Antimicrobial Resistance Studies Using Raman Spectroscopy on Clinically Relevant Bacterial Strains

There has been a steep rise in the emergence of antibiotic-resistant bacteria in the past few years. A timely diagnosis can help in initiating appropriate antibiotic therapy. However, conventional techniques for diagnosing antibiotic resistance are time-consuming and labor-intensive. Therefore, we investigated the potential of Raman spectroscopy as a rapid surveillance technology for tracking the emergence of antibiotic resistance. In this study, we used Raman spectroscopy to differentiate clinical isolates of antibiotic-resistant and -sensitive bacteria of Escherichia coli, Acinetobacter baumannii, and Enterobacter species. The spectra were collected with or without exposure to various antibiotics (ciprofloxacin, gentamicin, meropenem, and nitrofurantoin), each having a distinct mechanism of action. Ciprofloxacin- and meropenem-treated sensitive strains showed a decrease in the intensity of Raman bands associated with DNA (667, 724, 785, 1378, 1480, and 1575 cm^-1) and proteins (640 and 1662 cm^-1), coupled with an increase in the intensity of lipid bands (891, 960, and 1445 cm^-1). Gentamicin- and nitrofurantoin-treated sensitive strains showed an increase in the intensity of nucleic acid bands (668, 724, 780, 810, 1378, 1480, and 1575 cm^-1) while a decrease in the intensity of protein bands (640, 1003, 1606, and 1662 cm^-1) and the lipid band (1445 cm^-1). The Raman spectral changes observed in the antibiotic-resistant strains were opposite to that of antibiotic-sensitive strains. The Raman spectral data correlated well with the antimicrobial susceptibility test results. The Raman spectral dataset was used for partial least-squares (PLS) analysis to validate the biomarkers obtained from the univariate analysis. Overall, this study showcases the potential of Raman spectroscopy for detecting antibiotic-resistant and -sensitive bacteria.

Raman spectroscopy study of CdS nanorods and strain induced by the adsorption of 4-mercaptobenzoic acid

In this study, near- and off-resonance Raman spectra of cadmium sulfide (CdS) quantum rods (NRs) and 4-mercaptobenzoic acid (4-MBA) adsorbed CdS NRs are reported. The envelopes of characteristic optical phonon modes in the near-resonance Raman spectrum of CdS NRs are deconvoluted by following the phonon confinement model. As compared with off-resonant Raman spectra, optical phonon modes scattering cross section is amplified significantly in near-resonance Raman spectra through the Fröhlich interaction. The Huang–Rhys factor defining the strength of the Fröhlich interaction is estimated (∼0.468). Moreover, the adsorption of different concentrations of 4-mercaptobenzoic acid (4-MBA) onto CdS NRs produces surface strain in CdS NRs originating due to surface reconstruction and consequently blue and red shifts in off-resonance (514.5 nm) Raman spectra depending on the concentration of 4-MBA. These consequences are attributed to compressive and tensile strains, respectively. Relative to bulk CdS powder as the reference, strain in CdS NRs increases with decreasing 4-MBA concentrations. In off-resonance Raman spectra of 4-MBA adsorbed CdS NRs, the full width at half maxima of phonon modes (1-LO and 2-LO) and intensity ratio I2-LO/I1-LO increase with decreasing 4-MBA concentration.

Herbicides 2,4-Dichlorophenoxy Acetic Acid and Glyphosate Induce Distinct Biochemical Changes in E. coli during Phenotypic Antibiotic Resistance: A Raman Spectroscopic Study

Antibiotic resistance is a major global health concern. The increased use of herbicides may lead to multiple antibiotic resistance in bacteria. Conventional techniques for diagnosing antibiotic resistance are laborious, time-intensive, expensive, and lack information about antibiotic susceptibility. On the other hand, Raman spectroscopy is a rapid, label-free, noninvasive alternative to traditional techniques to detect antibiotic resistance. In this study, two popular herbicides 2,4-dichlorophenoxy acetic acid (2,4-D) and N-(phosphonomethyl)glycine (glyphosate) were used to study their effects on the emergence of antibiotic resistance. The Escherichia coli wild-type (WT) MG1655 strain and two isogenic mutants, Δlon and ΔacrB, were used together with Raman spectroscopy. The WT E. coli is sensitive to antibiotics, but exposure to both herbicides induces antibiotic resistance. Using an excitation wavelength of 785 nm, the intensity ratios (e.g., I₇₄₀/I₇₈₅, I₇₄₀/I₁₀₀₃, I₁₄₈₀/I₁₄₄₅, I₂₉₃₄/I₂₈₆₈, and I₂₉₃₄/I₂₈₄₅) were identified as biomarkers to study the induction of antibiotic resistance in bacteria but not NaCl-mediated stress. Using an excitation wavelength of 633 nm, the peak intensity at 740 cm^-1 assigned to cytochrome bd decreases under antibiotic stress but increases upon exposure to both herbicides and antibiotics, indicating the development of resistance. Thus, this study can be applied to monitor antibiotic resistance using Raman spectroscopy.

