Biological applications of synchrotron radiation infrared spectromicroscopy

Research updates and progress on nutritional significance of the amides I and II, alpha-helix and beta-sheet ratios, microbial protein synthesis, and steam pressure toasting condition with globar and synchrotron molecular microspectroscopic techniques with chemometrics

This article aims to review research updates and progress on the nutritional significance of the amides I and II, the alpha-helix and beta-sheet ratios, the microbial protein synthesis, and the steam pressure toasting condition in food and feed with globar and synchrotron molecular microspectroscopic techniques plus chemometrics (both univariate and multivariate techniques). The review focused on (I) impact of the amides I and II, and the alpha-helix and beta-sheet-structure ratios in food and feeds; (II) Current research progress and update in synchrotron technique and application in feed and food molecular structure studies that are associated with nutrition delivery; (III) Impact of thermal processing- steam pressure toasting condition on feed and food; (IV). Impact of the microbial protein synthesis and methodology on feed and food; and (V). Impact on performance and production of ruminants with Faba beans.

Quantitative biochemical phenotypic heterogeneity of senescent macrophage at a single cell level by Synchrotron Radiation Fourier Transform Infrared Microspectroscopy

Macrophage senescence plays an important role in pathophysiological process of age-related diseases such as atherosclerosis, chronic obstructive pulmonary disease (COPD), pulmonary fibrosis, and lung cancer. After macrophage senescence, the biochemical phenotypes related to biological functions showed great heterogeneity. However, the biochemical phenotype and phenotypic heterogeneity of senescent macrophage has not been fully understood. Exploring the phenotype of biochemical substances in senescent macrophage will be helpful for understanding the function of senescent macrophage and finding out the potential mechanism between immune macrophage senescence and age-related diseases. In this study, we employed SR-FTIR microspectroscopy to detect the biochemical phenotype and phenotypic heterogeneity of single macrophage. The whole infrared spectra of senescent macrophages shifted, indicating biochemical substance changes within senescent macrophages. PCA and intercellular Euclidean distance statistical analysis based on specific spectra regions revealed dynamic changes of lipids and proteins during macrophage senescence. This proved that SR-FTIR microspectroscopy is an effective tool to detect the single cell biochemical phenotype transformation and phenotypic heterogeneity during macrophage senescence. It is of great significance to provide an evaluation method or clue for the study of cellular functions related to intracellular biochemical substances.

Halide Perovskites Films for Ionizing Radiation Detection: An Overview of Novel Solid-State Devices

Halide perovskites are a novel class of semiconductors that have attracted great interest in recent decades due to their peculiar properties of interest for optoelectronics. In fact, their use ranges from the field of sensors and light emitters to ionizing radiation detectors. Since 2015, ionizing radiation detectors exploiting perovskite films as active media have been developed. Recently, it has also been demonstrated that such devices can be suitable for medical and diagnostic applications. This review collects most of the recent and innovative publications regarding solid-state devices for the detection of X-rays, neutrons, and protons based on perovskite thin and thick films in order to show that this type of material can be used to design a new generation of devices and sensors. Thin and thick films of halide perovskites are indeed excellent candidates for low-cost and large-area device applications, where the film morphology allows the implementation on flexible devices, which is a cutting-edge topic in the sensor sector.

Monitoring surface dynamics of electrodes during electrocatalysis using in situ synchrotron FTIR spectroscopy

Monitoring the surface dynamics of catalysts under working conditions is important for a deep understanding of the underlying electrochemical mechanisms towards efficient energy conversion and storage. Fourier transform infrared (FTIR) spectroscopy with high surface sensitivity has been considered as a powerful tool for detecting surface adsorbates, but it faces a great challenge when being adopted in surface dynamics investigations during electrocatalysis due to the complication and influence of aqueous environments. This work reports a well designed FTIR cell with tunable micrometre-scale water film over the surface of working electrodes and dual electrolyte/gas channels for in situ synchrotron FTIR tests. By coupling with a facile single-reflection infrared mode, a general in situ synchrotron radiation FTIR (SR-FTIR) spectroscopic method is developed for tracking the surface dynamics of catalysts during the electrocatalytic process. As an example, in situ formed key *OOH is clearly observed on the surface of commercial benchmark IrO₂ catalysts during the electrochemical oxygen evolution process based on the developed in situ SR-FTIR spectroscopic method, which demonstrates its universality and feasibility in surface dynamics studies of electrocatalysts under working conditions.

