1
|
Goett-Zink L, Klocke JL, Kottke T. Resolving Structural Changes of Photoreceptors in Living Escherichia coli via In-cell Infrared Difference Spectroscopy. Bio Protoc 2021; 11:e3909. [PMID: 33732796 DOI: 10.21769/bioprotoc.3909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 11/02/2022] Open
Abstract
Several in-cell spectroscopic techniques have been developed recently to investigate the structure and mechanism of proteins in their native environment. Conditions in vivo differ dramatically from those selected for in vitro experiments. Accordingly, the cellular environment can affect the protein mechanism for example by molecular crowding or binding of small molecules. Fourier transform infrared (FTIR) difference spectroscopy is a well-suited method to study the light-induced structural responses of photoreceptors including changes in cofactor, side chains and secondary structure. Here, we describe a protocol to study the response of cofactor and protein in living E. coli cells via in-cell infrared difference (ICIRD) spectroscopy using the attenuated total reflection (ATR) configuration. Proteins are overexpressed in E. coli, the cells are transferred into saline solution and the copy number per cell is determined using fluorescence spectroscopy. The suspension is centrifuged and the concentrated cells transferred onto the ATR cell inside the FTIR spectrometer. The thermostatted cell is sealed and illuminated from the top with an LED. Intensity spectra are recorded before and after illumination to generate the difference spectrum of the receptor inside the living cell. With ICIRD spectroscopy, structural changes of soluble photoreceptors are resolved in a near-native environment. The approach works in H2O at ambient conditions, is label free, without any limitations in protein size and does not require any purification step. Graphic abstract: In-cell infrared difference spectroscopy on photoreceptors in living E. coli using attenuated total reflection.
Collapse
Affiliation(s)
- Lukas Goett-Zink
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany.,Medical School OWL, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
2
|
Goett-Zink L, Klocke JL, Bögeholz LAK, Kottke T. In-cell infrared difference spectroscopy of LOV photoreceptors reveals structural responses to light altered in living cells. J Biol Chem 2020; 295:11729-11741. [PMID: 32580943 PMCID: PMC7450117 DOI: 10.1074/jbc.ra120.013091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the light, oxygen, or voltage (LOV) domains of the blue light receptors aureochrome and phototropin revealed a suppression of the response of specific secondary structure elements, indicating that the intracellular environment affects LOV photoreceptor mechanisms in general. Moreover, in-cell fluorescence spectroscopy disclosed that the intracellular environment slows down the recovery of the light-induced flavin adduct. Segment-resolved ICIRD spectroscopy on basic-region leucine zipper (bZIP)-LOV of aureochrome 1a from the diatom Phaeodactylum tricornutum indicated a signal progression from the LOV sensor to the bZIP effector independent of unfolding of the connecting A'α-helix, an observation that stood in contrast to in vitro results. This deviation was recapitulated in vitro by emulating the intracellular environment through the addition of the crowding agent BSA, but not by sucrose polymers. We conclude that ICIRD spectroscopy is a noninvasive, label-free approach for assessing conformational changes in receptors in living cells at ambient conditions. As demonstrated, these near-native responses may deviate from the mechanisms established under in vitro conditions.
