The project focused on provenance identification, an aspect of architectural conservation where missing inscriptions and incomplete archives can complicate efforts to establish material authenticity. The team combined three forms of analytical information: X-ray diffraction and Raman spectroscopy provided spectral data, while X-ray fluorescence measured elemental concentrations. Those features were used with a random forest classifier to distinguish the five regional groups represented in the dataset.

After this preprocessing, the random forest achieved 95% test accuracy and an area under the receiver operating characteristic curve of 0.973. The researchers also applied Shapley additive explanations, or SHAP, to identify the variables that discriminated most strongly among the provenance groups. Rubidium, aluminum and zirconium emerged as important discriminative variables, making the model’s reasoning less opaque than a prediction based only on its final output.

Interpretation also extended to the autoencoder’s latent representation through decoder-based analysis, which linked encoded features to mineral phases. Together, these analyses support the measured classification performance and the use of explainability tools in examining the information behind the model. The principal limitation is the study’s scale: only 52 bricks from five regions were evaluated.

The reported accuracy therefore does not establish how the framework would perform on larger collections, bricks from additional regions, or materials with different compositions and manufacturing histories. Within that boundary, the study presents a technically interpretable method for using laboratory measurements to support regional provenance identification in architectural conservation.

Subject of Research: Explainable machine learning for tracing the regional provenance of historic blue bricks

Article Title: A sparse autoencoder and explainable machine learning framework for provenance tracing of historic blue bricks in architectural conservation

Article References: Song, Z., Hou, F., Chen, S., Xu, W., & Zhang, L. (2026). A sparse autoencoder and explainable machine learning framework for provenance tracing of historic blue bricks in architectural conservation. npj Heritage Science. https://doi.org/10.1038/s40494-026-03066-6

Image Credits: AI Generated

DOI: 10.1038/s40494-026-03066-6

Keywords: historic blue bricks, provenance tracing, explainable AI, sparse autoencoders, random forests, X-ray fluorescence, Raman spectroscopy, X-ray diffraction, architectural conservation, SHAP explanations, sparse, autoencoder

The work, published in Scientific Reports on 21 October 2026, evaluated the as-grown nanotube preparation against a single laboratory strain of E. coli. Researchers used agar well diffusion, broth microdilution and viable-count plating to assess inhibition. The as-grown material was characterized by X-ray diffraction, Raman spectroscopy, field-emission scanning electron microscopy and energy-dispersive X-ray spectroscopy. These analyses supported the formation of graphitized multi-walled nanotube structures and detected iron-containing residues associated with the ferrocene precursor, which served as both the carbon source and iron catalyst during chemical vapor deposition.

The agar well-diffusion assay produced clear concentration-related differences in antibacterial activity. Inhibition-zone diameters measured 26 millimeters at 512 micrograms per milliliter, 21 millimeters at 256, 19 millimeters at 128, 9 millimeters at 64 and 7 millimeters at 32 micrograms per milliliter. No inhibition zone was observed for the negative control. Across the tested range of 1–512 micrograms per milliliter, the study reported a concentration-dependent reduction in bacterial growth, with the strongest measured inhibition at the upper end of that range.

Broth microdilution identified 256 micrograms per milliliter as the MIC, based on the absence of visible bacterial growth, and blank-corrected quantitative measurements provided supplementary confirmation of this endpoint. When cultures were subsequently plated on drug-free Mueller–Hinton agar, no recoverable colonies were found after exposure at 256 or 512 micrograms per milliliter. On the basis of that viable-count result, the researchers reported an MBC of 256 micrograms per milliliter for the conditions tested.

The results characterize the antibacterial performance of the complete preparation as tested, rather than isolating the contribution of the nanotube structure itself. The material was evaluated without post-synthesis purification, so the observed inhibition may also have involved contributions from iron-containing residues or other synthesis-derived components. The findings therefore demonstrate concentration-dependent antibacterial activity of as-grown ferrocene-derived multi-walled carbon nanotubes against E. coli ATCC 25922 in laboratory media; they do not by themselves establish the mechanism of action or performance outside the tested conditions.

Subject of Research: Laboratory antibacterial assessment of ferrocene-derived multi-walled carbon nanotubes against Escherichia coli ATCC 25922

Article Title: Antibacterial activity of ferrocene-derived multi-walled carbon nanotubes synthesized by chemical vapor deposition against Escherichia coli

Article References: Ahmed, S. K., Taay, Y. M., Ahmed, A. J., Khudhayer, H. H., Hussein, S. M. F., & Abbas, Z. S. (2026). Antibacterial activity of ferrocene-derived multi-walled carbon nanotubes synthesized by chemical vapor deposition against Escherichia coli. Scientific Reports. https://doi.org/10.1038/s41598-026-70564-9

Image Credits: AI Generated

DOI: 10.1038/s41598-026-70564-9

Keywords: E. coli, multi-walled carbon nanotubes, ferrocene, chemical vapor deposition, antibacterial activity, minimum inhibitory concentration, minimum bactericidal concentration, Raman spectroscopy, X-ray diffraction, laboratory assay, Antibacterial, activity

The crystal-engineering strategy was intended to produce a new crystalline phase of berberine, a natural-product medicine associated with antimicrobial properties. Hydrothermal screening experiments yielded the berberine–2-sulfobenzoate salt, and diffraction and thermal analysis supported successful formation of the intended material. The structural investigation found no classic hydrogen bonds within the reported salt system.

Instead, weak C–H···O contacts stabilize the interaction between berberine and 2-sulfobenzoate, while a strong dimeric intermolecular hydrogen bond forms between two 2-sulfobenzoate molecules. Spectroscopic observations showed that vibrational modes in the berberine–2-sulfobenzoate salt shifted relative to the modes of the individual components, with the change evident in the Raman spectra. The researchers interpreted these shifts in conjunction with the crystal structure and computational results, showing that salt formation alters the molecular environment experienced by berberine and 2-sulfobenzoate.

For the density functional calculations, they selected a 1:2 berberine–2-sulfobenzoate system so that the model would cover a larger number of intermolecular hydrogen bonds. The modeled system was examined with quantum theory of atoms in molecules and reduced-gradient density analysis to interpret the strength and type of the molecular interactions, while natural bond orbital analysis was used to assess the stability of the system. The calculations also produced molecular electrostatic potential surfaces for berberine, 2-sulfobenzoate and the salt system, identifying regions associated with electrophilic, nucleophilic and neutral behavior.

Frontier molecular orbital and global-descriptor calculations indicated that the modeled berberine–2-sulfobenzoate salt was more chemically reactive than berberine alone. Molar refractivity was used to characterize drug-likeness behavior, and the authors described the combined evidence as confirmation of a new berberine salt with improved physicochemical properties. These reactivity and drug-likeness results are properties predicted or modeled computationally; the study does not establish clinical advantages for the salt.

The research is a laboratory synthesis and solid-state characterization of a crystalline material rather than a clinical investigation of its effects in people.

