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Raman spectroscopy is increasingly being used in biology, forensics, diagnostics, pharmaceutics and food science applications. This growth is triggered not only by improvements in the computational and experimental setups but also by the development of chemometric techniques. Chemometric techniques are the analytical processes used to detect and extract information from subtle differences in Raman spectra obtained from related samples. This information could be used to find out, for example, whether a mixture of bacterial cells contains different species, or whether a mammalian cell is healthy or not. Chemometric techniques include spectral processing (ensuring that the spectra used for the subsequent computational processes are as clean as possible) as well as the statistical analysis of the data required for finding the spectral differences that are most useful for differentiation between, for example, different cell types. For Raman spectra, this analysis process is not yet standardized, and there are many confounding pitfalls. This protocol provides guidance on how to perform a Raman spectral analysis: how to avoid these pitfalls, and strategies to circumvent problematic issues. The protocol is divided into four parts: experimental design, data preprocessing, data learning and model transfer. We exemplify our workflow using three example datasets where the spectra from individual cells were collected in single-cell mode, and one dataset where the data were collected from a raster scanning–based Raman spectral imaging experiment of mice tissue. Our aim is to help move Raman-based technologies from proof-of-concept studies toward real-world applications. Raman spectroscopy is increasingly being used in biological assays and studies. This protocol provides guidance for performing chemometric analysis to detect and extract information relating to the chemical differences between biological samples.

Raman microscopy is a promising technology for visualizing the distribution of molecules in cells. A challenge for live-cell imaging using Raman microscopy has been long imaging times owing to the weak Raman signal. Here we present a protocol for constructing and using a Raman microscope equipped with both a slit-scanning excitation and detection system and a laser steering and nanoparticle-tracking system. Slit scanning allows Raman imaging with high temporal and spatial resolution, whereas the laser beam steering system enables dynamic surface-enhanced Raman imaging using gold nanoparticles. Both features enable mapping of the distributions of molecules in live cells and visualization of cellular transport pathways. Furthermore, its utility can be expanded to small-molecule imaging by using tiny Raman-active tags such as alkyne. For example, DNA synthesis in a cell can be visualized by detecting 5-ethynyl-2′-deoxyuridine (EdU), a deoxyuridine derivative with an alkyne moiety. We describe the optics, hardware and software to construct the Raman microscope, and discuss the conditions and parameters involved in live-cell imaging. The whole system can be built in ∼8 h.

Recently, surface-enhanced Raman scattering nanoprobes have shown tremendous potential in oncological imaging owing to the high sensitivity and specificity of their fingerprint-like spectra. As current Raman scanners rely on a slow, point-by-point spectrum acquisition, there is an unmet need for faster imaging to cover a clinically relevant area in real-time. Herein, we report the rational design and optimization of fluorescence-Raman bimodal nanoparticles (FRNPs) that synergistically combine the specificity of Raman spectroscopy with the versatility and speed of fluorescence imaging. DNA-enabled molecular engineering allows the rational design of FRNPs with a detection limit as low as 5 × 10 −15  M. FRNPs selectively accumulate in tumor tissue mouse cancer models and enable real-time fluorescence imaging for tumor detection, resection, and subsequent Raman-based verification of clean margins. Furthermore, FRNPs enable highly efficient image-guided photothermal ablation of tumors, widening the scope of the NPs into the therapeutic realm. Currently available Raman scanners are limited in speed to acquire images of clinically relevant sizes in cancer imaging. Here, the authors developed a DNA based design principle for Raman-Fluorescence bimodal nanoparticles and demonstrate real-time, high precision image-guided tumor resections and photothermal ablation of cancer.

Gold deposition with diagonal angle towards boehmite-based nanostructure creates random arrays of horse-bean-shaped nanostructures named gold-nanofève (GNF). GNF generates many electromagnetic hotspots as surface-enhanced Raman spectroscopy (SERS) excitation sources, and enables large-area visualization of molecular vibration fingerprints of metabolites in human cancer xenografts in livers of immunodeficient mice with sufficient sensitivity and uniformity. Differential screening of GNF-SERS signals in tumours and those in parenchyma demarcated tumour boundaries in liver tissues. Furthermore, GNF-SERS combined with quantum chemical calculation identified cysteine-derived glutathione and hypotaurine (HT) as tumour-dominant and parenchyma-dominant metabolites, respectively. CD44 knockdown in cancer diminished glutathione, but not HT in tumours. Mechanisms whereby tumours sustained HT under CD44-knockdown conditions include upregulation of PHGDH, PSAT1 and PSPH that drove glycolysis-dependent activation of serine/glycine-cleavage systems to provide one-methyl group for HT synthesis. HT was rapidly converted into taurine in cancer cells, suggesting that HT is a robust anti-oxidant for their survival under glutathione-suppressed conditions. Surface-enhanced Raman spectroscopy (SERS) visualizes fingerprints of intermolecular vibrations of many metabolites. Here the authors report a SERS imaging technique that enables the visualization of metabolites distribution and automated extraction of tumour boundaries in frozen tissues.