Culture-Independent Raman Spectroscopic Identification of Bacterial Pathogens from Clinical Samples Using Deep Transfer Learning

The rapid identification of bacterial pathogens in clinical samples like blood, urine, pus, and sputum is the need of the hour. Conventional bacterial identification methods like culturing and nucleic acid-based amplification have limitations like poor sensitivity, high cost, slow turnaround time, etc. Raman spectroscopy, a label-free and noninvasive technique, has overcome these drawbacks by providing rapid biochemical signatures from a single bacterium. Raman spectroscopy combined with chemometric methods has been used effectively to identify pathogens. However, a robust approach is needed to utilize Raman features for accurate classification while dealing with complex data sets such as spectra obtained from clinical isolates, showing high sample-to-sample heterogeneity. In this study, we have used Raman spectroscopy-based identification of pathogens from clinical isolates using a deep transfer learning approach at the single-cell level resolution. We have used the data-augmentation method to increase the volume of spectra needed for deep-learning analysis. Our ResNet model could specifically extract the spectral features of eight different pathogenic bacterial species with a 99.99% classification accuracy. The robustness of our model was validated on a set of blinded data sets, a mix of cultured and noncultured bacterial isolates of various origins and types. Our proposed ResNet model efficiently identified the pathogens from the blinded data set with high accuracy, providing a robust and rapid bacterial identification platform for clinical microbiology.

Potential of Raman spectroscopic techniques to study proteins

Proteins are large, complex molecules responsible for various biological processes. However, protein misfolding may lead to various life-threatening diseases. Therefore, it is vital to understand the shape and structure of proteins. Despite numerous techniques, a mechanistic understanding of the protein folding process is still unclear. Therefore, new techniques are continually being explored. In the present article, we have discussed the importance of Raman spectroscopy, Raman Optical Activity (ROA) and various other advancements in Raman spectroscopy to understand protein structure and conformational changes based on the review of our earlier work and recent literature. A Raman spectrum of a protein provides unique signatures for various secondary structures like helices, beta-sheets, turns, random structures, etc., and various amino acid residues such as tyrosine, tryptophan, and phenylalanine. We have shown how Raman spectra can differentiate between bovine serum albumin (BSA) and lysozyme protein based on their difference in sequence and structure (primary, secondary and tertiary). Although it is challenging to elucidate the structure of a protein using a Raman spectrum alone, Raman spectra can be used to differentiate small changes in conformations of proteins such as BSA during melting. Various new advancements in technique and data analyses in Raman spectroscopic studies of proteins have been discussed. The last part of the review focuses on the importance of the ROA spectrum to understand additional features about proteins. The ROA spectrum is rich in information about the protein backbone due to its rigidity compared to its side chains. Furthermore, the ROA spectra of lysozyme and BSA have been presented to show how ROA provides extra information about the solvent properties of proteins.

Cell-free hemoglobin is a marker of systemic inflammation in mouse models of sepsis: a Raman spectroscopic study

Sepsis is a life-threatening condition caused by heightened host immune responses post infection. Despite intensive research, most of the existing diagnostic methods remain non-specific, labour-intensive, time-consuming or are not sensitive enough for rapid and timely diagnosis of the onset and progression of sepsis. The present work was undertaken to explore the potential of Raman spectroscopy to identify the biomarkers of sepsis in a label-free and minimally invasive manner using different mouse models of inflammation. The sera of BALB/c mice infected with Salmonella Typhimurium reveal extensive hemolysis, as indicated by the Raman bands that are characteristic of the porphyrin ring of hemoglobin (668, 743, 1050, 1253 and 1397 cm-1) which increase in a kinetic manner. These markers are also observed in a lipopolysaccharide-induced endotoxic shock model, but not in a thioglycollate-induced sterile peritonitis model. These data demonstrate that hemolysis is a signature of systemic, but not localised, inflammation. To further validate our observations, sepsis was induced in the nitric oxide synthase 2 (Nos2-/-) deficient strain which is more sensitive to infection. Interestingly, Nos2-/- mice exhibit a higher degree of hemolysis than C57BL/6 mice. Sepsis-induced hemolysis was also confirmed using resonance Raman spectroscopy with 442 nm excitation which demonstrated a pronounced increase in the resonant Raman bands at 670 and 1350 cm-1 in sera of the infected mice. This is the first study to identify inflammation-induced hemolysis in mouse models of sepsis using Raman spectral signatures for hemoglobin. The possible implications of this method in detecting hemolysis in different inflammatory pathologies, such as the ongoing COVID-19 pandemic, are discussed.

Understanding phase transition and vibrational mode coupling in ammonium nitrate using 2D correlation Raman spectroscopy

Ammonium nitrate (AN) is an important component of the chemical industry such as an active ingredient in fertilizers, as an oxidizer in explosive compositions and propellants, and as a blasting agent in civil explosives. Numerous accidents have been reported in the past which concerns its thermal instability and poses a big threat to its processing, transportation, and storage. Despite much literature being reported to understand its thermal instability, a mechanistic view remains unclear. In the present work, we have studied the behavior of AN to temperature change using a mathematical approach called 2D correlation (2D Cos) Raman spectroscopy to provide complete insight into the detailed dynamical nature of the interactions between the species (ionic or molecular) occurring with an increase in temperature. We have analyzed various libration and translational modes of nitrate in the low-frequency region using this mathematical tool. It is observed from 2D maps that the phase transition of AN starts with changes in libration modes followed by various nitrate modes and ammonium modes which further precedes low-frequency translational modes. Further, the 2D correlation could differentiate between modes splitting and shifting based on specific 2D Cos pattern. The changes occurring in the N-O deformation modes, symmetric stretching modes as well as anti-symmetric stretching modes which have been attributed to the weakening of the hetero-ionic coupling between the NH₄⁺ and the NO₃^- ions could be clearly distinguished in the 2D synchronous and asynchronous plots. Besides, moving window analysis was performed to visualize the transition temperature at which phase change of AN takes place.

