Advances in Surface Plasmon Resonance Imaging and Microscopy and Their Biological Applications

Visualizing Single-Molecule Protein Conformational Transitions and Free Energy Landscape

Monitoring the conformational dynamics of individual proteins is essential to understand the relationship between structure and function in molecular regulatory mechanisms. However, the fast dynamics of single proteins remain poorly understood. Here, we construct a single-molecule sensing platform by introducing plasmonic imaging of single nanoparticles to sense and report the protein conformational changes at the single-molecule level. Tracking the fluctuations of individual nanoparticles with high resolution, we detect and characterize distinct conformational states of molecular chaperone heat shock protein 90 (Hsp90). We also explore the conformational changes of Hsp90 in situ under different nucleotide conditions. Analysis of the conformational fluctuations between the open and closed states of single Hsp90 provides important information on free energy profiles, effective spring constants, and multiphase behaviors. This method offers a strategy to visualize the conformational changes of single proteins in real-time and provides insights into the underlying molecular mechanisms.

Wavelength Division Multiplexing-Based High-Sensitivity Surface Plasmon Resonance Imaging Biosensor for High-Throughput Real-Time Molecular Interaction Analysis

In this study, we report the successful development of a novel high-sensitivity intensity-based Surface Plasmon Resonance imaging (SPRi) biosensor and its application for detecting molecular interactions. By optimizing the excitation wavelength and employing a wavelength division multiplexing (WDM) algorithm, the system can determine the optimal excitation wavelength based on the initial refractive index of the sample without adjusting the incidence angle. The experimental results demonstrate that the refractive index resolution of the system reaches 1.77×10-6 RIU. Moreover, it can obtain the optimal excitation wavelength for samples with an initial refractive index in the range of 1.333 to 1.370 RIU and accurately monitor variations within the range of 0.0037 RIU without adjusting the incidence angle. Additionally, our new SPRi technique realized real-time detection of high-throughput biomolecular binding processes, enabling analysis of kinetic parameters. This research is expected to advance the development of more accurate SPRi technologies for molecular interaction analysis.

Interactive biocatalysis achieved by driving enzyme cascades inside a porous conducting material

An emerging concept and platform, the electrochemical Leaf (e-Leaf), offers a radical change in the way tandem (multi-step) catalysis by enzyme cascades is studied and exploited. The various enzymes are loaded into an electronically conducting porous material composed of metallic oxide nanoparticles, where they achieve high concentration and crowding - in the latter respect the environment resembles that found in living cells. By exploiting efficient electron tunneling between the nanoparticles and one of the enzymes, the e-Leaf enables the user to interact directly with complex networks, rendering simultaneous the abilities to energise, control and observe catalysis. Because dispersion of intermediates is physically suppressed, the output of the cascade - the rate of flow of chemical steps and information - is delivered in real time as electrical current. Myriad enzymes of all major classes now become effectively electroactive in a technology that offers scalability between micro-(analytical, multiplex) and macro-(synthesis) levels. This Perspective describes how the e-Leaf was discovered, the steps in its development so far, and the outlook for future research and applications.

Enhanced Far-Field Thermal Radiation through a Polaritonic Waveguide

We experimentally demonstrate the enhancement of the far-field thermal radiation between two nonabsorbent Si microplates coated with energy-absorbent silicon dioxide (SiO_{2}) nanolayers supporting the propagation of surface phonon polaritons. By measuring the radiative thermal conductance between two coated Si plates, we find that its values are twice those obtained without the SiO_{2} coating. This twofold increase results from the hybridization of polaritons with guided modes inside Si and is well predicted by fluctuational electrodynamics and an analytical model based on a two-dimensional density of polariton states. These findings could be applied to thermal management in microelectronics, silicon photonics, energy conversion, atmospheric sciences, and astrophysics.

Combining plasmonic and electrochemical biosensing methods

The idea of combining electrochemical (EC) and plasmonic biosensor methods was introduced almost thirty years ago and the potential of electrochemical-plasmonic (EC-P) biosensors has been highlighted ever since. Despite that, the use of EC-P biosensors in analytics has been rather limited so far and the search for unique applications of the EC-P method continues. In this paper, we review the advances in the field of EC-P biosensors and discuss the features and benefits they can provide. In addition, we identify the main challenges for the development of EC-P biosensors and the limitations that prevent EC-P biosensors from more widespread use. Finally, we review applications of EC-P biosensors for the investigation and quantification of biomolecules, and for the study of biomolecular and cellular processes.

Coffee Ring Effect Enhanced Surface Plasmon Resonance Imaging Biosensor via 2-λ Fitting Detection Method

SPR biosensors have been extensively used for investigating protein-protein interactions. However, in conventional surface plasmon resonance (SPR) biosensors, detection is limited by the Brownian-motion-governed diffusion process of sample molecules in the sensor chip, which makes it challenging to detect biomolecule interactions at ultra-low concentrations. Here, we propose a highly sensitive SPR imaging biosensor which exploits the coffee ring effect (CRE) for in situ enrichment of molecules on the sensing surface. In addition, we designed a wavelength modulation system utilizing two LEDs to reduce the system cost and enhance the detection speed. Furthermore, a detection limit of 213 fM is achieved, which amounts to an approximately 365 times improvement compared to traditional SPR biosensors. With further development, we believe that this SPR imaging system with high sensitivity, less sample consumption, and faster detection speed can be readily applied to ultra-low-concentration molecular detection and interaction analysis.

Surface Plasmon Resonance Biosensors: A Review of Molecular Imaging with High Spatial Resolution

Surface plasmon resonance (SPR) is a powerful tool for determining molecular interactions quantitatively. SPR imaging (SPRi) further improves the throughput of SPR technology and provides the spatially resolved capability for observing the molecular interaction dynamics in detail. SPRi is becoming more and more popular in biological and chemical sensing and imaging. However, SPRi suffers from low spatial resolution due to the imperfect optical components and delocalized features of propagating surface plasmonic waves along the surface. Diverse kinds of approaches have been developed to improve the spatial resolution of SPRi, which have enormously impelled the development of the methodology and further extended its possible applications. In this minireview, we introduce the mechanisms for building a high-spatial-resolution SPRi system and present its experimental schemes from prism-coupled SPRi and SPR microscopy (SPRM) to surface plasmonic scattering microscopy (SPSM); summarize its exciting applications, including molecular interaction analysis, molecular imaging and profiling, tracking of single entities, and analysis of single cells; and discuss its challenges in recent decade as well as the promising future.

