Saccharomyces cerevisiae CellWall Remodeling in the Absence of Knr4 and Kre6 Revealed by Nano-FourierTransform Infrared Spectroscopy

The cell wall integrity (CWI) signaling pathway regulates yeast cell wall biosynthesis, cell division, and responses to external stress. The cell wall, comprised of a dense network of chitin, β-1,3- and β-1,6- glucans, and mannoproteins, is very thin, <100 nm. Alterations in cell wall composition may activate the CWI pathway. Saccharomyces cerevisiae, a model yeast, was used to study the role of individual wall components in altering the structure and biophysical properties of the yeast cell wall. Near-field Fourier transform infrared spectroscopy (nano-FT-IR) was used for the first direct, spectrochemical identification of cell wall composition in a background (wild-type) strain and two deletion mutants from the yeast knock-out collection: kre6Δ and knr4Δ. Killer toxin resistant 6 (Kre6) is an integral membrane protein required for biosynthesis of β-1,6-glucan, while Knr4 is a cell signaling protein involved in the control of cell wall biosynthesis, in particular, biosynthesis and deposition of chitin. Complementary spectral data were obtained with far-field (FF)-FT-IR, in transmission, and with attenuated total reflectance (ATR) spectromicroscopy with 3-10 μm wavelength-dependent spatial resolution. The FF-FT-IR spectra of cells and spectra of isolated cell wall components showed that components of the cell body dominated transmission spectra and were still evident in ATR spectra. In contrast, the nano-FT-IR at ∼25 nm spatial resolution could be used to characterize the yeast wall chemical structure. Our results show that the β-1,6-glucan content is decreased in kre6Δ, while all glucan content is decreased in the knr4Δ cell wall. The latter may be thinner than in wild type, since not only are mannan and chitin detectable by nano-FT-IR, but also lipid membranes and protein, indicative of cell interior.

Development of Line-Detected UV-Vis Absorption Microscope and Its Application to Quantitative Evaluation of Lithium Surface Reactivity

Electrochemical reactions in practical batteries occur in confined environments where anode and cathode electrodes are separated only by a thin separator. Therefore, their electrochemical behaviors may differ from those obtained in the conventional experimental cells, where the two electrodes (working and counter electrodes) are largely separated compared to the batteries. The spatial and temporal distributions of the chemical species in the vicinity of each electrode are highly expected to be determined for quantitatively understanding the phenomena in confined environments. In the present study, we developed a line-detected UV-vis absorption microscope that simultaneously measures space-resolved UV-vis absorption spectra. This novel technique has been successfully applied to evaluate the reactivities of the highly reactive lithium (Li) surfaces in organic electrolyte solutions under in situ conditions. The quantitative evaluations of the dissolution rate of Li and the diffusion constant of the product were successfully realized by analyzing the space- and time-resolved absorption spectra based on Fick's law of diffusion. The microscopic technique is expected to open the door to understanding the fundamental electrochemistry in batteries.

Piezoresistive Behavior of Polypyrrole:Carboxymethyl Cellulose Composites

The unique properties of conducting polymers make them ideally suited for applications in organic electronics, photovoltaics, and energy storage systems. Depending on the specific application, they can outperform metal-based electronics by cost, mechanical flexibility, molecular design opportunities, and environmental impact. Many composites of conducting polymers with polyanions can be processed in water. However, the facile processing of such composites comes at a cost of reduced conductivity. In this manuscript, electronic conductivity dependence on composition for a composite of polypyrrole (PPy) with carboxymethyl cellulose (CMC) has been studied. Secondary ion mass spectrometry and electron energy loss spectroscopy mapping indicate the formation of a nanostructure forming PPy-rich nanospheres with a CMC-rich surface coverage. This structure requires inter-particle electron conduction to occur via quantum tunneling. Variations in the tunneling distance are dependent on the applied pressure, giving rise to a pressure-dependent electronic conductivity and thus piezoresistance. This behavior opens new applications of conducting polymer composites in pressure-sensitive electronic devices, providing metal-free alternatives to quantum tunneling composites.

Infrared Spectroscopy–Quo Vadis?

Given the exquisite capability of direct, non-destructive label-free sensing of molecular transitions, IR spectroscopy has become a ubiquitous and versatile analytical tool. IR application scenarios range from industrial manufacturing processes, surveillance tasks and environmental monitoring to elaborate evaluation of (bio)medical samples. Given recent developments in associated fields, IR spectroscopic devices increasingly evolve into reliable and robust tools for quality control purposes, for rapid analysis within at-line, in-line or on-line processes, and even for bed-side monitoring of patient health indicators. With the opportunity to guide light at or within dedicated optical structures, remote sensing as well as high-throughput sensing scenarios are being addressed by appropriate IR methodologies. In the present focused article, selected perspectives on future directions for IR spectroscopic tools and their applications are discussed. These visions are accompanied by a short introduction to the historic development, current trends, and emerging technological opportunities guiding the future path IR spectroscopy may take. Highlighted state-of-the art implementations along with novel concepts enhancing the performance of IR sensors are presented together with cutting-edge developments in related fields that drive IR spectroscopy forward in its role as a versatile analytical technology with a bright past and an even brighter future.

