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Journal ArticleDOI

High-resolution Fourier-transform infrared chemical imaging with multiple synchrotron beams

TL;DR: This advance allows truly diffraction-limited high-resolution imaging over the entire mid-infrared spectrum with high chemical sensitivity and fast acquisition speed while maintaining high-quality SNR.
Abstract: Conventional Fourier-transform infrared (FTIR) microspectroscopic systems are limited by an inevitable trade-off between spatial resolution, acquisition time, signal-to-noise ratio (SNR) and sample coverage. We present an FTIR imaging approach that substantially extends current capabilities by combining multiple synchrotron beams with wide-field detection. This advance allows truly diffraction-limited high-resolution imaging over the entire mid-infrared spectrum with high chemical sensitivity and fast acquisition speed while maintaining high-quality SNR.

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Citations
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Journal ArticleDOI
TL;DR: This review comprises the main characteristics of O2(•-) followed by generation methods, and its potential applications including the destruction of hazardous chemicals, synthesis of organic compounds, and many other applications are highlighted.
Abstract: Superoxide ion (O2•–) is of great significance as a radical species implicated in diverse chemical and biological systems. However, the chemistry knowledge of O2•– is rather scarce. In addition, numerous studies on O2•– were conducted within the latter half of the 20th century. Therefore, the current advancement in technology and instrumentation will certainly provide better insights into mechanisms and products of O2•– reactions and thus will result in new findings. This review emphasizes the state-of-the-art research on O2•– so as to enable researchers to venture into future research. It comprises the main characteristics of O2•– followed by generation methods. The reaction types of O2•– are reviewed, and its potential applications including the destruction of hazardous chemicals, synthesis of organic compounds, and many other applications are highlighted. The O2•– environmental chemistry is also discussed. The detection methods of O2•– are categorized and elaborated. Special attention is given to the f...

1,356 citations

Journal ArticleDOI
TL;DR: This manuscript brings together 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.
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.

1,340 citations

Journal ArticleDOI
TL;DR: AFM-IR applications that will be discussed include those in polymers, life sciences, photonics, solar cells, semiconductors, pharmaceuticals, and cultural heritage.
Abstract: Atomic force microscopy-based infrared spectroscopy (AFM-IR) is a rapidly emerging technique that provides chemical analysis and compositional mapping with spatial resolution far below conventional optical diffraction limits. AFM-IR works by using the tip of an AFM probe to locally detect thermal expansion in a sample resulting from absorption of infrared radiation. AFM-IR thus can provide the spatial resolution of AFM in combination with the chemical analysis and compositional imaging capabilities of infrared spectroscopy. This article briefly reviews the development and underlying technology of AFM-IR, including recent advances, and then surveys a wide range of applications and investigations using AFM-IR. AFM-IR applications that will be discussed include those in polymers, life sciences, photonics, solar cells, semiconductors, pharmaceuticals, and cultural heritage. In the Supporting Information, the authors provide a theoretical section that reviews the physics underlying the AFM-IR measurement and d...

652 citations

Journal ArticleDOI
Renato Zenobi1
06 Dec 2013-Science
TL;DR: The fact that single-cell measurements exhibited a much larger spread in metabolite concentrations than population measurements was exploited to determine many metabolite-metabolite correlations, which were altered in 2DG-treated yeast cells relative to controls.
Abstract: Background In recent years, there has been a surge in the development and application of single-cell genomics, transcriptomics, proteomics, and metabolomics. The metabolome is defined as the full complement of small-molecule metabolites found in a specific cell, organ, or organism. The most interesting potential application of single-cell metabolomics may be in the area of cancer—for example, identification of circulating cancer cells that lead to metastasis. Other fields where single-cell metabolomics is expected to have an impact are systems biology, stem cell research, aging, and the development of drug resistance; more generally, it could be used to discover cells’ chemical strategies for coping with chemical or environmental stress. Relative to other single-cell “-omics” measurements, metabolomics provides a more immediate and dynamic picture of the functionality (i.e., of the phenotype) of a cell, but is arguably also the most difficult to measure. This is because the metabolome can dynamically react to the environment on a very short time scale (seconds or less), because of the large structural diversity and huge dynamic range of metabolites, because it is not possible to amplify metabolites, and because tagging them with fluorescent labels would distort their normal function. Single-cell analysis uses a wide variety of imaging and chemical analysis methods to study vastly different cell types and sizes. (A) Closterium acerosum (algal cells, ~300 μm × 40 μm; optical micrograph). (B) Euglena gracilis (algal cells, diameter ~20 μm); Raman image of β-carotene distribution (left) and fluorescence emission from proplastids (right). (C) Baker’s yeast (diameter ~5 μm); optical micrograph. (D) Escherichia coli (diameter ~0.75 μm, length 1 to 3 μm); fluorescence micrograph (image courtesy of M. Heinemann, University of Groningen). Advances Although deep biological insight based on single-cell metabolomics has not yet been obtained, important steps have been taken toward this goal. Advances in mass spectrometry (MS), MS imaging, capillary electrophoresis, optical spectroscopy, and in the development of fluorescence biosensors now allow the simultaneous determination of hundreds of metabolites in a single cell, with sensitivities in the attomole range. Modern array formats, in particular microfluidic platforms, contribute to our ability to perform such measurements rapidly and with high throughput. Several recent studies show how novel biological insight can be extracted from single-cell metabolomics. Substantial differences in the metabolomes of different snail neurons—for example, in B1 and B2 type neurons—have been found, immediately after isolating them and after overnight culturing. Glycosphingolipids could be labeled with a fluorescent tag, and in lysates of neurons incubated with such conjugates, all metabolic products derived from them were fluorescent and could be identified. Phosphorylation of 3′-deoxy-3′-fluorothymidine in lymphoma cells and solid tumors could be followed after treatment with cancer drugs. The biological effect of treating yeast cells by 2-deoxy-d-glucose (2DG) on the metabolome could be followed. The fact that single-cell measurements exhibited a much larger spread in metabolite concentrations than population measurements was exploited to determine many metabolite-metabolite correlations, which were altered in 2DG-treated yeast cells relative to controls. Outlook The metabolome is an excellent indicator of phenotypic heterogeneity and has been recognized as a key factor in rare-cell survival when populations are subjected to major chemical or environmental challenges. Metabolomics at the single-cell level, however, is only just coming of age. Improvements leading to more complete coverage of the metabolome, better and faster identification of metabolites, and nondestructive measurement are anticipated.