Extracellular vesicles associated microRNAs: Their biology and clinical significance as biomarkers in gastrointestinal cancers

Gastrointestinal (GI) cancers, including colorectal, gastric, esophageal, pancreatic, and liver, are associated with high mortality and morbidity rates worldwide. One of the underlying reasons for the poor survival outcomes in patients with these malignancies is late disease detection, typically when the tumor has already advanced and potentially spread to distant organs. Increasing evidence indicates that earlier detection of these cancers is associated with improved survival outcomes and, in some cases, allows curative treatments. Consequently, there is a growing interest in the development of molecular biomarkers that offer promise for screening, diagnosis, treatment selection, response assessment, and predicting the prognosis of these cancers. Extracellular vesicles (EVs) are membranous vesicles released from cells containing a repertoire of biological molecules, including nucleic acids, proteins, lipids, and carbohydrates. MicroRNAs (miRNAs) are the most extensively studied non-coding RNAs, and the deregulation of miRNA levels is a feature of cancer cells. EVs miRNAs can serve as messengers for facilitating interactions between tumor cells and the cellular milieu, including immune cells, endothelial cells, and other tumor cells. Furthermore, recent years have witnessed considerable technological advances that have permitted in-depth sequence profiling of these small non-coding RNAs within EVs for their development as promising cancer biomarkers -particularly non-invasive, liquid biopsy markers in various cancers, including GI cancers. Herein, we summarize and discuss the roles of EV-associated miRNAs as they play a seminal role in GI cancer progression, as well as their promising translational and clinical potential as cancer biomarkers as we usher into the area of precision oncology.

20(S)-ginsenoside Rg3 exerts anti-fibrotic effect after myocardial infarction by alleviation of fibroblasts proliferation and collagen deposition through TGFBR1 signaling pathways

Background

Myocardial fibrosis post-myocardial infarction (MI) can induce maladaptive cardiac remodeling as well as heart failure. Although 20(S)-ginsenoside Rg3 (Rg3) has been applied to cardiovascular diseases, its efficacy and specific molecular mechanism in myocardial fibrosis are largely unknown. Herein, we aimed to explore whether TGFBR1 signaling was involved in Rg3's anti-fibrotic effect post-MI.

Methods

Left anterior descending (LAD) coronary artery ligation-induced MI mice and TGF-β1-stimulated primary cardiac fibroblasts (CFs) were adopted. Echocardiography, hematoxlin-eosin and Masson staining, Western-blot and immunohistochemistry, CCK8 and Edu were used to study the effects of Rg3 on myocardial fibrosis and TGFBR1 signaling. The combination mechanism of Rg3 and TGFBR1 was explored by surface plasmon resonance imaging (SPRi). Moreover, myocardial Tgfbr1-deficient mice and TGFBR1 adenovirus were adopted to confirm the pharmacological mechanism of Rg3.

Results

In vivo experiments, Rg3 ameliorated myocardial fibrosis and hypertrophy and enhanced cardiac function. Rg3-TGFBR1 had the 1.78 × 10-7 M equilibrium dissociation constant based on SPRi analysis, and Rg3 inhibited the activation of TGFBR1/Smads signaling dose-dependently. Cardiac-specific Tgfbr1 knockdown abolished Rg3's protection against myocardial fibrosis post-MI. In addition, Rg3 down-regulated the TGF-β1-mediated CFs growth together with collagen production in vitro through TGFBR1 signaling. Moreover, TGFBR1 adenovirus partially blocked the inhibitory effect of Rg3.

Conclusion

Rg3 improves myocardial fibrosis and cardiac function through suppressing CFs proliferation along with collagen deposition by inactivation of TGFBR1 pathway.

Intensity Interrogation-Based High-Sensitivity Surface Plasmon Resonance Imaging Biosensor for Apoptosis Detection in Cancer

Intensity interrogation-based surface plasmon resonance imaging (ISPRi) sensing has a simple schematic design and is the most widely used surface plasmon resonance technology at present. In this study, we report the successful development of a novel high-sensitivity ISPRi biosensor and its application for apoptosis detection in cancer cells. By optimizing the excitation wavelength and excitation angle, we achieved a refractive index resolution (RIR) of 5.20 × 10-6 RIU. Importantly, the biosensor has been tested and validated for high-throughput and label-free detection of activated caspase-3 with its specific inhibitor Z-DEVD-FMK in apoptotic cells. Therefore, this study describes a novel molecular imaging system to monitor apoptosis in cancers for disease diagnosis and/or evaluation of therapeutic efficacy of anti-cancer drugs.

Advances in detection methods for viable Salmonella spp.: current applications and challenges

Salmonella is a common intestinal pathogen that can cause food poisoning and intestinal disease. The high prevalence of Salmonella necessitates efficient and sensitive methods for its identification, detection, and monitoring, especially of viable Salmonella. Conventional culture methods need to be more laborious and time-consuming. And they are relatively limited in their ability to detect Salmonella in the viable but non-culturable status if present in the sample to be tested. As a result, there is an increasing need for rapid and accurate techniques to detect viable Salmonella spp. This paper reviewed the status and progress of various methods reported in recent years that can be used to detect viable Salmonella, such as culture-based methods, molecular methods targeting RNAs and DNAs, phage-based methods, biosensors, and some techniques that have the potential for future application. This review can provide researchers with a reference for additional method options and help facilitate the development of rapid and accurate assays. In the future, viable Salmonella detection approaches will become more stable, sensitive, and fast and are expected to play a more significant role in food safety and public health.