Subject of Research: Experimental and quantum-chemical characterization of a crystalline berberine–2-sulfobenzoate salt

Article Title: Synthesis, crystal structure, and characterization of a new crystalline berberine–2-sulfobenzoate salt, integrating vibrational spectroscopy and quantum chemical investigation

Article References: Srivastava, D. A., Prajapati, P., Shimpi, M. R., & Tandon, P. (2026). Synthesis, Crystal Structure and Characterization of a New Crystalline Berberine-2-Sulfobenzoate Salt, Integrating Vibrational Spectroscopy and Quantum Chemical Investigation. Frontiers in Chemistry, 14, 1971429. https://doi.org/10.3389/fchem.2026.1971429

Image Credits: AI Generated

DOI: 10.3389/fchem.2026.1971429

Keywords: berberine, 2-sulfobenzoate, crystal synthesis, hydrogen bonding, vibrational spectroscopy, Raman spectroscopy, density functional theory, quantum chemistry, molecular reactivity, physicochemical properties, Synthesis, crystal

The review presents the techniques as potential non-invasive adjuncts to existing transplant assessment rather than established clinical tests. The analytical basis for this approach lies in the characteristic patterns produced when molecules scatter laser light. A Raman spectrum can represent the combined molecular composition of proteins, nucleic acids, lipids, metabolites and other substances within a sample.

In kidney transplantation, investigators have examined signals associated with collagen, creatinine, amino acids, extracellular-matrix remodeling, immune-complex deposition and oxidative stress, all of which are connected in the source material with acute or chronic rejection. Some of these processes may become detectable before changes appear in a standard biopsy. The method does not necessarily identify a single disease-specific molecule, however; much of its discriminatory power comes from mathematical analysis of the combined spectral pattern.

That distinction was evident in a study of serum collected from kidney-transplant recipients classified by contemporary biopsy, Banff scoring and immunohistochemistry. The sample included seven recipients with antibody-mediated rejection, three with T-cell-mediated rejection and seven with no major abnormality, with the last group serving as the control. A sensing chip with gold-coated zinc-oxide nanorods was used to amplify the SERS signal from 5 microliters of serum.

Although the raw spectra appeared broadly similar and did not show distinct group-specific peaks, two machine-learning approaches separated the groups with reported accuracies of 93.53 percent and 98.82 percent. The findings indicate that computational classification can extract information from complex differences in molecular signals, even when individual spectral features are not visually obvious. Urine has attracted attention because it can be obtained without a needle or incision and can contain both urinary and blood-derived indicators of graft status.

In one study, investigators collected 60 samples from 20 kidney-transplant recipients: one day before transplantation, on the first postoperative day and on postoperative day seven. The researchers used two SERS approaches, one based on a colloidal silver film and another incorporating a 4-mercaptopyridine probe to improve sensitivity for small metabolic structures. The principal metabolites examined were choline, creatinine and urea.

Classification models reported accuracies of 96 to 100 percent between transplantation stages, while postoperative samples showed increased signals associated with amino acids and lipids and decreased signals associated with creatinine and nucleic acids relative to preoperative samples. Because the comparison included only transplantation time points and no healthy or chronic-kidney-disease groups, the results demonstrate stage-dependent spectral differences but do not establish specificity for rejection. Animal experiments offer additional evidence that urine SERS can reflect disease-associated and treatment-associated biology.

In one rat model, renal-allograft recipients received either anti-TGF-beta antibody or a nonspecific control antibody rather than standard pharmaceutical immunosuppression, with 10 animals per group. A silver-nanoparticle substrate was used for SERS, and principal component-linear discriminant analysis distinguished the antibody-treated and control groups with 90 percent sensitivity and 70 percent specificity. A second model used obese, genetically diabetic ZSF1 rats, with 10 animals receiving control chow and 11 receiving chow supplemented with grape powder.

SERS analysis distinguished the diet groups with 72.7 percent sensitivity and 60 percent specificity. Receiver operating characteristic areas under the curve were approximately 0.85 for the transplant model and 0.80 for the diabetic model. These findings show that reproducible urine signatures occurred in experimentally induced renal disease, but they are animal-model observations and do not directly establish human transplant benefit.

The connection between spectral information and routine biochemical measures was examined in 110 transplant recipients whose urine and blood were collected within three days after transplantation. For SERS analysis, urine was mixed with silver nanoparticles, air-dried for one hour at room temperature and scanned. Partial least-squares regression then related the spectra to laboratory measurements.

Urine spectra correlated with urinary creatinine at R² = 0.8106, urinary urea at R² = 0.7808 and urinary protein at R² = 0.4660. Spectral analysis also predicted serum creatinine at R² = 0.7628 and blood urea nitrogen at R² = 0.6539, with all five relationships reported as statistically significant at p less than 0.01. These results show that urine-derived spectra can contain information about established biochemical indicators of kidney function, although the study did not report the detection of rejection itself.

Donor kidneys may present another potential application because Raman methods can examine molecular features before or after implantation. In a study of urine from 30 deceased donors, participants were divided into three groups of 10: donors with biopsy-proven acute tubular necrosis, donors whose recipients experienced delayed graft function, and controls with neither condition. SERS with iodide-modified silver nanoparticles generated distinct spectra for the groups, with sensitivity greater than 90 percent for distinguishing acute tubular necrosis from both delayed graft function and controls.

Differences were also observed between the delayed-graft-function and control groups. Many kidneys with acute tubular necrosis nevertheless produced acceptable transplant outcomes. The findings suggest that a urinary spectral profile may provide information beyond traditional donor-risk categories, but the study did not test whether applying those profiles to organ selection would change clinical decisions.

A separate label-free Raman-imaging study investigated hydroxyethyl starch, an expander used during donor resuscitation, in renal-allograft biopsies obtained three months after transplantation. The study included 26 recipients: 20 grafts came from donors exposed to hydroxyethyl starch within 72 hours before procurement, while six control grafts came from donors who received no colloid. A vibrational band near 480 inverse centimeters was associated with hydroxyethyl starch and was absent in the controls, although positivity was determined through a fitting algorithm that incorporated the full spectral profile rather than this band alone.

Approximately 40 percent of exposed biopsies had signals above the positivity threshold, and none of the controls did. Stronger relative signals correlated with higher estimated glomerular filtration rate at three months, with r = 0.88 and p less than 0.001, and with a lower kidney donor risk index, with r = −0.72 and p less than 0.001. The researchers indicated that the relationship between hydroxyethyl starch signal and graft function probably reflected underlying graft quality rather than a beneficial effect of the expander.

One possible explanation was that higher-functioning kidneys might reabsorb and retain more hydroxyethyl starch within tubular cells. Raman imaging is invasive in this setting because it was performed on biopsy tissue, despite the broader potential for non-invasive sampling through fluids. The donor-assessment evidence therefore spans pre-transplant urine analysis and post-transplant imaging of excised tissue rather than a single non-invasive donor-testing procedure.

