Highly Sensitive Detection of Proteins and Bacteria in Aqueous Solution Using Surface-Enhanced Raman Scattering and Optical Fibers

Simultaneous SERS-decoding detection of multiple pathogens in drinking water with home-made portable double-layer filtration and concentration device

The engineering of a home-made portable double-layer filtration and concentration device with the common syringe for rapid analysis of water samples is reported. The core elements of the device were two installed filtration membranes with different pore sizes for respective functions. The upper filtration membrane was used for preliminary intercepting large interfering impurities (interception membrane), while the lower filtration membrane was used for collecting multiple target pathogens (enrichment membrane) for determination. This combination can make the contaminated environmental water, exemplified by surface water, filtrated quickly through the device and just retained the target bacteria of Escherichia coli O157:H7, Staphylococcus aureus, and Listeria monocytogenes on the lower enrichment membrane. Integrating with surface-enhanced Raman spectra (SERS) platform to decode the SERS-Tags (SERS-TagCVa, SERS-TagR6G, and SERS-TagMB) already labeled on each of the enriched bacteria based the antibody-mediated immuno-recognition effect, fast separation, concentration, and detection of multiple pathogenic bacteria from the bulk of contaminated environmental water were realized. Results show that within 30 min, all target bacteria in the lake water can be simultaneously and accurately measured in the range from 101 to 106 CFU mL-1 with detection limit of 10.0 CFU mL-1 without any pre-culture procedures. This work highlights the simplicity, rapidness, cheapness, selectivity, and the robustness of the constructed method for simultaneous detecting multiple pathogens in aqueous samples. This protocol opens a new avenue for facilitating the development of versatile analytical tools for drinking water and food safety monitoring in underdeveloped or developing countries.

Surface-Enhanced Raman Scattering in Silver-Coated Suspended-Core Fiber

In this paper, the silver-coated large-core suspended-core fiber (LSCF) probe was fabricated by the dynamic chemical liquid phase deposition method for surface-enhanced Raman scattering (SERS) sensing. The 4-mercaptophenylboronic acid (4-MPBA) monolayer was assembled in the LSCF as the recognition monolayer. Taking advantage of the appropriate core size of the LSCF, a custom-made Y-type optical fiber patch cable was utilized to connect the semiconductor laser, Raman spectrometer, and the proposed fiber SERS probe. The SERS signal is propagated in the silver-coated air channels, which can effectively reduce the Raman and fluorescence background of the silica core. Experiments were performed to measure the Raman scattering spectra of the 4-MPBA in the silver-coated LSCF in a non-enhanced and enhanced case. The experiment results showed that the Raman signal strength was enhanced more than 6 times by the surface plasmon resonance compared with the non-enhanced case. The proposed LSCF for SERS sensing technology provides huge research value for the fiber SERS probes in biomedicine and environmental science. The combination of SERS and microstructured optical fibers offers a potential approach for SERS detection.

Antimicrobial Agent against Methicillin-Resistant Staphylococcus aureus Biofilm Monitored Using Raman Spectroscopy

The prevalence of antimicrobial-resistant bacteria has become a major challenge worldwide. Methicillin-resistant Staphylococcus aureus (MRSA)-a leading cause of infections-forms biofilms on polymeric medical devices and implants, increasing their resistance to antibiotics. Antibiotic administration before biofilm formation is crucial. Raman spectroscopy was used to assess MRSA biofilm development on solid culture media from 0 to 48 h. Biofilm formation was monitored by measuring DNA/RNA-associated Raman peaks and protein/lipid-associated peaks. The search for an antimicrobial agent against MRSA biofilm revealed that Eugenol was a promising candidate as it showed significant potential for breaking down biofilm. Eugenol was applied at different times to test the optimal time for inhibiting MRSA biofilms, and the Raman spectrum showed that the first 5 h of biofilm formation was the most antibiotic-sensitive time. This study investigated the performance of Raman spectroscopy coupled with principal component analysis (PCA) to identify planktonic bacteria from biofilm conglomerates. Raman analysis, microscopic observation, and quantification of the biofilm growth curve indicated early adhesion from 5 to 10 h of the incubation time. Therefore, Raman spectroscopy can help in monitoring biofilm formation on a solid culture medium and performing rapid antibiofilm assessments with new antibiotics during the early stages of the procedure.

Fiber Optic SERS Sensor with Silver Nanocubes Attached Based on Evanescent Wave for Detecting Pesticide Residues

Surface-enhanced Raman scattering (SERS) has great potential in the field of rapid detection of pesticide residues in food. In this paper, a fiber optic SERS sensor excited by evanescent waves was proposed for efficient detection of thiram. Silver nanocubes (Ag NCs) were prepared as SERS active substrates, which had much stronger electromagnetic field intensity than nanospheres under laser excitation due to much more "hot spots". By using the method of electrostatic adsorption and laser induction, Ag NCs were uniformly assembled at the fiber taper waist (FTW) for enhancing the Raman signal. Different from the traditional way of stimulation, evanescent wave excitation greatly increased the interaction area between the excitation and analyte, while reducing the damage of the excited light to the metal nanostructures. The methods proposed in this work have been successfully used to detect the pesticide residues of thiram and showed good detection performance. The detection limits for 4-Mercaptobenzoic acid (4-MBA) and thiram were determined to be 10^-9 and 10^-8 M, the corresponding enhancement factor could be 1.64 × 10⁵ and 6.38 × 10⁴. Low concentration of thiram was detected in the peels of tomatoes and cucumbers, indicating its feasibility in actual sample detection. The combination of evanescent waves and SERS provides a new direction for the application of SERS sensors, which had great application potential in the field of pesticide residue detection.