The aim of the study was to examine the biochemical and structural changes occurring in the periodontal ligament (PDL) during orthodontic-force application using micro-Raman spectroscopy ( μ -RS). Adolescent and young patients who needed orthodontic treatment with first premolar extractions were recruited. Before extractions, orthodontic forces were applied using a closed-coil spring that was positioned between the molar and premolar. Patients were randomly divided into three groups, whose extractions were performed after 2, 7, and 14 days of force application. From the extracted premolars, PDL samples were obtained, and a fixation procedure with paraformaldehyde was adopted. Raman spectra were acquired for each PDL sample in the range of 1000–3200 cm − 1 and the more relevant vibrational modes of proteins (Amide I and Amide III bands) and CH 2 and CH 3 modes were shown. Analysis indicated that the protein structure in the PDL samples after different time points of orthodontic-force application was modified. In addition, changes were observed in the CH 2 and CH 3 high wavenumber region due to local hypoxia and mechanical force transduction. The reported results indicated that μ -RS provides a valuable tool for investigating molecular interchain interactions and conformational modifications in periodontal fibers after orthodontic tooth movement, providing quantitative insight of time occurring for PDL molecular readjustment.

Development of rapid and sensitive methods to detect pathogens is important to food and water safety. This study aimed to detect and discriminate important food- and waterborne bacteria (i.e., Escherichia coli O157:H7, Staphylococcus epidermidis, Listeria monocytogenes, and Enterococcus faecelis) by surface-enhanced Raman spectroscopy (SERS) coupled with intracellular nanosilver as SERS substrates. An in vivo molecular probing using intracellular nanosilver for the preparation of bacterial samples was established and assessed. Satisfactory SERS performance and characteristic SERS spectra were obtained from different bacterial samples. Distinctive differences were observed in SERS spectral data, specifically in the Raman shift region of 500-1,800 cm^sup -1^, and between bacterial samples at the species and strain levels. The detection limit of SERS coupled with in vivo molecular probing using silver nanosubstrates could reach the level of single cells. Experiments with a mixture of E. coli O157:H7 and S. epidermidis for SERS measurement demonstrate that SERS could be used for classification of mixed bacterial samples. Transmission electron microscopy was used to characterize changes of morphology and cellular composition of bacterial cells after treatment of intracellular nanosilver. The results indicate that SERS coupled with intracellular silver nanosubstrates is a promising method for detection and characterization of food- and waterborne pathogenic and non-pathogenic bacterial samples.[PUBLICATION ABSTRACT]

The influence of a topically applied formulation containing components of natural moisturizing factor (NMF) on barrier-related parameters of the stratum corneum (SC) was investigated in vivo using confocal Raman microspectroscopy in a randomized, placebo-controlled double-blind study on 12 volunteers for 14 days. This method allowed for the elucidation of subtle differences between the verum and the placebo even though the components of the verum naturally occur in the SC. This differentiation is not possible non-invasively by conventional methods. In this study, we found that the applied verum and placebo formulations disrupted the equilibrium of water, NMF and lipids in the SC. The adverse effects of the formulation could be mitigated by incorporating it into a simplified supplementation of NMF molecules. As a long-term effect, the amount of strongly bound water increases at 30–40% SC depth (p < 0.05) and the amount of weakly bound water decreases at 30–40% SC depth (p < 0.05) for the verum. This supplement was also unexpectedly able to prevent intercellular lipids (ICL) disorganization in selected depths. In the long term, the verum treatment limited the lateral disorganization of the ICL to the upper 20% SC depth. Further research is required to elucidate the interplay of these factors in the SC, to better understand their contribution to the equilibrium and barrier function of the skin. This understanding of the interaction of these naturally occurring components could help in the future to develop and optimize topical treatments for diseases like psoriasis, atopic dermatitis, ichthyosis where the skin barrier is disrupted.

A detailed understanding of the structural organization of the cell wall of vascular plants is important from both the perspectives of plant biology and chemistry and of commercial utilization. A state-of-the-art 633-nm laser-based confocal Raman microscope was used to determine the distribution of cell wall components in the cross section of black spruce wood in situ. Chemical information from morphologically distinct cell wall regions was obtained and Raman images of lignin and cellulose spatial distribution were generated. While cell corner (CC) lignin concentration was the highest on average, lignin concentration in compound middle lamella (CmL) was not significantly different from that in secondary wall (S2 and S2-S3). Images generated using the 1,650 cm-1 band showed that coniferaldehyde and coniferyl alcohol distribution followed that of lignin and no particular cell wall layer/region was therefore enriched in the ethylenic residue. In contrast, cellulose distribution showed the opposite pattern--low concentration in CC and CmL and high in S2 regions. Nevertheless, cellulose concentration varied significantly in some areas, and concentrations of both lignin and cellulose were high in other areas. Though intensity maps of lignin and cellulose distributions are currently interpreted solely in terms of concentration differences, the effect of orientation needs to be carefully considered to reveal the organization of the wood cell wall.