Quasi-phase extraction-based surface plasmon resonance imaging method for coffee ring effect monitoring and biosensing

Wavelength interrogation surface plasmon resonance imaging (WSPRi) sensing has unique advantages in high-throughput imaging detection. The refractive index resolution (RIR) of WSPRi is limited to the order of 10-6 RIU. This paper demonstrates a novel WSPRi sensing system with a wavelength scanning device of an acousto-optic tunable filter (AOTF) and a low-cost speckle-free SPR excitation source of a halogen lamp. We developed a sensitive quasi-phase extraction method for data processing. The new technique achieved an RIR of 8.84×10-7 RIU, which is the first WSPRi system that has an RIR in the order of 10-7 RIU. Moreover, we performed a real-time recording of the formation of the coffee ring effect during brine evaporation and enhanced the biosensor performance of SPR for the first time. We believe the higher RIR and accuracy of the system will benefit more potential applications toward exploring the biomolecules' behaviors in biological and biochemistry studies.

Using surface plasmon resonance, capillary electrophoresis and diffusion-ordered NMR spectroscopy to study drug release kinetics

Nanomedicines, including polymer nanocarriers with controlled drug release, are considered next-generation therapeutics with advanced therapeutic properties and reduced side effects. To develop safe and efficient nanomedicines, it is crucial to precisely determine the drug release kinetics. Herein, we present application of analytical methods, i.e., surface plasmon resonance biosensor technology (SPR), capillary electrophoresis, and 1H diffusion-ordered nuclear magnetic resonance spectroscopy, which were innovatively applied for drug release determination. The methods were optimised to quantify the pH-triggered release of three structurally different drugs from a polymer carrier. The suitability of these methods for drug release characterisation was evaluated and compared using several parameters including applicability for diverse samples, the biological relevance of the experimental setup, method complexity, and the analysis outcome. The SPR method was the most universal method for the evaluation of diverse drug molecule release allowing continuous observation in the flow-through setting and requiring a small amount of sample.

Linking aberrant glycosylation of plasma glycoproteins with progression of myelodysplastic syndromes: a study based on plasmonic biosensor and lectin array

Aberrant glycosylation of glycoproteins has been linked with various pathologies. Therefore, understanding the relationship between aberrant glycosylation patterns and the onset and progression of the disease is an important research goal that may provide insights into cancer diagnosis and new therapy development. In this study, we use a surface plasmon resonance imaging biosensor and a lectin array to investigate aberrant glycosylation patterns associated with oncohematological disease-myelodysplastic syndromes (MDS). In particular, we detected the interaction between the lectins and glycoproteins present in the blood plasma of patients (three MDS subgroups with different risks of progression to acute myeloid leukemia (AML) and AML patients) and healthy controls. The interaction with lectins from Aleuria aurantia (AAL) and Erythrina cristagalli was more pronounced for plasma samples of the MDS and AML patients, and there was a significant difference between the sensor response to the interaction of AAL with blood plasma from low and medium-risk MDS patients and healthy controls. Our data also suggest that progression from MDS to AML is accompanied by sialylation of glycoproteins and increased levels of truncated O-glycans and that the number of lectins that allow discriminating different stages of disease increases as the disease progresses.

Metallic and Non-Metallic Plasmonic Nanostructures for LSPR Sensors

Localized surface plasmonic resonance (LSPR) provides a unique scheme for light management and has been demonstrated across a large variety of metallic nanostructures. More recently, non-metallic nanostructures of two-dimensional atomic materials and heterostructures have emerged as a promising, low-cost alternative in order to generate strong LSPR. In this paper, a review of the recent progress made on non-metallic LSPR nanostructures will be provided in comparison with their metallic counterparts. A few applications in optoelectronics and sensors will be highlighted. In addition, the remaining challenges and future perspectives will be discussed.

Label-free and dynamic monitoring of cell evolutions using wavelength-multiplexing surface plasmon resonance holographic microscopy

Dynamic characterizations of intracellular variations and cell-substrate interactions under different external environments are critical to study cell behaviors and exploring biological applications. However, techniques that are capable of dynamically and simultaneously measuring multiple parameters of living cells in a wide-field manner have rarely been reported. Here, we present a wavelength-multiplexing surface plasmon resonance holographic microscopy which allows wide-field, simultaneous, and dynamic measurements of cell parameters, including cell-substrate distance and cytoplasm refractive index (RI). We use two lasers of 632.8 nm and 690 nm as light sources. Two beam splitters are employed in the optical setup to separately adjust the incident angle of two light beams. Then, surface plasmon resonance (SPR) can be excited for each wavelength under SPR angles. We demonstrate the advances of the proposed apparatus by systematically studying the cell responses to osmotic pressure stimuli from the environmental medium at the cell-substrate interface. The SPR phase distributions of the cell are firstly mapped at two wavelengths, then the cell-substrate distance and cytoplasm RI are retrieved using a demodulation method. Based on phase response differences between two wavelengths and monotonic changes of SPR phase with cell parameters, cell-substrate distance, and cytoplasm RI can be determined simultaneously using an inverse algorithm. This work affords a new optical measurement technique to dynamically characterize cell evolutions and investigate cell properties in various cellular activities. It may become a useful tool in the bio-medical and bio-monitoring areas.

High-throughput spatiotemporal monitoring of single-cell secretions via plasmonic microwell arrays

Methods for the analysis of cell secretions at the single-cell level only provide semiquantitative endpoint readouts. Here we describe a microwell array for the real-time spatiotemporal monitoring of extracellular secretions from hundreds of single cells in parallel. The microwell array incorporates a gold substrate with arrays of nanometric holes functionalized with receptors for a specific analyte, and is illuminated with light spectrally overlapping with the device's spectrum of extraordinary optical transmission. Spectral shifts in surface plasmon resonance resulting from analyte-receptor bindings around a secreting cell are recorded by a camera as variations in the intensity of the transmitted light while machine-learning-assisted cell tracking eliminates the influence of cell movements. We used the microwell array to characterize the antibody-secretion profiles of hybridoma cells and of a rare subset of antibody-secreting cells sorted from human donor peripheral blood mononuclear cells. High-throughput measurements of spatiotemporal secretory profiles at the single-cell level will aid the study of the physiological mechanisms governing protein secretion.

