Raman Scattering: From Structural Biology to Medical Applications

Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy

The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.

Evading the Illusions: Identification of False Peaks in Micro-Raman Spectroscopy and Guidelines for Scientific Best Practice

Micro-Raman spectroscopy is an important analytical tool in a large variety of science disciplines. The technique is suitable for both identification of chemical bonds and studying more detailed phenomena like molecular interactions, material strain, crystallinity, defects, and bond formations. Raman scattering has one major weakness however: it is a very low probability process. The weak signals require very sensitive detection systems, which leads to a high probability of picking up signals from origins other than the sample. This complicates the analysis of the results and increases the risk of misinterpreting data. This work provides an overview of the sources of spurious signals occurring in Raman spectra, including photoluminescence, cosmic rays, stray light, artefacts caused by spectrometer components, and signals from other compounds in or surrounding the sample. The origins of these false Raman peaks are explained and means to identify and counteract them are provided.

Vibrational spectroscopies for biochemical investigation of X-ray exposure effects on SH-SY5Y human neuroblastoma cells

Neuroblastoma is the most recurring cancer in childhood and adolescence. The SH-SY5Y neuroblastoma cell line is generally adopted for elaborating new therapeutical approaches and/or elaborating strategies for the prevention of central nervous system disturbances. In fact, it represents a valid model system for investigating in vitro the effects on the brain of X-ray exposure using vibrational spectroscopies that can detect early radiation-induced molecular alterations of potential clinical usefulness. In recent years, we dedicated significant efforts in the use of Fourier-transform and Raman microspectroscopy techniques for characterizing such radiation-induced effects on SH-SY5Y cells by examining the contributions from different cell components (DNA, proteins, lipids, and carbohydrates) to the vibrational spectra. In this review, we aim at revising and comparing the main results of our studies to provide a wide outlook of the latest outcomes and a framework for future radiobiology research using vibrational spectroscopies. A short description of our experimental approaches and data analysis procedures is also reported.

Label-Free Quantification of Nanoencapsulated Piperonyl Esters in Cosmetic Hydrogels Using Raman Spectroscopy

Raman spectroscopy is a well-established technique for the molecular characterisation of samples and does not require extensive pre-analytical processing for complex cosmetic products. As an illustration of its potential, this study investigates the quantitative performance of Raman spectroscopy coupled with partial least squares regression (PLSR) for the analysis of Alginate nanoencapsulated Piperonyl Esters (ANC-PE) incorporated into a hydrogel. A total of 96 ANC-PE samples covering a 0.4% w/w-8.3% w/w PE concentration range have been prepared and analysed. Despite the complex formulation of the sample, the spectral features of the PE can be detected and used to quantify the concentrations. Using a leave-K-out cross-validation approach, samples were divided into a training set (n = 64) and a test set, samples that were previously unknown to the PLSR model (n = 32). The root mean square error of cross-validation (RMSECV) and prediction (RMSEP) was evaluated to be 0.142% (w/w PE) and 0.148% (w/w PE), respectively. The accuracy of the prediction model was further evaluated by the percent relative error calculated from the predicted concentration compared to the true value, yielding values of 3.58% for the training set and 3.67% for the test set. The outcome of the analysis demonstrated the analytical power of Raman to obtain label-free, non-destructive quantification of the active cosmetic ingredient, presently PE, in complex formulations, holding promise for future analytical quality control (AQC) applications in the cosmetics industry with rapid and consumable-free analysis.

Current decontamination challenges and potentially complementary solutions to safeguard the vulnerable seafood industry from recalcitrant human norovirus in live shellfish: Quo Vadis?