Collapse
Affiliation(s)
- Lukas Goett-Zink
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Lena A K Bögeholz
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
3
|
Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
Collapse
|
4
|
Infrared and 2-Dimensional Correlation Spectroscopy Study of the Effect of CH 3NH 3PbI 3 and CH 3NH 3SnI 3 Photovoltaic Perovskites on Eukaryotic Cells. Molecules 2020; 25:molecules25020336. [PMID: 31947578 PMCID: PMC7024238 DOI: 10.3390/molecules25020336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 11/30/2022] Open
Abstract
We studied the effect of the exposure of human A549 and SH-SY5Y cell lines to aqueous solutions of organic/inorganic halide perovskites CH3NH3PbI3 (MAPbI3) and CH3NH3SnI3 (MASnI3) at the molecular level by using Fourier transform infrared microspectroscopy. We monitored the infrared spectra of some cells over a few days following exposure to the metals and observed the spectroscopic changes dominated by the appearance of a strong band at 1627 cm−1. We used Infrared (IR) mapping to show that this change was associated with the cell itself or the cellular membrane. It is unclear whether the appearance of the 1627 cm−1 band and heavy metal exposure are related by a direct causal relationship. The spectroscopic response of exposure to MAPbI3 and MASnI3 was similar, indicating that it may arise from a general cellular response to stressful environmental conditions. We used 2D correlation spectroscopy (2DCOS) analysis to interpret spectroscopic changes. In a novel application of the method, we demonstrated the viability of 2DCOS for band assignment in spatially resolved spectra. We assigned the 1627 cm−1 band to the accumulation of an abundant amide or amine containing compound, while ruling out other hypotheses. We propose a few tentative assignments to specific biomolecules or classes of biomolecules, although additional biochemical characterization will be necessary to confirm such assignments.
Collapse
|
5
|
Doherty J, Raoof A, Hussain A, Wolna M, Cinque G, Brown M, Gardner P, Denbigh J. Live single cell analysis using synchrotron FTIR microspectroscopy: development of a simple dynamic flow system for prolonged sample viability. Analyst 2019; 144:997-1007. [PMID: 30403210 DOI: 10.1039/c8an01566j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Synchrotron radiation Fourier transform infrared microspectroscopy (SR-microFTIR) of live biological cells has the potential to provide far greater biochemical and morphological detail than equivalent studies using dehydrated, chemically-fixed single cells. Attempts to measure live cells using microFTIR are complicated by the aqueous environment required and corresponding strong infrared absorbance by water. There is also the additional problem of the limited lifetime of the cells outside of their preferred culture environment. In this work, we outline simple, cost-effective modifications to a commercially available liquid sample holder to perform single live cell analysis under an IR microscope and demonstrate cell viability up to at least 24 hours. A study using this system in which live cells have been measured at increasing temperature has shown spectral changes in protein bands attributed to α-β transition, consistent with other published work, and proves the ability to simultaneously induce and measure biochemical changes. An additional study of deuterated palmitic acid (D31-PA) uptake at different timepoints has made use of over 200 individual IR spectra collected over ∼4 hours, taking advantage of the ability to maintain viable cell samples for longer periods of time in the measurement environment, and therefore acquire greatly increased numbers of spectra without compromising on spectral quality. Further developments of this system are planned to widen the range of possible experiments, and incorporate more complex studies, including drug-cell interaction.
Collapse
Affiliation(s)
- James Doherty
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Byrne HJ, Bonnier F, Farhane Z. Two-dimensional correlation analysis of Raman microspectroscopy of subcellular interactions of drugs in vitro. JOURNAL OF BIOPHOTONICS 2019; 12:e201800328. [PMID: 30414254 DOI: 10.1002/jbio.201800328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 05/24/2023]
Abstract
Two-dimensional (2D) correlation analysis is explored to data mine the time evolution of the characteristic Raman microspectroscopic signatures of the subcellular responses of the nucleoli of human lung cancer cells to the uptake of doxorubicin. A simulated dataset of experimental control spectra, perturbed with systematically time-dependent spectral changes, constituted by a short-term response which represents the initial binding of the drug in the nucleolus, followed by a longer term response of the organelle metabolism, is used to validate the analysis protocol. Applying 2D correlation analysis, the in phase, synchronous correlation coefficients are seen to contain contributions of both response profiles, whereas they can be independently extracted from the out of phase, asynchronous correlation coefficients. The methodology is applied to experimental data of the uptake of doxorubicin in human lung cell lines to differentiate the signatures of chemical binding and subsequent cellular response.