Surface-Roughened SERS-Active Single Silver Nanowire for Simultaneous Detection of Intracellular and Extracellular pHs

The simultaneous and accurate detection of intracellular pH (pH_i) and extracellular pH (pH_e) is essential for studying the complex physiological activities of cancer cells and exploring pH-related therapeutic mechanisms. Here, we developed a super-long silver nanowire-based surface-enhanced Raman scattering (SERS) detection strategy for simultaneous sensing of pH_i and pH_e. A surface-roughened silver nanowire (AgNW) with a high aspect ratio is prepared at a nanoelectrode tip using a Cu-mediated oxidation process, which is then modified by pH-sensitive 4-mercaptobenzoic acid (4-MBA) to form 4-MBA@AgNW as a pH sensing probe. With the assistance of a 4D microcontroller, 4-MBA@AgNW is efficient in simultaneously detecting pH_i and pH_e in both 2D and 3D culture cancer cells by SERS, with minimal invasiveness, high sensitivity, and spatial resolution. Further investigation proves that the surface-roughened single AgNW can also be used in monitoring the dynamic variation of pH_i and pH_e of cancer cells upon stimulation with anticancer drugs or under a hypoxic environment.

A direct method for detecting proteins in body fluids by Surface-Enhanced Raman Spectroscopy under native conditions

Surface enhanced Raman spectroscopy (SERS) is widely used in biomolecular detection. However, maintaining the native structure of proteins while obtaining sensitive and reproducible SERS signals of unlabeled proteins remains a challenge. In this study, dichloromethane (DCM) and CaCl₂ were used to optimize the aggregation of Ag nanoparticles (AgNPs), and several proteins were analyzed comprehensively. Calcium ions removed citrate ions outside AgNPs, inducing hot spots and achieving high-sensitivity SERS signals of proteins. Furthermore, 20 random samples of 0.5 μg/mL hemoglobin were analyzed by this method. The obtained spectra showed good repeatability and a high quality. Using the peak intensity of DCM as internal parameter, the differences in peak intensities at the same position were analyzed to distinguish different proteins and evaluate changes in protein structure. Subsequently, the protein content in protein mixtures and serum was quantified and a good linear relationship between peak intensity and protein concentration was obtained. This method shows great promise in the fields of food testing and clinical diagnosis.

Monitoring allergic reaction to penicillin based on ultrasensitive detection of penicilloyl protein using alkyne response SERS immunosensor

The evaluation of true penicillin allergy is significant to reduce its occurrence and the overdiagnosis before anti-infective treatment. However, the currently available methods with high specificity still face the problem of low sensitivity, thereby easily leading to false negatives. Herein, an alkyne responsive surface-enhanced Raman scattering (SERS) immunosensor is reported for ultrasensitive detection of penicillin allergen penicilloyl protein (P-protein) by using Au-Ag alloy nanoparticles@(antibody + alkyne probe) (as SERS immunoprobe) together with Ag nanofilm modified by antibody (as SERS capture substrate). The SERS immunoassay integrates the interference-free Raman response of high wavenumber region (2212 cm^-1) and specific capture antibody with high affinity to selectively recognize P-protein from complicated sample. Meanwhile, the target-induced near-field coupling effect between localized surface plasmon resonances of individual SERS immunoprobe and capture substrate enables the detection of P-protein as low as pg/mL level, and the limit of detection can reach 0.329 pg/mL that is about 6 orders of magnitude lower than the limit defined protein residue (causing penicillin allergy). With the ultrasensitivity and specific selectivity, the proposed SERS immunoassay platform can precisely evaluate the content of P-protein in blood sample or penicillin drugs. It will be a potential tool to monitor allergic reaction to penicillin and better understand the mechanism of penicillin hypersensitivity.

Quantitative Assessment of Periodontal Bacteria Using a Cell-Based Immunoassay with Functionalized Quartz Crystal Microbalance

Periodontal disease is an inflammatory disorder that is triggered by bacterial plaque and causes the destruction of the tooth-supporting tissues leading to tooth loss. Several bacteria species, including Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, are considered to be associated with severe periodontal conditions. In this study, we demonstrated a quartz crystal microbalance (QCM) immunoassay for quantitative assessment of the periodontal bacteria, A. actinomycetemcomitans. An immunosensor was constructed using a self-assembled monolayer of 11-mercaptoundecanoic acid (11-MUA) on the gold surface of a QCM chip. The 11-MUA layer was evaluated using a cyclic voltammetry technique to determine its mass and packing density. Next, a monoclonal antibody was covalently linked to 11-MUA using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide to act as the biorecognition element. The specificity of the monoclonal antibody was confirmed by an enzyme-linked immunosorbent assay. A calibration curve, for the relationship between the frequency shifts and number of bacteria, was used to calculate the number of A. actinomycetemcomitans bacteria in a test sample. Based on a regression equation, the lower detection limit was 800 cells, with a dynamic range up to 2.32 × 106 cells. Thus, the QCM biosensor in this study provides a sensitive and label-free method for quantitative analysis of periodontal bacteria. The method can be used in various biosensing assays for practical application and routine detection of periodontitis pathogens.

AuNP array coated substrate for sensitive and homogeneous SERS-immunoassay detection of human immunoglobulin G

Owing to the high sensitivity, fast responsiveness and high specificity, immunoassays using surface-enhanced Raman scattering (SERS) as the readout signal displayed great potential in disease diagnosis. In this study, we developed a SERS-immunoassay method for the detection of human immunoglobulin G (HIgG). Upon involving well-ordered AuA on a SERSIA substrate, the LSPR effect was further enhanced to generate a strong and uniform Raman signal through the formation of sandwich structure with the addition of target HIgG and SERSIA tag. Optimization of the assay provided a wide linear range (0.1–200 μg mL⁻¹) and low limit of detection (0.1 μg mL⁻¹). In addition, the SERS-immunoassay method displayed excellent specificity and was homogeneous, which guaranteed the practical use of this method in the quantitative detection of HIgG. To validate this assay, human serum was analysed, which demonstrated the potential advantages of SERS-immunoassay technology in clinical diagnostics.