Safeguarding the seafood industry is important given its contribution to supporting our growing global population. However, shellfish are filter feeders that bioaccumulate microbial contaminants in their tissue from wastewater discharged into the same coastal growing environments leading to significant human disease outbreaks unless appropriately mitigated. Removal or inactivation of enteric viruses is very challenging particularly as human norovirus (hNoV) binds to specific histo-blood ligands in live oyster tissue that are consumed raw or lightly cooked. The regulatory framework that sets out use of clean seawater and UV disinfection is appropriate for bacterial decontamination at the post-harvest land-based depuration (cleaning) stage. However, additional non-thermal technologies are required to eliminate hNoV in live shellfish (particularly oysters) where published genomic studies report that low-pressure UV has limited effectiveness in inactivating hNoV. The use of the standard genomic detection method (ISO 15, 216-1:2017) is not appropriate for assessing the loss of infectious hNoV in treated live shellfish. The use of surrogate viral infectivity methods appear to offer some insight into the loss of hNoV infectiousness in live shellfish during decontamination. This paper reviews the use of existing and potentially other combinational treatment approaches to enhance the removal or inactivation of enteric viruses in live shellfish. The use of alternative and complementary novel diagnostic approaches to discern viable hNoV are discussed. The effectiveness and virological safety of new affordable hNoV intervention(s) require testing and validating at commercial shellfish production in conjunction with laboratory-based research. Appropriate risk management planning should encompass key stakeholders including local government and the wastewater industry. Gaining a mechanistic understanding of the relationship between hNoV response at molecular and structural levels in individually treated oysters as a unit will inform predictive modeling and appropriate treatment technologies. Global warming of coastal growing environments may introduce additional contaminant challenges (such as invasive species); thus, underscoring need to develop real-time ecosystem monitoring of growing environments to alert shellfish producers to appropriately mitigate these threats.

Vibrational Spectroscopy as a Tool for Bioanalytical and Biomonitoring Studies

The review briefly describes various types of infrared (IR) and Raman spectroscopy methods. At the beginning of the review, the basic concepts of biological methods of environmental monitoring, namely bioanalytical and biomonitoring methods, are briefly considered. The main part of the review describes the basic principles and concepts of vibration spectroscopy and microspectrophotometry, in particular IR spectroscopy, mid- and near-IR spectroscopy, IR microspectroscopy, Raman spectroscopy, resonance Raman spectroscopy, Surface-enhanced Raman spectroscopy, and Raman microscopy. Examples of the use of various methods of vibration spectroscopy for the study of biological samples, especially in the context of environmental monitoring, are given. Based on the described results, the authors conclude that the near-IR spectroscopy-based methods are the most convenient for environmental studies, and the relevance of the use of IR and Raman spectroscopy in environmental monitoring will increase with time.

Raman Scattering-Based Optical Sensing Of Chronic Liver Diseases

Chronic liver diseases (CLDs) are a major public health problem. Despite the progress achieved in fighting against viral hepatitis, the emergence of non-alcoholic fatty liver disease might pose a serious challenge to the public's health in the coming decades. Medical management of CLDs represents a substantial burden on the public health infrastructures. The health care cost of these diseases is an additional burden that weighs heavily on the economies of developing countries. Effective management of CLDs requires the adoption of reliable and cost-effective screening and diagnosing methods to ensure early detection and accurate clinical assessment of these diseases. Vibrational spectroscopies have emerged as universal analytical methods with promising applications in various industrial and biomedical fields. These revolutionary analytical techniques rely on analyzing the interaction between a light beam and the test sample to generate a spectral fingerprint. This latter is defined by the analyte's chemical structure and the molecular vibrations of its functional groups. Raman spectroscopy and surface-enhanced Raman spectroscopy have been used in combination with various chemometric tests to diagnose a wide range of malignant, metabolic and infectious diseases. The aim of the current review is to cast light on the use of these optical sensing methods in the diagnosis of CLDs. The vast majority of research works that investigated the potential application of these spectroscopic techniques in screening and detecting CLDs were discussed here. The advantages and limitations of these modern analytical methods, as compared with the routine and gold standard diagnostic approaches, were also reviewed in details.

