Exploiting Purine as an Internal Standard for SERS Quantification of Purine Derivative Molecules Released by Bacteria.

Surface-enhanced Raman scattering (SERS) is a highly sensitive technique used in diverse biomedical applications including rapid antibiotic susceptibility testing (AST). However, signal fluctuation in SERS, particularly the widespread of signals measured from different batches of SERS substrates, compromises its reliability and introduces potential errors in SERS-AST. In this study, we investigate the use of purine as an internal standard (IS) to recalibrate SERS signals and quantify the concentrations of two important purine derivatives, adenine and hypoxanthine, which are the most important biomarkers used in SERS-AST. Our findings demonstrate that purine IS effectively mitigates SERS signal fluctuations and enables accurate prediction of adenine and hypoxanthine concentrations across a wide range (5 orders of magnitude). Calibrations with purine as an IS outperform those without, exhibiting a 10-fold increase in predictive accuracy. Additionally, the calibration curve obtained from the first batch of SERS substrates remains effective for 64 additional substrates fabricated over a half-year period. Measurements of adenine and hypoxanthine concentrations in bacterial supernatants using SERS with purine IS closely align with the liquid chromatography-mass spectrometry results. The use of purine as an IS offers a simple and robust platform to enhance the speed and accuracy of SERS-AST, while also paving the way for in situ SERS quantification of purine derivatives released by bacteria under various stress conditions.

SERS-based rapid susceptibility testing of commonly administered antibiotics on clinically important bacteria species directly from blood culture of bacteremia patients.

Bloodstream infections are a growing public health concern due to emerging pathogens and increasing antimicrobial resistance. Rapid antibiotic susceptibility testing (AST) is urgently needed for timely and optimized choice of antibiotics, but current methods require days to obtain results. Here, we present a general AST protocol based on surface-enhanced Raman scattering (SERS-AST) for bacteremia caused by eight clinically relevant Gram-positive and Gram-negative pathogens treated with seven commonly administered antibiotics. Our results show that the SERS-AST protocol achieves a high level of agreement (96% for Gram-positive and 97% for Gram-negative bacteria) with the widely deployed VITEK 2 diagnostic system. The protocol requires only five hours to complete per blood-culture sample, making it a rapid and effective alternative to conventional methods. Our findings provide a solid foundation for the SERS-AST protocol as a promising approach to optimize the choice of antibiotics for specific bacteremia patients. This novel protocol has the potential to improve patient outcomes and reduce the spread of antibiotic resistance.

Sensible Functional Linear Discriminant Analysis Effectively Discriminates Enhanced Raman Spectra of Mycobacterium Species.

Tuberculosis caused by Mycobacterium tuberculosis complex (MTBC) is one of the major infectious diseases in the world. Identification of MTBC and differential diagnosis of nontuberculous mycobacteria (NTM) species impose challenges because of their taxonomic similarity. This study describes a differential diagnosis method using the surface-enhanced Raman scattering (SERS) measurement of molecules released by Mycobacterium species. Conventional principal component analysis and linear discriminant analysis methods successfully separated the acquired spectrum of MTBC from those of NTM species but failed to distinguish between the spectra of different NTM species. A novel sensible functional linear discriminant analysis (SLDA), projecting the averaged spectrum of a bacterial specie to the subspace orthogonal to the within-species random variation, thereby eliminating its influence in applying linear discriminant analysis, was employed to effectively discriminate not only MTBC but also species of NTM. The successful demonstration of this SERS-SLDA method opens up new opportunities for the rapid differentiation of Mycobacterium species.

Antibiotic Susceptibility Test with Surface-Enhanced Raman Scattering in a Microfluidic System.

Antibiotic susceptibility test (AST) is essential in clinical diagnosis of serious bacterial infection, such as sepsis, while it typically takes 2-5 days for sample culture, antibiotic treatment, and reading result. Detecting metabolites secreted from bacteria with surface-enhanced Raman scattering (SERS) enables rapid determination of antibiotic susceptibility, reducing the AST time to 1-2 days. However, it still requires 1 day of culture time to obtain sufficient quantity of bacteria for sample washing, bacterial extraction, and antibiotic treatment. Additionally, the whole procedure, manually performed in open environment, often suffers from contamination and human error. To address the above problems, a microfluidic system integrating membrane filtration and the SERS-active substrate (MF-SERS) was developed to perform on-chip bacterial enrichment, metabolite collection, and in situ SERS measurements for antibiotic susceptibility test. Using Escherichia coli as the prototype bacterium, the lowest SERS detection limit of bacterial concentration of the MF-SERS system is 103 CFU/mL, which is 4 orders of magnitude lower than that using centrifugation-purification procedure, significantly shortening the bacterial culture time. The bacteria and secreted metabolites are enclosed during bacterial trapping, metabolite filtration, and SERS detection, thus minimizing possible contamination and human errors. Finally, the successful demonstration of AST on E. coli with a concentration of 103 CFU/mL is presented. Overall, the MF-SERS system with a miniature size and well-confined microenvironment allows the integration of multiple bacteria processes for bacterial enrichment, culture, and determination of AST.