An AuNP array coated substrate was developed for the SERS-immunoassay detection of human immunoglobulin G.

Understanding the role of the gut in undernutrition: what can technology tell us?

Gut function remains largely underinvestigated in undernutrition, despite its critical role in essential nutrient digestion, absorption and assimilation. In areas of high enteropathogen burden, alterations in gut barrier function and subsequent inflammatory effects are observable but remain poorly characterised. Environmental enteropathy (EE)-a condition that affects both gut morphology and function and is characterised by blunted villi, inflammation and increased permeability-is thought to play a role in impaired linear growth (stunting) and severe acute malnutrition. However, the lack of tools to quantitatively characterise gut functional capacity has hampered both our understanding of gut pathogenesis in undernutrition and evaluation of gut-targeted therapies to accelerate nutritional recovery. Here we survey the technology landscape for potential solutions to improve assessment of gut function, focussing on devices that could be deployed at point-of-care in low-income and middle-income countries (LMICs). We assess the potential for technological innovation to assess gut morphology, function, barrier integrity and immune response in undernutrition, and highlight the approaches that are currently most suitable for deployment and development. This article focuses on EE and undernutrition in LMICs, but many of these technologies may also become useful in monitoring of other gut pathologies.

Fiber-cap biosensors for SERS analysis of liquid samples

Optical detection techniques based on surface enhanced Raman spectroscopy (SERS) are a powerful tool for biosensing applications. Meanwhile, due to technological advances, different approaches have been investigated to integrate SERS substrates on the tip of optical fibres for molecular probing in liquids. To further demonstrate the perspectives offered by SERS-on-fiber technology for diagnostic purposes, in this study, novel cap-shaped SERS sensors for reversible coupling with customized multimodal probes were prototyped via low-cost polymer casting of polydimethylsiloxane (PDMS) and further assembly of gold nanoparticles (Au NPs) of varied sizes and shapes. To demonstrate the feasibility of liquid sensing with cap sensors using backside illumination and detection, the spectra of rhodamine were acquired by coupling the caps with the fiber. As expected by UV-vis, the highest SERS efficiency was observed for NP-decorated substrates with plasmonic properties in resonance with the irradiation wavelength. Then, SERS biosensors for the specific detection of amyloid-β (Aβ) neurotoxic biomarkers were realized by covalent grafting of Aβ antibodies. As attested by fluorescence images and SERS measurements, the biosensors successfully exhibited enhanced Aβ affinity compared to the bare sensors without ligands. Finally, these versatile (bio)sensors are a powerful tool to transform any milli-sized fibers into functional (bio)sensing platforms with plasmonic and biochemical properties tailored for specific applications.

Determination of vibrational band positions in the E-hook of β-tubulin

Raman spectral characterization of the β-TUBB2A E-hook hexapeptide, EGEDEA, is determined through experimental analysis combined with full geometry optimizations and corresponding harmonic vibrational frequency computations employing DFT methods. The hexapeptide is first broken down into di- and tetrapeptide fragments which are analyzed both quantum chemically and experimentally, and then combined to achieve an energetic minimum of the large EGEDEA hexapeptide. The Raman spectral characterization of EGEDEA band positions are then verified via the literature and comparison to the small fragment's similarly located band positions. The approach employed provides further evidence for the use of fragments as a helpful tool in characterization of the vibrational band positions of large peptides. STATEMENT OF SIGNIFICANCE: To investigate β-TUBB2A E-hook hexapeptide, a unique approach is employed whereby the hexapeptide is broken into fragments, EG, ED, EA, EGED, and EDEA and analyzed via experimental Raman spectroscopy of the crystalline solids. The experimentally observed vibrational band positions are compared to those computed using and scaled from DFT methods and Pople's 6-311+G(2df,2pd) basis set. The reported vibrational band positions are also confirmed by previously reported bands of similar peptides in the literature. This methodology facilitates differentiation between the behaviors of various side chains and their influence on the structure of the hexapeptide, providing insight into not only the nature of the peptide but also defining regions for potential protein and cytoplasmic interactions, without requiring excessive computing resources or overly-sensitive experimental methods.

Functional BOD-Ad-Cmyc@BSA complex nanosensor for Cu(II) and the detection of live E. coli

Escherichia coli (E. coli) is abundantly present in nature. It is generally harmless to humans but some strains have been deemed very dangerous. Therefore, as an indicator of hygienic testing, the detection of E. coli is essential. In this work, a fluorescent assembly was synthesized and characterized by spectroscopic methods. It was found that the amantadine (Ad) conjugated dye (BOD-Ad) intercalated into Cmyc G4 (aptamer) forming a non-emission assembly (BOD-Ad-Cmyc), which could be lighted-up by BSA due to the formation of fluorescence nanoparticle BOD-Ad-Cmyc@BSA. Further, BOD-Ad-Cmyc@BSA can selectively bind Cu²⁺ forming non-emission species BOD-Ad-Cmyc@BSA-Cu²⁺. E. coli can turn-on the emission of BOD-Ad-Cmyc@BSA-Cu²⁺ system due to the copper accumulation or reduction by E. coli. Therefore, a fluorescence method for the determination of E. coli was built. The detection limit of BOD-Ad-Cmyc@BSA-Cu²⁺ of E. coli is 6.3 CFU/mL. Thus, this BOD-Ad-Cmyc@BSA-Cu²⁺ fluorescent assembly can be used for the detection of live E. coli in the environment.