Recent advances in surface plasmon resonance imaging and biological applications

Surface Plasmon Resonance Imaging (SPRI) is a robust technique for visualizing refractive index changes, which enables researchers to observe interactions between nanoscale objects in an imaging manner. In the past period, scholars have been attracted by the Prism-Coupled and Non-prism Coupled configurations of SPRI and have published numerous experimental results. This review describes the principle of SPRI and discusses recent developments in Prism-Coupled and Non-prism Coupled SPRI techniques in detail, respectively. And then, major advances in biological applications of SPRI are reviewed, including four sub-fields (cells, viruses, bacteria, exosomes, and biomolecules). The purpose is to briefly summarize the recent advances of SPRI and provide an outlook on the development of SPRI in various fields.

Live Cells versus Fixated Cells: Kinetic Measurements of Biomolecular Interactions with the LigandTracer Method and Surface Plasmon Resonance Microscopy

Cell-based kinetic studies of ligand or candidate drug binding to membrane proteins have produced affinity and kinetic values that are different from measurements using purified proteins. However, ligand binding to fixated cells whose membrane constituents (e.g., proteins and their glycosylated forms) are partially connected by a cross-linking reagent has not been compared to that to live cells. Under the same experimental conditions for the LigandTracer method, we measured the interactions of fluorophore-labeled lectins and antibody molecules with glycans at HFF cells and the human epithelial growth receptor 2 at SKBR3 cells, respectively. In conjunction with surface plasmon resonance microscopy, the effects of labels and cell/sub-cell heterogeneity on binding kinetics were investigated. Our results revealed that, for cell constituents whose structures and functions are not closely dependent on cell viability, the ligand binding kinetics at fixated cells is only slightly different from that at live cells. The altered kinetics is explained on the basis of a less mobile receptor confined in a local environment created by partially interconnected protein molecules. We show that cell/sub-cell heterogeneity and labels on the ligands can alter the binding reaction more significantly. Thus, fixating cells not only simplifies experimental procedures for drug screening and renders assays more robust but also provides reliable kinetic information about drug binding to cell constituents whose structures are not changed by chemical fixation.

Recent advances in label-free imaging of cell-matrix adhesions

Cell-matrix adhesions play an essential role in mediating and regulating many biological processes. The adhesion receptors, typically transmembrane integrins, provide dynamic correlations between intracellular environments and extracellular matrixes (ECMs) by bi-directional signaling. In-depth investigations of cell-matrix adhesion and integrin-mediated cell adhesive force are of great significance in biology and medicine. The emergence of advanced imaging techniques and principles has facilitated the understanding of the molecular composition and structure dynamics of cell-matrix adhesions, especially the label-free imaging methods that can be used to study living cell dynamics without immunofluorescence staining. This highlight article aims to give an overview of recent developments in imaging cell-matrix adhesions in a label-free manner. Electrochemiluminescence microscopy (ECLM) and surface plasmon resonance microscopy (SPRM) are briefly introduced and their applications in imaging analysis of cell-matrix adhesions are summarized. Then we highlight the advances in mapping cell-matrix adhesion force based on molecular tension probes and fluorescence microscopy (collectively termed as MTFM). The biomaterials including polyethylene glycol (PEG), peptides and DNA for constructing tension probes in MTFM are summarized. Finally, the outlook and perspectives on the further developments of cell-matrix adhesion imaging are presented.

Surface Plasmon Resonance Microscopy Based on Total Internal Reflection

Surface plasmon resonance microscopy (SPRM) has been widely employed in biological fields because of its high spatial resolution and label-free detection modality. In this study, SPRM based on total internal reflection (TIR) is studied via a home-built SPRM system, and the principle of imaging of a single nanoparticle is analyzed as well. By designing a ring filter and combining it with the deconvolution algorithm in Fourier space, the parabolic tail of the nanoparticle image is removed, in which a spatial resolution of 248 nm is obtained. In addition, we also measured the specific binding between the human IgG antigen and goat anti-human IgG antibody using the TIR-based SPRM. The experimental results have proved that the system can image sparse nanoparticles and monitor biomolecular interactions.

Quorum sensing-based interactions among drugs, microbes, and diseases

Many diseases and health conditions are closely related to various microbes, which participate in complex interactions with diverse drugs; nonetheless, the detailed targets of such drugs remain to be elucidated. Many existing studies have reported causal associations among drugs, gut microbes, or diseases, calling for a workflow to reveal their intricate interactions. In this study, we developed a systematic workflow comprising three modules to construct a Quorum Sensing-based Drug-Microbe-Disease (QS-DMD) database ( http://www.qsdmd.lbci.net/ ), which includes diverse interactions for more than 8,000 drugs, 163 microbes, and 42 common diseases. Potential interactions between microbes and more than 8,000 drugs have been systematically studied by targeting microbial QS receptors combined with a docking-based virtual screening technique and in vitro experimental validations. Furthermore, we have constructed a QS-based drug-receptor interaction network, proposed a systematic framework including various drug-receptor-microbe-disease connections, and mapped a paradigmatic circular interaction network based on the QS-DMD, which can provide the underlying QS-based mechanisms for the reported causal associations. The QS-DMD will promote an understanding of personalized medicine and the development of potential therapies for diverse diseases. This work contributes to a paradigm for the construction of a molecule-receptor-microbe-disease interaction network for human health that may form one of the key knowledge maps of precision medicine in the future.

