Ganesh D. Sockalingum

Using Fourier transform IR spectroscopy to analyze biological materials

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.

Estimating and correcting mie scattering in synchrotron-based microscopic fourier transform infrared spectra by extended multiplicative signal correction.

We present an approach for estimating and correcting Mie scattering occurring in infrared spectra of single cells, at diffraction limited probe size, as in synchrotron based microscopy. The Mie scattering is modeled by extended multiplicative signal correction (EMSC) and subtracted from the vibrational absorption. Because the Mie scattering depends non-linearly on α, the product of the radius and the refractive index of the medium/sphere causing it, a new method was developed for estimating the Mie scattering by EMSC for unknown radius and refractive index of the Mie scatterer. The theoretically expected Mie contributions for a range of different α values were computed according to the formulae developed by Van de Hulst (1957). The many simulated spectra were then summarized by a six-dimensional subspace model by principal component analysis (PCA). This subspace model was used in EMSC to estimate and correct for Mie scattering, as well as other additive and multiplicative interference effects. The approach was applied to a set of Fourier transform infrared (FT-IR) absorbance spectra measured for individual lung cancer cells in order to remove unwanted interferences and to estimate ranges of important α values for each spectrum. The results indicate that several cell components may contribute to the Mie scattering.

Micro-Raman Spectroscopy for Optical Pathology of Oral Squamous Cell Carcinoma

Micro-Raman spectra of formalin-fixed oral squamous normal and carcinoma tissues, stored at room temperature for 2 months, have been recorded. Spectra were recorded both in the epithelial and subepithelial regions of the tissues. No noticeable spectral contamination due to formalin was observed. Very significant differences between spectra of normal epithelial and malignant epithelial samples were found. No such differences in spectra of subepithelial malignant and subepithelial normal samples could be observed. This study shows that spectra from the epithelial region changes drastically because of malignancy-induced biochemical changes in this region. Major differences between normal and malignant spectra seem to arise from the protein composition, conformational/structural changes, and possible increase in protein content in malignant epithelia. The differences between normal epithelial and subepithelial spectra, as expected, arise mainly from the collagen in subepithelial tissue. Principal component analysis of the combined sets of spectra—epithelial and subepithelial, normal and malignant— showed that very good discrimination can be achieved by Raman microspectroscopy. This study thus validates the suitability of formalin-fixed tissues for optical pathology in oral malignancy.

Studies of chemical fixation effects in human cell lines using Raman microspectroscopy

AbstractThe in vitro study of cellular species using Raman spectroscopy has proven a powerful non-invasive modality for the analysis of cell constituents and processes. This work uses micro-Raman spectroscopy to study the chemical fixation mechanism in three human cell lines (normal skin, normal bronchial epithelium, and lung adenocarcinoma) employing fixatives that preferentially preserve proteins (formalin), and nucleic acids (Carnoy’s fixative and methanol–acetic acid). Spectral differences between the mean live cell spectra and fixed cell spectra together with principal components analysis (PCA), and clustering techniques were used to analyse and interpret the spectral changes. The results indicate that fixation in formalin produces spectral content that is closest to that in the live cell and by extension, best preserves the cellular integrity. Nucleic acid degradation, protein denaturation, and lipid leaching were observed with all fixatives and for all cell lines, but to varying degrees. The results presented here suggest that the mechanism of fixation for short fixation times is complex and dependent on both the cell line and fixative employed. Moreover, important spectral changes occur with all fixatives that have consequences for the interpretation of biochemical processes within fixed cells. The study further demonstrates the potential of vibrational spectroscopy in the characterization of complex biochemical processes in cells at a molecular level. FigureChemical preservation of cells for Raman microspectroscopy is shown to be strongly dependent on the cell type and the fixative used, in a variety of cell lines, with formalin fixation show to result in spectral content most comparable to that in the live cell

Fourier Transform Infrared and Raman Spectroscopy for Characterization of Listeria monocytogenes Strains

ABSTRACT The purpose of this study was to characterize the variation in biochemical composition of 89 strains of Listeria monocytogenes with different susceptibilities towards sakacin P, using Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. The strains were also analyzed using amplified fragment length polymorphism (AFLP) analysis. Based on their susceptibilities to sakacin P, the 89 strains have previously been divided into two groups. Using the FTIR spectra and AFLP data, the strains were basically differentiated into the same two groups. Analyses of the FTIR and Raman spectra revealed that the strains in the two groups contained differences in the compositions of carbohydrates and fatty acids. The relevance of the variation in the composition of carbohydrates with respect to the variation in the susceptibility towards sakacin P for the L. monocytogenes strains is discussed.

