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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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2
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Boseley RE, Sylvain NJ, Peeling L, Kelly ME, Pushie MJ. A review of concepts and methods for FTIR imaging of biomarker changes in the post-stroke brain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184287. [PMID: 38266967 DOI: 10.1016/j.bbamem.2024.184287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Stroke represents a core area of study in neurosciences and public health due to its global contribution toward mortality and disability. The intricate pathophysiology of stroke, including ischemic and hemorrhagic events, involves the interruption in oxygen and nutrient delivery to the brain. Disruption of these crucial processes in the central nervous system leads to metabolic dysregulation and cell death. Fourier transform infrared (FTIR) spectroscopy can simultaneously measure total protein and lipid content along with a number of key biomarkers within brain tissue that cannot be observed using conventional techniques. FTIR imaging provides the opportunity to visualize this information in tissue which has not been chemically treated prior to analysis, thus retaining the spatial distribution and in situ chemical information. Here we present a review of FTIR imaging methods for investigating the biomarker responses in the post-stroke brain.
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Affiliation(s)
- Rhiannon E Boseley
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Nicole J Sylvain
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Lissa Peeling
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - Michael E Kelly
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
| | - M Jake Pushie
- Department of Surgery, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada.
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3
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Song X, Liu X, Luo Z, Dong J, Zhong W, Wang G, He B, Li Z, Liu Q. High-resolution iterative reconstruction at extremely low sampling rate for Fourier single-pixel imaging via diffusion model. OPTICS EXPRESS 2024; 32:3138-3156. [PMID: 38297542 DOI: 10.1364/oe.510692] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
The trade-off between imaging efficiency and imaging quality has always been encountered by Fourier single-pixel imaging (FSPI). To achieve high-resolution imaging, the increase in the number of measurements is necessitated, resulting in a reduction of imaging efficiency. Here, a novel high-quality reconstruction method for FSPI imaging via diffusion model was proposed. A score-based diffusion model is designed to learn prior information of the data distribution. The real-sampled low-frequency Fourier spectrum of the target is employed as a consistency term to iteratively constrain the model in conjunction with the learned prior information, achieving high-resolution reconstruction at extremely low sampling rates. The performance of the proposed method is evaluated by simulations and experiments. The results show that the proposed method has achieved superior quality compared with the traditional FSPI method and the U-Net method. Especially at the extremely low sampling rate (e.g., 1%), an approximately 241% improvement in edge intensity-based score was achieved by the proposed method for the coin experiment, compared with the traditional FSPI method. The method has the potential to achieve high-resolution imaging without compromising imaging speed, which will further expanding the application scope of FSPI in practical scenarios.
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Tiwari S, Falahkheirkhah K, Cheng G, Bhargava R. Colon Cancer Grading Using Infrared Spectroscopic Imaging-Based Deep Learning. APPLIED SPECTROSCOPY 2022; 76:475-484. [PMID: 35332784 PMCID: PMC9202565 DOI: 10.1177/00037028221076170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tumor grade assessment is critical to the treatment of cancers. A pathologist typically evaluates grade by examining morphologic organization in tissue using hematoxylin and eosin (H&E) stained tissue sections. Fourier transform infrared spectroscopic (FT-IR) imaging provides an alternate view of tissue in which spatially specific molecular information from unstained tissue can be utilized. Here, we examine the potential of IR imaging for grading colon cancer in biopsy samples. We used a 148-patient cohort to develop a deep learning classifier to estimate the tumor grade using IR absorption. We demonstrate that FT-IR imaging can be a viable tool to determine colorectal cancer grades, which we validated on an independent cohort of surgical resections. This work demonstrates that harnessing molecular information from FT-IR imaging and coupling it with morphometry is a potential path to develop clinically relevant grade prediction models.
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Affiliation(s)
- Saumya Tiwari
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Kianoush Falahkheirkhah
- Department of Chemical and Biomolecular Engineering and Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Georgina Cheng
- Carle Foundation Hospital (Carle Health), Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rohit Bhargava
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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5
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Lux L, Phal Y, Hsieh PH, Bhargava R. On the Limit of Detection in Infrared Spectroscopic Imaging. APPLIED SPECTROSCOPY 2022; 76:105-117. [PMID: 34643135 PMCID: PMC10539114 DOI: 10.1177/00037028211050961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Infrared (IR) spectroscopic imaging instruments' performance can be characterized and optimized by an analysis of their limit of detection (LOD). Here we report a systematic analysis of the LOD for Fourier transform IR (FT-IR) and discrete frequency IR (DFIR) imaging spectrometers. In addition to traditional measurements of sample and blank data, we propose a decision theory perspective to pose the determination of LOD as a binary classification problem under different assumptions of noise uniformity and correlation. We also examine three spectral analysis approaches, namely, absorbance at a single frequency, average of absorbance over selected frequencies and total spectral distance - to suit instruments that acquire discrete or contiguous spectral bandwidths. The analysis is validated by refining the fabrication of a bovine serum albumin protein microarray to provide eight uniform spots from ∼2.8 nL of solution for each concentration over a wide range (0.05-10 mg/mL). Using scanning parameters that are typical for each instrument, we estimate a LOD of 0.16 mg/mL and 0.12 mg/mL for widefield and line scanning FT-IR imaging systems, respectively, using the spectral distance approach, and 0.22 mg/mL and 0.15 mg/mL using an optimal set of discrete frequencies. As expected, averaging and the use of post-processing techniques such as minimum noise fraction transformation results in LODs as low as ∼0.075 mg/mL that correspond to a spotted protein mass of ∼112 fg/pixel. We emphasize that these measurements were conducted at typical imaging parameters for each instrument and can be improved using the usual trading rules of IR spectroscopy. This systematic analysis and methodology for determining the LOD can allow for quantitative measures of confidence in imaging an analyte's concentration and a basis for further improving IR imaging technology.
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Affiliation(s)
- Laurin Lux
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yamuna Phal
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pei-Hsuan Hsieh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Deparment of Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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6
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Cefarin N, Bedolla DE, Surowka A, Donato S, Sepperer T, Tondi G, Dreossi D, Sodini N, Birarda G, Vaccari L. Study of the Spatio-Chemical Heterogeneity of Tannin-Furanic Foams: From 1D FTIR Spectroscopy to 3D FTIR Micro-Computed Tomography. Int J Mol Sci 2021; 22:ijms222312869. [PMID: 34884675 PMCID: PMC8658003 DOI: 10.3390/ijms222312869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/25/2022] Open
Abstract
Tannin-furanic rigid foams are bio-based copolymers of tannin plant extract and furfuryl alcohol, promising candidates to replace synthetic insulation foams, as for example polyurethanes and phenolics, in eco-sustainable buildings thanks to their functional properties, such as lightness of the material and fire resistance. Despite their relevance as environmental-friendly alternatives to petroleum derivatives, many aspects of the polymerization chemistry still remain unclear. One of the open issues is on the spatial heterogeneity of the foam, i.e., whether the foam constituents prevalently polymerize in spatially segregated blocks or distribute almost homogenously in the foam volume. To address this matter, here we propose a multiscale FTIR study encompassing 1D FTIR spectroscopy, 2D FTIR imaging and 3D FTIR micro-tomography (FTIR-μCT) on tannin-furanic rigid foams obtained by varying the synthesis parameters in a controlled way. Thanks to the implementation of the acquisition and processing pipeline of FTIR-μCT, we were able for the first time to demonstrate that the polymer formulations influence the spatial organization of the foam at the microscale and, at the same time, prove the reliability of FTIR-μCT data by comparing 2D FTIR images and the projection of the 3D chemical images on the same plane.
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Affiliation(s)
- Nicola Cefarin
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
- IOM-CNR, Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy
| | - Diana E. Bedolla
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
- Area Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Artur Surowka
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
- Faculty of Physics and Applied Computer Science, Department of Medical Physics and Biophysics, AGH University of Science and Technology, al. Mickiewicza 30, 30-059 Kraków, Poland
| | - Sandro Donato
- Department of Physics, University of Calabria, Via P.Bucci 31C, 87036 Rende, Italy;
- Division of Frascati, Istituto Nazionale di Fisica Nucleare, Via Fermi, 54, 00044 Frascati, Italy
| | - Thomas Sepperer
- Forest Products Technology & Timber Constructions Department, Salzburg University of Applied Sciences, Marktstrasse 136a, 5431 Kuchl, Austria; (T.S.); (G.T.)
