FT-IR spectroscopy supported by PCA–LDA analysis for the study of embryonic stem cell differentiation

Abstract

Abstract.As recently pointed out in the literature, Fourier transform infrared (FT-IR) spectroscopy is emerging as a powerful tool in stem cell research. In this work we characterized in situ by FT-IR microspectroscopy the differentiation of murine embryonic stem cells (ES) to monitor possible changes in the cell macromolecular content during the early stages of differentiation. Undifferentiated and differentiating cells at 4, 7, 9 and 14 days were measured. Data were analyzed by the principal component and subsequent linear discriminant analyses (PCA-LDA) that enabled us to segregate ES cell spectra into well separate clusters and to identify the most significant spectral changes. Important changes in the lipid (3050-2800 cm −1 ), protein (1700-1600 cm −1 ) and in the nucleic acid (1050-850 cm −1 ) absorption regions were observed between days 4 to 7 of differentiation, indicating the appearance -at day 7 -of the new phenotype into cardiomyocyte precursors. Also the presence of DNA/RNA hybrid bands (954 cm −1 and 899 cm −1 ) suggests that the transcriptional switch of the genome started at this stage of differentiation. Particularly noteworthy, we suggest that the 2936 cm −1 shoulder we observed could reflect methyl group vibrations thus allowing the detection of variations in methylation levels of the stem cell during differentiation. These infrared results were found to be in agreement with the biochemical characterization of these differentiating cells, underlying the great potential of FT-IR spectroscopy in stem cell research.

Effects of Cannabis Use on the Protein and Lipid Profile of Olfactory Neuroepithelium Cells from Schizophrenia Patients Studied by Synchrotron-Based FTIR Spectroscopy

“…Accordingly, AEA levels in cerebrospinal fluid of acute SCZ patients are increased, and correlate negatively with psychotic symptoms [46], pointing to a protective role of AEA in cannabis users and SCZ patients Additionally, our results also support the existence of an increase in DNA and histone methylation in ON cells of SCZ/nc and HC/c. The peak situated in the 2936 cm −1 band corresponds to CH 3 groups from DNA and histone methylation [31], which is increased in some brain areas that are highly affected by SCZ neuropathology. This increase has been mostly reported as an increase of DNA methyltransferases in GABAergic neurons of SCZ patients [47].…”

“…In the lipid region of the spectra, we analysed the amplitude of the most pronounced peaks at (2923 and 2852 cm −1 ), as well as, the ratio of symmetric CH2/CH3 vibrations (2952/2871 cm −1 ) after baseline correction and vector normalization ( Figure 2). The peak at 2923 cm −1 is mainly related to long phospholipidic chains [31]. This band is also influenced by CH groups, which result from oxidation of CH2 groups to hydroxymethine groups, pointing to a possible oxidation effect [32].…”

“…Moreover, another narrow peak was identified thanks to the PCA around the 2936 cm −1 ( Figure 4A). This peak was first found to be a shoulder peak from the 2923 cm −1 band, which could reflect variations in the methylation levels of DNA and histones [31,35]. After applying the Norris GAP derivative approach, we found a significant increase in peak amplitude in HC/c (p < 0.001), and in SCZ/nc (p < 0.01) as compared to HC/nc, while no significant differences were found in SCZ/c with respect to HC/nc (one-way ANOVA F(3,922) = 7.199; p < 0.001).…”

Reversible in vivo cellular changes occur during desiccation and recovery: Desiccation tolerance of the resurrection filmy fern Hymenophyllum dentatum Cav.

“…FT-IR is a non-destructive analytical technique that allows reliable, direct and fast determination of several properties without any sample pretreatment (Wang 2012). It has been used for the study of intact cells, tissues and whole organisms (Ami et al 2010). The entire FT-IR spectra of an organic compound provide A muestra una imagen de una posición representativa de la proyección en 3D de las frondes desecadas.…”

Random Forest as a Non-parametric Algorithm for Near-infrared (NIR) Spectroscopic Discrimination for Geographical Origin of Agricultural Samples

“…In this situation, multivariate discrimination methods are typically employed to establish empirical correlation between spectral features and relevant geographical origins. Although diverse discrimination methods have been developed, 7-12 three methods of principal component analysis-linear discriminant analysis (PCA-LDA), 8,9,[13][14][15] partial least squaresdiscriminant analysis (PLS-DA), 8,9,[16][17][18] and soft independent modeling of class analogy (SIMCA) 8,10,[19][20][21] have been most frequently adopted for many practical field applications.…”