Collapse
Affiliation(s)
- Hugh J Byrne
- FOCAS Research Institute, Dublin Institute of Technology, Dublin, Ireland
| | - Franck Bonnier
- Université François-Rabelais de Tours, Faculty of Pharmacy, EA 6295 Nanomédicaments et Nanosondes, Tours, France
| | - Zeineb Farhane
- FOCAS Research Institute, Dublin Institute of Technology, Dublin, Ireland
- School of Physics and Clinical & Optometric Sciences, Dublin Institute of Technology, Dublin, Ireland
| |
Collapse
|
7
|
Altharawi A, Rahman KM, Chan KLA. Towards identifying the mode of action of drugs using live-cell FTIR spectroscopy. Analyst 2019; 144:2725-2735. [DOI: 10.1039/c8an02218f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fourier transform infrared spectroscopy (FTIR) has been shown to be a promising tool for identifying the mode of action of drugs.
Collapse
Affiliation(s)
- Ali Altharawi
- School of Cancer and Pharmaceutical Science
- King's College London
- UK
| | | | | |
Collapse
|
8
|
Pahlow S, Weber K, Popp J, Wood BR, Kochan K, Rüther A, Perez-Guaita D, Heraud P, Stone N, Dudgeon A, Gardner B, Reddy R, Mayerich D, Bhargava R. Application of Vibrational Spectroscopy and Imaging to Point-of-Care Medicine: A Review. APPLIED SPECTROSCOPY 2018; 72:52-84. [PMID: 30265133 PMCID: PMC6524782 DOI: 10.1177/0003702818791939] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Susanne Pahlow
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Jena, Germany
- InfectoGnostics Research Campus Jena, Centre for Applied Research, Jena, Germany
| | - Karina Weber
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Jena, Germany
- InfectoGnostics Research Campus Jena, Centre for Applied Research, Jena, Germany
- Leibniz Institute of Photonic Technology-Leibniz Health Technologies, Jena, Germany
| | - Jürgen Popp
- Friedrich Schiller University Jena, Institute of Physical Chemistry and Abbe Center of Photonics, Jena, Germany
- InfectoGnostics Research Campus Jena, Centre for Applied Research, Jena, Germany
- Leibniz Institute of Photonic Technology-Leibniz Health Technologies, Jena, Germany
| | - Bayden R. Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Kamila Kochan
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Anja Rüther
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - David Perez-Guaita
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Philip Heraud
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Nick Stone
- University of Exeter, School of Physics and Astronomy, Exeter, UK
| | - Alex Dudgeon
- University of Exeter, School of Physics and Astronomy, Exeter, UK
| | - Ben Gardner
- University of Exeter, School of Physics and Astronomy, Exeter, UK
| | - Rohith Reddy
- Department of Electrical Engineering, University of Houston, Houston, USA
| | - David Mayerich
- Department of Electrical Engineering, University of Houston, Houston, USA
| | - Rohit Bhargava
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Departments of Mechanical Engineering, Bioengineering, Chemical and Biomolecular Engineering, Electrical and Computer Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, USA
| |
Collapse
|
9
|
Doherty J, Zhang Z, Wehbe K, Cinque G, Gardner P, Denbigh J. Increased optical pathlength through aqueous media for the infrared microanalysis of live cells. Anal Bioanal Chem 2018; 410:5779-5789. [PMID: 29968104 PMCID: PMC6096700 DOI: 10.1007/s00216-018-1188-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 12/13/2022]
Abstract
The study of live cells using Fourier transform infrared spectroscopy (FTIR) and FTIR microspectroscopy (FT-IRMS) intrinsically yields more information about cell metabolism than comparable experiments using dried or chemically fixed samples. There are, however, a number of barriers to obtaining high-quality vibrational spectra of live cells, including correction for the significant contributions of water bands to the spectra, and the physical stresses placed upon cells by compression in short pathlength sample holders. In this study, we present a water correction method that is able to result in good-quality cell spectra from water layers of 10 and 12 μm and demonstrate that sufficient biological detail is retained to separate spectra of live cells based upon their exposure to different novel anti-cancer agents. The IR brilliance of a synchrotron radiation (SR) source overcomes the problem of the strong water absorption and provides cell spectra with good signal-to-noise ratio for further analysis. Supervised multivariate analysis (MVA) and investigation of average spectra have shown significant separation between control cells and cells treated with the DNA cross-linker PL63 on the basis of phosphate and DNA-related signatures. Meanwhile, the same control cells can be significantly distinguished from cells treated with the protein kinase inhibitor YA1 based on changes in the amide II region. Each of these separations can be linked directly to the known biochemical mode of action of each agent. Graphical abstract ![]()
Collapse
Affiliation(s)
- James Doherty
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,School of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Zhe Zhang
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,School of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Katia Wehbe
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Gianfelice Cinque
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Peter Gardner
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. .,School of Chemical Engineering and Analytical Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Joanna Denbigh
- Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK.