Nanoscale Chemical Imaging of Human Cell Membranes Using Tip-Enhanced Raman Spectroscopy

Lack of appropriate tools for visualizing cell membrane molecules at the nanoscale in a non-invasive and label-free fashion limits our understanding of many vital cellular processes. Here, we use tip-enhanced Raman spectroscopy (TERS) to visualize the molecular distribution in pancreatic cancer cell (BxPC-3) membranes in ambient conditions without labelling, with a spatial resolution down to ca. 2.5 nm. TERS imaging reveals segregation of phenylalanine-, histidine-, phosphatidylcholine-, protein-, and cholesterol-rich BxPC-3 cell membrane domains at the nm length-scale. TERS imaging also showed a cell membrane region where cholesterol is mixed with protein. Interestingly, the higher resolution TERS imaging revealed that the molecular domains observed on the BxPC-3 cell membrane are not chemically "pure" but also contain other biomolecules. These results demonstrate the potential of TERS for non-destructive and label-free imaging of cell membranes with nanoscale resolution.

Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores

The structural organization of natural pigment-protein complexes provides a specific environment for the chromophore groups. Yet, proteins are inherently dynamic and conformationally mobile. In this work, we demonstrate the heterogeneity of chromophores of C-phycocyanin (C-PC) from Arthrospira platensis. Part of the population of trimeric C-PC is subject to spontaneous disturbances of protein-protein interactions resulting in increased conformational mobility of the chromophores. Upon fluorescence excitation in the visible range, the spectral signatures of these poorly populated states are masked by bulk chromophore states, but the former could be clearly discriminated when the fluorescence is excited by near-infrared quanta. Such selective excitation of conformationally mobile C-PC chromophores is due to the structure of their S₁ level, which is characterized by a significantly broadened spectral line. We demonstrate that the anti-Stokes C-PC fluorescence is the result of single-photon absorption. By combining spectral and structural methods, we characterize four distinct states of C-PC chromophores emitting at 620, 650, 665, and 720 nm and assigned the fast component in the anti-Stokes fluorescence decay kinetics in the range of 690-750 nm to the chromophores with increased conformational mobility. Our data suggest that the spectral and temporal characteristics of the anti-Stokes fluorescence can be used to study protein dynamics and develop methods to visualize local environment parameters such as temperature.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Current and Future Advancements of Raman Spectroscopy Techniques in Cancer Nanomedicine

Raman scattering is one of the most used spectroscopy and imaging techniques in cancer nanomedicine due to its high spatial resolution, high chemical specificity, and multiplexity modalities. The flexibility of Raman techniques has led, in the past few years, to the rapid development of Raman spectroscopy and imaging for nanodiagnostics, nanotherapy, and nanotheranostics. This review focuses on the applications of spontaneous Raman spectroscopy and bioimaging to cancer nanotheranostics and their coupling to a variety of diagnostic/therapy methods to create nanoparticle-free theranostic systems for cancer diagnostics and therapy. Recent implementations of confocal Raman spectroscopy that led to the development of platforms for monitoring the therapeutic effects of anticancer drugs in vitro and in vivo are also reviewed. Another Raman technique that is largely employed in cancer nanomedicine, due to its ability to enhance the Raman signal, is surface-enhanced Raman spectroscopy (SERS). This review also explores the applications of the different types of SERS, such as SERRS and SORS, to cancer diagnosis through SERS nanoprobes and the detection of small-size biomarkers, such as exosomes. SERS cancer immunotherapy and immuno-SERS (iSERS) microscopy are reviewed.

Label-Free Histology and Evaluation of Human Pancreatic Cancer with Coherent Nonlinear Optical Microscopy

Surgeries achieving maximal tumor resection remain the major effective treatment of pancreatic cancer. Rapid and precise intraoperative diagnosis of pancreatic tissues is critical for optimum surgical outcomes but is challenging for the current staining-based histological methods. We demonstrated that label-free coherent nonlinear optical microscopy with combined stimulated Raman scattering (SRS) and second harmonic generation (SHG) could reveal key diagnostic features of both normal and cancerous human pancreatic tissues. Adjacent pairs of tissue sections from resection margins of 37 patients were imaged by SRS and hematoxylin and eosin staining for direct comparison, demonstrating high diagnostic concordance (Cohen's kappa, κ > 0.97) between them. Fresh unprocessed tissues showed well-preserved histoarchitectures including pancreatic ducts, islets, acini, and nerves. Moreover, the area ratios of collagen fibers were analyzed and found to correlate with the drainage pancreatic amylase level (odds ratio = 28.0, p = 0.0017). Our results indicated that SRS/SHG histology provides potential for rapid intraoperative diagnosis of pancreatic cancer as well as a predictive value of postoperative pancreatic fistula.

Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex

Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII-NpHtrII) was performed. The influence of the polydispersity of NpSRII-NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

In Situ Water Quantification in Natural Deep Eutectic Solvents Using Portable Raman Spectroscopy

Raman spectroscopy is a label-free, non-destructive, non-invasive analytical tool that provides insight into the molecular composition of samples with minimum or no sample preparation. The increased availability of commercial portable Raman devices presents a potentially easy and convenient analytical solution for day-to-day analysis in laboratories and production lines. However, their performance for highly specific and sensitive analysis applications has not been extensively evaluated. This study performs a direct comparison of such a commercially available, portable Raman system, with a research grade Raman microscope system for the analysis of water content of Natural Deep Eutectic Solvents (NADES). NADES are renewable, biodegradable and easily tunable “green” solvents, outcompeting existing organic solvents for applications in extraction from biomass, biocatalysis, and nanoparticle synthesis. Water content in NADES is, however, a critical parameter, affecting their properties, optimal use and extraction efficiency. In the present study, portable Raman spectroscopy coupled with Partial Least Squares Regression (PLSR) is investigated for rapid determination of water content in NADES samples in situ, i.e., directly in glassware. Three NADES systems, namely Betaine Glycerol (BG), Choline Chloride Glycerol (CCG) and Glucose Glycerol (GG), containing a range of water concentrations between 0% (w/w) and 28.5% (w/w), were studied. The results are directly compared with previously published studies of the same systems, using a research grade Raman microscope. PLSR results demonstrate the reliability of the analysis, surrendering R² values above 0.99. Root Mean Square Errors Prediction (RMSEP) of 0.6805%, 0.9859% and 1.2907% w/w were found for respectively unknown CCG, BG and GG samples using the portable device compared to 0.4715%, 0.3437% and 0.7409% w/w previously obtained by analysis in quartz cuvettes with a Raman confocal microscope. Despite the relatively higher values of RMSEP observed, the comparison of the percentage of relative errors in the predicted concentration highlights that, overall, the portable device delivers accuracy below 5%. Ultimately, it has been demonstrated that portable Raman spectroscopy enables accurate quantification of water in NADES directly through glass vials without the requirement for sample withdrawal. Such compact instruments provide solvent and consumable free analysis for rapid analysis directly in laboratories and for non-expert users. Portable Raman is a promising approach for high throughput monitoring of water content in NADES that can support the development of new analytical protocols in the field of green chemistry in research and development laboratories but also in the industry as a routine quality control tool.

Effect of thiamethoxam on photosynthetic pigments and primary photosynthetic reactions in two maize genotypes (Zea mays)

Neonicotinoid insecticides are used against the wide range of pests to protect plants. The influence of neonicotinoids on target and non-target insects is well understood. Hence, there are controversial opinions about the effect of neonicotinoids on the plants. We investigated pigments and photosynthetic primary reactions in two maize genotypes (the inbred line zppl 225 and hybrid zp 341) under thiamethoxam (TMX) treatment by root irrigation. It was found that the effect of TMX depended on pesticide application techniques and selection of maize genotype. TMX was added to the soil by root irrigation on the 4th and 8th days after planting, and photosynthetic characteristics monitored on the 10th and 12th days after planting. The primary photochemical reactions in PSII (Fv/Fm) of both maize genotypes were not affected under two variants of TMX treatment during all growing period. The hybrid zp341 was shown to be more susceptible to both TMX treatments, demonstrating a decrease in photosynthetic characteristics (JIP-test parameters) as well as changes in the content of pigments and in the conformation of the carotenoid molecule. Our findings suggest that the combination of fluorescence method and Raman spectroscopy is a perspective tool for monitoring plant state under pesticide application.

