Statistical approaches to Raman imaging: principal component score mapping.

In this research, Raman imaging was employed to map various samples, and the resulting data were analyzed using a suite of automated tools to extract critical information, including intensity and signal-to-noise ratio. The acquired spectra were further processed to identify similarities and investigate patterns using principal component analysis. The objective of this study was to establish guidelines for investigating Raman imaging results, particularly when dealing with large datasets comprising thousands of relatively low-intensity spectra. The overall quality of the results was assessed, and representative locations were determined based on the main Raman bands. While automated software solutions are insufficient for removing baselines and fitting the data, statistical analysis proved to be a powerful tool for extracting valuable information directly from the raw spectral data. This approach enables the extraction of as much information as possible from large arrays of spectral data, even in complex cases where automated software may fall short. The findings of this study contribute to enhancing the analysis and interpretation of Raman imaging results, providing researchers with a robust methodology for extracting meaningful insights from complex datasets, reducing the amount of effort required during data interpretation and analysis.

Ammonia Toxicity and Associated Protein Oxidation: A Single-Cell Surface Enhanced Raman Spectroscopy Study.

Ammonia (NH3) is a commonly used industrial chemical to which exposure at high concentrations can result in severe skin damage. Moreover, high levels of ammonia in the human body can lead to hyperammonemia conditions and enhanced cancer metabolism. In this work, the toxicity mechanism of NH3 has been studied against human dermal fibroblast (HDF) cells using surface-enhanced Raman spectroscopy (SERS). For this purpose, gold nanoparticles of size 50 nm have been prepared and used as probes for Raman signal enhancement, after being internalized inside HDF cells. Following the exposure to ammonia, HDF cells showed a significant variation in the protein ternary structure's signals, demonstrating their denaturation and oxidation process, together with early signs of apoptosis. Meaningful changes were observed especially in the Raman vibrations of sulfur-containing amino acids (cysteine and methionine) together with aromatic residues. Fluorescence microscopy revealed the formation of reactive oxygen and nitrogen species in cells, which confirmed their stressed condition and to whom the causes of protein degradation can be attributed. These findings can provide new insights into the mechanism of ammonia toxicity and protein oxidation at a single-cell level, demonstrating the high potential of the SERS technique in investigating the cellular response to toxic compounds.

Raman Multi-Omic Snapshot and Statistical Validation of Structural Differences between Herpes Simplex Type I and Epstein-Barr Viruses.

Raman spectroscopy was applied to study the structural differences between herpes simplex virus Type I (HSV-1) and Epstein-Barr virus (EBV). Raman spectra were first collected with statistical validity on clusters of the respective virions and analyzed according to principal component analysis (PCA). Then, average spectra were computed and a machine-learning approach applied to deconvolute them into sub-band components in order to perform comparative analyses. The Raman results revealed marked structural differences between the two viral strains, which could mainly be traced back to the massive presence of carbohydrates in the glycoproteins of EBV virions. Clear differences could also be recorded for selected tyrosine and tryptophan Raman bands sensitive to pH at the virion/environment interface. According to the observed spectral differences, Raman signatures of known biomolecules were interpreted to link structural differences with the viral functions of the two strains. The present study confirms the unique ability of Raman spectroscopy for answering structural questions at the molecular level in virology and, despite the structural complexity of viral structures, its capacity to readily and reliably differentiate between different virus types and strains.

Raman Multi-Omic Snapshots of Koshihikari Rice Kernels Reveal Important Molecular Diversities with Potential Benefits in Healthcare.

This study exploits quantitative algorithms of Raman spectroscopy to assess, at the molecular scale, the nutritional quality of individual kernels of the Japanese short-grain rice cultivar Koshihikari in terms of amylose-to-amylopectin ratio, fractions of phenylalanine and tryptophan aromatic amino acid residues, protein-to-carbohydrate ratio, and fractions of protein secondary structures. Statistical assessments on a large number of rice kernels reveal wide distributions of the above nutritional parameters over nominally homogeneous kernel batches. This demonstrates that genetic classifications cannot catch omic fluctuations, which are strongly influenced by a number of extrinsic factors, including the location of individual grass plants within the same rice field and the level of kernel maturation. The possibility of collecting nearly real-time Raman "multi-omic snapshots" of individual rice kernels allows for the automatic (low-cost) differentiation of groups of kernels with restricted nutritional characteristics that could be used in the formulation of functional foods for specific diseases and in positively modulating the intestinal microbiota for protection against bacterial infection and cancer prevention.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions.