| |
Collapse
|
10
|
Vannocci T, Notario Manzano R, Beccalli O, Bettegazzi B, Grohovaz F, Cinque G, de Riso A, Quaroni L, Codazzi F, Pastore A. Adding a temporal dimension to the study of Friedreich's ataxia: the effect of frataxin overexpression in a human cell model. Dis Model Mech 2018; 11:dmm032706. [PMID: 29794127 PMCID: PMC6031361 DOI: 10.1242/dmm.032706] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/08/2018] [Indexed: 12/27/2022] Open
Abstract
The neurodegenerative disease Friedreich's ataxia is caused by lower than normal levels of frataxin, an important protein involved in iron-sulfur (Fe-S) cluster biogenesis. An important step in designing strategies to treat this disease is to understand whether increasing the frataxin levels by gene therapy would simply be beneficial or detrimental, because previous studies, mostly based on animal models, have reported conflicting results. Here, we have exploited an inducible model, which we developed using the CRISPR/Cas9 methodology, to study the effects of frataxin overexpression in human cells and monitor how the system recovers after overexpression. Using new tools, which range from high-throughput microscopy to in cell infrared, we prove that overexpression of the frataxin gene affects the cellular metabolism. It also leads to a significant increase of oxidative stress and labile iron pool levels. These cellular alterations are similar to those observed when the gene is partly silenced, as occurs in Friedreich's ataxia patients. Our data suggest that the levels of frataxin must be tightly regulated and fine-tuned, with any imbalance leading to oxidative stress and toxicity.
Collapse
Affiliation(s)
- Tommaso Vannocci
- Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Roberto Notario Manzano
- Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Ombretta Beccalli
- Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Barbara Bettegazzi
- Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Fabio Grohovaz
- Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianfelice Cinque
- Department of Physical Chemistry and Electrochemistry, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | | | - Luca Quaroni
- Department of Physical Chemistry and Electrochemistry, Faculty of Chemistry, Jagiellonian University, PL-30387, Kraków, Poland
| | - Franca Codazzi
- Division of Neuroscience, Vita-Salute San Raffaele University and IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Annalisa Pastore
- Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London, 5 Cutcombe Road, London SE5 9RT, UK
- Molecular Medicine Department, University of Pavia, I-27100 Pavia, Italy
| |
Collapse
|
11
|
|
12
|
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).
Collapse
Affiliation(s)
- Luca Quaroni
- Institute of Nuclear Physics, Polish Academy of Sciences
- Kraków
- Poland
| | | | | | | |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Graeme Clemens
- Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, Lancashire PR1 2HE, UK.