Tracking the Oxygen Dynamics of Solid-Liquid Electrochemical Interfaces by Correlative In Situ Synchrotron Spectroscopies

ConspectusOxygen-involved electrocatalytic processes, including the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR), are central to a series of advanced modern energy and conversion technologies, such as water electrolyzers, fuel cells, and CO₂ reduction or N₂ fixation devices. A comprehensive and in-depth understanding of the charge transfer and energy conversion process that ubiquitously occurs over solid-liquid electrochemical interfaces during oxygen electrocatalysis is crucial for understanding the key essence of oxygen-related electrochemistry. The huge challenges for dynamic studies over solid-liquid interfaces during oxygen electrocatalysis lie in the all-embracing electrochemical processes of the catalytic reactions, associated with both structural and reactive intermediates evolution on the electrode surface, and in the significant influence of the aqueous environments of electrolytes used. Hence, overcoming these challenges intrinsically calls for a great cooperation of multiple cutting-edge in situ technologies. Synchrotron radiation (SR) X-ray absorption fine structure (SR-XAFS) spectroscopy is highly sensitive to the local atomic structure of nanomaterials, and SR-based Fourier transform infrared (SR-FTIR) spectroscopy features unique molecular fingerprint identification to determine active species on the surface of electrodes. One can imagine that the correlative in situ SR-XAFS/FTIR spectroscopic investigations will potentially provide sufficient, reliable, and complementary information at the atomic/molecular level to depict vivid and comprehensive "dynamic movies" of solid-liquid electrochemical interfaces during oxygen electrocatalysis, which will help effectively promote/simplify the complicated screening process of advanced oxygen electrocatalysts for efficient high-energy-density energy systems.In this Account, starting with some fundamentals of SR-based spectroscopic technologies, tips for obtaining high-quality SR-XAFS and SR-FTIR spectroscopy results during the electrocatalytic process are comprehensively specified. Subsequently, the latest research achievements of dynamic investigations mainly from our group based on in situ SR-XAFS and/or SR-FTIR spectroscopies will be systematically scrutinized and properly emphasized in detail, where the currently attractive metal-organic-framework (MOF) nanomaterials and single-atom catalysts (SACs) are selected as the main object of research. Moreover, the vital contributions of correlative in situ SR-XAFS/FTIR studies on new discoveries of the dynamic evolution of solid-liquid interfaces during oxygen electrocatalysis are highlighted. In particular, our pioneering research found that the potential-dependent dynamically coupled oxygen formed in the precatalytic stage was a very useful promoter in SACs to promote efficient OER kinetics under acidic conditions. In addition, the in situ generated metastable Ni₁-N₂ centers with more structural degrees of freedom in SACs could potentially facilitate the fast 4e^- ORR kinetics. This Account is anticipated to stimulate broad interest in dynamic explorations in various catalytic processes of interest in the material science and electrochemistry communities using correlative SR-based technologies.

Halide perovskites and perovskite related materials for particle radiation detection

Radiation detectors are widely used in physics, materials science, chemistry, and biology. Halide perovskites are known for their superior properties including tunable bandgaps and chemical compositions, high defect tolerance, solution-processable synthesis of films and crystals, and high carrier diffusion length. Recently, halide perovskites have attracted enormous interest as particle radiation detectors for both charged (α and β) and uncharged (neutrons) particles. Solid-state detectors based on single crystal perovskites can detect α particles and thermal neutrons with energy-resolved spectra. Halide perovskite scintillators are also able to detect β particles and fast neutrons. In this review, we briefly introduce the fundamentals of radiation detection and summarize the recent progress on halide perovskite detectors for particle radiation.