High-resolution infrared microspectroscopic characterization of cartilage cell microenvironment

The lateral resolution of infrared spectroscopy has been inadequate for accurate biochemical characterization of the cell microenvironment, a region regulating biochemical and biomechanical signals to cells. In this study, we demonstrate the capacity of a high-resolution Fourier transform infrared microspectroscopy (HR-FTIR-MS) to characterize the collagen content of this region. Specifically, we focus on the collagen content in the cartilage cell (chondrocyte) microenvironment of healthy and osteoarthritic (OA) cartilage. Human tibial cartilage samples (N = 28) were harvested from 7 cadaveric donors and graded for OA severity (healthy, early OA, advanced OA). HR-FTIR-MS was used to analyze the collagen content of the chondrocyte microenvironment of five distinct zones across the tissue depth. HR-FTIR-MS successfully showed collagen content distribution across chondrocytes and their environment. In zones 2 and 3 (10 - 50% of the tissue thickness), we observed that collagen content was smaller (P < 0.05) in early OA compared to the healthy tissue in the vicinity of cells (pericellular region). The collagen content loss was extended to the extracellular matrix in advanced OA tissue. No significant differences in the collagen content of the chondrocyte microenvironment were observed between the groups in the most superficial (0-10%) and deep zones (50-100%). HR-FTIR-MS revealed collagen loss in the early OA cartilage pericellular region before detectable changes in the extracellular matrix in advanced OA. HR-FTIR-MS-based compositional assessment enables a better understanding of OA-related changes in tissues. This technique can be used to identify new disease mechanisms enabling better intervention strategies. STATEMENT OF SIGNIFICANCE: Osteoarthritis (OA) is the most common degenerative joint disease causing pain and disability. While significant progress has been made in OA research, OA pathogenesis is still poorly understood and current OA treatments are mainly palliative. This study demonstrates that high-resolution FTIR microspectroscopy (HR-FTIR-MS) can characterize OA-induced compositional changes in the cell microenvironment (pericellular matrix) during the early disease stages before tissue changes in the extracellular matrix become apparent. This technique may further enable the identification of new OA mechanisms and improve our current understanding of OA pathogenesis, thus, enabling the development of better treatment methods.

Design Considerations for Discrete Frequency Infrared Microscopy Systems

Discrete frequency infrared chemical imaging is transforming the practice of microspectroscopy by enabling a diversity of instrumentation and new measurement capabilities. While a variety of hardware implementations have been realized, design considerations that are unique to infrared (IR) microscopes have not yet been compiled in literature. Here, we describe the evolution of IR microscopes, provide rationales for design choices, and catalog some major considerations for each of the optical components in an imaging system. We analyze design choices that use these components to optimize performance, under their particular constraints, while providing illustrative examples. We then summarize a framework to assess the factors that determine an instrument's performance mathematically. Finally, we provide a validation approach by enumerating performance metrics that can be used to evaluate the capabilities of imaging systems or suitability for specific intended applications. Together, the presented concepts and examples should aid in understanding available instrument configurations, while guiding innovations in design of the next generation of IR chemical imaging spectrometers.

Fluorescence-Detected Mid-Infrared Photothermal Microscopy

Mid-infrared photothermal microscopy is a new chemical imaging technology in which a visible beam senses the photothermal effect induced by a pulsed infrared laser. This technology provides infrared spectroscopic information at submicrometer spatial resolution and enables infrared spectroscopy and imaging of living cells and organisms. Yet, current mid-infrared photothermal imaging sensitivity suffers from a weak dependence of scattering on the temperature, and the image quality is vulnerable to the speckles caused by scattering. Here, we present a novel version of mid-infrared photothermal microscopy in which thermosensitive fluorescent probes are harnessed to sense the mid-infrared photothermal effect. The fluorescence intensity can be modulated at the level of 1% per Kelvin, which is 100 times larger than the modulation of scattering intensity. In addition, fluorescence emission is free of interference, thus much improving the image quality. Moreover, fluorophores can target specific organelles or biomolecules, thus augmenting the specificity of photothermal imaging. Spectral fidelity is confirmed through fingerprinting a single bacterium. Finally, the photobleaching issue is successfully addressed through the development of a wide-field fluorescence-detected mid-infrared photothermal microscope which allows video rate bond-selective imaging of biological specimens.