| | | | | | | |
Collapse
|
14
|
Mitri E, Kenig S, Coceano G, Bedolla DE, Tormen M, Grenci G, Vaccari L. Time-Resolved FT-IR Microspectroscopy of Protein Aggregation Induced by Heat-Shock in Live Cells. Anal Chem 2015; 87:3670-7. [DOI: 10.1021/ac5040659] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Elisa Mitri
- Elettra−Sincrotrone Trieste, Strada Statale
14 km 163.5, 34149 Basovizza, Trieste Italy
- IOM-CNR, TASC Laboratory, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste Italy
| | - Saša Kenig
- Elettra−Sincrotrone Trieste, Strada Statale
14 km 163.5, 34149 Basovizza, Trieste Italy
| | - Giovanna Coceano
- IOM-CNR, TASC Laboratory, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste Italy
| | - Diana E. Bedolla
- Elettra−Sincrotrone Trieste, Strada Statale
14 km 163.5, 34149 Basovizza, Trieste Italy
| | - Massimo Tormen
- IOM-CNR, TASC Laboratory, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste Italy
| | - Gianluca Grenci
- IOM-CNR, TASC Laboratory, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste Italy
- MBI, National University of Singapore T-Lab, 5A Engineering Drive 1, Singapore
| | - Lisa Vaccari
- Elettra−Sincrotrone Trieste, Strada Statale
14 km 163.5, 34149 Basovizza, Trieste Italy
| |
Collapse
|
15
|
Park Y, Noda I, Jung YM. Two-dimensional correlation spectroscopy in polymer study. Front Chem 2015; 3:14. [PMID: 25815286 PMCID: PMC4356163 DOI: 10.3389/fchem.2015.00014] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 02/17/2015] [Indexed: 11/23/2022] Open
Abstract
This review outlines the recent works of two-dimensional correlation spectroscopy (2DCOS) in polymer study. 2DCOS is a powerful technique applicable to the in-depth analysis of various spectral data of polymers obtained under some type of perturbation. The powerful utility of 2DCOS combined with various analytical techniques in polymer studies and noteworthy developments of 2DCOS used in this field are also highlighted.
Collapse
Affiliation(s)
- Yeonju Park
- Department of Chemistry, Kangwon National University Chunchon, South Korea
| | - Isao Noda
- Department of Materials Science and Engineering, University of Delaware Newark, DE, USA
| | - Young Mee Jung
- Department of Chemistry, Kangwon National University Chunchon, South Korea
| |
Collapse
|
16
|
Chan KLA, Fale PLV. Label-Free in Situ Quantification of Drug in Living Cells at Micromolar Levels Using Infrared Spectroscopy. Anal Chem 2014; 86:11673-9. [DOI: 10.1021/ac503915c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- K. L. Andrew Chan
- Institute
of Pharmaceutical
Science, King's College London, London SE1 9NH, U.K
| | - Pedro L. V. Fale
- Institute
of Pharmaceutical
Science, King's College London, London SE1 9NH, U.K
| |
Collapse
|
17
|
Frontiers of two-dimensional correlation spectroscopy. Part 2. Perturbation methods, fields of applications, and types of analytical probes. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
18
|
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]
|
19
|
Quaroni L, Zlateva T. Real-time metabolic analysis of living cancer cells with correlated cellular spectro-microscopy. Anal Chem 2014; 86:6887-95. [PMID: 24914618 DOI: 10.1021/ac501561x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years, major efforts have been devoted to the application of microscopy with mid-infrared light to the study of living cells and tissue. Despite this interest, infrared (IR) microscopy has not realized its full potential in the molecular characterization of living systems. This is partly due to the fact that current approaches for data mining and analysis of IR absorption spectra have not evolved comparably to measurement technology and are not up to the interpretation of the complex spectra of living systems such as cells and tissue. In this work we show that the use of two-dimensional correlation spectroscopy coupled to IR absorption spectro-microscopy allows us to extract the spectral components of individual metabolites from time-resolved IR spectra of living cells. We call this method correlated cellular spectro-microscopy, and we implement it in the study of the glycolytic metabolism of cancer cells. We show that the method can detect intermediates of the glycolytic pathway, quantify their rate of formation, and correlate this with variations in pH, all in a single measurement. We propose the method as a useful tool for the quantitative description of metabolic processes in living cells and for the validation of drug candidates aimed at suppressing glycolysis in cancer cells.