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.

In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis.

The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid ß (Aß) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.

Forged to heal: The role of metallic cellular solids in bone tissue engineering.

Metallic cellular solids, made of biocompatible alloys like titanium, stainless steel, or cobalt-chromium, have gained attention for their mechanical strength, reliability, and biocompatibility. These three-dimensional structures provide support and aid tissue regeneration in orthopedic implants, cardiovascular stents, and other tissue engineering cellular solids. The design and material chemistry of metallic cellular solids play crucial roles in their performance: factors such as porosity, pore size, and surface roughness influence nutrient transport, cell attachment, and mechanical stability, while their microstructure imparts strength, durability and flexibility. Various techniques, including additive manufacturing and conventional fabrication methods, are utilized for producing metallic biomedical cellular solids, each offering distinct advantages and drawbacks that must be considered for optimal design and manufacturing. The combination of mechanical properties and biocompatibility makes metallic cellular solids superior to their ceramic and polymeric counterparts in most load bearing applications, in particular under cyclic fatigue conditions, and more in general in application that require long term reliability. Although challenges remain, such as reducing the production times and the associated costs or increasing the array of available materials, metallic cellular solids showed excellent long-term reliability, with high survival rates even in long term follow-ups.

Instantaneous Inactivation of Herpes Simplex Virus by Silicon Nitride Bioceramics.

Hydrolytic reactions taking place at the surface of a silicon nitride (Si3N4) bioceramic were found to induce instantaneous inactivation of Human herpesvirus 1 (HHV-1, also known as Herpes simplex virus 1 or HSV-1). Si3N4 is a non-oxide ceramic compound with strong antibacterial and antiviral properties that has been proven safe for human cells. HSV-1 is a double-stranded DNA virus that infects a variety of host tissues through a lytic and latent cycle. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) tests of HSV-1 DNA after instantaneous contact with Si3N4 showed that ammonia and its nitrogen radical byproducts, produced upon Si3N4 hydrolysis, directly reacted with viral proteins and fragmented the virus DNA, irreversibly damaging its structure. A comparison carried out upon testing HSV-1 against ZrO2 particles under identical experimental conditions showed a significantly weaker (but not null) antiviral effect, which was attributed to oxygen radical influence. The results of this study extend the effectiveness of Si3N4's antiviral properties beyond their previously proven efficacy against a large variety of single-stranded enveloped and non-enveloped RNA viruses. Possible applications include the development of antiviral creams or gels and oral rinses to exploit an extremely efficient, localized, and instantaneous viral reduction by means of a safe and more effective alternative to conventional antiviral creams. Upon incorporating a minor fraction of micrometric Si3N4 particles into polymeric matrices, antiherpetic devices could be fabricated, which would effectively impede viral reactivation and enable high local effectiveness for extended periods of time.

Effect of Carbonate Source on the Dehydrofluorination Process in Polyvinylidene Fluoride/Alkali Metal Carbonate Composites.

In this paper, Raman and X-ray photoelectron spectroscopies were applied to analyze compositional and structural variations of the generated activated carbon (AC), as induced by changing carbonate source in three different types of systems, PVDF/M2CO3 (M = Li, Na, and K). According to the variations of I D/I G and sp2/sp3 ratios, a strong dependence of the AC structure on the type and content of the initial carbonate was found, determined by practical dehydrofluorination reactions associated with oxygen incorporation in AC and side reactions, because of the property variation induced by the difference in the cation of the carbonate sources. This procedure clarified the process of PVDF dehydrofluorination and the formation of activated carbon, which helps to optimize the material performance of the percolative composite for flexible energy storage applications.

In Situ Raman Analysis of Biofilm Exopolysaccharides Formed in Streptococcus mutans and Streptococcus sanguinis Commensal Cultures.