Mapping sub-cellular protein aggregates and lipid inclusions using synchrotron ATR-FTIR microspectroscopy

Visualising direct biochemical markers of cell physiology and disease pathology at the sub-cellular level is an ongoing challenge in the biological sciences. A suite of microscopies exists to either visualise sub-cellular architecture or to indirectly view biochemical markers (e.g. histochemistry), but further technique developments and innovations are required to increase the range of biochemical parameters that can be imaged directly, in situ, within cells and tissue. Here, we report our continued advancements in the application of synchrotron radiation attenuated total reflectance Fourier transform infrared (SR-ATR-FTIR) microspectroscopy to study sub-cellular biochemistry. Our recent applications demonstrate the much needed capability to map or image directly sub-cellular protein aggregates within degenerating neurons as well as lipid inclusions within bacterial cells. We also characterise the effect of spectral acquisition parameters on speed of data collection and the associated trade-offs between a realistic experimental time frame and spectral/image quality. Specifically, the study highlights that the choice of 8 cm^-1 spectral resolutions provide a suitable trade-off between spectral quality and collection time, enabling identification of important spectroscopic markers, while increasing image acquisition by ∼30% (relative to 4 cm^-1 spectral resolution). Further, this study explores coupling a focal plane array detector with SR-ATR-FTIR, revealing a modest time improvement in image acquisition time (factor of 2.8). Such information continues to lay the foundation for these spectroscopic methods to be readily available for, and adopted by, the biological science community to facilitate new interdisciplinary endeavours to unravel complex biochemical questions and expand emerging areas of study.

Perspectives on infrared spectroscopic imaging from cancer diagnostics to process analysis

This perspective paper discusses the recent and potential developments in the application of infrared spectroscopic imaging, with a focus on Fourier transform infrared (FTIR) spectroscopic imaging. The current state-of-the-art has been briefly reported, that includes recent trends and advances in applications of FTIR spectroscopic imaging to biomedical systems. Here, some new opportunities for research in the biomedical field, particularly for cancer diagnostics, and also in the engineering field of process analysis; as well as challenges in FTIR spectroscopic imaging are discussed. Current and future prospects that will bring spectroscopic imaging technologies to the frontier of advanced medical diagnostics and to process analytics in engineering applications will be outlined in this opinion paper.

Multiscale Synchrotron-Based Imaging Analysis for the Transfer of PEGylated Gold Nanoparticles In Vivo

High spatial resolution imaging analysis is urgently needed to explore the biodistribution, transfer and clearance profiles, and biological impact of nanoparticles in the body, which will be helpful to clarify the efficacy of nanomedicine in clinical applications. Herein, by combination with multiscale synchrotron-based imaging techniques, including X-ray fluorescence (XRF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and micro X-ray phase contrast computed tomography (micro-XPCT), we visually displayed the transfer patterns and site-specific distribution of PEGylated gold nanoparticles (PEG-GNPs) in the suborgans of the liver, spleen, and kidney after an intravenous injection in mice. A combination of XRF and FTIR imaging analysis showed that the PEG bands presented similar distribution patterns with Au in the intraorgans, suggesting the stability of PEGylation on GNPs. We show that the PEG-GNPs presented heterogeneous distribution in the hepatic lobules with a large amount around the portal vein zone and then a gradient decrease in the sinusoidal region and the CV zone; in the spleen, it gradually accumulated in the splenic red pulp over time; and in the kidney, it quickly transported via the bloodstream to the renal pyramids and renal pelvis, and parts of PEG-GNPs finally accumulated in the renal medulla and renal cortex. Multidimensional micro-XPCT images further show that the PEG-GNP transfer in the liver induced hepatic blood vessel dilatation while they transferred in the liver, providing evidence of GNP transport across the blood vessel endothelial barrier.

Analysis of Fixed and Live Single Cells Using Optical Photothermal Infrared with Concomitant Raman Spectroscopy

This paper reports the first use of a novel completely optically based photothermal method (O-PTIR) for obtaining infrared spectra of both fixed and living cells using a quantum cascade laser (QCL) and optical parametric oscillator (OPO) laser as excitation sources, thus enabling all biologically relevant vibrations to be analyzed at submicron spatial resolution. In addition, infrared data acquisition is combined with concomitant Raman spectra from exactly the same excitation location, meaning the full vibrational profile of the cell can be obtained. The pancreatic cancer cell line MIA PaCa-2 and the breast cancer cell line MDA-MB-231 are used as model cells to demonstrate the capabilities of the new instrumentation. These combined modalities can be used to analyze subcellular structures in both fixed and, more importantly, live cells under aqueous conditions. We show that the protein secondary structure and lipid-rich bodies can be identified on the submicron scale.