Collapse
Affiliation(s)
- Luca Quaroni
- Swiss Light Source, Paul Scherrer Institut , CH-5232 Villigen, Switzerland
| | | |
Collapse
|
20
|
Quaroni L, Zlateva T, Sarafimov B, Kreuzer HW, Wehbe K, Hegg EL, Cinque G. Synchrotron based infrared imaging and spectroscopy via focal plane array on live fibroblasts in D2O enriched medium. Biophys Chem 2014; 189:40-8. [PMID: 24747675 DOI: 10.1016/j.bpc.2014.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/15/2014] [Accepted: 03/16/2014] [Indexed: 12/29/2022]
Abstract
We successfully tested the viability of using synchrotron-based full-field infrared imaging to study biochemical processes inside living cells. As a model system, we studied fibroblast cells exposed to a medium highly enriched with D2O. We could show that the experimental technique allows us to reproduce at the cellular level measurements that are normally performed on purified biological molecules. We can obtain information about lipid conformation and distribution, kinetics of hydrogen/deuterium exchange, and the formation of concentration gradients of H and O isotopes in water that are associated with cell metabolism. The implementation of the full field technique in a sequential imaging format gives a description of cellular biochemistry and biophysics that contains both spatial and temporal information.
Collapse
Affiliation(s)
- Luca Quaroni
- Paul Scherrer Institut, Villigen-PSI, CH-5232, Switzerland.
| | | | | | - Helen W Kreuzer
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Katia Wehbe
- Diamond Light Source, Harwell Campus, Chilton-Didcot, Oxon OX11 0DE, UK
| | - Eric L Hegg
- Michigan State University, Department of Biochemistry & Molecular Biology, East Lansing, MI 48824, USA
| | - Gianfelice Cinque
- Diamond Light Source, Harwell Campus, Chilton-Didcot, Oxon OX11 0DE, UK
| |
Collapse
|
21
|
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.
Collapse
Affiliation(s)
- Elisa Mitri
- CNR-IOM, TASC laboratory, S. S. 14 km 163.5 Basovizza, 34149 Trieste, Italy.
| | | | | | | | | | | |
Collapse
|
22
|
Zobi F, Quaroni L, Santoro G, Zlateva T, Blacque O, Sarafimov B, Schaub MC, Bogdanova AY. Live-fibroblast IR imaging of a cytoprotective PhotoCORM Activated with Visible Light. J Med Chem 2013; 56:6719-31. [PMID: 23927566 DOI: 10.1021/jm400527k] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Carbon monoxide releasing molecules (CORMs) are an emerging class of pharmaceutical compounds currently evaluated in several preclinical disease models. There is general consensus that the therapeutic effects elicited by the molecules may be directly ascribed to the biological function of the released CO. It remains unclear, however, if cellular internalization of CORMs is a critical event in their therapeutic action. To address the problem of cellular delivery, we have devised a general strategy which entails conjugation of a CO-releasing molecule (here a photoactivated CORM) to the 5'-OH ribose group of vitamin B12. Cyanocobalamin (B12) functions as the biocompatible water-soluble scaffold which actively transports the CORM against a concentration gradient into the cells. The uptake and cellular distribution of this B12-photoCORM conjugate is demonstrated via synchrotron FTIR spectromicroscopy measurements on living cells. Intracellular photoinduced CO release prevents fibroblasts from dying under conditions of hypoxia and metabolic depletion, conditions that may occur in vivo during insufficient blood supply to oxygen-sensitive tissues such as the heart or brain.