Sensitive fluorescence biosensor for SARS-CoV-2 nucleocapsid protein detection in cold-chain food products based on DNA circuit and g-CNQDs@Zn-MOF

SARS-CoV-2 isolation from cold-chain food products confirms the possibility of outbreaks through cold-chain food products. RNA extraction combined with RT-PCR is the primary method currently utilized for the detection of SARS-CoV-2. However, the requirement of hours of analytical time and the high price of RT-PCR hinder its worldwide implementation in food supervision. Here, we report a fluorescence biosensor for detection of SARS-CoV-2 N protein. The fluorescence biosensor was fabricated by aptamer-based conformational entropy-driven circuit where molecular beacon strands were labeled with graphitic carbon nitrides quantum dots@Zn-metal-organic framework (g-CNQDs@Zn-MOF) and Dabcyl. The detection of the N protein was achieved via swabbing followed by competitive assay using a fixed amount of N-48 aptamers in the analytical system. A fluorescence emission spectrum was employed for the detection. The detection limit of our fluorescence biosensor was 1.0 pg/mL for SARS-CoV-2 N protein, indicating very excellent sensitivity. The fluorescence biosensor did not exhibit significant cross-reactivity with other N proteins. Finally, the biosensor was successfully applied for the detection of SARS-CoV-2 N protein in actual cold-chain food products showing same excellent accuracy as RT-PCR method. Thus, our fluorescence biosensor is a promising analytical tool for rapid and sensitive detection of SARS-CoV-2 N protein.

Chip-DSF: A rapid screening strategy for drug protein targets

Identification of the drug target of lead compounds is an important means for rapid and efficient drug discovery. Protein chips are a high-throughput protein function analysis technology that has been widely used in screening drug protein targets in recent years. However, the verification of the results after high-throughput protein chip screening is still cumbersome. Based on our mature protein chip preparation platform, we prepared a protein chip containing 150 important high-frequency protein targets and used antibodies to prove the availability of the protein chip. To improve the accuracy of target screening, we combined the label-free differential scanning fluorimetry (DSF) with the protein chip, proposing the Chip-DSF strategy. Subsequently, we tested the method with small molecular ginsenoside-Rg2 (Rg2). The Chip-DSF strategy was used to successfully screen the potential target protein KRAS(G12C) of Rg2. Consistently, we found that Rg2 could inhibit NCI-H23 cell proliferation by inducing cell cycle arrest. Also, we found that Rg2 could reduce the amount of KRAS protein and inhibit the phosphorylation of KRAS downstream key signaling protein ERK1, RPS6, and P70S6K in NCI-H23 cells. Collectively, our Chip-DSF strategy could achieve rapid target verification which improved the accuracy and efficiency of target screening of protein chips.

Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants

The global pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly affected every human life and overloaded the health care system worldwide. Limited therapeutic options combined with the consecutive waves of the infection and emergence of novel SARS-CoV-2 variants, especially variants of concern (VOCs), have prolonged the COVID-19 pandemic and challenged its control. The Spike (S) protein on the surface of SARS-CoV-2 is the primary target exposed to the host and essential for virus entry into cells. The parental (Wuhan-Hu-1 or USA/WA1 strain) S protein is the virus-specific component of currently implemented vaccines. However, S is most prone to mutations, potentially shifting the dynamics of virus-host interactions by affecting S conformational/structural profiles. Scientists have rapidly resolved atomic structures of S VOCs and elucidated molecular details of these mutations, which can inform the design of S-directed novel therapeutics and broadly protective vaccines. Here, we discuss recent findings on S-associated virus transmissibility and immune evasion of SARS-CoV-2 VOCs and experimental approaches used to profile these properties. We summarize the structural studies that document the structural flexibility/plasticity of S VOCs and the potential roles of accumulated mutations on S structures and functions. We focus on the molecular interpretation of structures of the S variants and its insights into the molecular mechanism underlying antibody evasion and host cell-receptor binding.

Technique Evolutions for Microorganism Detection in Complex Samples: A Review

Rapid detection of microorganisms is a major challenge in the medical and industrial sectors. In a pharmaceutical laboratory, contamination of medical products may lead to severe health risks for patients, such as sepsis. In the specific case of advanced therapy medicinal products, contamination must be detected as early as possible to avoid late production stop and unnecessary costs. Unfortunately, the conventional methods used to detect microorganisms are based on time-consuming and labor-intensive approaches. Therefore, it is important to find new tools to detect microorganisms in a shorter time frame. This review sums up the current methods and represents the evolution in techniques for microorganism detection. First, there is a focus on promising ligands, such as aptamers and antimicrobial peptides, cheaper to produce and with a broader spectrum of detection. Then, we describe methods achieving low limits of detection, thanks to Raman spectroscopy or precise handling of samples through microfluids devices. The last part is dedicated to techniques in real-time, such as surface plasmon resonance, preventing the risk of contamination. Detection of pathogens in complex biological fluids remains a scientific challenge, and this review points toward important areas for future research.

Development and In-Depth Characterization of Bacteria Repellent and Bacteria Adhesive Antibody-Coated Surfaces Using Optical Waveguide Biosensing

Bacteria repellent surfaces and antibody-based coatings for bacterial assays have shown a growing demand in the field of biosensors, and have crucial importance in the design of biomedical devices. However, in-depth investigations and comparisons of possible solutions are still missing. The optical waveguide lightmode spectroscopy (OWLS) technique offers label-free, non-invasive, in situ characterization of protein and bacterial adsorption. Moreover, it has excellent flexibility for testing various surface coatings. Here, we describe an OWLS-based method supporting the development of bacteria repellent surfaces and characterize the layer structures and affinities of different antibody-based coatings for bacterial assays. In order to test nonspecific binding blocking agents against bacteria, OWLS chips were coated with bovine serum albumin (BSA), I-block, PAcrAM-g-(PMOXA, NH₂, Si), (PAcrAM-P) and PLL-g-PEG (PP) (with different coating temperatures), and subsequent Escherichia coli adhesion was monitored. We found that the best performing blocking agents could inhibit bacterial adhesion from samples with bacteria concentrations of up to 10⁷ cells/mL. Various immobilization methods were applied to graft a wide range of selected antibodies onto the biosensor's surface. Simple physisorption, Mix&Go (AnteoBind) (MG) films, covalently immobilized protein A and avidin-biotin based surface chemistries were all fabricated and tested. The surface adsorbed mass densities of deposited antibodies were determined, and the biosensor;s kinetic data were evaluated to divine the possible orientations of the bacteria-capturing antibodies and determine the rate constants and footprints of the binding events. The development of affinity layers was supported by enzyme-linked immunosorbent assay (ELISA) measurements in order to test the bacteria binding capabilities of the antibodies. The best performance in the biosensor measurements was achieved by employing a polyclonal antibody in combination with protein A-based immobilization and PAcrAM-P blocking of nonspecific binding. Using this setting, a surface sensitivity of 70 cells/mm² was demonstrated.

Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures

Proteins in biological fluids (blood, urine, cerebrospinal fluid) are important biomarkers of various pathological conditions. Protein biomarkers detection and quantification have been proven to be an indispensable diagnostic tool in clinical practice. There is a growing tendency towards using portable diagnostic biosensor devices for point-of-care (POC) analysis based on microfluidic technology as an alternative to conventional laboratory protein assays. In contrast to universally accepted analytical methods involving protein labeling, label-free approaches often allow the development of biosensors with minimal requirements for sample preparation by omitting expensive labelling reagents. The aim of the present work is to review the variety of physical label-free techniques of protein detection and characterization which are suitable for application in micro-fluidic structures and analyze the technological and material aspects of label-free biosensors that implement these methods. The most widely used optical and impedance spectroscopy techniques: absorption, fluorescence, surface plasmon resonance, Raman scattering, and interferometry, as well as new trends in photonics are reviewed. The challenges of materials selection, surfaces tailoring in microfluidic structures, and enhancement of the sensitivity and miniaturization of biosensor systems are discussed. The review provides an overview for current advances and future trends in microfluidics integrated technologies for label-free protein biomarkers detection and discusses existing challenges and a way towards novel solutions.

Nanoparticle-Enhanced Surface Plasmon Resonance Imaging Enables the Ultrasensitive Detection of Non-Amplified Cell-Free Fetal DNA for Non-Invasive Prenatal Testing

Although many potential applications in early clinical diagnosis have been proposed, the use of a surface plasmon resonance imaging (SPRI) technique for non-invasive prenatal diagnostic approaches based on maternal blood analysis is confined. Here, we report a nanoparticle-enhanced SPRI strategy for a non-invasive prenatal fetal sex determination based on the detection of a Y-chromosome specific sequence (single-gene SRY) in cell-free fetal DNA from maternal plasma. The SPR assay proposed here allows for detection of male DNA in mixtures of 2.5 aM male and female genomic DNAs with no preliminary amplification of the DNA target sequence, thus establishing an analytical protocol that does not require costly, time-consuming, and prone to sample contamination PCR-based procedures. Afterward, the developed protocol was successfully applied to reveal male cell-free fetal DNA in the plasma of pregnant women at different gestational ages, including early gestational ages. This approach would pave the way for the establishment of faster and cost-effective non-invasive prenatal testing.

High-Sensitive Surface Plasmon Resonance Imaging Biosensor Based on Dual-Wavelength Differential Method

Intensity interrogation surface plasmon resonance (ISPR) sensing has a simple schematic design and is the most widely used surface plasmon resonance technology at present. However, it has relatively low sensitivity, especially for ISPR imaging (ISPRi). In this paper, a new technique for the real-time monitoring of biomolecule binding on sensor surfaces via ISPRi detection is described. The technique is based on the interrogation of the differential value of two intensities at two specific wavelengths from the reflected light spectrum. In addition, we also optimized the selection of dual-wavelength parameters under different circumstances to achieve the highest sensitivity. The new technique achieved a refractive index resolution (RIR) of 2.24 × 10^–6 RIU, which is far beyond that of traditional ISPRi technique. Moreover, our new ISPRi technique also realized the real-time detection of high-throughput biomolecular binding. This study is expected to promote the development of faster and more accurate SPRi technologies.

Optimization of Gold Nanorod Features for the Enhanced Performance of Plasmonic Nanocavity Arrays

Nanoplasmonic biosensors incorporating noble metal nanocavity arrays are widely used for the detection of various biomarkers. Gold nanorods (GNRs) have unique properties that can enhance spectroscopic detection capabilities of such nanocavity-based biosensors. However, the contribution of the physical properties of multiple GNRs to resonance enhancement of gold nanocavity arrays requires further characterization and elucidation. In this work, we study how GNR aspect ratio (AR) and surface area (SA) modify the plasmonic resonance spectrum of a gold triangular nanocavity array by both simulations and experiments. The finite integration technique (FIT) simulated the extinction spectrum of the gold nanocavity array with 300 nm periodicity onto which the GNRs of different ARs and SAs are placed. Simulations showed that matching of the GNRs longitudinal peak, which is affected by AR, to the nanocavity array's spectrum minima can optimize signal suppression and shifting. Moreover, increasing SA of the matched GNRs increased the spectral variations of the array. Experiments confirmed that GNRs conjugated to a gold triangular nanocavity array of 300 nm periodicity caused spectrum suppression and redshift. Our findings demonstrate that tailoring of the GNR AR and SA parameters to nanoplasmonic arrays has the potential to greatly improve spectral variations for enhanced plasmonic biosensing.

Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins

Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.

Label-free methods for optical in vitro characterization of protein-protein interactions

Protein-protein interactions are involved in the regulation and function of the majority of cellular processes. As a result, much effort has been aimed at the development of methodologies capable of quantifying protein-protein interactions, with label-free methods being of particular interest due to the associated simplified workflows and minimisation of label-induced perturbations. Here, we review recent advances in optical technologies providing label-free in vitro measurements of affinities and kinetics. We provide an overview and comparison of existing techniques and their principles, discussing advantages, limitations, and recent applications.

AES and ToF-SIMS combination for single cell chemical imaging of gold nanoparticle-labeled Escherichia coli

A chemical fingerprint of the Escherichia coli cell surface labeled by gelatin coated gold nanoparticles was obtained by combining Auger Electron Spectroscopy (AES) for single cell level chemical images, and Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS) Tandem MS for unambiguous molecular identification of co-localized species.