519 citations


Additional excerpts

  • ...Synchrotron-based IR spectroscopy, with multiple low-emittance beams and a large focal plane array detector, was used to achieve a pixel size of 540 nm in the mid-IR, about two orders of magnitude smaller than is possible with conventional thermal or synchrotron IR sources (77)....

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Journal ArticleDOI
24 Aug 2012-ACS Nano
TL;DR: A dual-band perfect absorber based on a gold nanocross structure with two bands of maximum absorption of 94% is introduced and can be readily tuned throughout the mid-infrared with their associated resonances giving rise to large near-field enhancements.
Abstract: Metamaterial-based perfect absorbers utilize intrinsic loss, with the aid of appropriate structural design, to achieve near unity absorption at a certain wavelength. For most of the reported absorbers, the absorption occurs only at a single wavelength where plasmon resonances are excited in the nanostructures. Here we introduce a dual-band perfect absorber based on a gold nanocross structure. Two bands of maximum absorption of 94% are experimentally accomplished by breaking the symmetry of the cross structure. Furthermore, we demonstrate the two bands can be readily tuned throughout the mid-infrared with their associated resonances giving rise to large near-field enhancements. These features are ideal for multiband surface-enhanced infrared spectroscopy applications. We experimentally demonstrate this application by simultaneously detecting two molecular vibrational modes of a 4 nm thick polymer film utilizing our proposed absorber. Furthermore, in response to variations in the interaction strength betwee...

449 citations

References
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BookDOI
01 Jan 1990
TL;DR: Methods for Three-Dimensional Imaging and Tutorial on Practical Confocal Microscopy and Use of the Confocal Test Specimen.
Abstract: Foundations of Confocal Scanned Imaging in Light Microscopy -- Fundamental Limits in Confocal Microscopy -- Special Optical Elements -- Points, Pixels, and Gray Levels: Digitizing Image Data -- Laser Sources for Confocal Microscopy -- Non-Laser Light Sources for Three-Dimensional Microscopy -- Objective Lenses for Confocal Microscopy -- The Contrast Formation in Optical Microscopy -- The Intermediate Optical System of Laser-Scanning Confocal Microscopes -- Disk-Scanning Confocal Microscopy -- Measuring the Real Point Spread Function of High Numerical Aperture Microscope Objective Lenses -- Photon Detectors for Confocal Microscopy -- Structured Illumination Methods -- Visualization Systems for Multi-Dimensional Microscopy Images -- Automated Three-Dimensional Image Analysis Methods for Confocal Microscopy -- Fluorophores for Confocal Microscopy: Photophysics and Photochemistry -- Practical Considerations in the Selection and Application of Fluorescent Probes -- Guiding Principles of Specimen Preservation for Confocal Fluorescence Microscopy -- Confocal Microscopy of Living Cells -- Aberrations in Confocal and Multi-Photon Fluorescence Microscopy Induced by Refractive Index Mismatch -- Interaction of Light with Botanical Specimens -- Signal-to-Noise Ratio in Confocal Microscopes -- Comparison of Widefield/Deconvolution and Confocal Microscopy for Three-Dimensional Imaging -- Blind Deconvolution -- Image Enhancement by Deconvolution -- Fiber-Optics in Scanning Optical Microscopy -- Fluorescence Lifetime Imaging in Scanning Microscopy -- Multi-Photon Molecular Excitation in Laser-Scanning Microscopy -- Multifocal Multi-Photon Microscopy -- 4Pi Microscopy -- Nanoscale Resolution with Focused Light: Stimulated Emission Depletion and Other Reversible Saturable Optical Fluorescence Transitions Microscopy Concepts -- Mass Storage, Display, and Hard Copy -- Coherent Anti-Stokes Raman Scattering Microscopy -- Related Methods for Three-Dimensional Imaging -- Tutorial on Practical Confocal Microscopy and Use of the Confocal Test Specimen -- Practical Confocal Microscopy -- Selective Plane Illumination Microscopy -- Cell Damage During Multi-Photon Microscopy -- Photobleaching -- Nonlinear (Harmonic Generation) Optical Microscopy -- Imaging Brain Slices -- Fluorescent Ion Measurement -- Confocal and Multi-Photon Imaging of Living Embryos -- Imaging Plant Cells -- Practical Fluorescence Resonance Energy Transfer or Molecular Nanobioscopy of Living Cells -- Automated Confocal Imaging and High-Content Screening for Cytomics -- Automated Interpretation of Subcellular Location Patterns from Three-Dimensional Confocal Microscopy -- Display and Presentation Software -- When Light Microscope Resolution Is Not Enough:Correlational Light Microscopy and Electron Microscopy -- Databases for Two- and Three-Dimensional Microscopical Images in Biology -- Confocal Microscopy of Biofilms — Spatiotemporal Approaches -- Bibliography of Confocal Microscopy.