- Salzburg Center for Smart Materials, Jakob-Haringerstrasse 2a, 5020 Salzburg, Austria
| | - Gianluca Tondi
- Forest Products Technology & Timber Constructions Department, Salzburg University of Applied Sciences, Marktstrasse 136a, 5431 Kuchl, Austria; (T.S.); (G.T.)
- Department of Land, Environment, Agriculture & Forestry, University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy
| | - Diego Dreossi
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
| | - Nicola Sodini
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
| | - Giovanni Birarda
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
- Correspondence:
| | - Lisa Vaccari
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy; (N.C.); (D.E.B.); (A.S.); (D.D.); (N.S.); (L.V.)
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7
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Phal Y, Yeh K, Bhargava R. Design Considerations for Discrete Frequency Infrared Microscopy Systems. APPLIED SPECTROSCOPY 2021; 75:1067-1092. [PMID: 33876990 PMCID: PMC9993325 DOI: 10.1177/00037028211013372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Discrete frequency infrared chemical imaging is transforming the practice of microspectroscopy by enabling a diversity of instrumentation and new measurement capabilities. While a variety of hardware implementations have been realized, design considerations that are unique to infrared (IR) microscopes have not yet been compiled in literature. Here, we describe the evolution of IR microscopes, provide rationales for design choices, and catalog some major considerations for each of the optical components in an imaging system. We analyze design choices that use these components to optimize performance, under their particular constraints, while providing illustrative examples. We then summarize a framework to assess the factors that determine an instrument's performance mathematically. Finally, we provide a validation approach by enumerating performance metrics that can be used to evaluate the capabilities of imaging systems or suitability for specific intended applications. Together, the presented concepts and examples should aid in understanding available instrument configurations, while guiding innovations in design of the next generation of IR chemical imaging spectrometers.
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Affiliation(s)
- Yamuna Phal
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Kevin Yeh
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Rohit Bhargava
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, USA
- Departments of Bioengineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, USA
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8
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Time lapse synchrotron IR chemical imaging for observing the acclimation of a single algal cell to CO 2 treatment. Sci Rep 2021; 11:13246. [PMID: 34168226 PMCID: PMC8225881 DOI: 10.1038/s41598-021-92657-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/21/2021] [Indexed: 11/08/2022] Open
Abstract
Algae are the main primary producers in aquatic environments and therefore of fundamental importance for the global ecosystem. Mid-infrared (IR) microspectroscopy is a non-invasive tool that allows in principle studying chemical composition on a single-cell level. For a long time, however, mid-infrared (IR) imaging of living algal cells in an aqueous environment has been a challenge due to the strong IR absorption of water. In this study, we employed multi-beam synchrotron radiation to measure time-resolved IR hyperspectral images of individual Thalassiosira weissflogii cells in water in the course of acclimation to an abrupt change of CO2 availability (from 390 to 5000 ppm and vice versa) over 75 min. We used a previously developed algorithm to correct sinusoidal interference fringes from IR hyperspectral imaging data. After preprocessing and fringe correction of the hyperspectral data, principal component analysis (PCA) was performed to assess the spatial distribution of organic pools within the algal cells. Through the analysis of 200,000 spectra, we were able to identify compositional modifications associated with CO2 treatment. PCA revealed changes in the carbohydrate pool (1200-950 cm[Formula: see text]), lipids (1740, 2852, 2922 cm[Formula: see text]), and nucleic acid (1160 and 1201 cm[Formula: see text]) as the major response of exposure to elevated CO2 concentrations. Our results show a local metabolism response to this external perturbation.
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9
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Kochan K, Bedolla DE, Perez-Guaita D, Adegoke JA, Chakkumpulakkal Puthan Veettil T, Martin M, Roy S, Pebotuwa S, Heraud P, Wood BR. Infrared Spectroscopy of Blood. APPLIED SPECTROSCOPY 2021; 75:611-646. [PMID: 33331179 DOI: 10.1177/0003702820985856] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The magnitude of infectious diseases in the twenty-first century created an urgent need for point-of-care diagnostics. Critical shortages in reagents and testing kits have had a large impact on the ability to test patients with a suspected parasitic, bacteria, fungal, and viral infections. New point-of-care tests need to be highly sensitive, specific, and easy to use and provide results in rapid time. Infrared spectroscopy, coupled to multivariate and machine learning algorithms, has the potential to meet this unmet demand requiring minimal sample preparation to detect both pathogenic infectious agents and chronic disease markers in blood. This focal point article will highlight the application of Fourier transform infrared spectroscopy to detect disease markers in blood focusing principally on parasites, bacteria, viruses, cancer markers, and important analytes indicative of disease. Methodologies and state-of-the-art approaches will be reported and potential confounding variables in blood analysis identified. The article provides an up to date review of the literature on blood diagnosis using infrared spectroscopy highlighting the recent advances in this burgeoning field.
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Affiliation(s)
- Kamila Kochan
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Diana E Bedolla
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - David Perez-Guaita
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - John A Adegoke
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | | | - Miguela Martin
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Supti Roy
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Savithri Pebotuwa
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Philip Heraud
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Bayden R Wood
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
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10
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Hartnell D, Hollings A, Ranieri AM, Lamichhane HB, Becker T, Sylvain NJ, Hou H, Pushie MJ, Watkin E, Bambery KR, Tobin MJ, Kelly ME, Massi M, Vongsvivut J, Hackett MJ. Mapping sub-cellular protein aggregates and lipid inclusions using synchrotron ATR-FTIR microspectroscopy. Analyst 2021; 146:3516-3525. [PMID: 33881057 DOI: 10.1039/d1an00136a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Visualising direct biochemical markers of cell physiology and disease pathology at the sub-cellular level is an ongoing challenge in the biological sciences. A suite of microscopies exists to either visualise sub-cellular architecture or to indirectly view biochemical markers (e.g. histochemistry), but further technique developments and innovations are required to increase the range of biochemical parameters that can be imaged directly, in situ, within cells and tissue. Here, we report our continued advancements in the application of synchrotron radiation attenuated total reflectance Fourier transform infrared (SR-ATR-FTIR) microspectroscopy to study sub-cellular biochemistry. Our recent applications demonstrate the much needed capability to map or image directly sub-cellular protein aggregates within degenerating neurons as well as lipid inclusions within bacterial cells. We also characterise the effect of spectral acquisition parameters on speed of data collection and the associated trade-offs between a realistic experimental time frame and spectral/image quality. Specifically, the study highlights that the choice of 8 cm-1 spectral resolutions provide a suitable trade-off between spectral quality and collection time, enabling identification of important spectroscopic markers, while increasing image acquisition by ∼30% (relative to 4 cm-1 spectral resolution). Further, this study explores coupling a focal plane array detector with SR-ATR-FTIR, revealing a modest time improvement in image acquisition time (factor of 2.8). Such information continues to lay the foundation for these spectroscopic methods to be readily available for, and adopted by, the biological science community to facilitate new interdisciplinary endeavours to unravel complex biochemical questions and expand emerging areas of study.
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Affiliation(s)
- David Hartnell
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia. and Curtin Health Innovation Research Institute, Curtin University, Bentley, 6102, Western Australia
| | - Ashley Hollings
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia. and Curtin Health Innovation Research Institute, Curtin University, Bentley, 6102, Western Australia
| | - Anna Maria Ranieri
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia.
| | - Hum Bahadur Lamichhane
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia.
| | - Thomas Becker
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia.
| | - Nicole J Sylvain
- Division of Neurosurgery, Department of Surgery, College of Medicine, University of Saskatchewan, Saskatoon, Canada S7N 5E5
| | - Huishu Hou
- Division of Neurosurgery, Department of Surgery, College of Medicine, University of Saskatchewan, Saskatoon, Canada S7N 5E5
| | - M Jake Pushie
- Division of Neurosurgery, Department of Surgery, College of Medicine, University of Saskatchewan, Saskatoon, Canada S7N 5E5
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Bentley, Western Australia 6845
| | - Keith R Bambery
- ANSTO - Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, 3168, Australia
| | - Mark J Tobin
- ANSTO - Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, 3168, Australia
| | - Michael E Kelly
- Division of Neurosurgery, Department of Surgery, College of Medicine, University of Saskatchewan, Saskatoon, Canada S7N 5E5
| | - Massimiliano Massi
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia.
