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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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2
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Clède S, Sandt C, Dumas P, Policar C. Monitoring the Kinetics of the Cellular Uptake of a Metal Carbonyl Conjugated with a Lipidic Moiety in Living Cells Using Synchrotron Infrared Spectromicroscopy. APPLIED SPECTROSCOPY 2020; 74:63-71. [PMID: 31617373 DOI: 10.1177/0003702819877260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Presented here is the exploitation of synchrotron infrared spectromicroscopy to evaluate the feasibility of monitoring the cellular uptake of rhenium-tris-carbonyl-tagged (Re(CO)3) lipophilic chains in living cells. To this aim, an in-house thermostated microfluidic device was used to limit water absorption while keeping cells alive. Indeed, cells showed a high survival rate in the microfluidic device over the course of the experiment, proving the short-term biocompatibility of the device. We recorded spectra of single, living, fully hydrated breast cancer MDA-MB231 cells and could follow the penetration of the rhenium complexes for up to 2 h. Despite the strong variations observed in the uptake kinetics between individual cells, the Re(CO)3 complex was traced inside the cells at low concentration and shown to enter them on the hour time scale by active transport.
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Affiliation(s)
- Sylvain Clède
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne université, Paris, France
| | - Christophe Sandt
- SMIS beamline, SOLEIL synchrotron, L'orme des Merisiers, Gif sur Yvette, France
| | - Paul Dumas
- SMIS beamline, SOLEIL synchrotron, L'orme des Merisiers, Gif sur Yvette, France
| | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, Ecole normale supérieure, PSL University, Sorbonne université, Paris, France
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3
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Grenci G, Bertocchi C, Ravasio A. Integrating Microfabrication into Biological Investigations: the Benefits of Interdisciplinarity. MICROMACHINES 2019; 10:E252. [PMID: 30995747 PMCID: PMC6523848 DOI: 10.3390/mi10040252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/08/2019] [Accepted: 04/13/2019] [Indexed: 12/14/2022]
Abstract
The advent of micro and nanotechnologies, such as microfabrication, have impacted scientific research and contributed to meaningful real-world applications, to a degree seen during historic technological revolutions. Some key areas benefitting from the invention and advancement of microfabrication platforms are those of biological and biomedical sciences. Modern therapeutic approaches, involving point-of-care, precision or personalized medicine, are transitioning from the experimental phase to becoming the standard of care. At the same time, biological research benefits from the contribution of microfluidics at every level from single cell to tissue engineering and organoids studies. The aim of this commentary is to describe, through proven examples, the interdisciplinary process used to develop novel biological technologies and to emphasize the role of technical knowledge in empowering researchers who are specialized in a niche area to look beyond and innovate.
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Affiliation(s)
- Gianluca Grenci
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore.
- Biomedical Engineering Department, National University of Singapore, Singapore 117583, Singapore.
| | - Cristina Bertocchi
- Department of Physiology, School of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile.
| | - Andrea Ravasio
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile.
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4
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Investigation on Conversion Pathways in Degradative Solvent Extraction of Rice Straw by Using Liquid Membrane-FTIR Spectroscopy. ENERGIES 2019. [DOI: 10.3390/en12030528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Degradative solvent extraction (DSE) is effective in both dewatering and upgrading biomass wastes through the selective removal of oxygen functional groups. However, this conversion mechanism has yet to be elucidated. Here, liquid membrane-FTIR spectroscopy was utilized to examine the main liquid product (Solvent-soluble) without sample modification. Rice straw (RS) and 1-methylnaphthalene (as a non-hydrogen donor solvent) were used as materials, and measurements were performed at treatment temperatures of 200, 250, 300, and 350 °C for 0 min, and at 350 °C for 60 min. The Solvent-soluble spectra were quantitatively analyzed, and changes in the oxygen-containing functional groups and hydrogen bonds at each temperature were used to characterize the DSE mechanism. It was determined that the DSE reaction process can be divided into three stages. During the first stage, 200–300 °C (0 min), oxygen was removed via dehydration, and aromaticity was observed. In the second stage, 300–350 °C (0 min), deoxygenation reactions involving dehydration and decarboxylation were followed by reactions for aromatization. For the third stage, 350 °C (0–60 min), further aromatization and dehydration reactions were observed. Intramolecular reactions are indicated as the predominant mechanism for dehydration in RS DSE, and the final product is composed of smaller molecular compounds.