Infrared Microspectroscopy With Multivariate Analysis to Differentiate Oral Hyperplasia From Squamous Cell Carcinoma: A Proof of Concept for Early Diagnosis

BACKGROUND AND OBJECTIVES

Despite having numerous advances in therapeutics, mortality and morbidity due to oral cancer incidence are still very high. Early detection can improve the chances of survival in most patients. However, diagnosis at early stages can be challenging as premalignant conditions are usually asymptomatic. Currently, histological assessment remains the gold standard for diagnosis. Early diagnosis poses challenges to pathologists due to less severe morphological changes associated with early stages. Therefore, a fast and robust method of detection based on molecular changes is needed for early diagnosis. © 2021 Wiley Periodicals LLC.

STUDY DESIGN/MATERIAL AND METHODS

In the present study, Fourier transform infrared (FTIR) spectroscopic imaging has been used to differentiate early-stage oral hyperplasia from adjacent normal (AN) and oral squamous cell carcinoma (OSCC). Hyperplasia is often considered as an initial event in the pathogenesis of oral cancer and OSCC is the most common advanced stage of malignancy. Differentiating normal versus hyperplasia and hyperplasia versus OSCC can remain quite challenging on occasion using conventional staining as the histological assessment is based on morphological changes.

RESULTS

Unsupervised hierarchical cluster analysis (UHCA) has been performed on FTIR images of multiple tissues together that provided some degree of classification among tissue groups. The AN epithelium clustered distinctively using UHCA from both hyperplasia and grades 1 and 2 of OSCC. An increase in the content of DNA, denaturation of protein, and altered lipid structures were more clearly elucidated with spectral analysis.

CONCLUSION

This study demonstrates a simple strategy to differentiate early-stage oral hyperplasia from AN and OSCC using UHCA. This study also proposes a future alternative method where FTIR imaging can be used as a diagnostic tool for cancer at early stages.

Profiling antibiotic resistance in Escherichia coli strains displaying differential antibiotic susceptibilities using Raman spectroscopy

The rapid identification of antibiotic resistant bacteria is important for public health. In the environment, bacteria are exposed to sub-inhibitory antibiotic concentrations which has implications in the generation of multi-drug resistant strains. To better understand these issues, Raman spectroscopy was employed coupled with partial least squares-discriminant analysis to profile Escherichia coli strains treated with sub-inhibitory concentrations of antibiotics. Clear differences were observed between cells treated with bacteriostatic (tetracycline and rifampicin) and bactericidal (ampicillin, ciprofloxacin, and ceftriaxone) antibiotics for 6 hr: First, atomic force microscopy revealed that bactericidal antibiotics cause extensive cell elongation whereas short filaments are observed with bacteriostatic antibiotics. Second, Raman spectral analysis revealed that bactericidal antibiotics lower nucleic acid to protein (I₈₁₂ /I₈₃₀ ) and nucleic acid to lipid ratios (I₁₄₈₃ /I₁₄₅₂ ) whereas the opposite is seen with bacteriostatic antibiotics. Third, the protein to lipid ratio (I₂₉₃₆ /I₂₈₈₅ and I₂₉₃₆ /I₂₈₅₀ ) is a Raman stress signature common to both the classes. These signatures were validated using two mutants, Δlon and ΔacrB, that exhibit relatively high and low resistance towards antibiotics, respectively. In addition, these spectral markers correlated with the emergence of phenotypic antibiotic resistance. Overall, this study demonstrates the efficacy of Raman spectroscopy to identify resistance in bacteria to sub-lethal concentrations of antibiotics.

Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns

Mycobacterium chelonae is an environmental, non-tuberculous mycobacterial species, capable of causing infections in humans. Biofilm formation is a key strategy used by M. chelonae in colonising niches in the environment and in the host. We studied a water-air interface (pellicle) biofilm of M. chelonae using a wide array of approaches to outline the molecular structure and composition of the biofilm. Scanning electron micrographs showed that M. chelonae biofilms produced an extracellular matrix. Using a combination of biochemical analysis, Raman spectroscopy, and fluorescence microscopy, we showed the matrix to consist of proteins, carbohydrates, lipids and eDNA. Glucose was the predominant sugar present in the biofilm matrix, and its relative abundance decreased in late (established) biofilms. RNA-seq analysis of the biofilms showed upregulation of genes involved in redox metabolism. Additionally, genes involved in mycolic acid, other lipid and glyoxylate metabolism were also upregulated in the early biofilms.

Absent 'superimposed-line' sign: novel marker in early diagnosis of cleft of fetal secondary palate

OBJECTIVES

To describe a novel sign, the 'superimposed-line' sign, for early diagnosis of cleft of the fetal secondary palate on two-dimensional imaging of the vomeromaxillary junction in the midsagittal view.

METHODS

This was a prospective evaluation of the superimposed-line sign using two-dimensional sonography (midsagittal view) in 9576 singleton fetuses referred for routine screening between 12 and 20 weeks of gestation. In this view, the vomer bone appears as a line superimposed on the distal two-thirds of the maxillary line, as the vomer fuses with the secondary palate in the midline. If there is a midline cleft of the secondary palate, the line formed by the palate is absent and hence only the vomer bone is visualized, creating a single line instead of the normal superimposed double line. Multiplanar three-dimensional (3D) views were assessed in cases in which the superimposed-line sign was absent.

RESULTS

The superimposed line was absent in 17 fetuses with a cleft of the secondary palate that was confirmed by 3D evaluation. Of these, 13 had defects involving the premaxilla and four had an isolated cleft of the secondary palate. Postnatal confirmation was available in all cases. The sign was useful in ruling out cleft of the fetal secondary palate in 32 high-risk cases with a family history of cleft palate. The superimposed-line sign had a sensitivity of 89.5% in detecting cleft of the secondary palate.