Water-soluble ZnCuInSe quantum dots for bacterial classification, detection, and imaging

Bacteria are everywhere and pose severe threats to human health and safety. The rapid classification and sensitive detection of bacteria are vital steps of bacterial community research and the treatment of infection. Herein, we developed optical property-superior and heavy metal-free ZnCuInSe quantum dots (QDs) for achieving rapid discrimination of Gram-positive/Gram-negative bacteria by the naked eye; driven by the structural differences of bacteria, ZnCuInSe QDs are effective in binding to Gram-positive bacteria, especially Staphylococcus aureus (S. aureus), in comparison with Gram-negative bacteria and give discernable color viewed by the naked eye. Meanwhile, based on its distinctive fluorescence response, the accurate quantification of S. aureus was investigated with a photoluminescence system in the concentration ranges of 1 × 10³ to 1 × 10¹¹ CFU/mL, with a limit of detection of 1 × 10³ CFU/mL. Furthermore, we demonstrated the feasibility of ZnCuInSe QDs as a fluorescence probe for imaging S. aureus. This simple strategy based on ZnCuInSe QDs provides an unprecedented step for rapid and effective bacterial discrimination, detection, and imaging.

Modular protein-oligonucleotide signal exchange

While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

Wafer-level fabrication of 3D nanoparticles assembled nanopillars and click chemistry modification for sensitive SERS detection of trace carbonyl compounds

In this work, we develop a new method for fabricating wafer-level gold nanoparticles covered silicon nanopillars (SNPs) combined with surface chemical modification to detect trace level carbonyl compounds based on surface-enhanced Raman scattering (SERS) technique. The SNPs are fabricated with an etching process using nano masks synthesized in oxygen-plasma bombardment of photoresist, and further deposited with gold nanoparticles on the surface, thus forming a 3D 'particles on pillars' nanostructure for sensitive SERS detection. The enhancement factor (EF) of the devices for R6G detection can achieve 1.56 × 10⁶ times compared with a flat Si substrate. We also developed an oximation click chemistry reaction procedure by chemically modifying the nanostructures with aminooxy dodecane thiol (ADT) self-assemble modification. The chip is further integrated with a polydimethylsiloxane (PDMS) microfluidic chamber, which allows fast and convenient detection of trace carbonyl compounds in liquid samples. The SERS detection capability was demonstrated by the dropwise addition of fluorescent carbonyl compounds before and after elution. Furthermore, the device was proved with high surface consistency(<70%) for repeated measurement, which has the potential for ppb(parts per billion) level concentration of carbonyl compounds detection.

The integration of molecular imprinting and surface-enhanced Raman scattering for highly sensitive detection of lysozyme biomarker aided by density functional theory

Surface-enhanced Raman scattering (SERS) is a powerful bioanalytical technique that opens opportunities for early disease diagnosis and treatment by detecting biomarkers. However, the low sensitivity, selectivity, and reproducibility in the bioanalytical SERS are the main obstacles for clinical use. Herein, we demonstrate a high sensitive and selective label-free lysozyme biomarker detection platform based on coupling of SERS with molecular imprinting technique. The hierarchical silver microspheres with dendritic structure are controllably fabricated by a wet-chemical self-assembly approach. Based on selection of surface-active regions by density functional theory (DFT) simulations, a thin MIPs film (thickness < 15 nm) is then grafted on Ag microsphere surface through surface imprinting. As a result, the final synthesized Ag@MIPs hybrid exhibits as low as 5 ng mL^-1 detection limit for target lysozyme, and high selectivity and reproducibility. Intensive "hot spots" in Ag@MIPs confirmed by Raman mapping give rise to the high-performance SERS. Meanwhile, DFT calculations are employed to investigate the SERS spectra and assist the assignment for the characteristic peaks of lysozyme. We believe that the present study provides a reliable and high-sensitive protocol for label-free protein biomarkers detection.

Functionalized Microstructured Optical Fibers: Materials, Methods, Applications

Microstructured optical fiber-based sensors (MOF) have been widely developed finding numerous applications in various fields of photonics, biotechnology, and medicine. High sensitivity to the refractive index variation, arising from the strong interaction between a guided mode and an analyte in the test, makes MOF-based sensors ideal candidates for chemical and biochemical analysis of solutions with small volume and low concentration. Here, we review the modern techniques used for the modification of the fiber's structure, which leads to an enhanced detection sensitivity, as well as the surface functionalization processes used for selective adsorption of target molecules. Novel functionalized MOF-based devices possessing these unique properties, emphasize the potential applications for fiber optics in the field of modern biophotonics, such as remote sensing, thermography, refractometric measurements of biological liquids, detection of cancer proteins, and concentration analysis. In this work, we discuss the approaches used for the functionalization of MOFs, with a focus on potential applications of the produced structures.