Advances in mid-infrared spectroscopy enabled by supercontinuum laser sources

Supercontinuum sources are all-fiber pulsed laser-driven systems that provide high power spectral densities within ultra-broadband spectral ranges. The tailored process of generating broadband, bright, and spectrally flat supercontinua-through a complex interplay of linear and non-linear processes-has been recently pushed further towards longer wavelengths and has evolved enough to enter the field of mid-infrared (mid-IR) spectroscopy. In this work, we review the current state and perspectives of this technology that offers laser-like emission properties and instantaneous broadband spectral coverage comparable to thermal emitters. We aim to go beyond a literature review. Thus, we first discuss the basic principles of supercontinuum sources and then provide an experimental part focusing on the quantification and analysis of intrinsic emission properties such as typical power spectral densities, brightness levels, spectral stability, and beam quality (to the best of the authors' knowledge, the M² factor for a mid-IR supercontinuum source is characterized for the first time). On this basis, we identify key competitive advantages of these alternative emitters for mid-IR spectroscopy over state-of-the-art technologies such as thermal sources or quantum cascade lasers. The specific features of supercontinuum radiation open up prospects of improving well-established techniques in mid-IR spectroscopy and trigger developments of novel analytical methods and instrumentation. The review concludes with a structured summary of recent advances and applications in various routine mid-IR spectroscopy scenarios that have benefited from the use of supercontinuum sources.

Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status

Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.

Lipid distribution on ethnic hairs by Fourier transform infrared synchrotron spectroscopy

BACKGROUND

A synchrotron-based Fourier transform infrared micro-spectrometer (μ-FTIR) allows the spatial determination of lipids across the different layers of ethnic hairs and differentiates between the lipid order arrangement and quantity.

MATERIALS AND METHODS

The three ethnic fibers were delipidized, the lipid extracts were characterized, and the delipidized fibers were studied by dynamic vapor sorption experiments (DVS) and FTIR-synchrotron techniques.

RESULTS

The average spectra from the different hair regions exhibited the most intense CH₂ sym peaks on the medulla, followed by those from the cuticle and cortex for all hairs of different ethnicities. Differences in the lipid fraction of the three hair types have been observed, and they can explain some barrier properties. African virgin hair was demonstrated to have more lipids mainly in the medulla, which implies an important hydrophobicity with low hysteresis between absorption and desorption water vapor processes. In addition, these lipids are highly disordered, mainly in the cuticle, which can be related to its high water vapor diffusion. Asian and Caucasian virgin hairs presented a similar lipid order in all regions, with similar diffusion coefficients. Results indicate that the higher order of the lipid bilayer hinders water permeation kinetics in some way.

CONCLUSION

The differences in the presence and organization of the lipids in the different regions of the African hair can account for its differentiation with regards to moisturization and swelling from the other types of fibers.

Synchrotron Fourier transform infrared microspectroscopy (sFTIRM) analysis of unfolding behavior of electrospun collagen nanofibers

Collagen nanofibers are popular extracellular matrix (ECM) materials in regenerative medicine. Electrospinning of collagen dissolved in organic solvents is widely used for fabricating anisotropic collagen nanofibers; however, such fibers are water-soluble and require cross-linking before use as scaffolds for cell culture. Herein, in-situ crosslinking during electrospinning process is suggested by using different chemical agents, namely genipin and glutaraldehyde, and physical crosslinking method (UV light). sFTIRM; Synchrotron Fourier-Transform Infrared Microspectroscopy is a powerful tool that sheds light on the molecular structure of collagen nanofibers. Applied extraction methods caused shifts on protein band positions. Electrospinning process prevents self-assembly of collagen molecules and obtained electrospun collagen nanofibers have lower band positions. Crosslinkers have effect on the secondary structure of collagen molecules. Among different crosslinkers, genipin in-situ crosslinking process perform better in preserving the native structure of electrospun collagen nanofibers than the physical crosslinking method (UV).

Amyloid Structural Changes Studied by Infrared Microspectroscopy in Bigenic Cellular Models of Alzheimer's Disease