CONCLUSIONS

The superimposed-line sign is a new sonographic marker for evaluation of cleft of the fetal secondary palate; documentation of this sign proves the presence of both the palate and vomer in the midline. This marker can be demonstrated clearly in the late first trimester, allowing early diagnosis of secondary palatine cleft. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Identification of a resonance Raman marker for cytochrome to monitor stress responses in Escherichia coli

Raman spectroscopy and resonance Raman spectroscopy are widely used to study bacteria and their responses to different environmental conditions. In the present study, the identification of a novel resonance Raman peak for Escherichia coli, recorded with 633 nm laser excitation is discussed. A peak at 740 cm^-1 is observed exclusively with 633 nm excitation but not with 514 nm or 785 nm excitation. This peak is absent in the lag phase but appears in the log phase of bacterial growth. The intensity of the peak increases at high temperature (45 °C) compared with growth at low temperature (25 °C) or the physiological temperature (37 °C). Although osmotic stress lowered bacterial growth, the intensity of this peak was unaffected. However, treatment with chemical uncouplers of oxidative phosphorylation resulted in significantly lower intensity of this Raman band, indicating its possible involvement in respiration. Cytochromes, a component of bacterial respiration' can show resonance enhancement at 633 nm due to the presence of a shoulder in that region depending on the type and conformation of cytochrome. Therefore, the peak intensity was monitored in different genetic mutants of E. coli lacking cytochromes. This peak is absent in the Escherichia coli mutant lacking cydB, but not ccmE, demonstrating the contribution of cytochrome bd subunit II in the peak's origin. In future, this newly found cytochrome marker can be used for biochemical assessment of bacteria exposed to various conditions. Overall, this finding opens the scope for use of red laser excitation in resonance Raman in monitoring stress and respiration in bacteria. Graphical abstract.

Design of P-Doped Mesoporous Carbon Nitrides as High-Performance Anode Materials for Li-Ion Battery

Herein, we demonstrate a simple and unique strategy for the preparation of P-doped into the substructure of mesoporous carbon nitride materials (P-MCN-1) with ordered porous structures as a high-energy and high-power Li-ion battery (LIB) anode. The P-MCN-1 as an anode in LIB delivers a high reversible discharge capacity of 963 mAh g^-1 even after 1000 cycles at a current density of 1 A g^-1, which is much higher than that of other counterparts comprising s-triazine (C₃H₃N₃, g-C₃N₄), pristine MCN-1, and B-containing MCN-1 (B-MCN-1) subunits or carbon allotropes like CNT and graphene (rGO) materials. The P-MCN-1 electrode also exhibits exceptional rate capability even at high current densities of 5, 10, and 20 A g^-1 delivering 685, 539, and 274 mAh g^-1, respectively, after 2500 cycles. The high electrical conductivity and Li-ion diffusivity (D), estimated from electrochemical impedance spectra (EIS), very well support the extraordinary electrochemical performance of the P-MCN-1. Higher formation energy, lower bandgap value, and high Li-ion adsorption ability predicted by first principle calculations of P-MCN-1 are in good agreement with experimentally observed high lithium storage, stable cycle life, high power capability, and minimal irreversible capacity (IRC) loss. To the best of our knowledge, it is an entirely new material with the combination of ordered mesostructures with P codoping in carbon nitride substructure which offers superior performance for LIB, and hence we believe that this work will create new momentum for the design and development of clean energy storage devices.

Thermodynamically Stable Mesoporous C3 N7 and C3 N6 with Ordered Structure and Their Excellent Performance for Oxygen Reduction Reaction

Carbon nitrides with a high N/C atomic ratio (>2) are expected to offer superior basicity and unique electronic properties. However, the synthesis of these nanostructures is highly challenging since many parts of the CN frameworks in the carbon nitride should be replaced with thermodynamically less stable NN frameworks as the nitrogen content increases. Thermodynamically stable C₃ N₇ and C₃ N₆ with an ordered mesoporous structure are synthesized at 250 and 300 °C respectively via a pyrolysis process of 5-amino-1H-tetrazole (5-ATTZ). Polymerization of the precursor to the ordered mesoporous C₃ N₇ and C₃ N₆ is clearly proved by X-ray and electron diffraction analyses. A combined analysis including diverse spectroscopy and FDMNES and density functional theory (DFT) calculations demonstrates that the NN bonds are stabilized in the form of tetrazine and/or triazole moieties in the C₃ N₇ and C₃ N₆ . The ordered mesoporous C₃ N₇ represents the better oxygen reduction reaction (ORR) performances (onset potential: 0.81 V vs reversible hydrogen electrode (RHE), electron transfer number: 3.9 at 0.5 V vs RHE) than graphitic carbon nitride (g-C₃ N₄ ) and the ordered mesoporous C₃ N₆ . The study on the mechanism of ORR suggests that nitrogen atoms in the tetrazine moiety of the ordered mesoporous C₃ N₇ act as active sites for its improved ORR activity.

Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy

Infectious diseases caused by bacteria still pose major diagnostic challenges in spite of the availability of various molecular approaches. Irrespective of the type of infection, rapid identification of the causative pathogen with a high degree of sensitivity and specificity is essential for initiating appropriate treatment. While existing methods like PCR possess high sensitivity, they are incapable of identifying the viability status of the pathogen and those which can, like culturing, are inherently slow. To overcome these limitations, we developed a diagnostic platform based on Raman microspectroscopy, capable of detecting biochemical signatures from a single bacterium for identification as well as viability assessment. The study also establishes a decontamination protocol for handling live pathogenic bacteria which does not affect identification and viability testing, showing applicability in the analysis of sputum samples containing pathogenic mycobacterial strains. The minimal sample processing along with multivariate analysis of spectroscopic signatures provides an interface for automatic classification, allowing the prediction of unknown samples by mapping signatures onto available datasets. Also, the novelty of the current work is the demonstration of simultaneous identification and viability assessment at a single bacterial level for pathogenic bacteria. Graphical abstract.