Introduction Ceramides are essential epidermal constituents that play a critical role in skin moisturization treatment as a raw material in cosmetics formulation. Recently, ceramides have been known to be frequently applied in various cosmetic formulations. Despite ceramide's beneficial characteristics, academic research regarding ceramides and their skin absorption remains insufficient. Therefore, our study conducted clinical research employing Raman spectroscopy to investigate the effects of ceramides on skin absorption to enhance the understanding of ceramides’ dermatological functionality and their topical application in cosmetics science. Materials and Methods Twenty healthy individuals with dry skin have participated in this clinical trial. In this double‐arm designed trial, the test group received an investigational product with ceramides (5000 ppm) and a control group received an investigational product without the ceramides while all other components remained identical. The subjects visited the clinical research center and acclimatized for 30 min in constant humidity and temperature for equilibrium, subsequently conducting a measurement. Before the trial, the research subject's target site (lower arm area) was kept clean, devoid of any cosmetic administering 24 h before the trial when investigational product was topically applied. Results Our findings with Raman spectroscopy statistically demonstrate that skin absorption amount, speed and depth for both groups improved overall (p < 0.05) after administration of the investigational product. Notably, the test group received an investigational product with ceramides (5000 ppm) indicating superior effectiveness across all parameters compared to a control group from comparison analysis of each parameter (p < 0.05). Conclusion This study concludes that ceramide‐containing cosmetics provide a beneficial effect on skin absorption via visual and statistical results of Raman spectroscopy analysis.

Theory Theory of Coherent Raman Scattering, Eric Olaf Potma and Shaul MukamelCoherent Raman Scattering under Tightly Focused Conditions, Eric Olaf Potma, Xiaoliang Sunney Xie, Andreas Volkmer, and Ji-Xin ChengPlatformsConstruction of a Coherent Raman Microscope, Brian G. Sarr and Xiaoliang Sunney XieStimulated Raman Scattering Microscopy, Christian Freudiger and Xiaoliang Sunney XieFemtosecond versus Picosecond Pulses for Coherent Raman Microscopy, Mikhail N. Slipchenko, Delong Zhang, and Ji-Xin ChengWide-Field CARS Microscopy, Alexander Jesacher, Gregor Thalhammer, Stefan Bernet, and Monika Ritsch-MarteVibrational Spectromicroscopy by Coupling Coherent Raman Imaging with Spontaneous Raman Spectral Analysis, Mikhail N. Slipchenko and Ji-Xin ChengCoherent Control in CARS, Jonathan M. Levitt, Ori Katz, and Yaron SilberbergFourier Transform CARS Microscopy, Jennifer P. OgilvieCRS with Alternative Beam Profiles, Varun Raghunathan, Hyunmin Kim, Stephan Stranick, and Eric Olaf PotmaVibrational Phase Microscopy, Martin Jurna, Cees Otto, and Herman L. OfferhausMultiplex CARS Microscopy, James P.R. Day, Katrin F. Domke, Gianluca Rago, Erik M. Vartiainen, and Mischa BonnInterferometric Multiplex CARS, Sang-Hyun LimPhotonic Crystal Fiber-Based Broadband CARS Microscopy, Marcus T. Cicerone, Young Jong Lee, Sapun H. Parekh, and Khaled A. AamerMultiplex Stimulated Raman Scattering Microscopy, Dan Fu and Xiaoliang Sunney XieApplicationsImaging Myelin Sheath Ex Vivo and In Vivo by CARS Microscopy, Yan Fu, Yunzhou (Sophia) Shi, and Ji-Xin ChengImaging Lipid Metabolism in Caenorhabditis elegans and Other Model Organisms, Helen Fink, Christian Brackmann, and Annika EnejderLipid-Droplet Biology and Obesity-Related Health Risks, Thuc T. LeWhite Matter Injury: Cellular-Level Myelin Damage Quantification in Live Animals, Erik Bélanger, F.P. Henry, R. Vallée, M.A. Randolph, I.E. Kochevar, J.M. Winograd, Charles P. Lin, and Daniel CôtéCARS Microscopy Study of Liquid Crystals, Heung-Shik Park and Oleg D. LavrentovichLive Cell Imaging by Multiplex CARS Microspectroscopy, Hideaki Kano Coherent Raman Scattering Imaging of Drug Delivery Systems, Ling Tong and Ji-Xin ChengApplications of Stimulated Raman Scattering Microscopy, Christian Freudiger, Daniel A. Orringer, and Xiaoliang Sunney XieApplications of Coherent Anti-Stokes Raman Spectroscopy Imaging to Cardiovascular Diseases, Han-Wei Wang, Michael Sturek, and Ji-Xin ChengApplications of CARS Microscopy to Tissue Engineering, Annika Enejder and Christian BrackmannDietary Fat Absorption Visualized by CARS Microscopy, Kimberly K. BuhmanIndex.