Label-free vibrational imaging of different Aβ plaque types in Alzheimer's disease reveals sequential events in plaque development

The neuropathology of Alzheimer’s disease (AD) is characterized by hyperphosphorylated tau neurofibrillary tangles (NFTs) and amyloid-beta (Aβ) plaques. Aβ plaques are hypothesized to follow a development sequence starting with diffuse plaques, which evolve into more compact plaques and finally mature into the classic cored plaque type. A better molecular understanding of Aβ pathology is crucial, as the role of Aβ plaques in AD pathogenesis is under debate. Here, we studied the deposition and fibrillation of Aβ in different plaque types with label-free infrared and Raman imaging. Fourier-transform infrared (FTIR) and Raman imaging was performed on native snap-frozen brain tissue sections from AD cases and non-demented control cases. Subsequently, the scanned tissue was stained against Aβ and annotated for the different plaque types by an AD neuropathology expert. In total, 160 plaques (68 diffuse, 32 compact, and 60 classic cored plaques) were imaged with FTIR and the results of selected plaques were verified with Raman imaging. In diffuse plaques, we detect evidence of short antiparallel β-sheets, suggesting the presence of Aβ oligomers. Aβ fibrillation significantly increases alongside the proposed plaque development sequence. In classic cored plaques, we spatially resolve cores containing predominantly large parallel β-sheets, indicating Aβ fibrils. Combining label-free vibrational imaging and immunohistochemistry on brain tissue samples of AD and non-demented cases provides novel insight into the spatial distribution of the Aβ conformations in different plaque types. This way, we reconstruct the development process of Aβ plaques in human brain tissue, provide insight into Aβ fibrillation in the brain, and support the plaque development hypothesis.

Orientation Matters: Polarization Dependent IR Spectroscopy of Collagen from Intact Tendon Down to the Single Fibril Level

Infrared (IR) spectroscopy has been used for decades to study collagen in mammalian tissues. While many changes in the spectral profiles appear under polarized IR light, the absorption bands are naturally broad because of tissue heterogeneity. A better understanding of the spectra of ordered collagen will aid in the evaluation of disorder in damaged collagen and in scar tissue. To that end, collagen spectra have been acquired with polarized far-field (FF) Fourier Transform Infrared (FTIR) imaging with a Focal Plane Array detector, with the relatively new method of FF optical photothermal IR (O-PTIR), and with nano-FTIR spectroscopy based on scattering-type scanning near-field optical microscopy (s-SNOM). The FF methods were applied to sections of intact tendon with fibers aligned parallel and perpendicular to the polarized light. The O-PTIR and nano-FTIR methods were applied to individual fibrils of 100–500 nm diameter, yielding the first confirmatory and complementary results on a biopolymer. We observed that the Amide I and II bands from the fibrils were narrower than those from the intact tendon, and that both relative intensities and band shapes were altered. These spectra represent reliable profiles for normal collagen type I fibrils of this dimension, under polarized IR light, and can serve as a benchmark for the study of collagenous tissues.

Label-Free Infrared Spectral Histology of Skin Tissue Part II: Impact of a Lumican-Derived Peptide on Melanoma Growth

Melanoma is the most aggressive type of cutaneous malignancies. In addition to its role as a regulator of extracellular matrix (ECM) integrity, lumican, a small leucine-rich proteoglycan, also exhibits anti-tumor properties in melanoma. This work focuses on the use of infrared spectral imaging (IRSI) and histopathology (IRSH) to study the effect of lumican-derived peptide (L9Mc) on B16F1 melanoma primary tumor growth. Female C57BL/6 mice were injected with B16F1 cells treated with L9Mc (n = 10) or its scrambled peptide (n = 8), and without peptide (control, n = 9). The melanoma primary tumors were subjected to histological and IR imaging analysis. In addition, immunohistochemical staining was performed using anti-Ki-67 and anti-cleaved caspase-3 antibodies. The IR images were analyzed by common K-means clustering to obtain high-contrast IRSH that allowed identifying different ECM tissue regions from the epidermis to the tumor area, which correlated well with H&E staining. Furthermore, IRSH showed good correlation with immunostaining data obtained with anti-Ki-67 and anti-cleaved caspase-3 antibodies, whereby the L9Mc peptide inhibited cell proliferation and increased strongly apoptosis of B16F1 cells in this mouse model of melanoma primary tumors.

Synchrotron Photothermal Infrared Nanospectroscopy of Drug-Induced Phospholipidosis in Macrophages

Synchrotron resonance-enhanced infrared atomic force microscopy (RE-AFM-IR) is a near-field photothermal vibrational nanoprobe developed at Diamond Light Source (DLS), capable of measuring mid-infrared absorption spectra with spatial resolution around 100 nm. The present study reports a first application of synchrotron RE-AFM-IR to interrogate biological soft matter at the subcellular level, in this case, on a cellular model of drug-induced phospholipidosis (DIPL). J774A-1 macrophages were exposed to amiodarone (10 μM) or medium for 24 h and chemically fixed. AFM topography maps revealed amiodarone-treated cells with enlarged cytoplasm and very thin regions corresponding to collapsed vesicles. IR maps of the whole cell were analyzed by exploiting the RE-AFM-IR overall signal, i.e., the integrated RE-AFM-IR signal amplitude versus AFM-derived cell thickness, also on lateral resolution around 100 nm. Results show that vibrational band assignment was possible, and all characteristic peaks for lipids, proteins, and DNA/RNA were identified. Both peak ratio and unsupervised chemometric analysis of RE-AFM-IR nanospectra generated from the nuclear and perinuclear regions of untreated and amiodarone-treated cells showed that the perinuclear region (i.e., cytoplasm) of amiodarone-treated cells had significantly elevated band intensities in the regions corresponding to phosphate and carbonyl groups, indicating detection of phospholipid-rich inclusion bodies typical for cells with DIPL. The results of this study are of importance to demonstrate not only the applicability of Synchrotron RE-AFM-IR to soft biological matters with subcellular spatial resolution but also that the spectral information gathered from an individual submicron sample volume enables chemometric identification of treatment and biochemical differences between mammalian cells.