Quantification of biomolecules responsible for biomarkers in the surface-enhanced Raman spectra of bacteria using liquid chromatography-mass spectrometry.

Recently, specific biomarkers in the surface-enhanced Raman scattering (SERS) spectra of bacteria have been successfully exploited for rapid bacterial antibiotic susceptibility testing (AST) - dubbed SERS-AST. The biomolecules responsible for these bacterial SERS biomarkers have been identified as several purine derivative metabolites involved in bacterial purine salvage pathways (W. R. Premasiri, J. C. Lee, A. Sauer-Budge, R. Theberge, C. E. Costello and L. D. Ziegler, Anal. Bioanal. Chem., 2016, 408, 4631). Here we quantified these metabolites in the SERS spectra of Staphylococcus aureus and Escherichia coli using ultra-performance liquid chromatography/electrospray ionization-mass spectrometry (UPLC/ESI-MS). The time dependences of the concentrations of these molecules were measured using 13C- or 12C-purine derivatives as internal and external standards respectively in UPLC/ESI-MS measurements. Surprisingly, a single S. aureus and an E. coli cell were found to release millions of adenine and hypoxanthine into a water environment in an hour respectively. Furthermore, simulated SERS spectra of bacterial supernatants based on the mixtures of purine derivatives with measured concentrations also show great similarity with those of the corresponding bacterial samples. Our results not only provide a quantitative foundation for the emerging SERS-AST method but also suggest the potential of exploiting SERS for in situ monitoring the changes in bacterial purine salvage processes in response to different physical and chemical challenges.

Dependence of Adenine Raman Spectrum on Excitation Laser Wavelength: Comparison between Experiment and Theoretical Simulations.

We acquired the Raman spectra of adenine in powder and aqueous phase using excitation lasers with 532, 633, and 785 nm wavelengths for the region between 300 and 1500 cm-1. In comparison to the most distinct peak at 722 cm-1, the peaks between 1200 and 1500 cm-1 exhibited a characteristic increase in cross-section with decreasing excitation wavelength in both phases. This trend can be reproduced by different density functional theory (DFT) calculations for the adenine molecule in the gas phase as well as in the aqueous phase. Furthermore, from the calculation on the π-stacked dimer, hydrogen-bonded dimer, and trimer, we find that this trend toward excitation laser wavelength is not sensitive to the packing. When comparing the Raman spectra given by different excitation wavelength, one should take care in analyzing the cross-section, and present day DFT calculations are able to capture general trends in the excitation laser wavelength dependence of the Raman activity.

Highly active and stable hybrid catalyst of cobalt-doped FeS2 nanosheets-carbon nanotubes for hydrogen evolution reaction.

Hydrogen evolution reaction (HER) from water through electrocatalysis using cost-effective materials to replace precious Pt catalysts holds great promise for clean energy technologies. In this work we developed a highly active and stable catalyst containing Co doped earth abundant iron pyrite FeS(2) nanosheets hybridized with carbon nanotubes (Fe(1-x)CoxS(2)/CNT hybrid catalysts) for HER in acidic solutions. The pyrite phase of Fe(1-x)CoxS(2)/CNT was characterized by powder X-ray diffraction and absorption spectroscopy. Electrochemical measurements showed a low overpotential of ∼0.12 V at 20 mA/cm(2), small Tafel slope of ∼46 mV/decade, and long-term durability over 40 h of HER operation using bulk quantities of Fe(0.9)Co(0.1)S(2)/CNT hybrid catalysts at high loadings (∼7 mg/cm(2)). Density functional theory calculation revealed that the origin of high catalytic activity stemmed from a large reduction of the kinetic energy barrier of H atom adsorption on FeS(2) surface upon Co doping in the iron pyrite structure. It is also found that the high HER catalytic activity of Fe(0.9)Co(0.1)S(2) hinges on the hybridization with CNTs to impart strong heteroatomic interactions between CNT and Fe(0.9)Co(0.1)S(2). This work produces the most active HER catalyst based on iron pyrite, suggesting a scalable, low cost, and highly efficient catalyst for hydrogen generation.