| | - Jitraporn Vongsvivut
- ANSTO - Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, 3168, Australia
| | - Mark J Hackett
- School of Molecular and Life Sciences, Curtin University, Bentley, 6845, Western Australia. and Curtin Health Innovation Research Institute, Curtin University, Bentley, 6102, Western Australia
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11
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Primpke S, Christiansen SH, Cowger W, De Frond H, Deshpande A, Fischer M, Holland EB, Meyns M, O'Donnell BA, Ossmann BE, Pittroff M, Sarau G, Scholz-Böttcher BM, Wiggin KJ. Critical Assessment of Analytical Methods for the Harmonized and Cost-Efficient Analysis of Microplastics. APPLIED SPECTROSCOPY 2020; 74:1012-1047. [PMID: 32249594 DOI: 10.1177/0003702820921465] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Microplastics are of major concerns for society and is currently in the focus of legislators and administrations. A small number of measures to reduce or remove primary sources of microplastics to the environment are currently coming into effect. At the moment, they have not yet tackled important topics such as food safety. However, recent developments such as the 2018 bill in California are requesting the analysis of microplastics in drinking water by standardized operational protocols. Administrations and analytical labs are facing an emerging field of methods for sampling, extraction, and analysis of microplastics, which complicate the establishment of standardized operational protocols. In this review, the state of the currently applied identification and quantification tools for microplastics are evaluated providing a harmonized guideline for future standardized operational protocols to cover these types of bills. The main focus is on the naked eye detection, general optical microscopy, the application of dye staining, flow cytometry, Fourier transform infrared spectroscopy (FT-Ir) and microscopy, Raman spectroscopy and microscopy, thermal degradation by pyrolysis-gas chromatography-mass spectrometry (py-GC-MS) as well as thermo-extraction and desorption gas chromatography-mass spectrometry (TED-GC-MS). Additional techniques are highlighted as well as the combined application of the analytical techniques suggested. An outlook is given on the emerging aspect of nanoplastic analysis. In all cases, the methods were screened for limitations, field work abilities and, if possible, estimated costs and summarized into a recommendation for a workflow covering the demands of society, legislation, and administration in cost efficient but still detailed manner.
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Affiliation(s)
- Sebastian Primpke
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Silke H Christiansen
- Research Group Christiansen, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
- Max Planck Institute for the Science of Light, Erlangen, Germany
- Physics Department, Freie Universität Berlin, Berlin, Germany
| | - Win Cowger
- University of California, Riverside, Riverside, CA, USA
| | - Hannah De Frond
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ashok Deshpande
- NOAA Fisheries, James J. Howard Marine Sciences Laboratory at Sandy Hook, Highlands, NJ, USA
| | - Marten Fischer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Erika B Holland
- Department of Biological Sciences, California State University of Long Beach, Long Beach, CA, USA
| | - Michaela Meyns
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Bridget A O'Donnell
- HORIBA Instruments Incorporated, A HORIBA Scientific Company, Piscataway, NJ, USA
| | - Barbara E Ossmann
- Bavarian Health and Food Safety Authority, Erlangen, Germany
- Food Chemistry Unit, Department of Chemistry and Pharmacy-Emil Fischer Center, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Marco Pittroff
- TZW: DVGW-Technologiezentrum Wasser (German Water Centre), Karlsruhe, Germany
| | - George Sarau
- Research Group Christiansen, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
- Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Barbara M Scholz-Böttcher
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Kara J Wiggin
- Department of Biological Sciences, California State University of Long Beach, Long Beach, CA, USA
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12
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Beć KB, Grabska J, Huck CW. Biomolecular and bioanalytical applications of infrared spectroscopy - A review. Anal Chim Acta 2020; 1133:150-177. [PMID: 32993867 DOI: 10.1016/j.aca.2020.04.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 12/11/2022]
Abstract
Infrared (IR; or mid-infrared, MIR; 4000-400 cm-1; 2500-25,000 nm) spectroscopy has become one of the most powerful and versatile tools at the disposal of modern bioscience. Because of its high molecular specificity, applicability to wide variety of samples, rapid measurement and non-invasivity, IR spectroscopy forms a potent approach to elucidate qualitative and quantitative information from various kinds of biological material. For these reasons, it became an established bioanalytical technique with diverse applications. This work aims to be a comprehensive and critical review of the recent accomplishments in the field of biomolecular and bioanalytical IR spectroscopy. That progress is presented on a wider background, with fundamental characteristics, the basic principles of the technique outlined, and its scientific capability directly compared with other methods being used in similar fields (e.g. near-infrared, Raman, fluorescence). The article aims to present a complete examination of the topic, as it touches the background phenomena, instrumentation, spectra processing and data analytical methods, spectra interpretation and related information. To suit this goal, the article includes a tutorial information essential to obtain a thorough perspective of bio-related applications of the reviewed methodologies. The importance of the fundamental factors to the final performance and applicability of IR spectroscopy in various areas of bioscience is explained. This information is interpreted in critical way, with aim to gain deep understanding why IR spectroscopy finds extraordinarily intensive use in this remarkably diverse and dynamic field of research and utility. The major focus is placed on the diversity of the applications in which IR biospectroscopy has been established so far and those onto which it is expanding nowadays. This includes qualitative and quantitative analytical spectroscopy, spectral imaging, medical diagnosis, monitoring of biophysical processes, and studies of physicochemical properties and dynamics of biomolecules. The application potential of IR spectroscopy in light of the current accomplishments and the future prospects is critically evaluated and its significance in the progress of bioscience is comprehensively presented.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria.
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13
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Recent trends in the application of Fourier Transform Infrared (FT-IR) spectroscopy in Heritage Science: from micro- to non-invasive FT-IR. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The relevance of FT-IR spectroscopy in heritage science has experienced a constant grow in the last two decades owing to analytical peculiarities that make it an extremely useful tool to answer the questions posed by the study and conservation of art-historical and archaeological materials. High versatility, sensitivity and molecular specificity are, in fact, all requirements that FT-IR spectroscopy fulfils allowing for the investigation of the chemical properties of heritage materials spanning from the micro- to the macro-scale and offering a variety of approaches to minimize sample manipulation and maximize extracted information. Molecular identification and localisation at high lateral resolution of organic and inorganic components in micro-samples was, over recently, the mostly exploited use of FT-IR in heritage science; however, benefiting from technological progress and advances in optical materials and components achieved in the last decade, it now stands out also for non-invasive surface analysis of artworks by fully portable instrumentation.
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14
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Feng B, Zhu J, Lu B, Liu F, Zhou L, Chen Y. Achieving Infrared Detection by All-Si Plasmonic Hot-Electron Detectors with High Detectivity. ACS NANO 2019; 13:8433-8441. [PMID: 31268682 DOI: 10.1021/acsnano.9b04236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An improved architecture for all-Si based photoelectronic detectors has been developed, consisting of a specially designed metasurface as the antenna integrated into a Si nanowire array on the insulator by an electron beam lithography based self-alignment process. Simulation using the Finite Difference Time Domain (FDTD) method was carried out to ensure perfect absorption of light by the detector. Optic measurement shows a 90% absorption at 1.05 μm. Photoelectronic characterization demonstrates the responsivity and detectivity as high as 94.5 mA/W and 4.38 × 1011 cm Hz1/2/W, respectively, at 1.15 μm with the bandwidth of 480 nm, which is comparable to that of III-V/II-VI compound detectors. It is understood that the outstanding performances over other reported all-Si based detectors originate from the enhanced quantum efficiency in one-dimensional conduction channels with high density of states, which efficiently accommodate the emitted plasmonic hot electrons for high conduction in the Si nanowires, enabling the near-infrared detection by all-Si based detectors.