Direct label-free imaging of brain tissue using synchrotron light: a review of new spectroscopic tools for the modern neuroscientist

The incidence of brain disease and brain disorders is increasing on a global scale. Unfortunately, development of new therapeutic strategies has not increased at the same rate, and brain diseases and brain disorders now inflict substantial health and economic impacts. A greater understanding of the fundamental neurochemistry that underlies healthy brain function, and the chemical pathways that manifest in brain damage or malfunction, are required to enable and accelerate therapeutic development. A previous limitation to the study of brain function and malfunction has been the limited number of techniques that provide both a wealth of biochemical information, and spatially resolved information (i.e., there was a previous lack of techniques that provided direct biochemical or elemental imaging at the cellular level). In recent times, a suite of direct spectroscopic imaging techniques, such as Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence microscopy (XFM), and X-ray absorption spectroscopy (XAS) have been adapted, optimized and integrated into the field of neuroscience, to fill the above mentioned capability-gap. Advancements at synchrotron light sources, such as improved light intensity/flux, increased detector sensitivities and new capabilities of imaging/optics, has pushed the above suite of techniques beyond "proof-of-concept" studies, to routine application to study complex research problems in the field of neuroscience (and other scientific disciplines). This review examines several of the major advancements that have occurred over the last several years, with respect to FTIR, XFM and XAS capabilities at synchrotron facilities, and how the increases in technical capabilities have being integrated and used in the field of neuroscience.

Analysis of molecular orientation in polymeric spherulite using polarized micro attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic imaging

Micro ATR-FTIR spectroscopic imaging enables the visualization of two-dimensional chemical distribution at a higher spatial resolution than macro-transmission FTIR imaging approach. In this study, micro ATR-FTIR imaging was applied for analysis of a specific morphology in a spherulite of poly(3-hydroxybutyrate) (PHB). The PHB spherulites crystallized at an isothermal condition, showed the fine band structure due to the twisting lamellar crystals during the spherulite growth under the polarized optical microscope (POM). In addition, the band structure observed in the PHB spherulite was the double band pattern in which the higher and lower birefringence banded areas alternatively appear due to the three-dimensional orientation of crystallographic axes and the biaxial refractive index ellipsoid of PHB crystalline structure. Micro ATR-FTIR spectroscopic imaging was employed for detecting the double band structure in the PHB spherulite. However, the obtained spectral images did not indicate any band structures. To detect the difference of molecular orientation among the double band structures, the micro ATR-FTIR imaging was performed with a linear polarizer at four different angles. The mean values of absorbance in each measured area changed depending on the polarizer angle. The in-plane molecular orientation to the tangential direction of spherulite, caused by the dependence of the average absorbance on the polarizer angles, was determined by the position of measured area in the spherulite and the linear dicroism of each of the spectral band used. To visualize the small difference of molecular orientation in the double band structure, micro ATR-FTIR images of the dichroic differences at three spectral bands were calculated from two different sets of polarizer angles. The micro ATR-FTIR images representing the dichroic differences displayed their corresponding distributions among three spectral bands. The complementary distributions of the dichroic difference were caused by the crystallographic orientation of b- and c-axes and were successfully visualized to reveal the pattern with the features less than 10 μm in size. The results achieved in this study were due to two advantages of the polarized micro ATR-FTIR imaging: the high spatial resolution of micro ATR-FTIR imaging technique, and the high sensitivity of polarization measurements. Thus, this work demonstrates the power of this spectroscopic approach for such analytical investigation.

Detection of Aβ plaque-associated astrogliosis in Alzheimer's disease brain by spectroscopic imaging and immunohistochemistry

Correlative vibrational spectroscopy and immunohistochemistry reveal astroglial processes co-localised with the lipid-rich shell of Aβ plaques.