Pathogenic Escherichia coli (E. coli) detection through tuned nanoparticles enhancement study

OBJECTIVE

This study aims to detect pathogenic Escherichia coli (E. coli) bacteria using non-destructive fluorescence microscopy and micro-Raman spectroscopy.

RESULTS

Raman vibrational spectroscopy provides additional information regarding biochemical changes at the cellular level. We have used two nanomaterials zinc oxide nanoparticles (ZnO-NPs) and gold nanoparticles (Au-NPs) to detect pathogenic E. coli. The scanning electron microscope (SEM) with energy dispersive X-ray (EDAX) spectroscopy exhibit surface morphology and the elemental composition of the synthesized NPs. The metal NPs are useful contrast agents due to the surface plasmon resonance (SPR) to detect the signal intensity and hence the bacterial cells. The changes due to the interaction between cells and NPs are further correlated to the change in the surface charge and stiffness of the cell surface with the help of the fluorescence microscopic assay.

CONCLUSIONS

We conclude that when two E. coli strains (MTCC723 and MTCC443) and NPs are respectively mixed and kept overnight, the growth of bacteria are inhibited by ZnO-NPs due to changes in cell membrane permeability and intracellular metabolic system under fluorescence microscopy. However, SPR possessed Au-NPs result in enhanced fluorescence of both pathogens. In addition, with the help of Raman microscopy and element analysis, significant changes are observed when Au-NPs are added with the two strains as compared to ZnO-NPs due to protein, lipid and DNA/RNA induced conformational changes.

Understanding the effects of culture conditions in bacterial growth: A biochemical perspective using Raman microscopy

Rapid, sensitive and label-free methods to probe bacterial growth irrespective of the culture conditions can shed light on the mechanisms by which bacteria adapt to different environmental stimuli. Raman spectroscopy can rapidly and continuously monitor the growth of bacteria under varied conditions. In this study, the growth of Escherichia coli in Luria broth (nutrient rich conditions) and minimal media with either glucose or glycerol as carbon source (nutrient limiting conditions) is profiled using Raman spectroscopy. Moreover, the study also gives insights into the altered bacterial biochemistry upon exposure to low- (25°C) and high-temperature (45°C) stress. Raman spectral measurement was performed on bulk bacteria cultured under laboratory conditions. A detailed analysis of the spectra as a function of bacterial growth reveals changes in Raman band intensities/area of biomolecules such as DNA, proteins and lipids. We also report five novel ratiometric markers (I₈₃₀ /I₈₁₀ , I₁₁₂₆ /I₁₁₀₀ , I₁₃₄₀ /I₁₄₄₀ , I₁₂₀₇ /I₁₂₄₀ and I₁₅₈₀ /I₁₄₄₀ ) that can identify the phase of growth, independent of the culture condition. Unsupervised multivariate methods like Principal Component Analysis also corroborate the aforementioned markers of growth. Altogether, our findings highlight the potential of Raman spectroscopy in yielding universal biochemical signatures that may be indicative of stress and aging in a growth milieu.

Raman spectroscopy reveals distinct differences between two closely related bacterial strains, Mycobacterium indicus pranii and Mycobacterium intracellulare

A common technique used to differentiate bacterial species and to determine evolutionary relationships is sequencing their 16S ribosomal RNA genes. However, this method fails when organisms exhibit high similarity in these sequences. Two such strains that have identical 16S rRNA sequences are Mycobacterium indicus pranii (MIP) and Mycobacterium intracellulare. MIP is of significance as it is used as an adjuvant for protection against tuberculosis and leprosy; in addition, it shows potent anti-cancer activity. On the other hand, M. intracellulare is an opportunistic pathogen and causes severe respiratory infections in AIDS patients. It is important to differentiate these two bacterial species as they co-exist in immuno-compromised individuals. To unambiguously distinguish these two closely related bacterial strains, we employed Raman and resonance Raman spectroscopy in conjunction with multivariate statistical tools. Phenotypic profiling for these bacterial species was performed in a kinetic manner. Differences were observed in the mycolic acid profile and carotenoid pigments to show that MIP is biochemically distinct from M. intracellulare. Resonance Raman studies confirmed that carotenoids were produced by both MIP as well as M. intracellulare, though the latter produced higher amounts. Overall, this study demonstrates the potential of Raman spectroscopy in differentiating two closely related mycobacterial strains. Graphical abstract.