4,121 citations

Journal ArticleDOI
TL;DR: In this article, an infrared spectromicroscopy study of charge dynamics in graphene integrated in gated devices is presented, which reveals significant departures of the quasiparticle dynamics from predictions made for Dirac fermions in idealized, free-standing graphene.
Abstract: A remarkable manifestation of the quantum character of electrons in matter is offered by graphene, a single atomic layer of graphite. Unlike conventional solids where electrons are described with the Schrodinger equation, electronic excitations in graphene are governed by the Dirac hamiltonian. Some of the intriguing electronic properties of graphene, such as massless Dirac quasiparticles with linear energy-momentum dispersion, have been confirmed by recent observations. Here, we report an infrared spectromicroscopy study of charge dynamics in graphene integrated in gated devices. Our measurements verify the expected characteristics of graphene and, owing to the previously unattainable accuracy of infrared experiments, also uncover significant departures of the quasiparticle dynamics from predictions made for Dirac fermions in idealized, free-standing graphene. Several observations reported here indicate the relevance of many-body interactions to the electromagnetic response of graphene.

1,137 citations

Journal ArticleDOI
08 Oct 2010-Science
TL;DR: It is reported that the dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders, and the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.
Abstract: The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.

1,125 citations

Journal ArticleDOI
13 May 1999-Nature
TL;DR: In this article, the authors demonstrate the use of the apertureless approach to scan near field optical microscopy to obtain contrast in vibrational absorption on a scale of about 100 nanometres, about one-hundredth of a wavelength.
Abstract: Identification of chemical compounds by vibrational spectroscopy at infrared wavelengths requires macroscopic samples: the spatial resolution is diffraction-limited to a scale of about half the wavelength, or about five micrometres. The scanning near-field optical microscope1,2, however, can reveal sub-wavelength detail because it uses near-field probing rather than beam focusing. Here we demonstrate the use of the aperture-less approach to scanning near-field optical microscopy3,4,5,6 to obtain contrast in vibrational absorption on a scale of about 100 nanometres, about one-hundredth of a wavelength. We record infrared scattering from the tip of an atomic force microscope scanned over a composite polymer film. At the boundary between different polymers we observe contrast changes owing to changes in vibrational absorption. The contrast is strongly enhanced in the near field of the probe tip, which we interpret as evidence of surface-enhanced infrared absorption7. When extended to multi-wavelength operation, this approach should enable imaging of chemical composition at nanometre resolution.

864 citations

Journal ArticleDOI
12 Nov 2004-Science
TL;DR: It is shown that sea urchin spine regeneration proceeds via the initial deposition of amorphous calcium carbonate, which may have interesting implications for the development of sophisticated materials.
Abstract: The skeletons of adult echinoderms comprise large single crystals of calcite with smooth convoluted fenestrated morphologies, raising many questions about how they form. By using water etching, infrared spectroscopy, electron diffraction, and environmental scanning electron microscopy, we show that sea urchin spine regeneration proceeds via the initial deposition of amorphous calcium carbonate. Because most echinoderms produce the same type of skeletal material, they probably all use this same mechanism. Deposition of transient amorphous phases as a strategy for producing single crystals with complex morphology may have interesting implications for the development of sophisticated materials.

858 citations