Direct Discrimination of Edible Oil Type, Oxidation, and Adulteration by Liquid Interfacial Surface-Enhanced Raman Spectroscopy

The quality and safety of edible oils is a momentous but formidable challenge, especially regarding identification of oil type, oxidation, and adulteration. Most conventional analytical methods have bottlenecks in sensitivity, specificity, accessibility, or reliability. Surface-enhanced Raman spectroscopy (SERS) is promising as an unlabeled and ultrasensitive technique but limited by modification of inducers or surfactants on metal surfaces for oil analysis. Here, we develop a quantitative SERS analyzer on two-liquid interfacial plasmonic arrays for direct quality classification of edible oils by a portable Raman device. The interfacial plasmonic array is self-assembled through mixing the gold nanoparticle (GNP) sols and oil sample dissolved in chloroform without any surfactants or pretreatments. Different kinds of edible oils dissolved in chloroform directly participate in self-assembly of plasmonic arrays that finally localizes onto a three-dimensional (3D) oil/water interface. The 3D plasmonic array is self-healing, shape adaptive, and can be transferred to any glass containers as a substrate-free SERS analyzer for direct Raman measurements. It produces sensitive responses of SERS on different kinds of edible oils. By virtue of principal component analysis (PCA), this analyzer is able to quickly distinguish six edible oils, oxidized oils, and adulterated oils. Moreover, the solvent chloroform generates unique and stable SERS bands that can utilized as an inherent internal standard (IIS) to calibrate SERS fluctuation and greatly improve quantitation accuracy. Compared to conventional lab methods, this analyzer avoids complex and time-consuming preprocessing and provides significant advantages in cost, speed, and utility. Our study illuminates a facile way to determine edible oil quality and promises great potential in food quality and safety analysis.

Flexible and transparent Surface Enhanced Raman Scattering (SERS)-Active Ag NPs/PDMS composites for in-situ detection of food contaminants

The fabrication of flexible and transparent Surface Enhanced Raman Scattering (SERS) substrates enabling fast, sensitive and on site detection is relevant for the practical application of SERS for real world analysis, such as food safety and organic pollutants monitoring. In this work novel Ag NPs/PDMS composites were fabricated and employed for the SERS detection of food contaminants directly on food surfaces. Ag NPs/PDMS composites were obtained by self-assembly of organic Ag nanoparticle solutions on flexible PDMS surfaces. Preliminary evaluation of the suitability of Ag NPs/PDMS probes for SERS analysis showed that composites were characterized by a SERS enhancement factor (EF) of 3.1 × 10⁵, good stability and resistance to harsh conditions as well as good uniformity and batch to bach reproducibility. The "sticky" nature of Ag NPs/PDMS composites was exploited to "paste" them on irregular analytical surfaces, thus enabling the detection in situ of food contaminant crystal violet (CV) and pesticide thiram, respectively. Specifically, CV and thiram concentrations as low as 1 × 10^-7 M and 1 × 10^-5 M were measured on contaminated fish skin and orange peel, respectively. Furthermore, efficient SERS detection by micro-extraction of CV from fish skin and thiram from fruit surfaces was achieved, showing the analytical versatility of the fabricated SERS composites.

Volume-Enhanced Raman Scattering Detection of Viruses

Virus detection and analysis are of critical importance in biological fields and medicine. Surface-enhanced Raman scattering (SERS) has shown great promise in small molecule and even single molecule detection, and can provide fingerprint signals of molecules. Despite the powerful detection capabilities of SERS, the size discrepancy between the SERS "hot spots" (generally, <10 nm) and viruses (usually, sub-100 nm) yields poor detection reliability of viruses. Inspired by the concept of molecular imprinting, a volume-enhanced Raman scattering (VERS) substrate composed of hollow nanocones at the bottom of microbowls (HNCMB) is developed. The hollow nanocones of the resulting VERS substrates serve a twofold purpose: 1) extending the region of Raman signal enhancement from the nanocone surface (e.g., surface "hot spots") to the hollow area within the cone (e.g., volume "hot spots")-a novel method of Raman signal enhancement, and 2) directing analyte such as viruses of a wide range of sizes to those VERS "hot spots" while simultaneously increasing the surface area contributing to SERS. Using HNCMB VERS substrates, greatly improved Raman signals of single viruses are demonstrated, an achievement with important implications in disease diagnostics and monitoring, biomedical fields, as well as in clinical treatment.

Label-Free SERS Discrimination and In Situ Analysis of Life Cycle in Escherichia coli and Staphylococcus epidermidis

Surface enhanced Raman spectroscopy (SERS) has been proven suitable for identifying and characterizing different bacterial species, and to fully understand the chemically driven metabolic variations that occur during their evolution. In this study, SERS was exploited to identify the cellular composition of Gram-positive and Gram-negative bacteria by using mesoporous silicon-based substrates decorated with silver nanoparticles. The main differences between the investigated bacterial strains reside in the structure of the cell walls and plasmatic membranes, as well as their biofilm matrix, as clearly noticed in the corresponding SERS spectrum. A complete characterization of the spectra was provided in order to understand the contribution of each vibrational signal collected from the bacterial culture at different times, allowing the analysis of the bacterial populations after 12, 24, and 48 h. The results show clear features in terms of vibrational bands in line with the bacterial growth curve, including an increasing intensity of the signals during the first 24 h and their subsequent decrease in the late stationary phase after 48 h of culture. The evolution of the bacterial culture was also confirmed by fluorescence microscope images.

Surface-Enhanced Raman Scattering (SERS) With Silver Nano Substrates Synthesized by Microwave for Rapid Detection of Foodborne Pathogens

Rapid and sensitive methods have been developed to detect foodborne pathogens, a development that is important for food safety. The aim of this study is to explore Surface-enhanced Raman scattering (SERS) with silver nano substrates to detect and identify the following three foodborne pathogens: Escherichia coli O157: H7, Staphylococcus aureus and Salmonella. All the cells were resuspended with 10 mL silver colloidal nanoparticles, making a concentration of 107 CFU/mL, and were then exposed to 785 nm laser excitation. In this study, the results showed that all the bacteria can be sensitively and reproducibly detected directly by SERS. The distinctive differences can be observed in the SERS spectral data of the three food-borne pathogens, and the silver colloidal nanoparticles can be used as highly sensitive SERS-active substrates. In addition, the assay time required only a few minutes, which indicated that SERS coupled with the silver colloidal nanoparticles is a promising method for the detection and characterization of food-borne pathogens. At the same time, principle component analysis (PCA) and hierarchical cluster analysis (HCA) made the different bacterial strains clearly differentiated based on the barcode spectral data reduction. Therefore, the SERS methods hold great promise for the detection and identification of food-borne pathogens and even for applications in food safety.