Collapse
Affiliation(s)
- Fabio Zobi
- Institute of Inorganic Chemistry, University of Zürich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Eli Stavitski
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York 11973, United States
| | | | | | | | | | | |
Collapse
|
24
|
Carbone M, Zlateva T, Quaroni L. Monitoring and manipulation of the pH of single cells using infrared spectromicroscopy and a molecular switch. Biochim Biophys Acta Gen Subj 2013; 1830:2989-93. [PMID: 23291426 DOI: 10.1016/j.bbagen.2012.12.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/07/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND The pH of a biological system is a crucial determinant of the structures and reactivity of its components and cellular homeostasis of H(+) is critical for cell viability. Control and monitoring of cellular acidity are highly desirable for the purpose of studying biochemical processes in vivo. METHODS The effect of photolysis of a caged strong acid, the ester 1-(2-nitrophenyl)-ethylhexadecyl sulfonate (HDNS) is used to cause a controlled drop in pH in single cells. An isolated cell is selected under the IR microscope, irradiated with near-UV light and monitored by FTIR. RESULTS We demonstrate the use of FTIR spectromicroscopy to monitor light-induced acidification of the cellular medium by measuring the increased concentration of CO2 and corresponding decrease of HCO3(-) in the cell and in the surrounding medium. CONCLUSIONS We have demonstrated a method to control and accurately monitor the changes in pH of a cellular system by coupling a caged proton-releasing agent with FTIR spectromicroscopy detection. The overall implementation of photolysis and spectroscopic detection in a microscope optical configuration ensures single cell selectivity in both acidification and monitoring. We show the viability of monitoring of pH changes by FTIR spectromicroscopy with sensitivity comparable to that of glass electrodes, better than the existing methods for determining cell pH. GENERAL SIGNIFICANCE Reporting the effect of small variations of cellular acidity provides a major improvement in the understanding of the interplay between molecular properties as assessed in vitro and cell physiology.
Collapse
Affiliation(s)
- Marilena Carbone
- Department of Chemical Sciences and Technologies, University Tor Vergata, Via della Ricerca Scientifica 1 Rome, 0133, Italy.
| | | | | |
Collapse
|
25
|
Spegazzini N, Siesler HW, Ozaki Y. Sequential identification of model parameters by derivative double two-dimensional correlation spectroscopy and calibration-free approach for chemical reaction systems. Anal Chem 2012; 84:8330-9. [PMID: 22924791 DOI: 10.1021/ac301867u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A sequential identification approach by two-dimensional (2D) correlation analysis for the identification of a chemical reaction model, activation, and thermodynamic parameters is presented in this paper. The identification task is decomposed into a sequence of subproblems. The first step is the construction of a reaction model with the suggested information by model-free 2D correlation analysis using a novel technique called derivative double 2D correlation spectroscopy (DD2DCOS), which enables one to analyze intensities with nonlinear behavior and overlapped bands. The second step is a model-based 2D correlation analysis where the activation and thermodynamic parameters are estimated by an indirect implicit calibration or a calibration-free approach. In this way, a minimization process for the spectral information by sample-sample 2D correlation spectroscopy and kinetic hard modeling (using ordinary differential equations) of the chemical reaction model is carried out. The sequential identification by 2D correlation analysis is illustrated with reference to the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol. The reaction was investigated by FT-IR spectroscopy. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied by means of an integration of model-free and model-based 2D correlation analysis called a sequential identification approach. The study determined the enthalpy (ΔH = 15.25 kJ/mol) and entropy (TΔS = 13.20 kJ/mol) of C═O···H hydrogen bonding of diphenylurethane through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S) at equilibrium in the chemical reaction system.
Collapse
Affiliation(s)
- Nicolas Spegazzini
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan.
| | | | | |
Collapse
|
26
|
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]
|
27
|
Chen L, Holman HYN, Hao Z, Bechtel HA, Martin MC, Wu C, Chu S. Synchrotron Infrared Measurements of Protein Phosphorylation in Living Single PC12 Cells during Neuronal Differentiation. Anal Chem 2012; 84:4118-25. [DOI: 10.1021/ac300308x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Liang Chen
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Hoi-Ying N. Holman
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Zhao Hao
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Hans A. Bechtel
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Michael C. Martin
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California
94720, United States
| | - Chengbiao Wu
- Department
of Neurosciences, University of California at San Diego School of Medicine, La Jolla, California 92093, United
States
| | - Steven Chu
- Departments of Physics
and Molecular
and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative
Biosciences (QB3), University of California at Berkeley, Berkeley, California 94720, United States
| |
Collapse
|