Synchrotron Infrared Microspectroscopy Research Articles

Fire-induced shifts in stalagmite organic matter mapped using Synchrotron infrared microspectroscopy

Understanding organic matter (OM) in cave mineral deposits (speleothems) is essential for interpreting land use and climatic changes, and the incorporation of trace elements associated with organic compounds. However, the sources and composition of OM in speleothems are poorly understood due to challenges associated with measuring OM at low concentrations and the destructive nature of most speleothem OM analysis techniques. Synchrotron Fourier-transform infrared (FTIR) microspectroscopy is a promising non-destructive technique that can be used to investigate stalagmite OM composition. We use FTIR to analyse vegetation, soil, calcium carbonate and ash end-members and demonstrate the use of Synchrotron infrared microspectroscopy (IRM) mapping to detect temporal changes in the OM composition of a stalagmite from a shallow cave in south-west Western Australia. Our analysis reveals predominant FTIR peaks in the stalagmite linked to amides and CH2 groups, suggesting potential microbial contributions, with smaller proportions of aromatic, CH3 and CO groups. High-resolution transmission electron microscopy revealed that this OM is likely hosted in sets of nanopores spaced hundreds of nanometers apart, aligned along calcite crystallographic orientations. Furthermore, we assess the impact of known wildfire events as discrete short term environmental changes on the stalagmite’s OM composition. The temporal variability in OM functional group composition after fires implies complex fire-soil-vegetation-microbial interactions. This research demonstrates the effectiveness of Synchrotron IRM mapping in providing insights into the short and long-term environmental influences on stalagmite OM composition. Expanding this research to other regions and climates could further enhance the interpretation of OM changes in speleothem-based palaeoclimate reconstructions.

Synchrotron-Infrared Microspectroscopy of Live Leishmania major Infected Macrophages and Isolated Promastigotes and Amastigotes.

The prevalence of neglected tropical diseases (NTDs) is advancing at an alarming rate. The NTD leishmaniasis is now endemic in over 90 tropical and sub-tropical low socioeconomic countries. Current diagnosis for this disease involves serological assessment of infected tissue by either light microscopy, antibody tests, or culturing with in vitro or in vivo animal inoculation. Furthermore, co-infection by other pathogens can make it difficult to accurately determine Leishmania infection with light microscopy. Herein, for the first time, we demonstrate the potential of combining synchrotron Fourier-transform infrared (FTIR) microspectroscopy with powerful discrimination tools, such as partial least squares-discriminant analysis (PLS-DA), support vector machine-discriminant analysis (SVM-DA), and k-nearest neighbors (KNN), to characterize the parasitic forms of Leishmania major both isolated and within infected macrophages. For measurements performed on functional infected and uninfected macrophages in physiological solutions, the sensitivities from PLS-DA, SVM-DA, and KNN classification methods were found to be 0.923, 0.981, and 0.989, while the specificities were 0.897, 1.00, and 0.975, respectively. Cross-validated PLS-DA models on live amastigotes and promastigotes showed a sensitivity and specificity of 0.98 in the lipid region, while a specificity and sensitivity of 1.00 was achieved in the fingerprint region. The study demonstrates the potential of the FTIR technique to identify unique diagnostic bands and utilize them to generate machine learning models to predict Leishmania infection. For the first time, we examine the potential of infrared spectroscopy to study the molecular structure of parasitic forms in their native aqueous functional state, laying the groundwork for future clinical studies using more portable devices.

Synchrotron-infrared microspectroscopy of live Leishmania major infected macrophages and isolated promastigotes and amastigotes

Synchrotron-infrared microspectroscopy of live Leishmania major infected macrophages and isolated promastigotes and amastigotes

Investigating the history of volatiles in the solar system using synchrotron infrared micro-spectroscopy

