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

FTIR Analysis of Proteins and Protein-Membrane Interactions

Fourier transform infrared (FTIR) spectroscopy has become one of the major techniques of structural characterization of proteins, peptides, and protein-membrane interactions. While the method does not have the capability of providing the precise, atomic-resolution molecular structure, it is exquisitely sensitive to conformational changes occurring in proteins upon functional transitions or intermolecular interactions. The sensitivity of vibrational frequencies to atomic masses has led to development of "isotope-edited" FTIR spectroscopy, where structural effects in two proteins, one unlabeled and the other labeled with a heavier stable isotope, such as ¹³C, are resolved simultaneously based on spectral downshift (separation) of the amide I band of the labeled protein. The same isotope effect is used to identify site-specific conformational changes in proteins by site-directed or segmental isotope labeling. Negligible light scattering in the infrared region provides an opportunity to study intermolecular interactions between large protein complexes, interactions of proteins and peptides with lipid vesicles, or protein-nucleic acid interactions without light scattering problems often encountered in ultraviolet spectroscopy. Attenuated total reflection FTIR (ATR-FTIR) is a surface-sensitive version of infrared spectroscopy that has proved useful in studying membrane proteins and lipids, protein-membrane interactions, mechanisms of interfacial enzymes, the structural features of membrane pore forming proteins and peptides, and much more. The purpose of this chapter was to provide a practical guide to analyze protein structure and protein-membrane interactions by FTIR and ATR-FTIR techniques, including procedures of sample preparation, measurements, and data analysis. Basic background information on FTIR spectroscopy, as well as some relatively new developments in structural and functional characterization of proteins and peptides in lipid membranes, is also presented.

Anticancer drug impact on DNA – a study by neutron spectroscopy coupled with synchrotron-based FTIR and EXAFS

Complementary information on drug–DNA interplay has been achieved for Pt/Pd anticancer agents, by a combined QENS, SR-FTIR-ATR and EXAFS approach.

Current and future functional imaging techniques for post-traumatic stress disorder

Posttraumatic stress disorder (PTSD) is a trauma and stressor related psychiatric disorder associated with structural, metabolic, and molecular alternations in several brain regions including diverse cortical areas, neuroendocrine regions, the striatum, dopaminergic, adrenergic and serotonergic pathways, and the limbic system. We are in critical need of novel therapeutics and biomarkers for PTSD and a deep understanding of cutting edge imaging and spectroscopy methods is necessary for the development of promising new approaches to better diagnose and treat the disorder. According to the Diagnostic and Statistical Manual of Mental Disorders (DSM-V) criterion, all forms of traumatic stress-induced disorder are considered acute stress disorder for the first month following the stressor. Only after symptoms do not remit for one month can the disorder be deemed PTSD. It would be particularly useful to differentiate between acute stress disorder and PTSD during the one month waiting period so that more intensive treatments can be applied early on to patients with a high likelihood of developing PTSD. This would potentially enhance treatment outcomes and/or prevent the development of PTSD. Comprehension of the qualities and limitations of currently applied methods as well as the novel emerging techniques provide invaluable knowledge for fast paced development. Conventional methods of studying PTSD have proven to be insufficient for diagnosis, measurement of treatment efficacy, and monitoring disease progression. As the field currently stands, there is no diagnostic biomarker available for any psychiatric disease, PTSD included. Currently, emerging and available technologies are not utilized to their full capacity and in appropriate experimental designs for the most fruitful possible studies in this area. Therefore, there is an apparent need for improved methods in PTSD research. This review demonstrates the current state of the literature in PTSD, including molecular, cellular, and behavioral indicators, possible biomarkers and clinical and pre-clinical imaging techniques relevant to PTSD, and through this, elucidate the void of current practical imaging and spectroscopy methods that provide true biomarkers for the disorder and the significance of devising new techniques for future investigations. We are unlikely to develop a single biomarker for any psychiatric disorder however. As psychiatric disorders are incomparably complex compared to other medical diagnoses, its most likely that transcriptomic, metabolomic and structural and connectomic imaging data will have to be analyzed in concert in order to produce a dependable non-behavioral marker of PTSD. This can explain the necessity of bridging conventional approaches to novel technologies in order to create a framework for further discoveries in the treatment of PTSD.