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Affiliation(s)
- Bo Feng
- Nanolithography and Application Research Group, State Key Lab of Asic and System, School of Information Science and Technology , Fudan University , Shanghai 200433 , China
| | - Jingyuan Zhu
- Nanolithography and Application Research Group, State Key Lab of Asic and System, School of Information Science and Technology , Fudan University , Shanghai 200433 , China
| | - Bingrui Lu
- Nanolithography and Application Research Group, State Key Lab of Asic and System, School of Information Science and Technology , Fudan University , Shanghai 200433 , China
| | - Feifei Liu
- Department of Physics , Fudan University , Shanghai 200433 , China
| | - Lei Zhou
- Department of Physics , Fudan University , Shanghai 200433 , China
| | - Yifang Chen
- Nanolithography and Application Research Group, State Key Lab of Asic and System, School of Information Science and Technology , Fudan University , Shanghai 200433 , China
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15
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Zhong J, Liu Y, Ren J, Tang Y, Qi Z, Zhou X, Chen X, Shao Z, Chen M, Kaplan DL, Ling S. Understanding Secondary Structures of Silk Materials via Micro- and Nano-Infrared Spectroscopies. ACS Biomater Sci Eng 2019; 5:3161-3183. [PMID: 33405510 DOI: 10.1021/acsbiomaterials.9b00305] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The secondary structures (also termed conformations) of silk fibroin (SF) in animal silk fibers and regenerated SF materials are critical in determining mechanical performance and function of the materials. In order to understand the structure-mechanics-function relationships of silk materials, a variety of advanced infrared spectroscopic techniques, such as micro-infrared spectroscopies (micro-IR spectroscopies for short), synchrotron micro-IR spectroscopy, and nano-infrared spectroscopies (nano-IR spectroscopies for short), have been used to determine the conformations of SF in silk materials. These IR spectroscopic methods provide a useful toolkit to understand conformations and conformational transitions of SF in various silk materials with spatial resolution from the nano-scale to the micro-scale. In this Review, we first summarize progress in understanding the structure and structure-mechanics relationships of silk materials. We then discuss the state-of-the-art micro- and nano-IR spectroscopic techniques used for silk materials characterization. We also provide a systematic discussion of the strategies to collect high-quality spectra and the methods to analyze these spectra. Finally, we demonstrate the challenges and directions for future exploration of silk-based materials with IR spectroscopies.
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Affiliation(s)
- Jiajia Zhong
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yawen Liu
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Jing Ren
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yuzhao Tang
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Zeming Qi
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, China
| | - Xiaojie Zhou
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xin Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Zhengzhong Shao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | - Min Chen
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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16
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Christensen D, Rüther A, Kochan K, Pérez-Guaita D, Wood B. Whole-Organism Analysis by Vibrational Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:89-108. [PMID: 30978292 DOI: 10.1146/annurev-anchem-061318-115117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Vibrational spectroscopy has contributed to the understanding of biological materials for many years. As the technology has advanced, the technique has been brought to bear on the analysis of whole organisms. Here, we discuss advanced and recently developed infrared and Raman spectroscopic instrumentation to whole-organism analysis. We highlight many of the recent contributions made in this relatively new area of spectroscopy, particularly addressing organisms associated with disease with emphasis on diagnosis and treatment. The application of vibrational spectroscopic techniques to entire organisms is still in its infancy, but new developments in imaging and chemometric processing will likely expand in the field in the near future.
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Affiliation(s)
- Dale Christensen
- School of Chemistry, Monash University, Victoria 3800, Australia;
| | - Anja Rüther
- School of Chemistry, Monash University, Victoria 3800, Australia;
| | - Kamila Kochan
- School of Chemistry, Monash University, Victoria 3800, Australia;
| | | | - Bayden Wood
- School of Chemistry, Monash University, Victoria 3800, Australia;
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17
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Pushie MJ, Kelly ME, Hackett MJ. Direct label-free imaging of brain tissue using synchrotron light: a review of new spectroscopic tools for the modern neuroscientist. Analyst 2019; 143:3761-3774. [PMID: 29961790 DOI: 10.1039/c7an01904a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The incidence of brain disease and brain disorders is increasing on a global scale. Unfortunately, development of new therapeutic strategies has not increased at the same rate, and brain diseases and brain disorders now inflict substantial health and economic impacts. A greater understanding of the fundamental neurochemistry that underlies healthy brain function, and the chemical pathways that manifest in brain damage or malfunction, are required to enable and accelerate therapeutic development. A previous limitation to the study of brain function and malfunction has been the limited number of techniques that provide both a wealth of biochemical information, and spatially resolved information (i.e., there was a previous lack of techniques that provided direct biochemical or elemental imaging at the cellular level). In recent times, a suite of direct spectroscopic imaging techniques, such as Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence microscopy (XFM), and X-ray absorption spectroscopy (XAS) have been adapted, optimized and integrated into the field of neuroscience, to fill the above mentioned capability-gap. Advancements at synchrotron light sources, such as improved light intensity/flux, increased detector sensitivities and new capabilities of imaging/optics, has pushed the above suite of techniques beyond "proof-of-concept" studies, to routine application to study complex research problems in the field of neuroscience (and other scientific disciplines). This review examines several of the major advancements that have occurred over the last several years, with respect to FTIR, XFM and XAS capabilities at synchrotron facilities, and how the increases in technical capabilities have being integrated and used in the field of neuroscience.
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Affiliation(s)
- M J Pushie
- Department of Surgery, Division of Neurosurgery, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
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18
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Lasch P, Noda I. Two-Dimensional Correlation Spectroscopy (2D-COS) for Analysis of Spatially Resolved Vibrational Spectra. APPLIED SPECTROSCOPY 2019; 73:359-379. [PMID: 30488717 DOI: 10.1177/0003702818819880] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The last two decades have seen tremendous progress in the application of two-dimensional correlation spectroscopy (2D-COS) as a versatile analysis method for data series obtained using a large variety of different spectroscopic modalities, including infrared (IR) and Raman spectroscopy. The analysis technique is applicable to a series of spectra recorded under the influence of an external sample perturbation. Two-dimensional COS analysis is not only helpful to decipher correlations, which may exist between distinct spectral features, but can also be utilized to obtain the sequence of individual spectral changes. The focus of this review article is on the application of 2D-COS for analyzing spatially resolved data with special emphasis on hyperspectral imaging (HSI) study. In this review, we briefly introduce the fundamentals of the generalized 2D-COS analysis approach, discuss specific points of 2D-COS application to spatially resolved spectra and demonstrate essential aspects of data pre-processing for 2D-COS analysis of spatially resolved spectra. Based on illustrative examples, we show that 2D-COS is useful for spectral band assignment in HSI applications and demonstrate its utility for detecting subtle correlations between spectra features, or between features from different imaging modalities in the case of heterospectral (multimodal) HSI. Furthermore, a short overview on existing 2D-COS software tools is provided. It is hoped that this article represents not only a useful guideline for 2D-COS analyses of spatially resolved hyperspectral data but supports also further dissemination of the 2D-COS analysis method as a whole.
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Affiliation(s)
- Peter Lasch
- 1 Robert Koch-Institute, ZBS6-Proteomics and Spectroscopy, Berlin, Germany
| | - Isao Noda
- 2 Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
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19
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Aboualizadeh E, Ranji M, Sorenson CM, Sepehr R, Sheibani N, Hirschmugl CJ. Retinal oxidative stress at the onset of diabetes determined by synchrotron FTIR widefield imaging: towards diabetes pathogenesis. Analyst 2018; 142:1061-1072. [PMID: 28210739 DOI: 10.1039/c6an02603f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Diabetic retinopathy is a microvascular complication of diabetes that can lead to blindness. In the present study, we aimed to determine the nature of diabetes-induced, highly localized biochemical changes in the neuroretina at the onset of diabetes. High-resolution synchrotron Fourier transform infrared (s-FTIR) wide field microscopy coupled with multivariate analysis (PCA-LDA) was employed to identify biomarkers of diabetic retinopathy with spatial resolution at the cellular level. We compared the retinal tissue prepared from 6-week-old Ins2Akita/+ heterozygous (Akita/+, N = 6; a model of diabetes) male mice with the wild-type (control, N = 6) mice. Male Akita/+ mice become diabetic at 4-weeks of age. Significant differences (P < 0.001) in the presence of biomarkers associated with diabetes and segregation of spectra were achieved. Differentiating IR bands attributed to nucleic acids (964, 1051, 1087, 1226 and 1710 cm-1), proteins (1662 and 1608 cm-1) and fatty acids (2854, 2923, 2956 and 3012 cm-1) were observed between the Akita/+ and the WT samples. A comparison between distinctive layers of the retina, namely the photoreceptor retinal layer (PRL), outer plexiform layer (OPL), inner nucleus layer (INL) and inner plexiform layer (IPL) suggested that the photoreceptor layer is the most susceptible layer to oxidative stress in short-term diabetes. Spatially-resolved chemical images indicated heterogeneities and oxidative-stress induced alterations in the diabetic retina tissue morphology compared with the WT retina. In this study, the spectral biomarkers and the spatial biochemical alterations in the diabetic retina and in specific layers were identified for the first time. We believe that the conclusions drawn from these studies will help to bridge the gap in our understanding of the molecular and cellular mechanisms that contribute to the pathobiology of diabetic retinopathy.