This study probed in vitro the mechanisms of competition/coexistence between Streptococcus sanguinis (known for being correlated with health in the oral cavity) and Streptococcus mutans (responsible for aciduric oral environment and formation of caries) by means of quantitative Raman spectroscopy and imaging. In situ Raman assessments of live bacterial culture/coculture focusing on biofilm exopolysaccharides supported the hypothesis that both species engaged in antagonistic interactions. Experiments of simultaneous colonization always resulted in coexistence, but they also revealed fundamental alterations of the biofilm with respect to their water-insoluble glucan structure. Raman spectra (collected at fixed time but different bacterial ratios) showed clear changes in chemical bonds in glucans, which pointed to an action by Streptococcus sanguinis to discontinue the impermeability of the biofilm constructed by Streptococcus mutans. The concurrent effects of glycosidic bond cleavage in water-insoluble α - 1,3-glucan and oxidation at various sites in glucans' molecular chains supported the hypothesis that secretion of oxygen radicals was the main "chemical weapon" used by Streptococcus sanguinis in coculture.

Biomedical Applications of Titanium Alloys: A Comprehensive Review.

Titanium alloys have emerged as the most successful metallic material to ever be applied in the field of biomedical engineering. This comprehensive review covers the history of titanium in medicine, the properties of titanium and its alloys, the production technologies used to produce biomedical implants, and the most common uses for titanium and its alloys, ranging from orthopedic implants to dental prosthetics and cardiovascular devices. At the core of this success lies the combination of machinability, mechanical strength, biocompatibility, and corrosion resistance. This unique combination of useful traits has positioned titanium alloys as an indispensable material for biomedical engineering applications, enabling safer, more durable, and more efficient treatments for patients affected by various kinds of pathologies. This review takes an in-depth journey into the inherent properties that define titanium alloys and which of them are advantageous for biomedical use. It explores their production techniques and the fabrication methodologies that are utilized to machine them into their final shape. The biomedical applications of titanium alloys are then categorized and described in detail, focusing on which specific advantages titanium alloys are present when compared to other materials. This review not only captures the current state of the art, but also explores the future possibilities and limitations of titanium alloys applied in the biomedical field.

Raman Analyses of Laser Irradiation-Induced Microstructural Variations in Synthetic Hydroxyapatite and Human Teeth.

The microstructural and molecular-scale variations induced by laser irradiation treatment on human teeth enamel in comparison with synthetic hydroxyapatite (HAp) were examined through Raman microprobe spectroscopy as a function of irradiation power. The results demonstrated that laser irradiation could modify stoichiometry, microstructure, and the population of crystallographic defects, as well as the hardness of the materials. These modifications showed strong dependences on both laser power and initial nonstoichiometric structure (defective content of HPO4), because of the occurrence of distinct reactions and structural reconstruction. The reported observations can redirect future trends in tooth whitening by laser treatment and the production of HAp coatings because of the important role of stoichiometric defects.

Raman Metabolomics of Candida auris Clades: Profiling and Barcode Identification.

This study targets on-site/real-time taxonomic identification and metabolic profiling of seven different Candida auris clades/subclades by means of Raman spectroscopy and imaging. Representative Raman spectra from different Candida auris samples were systematically deconvoluted by means of a customized machine-learning algorithm linked to a Raman database in order to decode structural differences at the molecular scale. Raman analyses of metabolites revealed clear differences in cell walls and membrane structure among clades/subclades. Such differences are key in maintaining the integrity and physical strength of the cell walls in the dynamic response to external stress and drugs. It was found that Candida cells use the glucan structure of the extracellular matrix, the degree of α-chitin crystallinity, and the concentration of hydrogen bonds between its antiparallel chains to tailor cell walls' flexibility. Besides being an effective ploy in survivorship by providing stiff shields in the α-1,3-glucan polymorph, the α-1,3-glycosidic linkages are also water-insoluble, thus forming a rigid and hydrophobic scaffold surrounded by a matrix of pliable and hydrated ß-glucans. Raman analysis revealed a variety of strategies by different clades to balance stiffness, hydrophobicity, and impermeability in their cell walls. The selected strategies lead to differences in resistance toward specific environmental stresses of cationic/osmotic, oxidative, and nitrosative origins. A statistical validation based on principal component analysis was found only partially capable of distinguishing among Raman spectra of clades and subclades. Raman barcoding based on an algorithm converting spectrally deconvoluted Raman sub-bands into barcodes allowed for circumventing any speciation deficiency. Empowered by barcoding bioinformatics, Raman analyses, which are fast and require no sample preparation, allow on-site speciation and real-time selection of appropriate treatments.

Three-Dimensional Culture of Cartilage Tissue on Nanogel-Cross-Linked Porous Freeze-Dried Gel Scaffold for Regenerative Cartilage Therapy: A Vibrational Spectroscopy Evaluation.