Conventional methods of studying posttraumatic stress disorder (PTSD) have proven to be insufficient for diagnosis. We have reviewed clinical and preclinical imaging techniques as well as molecular, cellular, and behavioral indicators for PTSD.

Synchrotron macro ATR-FTIR microspectroscopy for high-resolution chemical mapping of single cells

Coupling synchrotron IR beam to an ATR element enhances spatial resolution suited for high-resolution single cell analysis in biology, medicine and environmental science.

Towards identifying the mode of action of drugs using live-cell FTIR spectroscopy

Fourier transform infrared spectroscopy (FTIR) has been shown to be a promising tool for identifying the mode of action of drugs.

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectromicroscopy Using Synchrotron Radiation and Micromachined Silicon Wafers for Microfluidic Applications

A custom-designed optical configuration compatible with the use of micromachined multigroove internal reflection elements (μ-groove IREs) for attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and imaging applications in microfluidic devices is described. The μ-groove IREs consist of several face-angled grooves etched into a single, monolithic silicon chip. The optical configuration permits individual grooves to be addressed by focusing synchrotron sourced IR light through a 150 µm pinhole aperture, restricting the beam spot size to a dimension smaller than that of the groove walls. The effective beam spot diameter at the ATR sampling plane is determined through deconvolution of the measured detector response and found to be 70 µm. The μ-groove IREs are highly compatible with standard photolithographic techniques as demonstrated by printing a 400 µm wide channel in an SU-8 film spin-coated on the IRE surface. Attenuated total reflection FT-IR mapping as a function of sample position across the channel illustrates the potential application of this approach for rapid prototyping of microfluidic devices.

Thermal effect on dispersive infrared spectroscopic imaging of prostate cancer tissue

A system that combines dispersive infrared micro-spectroscopic imaging and thermography has been developed to study the effect of thermal radiation on the infrared absorption spectra of prostate biopsy samples. The system allows the distribution of thermal signal intensity as a function of emissivity to be interpreted from the integrated absorbance obtained by spectroscopic imaging. Biochemical differences between cancer and benign areas within the specimens are identified in the spectra. Side-by-side comparison of H&E stained adjacent tissue sections with infrared images constructed before and after the removal of thermal effect showed that the latter strongly support differentiation of regions within tissues. The use of spectral bands at discrete wavelengths significantly reduced spectral acquisition time, making this technique promising as a future clinical diagnostic tool. A systemic methodology was implemented to process the data, first by k-means clustering on the second derivative spectra without a priori knowledge, followed by principal component analysis (PCA). Four distinct regions within the tissue samples were successfully classified based on the antisymmetric stretching mode of the methylene functional group. Separation between data in clusters occurs when projecting spectra on a PCA score plot on a plane made by first 2 principal components. The significance of the disparity was verified with statistical test. Regulation of signal to chopper and detector enables simultaneous acquisition of infrared and thermal images of the prostate biopsy tissues.

Digital de-waxing on FTIR images

This paper presents a procedure that digitally neutralizes the contribution of paraffin to FTIR hyperspectral images. A brief mathematical derivation of the procedure is demonstrated and applied on one normal human colon sample to exemplify the de-waxing procedure. The proposed method includes construction of a paraffin model based on PCA, EMSC normalization and application of two techniques for spectral quality control. We discuss every step in which the researcher needs to take a subjective decision during the de-waxing procedure, and we explain how to make an adequate choice of parameters involved. Application of this procedure to 71 hyperspectral images collected from 55 human colon biopsies (20 normal, 17 ulcerative colitis, and 18 adenocarcinoma) showed that paraffin was appropriately neutralized, which made the de-waxed images adequate for analysis by pattern-recognition techniques such as k-means clustering or PCA-LDA.

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.

Intermolecular Interactions in N, N-Dimethylacetamide without and with LiCl Studied by Infrared Spectroscopy and Quantum Chemical Model Calculations