Spectroscopic and computational insights into the ion-solvent interactions in hydrated aprotic and protic ionic liquids

Ionic liquids (ILs) and their aqueous solutions are emerging media for solving and manipulating biochemical molecules such as proteins. Unleashing the full potential however requires a detailed mechanistic understanding of how suitable protic and aprotic ILs behave in the presence of water in the first place. The present work aims at making an important step by performing a combined experimental and computational study of two selected ILs and their mixtures with water: the aprotic cholinium propionate ([Chl][Pro]) and the protic N-methyl-2-pyrrolidonium propionate ([NMP][Pro]). IR and Raman spectroscopy reveal stronger ion-solvent interactions in [Chl][Pro]-H₂O systems compared to [NMP][Pro]-H₂O mixtures. This can be explained by the tightly packed ion-pair associations in [NMP][Pro] comprising the protic -N⁺-H counterpart, which allows the establishment of highly directional and strong interionic hydrogen bonds. The spectral decomposition of the O-D stretching band into three sub-peaks showed that the protic [NMP][Pro] favors the self-association of water molecules. On the other hand, the predominant fraction of water-anion/cation aggregates exists in aprotic [Chl][Pro]. These hydrated systems can be envisaged using quantum-chemical calculations in the following way: H₂O[Chl]⁺H₂O[Pro]^-H₂O and H₂O[NMP]⁺[Pro]^-H₂O, which implied preferable solvent-shared ion-pair (SIP) configurations for [Chl][Pro]-H₂O systems, whereas the contact ion-pair (CIP) state prevails for the [NMP][Pro]-H₂O systems. The latter holds even in the water-rich regime. In future work, these findings will be the basis for an understanding of the underlying principles that govern the interactions of ions with bio-molecules in aqueous solutions.

Sulfur-Doped Mesoporous Carbon Nitride with an Ordered Porous Structure for Sodium-Ion Batteries

Mesoporous carbon nitride (MCN) with well-ordered porous structures is a promising anode material for secondary ion batteries owing to their unique physico- and electrochemical properties. However, the practical application of these MCNs in sodium-ion batteries (SIBs) is still limited because of their confined interlayer distance, which results in restricted accommodation of Na ions inside the lattice. Here, we report on the synthesis of highly ordered sulfur-doped MCN (S-MCN) through a hard template approach by employing dithiooxamide (DTO) as a single molecular precursor containing carbon, nitrogen, and sulfur elements. The interlayer distance of carbon nitride is significantly expanded upon the introduction of larger S ions on the MCN lattice, which enables high capability of Na ion accommodation. We also demonstrate through the first-principles density functional theory calculation that the present S-MCN is highly optimized not only for the chemical structure but also for uptaking abundant Na ions with high adsorption energy. The specific discharge capacity of SIBs appears to be remarkably enhanced for S-MCN (304.2 mA h g^-1) compared to the nonporous S-CN (167.9 mA h g^-1) and g-C₃N₄ (5.4 mA h g^-1), highlighting the pivotal roles of the highly ordered mesoporous structure and S-doping in enhancing the electrochemical functionality of carbon nitride as an anode material for SIBs.

Impact of cesium in methylammonium lead bromide perovskites: insights into the microstructures, stability and photophysical properties

The thermal and moisture instabilities of pure organic lead halide perovskites are the foremost concerns towards the commercialization of perovskite solar cells, which can be avoided by introducing an inorganic cation, such as cesium ion (Cs+) at the A-site of the perovskite crystals. In this report, the impacts of substituted Cs+ cations on the inherent properties such as microstructures, morphology, and photophysics of pure methylammonium lead bromide (MAPbBr3) perovskites have been investigated. Successful formation of mixed MA1-xCsxPbBr3 phases (with 0 ≤ x ≤ 1.0) was predicted from the theoretically calculated tolerance factor, which was further supported by the appearance of sharp diffraction peaks in X-ray diffraction (XRD) patterns without any additional peaks in the whole composition range. Substitution of Cs+ ions brings significant lattice contraction in the parent MAPbBr3 crystal due to the ion size disparity in the ionic radii between MA+ and Cs+ ions. We examine the vibrational signatures of the Raman bands related to the organic MA+ and infer the nature of interactions between the organic moiety and the surrounding inorganic cage as a function of Cs concentration. Raman spectroscopic analysis reveals structural distortion due to the altered H-bonding interaction of the N+-HBr- type between MA+ and the PbBr3- octahedral framework as a function of Cs content, which is responsible for the octahedral tilting in Cs substituted MAPbBr3. We also found hindered rotational motions of MA+ in the octahedral cage of mixed cationic systems, resulting in the orientational ordering of MA in the presence of Cs. These results certainly offer highly ordered mixed phase structures and promote superior thermal stability, as evident from the thermogravimetric analysis. The photoluminescence intensity becomes considerably enhanced at increased substitution levels, which highlights the capability of incorporated Cs+ cations in suppressing non-radiative recombination in a pure MA-based crystal, possibly related to the mitigation of trapping. The substitution of Cs+ with MAPbBr3 allows innovative strategies to improve the proficiency of tandem solar cells by modifying their structural and photophysical properties.

Molecular-Level Insights into the Microstructure of a Hydrated and Nanoconfined Deep Eutectic Solvent

Despite the recent advancements in the field of deep eutectic solvents (DESs), their high viscosity often prevents practical applications. A versatile strategy to overcome this problem is either to add a co-solvent or to confine the DES inside a nanoscaled self-organized system. This work assesses the microstructures of a hydrated and nanoconfined DES comprising benzyltripropylammonium chloride [BTPA]Cl and ethylene glycol (EG). They act as a hydrogen-bond acceptor and a donor, respectively. The hydrogen bonding between [BTPA]Cl and EG in the DES (i.e., BTEG) and the molecular states of water in the hydrated BTEG were studied by Raman spectroscopy. The results show different hydrogen-bonding associations between water-water and water-BTEG or EG molecules. In addition, we investigated the confinement effects of BTEG in a Polysorbate 80 (Tween-80)/cyclohexane reverse micellar (RM) system. The results are compared with those of an ionic liquid-encapsulated RM system. The formation, bonding characteristics, and thermal stability of the RM droplets were studied by solubilization, dynamic light scattering, rheology, and Raman spectroscopy experiments. Furthermore, it is shown that hydrogen bonding between the DES and the surfactant leads to a stable RM system. Interestingly, the viscosity of the RM system is significantly lower than that of the neat DES suggesting that DESs have a much wider practical applicability in the form of RMs.