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5
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Morhart TA, Read S, Wells G, Jacobs M, Rosendahl SM, Achenbach S, Burgess IJ. Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectromicroscopy Using Synchrotron Radiation and Micromachined Silicon Wafers for Microfluidic Applications. APPLIED SPECTROSCOPY 2018; 72:1781-1789. [PMID: 29893584 DOI: 10.1177/0003702818785640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A custom-designed optical configuration compatible with the use of micromachined multigroove internal reflection elements (μ-groove IREs) for attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and imaging applications in microfluidic devices is described. The μ-groove IREs consist of several face-angled grooves etched into a single, monolithic silicon chip. The optical configuration permits individual grooves to be addressed by focusing synchrotron sourced IR light through a 150 µm pinhole aperture, restricting the beam spot size to a dimension smaller than that of the groove walls. The effective beam spot diameter at the ATR sampling plane is determined through deconvolution of the measured detector response and found to be 70 µm. The μ-groove IREs are highly compatible with standard photolithographic techniques as demonstrated by printing a 400 µm wide channel in an SU-8 film spin-coated on the IRE surface. Attenuated total reflection FT-IR mapping as a function of sample position across the channel illustrates the potential application of this approach for rapid prototyping of microfluidic devices.
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Affiliation(s)
- Tyler A Morhart
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Stuart Read
- Canadian Light Source, Saskatoon, SK, Canada
| | - Garth Wells
- Canadian Light Source, Saskatoon, SK, Canada
| | | | | | - Sven Achenbach
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ian J Burgess
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK, Canada
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6
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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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7
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Loutherback K, Birarda G, Chen L, Holman HYN. Microfluidic approaches to synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy of living biosystems. Protein Pept Lett 2016; 23:273-82. [PMID: 26732243 PMCID: PMC4997923 DOI: 10.2174/0929866523666160106154035] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/30/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
Abstract
A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the water thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.
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Affiliation(s)
| | | | | | - Hoi-Ying N Holman
- Berkeley Synchrotron Infrared Structural Biology Program, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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8
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Birarda G, Ravasio A, Suryana M, Maniam S, Holman HYN, Grenci G. IR-Live: fabrication of a low-cost plastic microfluidic device for infrared spectromicroscopy of living cells. LAB ON A CHIP 2016; 16:1644-1651. [PMID: 27040369 DOI: 10.1039/c5lc01460c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Water is a strong mid-infrared absorber, which has hindered the full exploitation of label-free and non-invasive infrared (IR) spectromicroscopy techniques for the study of living biological samples. To overcome this barrier, many researchers have built sophisticated fluidic chambers or microfluidic chips wherein the depth of the liquid medium in the sample compartment is limited to 10 μm or less. Here we report an innovative and simple way to fabricate plastic devices with infrared transparent view-ports enabling infrared spectromicroscopy of living biological samples; therefore the device is named "IR-Live". Advantages of this approach include lower production costs, a minimal need to access a micro-fabrication facility, and unlimited mass or waste exchange for the living samples surrounding the view-port area. We demonstrate that the low-cost IR-Live in combination with microfluidic perfusion techniques enables long term (>60 h) cell culture, which broadens the capability of IR spectromicroscopy for studying living biological samples. To illustrate this, we first applied the device to study protein and lipid polarity in migrating REF52 fibroblasts by collecting 2-dimensional spectral chemical maps at a micrometer spatial resolution. Then, we demonstrated the suitability of our approach to study dynamic cellular events by collecting a time series of spectral maps of U937 monocytes during the early stage of cell attachment to a bio-compatible surface.