This study presents a set of vibrational characterizations on a nanogel-cross-linked porous freeze-dried gel (NanoCliP-FD gel) scaffold for tissue engineering and regenerative therapy. This scaffold is designed for the in vitro culture of high-quality cartilage tissue to be then transplanted in vivo to enable recovery from congenital malformations in the maxillofacial area or crippling jaw disease. The three-dimensional scaffold for in-plate culture is designed with interface chemistry capable of stimulating cartilage formation and maintaining its structure through counteracting the dedifferentiation of mesenchymal stem cells (MSCs) during the formation of cartilage tissue. The developed interface chemistry enabled high efficiency in both growth rate and tissue quality, thus satisfying the requirements of large volumes, high matrix quality, and superior mechanical properties needed in cartilage transplants. We characterized the cartilage tissue in vitro grown on a NanoCliP-FD gel scaffold by human periodontal ligament-derived stem cells (a type of MSC) with cartilage grown by the same cells and under the same conditions on a conventional (porous) atelocollagen scaffold. The cartilage tissues produced by the MSCs on different scaffolds were comparatively evaluated by immunohistochemical and spectroscopic analyses. Cartilage differentiation occurred at a higher rate when MSCs were cultured on the NanoCliP-FD gel scaffold compared to the atelocollagen scaffold, and produced a tissue richer in cartilage matrix. In situ spectroscopic analyses revealed the cell/scaffold interactive mechanisms by which the NanoCliP-FD gel scaffold stimulated such increased efficiency in cartilage matrix formation. In addition to demonstrating the high potential of human periodontal ligament-derived stem cell cultures on NanoCliP-FD gel scaffolds in regenerative cartilage therapy, the present study also highlights the novelty of Raman spectroscopy as a non-destructive method for the concurrent evaluation of matrix quality and cell metabolic response. In situ Raman analyses on living cells unveiled for the first time the underlying physiological mechanisms behind such improved chondrocyte performance.

Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics.

Raman spectroscopy uncovered molecular scale markers of the viral structure of the SARS-CoV-2 Delta variant and related viral inactivation mechanisms at the biological interface with silicon nitride (Si3N4) bioceramics. A comparison of Raman spectra collected on the TY11-927 variant (lineage B.1.617.2; simply referred to as the Delta variant henceforth) with those of the JPN/TY/WK-521 variant (lineage B.1.617.1; referred to as the Kappa variant or simply as the Japanese isolate henceforth) revealed the occurrence of key mutations of the spike receptor together with profound structural differences in the molecular structure/symmetry of sulfur-containing amino acid and altered hydrophobic interactions of the tyrosine residue. Additionally, different vibrational fractions of RNA purines and pyrimidines and dissimilar protein secondary structures were also recorded. Despite mutations, hydrolytic reactions at the surface of silicon nitride (Si3N4) bioceramics induced instantaneous inactivation of the Delta variant at the same rate as that of the Kappa variant. Contact between virions and micrometric Si3N4 particles yielded post-translational deimination of arginine spike residues, methionine sulfoxidation, tyrosine nitration, and oxidation of RNA purines to form formamidopyrimidines. Si3N4 bioceramics proved to be a safe and effective inorganic compound for instantaneous environmental sanitation.

A Polarized Raman Spectroscopic Method for Advanced Analyses of the Osteon Lamellar Structure of Human Bone.

Raman spectroscopy has recently been used for quantitative analyses of cortical bone tissue and related materials, such as dentin and enamel. While those analyses have proven useful as potential diagnostic tools, the Raman spectrum of bone encrypts a wealth of additional molecular scale details about structure and crystal arrangement, which are yet to be unfolded. Such details directly link to both bone physiology and pathology. In this work, a triple monochromator spectrometer with high spectral resolution, employed in polarized light configurations, was used to extract quantitative details about the preferential crystallographic orientation of apatite and collagen components in a human proximal femoral cortical bone sample. This body of information was then used to model the bone structure at the nanometric scale through a methodology that could be key in assessments of bone structure in health and disease.

Raman Study of Pathogenic Candida auris: Imaging Metabolic Machineries in Reaction to Antifungal Drugs.