The aqueously altered CM carbonaceous chondrite meteorites can be used to investigate the nature and transport of volatiles in the early solar system. We present the preliminary results of an effort to collect 2D infrared (IR) spectral maps from the matrix and fine-grained rims (FGRs) of material that surround chondrules and inclusions in the Murchison CM2 meteorite using synchrotron IR micro-spectroscopy. The main features in mid-IR spectra of the matrix and FGRs occur at ∼3500 cm−1 and ∼1000 cm−1 and are attributed to OH/H2O and SiO bonds in phyllosilicates and anhydrous silicates. Minor features in the spectra are attributed to organic species (3000–2800 cm−1), CO2 (2400–2000 cm−1), and carbonates (1500–1380 cm−1). In both the matrix and FGRs we observe correlations between the OH/H2O and phyllosilicate/silicate features confirming that phyllosilicates dominate the mineralogy. This is consistent with previous studies showing that Murchison contains ∼70 vol% phyllosilicates following aqueous alteration on an asteroid parent body. The presence of anhydrous silicates in the matrix indicates that the alteration was heterogeneous at the micron-scale and that the reactions did not reach completion. We highlight a possible correlation between the phyllosilicates and organic species in the matrix, supporting the hypothesis that phyllosilicates may have played an important role in the formation and preservation of simple organic molecules and compounds. In the FGRs variations in the distribution of the phyllosilicate minerals cronstedtite and Mg-serpentine/saponite likely reflect differences in the local geochemical conditions during aqueous alteration on the asteroid.

Reactions of Dimethylether in Single Crystals of the Silicoaluminophosphate STA-7 Studied via Operando Synchrotron Infrared Microspectroscopy

Synchrotron infrared micro-spectroscopy has been applied to measure in situ the reaction of dimethylether in single crystals of the silicoaluminophosphate STA-7. The crystals are found to contain a uniform and homogeneous distribution of acidic hydroxyl groups. Dimethylether is hydrogen bonded to the hydroxyl groups at low temperatures, but evidence is found for dissociation to form surface methoxy groups above 473 K, and aromatic hydrocarbon pool species above 573 K. From time resolved infrared measurements coupled with MS analysis of evolved products it is concluded that alkene formation occurs via a direct mechanism from reaction of dimethylether with surface methoxy groups.Graphical

Advanced Vibrational Microspectroscopic Study of Conformational Changes within a Craze in Poly(ethylene terephthalate)

Crazes constitute one of the most common failure mechanisms in polymers. They act as fracture precursors, severely degrading the mechanical properties of the material. Thus, a deep understanding of the chain rearrangement occurring inside crazes is of utmost fundamental and practical importance. We have employed synchrotron infrared microspectroscopy (SIRMS) and Raman microspectroscopy to investigate the conformational changes inside micron-sized crazes in poly(ethylene terephthalate), PET. A promotion of the full-extended chain conformational structure at the expense of mainly the trans amorphous mesomorphic phase along with an increase in crystallinity of around 4% has been found. These results differ from what we observed across the deformation neck during PET cold drawing, where no promotion of the all-trans crystalline conformation occurred for slow drawing speeds at temperatures well below the glass transition. Our results show the tremendous capabilities of advanced vibrational microspectroscopy te...

Determination of Phosphorus Fertilizer Soil Reactions by Raman and Synchrotron Infrared Microspectroscopy

The reaction mechanisms of phosphate-bearing mineral phases from sewage sludge ash-based fertilizers in soil were determined by Raman and synchrotron infrared microspectroscopy. Different reaction mechanisms in wet soil were found for calcium and magnesium (pyro-) phosphates. Calcium orthophosphates were converted over time to hydroxyapatite. Conversely, different magnesium phosphates were transformed to trimagnesium phosphate. Since the magnesium phosphates are unable to form an apatite structure, the plant-available phosphorus remains in the soil, leading to better growth results observed in agricultural pot experiments. The pyrophosphates also reacted very differently. Calcium pyrophosphate is unreactive in soil. In contrast, magnesium pyrophosphate quickly formed plant-available dimagnesium phosphate.