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Affiliation(s)
| | - Mahsa Ranji
- Biophotonics Laboratory, University of Wisconsin-Milwaukee, Milwaukee, USA
| | | | - Reyhaneh Sepehr
- Biophotonics Laboratory, University of Wisconsin-Milwaukee, Milwaukee, USA
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, USA
| | - Carol J Hirschmugl
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, USA.
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20
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Hanninen AM, Prince RC, Ramos R, Plikus MV, Potma EO. High-resolution infrared imaging of biological samples with third-order sum-frequency generation microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:4807-4817. [PMID: 30319904 PMCID: PMC6179410 DOI: 10.1364/boe.9.004807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 05/10/2023]
Abstract
We studied the use of vibrationally resonant, third-order sum-frequency generation (TSFG) for imaging of biological samples. We found that laser-scanning TSFG provides vibrationally sensitive imaging capabilities of lipid droplets and structures in sectioned tissue samples. Although the contrast is based on the infrared-activity of molecular modes, TSFG images exhibit a high lateral resolution of 0.5 µm or better. We observed that the imaging properties of TSFG resemble the imaging properties of coherent anti-Stokes Raman scattering (CARS) microscopy, offering a nonlinear infrared alternative to coherent Raman methods. TSFG microscopy holds promise as a high-resolution imaging technique in the fingerprint region where coherent Raman techniques often provide insufficient sensitivity.
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Affiliation(s)
- Adam M. Hanninen
- Department of Astronomy and Physics, University of California, Irvine, CA 92697,
USA
| | - Richard C. Prince
- Department of Biomedical Engineering, University of California, Irvine, CA 92697,
USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, Sue and Bill Gross Stem Cell Research Center, Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Maksim V. Plikus
- Department of Developmental and Cell Biology, Sue and Bill Gross Stem Cell Research Center, Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Eric O. Potma
- Department of Chemistry, University of California, Irvine, CA 92697,
USA
- Beckman Laser Institute, Laser Microbeam and Medical Program, Irvine, CA 92617,
USA
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21
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Azarfar G, Aboualizadeh E, Walter NM, Ratti S, Olivieri C, Norici A, Nasse M, Kohler A, Giordano M, Hirschmugl CJ. Estimating and correcting interference fringes in infrared spectra in infrared hyperspectral imaging. Analyst 2018; 143:4674-4683. [PMID: 30176033 DOI: 10.1039/c8an00093j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Short-term acclimation response of individual cells of Thalassiosira weissflogii was monitored by Synchrotron FTIR imaging over the span of 75 minutes. The cells, collected from batch cultures, were maintained in a constant flow of medium, at an irradiance of 120 μmol m-2 s-1 and at 20 °C. Multiple internal reflections due to the micro fluidic channel were modeled, and showed that fringes are additive sinusoids to the pure absorption of the other components of the system. Preprocessing of the hyperspectral cube (x, y, Abs(λ)) included removing spectral fringe using an EMSC approach. Principal component analysis of the time series of hyperspectral cubes showed macromolecular pool variations (carbohydrates, lipids and DNA/RNA) of less than 2% after fringe correction.
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Affiliation(s)
- Ghazal Azarfar
- Department of Electrical Engineering, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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22
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Mouras R, Noor MR, Pastorino L, Bagnoli E, Mani A, Durack E, Antipov A, D’Autilia F, Bianchini P, Diaspro A, Soulimane T, Silien C, Ruggiero C, Tofail SAM. Image-Based Tracking of Anticancer Drug-Loaded Nanoengineered Polyelectrolyte Capsules in Cellular Environments Using a Fast Benchtop Mid-Infrared (MIR) Microscope. ACS OMEGA 2018; 3:6143-6150. [PMID: 30023942 PMCID: PMC6044925 DOI: 10.1021/acsomega.7b01859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
Drug delivery monitoring and tracking in the human body are two of the biggest challenges in targeted therapy to be addressed by nanomedicine. The ability of imaging drugs and micro-/nanoengineered drug carriers and of visualizing their interactions at the cellular interface in a label-free manner is crucial in providing the ability of tracking their cellular pathways and will help understand their biological impact, allowing thus to improve the therapeutic efficacy. We present a fast, label-free technique to achieve high-resolution imaging at the mid-infrared (MIR) spectrum that provides chemical information. Using our custom-made benchtop infrared microscope using a high-repetition-rate pulsed laser (80 MHz, 40 ps), we were able to acquire images with subwavelength resolution (0.8 × λ) at very high speeds. As a proof-of-concept, we embarked on the investigation of nanoengineered polyelectrolyte capsules (NPCs) containing the anticancer drug, docetaxel. These NPCs were synthesized using a layer-by-layer approach built upon a calcium carbonate (CaCO3) core, which was then removed away with ethylenediaminetetraacetic acid. The obtained MIR images show that NPCs are attached to the cell membrane, which is a good step toward an efficient drug delivery. This has been confirmed by both three-dimensional confocal fluorescence and stimulated emission depletion microscopy. Coupled with additional instrumentation and data processing advancements, this setup is capable of video-rate imaging speeds and will be significantly complementing current super-resolution microscopy techniques while providing an unperturbed view into living cells.
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Affiliation(s)
- Rabah Mouras
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
| | - Mohamed R. Noor
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
| | - Laura Pastorino
- Department
of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genova, Via Opera Pia, 13, 16145 Genova, Italy
| | - Enrico Bagnoli
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
- Department
of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genova, Via Opera Pia, 13, 16145 Genova, Italy
| | - Aladin Mani
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
| | - Edel Durack
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
| | - Alexei Antipov
- PlasmaChem
GmbH, Schwarzschildstr.
10, 12489 Berlin, Germany
| | - Francesca D’Autilia
- Nanophysics, Istituto Italiano di Tecnologia, Via Morego, 30, 16163 Genova, Italy
| | - Paolo Bianchini
- Nanophysics, Istituto Italiano di Tecnologia, Via Morego, 30, 16163 Genova, Italy
| | - Alberto Diaspro
- Nanophysics, Istituto Italiano di Tecnologia, Via Morego, 30, 16163 Genova, Italy
| | - Tewfik Soulimane
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
| | - Christophe Silien
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
| | - Carmelina Ruggiero
- Department
of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genova, Via Opera Pia, 13, 16145 Genova, Italy
| | - Syed A. M. Tofail
- Department
of Physics, Bernal Institute and Department of Chemical Sciences,
Bernal Institute, University of Limerick, Castletroy, Limerick V94
T9PX, Ireland
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23
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Liu P, Wang S, He P, Zhang Z. Dual-channel operation in a synchronously pumped optical parametric oscillator for the generation of broadband mid-infrared coherent light sources. OPTICS LETTERS 2018; 43:2217-2220. [PMID: 29714794 DOI: 10.1364/ol.43.002217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
We report, to the best of our knowledge, a novel approach for generating broadband mid-infrared (mid-IR) light by implementing a dual-channel scheme in a synchronously pumped optical parametric oscillator (SPOPO). Two-channel operation was achieved by inserting a prism pair and two reflection mirrors inside an optical parametric oscillator (OPO) cavity. Pumped by a Yb-fiber laser, the OPO generated an idler wave at ∼3150 nm with a -10 dB bandwidth of ∼13.2 THz, which was twice as much as that of the pump source. This scheme represents a promising technical route to transform conventional SPOPOs into a device capable of generating mid-IR light with very broad instantaneous bandwidth.
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24
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Yesiltas M. Investigation of carbonates in the Sutter's Mill meteorite grains with hyperspectral infrared imaging micro-spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 194:92-101. [PMID: 29328955 DOI: 10.1016/j.saa.2018.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/25/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Synchrotron-based high spatial resolution hyperspectral infrared imaging technique provides thousands of infrared spectra with high resolution, thus allowing us to acquire detailed spatial maps of chemical molecular structures for many grains in short times. Utilizing this technique, thousands of infrared spectra were analyzed at once instead of inspecting each spectrum separately. Sutter's Mill meteorite is a unique carbonaceous type meteorite with highly heterogeneous chemical composition. Multiple grains from the Sutter's Mill meteorite have been studied using this technique and the presence of both hydrous and anhydrous silicate minerals have been observed. It is observed that the carbonate mineralogy varies from simple to more complex carbonates even within a few microns in the meteorite grains. These variations, the type and distribution of calcite-like vs. dolomite-like carbonates are presented by means of hyperspectral FTIR imaging spectroscopy with high resolution. Various scenarios for the formation of different carbonate compositions in the Sutter's Mill parent body are discussed.