Recent work using micro-Fourier transform infrared (μFTIR) imaging has revealed that a lipid-rich layer surrounds many plaques in post-mortem Alzheimer's brain. However, the origin of this lipid layer is not known, nor is its role in the pathogenesis of Alzheimer's disease (AD). Here, we studied the biochemistry of plaques in situ using a model of AD. We combined FTIR, Raman and immunofluorescence images, showing that astrocyte processes co-localise with the lipid ring surrounding many plaques. We used μFTIR imaging to rapidly measure chemical signatures of plaques over large fields of view, and selected plaques for higher resolution analysis with Raman microscopy. Raman maps showed similar lipid rings and dense protein cores as in FTIR images, but also revealed cell bodies. We confirmed the presence of plaques using amylo-glo staining, and detected astrocytes using immunohistochemistry, revealing astrocyte co-localisation with lipid rings. This work is important because it correlates biochemical changes surrounding the plaque with the biological process of astrogliosis.

Subcellular mapping of living cells via synchrotron microFTIR and ZnS hemispheres

FTIR imaging is a label-free, non-destructive method valuably exploited in the study of the biological process in living cells. However, the long wavelength/low spatial resolution and the strong absorbance of water are still key constrains in the application of IR microscopy ex vivo. In this work, a new retrofit approach based on the use of ZnS hemispheres is introduced to significantly improve the spatial resolution on live cell FTIR imaging. By means of two high refractive index domes sandwiching the sample, a lateral resolution close to 2.2 μm at 6 μm wavelength has been achieved, i.e. below the theoretical diffraction limit in air and more than twice the improvement (to ~λ/2.7) from our previous attempt using CaF₂ lenses. The ZnS domes also allowed an extended spectral range to 950 cm⁻¹, in contrast to the cut-off at 1050 cm⁻¹ using CaF₂. In combination with synchrotron radiation source, microFTIR provides an improved signal-to-noise ratio through the circa 12 μm thin layer of medium, thus allowing detailed distribution of lipids, protein and nucleic acid in the surround of the nucleus of single living cells. Endoplasmic reticula were clearly shown based on the lipid ν(CH) and ν(C=O) bands, while the DNA was imaged based on the ν(PO₂⁻) band highlighting the nucleus region. This work has also included a demonstration of drug (doxorubicin) in cell measurement to highlight the potential of this approach.

High spatial resolution (1.1 μm and 20 nm) FTIR polarization contrast imaging reveals pre-rupture disorder in damaged tendon

Collagen is a major constituent in many life forms; in mammals, collagen appears as a component of skin, bone, tendon and cartilage, where it performs critical functions. Vibrational spectroscopy methods are excellent for studying the structure and function of collagen-containing tissues, as they provide molecular insight into composition and organization. The latter is particularly important for collagenous materials, given that a key feature is their hierarchical, oriented structure, organized from molecular to macroscopic length scales. Here, we present the first results of high-resolution FTIR polarization contrast imaging, at 1.1 μm and 20 nm scales, on control and mechanically damaged tendon. The spectroscopic data are supported with parallel SEM and correlated AFM imaging. Our goal is to explore the changes induced in tendon after the application of damaging mechanical stress, and the consequences for the healing processes. The results and possibilities for the application of these high-spatial-resolution FTIR techniques in spectral pathology, and eventually in clinical applications, are discussed.

Spectroscopic imaging of biomaterials and biological systems with FTIR microscopy or with quantum cascade lasers

Spectroscopic imaging of biomaterials and biological systems has received increased interest within the last decade because of its potential to aid in the detection of disease using biomaterials/biopsy samples and to probe the states of live cells in a label-free manner. The factors behind this increased attention include the availability of improved infrared microscopes and systems that do not require the use of a synchrotron as a light source, as well as the decreasing costs of these systems. This article highlights the current technical challenges and future directions of mid-infrared spectroscopic imaging within this field. Specifically, these are improvements in spatial resolution and spectral quality through the use of novel added lenses and computational algorithms, as well as quantum cascade laser imaging systems, which offer advantages over traditional Fourier transform infrared systems with respect to the speed of acquisition and field of view. Overcoming these challenges will push forward spectroscopic imaging as a viable tool for disease diagnostics and medical research.

Graphical abstract

Absorbance images of a biopsy obtained using an FTIR imaging microscope with and without an added lens, and also using a QCL microscope with high-NA objective.

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Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples

Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.

Thermal source Fourier transform infrared microtomography applied to Arctic sea ice diatoms

We have used thermal source Fourier Transform Infrared (FTIR) microtomographic imaging to compare sea ice diatoms growing under different light conditions. A prototype tomography accessory was designed to have sufficient degrees of freedom to align any tilted cylindrical sample relative to the axis of rotation, minimizing the off-axis path traced during rotation. The lightweight device rests on the motorized stage to position the sample in the field-of-view and enable mosaic imaging. Reconstruction routines were tested with simulated and real phantoms, to assess limitations in the Radon back-projection method employed. The distribution and abundance of biochemicals is analysed for targets larger than a single FPA tile. Two and three dimensional (2D and 3D) FTIR spectrochemical images were obtained with a Focal Plane Array (FPA, nominal 1.1 μm pixel edges) for phantoms (polystyrene beads in polyvinyl alcohol matrix) and diatom cells harvested from land fast, first-year ice sites in Resolute Passage (74 43.628'N; 95 33.330'W) and Dease Strait (69° 1.11'N; 105° 21.29'W), Nunavut, Canada. The analysis of relative concentrations of organic matter within the encapsulating silica frustules of diatoms is important for a better understanding of both the physiological state and the individual cellular response to environmental pressures. Analysis of 3D FTIR images of Nitzschia frigida collected from beneath high (17-19 cm) and low (3-7 cm) snow depth revealed higher concentrations of lipids in diatoms collected under low snow cover, uniquely based on spectroscopically determined total 3D cell volume and biochemical content.