Beyond organ chemistry, Raman spectroscopy can detect the biochemical remodeling that accompanies T-cell activation, a process involved in acute rejection. In one in-vitro experiment, human T lymphocytes isolated from healthy participants were divided among resting, nonspecifically activated and alloantigen-activated conditions. Nonspecific activation used CD3/CD28-coated beads and interleukin-2, whereas alloantigen activation was produced through a two-way mixed lymphocyte culture involving cells from nonrelated individuals and antigen-presenting cells.

The researchers measured 75 resting-cell samples, 75 CD3/CD28-activated samples and 40 alloantigen-activated samples. At selected wavelengths assigned to nucleic acids, amino acids and mixed protein–nucleic-acid contributions, nonspecifically activated cells had peak magnitudes approximately 4.3 to 32 percent below those of resting cells. Classification between nonspecific and alloantigen activation reported 100 percent sensitivity and specificity under the experimental conditions.

A related study compared resting, mitomycin-C-inactivated and alloimmune-activated human T cells, yielding 35 spectra for resting cells, 28 for inactivated cells and 51 for alloimmune-activated cells. Significant differences appeared at 1182 and 1195 inverse centimeters, wavelengths associated with amino-acid vibrations and protein structures. One statistical analysis reported 95.7 percent sensitivity and 100 percent specificity for distinguishing the three conditions, while discriminant-function analysis reported 89.3 percent sensitivity and 93.8 percent specificity.

Together, the two experiments indicate that Raman spectra contain measurable differences associated with immune-cell activation. They were performed with isolated cells manipulated in vitro, however, rather than demonstrating clinical detection of acute rejection in transplant recipients. The review identifies sample standardization and computational interpretation as central requirements for translating Raman methods into clinical use.

Subtle differences may require advanced methods such as machine learning, while the reviewed studies differ in their samples, endpoints and statistical approaches. The reported applications span three areas: monitoring graft-related changes in urine, blood or serum; assessing donor-associated molecular features and potential risk markers; and identifying biochemical changes in activated T lymphocytes. Within the evidence presented, the strongest conclusion is that Raman spectroscopy and SERS can reveal transplantation-associated molecular patterns with non-invasive sampling in some settings and may serve as useful additions to biopsy, laboratory testing and clinical assessment.

Whether those capabilities can improve graft outcomes, reduce biopsy use or expand safe use of donor organs remains an unanswered clinical question rather than an established result of the studies reviewed.

Subject of Research: Raman spectroscopy and SERS for kidney-transplant monitoring, donor assessment and immune-activation analysis

Article Title: From Spectra to Clinical Insight: Raman Spectroscopy in Kidney Transplant Monitoring and Donor Assessment

Article References: Peveri, E., Asthana, A., Byers, L. N., Senger, R., Issa, S., Robertson, J., Dehoff, D. M., & Orlando, G. (2026). From Spectra to Clinical Insight: Raman Spectroscopy in Kidney Transplant Monitoring and Donor Assessment. Current Transplantation Reports, 13(1), Article 34. https://doi.org/10.1007/s40472-026-00531-w

Image Credits: AI Generated

DOI: 10.1007/s40472-026-00531-w

Keywords: Raman spectroscopy, surface-enhanced Raman scattering, kidney transplantation, graft rejection, donor assessment, urine biomarkers, T-cell activation, graft dysfunction, non-invasive diagnostics, Spectra, Clinical, Insight

MBN is a disubstituted naphthalene: a bromine atom occupies the 6-position and a methyl carboxylate group occupies the 2-position. Before this work, the authors reported no published crystallographic structure and no experimental or computational study of MBN’s structural, vibrational, optical and electronic properties. The resulting findings are a molecular characterization of a synthesis intermediate, not evidence of clinical performance or a demonstration of a working optical device.

At the B3LYP-D3/6-311++G(d,p) level of theory, a relaxed potential-energy scan generated 1,369 optimized molecular geometries by varying the C3C2C11O14 and C11O14C12H22 dihedral angles in 10-degree increments from 0 to 360 degrees. Three equivalent global minima were found, each with an energy of −3187.4993 Hartree, corresponding to the same preferred molecular geometry because of the threefold symmetry of the methyl group. No imaginary frequencies were obtained from the subsequent harmonic analysis, confirming that the optimized structure was a minimum on the calculated potential-energy surface.

The calculations treated an isolated molecule, however, so they did not include intermolecular interactions or crystal-packing effects. That limitation matters because no X-ray structure was available for direct comparison. The researchers instead compared calculated bond lengths and angles with experimental values reported for the related compound methyl 1-bromo-2-naphthoate.

The authors described general agreement but did not present the comparison as a direct structural validation of MBN. For the aromatic carbon–hydrogen bonds, isolated-molecule calculations overestimated distances relative to the comparison data, with a root-mean-square error of about 0.154 angstroms. MBN’s carbon–hydrogen stretching frequencies were nevertheless higher than those of naphthalene, and potential-energy-distribution analysis identified all six as distinct modes.

The strongest changes occurred near the bromine and ester substituents, which removed the local equivalence among naphthalene’s carbon–hydrogen sites. The vibrational comparison drew on an FT-IR spectrum recorded from a potassium bromide pellet at room temperature over 400–4,000 inverse centimeters, and a Raman spectrum measured with 785-nanometer excitation over 250–3,200 inverse centimeters. The principal aromatic carbon–hydrogen stretches were calculated near 3,047–3,079 inverse centimeters, with observed bands at 3,063, 3,040 and 3,058 inverse centimeters.

The strong carbonyl feature appeared at 1,705 inverse centimeters in FT-IR and 1,716 inverse centimeters in Raman and was assigned 87% to the C=O stretching contribution. A band at 1,096 inverse centimeters in FT-IR, with a Raman counterpart at 1,098 inverse centimeters, was characterized as a mixed carbon–oxygen stretching and in-plane carbon–hydrogen bending mode. The researchers applied harmonic calculations to the 400–1,770 and 2,880–3,100 inverse-centimeter regions, where fundamental bands dominate, and used anharmonic calculations for the 1,770–2,880 and 3,100–4,000 inverse-centimeter regions.

The latter treatment separated overtones from combination bands and allowed weak experimental features to be assigned. A relatively resolved FT-IR band at 3,410 inverse centimeters was assigned to the overtone of the carbonyl vibration, with a calculated position of 3,443 inverse centimeters. An observed band at 2,847 inverse centimeters was matched to a calculated overtone at 2,837 inverse centimeters.

Below 2,200 inverse centimeters, overlapping overtone and combination bands were assigned individually at experimental positions of 2,292, 2,183, 1,944, 1,913, 1,829 and 1,775 inverse centimeters. The study indicates that anharmonic calculations can recover information missed when analysis is restricted to conventional fundamental-frequency windows, but it does not establish that every weak band has a single unique physical origin. Ultraviolet–visible measurements were performed on six MBN solutions in chloroform spanning reported concentrations from 10⁻² to 10⁻⁷ M.