The mixture of LiCl and N, N-dimethylacetamide (DMAc) is an important laboratory-scale solvent for cellulose. However, the mechanism of cellulose dissolution in DMAc/LiCl could not be fully established due to the limited knowledge about the interactions between DMAc and LiCl. To address this issue, we studied neat DMAc and DMAc/LiCl mixtures by ATR FTIR spectroscopy and quantum chemical model calculations. On the basis of the calculations, we newly assigned the bands at 1660 and 1642 cm^-1 in the ν(C═O) region of the spectra to DMAc monomeric and dimeric structures. The latter are presumably stabilized by the C-H···O═C weak hydrogen bonds that prevail in both neat DMAc and DMAc/LiCl mixtures. The analysis of the concentrated (7.9 wt % of LiCl) DMAc/LiCl mixture revealed that only about half of DMAc molecules interact directly with LiCl. The resulting average stoichiometry of about 2.8:1 (DMAc:LiCl), indicating the predominance of [(DMAc)₂-LiCl] and [(DMAc)₃-LiCl] complexes, was found to be temperature independent. Conversely, the stoichiometry was considerably temperature sensitive for the diluted DMAc/LiCl mixture (2.6 wt % of LiCl), indicating that further DMAc molecules can be incorporated into the primary solvation shell of LiCl at higher temperatures. These results highlight the dynamic character of the DMAc/LiCl system that needs to be considered when studying the cellulose dissolution mechanism.

Optimization for vertically scanning terahertz attenuated total reflection imaging

Terahertz attenuated total reflection imaging has been used to develop preliminary applications without any in-depth analysis of the nature of present systems. Based on our proposed vertically scanning imaging system, an analysis of optimum prism design and polarization selection for error reduction is presented theoretically and experimentally, showing good agreement. By taking the secondary reflection inside the prism and the prism deflection into consideration, p-polarized terahertz waves are recommended for prisms with a base angle below 31°, leading to minimum error. This work will contribute to the development of more practical application of terahertz attenuated total reflection scanning imaging in various fields with enhanced performance.

A benzoic acid terpyridine-based cyclometalated iridium(iii) complex as a two-photon fluorescence probe for imaging nuclear histidine

A series of two-photon active cyclometalated iridium(iii) complexes (Ir1, Ir2 and Ir3) were designed. Ir1 with a two-photon action cross-section of 40 GM in the NIR region has been developed for targeting intracellular histidine. Two-photon micrographs showed that Ir1 could rapidly and selectively light up the nucleus in both fixed and live cells and is capable of displaying nuclear histidine distribution in ultra-detail using a super resolution (SR) technique under stimulated emission depletion (STED) microscopy.

Infrared spectroscopy and spectroscopic imaging in forensic science

Infrared spectroscopy and spectroscopic imaging, are robust, label free and inherently non-destructive methods with a high chemical specificity and sensitivity that are frequently employed in forensic science research and practices. This review aims to discuss the applications and recent developments of these methodologies in this field. Furthermore, the use of recently emerged Fourier transform infrared (FT-IR) spectroscopic imaging in transmission, external reflection and Attenuated Total Reflection (ATR) modes are summarised with relevance and potential for forensic science applications. This spectroscopic imaging approach provides the opportunity to obtain the chemical composition of fingermarks and information about possible contaminants deposited at a crime scene. Research that demonstrates the great potential of these techniques for analysis of fingerprint residues, explosive materials and counterfeit drugs will be reviewed. The implications of this research for the examination of different materials are considered, along with an outlook of possible future research avenues for the application of vibrational spectroscopic methods to the analysis of forensic samples.

Characterization of inflammatory breast cancer: a vibrational microspectroscopy and imaging approach at the cellular and tissue level

Inflammatory breast cancer (IBC) has a poor prognosis because of the lack of specific biomarkers and its late diagnosis.

Clinical applications of infrared and Raman spectroscopy: state of play and future challenges

This review examines the state-of-the-art of clinical applications of infrared absorption and Raman spectroscopy, outstanding challenges, and progress towards translation.

A molecular probe based on pyrimidine imidazole derivatives for stable super-resolution endoplasmic reticulum imaging in living cells

Multi-functional florescent dyes capable of acting as molecular probes in living systems under two-photon microscopy, as well as super-resolution nanoscopy, are of great interest.