Can mid-infrared biomedical spectroscopy of cells, fluids and tissue aid improvements in cancer survival? A patient paradigm

This review will take a fresh approach from the patient perspective; offering insight into the applications of mid-infrared biomedical spectroscopy in a scenario whereby the patient presents with non-specific symptoms and via an extensive diagnostic process multiple lesions are discovered but no clear sign of the primary tumour; a condition known as cancer of unknown primary (CUP). With very limited options to diagnose the cancer origin, treatment options are likely to be ineffective and prognosis is consequentially very poor. CUP has not yet been targeted by infrared biospectroscopy, however, this timely, concise dissemination will focus on a series of research highlights and breakthroughs from the field for the management of a variety of cancer-related diseases - many examples of which have occurred within this year alone. The case for integration of mid-infrared (MIR) technology into clinical practice will be demonstrated largely via diagnostic, but also therapeutic and prognostic avenues by means of including cytological, bio-fluid and tissue analysis. The review is structured around CUP but is relevant for all cancer diagnoses. Infrared spectroscopy is fast developing a reputation as a valid and powerful tool for the detection and diagnosis of cancer using a variety of sample formats. The technology will produce data and tools that are designed to complement routine clinical practice; enhancing the ability of the clinician to make a reliable and non-subjective decision and enabling decreased levels of mortality and morbidity and gains in patient quality of life.

FTIR imaging of the molecular burden around Aβ deposits in an early-stage 3-Tg-APP-PSP1-TAU mouse model of Alzheimer's disease

High spatial resolution FTIR imaging of early-stage 3-Tg-APP-PSP1-TAU mouse brain identifies molecular burden around Aβ deposits.

Attenuated total reflection Fourier-transform infrared (ATR-FTIR) imaging of tissues and live cells

FTIR spectroscopic imaging is a label-free, non-destructive and chemically specific technique that can be utilised to study a wide range of biomedical applications such as imaging of biopsy tissues, fixed cells and live cells, including cancer cells. In particular, the use of FTIR imaging in attenuated total reflection (ATR) mode has attracted much attention because of the small, but well controlled, depth of penetration and corresponding path length of infrared light into the sample. This has enabled the study of samples containing large amounts of water, as well as achieving an increased spatial resolution provided by the high refractive index of the micro-ATR element. This review is focused on discussing the recent developments in FTIR spectroscopic imaging, particularly in ATR sampling mode, and its applications in the biomedical science field as well as discussing the future opportunities possible as the imaging technology continues to advance.

Fundamental developments in infrared spectroscopic imaging for biomedical applications

Infrared chemical imaging is a rapidly emerging field with new advances in instrumentation, data acquisition and data analysis. These developments have had significant impact in biomedical applications and numerous studies have now shown that this technology offers great promise for the improved diagnosis of the diseased state. Relying on purely biochemical signatures rather than contrast from exogenous dyes and stains, infrared chemical imaging has the potential to revolutionise histopathology for improved disease diagnosis. In this review we discuss the recent advances in infrared spectroscopic imaging specifically related to spectral histopathology (SHP) and consider the current state of the field. Finally we consider the practical application of SHP for disease diagnosis and consider potential barriers to clinical translation highlighting current directions and the future outlook.

High-resolution FTIR imaging of colon tissues for elucidation of individual cellular and histopathological features

Comparison of spectral-histopathological features of a colon tissue measured using a conventional (5.5 μm × 5.5 μm, left) and a high-magnification (1.1 μm × 1.1 μm, right) FTIR imaging system with respect to HE stained tissue (middle).