Spectra at the highest concentrations were broad and noisy, while a sample of 2.305 × 10⁻⁵ M produced the clearest structured absorption profile, which was used for comparison with calculations. The experimental spectrum showed bands at 291, 279, 246 and 239 nanometers. Time-dependent density functional calculations at the same B3LYP-D3/6-311++G(d,p) level predicted solution-phase transitions at 316.48, 298.02, 254.21 and 228.04 nanometers.

Among three tested approaches, B3LYP-D3 gave the smallest relative error in the experimental maximum absorption wavelength, 3.34%, compared with 5.60% for CAM-B3LYP-D3 and 6.36% for wB97XD. Frontier-orbital calculations assigned the predicted 316.48-nanometer shoulder mainly to a HOMO-to-LUMO transition with an 84% contribution, while the strongest calculated transition at 254.21 nanometers, with an oscillator strength of 1.1840, combined HOMO−1-to-LUMO and HOMO-to-LUMO+1 contributions. The calculated HOMO–LUMO energy gap was 4.405 eV in solution and 4.426 eV in the gas phase.

The study also estimated a total dipole moment of 2.0676 debye, a mean polarizability of 26.8085 × 10⁻²⁴ electrostatic units and a first hyperpolarizability of 11,902.1478 × 10⁻³³ electrostatic units. These calculated values were respectively about five and 31 times the corresponding reference values for urea, and the hyperpolarizability was nonzero unlike that of centrosymmetric naphthalene. These are theoretical molecular properties; the research did not fabricate a nonlinear-optical device or measure device-level performance.

Calculated reactivity descriptors gave a vertical ionization potential of 8.070 eV, vertical electron affinity of 0.815 eV, electronegativity of 4.442 eV and absolute hardness of 3.628 eV. Relative to values cited for naphthalene, the results characterize substituted MBN as less basic, more electron-accepting and less resistant to electron-density perturbation. Overall, the experiments and calculations provide a detailed baseline for MBN’s geometry, spectra and electronic structure, including assignments that would be inaccessible from a standard harmonic analysis alone.

Their potential relevance to drug, dye and optical-material synthesis lies in improving molecular understanding; the study did not test MBN in a finished pharmaceutical, establish biological efficacy, or demonstrate an application beyond the laboratory characterization.

Subject of Research: Experimental and computational characterization of methyl 6-bromo-2-naphthoate using spectroscopy and density functional theory.

Article Title: Conformational, harmonic/anharmonic vibrational frequencies, and molecular electronic investigations of methyl 6-bromo-2-naphthoate: when experiments (FT-IR, Raman, UV–Vis) meet DFT calculations

Article References: Benalia, A., Amrani, R., Boukaoud, A., Chiba, Y., Sebbar, D., Krid, A., Lekoui, F., & Abdelouahed, L. (2026). Conformational, harmonic/anharmonic vibrational frequencies, and molecular electronic investigations of methyl 6-bromo-2-naphthoate: when experiments (FT-IR, Raman, UV–Vis) meet DFT calculations. Results in Chemistry, 31, Article 103973. https://doi.org/10.1016/j.rechem.2026.103973

Image Credits: AI Generated

DOI: 10.1016/j.rechem.2026.103973

Keywords: methyl 6-bromo-2-naphthoate, density functional theory, FT-IR spectroscopy, Raman spectroscopy, UV–Vis spectroscopy, anharmonic vibrations, molecular geometry, electronic structure, nonlinear optics, naphthalene derivatives, Conformational, harmonic

The study addresses the fact that viral RNA contains information beyond the order and abundance of its four nucleotide bases. RNA molecules fold into complex three-dimensional structures through interactions between neighboring nucleotides and complementary bases. These secondary structures can include hairpins, stems and paired regions, and they can differ among viruses even when their overall nucleotide composition appears remarkably similar. Raman spectroscopy detects characteristic molecular vibrations when a sample interacts with light. In the experiment, the resulting signals reflected contributions from the RNA backbone, ribose rings, phosphate linkages and nitrogenous bases, allowing the investigators to characterize patterns associated with RNA organization rather than reading the sequence letter by letter.

For the experiment, the team extracted RNA nucleotide strands from 20 SARS-CoV-2 strains. The panel comprised the original Japanese isolate, seven named non-Omicron variants—Alpha, Beta, Gamma, Delta, Lambda, Theta and Mu—and 12 Omicron subvariants. The researchers systematically acquired the Raman spectra of these samples and mathematically deconvoluted them to identify their individual molecular components. All samples shared characteristic signals associated with common RNA chemistry, including the backbone, ribofuranose rings, phosphate groups and nitrogenous bases. At the same time, subtle but reproducible differences emerged among the strains and subvariants.

Those differences were then encoded as Raman barcodes, defined in the study as characteristic patterns of Raman signals that capture distinctive molecular features of viral RNA. The approach was intended to preserve structural information that might not be apparent from a simple comparison of nucleotide composition. In the authors’ conception, a “Raman genome” represents an RNA genome through its molecular architecture and spectral fingerprint rather than through a direct reading of its nucleotide sequence. This is a conceptual extension of genome characterization: the barcode captures molecular features associated with RNA folding and conformation, including the physical contributions of the sugar-phosphate framework, ribose and the bases.

A central finding was that the observed spectral distinctions could not be explained only by variation in the relative abundance of the four RNA bases. When the genome sequences were used to assess those proportions, the investigated strains had highly similar base fractions. Their Raman spectra nevertheless exhibited markedly different molecular signatures. This separation between sequence-based composition and measured spectra indicates that the Raman measurement was sensitive to information beyond base abundance. The authors investigated the molecular origins of the differences by relating particular Raman bands to features of RNA secondary structure, including backbone conformation, nucleotide-chain characteristics, ribofuranose dynamics, hairpin formation, stem length and base-pairing environments.

The resulting barcodes discriminated all 20 strains and subvariants examined, including multiple Omicron subvariants. Conventional principal component analysis, by comparison, provided only limited separation among the same material. The distinction between these two analyses is important to the reported result: the successful classification was based on explicitly encoded Raman spectral features, rather than on the limited discrimination produced by the conventional PCA approach. The finding also shows why the spectral differences matter. They were not merely an incidental effect of broad base composition; instead, selected bands could be associated with interpretable structural features of the RNA strands and used to distinguish the tested panel.

Technical interpretation of the spectra depends partly on changes in Raman signal intensity caused by molecular interactions. Hyperchromic and hypochromic responses involving nitrogenous bases provide clues about pairing environments and RNA secondary structure. Bands associated with ribose vibrations, phosphate linkages and RNA backbone conformation also contribute to the encoded barcode. These physically interpretable features connect the classification result to molecular architecture rather than leaving it as an unexplained statistical separation. The work therefore combines two aspects of the proposed method: a Raman fingerprint capable of differentiating samples and an analysis linking parts of that fingerprint to secondary-structure characteristics such as stem formation, hairpins and the environments in which bases are paired.