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Affiliation(s)
- Mehmet Yesiltas
- Faculty of Aeronautics and Space Sciences, Kirklareli University, Kirklareli 39000, Turkey.
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25
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Wrobel TP, Bhargava R. Infrared Spectroscopic Imaging Advances as an Analytical Technology for Biomedical Sciences. Anal Chem 2018; 90:1444-1463. [PMID: 29281255 PMCID: PMC6421863 DOI: 10.1021/acs.analchem.7b05330] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Tomasz P. Wrobel
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States
- Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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26
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Ran S, Berisha S, Mankar R, Shih WC, Mayerich D. Mitigating fringing in discrete frequency infrared imaging using time-delayed integration. BIOMEDICAL OPTICS EXPRESS 2018; 9:832-843. [PMID: 29552416 PMCID: PMC5854082 DOI: 10.1364/boe.9.000832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 05/14/2023]
Abstract
Infrared (IR) spectroscopic microscopes provide the potential for label-free quantitative molecular imaging of biological samples, which can be used to aid in histology, forensics, and pharmaceutical analysis. Most IR imaging systems use broadband illumination combined with a spectrometer to separate the signal into spectral components. This technique is currently too slow for many biomedical applications such as clinical diagnosis, primarily due to the availability of bright mid-infrared sources and sensitive MCT detectors. There has been a recent push to increase throughput using coherent light sources, such as synchrotron radiation and quantum cascade lasers. While these sources provide a significant increase in intensity, the coherence introduces fringing artifacts in the final image. We demonstrate that applying time-delayed integration in one dimension can dramatically reduce fringing artifacts with minimal alterations to the standard infrared imaging pipeline. The proposed technique also offers the potential for less expensive focal plane array detectors, since linear arrays can be more readily incorporated into the proposed framework.
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27
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Dazzi A, Prater CB. AFM-IR: Technology and Applications in Nanoscale Infrared Spectroscopy and Chemical Imaging. Chem Rev 2016; 117:5146-5173. [DOI: 10.1021/acs.chemrev.6b00448] [Citation(s) in RCA: 532] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexandre Dazzi
- Laboratoire
de Chimie Physique, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Craig B. Prater
- Anasys Instruments, 325 Chapala
St., Santa Barbara, California 93101, United States
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28
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Rüger J, Unger N, Schie IW, Brunner E, Popp J, Krafft C. Assessment of growth phases of the diatom Ditylum brightwellii by FT-IR and Raman spectroscopy. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Nallala J, Lloyd GR, Shepherd N, Stone N. High-resolution FTIR imaging of colon tissues for elucidation of individual cellular and histopathological features. Analyst 2016; 141:630-9. [DOI: 10.1039/c5an01871d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comparison of spectral-histopathological features of a colon tissue measured using a conventional (5.5 μm × 5.5 μm, left) and a high-magnification (1.1 μm × 1.1 μm, right) FTIR imaging system with respect to HE stained tissue (middle).
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Affiliation(s)
| | - Gavin Rhys Lloyd
- Biophotonics Research Unit
- Gloucestershire Royal Hospital
- Gloucester
- UK
| | - Neil Shepherd
- Department of Pathology
- Gloucestershire Hospitals NHS Foundation Trust
- Gloucester
- UK
| | - Nick Stone
- Biomedical Physics
- School of Physics
- University of Exeter
- UK
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30
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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31
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Wood BR, Bambery KR, Dixon MWA, Tilley L, Nasse MJ, Mattson E, Hirschmugl CJ. Diagnosing malaria infected cells at the single cell level using focal plane array Fourier transform infrared imaging spectroscopy. Analyst 2015; 139:4769-74. [PMID: 25055796 DOI: 10.1039/c4an00989d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New methods are needed to rapidly identify malaria parasites in blood smears. The coupling of a Focal Plane Array (FPA) infrared microscope system to a synchrotron light source at IRENI enables rapid molecular imaging at high spatial resolution. The technique, in combination with hyper-spectral processing, enables imaging and diagnosis of early stage malaria parasites at the single cell level in a blood smear. The method relies on the detection of distinct lipid signatures associated with the different stages of the malaria parasite and utilises resonant Mie extended multiplicative scatter correction to pre-process the spectra followed by full bandwidth image deconvolution to resolve the single cells. This work demonstrates the potential of focal plane technology to diagnose single cells in a blood smear. Brighter laboratory based infrared sources, optical refinements and higher sensitive detectors will soon see the emergence of focal plane array imaging in the clinical environment.
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Affiliation(s)
- Bayden R Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University, VIC 3800, Australia.
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32
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Clemens G, Hands JR, Dorling KM, Baker MJ. Vibrational spectroscopic methods for cytology and cellular research. Analyst 2015; 139:4411-44. [PMID: 25028699 DOI: 10.1039/c4an00636d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of vibrational spectroscopy, FTIR and Raman, for cytology and cellular research has the potential to revolutionise the approach to cellular analysis. Vibrational spectroscopy is non-destructive, simple to operate and provides direct information. Importantly it does not require expensive exogenous labels that may affect the chemistry of the cell under analysis. In addition, the advent of spectroscopic microscopes provides the ability to image cells and acquire spectra with a subcellular resolution. This introductory review focuses on recent developments within this fast paced field and highlights potential for the future use of FTIR and Raman spectroscopy. We particularly focus on the development of live cell research and the new technologies and methodologies that have enabled this.
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Affiliation(s)
- Graeme Clemens
- Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, Lancashire PR1 2HE, UK.
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33
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Leslie LS, Wrobel TP, Mayerich D, Bindra S, Emmadi R, Bhargava R. High definition infrared spectroscopic imaging for lymph node histopathology. PLoS One 2015; 10:e0127238. [PMID: 26039216 PMCID: PMC4454651 DOI: 10.1371/journal.pone.0127238] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
Abstract
Chemical imaging is a rapidly emerging field in which molecular information within samples can be used to predict biological function and recognize disease without the use of stains or manual identification. In Fourier transform infrared (FT-IR) spectroscopic imaging, molecular absorption contrast provides a large signal relative to noise. Due to the long mid-IR wavelengths and sub-optimal instrument design, however, pixel sizes have historically been much larger than cells. This limits both the accuracy of the technique in identifying small regions, as well as the ability to visualize single cells. Here we obtain data with micron-sized sampling using a tabletop FT-IR instrument, and demonstrate that the high-definition (HD) data lead to accurate identification of multiple cells in lymph nodes that was not previously possible. Highly accurate recognition of eight distinct classes - naïve and memory B cells, T cells, erythrocytes, connective tissue, fibrovascular network, smooth muscle, and light and dark zone activated B cells was achieved in healthy, reactive, and malignant lymph node biopsies using a random forest classifier. The results demonstrate that cells currently identifiable only through immunohistochemical stains and cumbersome manual recognition of optical microscopy images can now be distinguished to a similar level through a single IR spectroscopic image from a lymph node biopsy.
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Affiliation(s)
- L. Suzanne Leslie
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Tomasz P. Wrobel
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - David Mayerich
- Department of Electrical and Computer Engineering, University of Houston, Houston, Texas, United States America
| | - Snehal Bindra
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Rajyasree Emmadi
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Illinois, United States of America
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, United States of America
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Illinois, United States of America
- * E-mail:
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34
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Findlay CR, Wiens R, Rak M, Sedlmair J, Hirschmugl CJ, Morrison J, Mundy CJ, Kansiz M, Gough KM. Rapid biodiagnostic ex vivo imaging at 1 μm pixel resolution with thermal source FTIR FPA. Analyst 2015; 140:2493-503. [DOI: 10.1039/c4an01982b] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel high spatial resolution (1 × 1 μm pixel) FTIR imaging with commercial benchtop instrument yields data comparable to that from synchrotron sources.