Data evaluation for surface-sensitive label-free methods to obtain real-time kinetic and structural information of thin films: A practical review with related software packages

Interfacial layers are important in a wide range of applications in biomedicine, biosensing, analytical chemistry and the maritime industries. Given the growing number of applications, analysis of such layers and understanding their behavior is becoming crucial. Label-free surface sensitive methods are excellent for monitoring the formation kinetics, structure and its evolution of thin layers, even at the nanoscale. In this paper, we review existing and commercially available label-free techniques and demonstrate how the experimentally obtained data can be utilized to extract kinetic and structural information during and after formation, and any subsequent adsorption/desorption processes. We outline techniques, some traditional and some novel, based on the principles of optical and mechanical transduction. Our special focus is the current possibilities of combining label-free methods, which is a powerful approach to extend the range of detected and deduced parameters. We summarize the most important theoretical considerations for obtaining reliable information from measurements taking place in liquid environments and, hence, with layers in a hydrated state. A thorough treamtmaent of the various kinetic and structural quantities obtained from evaluation of the raw label-free data are provided. Such quantities include layer thickness, refractive index, optical anisotropy (and molecular orientation derived therefrom), degree of hydration, viscoelasticity, as well as association and dissociation rate constants and occupied area of subsequently adsorbed species. To demonstrate the effect of variations in model conditions on the observed data, simulations of kinetic curves at various model settings are also included. Based on our own extensive experience with optical waveguide lightmode spectroscopy (OWLS) and the quartz crystal microbalance (QCM), we have developed dedicated software packages for data analysis, which are made available to the scientific community alongside this paper.

Microfluidics-Based Plasmonic Biosensing System Based on Patterned Plasmonic Nanostructure Arrays

This review aims to summarize the recent advances and progress of plasmonic biosensors based on patterned plasmonic nanostructure arrays that are integrated with microfluidic chips for various biomedical detection applications. The plasmonic biosensors have made rapid progress in miniaturization sensors with greatly enhanced performance through the continuous advances in plasmon resonance techniques such as surface plasmon resonance (SPR) and localized SPR (LSPR)-based refractive index sensing, SPR imaging (SPRi), and surface-enhanced Raman scattering (SERS). Meanwhile, microfluidic integration promotes multiplexing opportunities for the plasmonic biosensors in the simultaneous detection of multiple analytes. Particularly, different types of microfluidic-integrated plasmonic biosensor systems based on versatile patterned plasmonic nanostructured arrays were reviewed comprehensively, including their methods and relevant typical works. The microfluidics-based plasmonic biosensors provide a high-throughput platform for the biochemical molecular analysis with the advantages such as ultra-high sensitivity, label-free, and real time performance; thus, they continue to benefit the existing and emerging applications of biomedical studies, chemical analyses, and point-of-care diagnostics.

Recent Advancements in Aptamer-Based Surface Plasmon Resonance Biosensing Strategies

Surface plasmon resonance (SPR) can track molecular interactions in real time, and is a powerful as well as widely used biological and chemical sensing technique. Among the different SPR-based sensing applications, aptamer-based SPR biosensors have attracted significant attention because of their simplicity, feasibility, and low cost for target detection. Continuous developments in SPR aptasensing research have led to the emergence of abundant technical and design concepts. To understand the recent advances in SPR for biosensing, this paper reviews SPR-based research from the last seven years based on different sensing-type strategies and sub-directions. The characteristics of various SPR-based applications are introduced. We hope that this review will guide the development of SPR aptamer sensors for healthcare.

Recent Advances in Antifouling Materials for Surface Plasmon Resonance Biosensing in Clinical Diagnostics and Food Safety

Strategies to develop antifouling surface coatings are crucial for surface plasmon resonance (SPR) sensing in many analytical application fields, such as detecting human disease biomarkers for clinical diagnostics and monitoring foodborne pathogens and toxins involved in food quality control. In this review, firstly, we provide a brief discussion with considerations about the importance of adopting appropriate antifouling materials for achieving excellent performances in biosensing for food safety and clinical diagnosis. Secondly, a non-exhaustive landscape of polymeric layers is given in the context of surface modification and the mechanism of fouling resistance. Finally, we present an overview of some selected developments in SPR sensing, emphasizing applications of antifouling materials and progress to overcome the challenges related to the detection of targets in complex matrices relevant for diagnosis and food biosensing.

Dual-channel illumination surface plasmon resonance holographic microscopy for resolution improvement

Surface plasmon resonance holographic microscopy (SPRHM), combining digital holographic microscopy with surface plasmon resonance (SPR), can simultaneously obtain the amplitude and phase distributions of the reflected beam carrying specimen information in SPR. Due to the decaying length of the surface plasmon wave as large as tens of micrometers, the spatial resolution of SPRHM is lower than that of ordinary optical microscopes. In this work, we propose a scheme to improve the spatial resolution of SPRHM by applying dual-channel SPR excitations. Through the polarization multiplexing technique, two holograms carrying the information of SPR excited in orthogonal directions are simultaneously acquired. Via a numerical reconstruction and filtering algorithm for holograms, the lateral spatial resolution of SPRHM can be effectively enhanced to reach nearly 1 µm at a wavelength of 632.8 nm. This is comparable to the resolution of traditional optical microscopes, while possessing the advantages of wide-field imaging and high measurement sensitivity of SPR.

Real-time and wide-field mapping of cell-substrate adhesion gap and its evolution via surface plasmon resonance holographic microscopy

As one of the most common biological phenomena, cell adhesion plays a vital role in the cellular activities such as the growth and apoptosis, attracting tremendous research interests over the past decades. Taking the cell evolution under drug injection as an example, the dynamics of cell-substrate adhesion gap can provide valuable information in the fundamental research of cell contacts. A robust technique of monitoring the cell adhesion gap and its evolution in real time is highly desired. Herein, we develop a surface plasmon resonance holographic microscopy to achieve the novel functionality of real-time and wide-field mapping of the cell-substrate adhesion gap and its evolution in situ. The cell adhesion gap images of mouse osteoblast cells and human breast cancer cells have been effectively extracted in a dynamic and label-free manner. The proposed technique opens up a new avenue of revealing the cell-substrate interaction mechanism and renders the wide applications in the biosensing area.

