Raman spectroscopy in cell biology and microbiology

Pezzotti, Giuseppe

doi:10.1002/jrs.6204

Cited by 111 publications

(101 citation statements)

References 453 publications

(699 reference statements)

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“…The spectroscopic characteristics obtained on average spectra for both clades/treatments were then subjected to confirmation by means of further characterizations based on Raman mapping and imaging, according to protocols described in previous works (Pezzotti, 2021 ; Pezzotti et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Resultsmentioning

confidence: 99%

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

et al. 2022

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“…This study is in line with our previous studies of variants of Influenza virus. [ 39 ] The Raman characteristics yield molecular‐scale information uniquely discriminating among different variants. Facilitating real‐time data access and exchange is an essential step in tracking variants and in estimating their spread and evolutionary mutation rate.…”

Section: Discussionmentioning

confidence: 99%

Raman Molecular Fingerprints of SARS‐CoV‐2 British Variant and the Concept of Raman Barcode

et al. 2021

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The multiple mutations of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus have created variants with structural differences in both their spike and nucleocapsid proteins. While the functional relevance of these mutations is under continuous scrutiny, current findings have documented their detrimental impact in terms of affinity with host receptors, antibody resistance, and diagnostic sensitivity. Raman spectra collected on two British variant sub‐types found in Japan (QK002 and QHN001) are compared with that of the original Japanese isolate (JPN/TY/WK‐521), and found bold vibrational differences. These included: i) fractions of sulfur‐containing amino acid rotamers, ii) hydrophobic interactions of tyrosine phenol ring, iii) apparent fractions of RNA purines and pyrimidines, and iv) protein secondary structures. Building upon molecular scale results and their statistical validations, the authors propose to represent virus variants with a barcode specially tailored on Raman spectrum. Raman spectroscopy enables fast identification of virus variants, while the Raman barcode facilitates electronic recordkeeping and translates molecular characteristics into information rapidly accessible by users.

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“…The computational work produced two important outcomes: (a) spectra could be screened automatically and an appropriate deconvolution could be suggested through finding the closest match with the experimentally collected spectrum through eq 1 , while additionally identifying the molecules/compounds primarily contributing to each sub-band, and (b) sub-bands having primarily single-reference-molecule sourced signal intensity (>90%) could be isolated. A number of reference spectra from basic molecules used in the above-described machine learning algorithm could be found in ref ( 112 ).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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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 (Si 3 N 4 ) 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 (Si 3 N 4 ) bioceramics induced instantaneous inactivation of the Delta variant at the same rate as that of the Kappa variant. Contact between virions and micrometric Si 3 N 4 particles yielded post-translational deimination of arginine spike residues, methionine sulfoxidation, tyrosine nitration, and oxidation of RNA purines to form formamidopyrimidines. Si 3 N 4 bioceramics proved to be a safe and effective inorganic compound for instantaneous environmental sanitation.

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Raman spectroscopy in cell biology and microbiology

Cited by 111 publications

References 453 publications

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

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

Raman Molecular Fingerprints of SARS‐CoV‐2 British Variant and the Concept of Raman Barcode

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

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