Fitting an Optical Fiber Background with a Weighted Savitzky-Golay Smoothing Filter for Raman Spectroscopy

The Raman background arising from optical fiber materials poses a critical problem for fiber optic surface-enhanced Raman spectroscopy (SERS). A novel filter is developed to fit the optical fiber background from the measured SERS spectrum of the target sample. The general model of the filter is built by incorporating a weighted term of matching the similarity between the estimated background spectrum and the measured background spectrum into the classic Savitzky-Golay (SG) smoothing filter model. Through respectively selecting Euclidean cosine coefficient (ECos) and Pearson correlation coefficient (PCor) as the similarity index, two different models of the weighted SG smoothing filter are derived and named as SG-ECos and SG-PCor accordingly. Furthermore, the algorithm is presented, implemented, successfully applied to experimentally measured SERS spectra of rhodamine 6G and crystal violet, and validated with mathematically simulated Raman spectra. Experimental and simulation results show that the SG-ECos filter is effective, fast, flexible, and of certain anti-noise capability in background fitting. It is suggested that the proposed filter may be also applicable for other Raman spectra measurements to remove spectral contaminants originated from sampling substrates such as glass slides.

Micro-scale fiber-optic force sensor fabricated using direct laser writing and calibrated using machine learning

Fiber-optic sensors have numerous existing and emerging applications spanning areas from industrial process monitoring to medical diagnosis. Two of the most common fiber sensors are based on the fabrication of Bragg gratings or Fabry-Perot etalons. While these techniques offer a large array of sensing targets, their utility can be limited by the difficulties involved in fabricating forward viewing probes (Bragg gratings) and in obtaining sufficient signal-to-noise ratios (Fabry-Perot systems). In this article we present a micro-scale fiber-optic force sensor produced using direct laser writing (DLW). The fabrication entails a single-step process that can be undertaken in a reliable and repeatable manner using a commercial DLW system. The sensor is made of a series of thin plates (i.e. Fabry-Perot etalons), which are supported by springs that compress under an applied force. At the proximal end of the fiber, the interferometric changes that are induced as the sensor is compressed are read out using reflectance spectroscopy, and the resulting spectral changes are calibrated with respect to applied force. This calibration is performed using either singular value decomposition (SVD) followed by linear regression or artificial neural networks. We describe the design and optimization of this device, with a particular focus on the data analysis required for calibration. Finally, we demonstrate proof-of-concept force sensing over the range 0-50 μN, with a measurement error of approximately 1.5 μN.

Optofluidics in Microstructured Optical Fibers

In this paper, we review the development and applications of optofluidics investigated based on the platform of microstructured optical fibers (MOFs) that have miniature air channels along the light propagating direction. The flexibility of the customizable air channels of MOFs provides enough space to implement light-matter interaction, as fluids and light can be guided simultaneously along a single strand of fiber. Different techniques employed to achieve the fluidic inlet/outlet as well as different applications for biochemical analysis are presented. This kind of miniature platform based on MOFs is easy to fabricate, free of lithography, and only needs a tiny volume of the sample. Compared to optofluidics on the chip, no additional waveguide is necessary to guide the light since the core is already designed in MOFs. The measurements of flow rate, refractive index of the filled fluids, and chemical reactions can be carried out based on this platform. Furthermore, it can also demonstrate some physical phenomena. Such devices show good potential and prospects for applications in bio-detection as well as material analysis.

Optical Aggregation of Gold Nanoparticles for SERS Detection of Proteins and Toxins in Liquid Environment: Towards Ultrasensitive and Selective Detection

Optical forces are used to aggregate plasmonic nanoparticles and create SERS-active hot spots in liquid. When biomolecules are added to the nanoparticles, high sensitivity SERS detection can be accomplished. Here, we pursue studies on Bovine Serum Albumin (BSA) detection, investigating the BSA-nanorod aggregations in a range from 100 µM to 50 nM by combining light scattering, plasmon resonance and SERS, and correlating the SERS signal with the concentration. Experimental data are fitted with a simple model describing the optical aggregation process. We show that BSA-nanorod complexes can be optically printed on non-functionalized glass surfaces, designing custom patterns stable with time. Furthermore, we demonstrate that this methodology can be used to detect catalase and hemoglobin, two Raman resonant biomolecules, at concentrations of 10 nM and 1 pM, respectively, i.e., well beyond the limit of detection of BSA. Finally, we show that nanorods functionalized with specific aptamers can be used to capture and detect Ochratoxin A, a fungal toxin found in food commodities and wine. This experiment represents the first step towards the addition of molecular specificity to this novel biosensor strategy.

Bioanalytical applications of surface-enhanced Raman spectroscopy: de novo molecular identification

Surface enhanced Raman scattering (SERS) has become a powerful technique for trace analysis of biomolecules. The use of SERS-tags has evolved into clinical diagnostics, the enhancement of the intrinsic signal of biomolecules on SERS active materials shows tremendous promise for the analysis of biomolecules and potential biomedical assays. The detection of the de novo signal from a wide range of biomolecules has been reported to date. In this review, we examine different classes of biomolecules for the signals observed and experimental details that enable their detection. In particular, we survey nucleic acids, amino acids, peptides, proteins, metabolites, and pathogens. The signals observed show that the interaction of the biomolecule with the enhancing nanostructure has a significant influence on the observed spectrum. Additional experiments demonstrate that internal standards can correct for intensity fluctuations and provide quantitative analysis. Experimental methods that control the interaction at the surface are providing for reproducible SERS signals. Results suggest that combining advances in methodology with the development of libraries for SERS spectra may enable the characterization of biomolecules complementary to other existing methods.