The researchers present the result as a first step toward a broader strategy for characterizing viral RNA through spectroscopy. They propose that future development could combine physically interpretable Raman markers with automated spectral analysis, theoretical calculations and artificial intelligence. Such systems could potentially provide a rapid layer of molecular information alongside sequencing, particularly during outbreaks, epidemics and emergency or critical-care situations where timely characterization may be important. The release does not report the implementation of such a clinical system. The reported evidence concerns an experimental comparison of RNA strands from a defined set of 20 strains and subvariants, not prospective surveillance or routine diagnostic validation.

Several limitations follow directly from that experimental scope. The panel was limited to 20 SARS-CoV-2 strains and subvariants, so the result demonstrates discrimination within the tested collection rather than universal performance across the full diversity of SARS-CoV-2 or other viruses. The researchers used RNA nucleotide strands extracted from the strains, meaning the measurements were performed downstream of sample preparation and did not by themselves demonstrate direct identification in unprocessed patient material. The news release also does not report prospective clinical comparisons, blinded diagnostic performance, turnaround time, cost, sensitivity, specificity or reproducibility across laboratories. It likewise does not describe testing under changing sample conditions or a clinical workflow for detecting newly emerging variants.

Even with these qualifications, the experiments offer a technically distinct route for viral science. Conventional sequencing determines the order of nucleotides, whereas the proposed Raman method captures a molecular fingerprint associated with RNA structure and conformation. By successfully discriminating 20 strains and subvariants whose evaluated base fractions were highly similar, the study shows that structural variation supplied information that was not captured by simple composition estimates alone. The authors do not claim that Raman analysis will replace RNA sequencing. Instead, they describe it as a complementary approach that may eventually support faster variant screening and broaden molecular surveillance. The work was financially supported by a Japan Society for the Promotion of Science grant, and the authors declared no conflicts of interest.

Subject of Research: Experimental Raman spectroscopy of SARS-CoV-2 RNA secondary structure for distinguishing variants and subvariants

Article Title: “Raman Genome” for SARS-CoV-2: new Raman technology distinguishes viral variants by their molecular RNA architecture

Article References: “Raman Genome” for SARS-CoV-2: new Raman technology distinguishes viral variants by their molecular RNA architecture. Original publication (Bibliographic details unavailable.)

Image Credits: AI Generated

DOI: Not provided

Keywords: SARS-CoV-2, Raman spectroscopy, Raman barcodes, RNA structure, viral variants, Omicron subvariants, molecular diagnostics, viral surveillance, secondary structure, Advanced Science, Raman, Genome

The team collected samples in October 2022, during the Amazonian dry season, when falling water levels cut the hydrological connections between the lake, adjacent channels, and the main river. This low-water phase matters because reduced connectivity tends to trap particles within the lake rather than flushing them out. The researchers chose two contrasting areas: one dominated by artisanal fishing activity, with boats, nets, and lines in regular use, and another marked by riverside dwellings, visible solid waste, and direct domestic use of the water. At seven points in each area, spaced ten meters apart along the margins, they drew six liters of near-surface water from the top thirty centimeters and scraped 150 grams of sediment from the upper five centimeters of the lake bed.

The laboratory work followed rigorous contamination-control protocols. Water samples were vacuum-filtered through paper filters with a five-micrometer pore size, while sediments were dried, subjected to density separation in saturated salt solution to float plastic particles away from mineral grains, and then treated with hydrogen peroxide to digest organic matter. The researchers wore only cotton clothing in the field, rinsed glass containers with filtered water, and ran sixteen blank controls, fourteen in the field and two in the laboratory. Just three particles appeared in those blanks, roughly 1.5 percent of the count in the environmental samples, indicating that background contamination was minimal and that the particles they counted were genuinely present in the lake.

The numbers were striking. Surface water concentrations ranged from zero, in a single sample where no particles were found, to 1,000 microplastics per cubic meter, with a mean of 405 plus or minus 298. Sediments held between 7 and 307 particles per kilogram of dry sediment, averaging 77 plus or minus 104. Perhaps the most telling result was what the researchers did not find: no statistically significant difference in concentrations between the fishing area and the settlement area. Both human activities, it seems, are feeding plastic into the lake at comparable rates, whether through worn fishing gear and boat materials on one side or inadequate waste disposal and untreated effluents on the other.

The physical character of the particles told its own story. In surface water, the particles were overwhelmingly fibers, predominantly blue and red, with sizes spanning 115 to 3,615 micrometers. In sediments, the picture split by land use: fragments dominated near the human settlements, consistent with the breakdown of domestic plastic waste, while fibers were more abundant in the fishing zone, where synthetic nets, lines, and ropes shed filaments as they wear. Sediment particle sizes also differed significantly between the two areas, with smaller to intermediate particles concentrated near the settlements and larger ones near the fishing grounds. The authors caution that because source-specific morphology was not statistically tested, these attributions remain plausible interpretations rather than proven links.

To identify what the particles were actually made of, the team turned to Fourier-transform infrared and Raman spectroscopy, analyzing roughly eight percent of the visually identified particles. Polyethylene emerged as the most frequently identified polymer, a finding that points to everyday sources such as packaging, bags, and household items. The spectra also revealed something less expected: copper phthalocyanine pigments, specifically Pigment Blue 15 and Pigment Green 7, the same organic colorants used in paints, coatings, and dyed plastics. One Raman spectrum showed the characteristic polyethylene bands, including carbon-carbon stretching signals near 1063 and 1130 inverse centimeters, alongside the fingerprint of Pigment Blue 15. The researchers note that such pigments can accelerate photodegradation under ultraviolet light, potentially speeding the fragmentation of plastic debris and the release of degradation products.

The ecological implications are significant. Blue fibers are a known hazard in aquatic food webs because fish and invertebrates can mistake them for prey, and previous work by some of the same team has already documented microplastics in catfish species sold in local markets near Lake Canaçari. Smaller particles, with their high surface-to-volume ratios, tend to stay suspended longer and interact readily with clays and organic matter, forming aggregates that settle into the sediment. In a low-energy floodplain lake during the dry season, when water exchange with the river is minimal, these particles may accumulate where fish feed and where riverside communities harvest their food. The Amazon’s limited sanitation infrastructure, particularly the absence of wastewater treatment and organized solid waste collection, ensures a continuous supply of new material.

The study also carries a broader geographic message. Model-based estimates suggest the Amazon River discharges somewhere between 38,000 and 182,000 tons of plastic to the ocean each year, though the wide range reflects sparse data. Floodplain lakes like Canaçari sit squarely within this conveyor belt. The authors propose that the lake functions simultaneously as a transport pathway, a redistribution zone, and a retention compartment for microplastics, storing particles during low water and potentially releasing them when the flood pulse reconnects the system. If that hypothesis holds, floodplain lakes could modulate the timing and magnitude of plastic delivery from the Andes to the Atlantic, a dynamic that global plastic transport models have largely ignored.