Discrimination Between Paraffin-Embedded and Frozen Skin Sections Using Synchrotron Infrared Microspectroscopy

The difference between paraffin-embedded and frozen skin sections is always questionable. Ten patients of early stage mycosis fungoides, ten patients with psoriasis and ten normal controls were included in this study. Aim of this study is to differentiate between paraffin-embedded and frozen skin sections in inflammatory and malignant dermatoses using synchrotron infrared microspectroscopy (SIRM). It was found that epidermal beta sheets in paraffin-embedded sections were higher in a highly significant manner than frozen sections (P < 0.001). Also, epidermal nucleic acids in paraffin-embedded sections were lower in a highly significant manner than frozen sections (P < 0.001). However, when various skin diseases were compared with the control. It was found that the difference between paraffin-embedded and frozen skin sections were almost similar. In conclusion SIRM is a unique promising diagnostic technique and it seems that frozen processing preserve skin tissue more, this was represented by less apoptosis (beta sheets) and more nucleic acids than paraffin processing. However, there are still many advantages of both approaches over the other depending on the goal of the study.

Synchrotron-Based Microspectroscopic Study on the Effects of Heat Treatments on Cotyledon Tissues in Yellow-Type Canola (Brassica) Seeds

Synchrotron-based infrared (IR) microspectroscopy is able to reveal structural features of biomaterials within intact tissue at both cellular and molecular levels. Heat-related treatments have been used to improve nutrient availability of canola seeds and meal. However, hitherto, there has been no study on the sensitivity and response of each layer in canola seeds to heat-related treatments. It is not known which layer (epiderm/mucllage, spermoderm, endosperm, or cotyledon) is the most sensitive to heat when heat treatment is applied to the seeds. Traditional wet chemical analysis is unable to answer such questions. The objective of this study is to use synchrotron IR microspectroscopy with multivariate molecular spectral analyses as a research tool to study heat treatment effects in a fast way on the structural changes in cotyledon tissues of yellow-type canola (Brassica) seeds among raw (treatment code "A"), wet heating (autoclaving at 121 °C for 60 min, treatment code "B"), and dry heating (dry roasting at 120 °C for 60 min, treatment code "C"). The hypothesis of this study was that different heat treatments have different heat penetration abilities on cotyledon tissues in yellow-type canola seeds. The multivariate analytical tools principal component analysis (PCA) and agglomerative hierarchal cluster analysis (AHCA) were applied to investigate variance and groupings within the spectral data set [whole spectral range of ca. 4000-650 cm(-1), spectral range of ca. 1300-900 cm(-1) (cellulose or saccarides), spectral range of ca. 1800-1500 cm(-1) (secondary structures of protein) and spectral range of ca. 1500-1300 cm(-1) (bending motion of methylene and methyl group; this change is consistent with the change in the range of ca. 3000-2800 cm(-1))]. The results showed that there were no clear cluster and groups formed in the cotyledon tissues among the three treatments (A, B, and C). There were no clear distinguished responses of the cotyledon tissues to different types of heat treatments using multivariate molecular spectral analyses. The results indicate that the cotyledon tissues might not be sufficiently penetrated by both heat treatments (autoclaving and dry roasting) under the specified conditions. A future study is needed to analyze individual functional group band intensity among the treatments using univariate molecular spectral analysis to confirm multivariate PCA and cluster analyses.

Biochemical Changes Observed After PUVA Versus PUVA Plus Methotrexate Therapy in Mycosis Fungoides Using Synchrotron Infrared Microspectroscopy

Mycosis fungoides (MF) is the most common type of cutaneous T cell lymphoma in which the distinction between early stage MF and other inflammatory dermatosis remains difficult. Twenty patients of early stage MF and nine patients with psoriasis and lichen planus were included in this study. Ten MF patients were treated with psoralen plus UVA (PUVA) and the other 10 MF patients were treated with PUVA plus methotrexate (MTX) until complete clinical remission. Synchrotron infrared microspectroscopy (SIRM) found that MF lesions were biochemically different compared to inflammatory diseases. After treating MF with either therapeutic modality, the lymphocytic count decreased significantly in both the epidermis and dermis (P < 0.001) but no biochemical changes were observed in the remaining lymphocytes after treatment, indicating the disease process was slowed by treatment but not eradicated. In conclusion SIRM is a promising method for distinguishing MF from other inflammatory diseases such as psoriasis and lichen planus. A significant reduction in lymphocyte count indicated that PUVA therapy is an effective treatment for early stage MF, and MTX could be reserved for more advanced cases that are not PUVA responsive. However, SIRM evidence of persistent disease suggests that maintenance therapy is recommended after clinical remission.