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Affiliation(s)
- G Birarda
- Berkeley Synchrotron Infrared Structural Biology Program, Lawrence Berkeley National Laboratory, 1 Cyclotron road, 94720 Berkeley, USA and Elettra - Sincrotrone Trieste, Strada Statale 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - A Ravasio
- Mechanobiology Institute (MBI), National University of Singapore, 5A Engineering Drive 1, 117411 Singapore, Singapore.
| | - M Suryana
- Mechanobiology Institute (MBI), National University of Singapore, 5A Engineering Drive 1, 117411 Singapore, Singapore.
| | - S Maniam
- Mechanobiology Institute (MBI), National University of Singapore, 5A Engineering Drive 1, 117411 Singapore, Singapore.
| | - H-Y N Holman
- Berkeley Synchrotron Infrared Structural Biology Program, Lawrence Berkeley National Laboratory, 1 Cyclotron road, 94720 Berkeley, USA
| | - G Grenci
- Mechanobiology Institute (MBI), National University of Singapore, 5A Engineering Drive 1, 117411 Singapore, Singapore.
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9
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Quaroni L, Zlateva T, Wehbe K, Cinque G. Infrared imaging of small molecules in living cells: from in vitro metabolic analysis to cytopathology. Faraday Discuss 2016; 187:259-71. [DOI: 10.1039/c5fd00156k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A major topic in InfraRed (IR) spectroscopic studies of living cells is the complexity of the vibrational spectra, involving hundreds of overlapping absorption bands from all the cellular components present at detectable concentrations. We focus on the relative contribution of both small-molecule metabolites and macromolecules, while defining the spectroscopic properties of cells and tissue in the middle IR (midIR) region. As a consequence, we show the limitations of current interpretative schemes that rely on a small number of macromolecules for IR band assignment. The discussion is framed specifically around the glycolytic metabolism of cancer cells because of the potential pharmacological applications. Several metabolites involved in glycolysis by A549 lung cancer cells can be identified by this approach, which we refer to as Correlated Cellular Spectro-Microscopy (CSM). It is noteworthy that the rate of formation or consumption of specific molecules could be quantitatively assessed by this approach. We now extend this analysis to the two-dimensional case by performing IR imaging on single cells and cell clusters, detecting variations of metabolite concentration in time and space across the sample. The molecular detail obtained from this analysis allows its use in evaluating the pharmacological effect of inhibitors of glycolytic enzymes with potential consequences for in vitro drug testing. Finally we highlight the implications of the spectral contribution from cellular metabolites on applications in IR spectral cytopathology (SCP).
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Affiliation(s)
- Luca Quaroni
- Institute of Nuclear Physics, Polish Academy of Sciences
- Kraków
- Poland
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10
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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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11
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Gelfand P, Smith RJ, Stavitski E, Borchelt DR, Miller LM. Characterization of Protein Structural Changes in Living Cells Using Time-Lapsed FTIR Imaging. Anal Chem 2015; 87:6025-31. [PMID: 25965274 DOI: 10.1021/acs.analchem.5b00371] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fourier-transform infrared (FTIR) spectroscopic imaging is a widely used method for studying the chemistry of proteins, lipids, and DNA in biological systems without the need for additional tagging or labeling. This technique can be especially powerful for spatially resolved, temporal studies of dynamic changes such as in vivo protein folding in cell culture models. However, FTIR imaging experiments have typically been limited to dry samples as a result of the significant spectral overlap between water and the protein Amide I band centered at 1650 cm(-1). Here, we demonstrate a method to rapidly obtain high quality FTIR spectral images at submicron pixel resolution in vivo over a duration of 18 h and longer through the development and use of a custom-built, demountable, microfluidic-incubator and a FTIR microscope coupled to a focal plane array (FPA) detector and a synchrotron light source. The combined system maximizes ease of use by allowing a user to perform standard cell culture techniques and experimental manipulation outside of the microfluidic-incubator, where assembly can be done just before the start of experimentation. The microfluidic-incubator provides an optimal path length of 6-8 μm and a submillimeter working distance in order to obtain FTIR images with 0.54-0.77 μm pixel resolution. In addition, we demonstrate a novel method for the correction of spectral distortions caused by varying concentrations of water over a subconfluent field of cells. Lastly, we use the microfluidic-incubator and time-lapsed FTIR imaging to determine the misfolding pathway of mutant copper-zinc superoxide dismutase (SOD1), the protein known to be a cause of familial amyotrophic lateral sclerosis (FALS).