Surface-enhanced Raman spectroscopy study on the structure changes of 4-Mercaptophenylboronic Acid under different pH conditions

4-Mercaptophenylboronic Acid (4-MPBA) plays pivotal role in various fields. The orientation and existing form of the 4-MPBA strongly depend on the pH value of the media. The general aim of this work is to obtain information about the structure changes of 4-MPBA absorbed on Ag nanoparticles in different pH environment. Surface-enhanced Raman spectroscopy (SERS) technique is a simple and rapid method to study adsorption phenomena at molecule level. The investigation is done by means of SERS. In order to interpret the experimental information, a series of SERS spectra is carried out. The relative intensities of the totally symmetric (a₁ mode) and non-totally symmetric (b₂ mode) bands in the SERS spectra of 4-MPBA change depend on the environmental pH values, which is a manifestation of charge transfer (CT) processes. The degree of charge transfer increases with the pH value of the media changing from acidity to alkalinity. The structure changes of MPBA had been carried out in different pH environment. We envision that this approach will be of great significance in related fields of 4-MPBA-involved detection.

Decomposable quantum-dots/DNA nanosphere for rapid and ultrasensitive detection of extracellular respiring bacteria

Extracellular respiring bacteria (ERB) are a group of bacteria capable of transferring electrons to extracellular acceptors and have important application in environmental remediation. In this study, a decomposable quantum-dots (QDs)/DNA nanosphere probe was developed for rapid and ultrasensitive detection of ERB. The QDs/DNA nanosphere was self-assembled from QDs-streptavidin conjugate (QDs-SA) and Y-shaped DNA nanostructure that is constructed based on toehold-mediated strand displacement. It can release numerous fluorescent QDs-SA in immunomagnetic separation (IMS)-based immunoassay via simple biotin displacement, which remarkably amplifies the signal of antigen-antibody recognizing event. This QDs/DNA-nanosphere-based IMS-fluorescent immunoassay is ultrasensitive for model ERB Shewanella oneidensis, showing a wide detection range between 1.0 cfu/mL and 1.0 × 10⁸ cfu/mL with a low detection limit of 1.37 cfu/mL. Moreover, the proposed IMS-fluorescent immunoassay exhibits high specificity, acceptable reproducibility and stability. Furthermore, the proposed method shows acceptable recovery (92.4-101.4%) for detection of S. oneidensis spiked in river water samples. The proposed IMS-fluorescent immunoassay advances an intelligent strategy for rapid and ultrasensitive quantitation of low-abundance analyte and thus holds promising potential in food, medical and environmental applications.

Extracting Optical Fiber Background from Surface-Enhanced Raman Spectroscopy Spectra Based on Bi-Objective Optimization Modeling

We propose a bi-objective optimization model for extracting optical fiber background from the measured surface-enhanced Raman spectroscopy (SERS) spectrum of the target sample in the application of fiber optic SERS. The model is built using curve fitting to resolve the SERS spectrum into several individual bands, and simultaneously matching some resolved bands with the measured background spectrum. The Pearson correlation coefficient is selected as the similarity index and its maximum value is pursued during the spectral matching process. An algorithm is proposed, programmed, and demonstrated successfully in extracting optical fiber background or fluorescence background from the measured SERS spectra of rhodamine 6G (R6G) and crystal violet (CV). The proposed model not only can be applied to remove optical fiber background or fluorescence background for SERS spectra, but also can be transferred to conventional Raman spectra recorded using fiber optic instrumentation.

SERS substrates fabricated using ceramic filters for the detection of bacteria: Eliminating the citrate interference

It was found that spectra obtained for bacteria on SERS substrates fabricated by filtering citrate-generated Ag nanoparticles (NPs) onto rigid, ceramic filters exhibited peaks due to citrate as well as the bacteria. In many cases the citrate spectrum overwhelmed that of the bacteria. Given the simplicity of the method to prepare these substrates, means of eliminating this citrate interference were explored. It was found that allowing a mixture of bacteria suspension and citrate-generated Ag NPs to incubate prior to filtering onto the ceramic filter eliminated this interference.

Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays

A distinct advantage of nanosensor arrays is their ability to achieve ultralow detection limits in solution by proximity placement to an analyte. Here, we demonstrate label-free detection of individual proteins from Escherichia coli (bacteria) and Pichia pastoris (yeast) immobilized in a microfluidic chamber, measuring protein efflux from single organisms in real time. The array is fabricated using non-covalent conjugation of an aptamer-anchor polynucleotide sequence to near-infrared emissive single-walled carbon nanotubes, using a variable chemical spacer shown to optimize sensor response. Unlabelled RAP1 GTPase and HIV integrase proteins were selectively detected from various cell lines, via large near-infrared fluorescent turn-on responses. We show that the process of E. coli induction, protein synthesis and protein export is highly stochastic, yielding variability in protein secretion, with E. coli cells undergoing division under starved conditions producing 66% fewer secreted protein products than their non-dividing counterparts. We further demonstrate the detection of a unique protein product resulting from T7 bacteriophage infection of E. coli, illustrating that nanosensor arrays can enable real-time, single-cell analysis of a broad range of protein products from various cell types.