Alzheimer's disease affects millions of lives worldwide. This terminal disease is characterized by the formation of amyloid aggregates, so-called amyloid oligomers. These oligomers are composed of β-sheet structures, which are believed to be neurotoxic. However, the actual secondary structure that contributes most to neurotoxicity remains unknown. This lack of knowledge is due to the challenging nature of characterizing the secondary structure of amyloids in cells. To overcome this and investigate the molecular changes in proteins directly in cells, we used synchrotron-based infrared microspectroscopy, a label-free and non-destructive technique available for in situ molecular imaging, to detect structural changes in proteins and lipids. Specifically, we evaluated the formation of β-sheet structures in different monogenic and bigenic cellular models of Alzheimer's disease that we generated for this study. We report on the possibility to discern different amyloid signatures directly in cells using infrared microspectroscopy and demonstrate that bigenic (amyloid-β, α-synuclein) and (amyloid-β, Tau) neuron-like cells display changes in β-sheet load. Altogether, our findings support the notion that different molecular mechanisms of amyloid aggregation, as opposed to a common mechanism, are triggered by the specific cellular environment and, therefore, that various mechanisms lead to the development of Alzheimer's disease.

Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra

Heavy metal acclimated bacteria are profoundly the preferred choice for bioremediation studies. Bacteria get acclimated to toxic concentrations of heavy metals by induction of specific enzymes and genetic selection favoring new metabolic abilities leading to activation of one or several of resistance mechanisms creating bacterial populations with differences in resistance profile and/or level. Therefore, to use in bioremediation processes, it is important to discriminate acclimated bacterial populations and choose a more resistant strain. In this study, we discriminated heavy metal acclimated bacteria by using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy and multivariate analysis methods namely Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). Two acclimation methods, acute and gradual, were used which cause differences in molecular changes resulting in bacterial populations with different molecular and resistance profiles. Brevundimonas sp., Gordonia sp., and Microbacterium oxydans were exposed to the toxic concentrations of Cd (30 μg/ml) or Pb (90 μg/ml) by using broth medium as a growth media. Our results revealed that PCA and HCA clearly discriminated the acute-acclimated, gradual-acclimated, and control bacteria from each other in protein, carbohydrate, and whole spectral regions. Furthermore, we classified acclimated (acute and gradual) and control bacteria more accurately by using SIMCA with 99.9% confidence. This study demonstrated that heavy metal acclimated and control group bacteria can be discriminated by using chemometric analysis of FTIR spectra in a powerful, cost-effective, and handy way. In addition to the determination of the most appropriate acclimation procedure, this approach can be used in the detection of the most resistant bacterial strains to be used in bioremediation studies.

Retinal oxidative stress at the onset of diabetes determined by synchrotron FTIR widefield imaging: towards diabetes pathogenesis

Diabetic retinopathy is a microvascular complication of diabetes that can lead to blindness. In the present study, we aimed to determine the nature of diabetes-induced, highly localized biochemical changes in the neuroretina at the onset of diabetes. High-resolution synchrotron Fourier transform infrared (s-FTIR) wide field microscopy coupled with multivariate analysis (PCA-LDA) was employed to identify biomarkers of diabetic retinopathy with spatial resolution at the cellular level. We compared the retinal tissue prepared from 6-week-old Ins2^Akita/+ heterozygous (Akita/+, N = 6; a model of diabetes) male mice with the wild-type (control, N = 6) mice. Male Akita/+ mice become diabetic at 4-weeks of age. Significant differences (P < 0.001) in the presence of biomarkers associated with diabetes and segregation of spectra were achieved. Differentiating IR bands attributed to nucleic acids (964, 1051, 1087, 1226 and 1710 cm^-1), proteins (1662 and 1608 cm^-1) and fatty acids (2854, 2923, 2956 and 3012 cm^-1) were observed between the Akita/+ and the WT samples. A comparison between distinctive layers of the retina, namely the photoreceptor retinal layer (PRL), outer plexiform layer (OPL), inner nucleus layer (INL) and inner plexiform layer (IPL) suggested that the photoreceptor layer is the most susceptible layer to oxidative stress in short-term diabetes. Spatially-resolved chemical images indicated heterogeneities and oxidative-stress induced alterations in the diabetic retina tissue morphology compared with the WT retina. In this study, the spectral biomarkers and the spatial biochemical alterations in the diabetic retina and in specific layers were identified for the first time. We believe that the conclusions drawn from these studies will help to bridge the gap in our understanding of the molecular and cellular mechanisms that contribute to the pathobiology of diabetic retinopathy.