Looking into meta-atoms of plasmonic nanowire metamaterial.

Nanowire-based plasmonic metamaterials exhibit many intriguing properties related to the hyperbolic dispersion, negative refraction, epsilon-near-zero behavior, strong Purcell effect, and nonlinearities. We have experimentally and numerically studied the electromagnetic modes of individual nanowires (meta-atoms) forming the metamaterial. High-resolution, scattering-type near-field optical microscopy has been used to visualize the intensity and phase of the modes. Numerical and analytical modeling of the mode structure is in agreement with the experimental observations and indicates the presence of the nonlocal response associated with cylindrical surface plasmons of nanowires.

Enhancing bright-field image of microorganisms by local plasmon of Ag nanoparticle array.

Inspecting biological cells with bright-field light microscopy often engenders a challenge, owing to their optical transparency. We show that imaging contrast can be greatly enhanced as yeast cells are placed on a silver nanoparticle array. Its near- and far-field traits, revealed by electrodynamic simulations, illustrate that the enhancement is attributed to the sensitivity of its plasmonic characteristics to the attached cells. This study demonstrates that the silver nanoparticle array can serve as the agent for concurrently enhancing Raman scattering and imaging contrast of microorganisms for identification and examination.

Custom-designed arrays of anodic alumina nanochannels with individually tunable pore sizes.

We demonstrate a process to selectively tune the pore size of an individual nanochannel in an array of high-aspect-ratio anodic aluminum oxide (AAO) nanochannels in which the pore sizes were originally uniform. This novel process enables us to fabricate arrays of AAO nanochannels of variable sizes arranged in any custom-designed geometry. The process is based on our ability to selectively close an individual nanochannel in an array by using focused ion beam (FIB) sputtering, which leads to redeposition of the sputtered material and closure of the nanochannel with a capping layer of a thickness depending on the energy of the FIB. When such a partially capped array is etched in acid, the capping layers are dissolved after different time delays due to their different thicknesses, which results in differences in the time required for the following pore-widening etching processes and therefore creates an array of nanochannels with variable pore sizes. The ability to fabricate such AAO templates with high-aspect-ratio nanochannels of tunable sizes arranged in a custom-designed geometry paves the way for the creation of nanophotonic and nanoelectronic devices.

A novel vertical fan-out platform based on an array of curved anodic alumina nanochannels.

Focused ion beam lithography and a two-step anodization have been combined to fabricate a vertical fan-out platform containing an array of unique probes. Each probe comprises three anodic alumina nanochannels with a fan-out arrangement. The lithography is used to pattern an aluminum sheet with a custom-designed array of triangular 'cells' whose apexes are composed of nanoholes. The nanoholes grow into straight nanochannels under proper voltage in the first-step anodization. The second step uses a doubled voltage to induce lateral repulsion among the nanochannels' growth fronts originating in the same cell. Therefore, the fronts fan out. The repulsion roots in the inter-front distance being shorter than the naturally favoured length, which increases with anodization voltage. The fan-out evolution continues until the growth fronts originating in all the cells evolve into a close-packed two-dimensional hexagonal lattice whose spacing is identical to the favoured one. The chemical and physical mechanisms behind the fan-out fabrication are discussed. This novel fan-out platform facilitates probing and handling of many signals from different areas on a sample's surface and is therefore promising for applications in detection and manipulation at the nanoscale level.

Automated quantitative analysis of lipid accumulation and hydrolysis in living macrophages with label-free imaging.

The accumulation of lipids in macrophages is a key factor that promotes the formation of atherosclerotic lesions. Several methods such as biochemical assays and neutral lipid staining have been used for the detection of lipids in cells. However, a method for real-time quantitative assessment of the lipid content in living macrophages has yet to be shown, particularly for its kinetic process with drugs, due to the lack of suitable tools for non-invasive chemical detection. Here we demonstrate label-free real-time monitoring of lipid droplets (LDs) in living macrophages by using coherent anti-Stokes Raman scattering (CARS) microscopy. In addition, we have established an automated image analysis method based on maximum entropy thresholding (MET) to quantify the cellular lipid content. The result of CARS image analysis shows a good correlation (R(2) > 0.9) with the measurement of biochemical assay. Using this method, we monitored the processes of lipid accumulation and hydrolysis in macrophages. We further characterized the effect of a lipid hydrolysis inhibitor (diethylumbelliferyl phosphate, DEUP) and determined the kinetic parameters such as the inhibition constant, K(i). Our work demonstrates that the automated quantitative analysis method is useful for the studies of cellular lipid metabolism and has potential for preclinical high-throughput screening of therapeutic agents related to atherosclerosis and lipid-associated disorders.