A study of the single SGC7901 and GES1 cell using synchrotron infrared microspectroscopy and imaging

In order to obtain unique information of the single gastric cancer cell and investigate gastric cancer further at the cellular and subcellular level, synchrotron infrared (SR-IR) microspectroscopy and imaging was used to study human gastric adenocarcinoma cell line SGC7901 and normal gastric mucosal epithelial cell line GES1. When we compared the infrared micro-spectra of the SGC7901 cells with those of the GES1 cells, the peak height ratios of 1121 cm −1/1020 cm −1 (RNA/DNA) of the SGC7901 cells were significantly higher than those of the GES1 cells, which might be useful for distinguishing malignant cells from normal cells. Furthermore, chemical imaging reveals that the amide II/the amide I ratio of the SGC7901 cell is lower than that of the GES1 cell in the most intense absorption region of v as PO 2 - . The result indicates the study of the single gastric cancer cell at subcellular level by synchrotron infrared microspectroscopy and imaging can provide more detailed information which is very helpful for the research and diagnosis of gastric cancer.

Laser microperforated biodegradable microbial polyhydroxyalkanoate substrates for tissue repair strategies: an infrared microspectroscopy study

Flexible and biodegradable film substrates prepared by solvent casting from poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBHV) solutions in chloroform were microperforated by ultraviolet laser ablation and subsequently characterized using infrared (IR) microspectroscopy and imaging techniques and scanning electron microscopy (SEM). Both transmission synchrotron IR microspectroscopy and attenuated total reflectance microspectroscopy measurements demonstrate variations in the polymer at the ablated pore rims, including evidence for changes in chemical structure and crystallinity. SEM results on microperforated PHBHV substrates after cell culture demonstrated that the physical and chemical changes observed in the biomaterial did not hinder cell migration through the pores.

Role of Synchrotron infra red microspectroscopy in studying epidermotropism of cutaneous T‐cell lymphoma

The molecular mechanisms of epidermotropism in mycosis fungoides (MF) are not well understood to date. The aim of this study was to differentiate between epidermal and dermal lymphocytes within the skin of MF patients. This study was done on 10 MF patients with a mean age of 50 years diagnosed clinically in the Department of Dermatology, Cairo University, Egypt. A 6 mm biopsy was taken from each patient in order to confirm the diagnosis. Skin biopsies were cut, put on low e-slides and then stained with H&E. Further examination with Synchrotron infrared (IR) microspectroscopy was done in National Synchrotron Light Source--Brookhaven National Laboratory, New York, USA. Immunophenotyping using antibodies CD3, CD4, CD8, CD20 and CD30 was also done. Statistical analysis was done by Student's t-test and cluster analysis. Both epidermal and dermal lymphocytes were clustered separately. Also, Amide I and RNA and DNA within the lymphocytes were significantly different between the epidermis and the dermis. The biochemical analysis of protein, RNA and DNA with Synchrotron IR microspectroscopy is a promising tool for studying epidermotropism in cutaneous T-cell lymphoma.

Evolution Of Protein Misfolding And Cell Apoptosis In Huntington's Disease Studied By Synchrotron Infra-Red Microspectroscopy