Quantitative Detection of NADH Using a Novel Enzyme-Assisted Method Based on Surface-Enhanced Raman Scattering

An enzymatic method for quantitative detection of the reduced form of nicotinamide-adenine dinucleotide (NADH) using surface-enhanced Raman scattering was developed. Under the action of NADH oxidase and horseradish peroxidase, NADH can generate hydrogen peroxide (H₂O₂) in a 1:1 molar ratio, and the H₂O₂ can oxidize a chromogen into pigment with a 1:1 molar ratio. Therefore, the concentration of NADH can be determined by detecting the generated pigment. In our experiments, eight chromogens were studied, and o-tolidine (OT) was selected because of the unique Raman peaks displayed by its corresponding pigment. The optimal OT concentration was 2 × 10⁻³ M, and this gave the best linear relationship and the widest linear range between the logarithmic H₂O₂ concentration and the logarithmic integrated SERS intensity of the peak centered at 1448 cm⁻¹. Under this condition, the limit of detection for NADH was as low as 4 × 10⁻⁷ M. Two NADH samples with concentrations of 2 × 10⁻⁴ and 2 × 10⁻⁵ M were used to validate the linear relationship, and the logarithmic deviations were less than 3%.

Optical Biosensing of Bacteria and Bacterial Communities

Bacterial sensing is important for understanding the numerous roles bacteria play in nature and in technology, understanding and managing bacterial populations, detecting pathogenic bacterial infections, and preventing the outbreak of illness. Current analytical challenges in bacterial sensing center on the dilemma of rapidly acquiring quantitative information about bacteria with high detection efficiency, sensitivity, and specificity, while operating within a reasonable budget and optimizing the use of ancillary tools, such as multivariate statistics. This review starts from a general description of bacterial sensing methods and challenges, and then focuses on bacterial characterization using optical methods including Raman spectroscopy and imaging, infrared spectroscopy, fluorescence spectroscopy and imaging, and plasmonics, including both extended and localized surface plasmon resonance spectroscopy. The advantages and drawbacks of each method in relation to the others are discussed, as are their applications. A particularly promising direction in bacterial sensing lies in combining multiple approaches to achieve multiplex analysis, and examples where this has been achieved are highlighted.

Surface-enhanced Raman spectroscopy introduced into the International Standard Organization (ISO) regulations as an alternative method for detection and identification of pathogens in the food industry

We show that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) can serve as a fast, reliable, and easy method for detection and identification of food-borne bacteria, namely Salmonella spp., Listeria monocytogenes, and Cronobacter spp., in different types of food matrices (salmon, eggs, powdered infant formula milk, mixed herbs, respectively). The main aim of this work was to introduce the SERS technique into three ISO (6579:2002; 11290-1:1996/A1:2004; 22964:2006) standard procedures required for detection of these bacteria in food. Our study demonstrates that the SERS technique is effective in distinguishing very closely related bacteria within a genus grown on solid and liquid media. The advantages of the proposed ISO-SERS method for bacteria identification include simplicity and reduced time of analysis, from almost 144 h required by standard methods to 48 h for the SERS-based approach. Additionally, PCA allows one to perform statistical classification of studied bacteria and to identify the spectrum of an unknown sample. Calculated first and second principal components (PC-1, PC-2) account for 96, 98, and 90% of total variance in the spectra and enable one to identify the Salmonella spp., L. monocytogenes, and Cronobacter spp., respectively. Moreover, the presented study demonstrates the excellent possibility for simultaneous detection of analyzed food-borne bacteria in one sample test (98% of PC-1 and PC-2) with a goal of splitting the data set into three separated clusters corresponding to the three studied bacteria species. The studies described in this paper suggest that SERS represents an alternative to standard microorganism diagnostic procedures. Graphical Abstract New approach of the SERS strategy for detection and identification of food-borne bacteria, namely S. enterica, L. monocytogenes, and C. sakazakii in selected food matrices.

Combined Dielectrophoresis and Impedance Systems for Bacteria Analysis in Microfluidic On-Chip Platforms

Bacteria concentration and detection is time-consuming in regular microbiology procedures aimed to facilitate the detection and analysis of these cells at very low concentrations. Traditional methods are effective but often require several days to complete. This scenario results in low bioanalytical and diagnostic methodologies with associated increased costs and complexity. In recent years, the exploitation of the intrinsic electrical properties of cells has emerged as an appealing alternative approach for concentrating and detecting bacteria. The combination of dielectrophoresis (DEP) and impedance analysis (IA) in microfluidic on-chip platforms could be key to develop rapid, accurate, portable, simple-to-use and cost-effective microfluidic devices with a promising impact in medicine, public health, agricultural, food control and environmental areas. The present document reviews recent DEP and IA combined approaches and the latest relevant improvements focusing on bacteria concentration and detection, including selectivity, sensitivity, detection time, and conductivity variation enhancements. Furthermore, this review analyses future trends and challenges which need to be addressed in order to successfully commercialize these platforms resulting in an adequate social return of public-funded investments.

Photoreduced silver nanoparticles grown on femtosecond laser ablated, D-shaped fiber probe for surface-enhanced Raman scattering

Surface-enhanced Raman scattering (SERS) probes are made by facile photochemical deposition of silver nanoparticles on a femtosecond (fs) laser ablated, D-shaped fiber. The structure and surface morphology of the probe are investigated by scanning electron microscopy. High-quality SERS signals are detected using Rhodamine 6G molecules via an in situ sensing mode. Experimental results show that the SERS signals increase with the increase of the length of fs laser ablated, D-shaped zone. Our D-shaped fiber SERS probe shows a feasible method for a large active area, high performance, and real-time and remote measurement of SERS signals in biochemical analysis.