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Affiliation(s)
- Paul Gelfand
- †Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Randy J Smith
- ‡National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Eli Stavitski
- ‡National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - David R Borchelt
- §Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, Santa Fe HealthCare Alzheimer's Disease Research Center, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Lisa M Miller
- †Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.,‡National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
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12
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Loutherback K, Chen L, Holman HYN. Open-Channel Microfluidic Membrane Device for Long-Term FT-IR Spectromicroscopy of Live Adherent Cells. Anal Chem 2015; 87:4601-6. [DOI: 10.1021/acs.analchem.5b00524] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kevin Loutherback
- Berkeley Synchrotron Infrared
Structural Biology (BSISB) Program, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Liang Chen
- Berkeley Synchrotron Infrared
Structural Biology (BSISB) Program, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hoi-Ying N. Holman
- Berkeley Synchrotron Infrared
Structural Biology (BSISB) Program, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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13
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Yang H, Yang S, Kong J, Dong A, Yu S. Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy. Nat Protoc 2015; 10:382-96. [PMID: 25654756 DOI: 10.1038/nprot.2015.024] [Citation(s) in RCA: 657] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fourier transform IR (FTIR) spectroscopy is a nondestructive technique for structural characterization of proteins and polypeptides. The IR spectral data of polymers are usually interpreted in terms of the vibrations of a structural repeat. The repeat units in proteins give rise to nine characteristic IR absorption bands (amides A, B and I-VII). Amide I bands (1,700-1,600 cm(-1)) are the most prominent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary structural components. In this protocol, we have detailed the principles that underlie the determination of protein secondary structure by FTIR spectroscopy, as well as the basic steps involved in protein sample preparation, instrument operation, FTIR spectra collection and spectra analysis in order to estimate protein secondary-structural components in aqueous (both H2O and deuterium oxide (D2O)) solution using algorithms, such as second-derivative, deconvolution and curve fitting. Small amounts of high-purity (>95%) proteins at high concentrations (>3 mg ml(-1)) are needed in this protocol; typically, the procedure can be completed in 1-2 d.
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Affiliation(s)
- Huayan Yang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Shouning Yang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, China
| | - Aichun Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, Colorado, USA
| | - Shaoning Yu
- Department of Chemistry, Fudan University, Shanghai, China
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14
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Mattson E, Pande K, Cui S, Weinert M, Chen J, Hirschmugl C. Investigation of NO 2 adsorption on reduced graphene oxide. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Vasdekis AE, Stephanopoulos G. Review of methods to probe single cell metabolism and bioenergetics. Metab Eng 2015; 27:115-135. [PMID: 25448400 PMCID: PMC4399830 DOI: 10.1016/j.ymben.2014.09.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/26/2022]
Abstract
Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed.
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Affiliation(s)
- Andreas E Vasdekis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99354, USA.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139, USA.