The researchers are careful about the limits of their work. Sampling covered a single dry-season campaign with modest spatial coverage, land-use categories were defined from qualitative field observations, and the salt-based density separation used for sediments may have under-recovered denser polymers such as PVC or PET. Only a subset of particles received spectroscopic confirmation, and degraded, pigment-coated particles sometimes resisted identification. They call for future studies spanning multiple hydrological seasons, deeper sediment cores, quantitative measures of human pressure, and denser separation solutions to capture the full polymer spectrum. Even so, the baseline is now established: an Amazonian floodplain lake, far from any city, carries microplastics in its water and its bed, and the particles bear the chemical signatures of both fishing livelihoods and everyday domestic life. Managing the Amazon’s plastic problem, the study suggests, will require monitoring strategies that follow the region’s dramatic seasonal pulse of water rather than treating the river system as a static environment.

Subject of Research: Microplastic contamination in the surface water and sediments of an Amazonian floodplain lake

Article Title: Microplastic contamination in surface water and sediments of Lake Canaçari, Central Amazon, during the dry season

Article References: Guimarães, G. D. A., da Fonseca, R. V., de Moraes, B. R., Ando, R. A., de Azevedo Rodrigues, I. J., Perotti, G. F., Sant’Anna, B. S., & Hattori, G. Y. (2026). Microplastic contamination in surface water and sediments of Lake Canaçari, Central Amazon, during the dry season. Environmental Monitoring and Assessment, 198(11), Article 1221. https://doi.org/10.1007/s10661-026-16079-2

Image Credits: AI Generated

DOI: 10.1007/s10661-026-16079-2

Keywords: microplastics, Amazon, Lake Canaçari, floodplain lake, polyethylene, Raman spectroscopy, FTIR, sediments, fishing activity, water pollution, Pigment Blue 15, dry season

Organophosphorus nerve agents, a class that includes sarin, VX and tabun, work by disrupting the enzymes that regulate the nervous system, and even minute quantities can be fatal within minutes. Because of this extreme toxicity, the ability to screen for these substances quickly and reliably has become a pressing priority for public safety officials worldwide. Airports, border checkpoints, subway systems and large public gatherings all represent environments where a rapid, on-site detection capability could mean the difference between a contained incident and a mass casualty event. Yet the analytical instruments traditionally used to confirm the presence of nerve agents, such as chromatography-mass spectrometry and ion mobility spectrometry, while highly accurate, tend to be bulky, expensive and dependent on laboratory infrastructure, which severely limits their usefulness in the field when minutes matter.

The breakthrough hinges on a deceptively simple chemical insight. Every organophosphorus nerve agent shares a defining structural feature: a phosphorus-carbon bond, abbreviated P–C, that sits at the heart of the molecule. Rather than trying to recognize each agent individually, the research team designed a probe molecule that targets this bond directly, creating what they describe as a directed and precise recognition mechanism built on the inherent characteristics of the P–C linkage. This strategy means the sensor is not locked into detecting one specific compound but can, in principle, flag any molecule carrying that telltale bond, which covers the full spectrum of organophosphorus warfare agents.

The probe itself, named pyridylamidoxime-mercapto, or PAOM, is a masterclass in multifunctional molecular design. At one end sits an oxime group, a reactive chemical handle that engages with the target molecules and captures them from the surrounding environment. At the other end, a thiol group performs a crucial anchoring role, bonding the probe firmly to the gold surface of the SERS chip. Gold-thiol chemistry is a well-established workhorse of nanotechnology, and here it ensures the probe layer stays put during measurement. Between these two functional ends lies a pyridine ring, whose job is purely optical: it boosts the Raman signal, amplifying the vibrational spectrum so that even trace amounts of the captured nerve agent become detectable above background noise.

Designing a probe molecule is rarely a one-shot affair, and the team synthesized and tested three different versions of PAOM, distinguished by the positional arrangement of their functional groups on the central ring structure. These variants, known as isomers, differ only in where the reactive groups attach relative to one another, yet that subtle geometric difference has outsized consequences for performance. The researchers found that the para isomer, dubbed p-PAOM, in which the groups occupy positions directly opposite each other on the ring, showed the strongest interaction with organophosphorus agents and the lowest reaction energy barrier. In practical terms, a lower energy barrier means the oxime group reacts with the target more readily and at a faster rate, translating directly into the sensor’s impressive speed.

When the team coupled the p-PAOM-functionalized chip to a portable Raman spectrometer, the results were striking. The sensor detected sarin in liquid samples in less than twenty seconds, achieving a detection limit of ten parts per billion, a concentration so low it corresponds to roughly ten grams of sarin dispersed in a thousand tonnes of liquid. For context, many regulatory thresholds for toxic industrial chemicals sit in the hundreds of parts per billion range, so a ten ppb limit places this sensor firmly in the ultrasensitive category. The speed is equally remarkable; conventional laboratory confirmations of nerve agent exposure can take hours from sample collection to final result, while this device delivers an answer before first responders have finished setting up their perimeter.

Real-world environments are messy, and a sensor that works only on pristine samples would be of limited value. The researchers therefore subjected their device to a battery of interference tests, spiking samples with common substances that might plausibly coexist with nerve agents in field conditions. The sensor maintained good selectivity throughout, correctly identifying the target molecules even in the presence of these interfering compounds. This robustness stems from the probe’s directed recognition mechanism: because the oxime group reacts specifically with the P–C bond chemistry rather than engaging in generic adsorption, unrelated molecules simply do not trigger the same response, leaving the Raman spectrum clean and unambiguous.

Environmental tolerance proved equally impressive. The sensor remained effective at temperatures reaching one hundred degrees Celsius and across a pH range spanning from three to twelve, conditions that cover everything from acidic rainwater to alkaline industrial runoff. This wide operating window suggests the device could function reliably in deserts, tropical climates, contaminated water sources or the aftermath of a chemical release where ambient conditions are far from controlled. For a technology intended for deployment at the sites of potential incidents rather than in climate-controlled laboratories, this kind of environmental resilience is not a luxury but a baseline requirement.

The detection capability extends beyond liquid samples. The team demonstrated that the sensor can identify sarin in the gas phase as well, which is critical because nerve agents released in an attack would primarily exist as vapors or aerosols drifting through the air. A gas-phase detection capability combined with the compact footprint of a portable Raman spectrometer means the device could be carried by security personnel, integrated into fixed screening stations or deployed rapidly to suspected contamination zones, screening the air itself for the presence of lethal compounds before people are exposed.

According to the research team, the technology is now being developed further for technology transfer and industrial applications, signaling a move from the laboratory bench toward commercial production. The work, published under the title Rational design of an oxime-functionalized probe for ultrasensitive and portable SERS detection of organophosphorus nerve agents, appeared in Chemical Engineering Journal on 28 August 2026. As concerns over chemical warfare and industrial chemical safety continue to grow, the marriage of rational molecular design with portable spectroscopy offers a glimpse of a future where the tools to unmask invisible threats fit in a briefcase, respond in seconds and speak a chemical language that no nerve agent can escape.