Huntington's disease (HD), caused by a mutation of the HD gene encoding the protein huntingtin (htt), is characterized by progressive deterioration of cognitive and motor functions, paralleled by extensive loss of striatal neurons. At the cellular level, pathogenesis involves an early and prolonged period of neuronal dysfunction and a later period of neuronal death. Understanding the molecular events driving these deleterious processes is critical to the successful development of therapies to slow down or halt the progression of the disease.Here, we used synchrotron-assisted Fourier transform infrared microspectroscopy (FTIRM) to examine the chemical makeup of brain slices taken from the striatum of a genetic rat model of HD. This model, based on lentiviral-mediated delivery of a fragment of the HD gene, expresses the mutant form of htt in one brain hemisphere, and the wild-type form in the control hemisphere. By optical microscopy, sequential appearance of htt inclusions and cell death is observed in the mutant htt-expressing striatum over 2 months. FTIRM results show a higher content of β-sheet protein in the mutant gray matter as early as 6 weeks after infection. Signs of apoptosis are not detected in the neuron-rich grey matter up to 8 weeks. In contrast, white matter tracts crossing through the striatum do not show any changes in protein structure, but surprisingly show a significant increase in peaks associated with fragmented DNA and protein phosphorylation, indicative of apoptosis. Results from a parallel study conducted on cultured neurons expressing wild-type or mutated htt are in accordance with the data from brain tissue. These findings are consistent with the accumulation of misfolded mutant htt polypeptides, which are known to polymerize in vitro through β-sheet folding.

Cross-linking of chitosan and chitosan/poly(ethylene oxide) beads: A theoretical treatment

The major aim of this study was to get deeper insight into the process of polymer cross-linking and the resulting structure of beads based on chitosan (CS) or chitosan/poly(ethylene oxide) (CS/PEO) semi-interpenetrating networks (semi-IPNs) as new carrier materials for oral drug delivery. Spherical hydrogels were prepared by a dropping method. The uptake kinetics of the cross-linking agent glyoxal into the beads were monitored and quantitatively described using Fick’s second law of diffusion. High-resolution synchrotron infrared microspectroscopy (SIRM) was used to characterize the inner structures of the beads. Importantly, the diffusion of glyoxal through the hydrogels was found to be much slower than the cross-linking reaction and the mesh size of the created networks to be much larger than the hydrodynamic diameter of glyoxal. The presence of PEO chains slightly decreased the diffusivity of glyoxal due to obstruction effects. However, the cross-linking reaction was not affected. Interestingly, the polymers were homogeneously cross-linked throughout the beads, except for a thin outer shell showing an elevated cross-linking density. Thus, the obtained cross-linked hydrogel-based beads exhibit well-defined polymeric structures and offer an interesting potential as novel oral drug delivery systems.

Candida antarctica lipase B catalyzed polymerization of lactones: Effects of immobilization matrices on polymerization kinetics &amp; molecular weight

This study investigated the effect of enzyme immobilization on its activity for the ring-opening polymerizations of lactones with differing ring sizes. Candida antarctica lipase B (CALB) was immobilized on a wide array of support materials that varied in polymer composition, relative hydrophobicity, pore diameter, and surface area. The reaction rates and polymer molecular weights were monitored by in situ NMR measurements. Synchrotron infrared microspectroscopy (SIRMS) was used to study the enzyme distribution and secondary structure within the support matrix. The fastest reaction rates resulted by immobilization of CALB on the macroporous matrices QDM 2-3-4 and Accurel. Both of these are constructed from polypropylene and had CALB distributed throughout the matrix particles. Immobilized CALB on QDM 2-3-4 gave ε-caprolactone (ε-CL) conversion that reached 50 and 95% in 12 and 60 min, respectively. In comparison, by using CALB immobilized on Deloxan HAP, a 50% CL conversion required 120 h. Other changes that were found by immobilization of CALB on different matrices are shifts in CALB selectivity and the frequency of step-condensation reactions at monomer conversions >50%. By changing the immobilization matrix, PCL molecular weight was increased from 5,000 to 15,000. All of the CALB-matrix systems investigated in this study gave polymerizations with ε-CL conversions that followed a first-order rate law. Changes in CALB catalytic activity and specificity imply variations in CALB conformation induced by the different surfaces. However, these conformational changes must be subtle since they were not found by synchrotron IR Microspectroscopy. Two common features observed that led to CALB-matrix systems with higher activity for polyester synthesis are: i) increased density of CALB molecules within the pores of matrices, and ii) distribution of CALB throughout the matrix.