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16
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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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17
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Baker MJ, Trevisan J, Bassan P, Bhargava R, Butler HJ, Dorling KM, Fielden PR, Fogarty SW, Fullwood NJ, Heys KA, Hughes C, Lasch P, Martin-Hirsch PL, Obinaju B, Sockalingum GD, Sulé-Suso J, Strong RJ, Walsh MJ, Wood BR, Gardner P, Martin FL. Using Fourier transform IR spectroscopy to analyze biological materials. Nat Protoc 2014; 9:1771-91. [PMID: 24992094 PMCID: PMC4480339 DOI: 10.1038/nprot.2014.110] [Citation(s) in RCA: 985] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
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Affiliation(s)
- Matthew J Baker
- 1] Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK. [2] Present address: WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Júlio Trevisan
- 1] Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK. [2] School of Computing and Communications, Lancaster University, Lancaster, UK
| | - Paul Bassan
- Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK
| | - Rohit Bhargava
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Holly J Butler
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Konrad M Dorling
- Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK
| | - Peter R Fielden
- Department of Chemistry, Lancaster University, Lancaster, UK
| | - Simon W Fogarty
- 1] Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK. [2] Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Nigel J Fullwood
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Kelly A Heys
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Caryn Hughes
- Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK
| | - Peter Lasch
- Proteomics and Spectroscopy (ZBS 6), Robert-Koch-Institut, Berlin, Germany
| | - Pierre L Martin-Hirsch
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Blessing Obinaju
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Ganesh D Sockalingum
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims, France
| | - Josep Sulé-Suso
- Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent, UK
| | - Rebecca J Strong
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Michael J Walsh
- Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois, USA
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Peter Gardner
- Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK
| | - Francis L Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
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18
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Mitri E, Birarda G, Vaccari L, Kenig S, Tormen M, Grenci G. SU-8 bonding protocol for the fabrication of microfluidic devices dedicated to FTIR microspectroscopy of live cells. LAB ON A CHIP 2014; 14:210-218. [PMID: 24195959 DOI: 10.1039/c3lc50878a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Here we present a new bonding protocol for SU-8 negative tone photoresist that exploits the chemical modifications induced in the resin by exposure to 254 nm (UVC) light. Fourier Transform Infrared microspectroscopy (μ-FTIR) was used to carry out a thorough study on the chemical processes and modifications occurring within the epoxy resin by exposure to 365 nm and 254 nm light. In particular, we established that UVC light promotes the opening of the epoxy rings bypassing the post-exposure bake. The possibility to promote a further activation of the resin, already patterned with standard UV lithography, was exploited to produce closed microfluidic devices. Specifically, we were able to fabricate fluidic chips, characterized by broadband transparency from mid-IR to UV and long term stability in continuous flow conditions. CaF2 was used as substrate, coated by sputtering with a nanometric silicon film, in order to make surface properties of this material more suitable for standard fabrication processes with respect to the original substrate. The fabricated microfluidic chips were used to study by μ-FTIR the biochemical response of live breast cancer MCF-7 cells to osmotic stress and their subsequent lysis induced by the injection of deionized water in the device. μ-FTIR analyses detected fast changes in protein, lipid and nucleic acid content as well as cytosol acidification.
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Affiliation(s)
- Elisa Mitri
- CNR-IOM, TASC laboratory, S. S. 14 km 163.5 Basovizza, 34149 Trieste, Italy.
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19
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Hughes C, Brown MD, Ball FJ, Monjardez G, Clarke NW, Flower KR, Gardner P. Highlighting a need to distinguish cell cycle signatures from cellular responses to chemotherapeutics in SR-FTIR spectroscopy. Analyst 2013; 137:5736-42. [PMID: 23095763 DOI: 10.1039/c2an35633c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Previous research has seen difficulties in establishing clear discrimination by principal component analysis (PCA) between drug-treated cells analysed by single point SR-FTIR spectroscopy, relative to multisampling cell monolayers by conventional FTIR. It is suggested that the issue arises due to signal mixing between cellular-response signatures and cell cycle phase contributions in individual cells. Consequently, chemometric distinction of cell spectra treated with multiple drugs is difficult even with supervised methods. In an effort to separate cell cycle chemistry from cellular response chemistry in the spectra, renal carcinoma cells were stained with propidium iodide and fluorescent-activated cell sorted (FACS) after exposure to a number of chemotherapeutic compounds; 5-fluorouracil (5FU) and a set of novel gold-based experimental compounds. The cell spectra were analysed separately by PCA in G(1), S or G(2)/M phase. The mode of action of established drug 5FU, known to disrupt S phase, was confirmed by FACS analysis. The chemical signature of 5FU-treated cells discriminated against both the control and gold-compound (KF0101)-treated cell spectra, suggesting a different mode of action due to a difference in cellular response.