Subject of Research: Portable SERS sensor for rapid detection of sarin and organophosphorus nerve agents

Article Title: Researchers develop portable sensor for rapid detection of sarin

Article References: Researchers develop portable sensor for rapid detection of sarin. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: SERS, sarin, nerve agents, organophosphorus, Raman spectroscopy, chemical detection, public safety, molecular probe, Hefei Institutes of Physical Science, Chemical Engineering Journal, Researchers, develop

SERS works by amplifying the inherently weak Raman scattering signal of molecules placed near nanostructured metal surfaces. When light strikes a plasmonic metal such as silver, collective oscillations of conduction electrons, known as surface plasmons, concentrate electromagnetic energy into nanoscale regions called hot spots. Molecules residing in these regions experience Raman signals enhanced by factors of millions or more, allowing trace detection that conventional Raman spectroscopy could never achieve. The challenge has always been engineering substrates that generate abundant hot spots while remaining uniform enough for quantitative analysis, since random nanoparticle aggregation produces erratic enhancements that vary wildly from point to point across a surface.

The new substrate tackles this challenge with a suspended architecture. Rather than depositing silver nanoparticles on a flat support, the team created a composite nanopore array in which discrete silver nanoparticles are isolated by silicon dioxide, forming ordered pore structures that hang suspended in space. This geometry is critical. The silicon dioxide spacers fix the separation between neighboring silver nanoparticles, preserving the nanoscale gaps where electromagnetic coupling is strongest. Because the particles are discrete rather than continuous, strong electromagnetic coupling occurs both between adjacent silver nanoparticles and along each nanopore structure, multiplying the number of active hot spots available to incoming analyte molecules.

Computer simulations using COMSOL confirmed the physical basis of the enhancement. The modeling revealed intense electromagnetic field localization within the gaps of the suspended pore walls and between the isolated silver particles, exactly the 3D hot spot distribution the experimental design intended. Unlike planar substrates, where hot spots concentrate only at the surface, the suspended pore geometry creates hot spots throughout the 3D volume of each pore. Analyte molecules that diffuse into the pores encounter enhanced fields along their entire pathway, effectively increasing the probability that any given molecule will land in a signal-boosting region. This volumetric hot spot availability is a key reason the substrate achieves such low detection limits.

The self-assembly strategy underlying the fabrication deserves attention because it addresses the scalability problem that plagues many high-performance SERS substrates. Lithographic approaches can produce exquisitely ordered plasmonic structures but require expensive equipment and small working areas. Self-assembly, by contrast, exploits spontaneous organization of materials into ordered patterns, potentially allowing larger substrates at lower cost. The team demonstrated that their assembled arrays exhibit high uniformity, meaning the Raman signal remains consistent across different positions on the substrate. Uniformity is the difference between a laboratory curiosity and a quantitative analytical tool, because reproducible signal intensity allows researchers to correlate peak heights directly with analyte concentration.

Stability proved equally impressive in the reported observations. Silver is famously reactive, tarnishing in air and degrading in aqueous environments, which limits the shelf life of many silver-based SERS substrates. The silicon dioxide isolation in the composite array appears to protect the silver nanoparticles, preserving the plasmonic response over time. The researchers report excellent stability alongside the ultra-low detection limit and high sensitivity, suggesting the substrate could withstand the handling and storage conditions of real-world analytical workflows rather than requiring immediate use after fabrication.

The target analyte, pyridaben, is a widely used acaricide employed against mites on fruit trees, vegetables, and ornamental crops. Like many pesticides, pyridaben residues on food products are regulated because excessive exposure poses health risks to consumers. Conventional detection methods such as chromatography coupled with mass spectrometry deliver excellent accuracy but demand costly instrumentation, skilled operators, and lengthy sample preparation. SERS offers a compelling alternative: rapid, label-free detection with minimal sample processing. The new substrate detected pyridaben at 1.19 × 10⁻¹⁰ M, a concentration low enough to satisfy stringent food safety monitoring requirements, and the technique requires only that a droplet of sample be applied to the substrate and measured with a Raman microscope.

The significance of this work extends beyond pesticide detection. The suspended composite nanopore concept could be adapted to sense a broad range of molecules, from environmental pollutants and foodborne pathogen markers to biomolecules in medical diagnostics. SERS platforms are already being explored for detecting nanoplastics in water, identifying explosive residues, monitoring human metabolites, and diagnosing diseases from biofluid samples. A substrate architecture that combines abundant 3D hot spots, high uniformity, and long-term stability addresses the three most persistent obstacles to translating SERS from specialized laboratories into routine analytical practice. The researchers suggest their design philosophy, using insulating spacers to lock plasmonic particles into optimal geometries, offers a general template for future substrate engineering.

There are still hurdles between this demonstration and widespread deployment. Real samples such as fruit extracts or river water contain complex mixtures of molecules that can compete for hot spot access or produce overlapping Raman peaks, and the suspended pores must prove their selectivity in such messy environments. Quantitative calibration across different instruments and operators will also require the kind of robust uniformity the team reports but has not yet validated at industrial scale. Nevertheless, the combination of a detection limit below one nanomolar, simulated confirmation of the hot spot physics, and a fabrication route based on self-assembly marks a substantial advance. As food safety agencies tighten residue limits and consumers demand transparency about what is on their produce, substrates like this suspended silver-silica array may soon become the workhorses of rapid, on-site chemical screening.

Subject of Research: Nanotechnology and analytical chemistry

Article Title: Suspended Ag-SiO2 composite nanopore array as SERS substrate for pyridaben detection

Article References: Tian, H., Zhang, Y., Wang, Y., Zhao, X., & Gao, R. (2026). Suspended Ag-SiO2 composite nanopore array as SERS substrate for pyridaben detection. Journal of Materials Science, 61(42), 32985-32994. https://doi.org/10.1007/s10853-026-13500-6

Image Credits: AI Generated

DOI: 10.1007/s10853-026-13500-6

Keywords: SERS, nanopore array, pyridaben, pesticide detection, silver nanoparticles, Raman spectroscopy, food safety, hot spots, Suspended, Ag-SiO2, composite, nanopore

Pseudomonas aeruginosa is a gram-negative rod-shaped bacterium measuring roughly one to five micrometers long and half a micrometer to one micrometer wide. According to the Centers for Disease Control and Prevention, it is the most common disease-causing member of the Pseudomonas group. It thrives in healthcare settings, where it causes severe infections in vulnerable patients, but it also lurks in hot tubs, swimming pools, and on contact surfaces associated with free-living animals. The authors note that the bacterium is a principal etiological factor in more than 65 percent of purulent-septic skin lesions, making rapid and reliable identification a pressing task for modern medicine.