In vivo chemical investigation of human skin using a confocal Raman fiber optic microprobe

To evaluate the potential of a new in vivo confocal Raman microprobe, we undertake a pilot study in human skin. A fiber optic probe is operated with a 633-nm laser and trials are conducted in healthy volunteers. We examine changes in molecular composition and structure of the stratum corneum, from different volunteers, from different anatomical sites and skin layers. Main spectral variations are detected in the following regions: 800 to 900 cm(-1) (amino acids); 1200 to 1290 cm(-1) (proteins); and 1030 to 1130 cm(-1), 1300 to 1450 cm(-1), and 2800 to 2900 cm(-1) (lipids). Curve fitting of the amide 1 region performs in detail protein secondary structural variations of the amide 1 band. Protein conformation is also found to vary depending on the anatomical site and volunteer. Similar analysis of the 730- to 1170-cm(-1) spectral window reveals a different organization of lamellar lipids: gel for forearm and palm, and liquid-crystalline phase for fingertips. All these variations result from changes in the stratum corneum components such as natural moisturizing factor (NMF), lipids (namely ceramides), and water. Hierarchical clustering classification is also performed to sort out Raman data obtained from different subjects. Further improvement of the confocal probe would be to adapt a 360-deg configuration enabling access to other anatomical sites.

An in vivo Randomized Study of Human Skin Moisturization by a New Confocal Raman Fiber-Optic Microprobe: Assessment of a Glycerol-Based Hydration Cream

Background: In a recent study, we demonstrated the ability of the new confocal Raman microprobe to investigate molecular and structural human skin composition under in vivo conditions. Experiments were performed at different anatomical sites, different layers, and with intervolunteer comparison. We also carried out feasibility tests using this probe to determine depth profiles of water content within the skin. Objective: In the present investigation we employed this confocal Raman optical microprobe to rigorously objectify the resulting hydration capacities after application of a moisturizing enhancer. Method: The in vivo experiments were performed on 26 healthy volunteers and measurements were undertaken on six areas of the volar forearm after a randomized application of hydrating agents. Responses were evaluated by calculating the water/protein band ratio, which determines the water content in the skin. Results: Data collected with the Raman microprobe showed significant changes between baseline values of control and treated skins. Statistical analysis performed on these data revealed an increase in skin moisture after application of a glycerol-based cream, which is the most widely used hydrating agent. Conclusion: Our results demonstrate clearly the potentials of this confocal Raman microprobe in the screening of hydrating agents or molecules under in vivo conditions. In the cosmetics field, this promising and suitable technique will undoubtedly offer new opportunities of hydration skin test evaluation.

Revealing Covariance Structures in Fourier Transform Infrared and Raman Microspectroscopy Spectra: A Study on Pork Muscle Fiber Tissue Subjected to Different Processing Parameters