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Affiliation(s)
- C Hughes
- Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, UK M1 7DN
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20
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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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21
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Chan KLA, Kazarian SG. Aberration-free FTIR spectroscopic imaging of live cells in microfluidic devices. Analyst 2013; 138:4040-7. [PMID: 23515344 DOI: 10.1039/c3an00327b] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The label-free, non-destructive chemical analysis offered by FTIR spectroscopic imaging is a very attractive and potentially powerful tool for studies of live biological cells. FTIR imaging of live cells is a challenging task, due to the fact that cells are cultured in an aqueous environment. While the synchrotron facility has proven to be a valuable tool for FTIR microspectroscopic studies of single live cells, we have demonstrated that high quality infrared spectra of single live cells using an ordinary Globar source can also be obtained by adding a pair of lenses to a common transmission liquid cell. The lenses, when placed on the transmission cell window, form pseudo hemispheres which removes the refraction of light and hence improve the imaging and spectral quality of the obtained data. This study demonstrates that infrared spectra of single live cells can be obtained without the focus shifting effect at different wavenumbers, caused by the chromatic aberration. Spectra of the single cells have confirmed that the measured spectral region remains in focus across the whole range, while spectra of the single cells measured without the lenses have shown some erroneous features as a result of the shift of focus. It has also been demonstrated that the addition of lenses can be applied to the imaging of cells in microfabricated devices. We have shown that it was not possible to obtain a focused image of an isolated cell in a droplet of DPBS in oil unless the lenses are applied. The use of the approach described herein allows for well focused images of single cells in DPBS droplets to be obtained.
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Affiliation(s)
- K L Andrew Chan
- Department of Chemical Engineering, Imperial College London, SW7 2AZ, London, UK
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22
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Stavitski E, Smith RJ, Bourassa MW, Acerbo AS, Carr GL, Miller LM. Dynamic full-field infrared imaging with multiple synchrotron beams. Anal Chem 2013; 85:3599-605. [PMID: 23458231 DOI: 10.1021/ac3033849] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microspectroscopic imaging in the infrared (IR) spectral region allows for the examination of spatially resolved chemical composition on the microscale. More than a decade ago, it was demonstrated that diffraction-limited spatial resolution can be achieved when an apertured, single-pixel IR microscope is coupled to the high brightness of a synchrotron light source. Nowadays, many IR microscopes are equipped with multipixel Focal Plane Array (FPA) detectors, which dramatically improve data acquisition times for imaging large areas. Recently, progress been made toward efficiently coupling synchrotron IR beamlines to multipixel detectors, but they utilize expensive and highly customized optical schemes. Here we demonstrate the development and application of a simple optical configuration that can be implemented on most existing synchrotron IR beamlines to achieve full-field IR imaging with diffraction-limited spatial resolution. Specifically, the synchrotron radiation fan is extracted from the bending magnet and split into four beams that are combined on the sample, allowing it to fill a large section of the FPA. With this optical configuration, we are able to oversample an image by more than a factor of 2, even at the shortest wavelengths, making image restoration through deconvolution algorithms possible. High chemical sensitivity, rapid acquisition times, and superior signal-to-noise characteristics of the instrument are demonstrated. The unique characteristics of this setup enabled the real-time study of heterogeneous chemical dynamics with diffraction-limited spatial resolution for the first time.
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Affiliation(s)
- Eli Stavitski
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973, United States
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23
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Miller LM, Bourassa MW, Smith RJ. FTIR spectroscopic imaging of protein aggregation in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2339-46. [PMID: 23357359 DOI: 10.1016/j.bbamem.2013.01.014] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/16/2013] [Indexed: 01/22/2023]
Abstract
Protein misfolding and aggregation are the hallmark of a number of diseases including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and the prion diseases. In all cases, a naturally-occurring protein misfolds and forms aggregates that are thought to disrupt cell function through a wide range of mechanisms that are yet to be fully unraveled. Fourier transform infrared (FTIR) spectroscopy is a technique that is sensitive to the secondary structure of proteins and has been widely used to investigate the process of misfolding and aggregate formation. This review focuses on how FTIR spectroscopy and spectroscopic microscopy are being used to evaluate the structural changes in disease-related proteins both in vitro and directly within cells and tissues. Finally, ongoing technological advances will be presented that are enabling time-resolved FTIR imaging of protein aggregation directly within living cells, which can provide insight into the structural intermediates, time scale, and mechanisms of cell toxicity associated with aggregate formation. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Lisa M Miller
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973, USA.