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Affiliation(s)
- C. R. Findlay
- Department of Chemistry
- University of Manitoba
- Winnipeg MB
- Canada R3T2N2
| | - R. Wiens
- Department of Chemistry
- University of Manitoba
- Winnipeg MB
- Canada R3T2N2
| | - M. Rak
- Department of Chemistry
- University of Manitoba
- Winnipeg MB
- Canada R3T2N2
| | - J. Sedlmair
- Physics Department
- University of Wisconsin-Milwaukee
- USA
| | | | - Jason Morrison
- Department of Biosystems Engineering
- University of Manitoba
- Winnipeg MB
- Canada R3T2N2
| | - C. J. Mundy
- Centre for Earth Observation Science
- Department of Environment and Geography
- University of Manitoba
- Winnipeg MB
- Canada
| | - M. Kansiz
- Agilent Technologies Pty Ltd
- Mulgrave
- Australia
| | - K. M. Gough
- Department of Chemistry
- University of Manitoba
- Winnipeg MB
- Canada R3T2N2
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35
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Hughes C, Henderson A, Kansiz M, Dorling KM, Jimenez-Hernandez M, Brown MD, Clarke NW, Gardner P. Enhanced FTIR bench-top imaging of single biological cells. Analyst 2015; 140:2080-5. [DOI: 10.1039/c4an02053g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new optical system has recently been developed that enables infrared images to be obtained with a pixel resolution of 1 micron on a bench-top instrument using a thermal source.
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Affiliation(s)
- C. Hughes
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
- Genito Urinary Cancer Research Group
| | - A. Henderson
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
| | - M. Kansiz
- Agilent Technologies Australia Pty Ltd
- Mulgrave
- Australia
| | | | - M. Jimenez-Hernandez
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
- Genito Urinary Cancer Research Group
| | - M. D. Brown
- Genito Urinary Cancer Research Group
- Institute of Cancer Sciences
- Paterson Building
- The University of Manchester
- Manchester Academic Health Science Centre
| | - N. W. Clarke
- Genito Urinary Cancer Research Group
- Institute of Cancer Sciences
- Paterson Building
- The University of Manchester
- Manchester Academic Health Science Centre
| | - P. Gardner
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
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36
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Abstract
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Infrared
(IR) spectroscopic imaging systems are a powerful tool
for visualizing molecular microstructure of a sample without the need
for dyes or stains. Table-top Fourier transform infrared (FT-IR) imaging
spectrometers, the current established technology, can record broadband
spectral data efficiently but requires scanning the entire spectrum
with a low throughput source. The advent of high-intensity, broadly
tunable quantum cascade lasers (QCL) has now accelerated IR imaging
but results in a fundamentally different type of instrument and approach,
namely, discrete frequency IR (DF-IR) spectral imaging. While the
higher intensity of the source provides a higher signal per channel,
the absence of spectral multiplexing also provides new opportunities
and challenges. Here, we couple a rapidly tunable QCL with a high
performance microscope equipped with a cooled focal plane array (FPA)
detector. Our optical system is conceptualized to provide optimal
performance based on recent theory and design rules for high-definition
(HD) IR imaging. Multiple QCL units are multiplexed together to provide
spectral coverage across the fingerprint region (776.9 to 1904.4 cm–1) in our DF-IR microscope capable of broad spectral
coverage, wide-field detection, and diffraction-limited spectral imaging.
We demonstrate that the spectral and spatial fidelity of this system
is at least as good as the best FT-IR imaging systems. Our configuration
provides a speedup for equivalent spectral signal-to-noise ratio (SNR)
compared to the best spectral quality from a high-performance linear
array system that has 10-fold larger pixels. Compared to the fastest
available HD FT-IR imaging system, we demonstrate scanning of large
tissue microarrays (TMA) in 3-orders of magnitude smaller time per
essential spectral frequency. These advances offer new opportunities
for high throughput IR chemical imaging, especially for the measurement
of cells and tissues.
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Affiliation(s)
- Kevin Yeh
- Department of Bioengineering, ‡Department of Mechanical Science and Engineering, and §Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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37
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Walsh Z, Janeček ER, Hodgkinson JT, Sedlmair J, Koutsioubas A, Spring DR, Welch M, Hirschmugl CJ, Toprakcioglu C, Nitschke JR, Jones M, Scherman OA. Multifunctional supramolecular polymer networks as next-generation consolidants for archaeological wood conservation. Proc Natl Acad Sci U S A 2014; 111:17743-8. [PMID: 25385610 PMCID: PMC4273396 DOI: 10.1073/pnas.1406037111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The preservation of our cultural heritage is of great importance to future generations. Despite this, significant problems have arisen with the conservation of waterlogged wooden artifacts. Three major issues facing conservators are structural instability on drying, biological degradation, and chemical degradation on account of Fe(3+)-catalyzed production of sulfuric and oxalic acid in the waterlogged timbers. Currently, no conservation treatment exists that effectively addresses all three issues simultaneously. A new conservation treatment is reported here based on a supramolecular polymer network constructed from natural polymers with dynamic cross-linking formed by a combination of both host-guest complexation and a strong siderophore pendant from a polymer backbone. Consequently, the proposed consolidant has the ability to chelate and trap iron while enhancing structural stability. The incorporation of antibacterial moieties through a dynamic covalent linkage into the network provides the material with improved biological resistance. Exploiting an environmentally compatible natural material with completely reversible chemistries is a safer, greener alternative to current strategies and may extend the lifetime of many culturally relevant waterlogged artifacts around the world.
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Affiliation(s)
- Zarah Walsh
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Emma-Rose Janeček
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - James T Hodgkinson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Julia Sedlmair
- US Forest Service, US Department of Agriculture, Forest Products Laboratory, Madison, WI 53276; Department of Agriculture and Biological Engineering, Pennsylvania State University, University Park, PA 16802; Synchrotron Radiation Center, Stoughton, WI 53589
| | - Alexandros Koutsioubas
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, D-85747 Garching, Germany
| | - David R Spring
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Carol J Hirschmugl
- Synchrotron Radiation Center, Stoughton, WI 53589; Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | | | - Jonathan R Nitschke
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Mark Jones
- The Mary Rose Trust, HM Naval Base, Portsmouth PO1 3LX, United Kingdom
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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38
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Clède S, Policar C. Metal-carbonyl units for vibrational and luminescence imaging: towards multimodality. Chemistry 2014; 21:942-58. [PMID: 25376740 DOI: 10.1002/chem.201404600] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metal-carbonyl complexes are attractive structures for bio-imaging. In addition to unique vibrational properties due to the CO moieties enabling IR and Raman cell imaging, the appropriate choice of ancillary ligands opens up the opportunity for luminescence detection. Through a classification by techniques, past and recent developments in the application of metal-carbonyl complexes for vibrational and luminescence bio-imaging are reviewed. Finally, their potential as bimodal IR and luminescent probes is addressed.
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Affiliation(s)
- Sylvain Clède
- Ecole Normale Supérieure, PSL Research University, Département de Chimie, Sorbonne Universités-UPMC Univ Paris 06, CNRS-ENS-UPMC, Laboratoire des Biomolécules, UMR7203, 24, rue Lhomond, 75005 Paris (France), Fax: (+33) 1-4432-3389
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39
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Noda I. Frontiers of Two-Dimensional Correlation Spectroscopy. Part 1. New concepts and noteworthy developments. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.025] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Surveillance of C-allocation in microalgal cells. Metabolites 2014; 4:453-64. [PMID: 24957036 PMCID: PMC4101516 DOI: 10.3390/metabo4020453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 11/16/2022] Open
Abstract
When microalgae are exposed to changing environmental conditions, e.g., light-dark cycles or oscillations in nutrient availability (CO2, nitrogen, phosphate or silicate) they respond with metabolic changes in the carbon allocation pattern. Short time regulations in the time range of few seconds to minutes can be mirrored best by mass spectroscopy based metabolomics. However, these snap shots do not reflect the alterations in the carbon flow to the cellular macromolecules like protein, carbohydrate or lipid. In this review it is shown how the combination of FTIR spectroscopy and Chla-in-vivo-fluorescence based electron transport rates can reveal changes in the metabolic flux rates of carbon during a shift of the environmental conditions. The review will demonstrate in which time range FTIR spectroscopy can deliver significant information and how FTIR spectroscopy data can synergistically support metabolome analysis by mass-spectroscopy.