Unraveling structural dynamics in isoenergetic excited S1 and multi-excitonic 1(TT) states of 9,10-bis(phenylethynyl)anthracene (BPEA) in solution via ultrafast Raman loss spectroscopy

Ultrafast Raman loss spectroscopy provides a direct evidence for the structural changes that occur during the evolution from the S₁ to the ₁(TT) state of BPEA in solution.

Assessment of Radiation Resistance and Therapeutic Targeting of Cancer Stem Cells: A Raman Spectroscopic Study of Glioblastoma

Radiation is the standard therapy used for treating Glioblastoma (GBM), a grade IV brain cancer. Glioma Stem-like Cells (GSCs), an integral part of GBM, enforces resistance to radiation therapy of GBM. Studying the differential biomolecular composition of GSCs with varying levels of radiation sensitivity can aid in identifying the molecules and their associated pathways which impose resistance to cells thereby unraveling new targets which would serve as potential adjuvant therapy. Raman spectroscopy being a noninvasive, label free technique can determine the biomolecular constituent of cells under live conditions. In this study, we have deduced Raman spectral signatures to predict the radiosensitivity of any GSC accurately using the inherent and radiation induced biomolecular composition. Our study identified the differential regulation of several biomolecules which can be potential targets for adjuvant therapy. We radiosensitized the resistant GSCs using small molecule inhibitors specific to the metabolic pathways of these biomolecules. Efficient antitumor therapy can be attained with lower dosage of radiation along with these inhibitors and thus improving the survival rate of GBM patients with reduced side-effects from radiation.

Challenges in application of Raman spectroscopy to biology and materials

Raman spectroscopy has become an essential tool for chemists, physicists, biologists and materials scientists. In this article, we present the challenges in unravelling the molecule-specific Raman spectral signatures of different biomolecules like proteins, nucleic acids, lipids and carbohydrates based on the review of our work and the current trends in these areas. We also show how Raman spectroscopy can be used to probe the secondary and tertiary structural changes occurring during thermal denaturation of protein and lysozyme as well as more complex biological systems like bacteria. Complex biological systems like tissues, cells, blood serum etc. are also made up of such biomolecules. Using mice liver and blood serum, it is shown that different tissues yield their unique signature Raman spectra, owing to a difference in the relative composition of the biomolecules. Additionally, recent progress in Raman spectroscopy for diagnosing a multitude of diseases ranging from cancer to infection is also presented. The second part of this article focuses on applications of Raman spectroscopy to materials. As a first example, Raman spectroscopy of a melt cast explosives formulation was carried out to monitor the changes in the peaks which indicates the potential of this technique for remote process monitoring. The second example presents various modern methods of Raman spectroscopy such as spatially offset Raman spectroscopy (SORS), reflection, transmission and universal multiple angle Raman spectroscopy (UMARS) to study layered materials. Studies on chemicals/layered materials hidden in non-metallic containers using the above variants are presented. Using suitable examples, it is shown how a specific excitation or collection geometry can yield different information about the location of materials. Additionally, it is shown that UMARS imaging can also be used as an effective tool to obtain layer specific information of materials located at depths beyond a few centimeters.

This paper reviews various facets of Raman spectroscopy. This encompasses biomolecule fingerprinting and conformational analysis, discrimination of healthy vs. diseased states, depth-specific information of materials and 3D Raman imaging.

Hydrophobic mediated growth of galvanic-nanobuds from germanium nanowires for a highly tunable SERS substrate

A SERS substrate is fabricated through a scalable process exhibiting suitable hotspot distribution, shelf life, tunability, and biological applications.

Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T1 and T2 states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S0 state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S0, T1, and T2 states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the nπ(∗) triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents.

Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis

We demonstrate how ratioing spectral bands can circumvent experimental artefacts, and present a library of ratios from the biomedical literature.

Molecular profiling of sepsis in mice using Fourier Transform Infrared Microspectroscopy

Sepsis is a life threatening condition resulting from a high burden of infection. It is a major health care problem and associated with inflammation, organ dysfunction and significant mortality. However, proper understanding and delineating the changes that occur during this complex condition remains a challenge. A comparative study involving intra-peritoneal injection of BALB/c mice with Salmonella Typhimurium (infection), lipopolysaccharide (endotoxic shock) or thioglycollate (sterile peritonitis) was performed. The changes in organs and sera were profiled using immunological assays and Fourier Transform Infrared (FTIR) micro-spectroscopy. There is a rapid rise in inflammatory cytokines accompanied with lowering of temperature, respiratory rate and glucose amounts in mice injected with S. Typhimurium or lipopolysaccharide. FTIR identifies distinct changes in liver and sera: decrease in glycogen and protein/lipid ratio and increase in DNA and cholesteryl esters. These changes were distinct from the pattern observed in mice treated with thioglycollate and the differences in the data obtained between the three models are discussed. The combination of FTIR spectroscopy and other biomarkers will be valuable in monitoring molecular changes during sepsis.