The multidrug-resistant Candida auris often defies treatments and presently represents a worldwide public health threat. Currently, the ergosterol-targeting Amphotericin B (AmB) and the DNA/RNA-synthesis inhibitor 5-flucytosine (5-FC) are the two main drugs available for first-line defense against life-threatening Candida auris infections. However, important aspects of their mechanisms of action require further clarification, especially regarding metabolic reactions of yeast cells. Here, we applied Raman spectroscopy empowered with specifically tailored machine-learning algorithms to monitor and to image in situ the susceptibility of two Candida auris clades to different antifungal drugs (LSEM 0643 or JCM15448T, belonging to the East Asian Clade II; and, LSEM 3673 belonging to the South African Clade III). Raman characterizations provided new details on the mechanisms of action against Candida auris Clades II and III, while also unfolding differences in their metabolic reactions to different drugs. AmB treatment induced biofilm formation in both clades, but the formed biofilms showed different structures: a dense and continuous biofilm structure in Clade II, and an extra-cellular matrix with a "fluffy" and discontinuous structure in Clade III. Treatment with 5-FC caused no biofilm formation but yeast-to-hyphal or pseudo-hyphal morphogenesis in both clades. Clade III showed a superior capacity in reducing membrane permeability to the drug through chemically tailoring chitin structure with a high degree of acetylation and fatty acids networks with significantly elongated chains. This study shows the suitability of the in situ Raman method in characterizing susceptibility and stress response of different C. auris clades to antifungal drugs, thus opening a path to identifying novel clinical solutions counteracting the spread of these alarming pathogens.

Cytotoxicity and osteogenic effects of aluminum ions.

In this study, we monitored the effect of Al3+ ions on mesenchymal cells (KUSA-A1) and human fibroblasts (NHDF) by means of in vitro experiments by culturing the cells with addition of small concentrations of aluminum ions (i.e., 0.1, 1, 10, and 100 ppm). Bone formation test was then conducted using KUSA-A1. Small concentrations of aluminum ions delayed but did not completely inhibit cell proliferation. The amount of bone tissue decreased as the concentration of Al3+ increased and crystallinity changes were also detected by Raman spectroscopic experiments. Moreover, Al3+ ions greatly affected both structure and chemistry of bone tissues with mineral nodules becoming larger and atomic substitution of Ca with Al in bone tissue being more preponderant with increasing Al3+ concentration. Such effects in turn impaired the balance between mineral and collagen in the formed bone tissue.

Innovative electrospun PCL/fibroin/l-dopa scaffolds scaffolds supporting bone tissue regeneration.

Poly-caprolactone is one of the most promising biocompatible polymers on the market, in particular for temporary devices that are not subjected to high physiological loads. Even if completely resorbable in various biological environments, poly-caprolactione does not play any specific biological role in supporting tissue regeneration and for this reason has a limited range of possible applications. In this preliminary work, for the first time l-dopa and fibroin have been combined with electrospun poly-caprolactone fibers in order to induce bioactive effects and, in particular, stimulate the proliferation, adhesion and osteoconduction of the polymeric fibers. Results showed that addition of low-molecular weight fibroin reduces the mechanical strength of the fibers while promoting the formation of mineralized deposits, when testedin vitrowith KUSA-A1 mesenchymal cells. l-dopa, on the other hand, improved the mechanical properties and stimulated the formation of agglomerates of mineralized deposits containing calcium and phosphorous with high specific volume. The combination of the two substances resulted in good mechanical properties and higher amounts of mineralized deposits formedin vitro.

Raman Spectroscopy of Oral Candida Species: Molecular-Scale Analyses, Chemometrics, and Barcode Identification.

Oral candidiasis, a common opportunistic infection of the oral cavity, is mainly caused by the following four Candida species (in decreasing incidence rate): Candida albicans, Candida glabrata, Candida tropicalis, and Candida krusei. This study offers in-depth Raman spectroscopy analyses of these species and proposes procedures for an accurate and rapid identification of oral yeast species. We first obtained average spectra for different Candida species and systematically analyzed them in order to decode structural differences among species at the molecular scale. Then, we searched for a statistical validation through a chemometric method based on principal component analysis (PCA). This method was found only partially capable to mechanistically distinguish among Candida species. We thus proposed a new Raman barcoding approach based on an algorithm that converts spectrally deconvoluted Raman sub-bands into barcodes. Barcode-assisted Raman analyses could enable on-site identification in nearly real-time, thus implementing preventive oral control, enabling prompt selection of the most effective drug, and increasing the probability to interrupt disease transmission.