The classical bacteriological method—growing a pure culture and identifying it from the totality of its properties—remains the gold standard for reliability, but it is laborious, costly, and slow, sometimes taking several days to deliver an answer. Automated systems such as VITEK2, Phoenix, MALDI-TOF mass spectrometry, and next-generation sequencing can shave 24 to 48 hours off the process, yet they still require substantial time and financial investment. There is also a logistics problem that is easy to overlook: roughly 30 percent of bacterial strains fail to reach laboratory testing at all, so they can never be identified. Any method that shortens the chain between sample and answer therefore carries real clinical value.

Raman spectroscopy attacks the problem from a different direction. The technique detects the vibrations of molecular bonds in a sample, producing a spectrum that acts like a chemical fingerprint. Because bacteria are built from characteristic proportions of proteins, lipids, carbohydrates, and nucleic acids, each species is thought to produce its own ensemble of Raman lines—what the researchers describe as biomolecule fingerprinting—that can be matched against a spectral library in as little as one to two minutes. Crucially, the method does not require long-term cultivation, special sample preparation, additional expensive reagents, or consumables.

Most Raman-based bacterial identification reported to date has relied on surface-enhanced Raman spectroscopy, or SERS, in which the sample is placed on a substrate coated with metallic gold or silver nanoparticles that dramatically amplify the Raman signal. These substrates are expensive and add a layer of complexity to the workflow. The goal of the new study was to demonstrate that P. aeruginosa could be identified with plain, standard Raman spectroscopy—no enhancement, no nanoparticles—by comparing the spectra of wild isolates against a well-characterized control strain, P. aeruginosa ATCC 27853 from the American Type Culture Collection.

The fieldwork began in Silene Nature Park, a NATURA2000 site in Latvia, where ten free-living European pond turtles were collected and samples were taken from the skin surface using sterile transport swabs. In the laboratory, Pseudomonas spp. were isolated by classical bacteriological methods on CHROMagar Orientation and Trypticasein Soy Lab-Agar. Colonies identified as P. aeruginosa were stored at 4 degrees Celsius, then warmed to room temperature, transferred into Brain Heart Infusion Broth, and incubated at 37 degrees Celsius for 24 hours. The cultures were then swabbed onto fresh nutrient agar and incubated for a further 24 to 48 hours before isolated colonies were emulsified in sterile distilled water, vortexed, and adjusted visually to McFarland 0.5 Standard—approximately 1.5 x 10^8 cells per milliliter. One hundred microliters of each suspension was placed on a sterile microscope slide for analysis.

Spectra were recorded with a Renishaw inVia Raman Microscope coupled to a Leica DM 2500 optical microscope, using a 50x objective and an air-cooled CCD array detector. The excitation source was an argon-ion laser operating at a short wavelength of 514 nanometers, chosen to minimize sample self-fluorescence. Laser power was kept remarkably low—no more than 50 milliwatts at the laser head and only about 0.016 milliwatts at the sample surface. More than 50 scans were accumulated for each sample, with integration times of 2 to 40 seconds per exposure and an optimal spectral resolution of 2 per centimeter. Full-length spectra covered the range from 3200 to 200 inverse centimeters, while short-length spectra focused on the 2000 to 600 inverse centimeter window. All data were collected and processed with Renishaw WiRE 5.5 software, and cosmic-ray artifacts were suppressed with dedicated removal functions.

The resulting spectra of the turtle-skin isolates and the control strain coincided closely in both intensity and the localization of their peaks. Fifteen individual Raman shifts stood out: 624, 760, 808, 1002, 1032, 1145, 1150, 1178, 1207, 1330, 1359, 1445, 1580, 1600, and 1620 inverse centimeters. Each peak could be tentatively assigned to a molecular component of the bacterial cell. The 624 line corresponds to skeletal vibrations of aromatic rings in amino acids; the 1002 and 1032 lines to phenylalanine; the 1178 and 1207 lines to aromatic amino acids such as tyrosine, phenylalanine, and tryptophan and to protein C–H stretching regions; the 1445 and 1330 lines to CH deformations in polysaccharides, lipids, and proteins; and the 1580, 1600, and 1620 lines to in-ring C=C and C–C stretching, Amide II, and Amide I vibrations of proteins and unsaturated lipids. The 1145 line was attributed to sulfonic acid residues, while the 1150 line was associated with symmetric glycosidic linkages in polysaccharides or C–C stretching vibrations, possibly including ATP.

Several practical lessons emerged from the experimental work. Taking spectra directly from colonies growing on nutrient agar in Petri dishes proved problematic: the transparent polystyrene base and the agar itself injected extra noise into the measurements. The researchers solved this by measuring drops of bacterial suspension instead, which neutralized any substrate distortion. They also confirmed that the McFarland 0.5 Standard suspension—1.5 x 10^8 cells per unit volume—is suitable for Raman analysis of this bacterium without any surface signal enhancement. The intensity of the Raman signal varied slightly with the concentration of the bacterial suspension, but measurements across different sample groups revealed no significant differences in the spectral positions. The team further noted that high-quality, reproducible spectra require keeping the exposure from any single point on the object to no more than 60 seconds, which also kept spontaneous luminescence minimal and avoided any noticeable effect of laser radiation on the cells.

The authors conclude that Raman spectroscopy, operated under these parameters, can be considered an express method for identifying microorganisms—one that detects the presence of P. aeruginosa even at the tested concentration, delivers quantitative and qualitative results within one to ten minutes for a full-range spectrum, and theoretically allows a large number of cultures to be identified simultaneously. The laser excitation parameters used did not cause destructive changes in the bacterial cells, which retained their integrity and cellular organelles. With high analytical and diagnostic sensitivity and specificity, no additional cultivation stages, and no special sample preparation, the approach offers analytical reliability at high speed. The researchers emphasize that the technology is promising for further research on other microorganisms, though interpreting spectral changes and extending the method to additional bacteria will require further study. If those follow-up efforts succeed, the humble pond turtle may have helped point the way toward a faster, cheaper era of microbial diagnosis.

Subject of Research: Rapid identification of Pseudomonas aeruginosa from European pond turtle skin using standard Raman spectroscopy

Article Title: Prospects and possibilities of using Raman spectroscopy for the identification of Pseudomonas aeruginosa from turtle Emys orbicularis (Linnaeus, 1758) skin

Article References: Petjukevičs, A., Umbraško, I., & Škute, N. (2023). Prospects and possibilities of using Raman spectroscopy for the identification of Pseudomonas aeruginosa from turtle Emys orbicularis (Linnaeus, 1758) skin. BioRisk, 21, 19-28. https://doi.org/10.3897/biorisk.21.111983

Image Credits: AI Generated

DOI: 10.3897/biorisk.21.111983

Keywords: Raman spectroscopy, Pseudomonas aeruginosa, Emys orbicularis, European pond turtle, bacterial identification, microbiology, diagnostics, SERS, spectral fingerprinting, gram-negative bacteria, Latvia, express method