Applications of mid-infrared spectroscopy in the clinical laboratory setting

Fourier transform mid-infrared (MIR-FTIR) spectroscopy is a nondestructive, label-free, highly sensitive and specific technique that provides complete information on the chemical composition of biological samples. The technique both can offer fundamental structural information and serve as a quantitative analysis tool. Therefore, it has many potential applications in different fields of clinical laboratory science. Although considerable technological progress has been made to promote biomedical applications of this powerful analytical technique, most clinical laboratory analyses are based on spectroscopic measurements in the visible or ultraviolet (UV) spectrum and the potential role of FTIR spectroscopy still remains unexplored. In this review, we present some general principles of FTIR spectroscopy as a useful method to study molecules in specimens by MIR radiation together with a short overview of methods to interpret spectral data. We aim at illustrating the wide range of potential applications of the proposed technique in the clinical laboratory setting with a focus on its advantages and limitations and discussing the future directions. The reviewed applications of MIR spectroscopy include (1) quantification of clinical parameters in body fluids, (2) diagnosis and monitoring of cancer and other diseases by analysis of body fluids, cells, and tissues, (3) classification of clinically relevant microorganisms, and (4) analysis of kidney stones, nails, and faecal fat.

Optical probing of gastrocnemius in patients with peripheral artery disease characterizes myopathic biochemical alterations and correlates with stage of disease

Peripheral artery disease (PAD) is a condition caused by atherosclerotic blockages in the arteries supplying the lower limbs and is characterized by ischemia of the leg, progressive myopathy, and increased risk of limb loss. The affected leg muscles undergo significant changes of their biochemistry and metabolism including variations in the levels of many key proteins, lipids, and nucleotides. The mechanisms behind these changes are poorly understood. The objective of this study was to correlate the severity of the PAD disease stage and associated hemodynamic limitation (determined by the ankle brachial index, ABI) in the legs of the patients with alterations in the biochemistry of chronically ischemic leg muscle as determined by ATR‐Fourier transform infrared micro‐spectroscopy. Muscle (gastrocnemius) biopsies were collected from 13 subjects including four control patients (ABI≥0.9), five claudicating patients (0.4 ≤ ABI<0.9), and four critical limb ischemia (CLI) patients (ABI<0.4). Slide mounted specimens were analyzed by ATR‐Fourier transform infrared micro‐spectroscopy. An analysis of variance and a partial least squares regression model were used to identify significant differences in spectral peaks and correlate them with the ABI. The spectra revealed significant differences (P < 0.05) across control, claudicating, and CLI patients in the fingerprint and functional group regions. Infrared microspectroscopic probing of ischemic muscle biopsies demonstrates that PAD produces significant and unique changes to muscle biochemistry in comparison to control specimens. These distinctive biochemical profiles correlate with disease progression and may provide insight and direction for new targets in the diagnosis and therapy of muscle degeneration in PAD.

ATR-FTIR spectral discrimination between normal and tumorous mouse models of lymphoma and melanoma from serum samples

This study presents, attenuated total reflection Fourier transforms infrared spectroscopy of dried serum samples in an effort to assess biochemical changes induced by non-Hodgkin's lymphoma and subcutaneous melanoma. An EL4 mouse model of non-Hodgkin lymphoma and a B16 mouse model of subcutaneous melanoma are used to extract a snapshot of tumor-associated alteration in the serum. The study of both cancer-bearing mouse models in wild types and their corresponding control types, emphasizes the diagnostic potential of this approach as a screening technique for non-Hodgkin lymphoma and melanoma skin cancer. Infrared absorbance values of the different spectral bands, hierarchical clustering and integral values of the component bands by curve fitting, show statistically significant differences (student's t-test, two-tailed unequal variance p-value < 0.05) between spectra representing healthy and tumorous mouse. This technique may thus be useful for having individualized route maps for rapid evaluation of lymphoma and melanoma status and associated therapeutic modalities.

Vibrational spectroscopy and imaging: applications for tissue engineering

Tissue engineering (TE) approaches strive to regenerate or replace an organ or tissue. The successful development and subsequent integration of a TE construct is contingent on a series of in vitro and in vivo events that result in an optimal construct for implantation. Current widely used methods for evaluation of constructs are incapable of providing an accurate compositional assessment without destruction of the construct. In this review, we discuss the contributions of vibrational spectroscopic assessment for evaluation of tissue engineered construct composition, both during development and post-implantation. Fourier transform infrared (FTIR) spectroscopy in the mid and near-infrared range, as well as Raman spectroscopy, are intrinsically label free, can be non-destructive, and provide specific information on the chemical composition of tissues. Overall, we examine the contribution that vibrational spectroscopy via fiber optics and imaging have to tissue engineering approaches.

