes in tissue in a label-free manner, eliminating the need for antibodies.
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Affiliation(s)
- Aaran T Lewis
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Riana Gaifulina
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Naomi J Guppy
- UCL-Advanced Diagnostics, University College London, London, UK
| | - Martin Isabelle
- Biophotonics Research Unit, Gloucester Royal Hospitals NHS Foundation Trust, Gloucestershire, UK
| | - Jennifer Dorney
- School of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Gavin R Lloyd
- Biophotonics Research Unit, Gloucester Royal Hospitals NHS Foundation Trust, Gloucestershire, UK
| | | | - Catherine Kendall
- Biophotonics Research Unit, Gloucester Royal Hospitals NHS Foundation Trust, Gloucestershire, UK
| | - Nicholas Stone
- School of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Geraint M Thomas
- Department of Cell and Developmental Biology, University College London, London, UK
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19
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Baker MJ, Byrne HJ, Chalmers J, Gardner P, Goodacre R, Henderson A, Kazarian SG, Martin FL, Moger J, Stone N, Sulé-Suso J. Clinical applications of infrared and Raman spectroscopy: state of play and future challenges. Analyst 2018; 143:1735-1757. [DOI: 10.1039/c7an01871a] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review examines the state-of-the-art of clinical applications of infrared absorption and Raman spectroscopy, outstanding challenges, and progress towards translation.
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Affiliation(s)
- Matthew J. Baker
- WestCHEM
- Technology and Innovation Centre
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1RD
| | - Hugh J. Byrne
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
| | | | - Peter Gardner
- Manchester Institute of Biotechnology (MIB)
- University of Manchester
- Manchester
- UK
| | - Royston Goodacre
- Manchester Institute of Biotechnology (MIB)
- University of Manchester
- Manchester
- UK
| | - Alex Henderson
- Manchester Institute of Biotechnology (MIB)
- University of Manchester
- Manchester
- UK
| | - Sergei G. Kazarian
- Department of Chemical Engineering
- Imperial College London
- South Kensington Campus
- London
- UK
| | - Francis L. Martin
- School of Pharmacy and Biomedical Sciences
- University of Central Lancashire
- Preston PR1 2HE
- UK
| | - Julian Moger
- Biomedical Physics
- School of Physics and Astronomy
- University of Exeter
- Exeter EX4 4QL
- UK
| | - Nick Stone
- Biomedical Physics
- School of Physics and Astronomy
- University of Exeter
- Exeter EX4 4QL
- UK
| | - Josep Sulé-Suso
- Institute for Science and Technology in Medicine
- Keele University
- Guy Hilton Research Centre
- Stoke on Trent ST4 7QB
- UK
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