Revealing local, enhanced optical field characteristics of Au nanoparticle arrays with 10 nm gap using scattering-type scanning near-field optical microscopy.

Anomalous optical properties displayed by plasmonic structures are commonly attributed to the enhanced, local field within their corrugations. Though theoretical calculations of such field enhancements abound, experimental observations are relatively few, because only few optical microscopic techniques have enough spatial resolution. We used scattering-type scanning near-field optical microscopy to resolve local optical characteristics of a gold nanoparticle array with 10 nm gap between adjacent particles. Subnanometer-resolution measurement of the optical field intensity was achieved by use of etched silicon atomic force microscopy probe tip. The result shows that, with a p-polarized excitation scheme, the induced field is enhanced and the phase undergoes a large change in the gap region. The spatially-resolved signals are attributed to the electromagnetic interaction within an array of vertical dipoles. We show that scattering-type near-field optical microscopy is well-suited to the investigation of field enhancements in plasmon-enhanced sensing and spectroscopy array structures.

Rapid detection of nicotine and benzoic acid in e-liquids with surface-enhanced Raman scattering and artificial intelligence-assisted spectrum interpretation.

Electronic cigarettes have rapidly gained acceptance recently. Nicotine-containing electronic cigarette liquids (e-liquids) are prohibited in some countries, but are permitted and simply available online in others. A rapid detection method is therefore required for on-site inspection or screening of a large amount of samples. Our previous study demonstrated a surface-enhanced Raman scattering (SERS)-based approach to identify nicotine-containing e-liquids; without any pre-treatment, e-liquid can be directly tested on our solid-phase SERS substrates, made of silver nanoparticle arrays embedded in anodic aluminium oxide nanochannels (Ag/AAO). However, this approach required manual determination of spectral signatures and negative samples should be validated in the second round detection. Here, after examining 406 commercial e-liquids, we refined this approach by developing artificial intelligence (AI)-assisted spectrum interpretations. We also found that nicotine and benzoic acid can be simultaneously detected in our platform. This increased test sensitivity because benzoic acid is usually used in nicotine salts. Around 64% of nicotine-positive samples in this study showed both signatures. Using either cutoffs of nicotine and benzoic acid peak intensities or a machine learning model based on the CatBoost algorithm, over 90% of tested samples can be correctly discriminated with only one round of SERS measurement. False negative and false positive rates were 2.5-4.4% and 4.4-8.9%, respectively, depending on the interpretation method and thresholds applied. The new approach takes only 1 microliter of sample and can be performed in 1-2 min, suitable for on-site inspection with portable Raman detectors. It could also be a complementary platform to reduce samples that need to be analyzed in the central labs and has the potential to identify other prohibited additives.

Periodic Si nanopillar arrays by anodic aluminum oxide template and catalytic etching for broadband and omnidirectional light harvesting.

Large-area, periodic Si nanopillar arrays (NPAs) with the periodicity of 100 nm and the diameter of 60 nm were fabricated by metal-assisted chemical etching with anodic aluminum oxide as a patterning mask. The 100-nm-periodicity NPAs serve an antireflection function especially at the wavelengths of 200~400 nm, where the reflectance is decreased to be almost tenth of the value of the polished Si (from 62.9% to 7.9%). These NPAs show very low reflectance for broadband wavelengths and omnidirectional light incidence, attributed to the small periodicity and the stepped refractive index of NPA layers. The experimental results are confirmed by theoretical calculations. Raman scattering intensity was also found to be significantly increased with Si NPAs. The introduction of this industrial-scale self-assembly methodology for light

Thermometric lateral flow immunoassay with colored latex beads as reporters for COVID-19 testing.

Temperature sensing is a promising method of enhancing the detection sensitivity of lateral flow immunoassay (LFIA) for point-of-care testing. A temperature increase of more than 100 °C can be readily achieved by photoexcitation of reporters like gold nanoparticles (GNPs) or colored latex beads (CLBs) on LFIA strips with a laser power below 100 mW. Despite its promise, processes involved in the photothermal detection have not yet been well-characterized. Here, we provide a fundamental understanding of this thermometric assay using non-fluorescent CLBs as the reporters deposited on nitrocellulose membrane. From a measurement for the dependence of temperature rises on the number density of membrane-bound CLBs, we found a 1.3-fold (and 3.2-fold) enhancement of the light absorption by red (and black) latex beads at 520 nm. The enhancement was attributed to the multiple scattering of light in this highly porous medium, a mechanism that could make a significant impact on the sensitivity improvement of LFIA. The limit of detection was measured to be 1 × 105 particles/mm2. In line with previous studies using GNPs as the reporters, the CLB-based thermometric assay provides a 10× higher sensitivity than color visualization. We demonstrated a practical use of this thermometric immunoassay with rapid antigen tests for COVID-19.