The prospects of tumor chemosensitivity testing at the single-cell level

Tumor chemosensitivity testing plays a pivotal role in the optimal selection of chemotherapeutic regimens for cancer patients in a personalized manner. High-throughput drug screening approaches have been developed but they failed to take into account intratumor heterogeneity and therefore only provided limited predictive power of therapeutic response to individual cancer patients. Single cancer cell drug sensitivity testing (SCC-DST) has been recently developed to evaluate the variable sensitivity of single cells to different anti-tumor drugs. In this review, we discuss how SCC-DST overcomes the obstacles of traditional drug screening methodologies. We outline critical procedures of SCC-DST responsible for single-cell generation and sorting, cell-drug encapsulation on a microfluidic chip and detection of cell-drug interactions. In SCC-DST, droplet-based microfluidics is emerging as an important platform that integrated various assays and analyses for drug susceptibility tests for individual patients. With the advancement of technology, both fluorescence imaging and label-free analysis have been used for detecting single cell-drug interactions. We also discuss the feasibility of integrating SCC-DST with single-cell RNA sequencing to unravel the mechanisms leading to drug resistance, and utilizing artificial intelligence to facilitate the analysis of various omics data in the evaluation of drug susceptibility. SCC-DST is setting the stage for better drug selection for individual cancer patients in the era of precision medicine.

Label-Free Immunoassay for Multiplex Detections of Foodborne Bacteria in Chicken Carcass Rinse with Surface Plasmon Resonance Imaging

The frequent outbreaks of foodborne pathogens have stimulated the demand of biosensors capable of rapid and multiplex detection of contaminated food. In this study, surface plasmon resonance imaging (SPRi) was used in simultaneous label-free detection of multiple foodborne pathogens, mainly Salmonella spp. and Shiga-toxin producing Escherichia coli (STEC), in commercial chicken carcass rinse. The antibodies were immobilized on the same SPRi sensor chip as a label-free immunoassay. Their immobilization concentrations were optimized to be ranging from 0.25 to 1.0 mg/mL, and independent of pH values. This label-free immunoassay achieved 10⁶ colony-forming unit (CFU)/mL limit of detection for Salmonella, which was further improved to 1.0 CFU/mL with overnight bacteria enrichment. The injected samples with different bacteria, Salmonella Enteritidis, STEC, and Listeria monocytogenes, have been identified by the same biochip. Moreover, the SPRi signals revealed complex interference effects among coexisting bacteria species in heterogeneous bacteria solutions. This SPRi-based immunoassay demonstrates the great potential in high-throughput screening of multiple pathogenic bacteria coexisting in chicken carcass rinse. The reliability of antibody immobilization and cross-reactions of different antibodies on the same biochip are the major challenges of practical application of SPRi.

Enhancing the sensitivity of plasmonic optical fiber sensors by analyzing the distribution of the optical modes intensity

Improving the sensitivity of plasmonic optical fiber sensors constitutes a major challenge as it could significantly enhance their sensing capabilities for the label-free detection of biomolecular interactions or chemical compounds. While many efforts focus on developing more sensitive structures, we present here how the sensitivity of a sensor can be significantly enhanced by improving the light analysis. Contrary to the common approach where the global intensity of the light coming from the core is averaged, our approach is based on the full analysis of the retro-reflected intensity distribution that evolves with the refractive index of the medium being analyzed. Thanks to this original and simple approach, the refractive index sensitivity of a plasmonic optical fiber sensor used in reflection mode was enhanced by a factor of 25 compared to the standard method. The reported approach opens exciting perspectives for improving the remote detection as well as for developing new sensing strategies.

Direct plasmonic detection of circulating RAS mutated DNA in colorectal cancer patients

RAS mutations in the blood of colorectal cancer (CRC) patients are emerging as biomarkers of acquired resistance to Epidermal Growth Factor Receptor therapy. Unfortunately, reliable assays granting fast, real-time monitoring of treatment response, capable of refining retrospective, tissue-based analysis, are still needed. Recently, several methods for detecting blood RAS mutations have been proposed, generally relying on multi-step and PCR-based, time-consuming and cost-ineffective procedures. By exploiting a liquid biopsy approach, we developed an ultrasensitive nanoparticle-enhanced plasmonic method for detecting ~1 aM RAS single nucleotide variants (SNVs) in the plasma of CRC patients. The assay does not require the extraction of tumor DNA from plasma and detects it in volumes as low as 40 μL of plasma, which is at least an order of magnitude smaller than that required by state of the art liquid biopsy technologies. The most prevalent RAS mutations are detected in DNA from tumor tissue with 100% sensitivity and 83.33% specificity. Spike-in experiments in human plasma further encouraged assay application on clinical specimens. The assay was proven in plasma from CRC patients and healthy donors, and full discrimination between mutated DNA from patients over wild-type DNA from healthy volunteers was obtained thus demonstrating its promising avenue for cancer monitoring based on liquid biopsy.

Atomic Force Microscope Study of Ag-Conduct Polymer Hybrid Films: Evidence for Light-Induced Charge Separation

Scanning Kelvin probe microscopy (SKPM), electrostatic force microscopy (EFM) are used to study the microscopic processes of the photo-induced charge separation at the interface of Ag and conductive polymers, i.e., poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-bʹ]dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)] (PCPDTBT) and poly(3-hexylthiophene-2,5-diyl) (P3HT). They are also widely used in order to directly observe the charge distribution and dynamic changes at the interfaces in nanostructures, owing to their high sensitivity. Using SKPM, it is proved that the charge of the photo-induced polymer PCPDTBT is transferred to Ag nanoparticles (NPs). The surface charge of the Ag-induced NPs is quantified while using EFM, and it is determined that the charge is injected into the polymer P3HT from the Ag NPs. We expect that this technology will provide guidance to facilitate the separation and transfer of the interfacial charges in the composite material systems and it will be applicable to various photovoltaic material systems.