Blood mononuclear cells as speculum of emotional stress analyzed by synchrotron infrared spectroscopy and a nootropic drug

Chronic psychological stress is an important public health issue which generates behavioral changes, anxiety, immunosuppression and oxidative damage. Piracetam is a cognitive enhancer, at cellular level it protects from oxidative stress. The aim of this study was to evaluate the effect of psychological stress and of piracetam on circulating mononuclear cells by analyzing the biochemical spectrome using Synchrotron Radiation Fourier Transform Infrared Microspectroscopy (SR-μFTIR). Rats were exposed for five days to a stressor (cat odor) under oral administration of piracetam (600 mg/kg). SR-μFTIR analysis showed a decrease in bands associated to the lipids region (2852 cm^-1, 2923 cm^-1 and 2962 cm^-1) and an increase absorption of the amide I band (1654 cm^-1) under stress conditions. The principal component analysis showed increase oxidation of lipids (decrease of 3010 cm^-1, 2923 cm^-1 and 2852 cm^-1 bands) as well as proteins denaturation (increase of 1610 cm^-1 and 1690 cm^-1 bands) under stress. Piracetam provided protection to polyunsaturated lipids (p ≤ 0.001) and lipids/proteins ratio (p ≤ 0.001). Behaviorally, this drug diminished fear and anxiety in stressed animals by the plus maze test (p ≤ 0.002). However, this drug induced oxidative stress in mononuclear cells from unstressed animals and altered their behavior.

A FTIRM study of the interactive effects of metals (zinc, copper and cadmium) in binary mixtures on the biochemical constituents of the gills in rainbow trout (Oncorhynchus mykiss)

We employed Fourier Transform Infrared Microspectroscopy to examine, in situ, the effects of waterborne Cu, Cd and Zn, alone and in binary mixtures, during acute exposure on the integrity of major lipid and protein constituents of the gill of a model teleost species, rainbow trout (Oncorhynchus mykiss). Our findings demonstrated that acute exposure to metals, both individually and in binary mixture, resulted in the degradations of various components of proteins and lipids in the gill tissue. Generally, when comparing the effects of individual metals, Cu was found to induce the maximum adverse effects followed by Cd and Zn, respectively. Among the binary metal-mixture combinations, Cu and Cd produced additive effects on the degradation of major proteins and lipid moieties, whereas the co-exposure of Zn with Cd or Cu elicited ameliorative effects, indicating antagonistic (less than additive) interactions between Zn and Cd or Cu in the rainbow trout gill. Overall, the present study demonstrates that FTIRM can be a useful tool to gain novel mechanistic insights into the biochemical changes induced by metals in the fish gill, which could influence the overall toxicity of metals to fish.

SR-FTIR as a tool for quantitative mapping of the content and distribution of extracellular matrix in decellularized book-shape bioscaffolds

Background

To evaluate synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIR) as a tool for quantitative mapping of the content and distribution of the extracellular matrix in decellularized fibrocartilage bioscaffolds, and to provide a new platform for quantitatively characterizing bioscaffolds for tissue engineering.

Methods

Fibrocartilage was harvested and cut into book-shape bioscaffolds (N = 54), which were then decellularized. The structures and distribution of collagen fibrous and intrinsic ultrastructure in decellularized fibrocartilage bioscaffolds were evaluated by histological staining and scanning electron microscopy (SEM), respectively. The content of collagen and proteoglycan in the cellularized or decellularized bioscaffolds were also measured by SR-FTIR and biochemical assay.

Results

Book-shape fibrocartilage decellularized bioscaffolds were successfully obtained. Histological examination revealed that the structure of extracellular matrix endured during decellularization. Histology and DNA quantification analysis confirmed substantial removal of cells during decellularization. SEM demonstrated that intrinsic ultrastructure of the fibrocartilage bioscaffold was also well preserved. SR-FTIR quantitative analysis confirmed that decellularization had a significant effect on the content and distribution of collagen and proteoglycan in fibrocartilage bioscaffolds, these results are confirmed with the biochemical assay results.

Conclusion

SR-FTIR imaging can capture the histological morphology of decellularized bioscaffolds. Moreover, it can be used for quantitative mapping of the content and distribution of collagen in the bioscaffolds.