The aim of this study was to investigate the correlation patterns between Fourier transform infrared (FT-IR) and Raman microspectroscopic data obtained from pork muscle tissue, which helped to improve the interpretation and band assignment of the observed spectral features. The pork muscle tissue was subjected to different processing factors, including aging, salting, and heat treatment, in order to induce the necessary degree of variation of the spectra. For comparing the information gained from the two spectroscopic techniques with respect to the experimental design, multiblock principal component analysis (MPCA) was utilized for data analysis. The results showed that both FT-IR and Raman spectra were mostly affected by heat treatment, followed by the variation in salt content. Furthermore, it could be observed that IR amide I, II, and III band components appear to be effected to a different degree by brine-salting and heating. FT-IR bands assigned to specific protein secondary structures could be related to different Raman C–C stretching bands. The Raman C–C skeletal stretching bands at 1031, 1061, and 1081 cm−1 are related to the IR bands indicative of aggregated β-structures, while the Raman bands at 901 cm−1 and 934 cm−1 showed a strong correlation with IR bands assigned to α-helical structures. At the same time, the IR band at 1610 cm−1, which formerly was assigned to tyrosine in spectra originating from pork muscle, did not show a correlation to the strong tyrosine doublet at 827 and 852 cm−1 found in Raman spectra, leading to the conclusion that the IR band at 1610 cm−1 found in pork muscle tissue is not originating from tyrosine.

The Ratio 1660/1690 cm−1 Measured by Infrared Microspectroscopy Is Not Specific of Enzymatic Collagen Cross-Links in Bone Tissue

In postmenopausal osteoporosis, an impairment in enzymatic cross-links (ECL) occurs, leading in part to a decline in bone biomechanical properties. Biochemical methods by high performance liquid chromatography (HPLC) are currently used to measure ECL. Another method has been proposed, by Fourier Transform InfraRed Imaging (FTIRI), to measure a mature PYD/immature DHLNL cross-links ratio, using the 1660/1690 cm−1 area ratio in the amide I band. However, in bone, the amide I band composition is complex (collagens, non-collagenous proteins, water vibrations) and the 1660/1690 cm−1 by FTIRI has never been directly correlated with the PYD/DHLNL by HPLC. A study design using lathyritic rats, characterized by a decrease in the formation of ECL due to the inhibition of lysyl oxidase, was used in order to determine the evolution of 1660/1690 cm−1 by FTIR Microspectroscopy in bone tissue and compare to the ECL quantified by HPLC. The actual amount of ECL was quantified by HPLC on cortical bone from control and lathyritic rats. The lathyritic group exhibited a decrease of 78% of pyridinoline content compared to the control group. The 1660/1690 cm−1 area ratio was increased within center bone compared to inner bone, and this was also correlated with an increase in both mineral maturity and mineralization index. However, no difference in the 1660/1690 cm−1 ratio was found between control and lathyritic rats. Those results were confirmed by principal component analysis performed on multispectral infrared images. In bovine bone, in which PYD was physically destructed by UV-photolysis, the PYD/DHLNL (measured by HPLC) was strongly decreased, whereas the 1660/1690 cm−1 was unmodified. In conclusion, the 1660/1690 cm−1 is not related to the PYD/DHLNL ratio, but increased with age of bone mineral, suggesting that a modification of this ratio could be mainly due to a modification of the collagen secondary structure related to the mineralization process.

Correcting attenuated total reflection-Fourier transform infrared spectra for water vapor and carbon dioxide.

Fourier transform infrared (FT-IR) spectroscopy is a valuable technique for characterization of biological samples, providing a detailed fingerprint of the major chemical constituents. However, water vapor and CO2 in the beam path often cause interferences in the spectra, which can hamper the data analysis and interpretation of results. In this paper we present a new method for removal of the spectral contributions due to atmospheric water and CO2 from attenuated total reflection (ATR)-FT-IR spectra. In the IR spectrum, four separate wavenumber regions were defined, each containing an absorption band from either water vapor or CO2. From two calibration data sets, gas model spectra were estimated in each of the four spectral regions, and these model spectra were applied for correction of gas absorptions in two independent test sets (spectra of aqueous solutions and a yeast biofilm (C. albicans) growing on an ATR crystal, respectively). The amounts of the atmospheric gases as expressed by the model spectra were estimated by regression, using second-derivative transformed spectra, and the estimated gas spectra could subsequently be subtracted from the sample spectra. For spectra of the growing yeast biofilm, the gas correction revealed otherwise hidden variations of relevance for modeling the growth dynamics. As the presented method improved the interpretation of the principle component analysis (PCA) models, it has proven to be a valuable tool for filtering atmospheric variation in ATR-FT-IR spectra.