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41
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Jiang X, Yang Z, Han L. A Markov random field based approach to the identification of meat and bone meal in feed by near-infrared spectroscopic imaging. Anal Bioanal Chem 2014; 406:4705-14. [DOI: 10.1007/s00216-014-7854-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/14/2014] [Accepted: 04/24/2014] [Indexed: 10/25/2022]
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42
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Clède S, Policar C, Sandt C. Fourier transform infrared (FT-IR) spectromicroscopy to identify cell organelles: correlation with fluorescence staining in MCF-7 breast cancer cells. APPLIED SPECTROSCOPY 2014; 68:113-117. [PMID: 24405961 DOI: 10.1366/13-07139] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecules display specific vibrational signatures in the infrared (IR) range, and organelles that concentrate these biomolecules can be identified by these IR signatures. Subcellular identification and location of cell organelles using IR signatures is attractive as it does not require the use of any specific trackers and is thus non-invasive and non-destructive. We show here that endogenous IR absorptions are relevant to detecting and imaging the nucleus, the cytoplasm, and the Golgi apparatus/endoplasmic reticulum in MCF-7 breast cancer cells, and we compare these results with our previous work on the HeLa cell line. We correlate maps of fixed and dried cells obtained by synchrotron radiation Fourier transform infrared (SR FT-IR) spectromicroscopy with epifluorescence images using fluorescent trackers for Golgi apparatus and nucleus, namely BODIPY TR C5-ceramide complexed to BSA and DAPI, respectively. Interestingly, the ratios of the IR bands CH2 : CH3 (both asymmetric and symmetric) and CO((ester)):amide I were shown to be reliable gauges of the lipidic character of a cellular compartment, the -CH2 and the CO((ester)) absorptions increasing with the presence of inner membranes like in the Golgi apparatus.
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43
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Liao CR, Rak M, Lund J, Unger M, Platt E, Albensi BC, Hirschmugl CJ, Gough KM. Synchrotron FTIR reveals lipid around and within amyloid plaques in transgenic mice and Alzheimer's disease brain. Analyst 2013; 138:3991-7. [PMID: 23586070 DOI: 10.1039/c3an00295k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
While the basis of neuronal degeneration in Alzheimer's disease (AD) continues to be debated, the amyloid cascade hypothesis remains central. Amyloid plaques are a required pathological marker for post mortem diagnosis, and Aβ peptide is regarded by most as a critical trigger at the very least. We present spectrochemical image analysis of brain tissue sections obtained with the mid-infrared beamline IRENI (InfraRed ENvironmental Imaging, Synchrotron Radiation Center, U Wisconsin-Madison), where the pixel resolution of 0.54 × 0.54 µm(2) permits analysis at sub-cellular dimensions. Spectrochemical images of dense core plaque found in hippocampus and cortex sections of two transgenic mouse models of AD (TgCRND8 and 3×Tg) are compared with plaque images from a 91 year old apoE43 human AD case. Spectral analysis was done in conjunction with histochemical stains of serial sections. A lipid membrane-like spectral signature surrounded and infiltrated the dense core plaques in all cases. Remarkable compositional similarities in early stage plaques suggest similar routes to plaque formation, regardless of genetic predisposition or mammalian origin.
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Affiliation(s)
- Catherine R Liao
- Department of Chemistry, University of Manitoba, 360 Parker Building,144 Dysart Road, Winnipeg, Manitoba, Canada.
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Opportunities for live cell FT-infrared imaging: macromolecule identification with 2D and 3D localization. Int J Mol Sci 2013; 14:22753-81. [PMID: 24256815 PMCID: PMC3856089 DOI: 10.3390/ijms141122753] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/22/2022] Open
Abstract
Infrared (IR) spectromicroscopy, or chemical imaging, is an evolving technique that is poised to make significant contributions in the fields of biology and medicine. Recent developments in sources, detectors, measurement techniques and speciman holders have now made diffraction-limited Fourier transform infrared (FTIR) imaging of cellular chemistry in living cells a reality. The availability of bright, broadband IR sources and large area, pixelated detectors facilitate live cell imaging, which requires rapid measurements using non-destructive probes. In this work, we review advances in the field of FTIR spectromicroscopy that have contributed to live-cell two and three-dimensional IR imaging, and discuss several key examples that highlight the utility of this technique for studying the structure and chemistry of living cells.
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Martin MC, Dabat-Blondeau C, Unger M, Sedlmair J, Parkinson DY, Bechtel HA, Illman B, Castro JM, Keiluweit M, Buschke D, Ogle B, Nasse MJ, Hirschmugl CJ. 3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography. Nat Methods 2013; 10:861-4. [PMID: 23913258 DOI: 10.1038/nmeth.2596] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/02/2013] [Indexed: 10/26/2022]
Abstract
We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical and morphological localization by determining a complete infrared spectrum for every voxel (millions of spectra determined per sample).
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Affiliation(s)
- Michael C Martin
- Advanced Light Source Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
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Ling S, Qi Z, Knight DP, Huang Y, Huang L, Zhou H, Shao Z, Chen X. Insight into the structure of single Antheraea pernyi silkworm fibers using synchrotron FTIR microspectroscopy. Biomacromolecules 2013; 14:1885-92. [PMID: 23607809 DOI: 10.1021/bm400267m] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synchrotron FTIR (S-FTIR) microspectroscopy was used to monitor both protein secondary structures (conformations) and their orientations in single cocoon silk fibers of the Chinese Tussah silk moth ( Antheraea pernyi ). In addition, to understand further the relationship between structure and properties of single silk fibers, we studied the changes of orientation and content of different secondary structures in single A. pernyi silk fibers when subjected to different strains. The results showed that the content and orientation of β-sheet was almost unchanged for strains from 0 to 0.3. However, the orientation of α-helix and random coil improved progressively with increasing strain, with a parallel decrease in α-helix content and an increase in random coil. This clearly indicates that most of the deformation upon stretching of the single fiber is due to the change of orientation in the amorphous regions coupled with a conversion of some of the α-helix to random coil. These observations provide an explanation for the supercontraction behavior of certain animal silks and are likely to facilitate understanding and optimization of postdrawing used in the conjunction with the wet-spinning of silk fibers from regenerated silk solutions. Thus, our work demonstrates the power of S-FTIR microspectroscopy for studying biopolymers.
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Affiliation(s)
- Shengjie Ling
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University , Shanghai, 200433, People's Republic of China
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Clemons C, Sedlmair J, Illman B, Ibach R, Hirschmugl C. Chemically imaging the effects of the addition of nanofibrillated cellulose on the distribution of poly(acrylic acid) in poly(vinyl alcohol). POLYMER 2013. [DOI: 10.1016/j.polymer.2013.02.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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48
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Wagner H, Dunker S, Liu Z, Wilhelm C. Subcommunity FTIR-spectroscopy to determine physiological cell states. Curr Opin Biotechnol 2013; 24:88-94. [DOI: 10.1016/j.copbio.2012.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/11/2012] [Accepted: 09/12/2012] [Indexed: 11/28/2022]
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49
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Kazarian SG, Chan KLA. ATR-FTIR spectroscopic imaging: recent advances and applications to biological systems. Analyst 2013; 138:1940-51. [DOI: 10.1039/c3an36865c] [Citation(s) in RCA: 267] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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50
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Janssens K, Alfeld M, Van der Snickt G, De Nolf W, Vanmeert F, Radepont M, Monico L, Dik J, Cotte M, Falkenberg G, Miliani C, Brunetti BG. The use of synchrotron radiation for the characterization of artists' pigments and paintings. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:399-425. [PMID: 23772661 DOI: 10.1146/annurev-anchem-062012-092702] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We review methods and recent studies in which macroscopic to (sub)microscopic X-ray beams were used for nondestructive analysis and characterization of pigments, paint microsamples, and/or entire paintings. We discuss the use of portable laboratory- and synchrotron-based instrumentation and describe several variants of X-ray fluorescence (XRF) analysis used for elemental analysis and imaging and combined with X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS). Macroscopic and microscopic (μ-)XRF variants of this method are suitable for visualizing the elemental distribution of key elements in paint multilayers. Technical innovations such as multielement, large-area XRF detectors have enabled such developments. The use of methods limited to elemental analysis or imaging usually is not sufficient to elucidate the chemical transformations that take place during natural pigment alteration processes. However, synchrotron-based combinations of μ-XRF, μ-XAS, and μ-XRD are suitable for such studies.
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Affiliation(s)
- Koen Janssens
- Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
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