Biosorption of malachite green onto Haematococcus pluvialis observed through synchrotron Fourier-transform infrared microspectroscopy

Microalgae have emerged as promising biosorbents for the treatment of malachite green (MG) in wastewater. However, the underlying mechanism for the biosorption of MG onto microalgae is still unclear and needs further intensive study. In this work, synchrotron Fourier-transform infrared (s-FTIR) microspectroscopy in combination with biochemical assay is employed to evaluate MG removal efficiency (95·2%, 75·6% and 66·5%) by three stages of Haematococcus pluvialis. Meanwhile, the various vital changes of algal cells including lipids, proteins, polysaccharides and carotenoids is distinguished and quantified in situ. This study illustrates that s-FTIR microspectroscopy is an effective and powerful tool to scrutinize the mechanism for the interactions between the MG dye and microalgal cells, and it even provides an effective and noninvasive new approach to screen potentially proper biosorbents for the removal of dyes from wastewater.

SIGNIFICANCE AND IMPACT OF THE STUDY

Microalgae have potential application for their ability to absorb dyes from industrial wastewater. In this study, we initiated the application of synchrotron Fourier-transform infrared (s-FTIR) microspectroscopy to investigate malachite green dye removal efficiency by three stages of Haematococcus pluvialis, demonstrating that s-FTIR is a very powerful tool in exploring the mechanism of the biosorption of dyes onto microalgae.

Chemotherapeutic response to cisplatin-like drugs in human breast cancer cells probed by vibrational microspectroscopy

Studies of drug-cell interactions in cancer model systems are essential in the preclinical stage of rational drug design, which relies on a thorough understanding of the mechanisms underlying cytotoxic activity and biological effects, at a molecular level. This study aimed at applying complementary vibrational spectroscopy methods to evaluate the cellular impact of two Pt(ii) and Pd(ii) dinuclear chelates with spermine (Pt2Spm and Pd2Spm), using cisplatin (cis-Pt(NH3)2Cl2) as a reference compound. Their effects on cellular metabolism were monitored in a human triple-negative metastatic breast cancer cell line (MDA-MB-231) by Raman and synchrotron-radiation infrared microspectroscopies, for different drug concentrations (2-8 μM) at 48 h exposure. Multivariate data analysis was applied (unsupervised PCA), unveiling drug- and concentration-dependent effects: apart from discrimination between control and drug-treated cells, a clear separation was obtained for the different agents studied - mononuclear vs. polynuclear, and Pt(ii) vs. Pd(ii). Spectral biomarkers of drug action were identified, as well as the cellular response to the chemotherapeutic insult. The main effect of the tested compounds was found to be on DNA, lipids and proteins, the Pd(ii) agent having a more significant impact on proteins while its Pt(ii) homologue affected the cellular lipid content at lower concentrations, which suggests the occurrence of distinct and unconventional pathways of cytotoxicity for these dinuclear polyamine complexes. Raman and FTIR microspectroscopies were confirmed as powerful non-invasive techniques to obtain unique spectral signatures of the biochemical impact and physiological reaction of cells to anticancer agents.

Nano-spectroscopic imaging of proteins with near-field scanning optical microscopy (NSOM)

Understanding the hierarchical structure of proteins at their fundamental length scales is essential to get insights into their functions and roles in fundamental biological processes. Near-field scanning optical microscopy (NSOM), which overcomes the diffraction limits of conventional optics, provides a powerful analytical tool to image target proteins at nanoscale resolution. Especially, by combining NSOM with infrared (IR) or Raman spectroscopy, near-field nanospectroscopic imaging of a single protein is achieved. In this review, we present the recent technical progress of NSOM setup for nanospectroscopic imaging of proteins, and its application to nanospectroscopic analysis of protein structures is highlighted and critically reviewed. Finally, current challenges and perspectives on application of NSOM in emerging areas of industrial, environmental and medical biotechnology are discussed.