Pericellular interphotoreceptor matrix dictates outer retina critical surface tension

Retinal detachments create two pathological surfaces, the surface of the outer neural retinal, and an apical retinal-pigmented epithelium (RPE) surface. The physicochemical properties of these two new surfaces are poorly understood. At a molecular level little is known how detachments form, how to optimize reattachment, or prevent extension of the detachment. A major limitation is lack of information about the biophysical consequences of the retina-RPE separation. The primary challenge is determining the molecular properties of the pathological interface surfaces. Here, using detached bovine retina, we show that this hurdle can be overcome through a combination of biophysical and ultrastructural approaches. The outer surface of freshly detached bovine neural retina, and isolated molecular components of the outer retina were subjected to: 1) Contact angle goniometry to determine the critical surface tension of the outer retinal surface, isolated insoluble interphotoreceptor matrix (IPM) and purified interphotoreceptor retinoid binding protein (IRBP); 2) Multiple attenuated internal reflectance infrared (MAIR-IR) spectroscopy was used to characterize the molecular composition of the retinal surface. MAIR-IR depth penetration was established through ellipsometric measurement of barium-stearate films. Light microscopy, immunohistochemistry and electron microscopy defined the structures probed spectroscopically. Furthermore, the data were correlated to IR spectra of docosahexaenoic acid, hyaluronan, chondroitin-6-sulfate and IRBP, and imaging by IR-microscopy. We found that the retinal critical surface tension is 24 mN/m, similar to isolated insoluble IPM and lower than IRBP. Barium-stearate calibration studies established that the MAIR-IR spectroscopy penetration depth was 0.2 μm. Ultrastructural observations and MAIR-IR studies of isolated outer retina components determined that the pericellular IPM coating the outer retinal surface is primarily responsible for these surface properties. The critical surface tension of detached bovine retina is dictated not by the outer segments, but by a pericellular IPM covering the outer segment tips.

Dielectric Sphere Clusters as a Model to Understand Infrared Spectroscopic Imaging Data Recorded from Complex Samples

Understanding the infrared (IR) spectral response of materials as a function of their morphology is not only of fundamental importance but also of contemporary practical need in the analysis of biological and synthetic materials. While significant work has recently been reported in understanding the spectra of particles with well-defined geometries, we report here on samples that consist of collections of particles. First, we theoretically model the importance of multiple scattering effects and computationally predict the impact of local particles' environment on the recorded IR spectra. Both monodisperse and polydisperse particles are considered in clusters with various degrees of packing. We show that recorded spectra are highly dependent on the cluster morphology and size of particles but the origin of this dependence is largely due to the scattering that depends on morphology and not absorbance that largely depends on the volume of material. The effect of polydispersity is to reduce the fine scattering features in the spectrum, resulting in a closer resemblance to bulk spectra. Fourier transform-IR (FT-IR) spectra of clusters of electromagnetically coupled poly(methyl methacrylate) (PMMA) spheres with wavelength-scale diameters were recorded and compared to simulated results. Measured spectra agreed well with those predicted. Of note, when PMMA spheres occupy a volume greater than 18% of the focal volume, the recorded IR spectrum becomes almost independent of the cluster's morphological changes. This threshold, where absorbance starts to dominate the signal, exactly matches the percolation threshold for hard spheres and quantifies the transition between the single particle and bulk behavior. Our finding enables an understanding of the spectral response of structured samples and points to appropriate models for recovering accurate chemical information from in IR microspectroscopy data.

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

Chemical and Biological Dynamics Using Droplet-Based Microfluidics

Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas. We then discuss a wide range of analytical methods that have been successfully adapted for analyte detection in droplets. Finally, we highlight a diversity of studies where droplet-based microfluidic strategies have enabled the characterization of dynamic systems that would otherwise have remained unexplorable.

Identification of trace additives in polymer materials by attenuated total reflection Fourier transform infrared mapping coupled with multivariate curve resolution

Although multivariate curve resolution (MCR) has been applied to the analysis of Fourier transform infrared (FTIR) imaging, it is still problematic to determine the number of components. The reported methods at present tend to cause the components of low concentration missed. In this paper a new idea was proposed to resolve this problem. First, MCR calculation was repeated by increasing the number of components sequentially, then each retrieved pure spectrum of as-resulted MCR component was directly compared with a real-world pixel spectrum of the local high concentration in the corresponding MCR map. One component was affirmed only if the characteristic bands of the MCR component had been included in its pixel spectrum. This idea was applied to attenuated total reflection (ATR)/FTIR mapping for identifying the trace additives in blind polymer materials and satisfactory results were acquired. The successful demonstration of this novel approach opens up new possibilities for analyzing additives in polymer materials.