Molecular and cellular features of mandibular autografts studied using raman spectroscopy

Currently, biophysical studies are of great interest, the results of which are important for development of a method for diagnosis of the cells and tissue condition to be used in clinical practice. The study was aimed to use a non-invasive optical method (Raman spectroscopy) for assessment of changes in the composition and conformation of the molecules of the patient’s mandibular cells and tissues. This approach was proposed to increase the informativeness and effectiveness of studying the composition of autografts harvested for augmentation of alveolar processes with bone tissue deficiency (elective bone grafting). In the course of the study the bone tissue samples obtained from three patients aged 51–73 (two men and one woman) were assessed. Raman signals were detected, indicating the presence of phosphate groups and carbonate ions (such as СО3–2) of the inorganic bone components. Raman bands indicating the presence of collagen, red blood cell hemoglobin, proteins (C–N bonds), lipids (С–Н groups of fatty acids and phosphate groups of phospholipids), as well as their OH groups may be considered the markers of periosteum tissue. The general possibility was suggested of studying single cells of autografts using the markers, indicating the presence of collagen, hemoglobin, proteins, lipids (С–Н groups of fatty acids of lipids; phosphate groups of phospholipids), and their OH groups. According to the authors, the results obtained can provide a basis for development of the new method for diagnosis of autograft bone using the combination of Raman spectroscopy and light guides.

Windowless detection geometry for sum frequency scattering spectroscopy in the C-D and amide I regions

Understanding the structure and chemistry of nanoscopic surfaces is an important challenge for biointerface sciences. Sum frequency scattering (SFS) spectroscopy can specifically probe the surfaces of nanoparticles, vesicles, liposomes, and other materials relevant to biomaterial research, and, as a vibrational spectroscopy method, it can provide molecular level information about the surface chemistry. SFS is particularly promising to probe the structure of proteins, and other biological molecules, at nanoparticle surfaces. Here, amide I spectra can provide information about protein folding and orientation, while spectra in the C-D and C-H stretching regions allow experiments to determine the mode of interaction between particle surfaces and proteins. Methods used currently employ a closed liquid cell or cuvette, which works extremely well for C-H and phosphate regions but is often impeded in the amide I and C-D regions by a strong background signal that originates from the window material of the sample cells. Here, we discuss a windowless geometry for collecting background-free and high-fidelity SFS spectra in the amide I and C-D regions. We demonstrate the improvement in spectra quality by comparing SFS spectra of unextruded, multilamellar vesicles in a sample cuvette with those recorded using the windowless geometry. The sample geometry we propose will enable new experiments using SFS as a probe for protein-particle interactions.

Detection of SARS-CoV-2 and its S and N proteins using surface enhanced Raman spectroscopy

The COVID-19 pandemic demonstrated the critical need for accurate and rapid testing for virus detection. This need has generated a high number of new testing methods aimed at replacing RT-PCR, which is the golden standard for testing. Most of the testing techniques are based on biochemistry methods and require chemicals that are often expensive and the supply might become scarce in a large crisis. In the present paper we suggest the use of methods based on physics that leverage novel nanomaterials. We demonstrate that using Surface Enhanced Raman Spectroscopy (SERS) of virion particles a very distinct spectroscopic signature of the SARS-CoV-2 virus can be obtained. We demonstrate that the spectra are mainly composed by signals from the spike (S) and nucleocapsid (N) proteins. It is believed that a clinical test using SERS can be developed. The test will be fast, inexpensive, and reliable. It is also clear that SERS can be used for analysis of structural changes on the S and N proteins. This will be an example of application of nanotechnology and properties of nanoparticles for health and social related matters.

The COVID-19 pandemic demonstrated the critical need for accurate and rapid testing for virus detection.

Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing

This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.