3D Digital Pathology for a Chemical-Functional Analysis of Glomeruli in Health and Pathology

Determining the filtration function and biochemical status of kidney at the single glomerulus level remains hardly accessible, even from biopsies. Here, we provide evidence that IR spectro-microscopy is a suitable method to account for the filtration capacity of individual glomeruli along with related physio-pathological condition. A ∼4 μm voxel resolution 3D IR image reconstruction is built from consecutive tissue sections, thus, providing a 3D IR spectrum matrix of an individual glomerulus. The filtration capacity of glomeruli was quantitatively determined after BaSO₄ perfusion, and additional chemical data could be used to determined oxidative stress effects and fibrosis, thus, combining functional and biochemical information from the same 3D IR spectrum matrix. This analytical approach was applied on mice with unilateral ureteral obstruction (UUO) inducing chronic kidney disease. Compared to the healthy condition, UUO induced a significant drop in glomeruli filtration capacity (-17 ± 8% at day 4 and -48 ± 14% at day 14) and volume (36 ± 10% at day 4 and 67 ± 13% at day 14), along a significant increase of oxidative stress (+61 ± 19% at day 4 and +84 ± 17% at day 14) and a change in the lipid-to-protein ratio (-8.2 ± 3.6% at day 4 and -18.1 ± 5.9% at day 14). Therefore, IR spectro-microscopy might be developed as a new 3D pathology resource for analyzing functional and biochemical parameters of glomeruli.

3D chemical imaging of the brain using quantitative IR spectro-microscopy

Three-dimensional (3D) histology is the next frontier for modern anatomo-pathology. Characterizing abnormal parameters in a tissue is essential to understand the rationale of pathology development. However, there is no analytical technique, in vivo or histological, that is able to discover such abnormal features and provide a 3D distribution at microscopic resolution. Here, we introduce a unique high-throughput infrared (IR) microscopy method that combines automated image correction and subsequent spectral data analysis for 3D-IR image reconstruction. We performed spectral analysis of a complete organ for a small animal model, a mouse brain with an implanted glioma tumor. The 3D-IR image is reconstructed from 370 consecutive tissue sections and corrected using the X-ray tomogram of the organ for an accurate quantitative analysis of the chemical content. A 3D matrix of 89 × 106 IR spectra is generated, allowing us to separate the tumor mass from healthy brain tissues based on various anatomical, chemical, and metabolic parameters. We demonstrate that quantitative metabolic parameters can be extracted from the IR spectra for the characterization of the brain vs. tumor metabolism (assessing the Warburg effect in tumors). Our method can be further exploited by searching for the whole spectral profile, discriminating tumor vs. healthy tissue in a non-supervised manner, which we call 'spectromics'.

Nanoantenna-Enhanced Infrared Spectroscopic Chemical Imaging

Spectroscopic infrared chemical imaging is ideally suited for label-free and spatially resolved characterization of molecular species, but often suffers from low infrared absorption cross sections. Here, we overcome this limitation by utilizing confined electromagnetic near-fields of resonantly excited plasmonic nanoantennas, which enhance the molecular absorption by orders of magnitude. In the experiments, we evaporate microstructured chemical patterns of C₆₀ and pentacene with nanometer thickness on top of homogeneous arrays of tailored nanoantennas. Broadband mid-infrared spectra containing plasmonic and vibrational information were acquired with diffraction-limited resolution using a two-dimensional focal plane array detector. Evaluating the enhanced infrared absorption at the respective frequencies, spatially resolved chemical images were obtained. In these chemical images, the microstructured chemical patterns are only visible if nanoantennas are used. This confirms the superior performance of our approach over conventional spectroscopic infrared imaging. In addition to the improved sensitivity, our technique provides chemical selectivity, which would not be available with plasmonic imaging that is based on refractive index sensing. To extend the accessible spectral bandwidth of nanoantenna-enhanced spectroscopic imaging, we employed nanostructures with dual-band resonances, providing broadband plasmonic enhancement and sensitivity. Our results demonstrate the potential of nanoantenna-enhanced spectroscopic infrared chemical imaging for spatially resolved characterization of organic layers with thicknesses of several nanometers. This is of potential interest for medical applications which are currently hampered by state-of-art infrared techniques, e.g., for distinguishing cancerous from healthy tissues.