Ascorbate protects neurons against oxidative stress: a Raman microspectroscopic study

Oxidative stress due to excessive accumulation of reactive oxygen or nitrogen species in the brain as seen in certain neurodegenerative diseases can have deleterious effects on neurons. Hydrogen peroxide, endogenously generated in neurons under normal physiological conditions, can produce an excess of hydroxyl radical via a Fenton mediated mechanism. This may induce acute oxidative injury if not scavenged or removed effectively by antioxidants. There are several biochemical assay methods to estimate oxidative injury in cells; however, they do not provide information on the biochemical changes as the cells get damaged progressively under oxidative stress. Raman microspectroscopy offers the possibility of real time monitoring of the chemical composition of live cells undergoing oxidative stress under physiological conditions. In the present study, a hippocampal neuron coculture was used to observe the acute impact of hydroxyl radicals generated by hydrogen peroxide in the presence of Fe(2+) (Fenton reaction). Raman peaks related to nucleic acids (725, 782, 1092, 1320, 1340, 1420, and 1576 cm(-1)) showed time-dependent changes over the experimental period (60 min), indicating the breakdown of the phosphodiester backbone as well as nuclear bases. Interestingly, ascorbic acid (a potent antioxidant) when cotreated with Fenton reactants showed protection of cells as inferred from the Raman spectra, presumably by scavenging hydroxyl radicals. Little or no change in the Raman spectra was observed for untreated control cells and for cells exposed to Fe(2+) only, H2O2 only, and ascorbate only. A live-dead assay study also supported the current observations. Hence, Raman microspectroscopy has the potential to be an excellent noninvasive tool for early detection of oxidative stress that is seen in neurodegenerative diseases.

Direct Observation of Thermal Equilibrium of Excited Triplet States of 9,10-Phenanthrenequinone. A Time-Resolved Resonance Raman Study

The photochemistry of aromatic ketones plays a key role in various physicochemical and biological processes, and solvent polarity can be used to tune their triplet state properties. Therefore, a comprehensive analysis of the conformational structure and the solvent polarity induced energy level reordering of the two lowest triplet states of 9,10-phenanthrenequinone (PQ) was carried out using nanosecond-time-resolved absorption (ns-TRA), time-resolved resonance Raman (TR(3)) spectroscopy, and time dependent-density functional theory (TD-DFT) studies. The ns-TRA of PQ in acetonitrile displays two bands in the visible range, and these two bands decay with similar lifetime at least at longer time scales (μs). Interestingly, TR(3) spectra of these two bands indicate that the kinetics are different at shorter time scales (ns), while at longer time scales they followed the kinetics of ns-TRA spectra. Therefore, we report a real-time observation of the thermal equilibrium between the two lowest triplet excited states of PQ, assigned to nπ* and ππ* of which the ππ* triplet state is formed first through intersystem crossing. Despite the fact that these two states are energetically close and have a similar conformational structure supported by TD-DFT studies, the slow internal conversion (∼2 ns) between the T(2)(1(3)nπ*) and T(1)(1(3)ππ*) triplet states indicates a barrier. Insights from the singlet excited states of PQ in protic solvents [ J. Chem. Phys. 2015 , 142 , 24305 ] suggest that the lowest nπ* and ππ* triplet states should undergo hydrogen bond weakening and strengthening, respectively, relative to the ground state, and these mechanisms are substantiated by TD-DFT calculations. We also hypothesize that the different hydrogen bonding mechanisms exhibited by the two lowest singlet and triplet excited states of PQ could influence its ISC mechanism.

Nuclear magnetic resonance, vibrational spectroscopic studies, physico-chemical properties and computational calculations on (nitrophenyl) octahydroquinolindiones by DFT method

In the present study, 2'-nitrophenyloctahydroquinolinedione and its 3'-nitrophenyl isomer were synthesized and characterized by FT-IR, FT-Raman, (1)H NMR and (13)C NMR spectroscopy. The molecular geometry, vibrational frequencies, (1)H and (13)C NMR chemical shift values of the synthesized compounds in the ground state have been calculated by using the density functional theory (DFT) method with the 6-311++G (d,p) basis set and compared with the experimental data. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution using GAR2PED programme. Isotropic chemical shifts for (1)H and (13)C NMR were calculated using gauge-invariant atomic orbital (GIAO) method. The experimental vibrational frequencies, (1)H and (13)C NMR chemical shift values were found to be in good agreement with the theoretical values. On the basis of vibrational analysis, molecular electrostatic potential and the standard thermodynamic functions have been investigated.

Raman spectroscopic studies on screening of myopathies

Myopathies are among the major causes of mortality in the world. There is no complete cure for this heterogeneous group of diseases, but a sensitive, specific, and fast diagnostic tool may improve therapy effectiveness. In this study, Raman spectroscopy is applied to discriminate between muscle mutants in Drosophila on the basis of associated changes at the molecular level. Raman spectra were collected from indirect flight muscles of mutants, upheld(1) (up(1)), heldup(2) (hdp(2)), myosin heavy chain(7) (Mhc(7)), actin88F(KM88) (Act88F(KM88)), upheld(101) (up(101)), and Canton-S (CS) control group, for both 2 and 12 days old flies. Difference spectra (mutant minus control) of all the mutants showed an increase in nucleic acid and β-sheet and/or random coil protein content along with a decrease in α-helix protein. Interestingly, the 12th day samples of up(1) and Act88F(KM88) showed significantly higher levels of glycogen and carotenoids than CS. A principal components based linear discriminant analysis classification model was developed based on multidimensional Raman spectra, which classified the mutants according to their pathophysiology and yielded an overall accuracy of 97% and 93% for 2 and 12 days old flies, respectively. The up(1) and Act88F(KM88) (nemaline-myopathy) mutants form a group that is clearly separated in a linear discriminant plane from up(101) and hdp(2) (cardiomyopathy) mutants. Notably, Raman spectra from a human sample with nemaline-myopathy formed a cluster with the corresponding Drosophila mutant (up(1)). In conclusion, this is the first demonstration in which myopathies, despite their heterogeneity, were screened on the basis of biochemical differences using Raman spectroscopy.