Pre-plaque conformational changes in Alzheimer's disease-linked Aβ and APP

Reducing levels of the aggregation-prone Aβ peptide that accumulates in the brain with Alzheimer's disease (AD) has been a major target of experimental therapies. An alternative approach may be to stabilize the physiological conformation of Aβ. To date, the physiological state of Aβ in brain remains unclear, since the available methods used to process brain tissue for determination of Aβ aggregate conformation can in themselves alter the structure and/or composition of the aggregates. Here, using synchrotron-based Fourier transform infrared micro-spectroscopy, non-denaturing gel electrophoresis and conformational specific antibodies we show that the physiological conformations of Aβ and amyloid precursor protein (APP) in brain of transgenic mouse models of AD are altered before formation of amyloid plaques. Furthermore, focal Aβ aggregates in brain that precede amyloid plaque formation localize to synaptic terminals. These changes in the states of Aβ and APP that occur prior to plaque formation may provide novel targets for AD therapy.

Lighting the Way to See Inside Two-Photon Absorption Materials: Structure-Property Relationship and Biological Imaging

The application of two-photon absorption (2PA) materials is a classical research field and has recently attracted increasing interest. It has generated a demand for new dyes with high 2PA cross-sections. In this short review, we briefly cover the structure-2PA property relationships of organic fluorophores, organic-inorganic nanohybrids and metal complexes explored by our group. (1) The two-photon absorption cross-section (δ) of organic fluorophores increases with the extent of charge transfer, which is important to optimize the core, donor-acceptor pair, and conjugation-bridge to obtain a large δ value. Among the various cores, triphenylamine appears to be an efficient core. Lengthening of the conjugation with styryl groups in the D-π-D quadrupoles and D-π-A dipoles increased δ over a long wavelength range than when vinylene groups were used. Large values of δ were observed for extended conjugation length and moderate donor-acceptors in the near-IR wavelengths. The δ value of the three-arm octupole is larger than that of the individual arm, if the core has electron accepting groups that allow significant electronic coupling between the arms; (2) Optical functional organic/inorganic hybrid materials usually show high thermal stability and excellent optical activity; therefore the design of functional organic molecules to build functional organic-inorganic hybrids and optimize the 2PA properties are significant. Advances have been made in the design of organic-inorganic nanohybrid materials of different sizes and shapes for 2PA property, which provide useful examples to illustrate the new features of the 2PA response in comparison to the more thoroughly investigated donor-acceptor based organic compounds and inorganic components; (3) Metal complexes are of particular interest for the design of new materials with large 2PA ability. They offer a wide range of metals with different ligands, which can give rise to tunable electronic and 2PA properties. The metal ions, including transition metals and lanthanides, can serve as an important part of the structure to control the intramolecular charge-transfer process that drives the 2PA process. As templates, transition metal ions can assemble simple to more sophisticated ligands in a variety of multipolar arrangements resulting in interesting and tailorable electronic and optical properties, depending on the nature of the metal center and the energetics of the metal-ligand interactions, such as intraligand charge-transfer (ILCT) and metal-ligand charge-transfer (MLCT) processes. Lanthanide complexes are attractive for a number of reasons: (i) their visible emissions are quite long-lived; (ii) their absorption and emission can be tuned with the aid of appropriate photoactive ligands; (iii) the accessible energy-transfer path between the photo-active ligands and the lanthanide ion can facilitate efficient lanthanide-based 2PA properties. Thus, the above materials with excellent 2PA properties should be applied in two-photon applications, especially two-photon fluorescence microscopy (TPFM) and related emission-based applications. Furthermore, the progress of research into the use of those new 2PA materials with moderate 2PA cross section in the near-infrared region, good Materials 2017, 10, 223 2 of 37 biocompatibility, and enhanced two-photon excited fluorescence for two-photon bio-imaging is summarized. In addition, several possible future directions in this field are also discussed (146 references).