Quantitative IR microscopy and spectromics open the way to 3D digital pathology

Currently, only mass-spectrometry (MS) microscopy brings a quantitative analysis of chemical contents of tissue samples in 3D. Here, the reconstruction of a 3D quantitative chemical images of a biological tissue by FTIR spectro-microscopy is reported. An automated curve-fitting method is developed to extract all intense absorption bands constituting IR spectra. This innovation benefits from three critical features: (1) the correction of raw IR spectra to make them quantitatively comparable; (2) the automated and iterative data treatment allowing to transfer the IR-absorption spectrum into a IR-band spectrum; (3) the reconstruction of an 3D IR-band matrix (x, y, z for voxel position and a 4^th dimension with all IR-band parameters). Spectromics, which is a new method for exploiting spectral data for tissue metadata reconstruction, is proposed to further translate the related chemical information in 3D, as biochemical and anatomical tissue parameters. An example is given with oxidative stress distribution and the reconstruction of blood vessels in tissues. The requirements of IR microscopy instrumentation to propose 3D digital histology as a clinical routine technology is briefly discussed.

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.

Biomedical investigations using Fourier transform-infrared microspectroscopy

One of the most exciting recent developments in infrared spectroscopy has been the coupling of the spectrometer to an infrared microscope. The combination of the new infrared spectrometer and a microscope was a natural thought of scientists in these fields. This development has been so rewarding and so useful in solving today's chemical problems that infrared microspectroscopy has quickly become a significant subclassification of infrared spectroscopy. Infrared microspectroscopy has a much longer history than the recent enthusiasm would imply, however. The great interest in the use of infrared spectroscopy to solve biomedical problems that occurred in recent years shortly spread into the medical and biological fields. The aim of this review is to discuss the new developments in applications of FT-IR microspectroscopy in biomedical analysis, covering the period between 2008 and 2013.

FTIR imaging of structural changes in visceral and subcutaneous adiposity and brown to white adipocyte transdifferentiation

FTIR microspectroscopy coupled with UCP1 immunohistological staining enables the detection of obesity-related molecular alterations and transdifferentiations in visceral and subcutaneous adipose tissues in spontaneously obese mice lines.

Ultrabroadband infrared nanospectroscopic imaging

Characterizing and ultimately controlling the heterogeneity underlying biomolecular functions, quantum behavior of complex matter, photonic materials, or catalysis requires large-scale spectroscopic imaging with simultaneous specificity to structure, phase, and chemical composition at nanometer spatial resolution. However, as with any ultrahigh spatial resolution microscopy technique, the associated demand for an increase in both spatial and spectral bandwidth often leads to a decrease in desired sensitivity. We overcome this limitation in infrared vibrational scattering-scanning probe near-field optical microscopy using synchrotron midinfrared radiation. Tip-enhanced localized light-matter interaction is induced by low-noise, broadband, and spatially coherent synchrotron light of high spectral irradiance, and the near-field signal is sensitively detected using heterodyne interferometric amplification. We achieve sub-40-nm spatially resolved, molecular, and phonon vibrational spectroscopic imaging, with rapid spectral acquisition, spanning the full midinfrared (700-5,000 cm(-1)) with few cm(-1) spectral resolution. We demonstrate the performance of synchrotron infrared nanospectroscopy on semiconductor, biomineral, and protein nanostructures, providing vibrational chemical imaging with subzeptomole sensitivity.

Fourier transform infrared (FT-IR) spectromicroscopy to identify cell organelles: correlation with fluorescence staining in MCF-7 breast cancer cells

Biomolecules display specific vibrational signatures in the infrared (IR) range, and organelles that concentrate these biomolecules can be identified by these IR signatures. Subcellular identification and location of cell organelles using IR signatures is attractive as it does not require the use of any specific trackers and is thus non-invasive and non-destructive. We show here that endogenous IR absorptions are relevant to detecting and imaging the nucleus, the cytoplasm, and the Golgi apparatus/endoplasmic reticulum in MCF-7 breast cancer cells, and we compare these results with our previous work on the HeLa cell line. We correlate maps of fixed and dried cells obtained by synchrotron radiation Fourier transform infrared (SR FT-IR) spectromicroscopy with epifluorescence images using fluorescent trackers for Golgi apparatus and nucleus, namely BODIPY TR C5-ceramide complexed to BSA and DAPI, respectively. Interestingly, the ratios of the IR bands CH2 : CH3 (both asymmetric and symmetric) and CO((ester)):amide I were shown to be reliable gauges of the lipidic character of a cellular compartment, the -CH2 and the CO((ester)) absorptions increasing with the presence of inner membranes like in the Golgi apparatus.