Studies on the repassivation behavior of aluminum and aluminum alloy exposed to chromate solutions

AbstractThis study explores the repassivation ability of a scratch in a chromate conversion coating (CCC) on aluminum alloy, AA2024‐T3, and hence evaluates the theory of migration of hexavalent chromium ions from the protected surface of the aluminum alloy to the exposed surface. To confirm that protection was indeed restored by hexavalent chromium ions, the repassivation of a scratch on pure aluminum exposed to a dichromate solution was studied. This forms the simplest subsystem model of the CCC on the alloy in which the CCC is replaced by pure hexavalent chromium and alloy with pure aluminum. Open‐circuit potential measurements, synchrotron infrared microspectroscopy (SIRMS) and secondary ion mass spectroscopy (SIMS) have been used judiciously to evaluate the repassivation behavior. Results indicate that the dichromate ions have high mobility. The slow migration of Cr(VI) ions from the protected surface to the scratch is observed to result in repassivation, as seen from the steady increase in the potential in 0.05 M NaCl solution. The results obtained from SIMS and SIRMS confirm the migration of the oxyanions from the protected region to the metal surface exposed by the scratch. The SIRMS results indicate the formation of an Al(III)–Cr(VI) complex, proposed and shown to be formed in the pits. Copyright © 2003 John Wiley &amp; Sons, Ltd.

Imaging the distribution and secondary structure of immobilized enzymes using infrared microspectroscopy.

Synchrotron infrared microspectroscopy (SIRMS) was used for the first time to image the distribution and secondary structure of an enzyme (lipase B from Candida antarctica, CALB) immobilized within a macroporous polymer matrix (poly(methyl methacrylate)) at 10 microm resolution. The beads of this catalyst (Novozyme435) were cut into thin sections (12 microm). SIRMS imaging of these thin sections revealed that the enzyme is localized in an external shell of the bead with a thickness of 80-100 microm. Also, the enzyme was unevenly distributed throughout this shell. Furthermore, by SIRMS-generated spectra, it was found that CALB secondary structure was not altered by immobilization. Unlike CALB, polystyrene molecules of similar molecular weight diffuse easily throughout Novozyme435 beads. Scanning electron micrograph (SEM) images of the Novozyme435 beads showed that the average pore size is 10 times larger than CALB or polystyrene molecules, implying that there is no physical barrier to enzyme or substrate diffusion throughout the bead. Thus, the difference between polystyrene and enzyme diffusivity suggests that protein-matrix and protein-protein interactions govern the distribution of the enzyme within the macroporous resin.

The application of synchrotron-based spectroscopic techniques to the study of chromate conversion coatings

This work utilized synchrotron spectroscopic techniques such as extended X-ray absorption fine structure (EXAFS), X-ray absorption near edge structure (XANES) and synchrotron infrared microspectroscopy (SIRMS) to understand the chemistry, formation, structure and aging of protective chromate conversion coatings (CCC). We shall discuss issues related CCC formed on aluminum–copper alloys. SIRMS combined with argon ion sputtering demonstrated spatial and depth chemical variations of the CCC formed on AA2024-T3. XANES indicated that in the first stages of CCC formation the thickness depends on the Cu content of the substrate and that thinner CCC appears to contain less Cr 6+ for protection. Micro-XANES shows that even monolayer coverage of chromate can protect the alloy surface. EXAFS and XANES measurements were used to monitor the structural changes of the CCC with time. It was observed that a slight decrease in the Cr(VI)Cr(III) ratio occurred during the first 24 h following coating. The structure of the CCC is in close agreement with a Cr mixed oxide. EXAFS data appeared to indicate an increase in ordering in the CCC structure with time.

Combining IR spectroscopy with fluorescence imaging in a single microscope: Biomedical applications using a synchrotron infrared source (invited)

It has become increasingly clear that infrared microspectroscopy (IRMS) can be an extremely valuable analysis tool when determining the chemical composition of biological and biomedical samples. Frequently, fluorescence illumination is required for sample characterization, and is usually achieved on a separate and dedicated optical microscope. We report the development and use of a single microscope for concomitant fluorescence and synchrotron IRMS. This unique combination has been used to identify changes in the composition of newly remodeled bone after the onset of osteoporosis, misfolded protein structure in Alzheimer’s disease, and cellular changes in apoptosis.