FTIR spectroscopic imaging and mapping with correcting lenses for studies of biological cells and tissues

Histopathology of tissue samples is used to determine the progression of cancer usually by staining and visual analysis. It is recognised that disease progression from healthy tissue to cancerous is accompanied by spectral signature changes in the mid-infrared range. In this work, FTIR spectroscopic imaging in transmission mode using a focal plane array (96 × 96 pixels) has been applied to the characterisation of Barrett's oesophageal adenocarcinoma. To correct optical aberrations, infrared transparent lenses were used of the same material (CaF₂) as the slide on which biopsies were fixed. The lenses acted as an immersion objective, reducing scattering and improving spatial resolution. A novel mapping approach using a sliding lens is presented where spectral images obtained with added lenses are stitched together such that the dataset contained a representative section of the oesophageal tissue. Images were also acquired in transmission mode using high-magnification optics for enhanced spatial resolution, as well as with a germanium micro-ATR objective. The reduction of scattering was assessed using k-means clustering. The same tissue section map, which contained a region of high grade dysplasia, was analysed using hierarchical clustering analysis. A reduction of the trough at 1077 cm⁻¹ in the second derivative spectra was identified as an indicator of high grade dysplasia. In addition, the spatial resolution obtained with the lens using high-magnification optics was assessed by measurements of a sharp interface of polymer laminate, which was also compared with that achieved with micro ATR-FTIR imaging. In transmission mode using the lens, it was determined to be 8.5 μm and using micro-ATR imaging, the resolution was 3 μm for the band at a wavelength of ca. 3 μm. The spatial resolution was also assessed with and without the added lens, in normal and high-magnification modes using a USAF target. Spectroscopic images of cells in transmission mode using two lenses are also presented, which are necessary for correcting chromatic aberration and refraction in both the condenser and objective. The use of lenses is shown to be necessary for obtaining high-quality spectroscopic images of cells in transmission mode and proves the applicability of the pseudo hemisphere approach for this and other microfluidic systems.

Novel bio-spectroscopic imaging reveals disturbed protein homeostasis and thiol redox with protein aggregation prior to hippocampal CA1 pyramidal neuron death induced by global brain ischemia in the rat

Global brain ischemia resulting from cardiac arrest and cardiac surgery can lead to permanent brain damage and mental impairment. A clinical hallmark of global brain ischemia is delayed neurodegeneration, particularly within the CA1 subsector of the hippocampus. Unfortunately, the biochemical mechanisms have not been fully elucidated, hindering optimization of current therapies (i.e., therapeutic hypothermia) or development of new therapies. A major limitation to elucidating the mechanisms that contribute to neurodegeneration and understanding how these are influenced by potential therapies is the inability to relate biochemical markers to alterations in the morphology of individual neurons. Although immunocytochemistry allows imaging of numerous biochemical markers at the sub-cellular level, it is not a direct chemical imaging technique and requires successful "tagging" of the desired analyte. Consequently, important biochemical parameters, particularly those that manifest from oxidative damage to biological molecules, such as aggregated protein levels, have been notoriously difficult to image at the cellular or sub-cellular level. It has been hypothesized that reactive oxygen species (ROS) generated during ischemia and reperfusion facilitate protein aggregation, impairing neuronal protein homeostasis (i.e., decreasing protein synthesis) that in turn promotes neurodegeneration. Despite indirect evidence for this theory, direct measurements of morphology and ROS induced biochemical damage, such as increased protein aggregates and decreased protein synthesis, within the same neuron is lacking, due to the unavailability of a suitable imaging method. Our experimental approach has incorporated routine histology with novel wide-field synchrotron radiation Fourier transform infrared imaging (FTIRI) of the same neurons, ex vivo within brain tissue sections. The results demonstrate for the first time that increased protein aggregation and decreased levels of total protein occur in the same CA1 pyramidal neurons 1 day after global ischemia. Further, analysis of serial tissue sections using X-ray absorption spectroscopy at the sulfur K-edge has revealed that CA1 pyramidal neurons have increased disulfide levels, a direct indicator of oxidative stress, at this time point. These changes at 1 day after ischemia precede a massive increase in aggregated protein and disulfide levels concomitant with loss of neuron integrity 2 days after ischemia. Therefore, this study has provided direct support for a correlative mechanistic link in both spatial and temporal domains between oxidative stress, protein aggregation and altered protein homeostasis prior to irreparable neuron damage following global ischemia.

High definition infrared spectroscopic imaging for lymph node histopathology

Chemical imaging is a rapidly emerging field in which molecular information within samples can be used to predict biological function and recognize disease without the use of stains or manual identification. In Fourier transform infrared (FT-IR) spectroscopic imaging, molecular absorption contrast provides a large signal relative to noise. Due to the long mid-IR wavelengths and sub-optimal instrument design, however, pixel sizes have historically been much larger than cells. This limits both the accuracy of the technique in identifying small regions, as well as the ability to visualize single cells. Here we obtain data with micron-sized sampling using a tabletop FT-IR instrument, and demonstrate that the high-definition (HD) data lead to accurate identification of multiple cells in lymph nodes that was not previously possible. Highly accurate recognition of eight distinct classes - naïve and memory B cells, T cells, erythrocytes, connective tissue, fibrovascular network, smooth muscle, and light and dark zone activated B cells was achieved in healthy, reactive, and malignant lymph node biopsies using a random forest classifier. The results demonstrate that cells currently identifiable only through immunohistochemical stains and cumbersome manual recognition of optical microscopy images can now be distinguished to a similar level through a single IR spectroscopic image from a lymph node biopsy.