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24
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Chan KLA, Kazarian SG. Correcting the Effect of Refraction and Dispersion of Light in FT-IR Spectroscopic Imaging in Transmission through Thick Infrared Windows. Anal Chem 2012; 85:1029-36. [DOI: 10.1021/ac302846d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. L. Andrew Chan
- Department of Chemical
Engineering, Imperial College London, SW7 2AZ, United Kingdom
| | - Sergei G. Kazarian
- Department of Chemical
Engineering, Imperial College London, SW7 2AZ, United Kingdom
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25
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Vaccari L, Birarda G, Businaro L, Pacor S, Grenci G. Infrared Microspectroscopy of Live Cells in Microfluidic Devices (MD-IRMS): Toward a Powerful Label-Free Cell-Based Assay. Anal Chem 2012; 84:4768-75. [DOI: 10.1021/ac300313x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Vaccari L, Birada G, Grenci G, Pacor S, Businaro L. Synchrotron radiation infrared microspectroscopy of single living cells in microfluidic devices: advantages, disadvantages and future perspectives. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/359/1/012007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Hirschmugl CJ, Gough KM. Fourier transform infrared spectrochemical imaging: review of design and applications with a focal plane array and multiple beam synchrotron radiation source. APPLIED SPECTROSCOPY 2012; 66:475-91. [PMID: 22524953 DOI: 10.1366/12-06629] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The beamline design, microscope specifications, and initial results from the new mid-infrared beamline (IRENI) are reviewed. Synchrotron-based spectrochemical imaging, as recently implemented at the Synchrotron Radiation Center in Stoughton, Wisconsin, demonstrates the new capability to achieve diffraction limited chemical imaging across the entire mid-infrared region, simultaneously, with high signal-to-noise ratio. IRENI extracts a large swath of radiation (320 hor. × 25 vert. mrads(2)) to homogeneously illuminate a commercial infrared (IR) microscope equipped with an IR focal plane array (FPA) detector. Wide-field images are collected, in contrast to single-pixel imaging from the confocal geometry with raster scanning, commonly used at most synchrotron beamlines. IRENI rapidly generates high quality, high spatial resolution data. The relevant advantages (spatial oversampling, speed, sensitivity, and signal-to-noise ratio) are discussed in detail and demonstrated with examples from a variety of disciplines, including formalin-fixed and flash-frozen tissue samples, live cells, fixed cells, paint cross-sections, polymer fibers, and novel nanomaterials. The impact of Mie scattering corrections on this high quality data is shown, and first results with a grazing angle objective are presented, along with future enhancements and plans for implementation of similar, small-scale instruments.
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Affiliation(s)
- Carol J Hirschmugl
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA.
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28
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Affiliation(s)
- Francisco Zaera
- Department of Chemistry, University of California, Riverside, California 92521, United States
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29
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Quaroni L, Zlateva T. Infrared spectromicroscopy of biochemistry in functional single cells. Analyst 2011; 136:3219-32. [DOI: 10.1039/c1an15060j] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Holman HYN, Hao Z, Martin MC, Bechtel HA. Infrared Spectromicroscopy: Probing Live Cellular Responses to Environmental Changes. ACTA ACUST UNITED AC 2010. [DOI: 10.1080/08940886.2010.516737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Holman HYN, Bechtel HA, Hao Z, Martin MC. Synchrotron IR spectromicroscopy: chemistry of living cells. Anal Chem 2010; 82:8757-65. [PMID: 20839782 DOI: 10.1021/ac100991d] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Advanced analytical capabilities of synchrotron IR spectromicroscopy meet the demands of modern biological research for studying molecular reactions in individual living cells. (To listen to a podcast about this article, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).
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