Direct and model-free detection of carbohydrate excipients in traditional Chinese medicine formula granules by ATR-FTIR microspectroscopic imaging

A formula granule is a traditional Chinese medicine preparation made from the decoction of a single herbal medicinal. Because of the flexibility for combination and the convenience for utilization, formula granules are becoming popular in clinical applications. However, the efficacy and safety of commercial formula granules often suffer from the improper addition of carbohydrate excipients. Therefore, the detection of carbohydrate excipients is indispensable for the quality control of formula granules. FTIR spectroscopy has been used for the detection of carbohydrate excipients in formula granules. But the overlapped absorption signals limit the sensitivity and specificity of detection. Besides, a large number of multivariate calibration models are needed for quantitative determination. To overcome the above disadvantages, this research utilizes FTIR microspectroscopy for the model-free and universal detection of carbohydrate excipients in formula granules. Using ATR-FTIR imaging, excipient particles and herbal extract particles in formula granules can be measured individually, which resolves the absorption signals of excipients and herbal extract spatially and thus improves the sensitivity and specificity of detection. The content of excipients can be estimated directly from the number of excipient particles, which is robust to the variations of herb extracts and free of calibration models. The case study of Gardeniae Fructus formula granules shows the potential of FTIR microspectroscopy in the direct and rapid detection of carbohydrate excipients in formula granules. Graphical Abstract Excipient particles in TCM formula granules can be measured and recognized individually by FTIR microspectroscopy.

Structural transformation of synthetic hydroxyapatite under simulated in vivo conditions studied with ATR-FTIR spectroscopic imaging

Hydroxyapatite and carbonate-substituted hydroxyapatite are widely used in bone tissue engineering and regenerative medicine. Both apatite materials were embedded into recently developed ceramic/polymer composites, subjected to Simulated Body Fluid (SBF) for 30days and characterized using ATR-FTIR spectroscopic imaging to assess their behaviour and structures. The specific aim was to detect the transition phases between both types of hydroxyapatite during the test and to analyze the surface modification caused by SBF. ATR-FTIR spectroscopic imaging was successfully applied to characterise changes in the hydroxyapatite lattice due to the elastic properties of the scaffolds. It was observed that SBF treatment caused a replacement of phosphates in the lattice of non-substituted hydroxyapatite by carbonate ions. A detailed study excluded the formation of pure A type carbonate apatite. In turn, CO₃^2- content in synthetic carbonate-substituted hydroxyapatite decreased. The usefulness of ATR-FTIR spectroscopic imaging studies in the evaluation of elastic and porous β-glucan hydroxyapatite composites has been demonstrated.

Protein hydration in living cells probed by Fourier transform infrared (FT-IR) spectroscopic imaging

FT-IR spectra of a HEK cell were analyzed with 2D disrelation mapping to reveal molecular states of water and protein hydration.

In-column ATR-FTIR spectroscopy to monitor affinity chromatography purification of monoclonal antibodies

In recent years many monoclonal antibodies (mAb) have entered the biotherapeutics market, offering new treatments for chronic and life-threatening diseases. Protein A resin captures monoclonal antibody (mAb) effectively, but the binding capacity decays over repeated purification cycles. On an industrial scale, replacing fouled Protein A affinity chromatography resin accounts for a large proportion of the raw material cost. Cleaning-in-place (CIP) procedures were developed to extend Protein A resin lifespan, but chromatograms cannot reliably quantify any remaining contaminants over repeated cycles. To study resin fouling in situ, we coupled affinity chromatography and Fourier transform infrared (FTIR) spectroscopy for the first time, by embedding an attenuated total reflection (ATR) sensor inside a micro-scale column while measuring the UV 280 nm and conductivity. Our approach quantified the in-column protein concentration in the resin bed and determined protein conformation. Our results show that Protein A ligand leached during CIP. We also found that host cell proteins bound to the Protein A resin even more strongly than mAbs and that typical CIP conditions do not remove all fouling contaminants. The insights derived from in-column ATR-FTIR spectroscopic monitoring could contribute to mAb purification quality assurance as well as guide the development of more effective CIP conditions to optimise resin lifespan.

A two-photon fluorescent RNA probe screened from a series of oxime-functionalized 2,2′:6′,2′′-terpyridine ZnX2(X = Cl, Br, I) complexes

An oxime-functionalized terpyridine ZnCl₂complex is a RNA two-photon fluorescent probe exhibiting RNA binding, fluorescence intensity enhancement and compatibility with Hoechst 33342.

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.