An antibiotic concentration gradient microfluidic device integrating surface-enhanced Raman spectroscopy for multiplex antimicrobial susceptibility testing.

Antimicrobial susceptibility testing (AST) is a key measure in clinical microbiology laboratories to enable appropriate antimicrobial administration. During an AST, the determination of the minimum inhibitory concentration (MIC) is an important step in which the bacterial responses to an antibiotic at a series of concentrations obtained in separate bacterial growth chambers or sites are compared. However, the preparation of different antibiotic concentrations is time-consuming and labor-intensive. In this paper, we present a microfluidic device that generates a concentration gradient for antibiotics that is produced by diffusion in the laminar flow regime along a series of lateral microwells to encapsulate bacteria for antibiotic treatment. All the AST preparation steps (including bacterium loading, antibiotic concentration generation, buffer washing, and isolated bacterial growth with an antibiotic) can be performed in a single chip. The viable bacterial cells in each microwell after the antibiotic treatment are then quantified by their surface-enhanced Raman scattering (SERS) signals that are acquired after placing a uniform SERS-active substrate in contact with all the microwells. For proof-of-concept, we demonstrated the AST performance of this system on ampicillin (AMP)-susceptible and -resistant E. coli strains. Compared with the parameters for conventional AST methods, the AST procedure based on this chip requires only 20 µL of bacteria solution and 5 h of operation time. This result indicates that this integrated system can greatly shorten and simplify the tedious and labor-intensive procedures required for current standard AST methods.

Morphological evolution of porous nanostructures grown from a single isolated anodic alumina nanochannel.

Porous anodic aluminum oxide (AAO) membranes have been widely used as templates for growing nanomaterials because of their ordered nanochannel arrays with high aspect ratio and uniform pore diameter. However, the intrinsic growth behavior of an individual AAO nanochannel has never been carefully studied for the lack of a means to fabricate a single isolated anodic alumina nanochannel (SIAAN). In this study, we develop a lithographic method for fabricating a SIAAN, which grows into a porous hemispherical structure with its pores exhibiting fascinating morphological evolution during anodization. We also discover that the mechanical stress affects the growth rate and pore morphology of AAO porous structures. This study helps reveal the growth mechanism of arrayed AAO nanochannels grown on a flat aluminum surface and provides insights to help pave the way to altering the geometry of nanochannels on AAO templates for the fabrication of advanced nanocomposite materials.

Transparent Raman-enhancing substrates for microbiological monitoring and in situ pollutant detection.

Opaque Raman-enhancing substrates made of Ag nanoparticles on incompletely oxidized aluminum templates have been rendered transparent by an ion-drift process to complete the oxidation. The result shows that the transparent substrates exhibit high/uniform surface-enhanced Raman scattering (SERS) capability and good optical transmissivity, allowing for concurrent SERS characterization and high contrast transmission-mode optical imaging of S. aureus bacteria. We also demonstrate that the transparent substrates can used in conjunction with optical fibers as SERS sensors for in situ detection of malachite green down to 10(-9) M.

Autocatalytic reaction in hydrolysis of difructose anhydride III.

Hydrolysis of several polysaccharides in neutral and weak acid environment has been shown to exhibit autocatalytic behavior. Because the pH value of the solution decreases during hydrolysis, it has been proposed that proton is the catalyst of the autocatalytic reaction. We monitored the hydrolysis of difructose anhydride III (DFA III) in both strong and weak acid environment using Raman spectroscopy and found that it is also an autocatalytic reaction. Its Raman signatures were analyzed with ab initio method. When the reaction product, fructose, is added in the beginning of the reaction, the speed of hydrolysis increases to a magnitude that cannot be explained by the rate enhancement due to a decrease in the pH value, indicating that proton alone is not an effective catalyst for the reaction. It is the combination of proton and a certain form of reaction product such as monosaccharide or its derivatives that catalyzes the hydrolysis of difructose anhydride III. Similar results are observed in the hydrolysis of cellobiose, suggesting the universality of this autocatalytic reaction. Our findings provide the first clue to a new autocatalytic pathway in the hydrolysis of polysaccharides.