Laser spectroscopic technique for direct identification of a single virus I: FASTER CARS

Integrated analysis of restraint stress in rat serum using ATR-FTIR and Raman spectroscopy with Machine learning

In forensic practice, accurately determining whether an individual has been subjected to prolonged restraint or assessing injuries resulting from restraint can be challenging. To address this, we explored a novel approach using attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and Raman spectroscopy combined with machine learning to jointly identify restraint stress. We randomly assigned rats into three experimental groups: a restraint stress group (subjected to fasting and water deprivation), a control group (subjected to fasting and water deprivation without restraint), and a normal group. After collecting the serum spectra of the animals, a principal component analysis (PCA) model was established to explore the separation trends among the groups and to identify relevant characteristic peaks. Subsequently, a random forest (RF) model was established to compare the restraint stress group with the other two groups. The analysis identified key substances that indicated the presence of restraint stress: 1161 cm-1, 1167 cm-1 (anti-symmetric C-O-C stretch) and 980 cm-1, 976 cm-1, 974 cm-1 (-N+(CH3)3, antisymmetric stretch). And the RF model was used to compare the restraint stress groups at different time points, revealing substances that may help determine the duration of restraint stress: 1747 cm-1 (ester carbonyl band), 1626 cm-1 (β-pleated sheet), 1211 cm-1 (Amide III, -N+(CH3)3, antisymmetric stretch), 1180 cm-1 (phosphodiester), 1128 cm-1 (-C-C-), 1024 cm-1 (C-O stretching coupled with C-O bending) and 1389 cm-1, 1335 cm-1, 1321 cm-1 (Trp, α helix, phospholipids), 710 cm-1 (Polysaccharides), 1266 cm-1 (Amide Ⅲ), 1015 cm-1 (β-carotene). These findings suggest that ATR-FTIR and Raman spectroscopy together, when combined with machine learning, has significant potential as a powerful tool for analyzing and characterizing restraint stress, offering new insights and directions for future research in this area.

Fiber Vector Light-Field-Based Tip-Enhanced Raman Spectroscopy

Tip-enhanced Raman spectroscopy (TERS) has been extensively employed to investigate the light-matter interaction at the nanoscale. However, the current TERS strategies lack the ability to excite the low-background inhomogeneous electromagnetic field with significant enhancement of electric field, electric field gradient, and optomagnetic field, simultaneously. To overcome this, we developed a fiber vector light-field-based TERS strategy aimed at exploring the multipole Raman scattering processes of molecules. By modulating the excitation power, we have observed for the first time the Stark effect associated with Raman-forbidden transitions, revealing a strong electric-field gradient and optomagnetic effect within the plasmon cavity. Furthermore, by manipulating the plasmon tip to minimize the nanogap, we demonstrate that splitting occurs in the dipole Raman spectrum, indicating that the plasmon cavity enters a strong coupling regime. This fiber vector light-field-based TERS approach offers a unique opportunity to investigate weak matter responses with potential applications in single-molecule spectroscopy, sensors, and catalysis monitoring.

Recent progress in online detection methods of bioaerosols

The aerosol transmission of coronavirus disease in 2019, along with the spread of other respiratory diseases, caused significant loss of life and property; it impressed upon us the importance of real-time bioaerosol detection. The complexity, diversity, and large spatiotemporal variability of bioaerosols and their external/internal mixing with abiotic components pose challenges for effective online bioaerosol monitoring. Traditional methods focus on directly capturing bioaerosols before subsequent time-consuming laboratory analysis such as culture-based methods, preventing the high-resolution time-based characteristics necessary for an online approach. Through a comprehensive literature assessment, this review highlights and discusses the most commonly used real-time bioaerosol monitoring techniques and the associated commercially available monitors. Methods applied in online bioaerosol monitoring, including adenosine triphosphate bioluminescence, laser/light-induced fluorescence spectroscopy, Raman spectroscopy, and bioaerosol mass spectrometry are summarized. The working principles, characteristics, sensitivities, and efficiencies of these real-time detection methods are compared to understand their responses to known particle types and to contrast their differences. Approaches developed to analyze the substantial data sets obtained by these instruments and to overcome the limitations of current real-time bioaerosol monitoring technologies are also introduced. Finally, an outlook is proposed for future instrumentation indicating a need for highly revolutionized bioaerosol detection technologies.

Mosaic quadrivalent influenza vaccine single nanoparticle characterization

Recent work by our laboratory and others indicates that co-display of multiple antigens on protein-based nanoparticles may be key to induce cross-reactive antibodies that provide broad protection against disease. To reach the ultimate goal of a universal vaccine for seasonal influenza, a mosaic influenza nanoparticle vaccine (FluMos-v1) was developed for clinical trial (NCT04896086). FluMos-v1 is unique in that it is designed to co-display four recently circulating haemagglutinin (HA) strains; however, current vaccine analysis techniques are limited to nanoparticle population analysis, thus, are unable to determine the valency of an individual nanoparticle. For the first time, we demonstrate by total internal reflection fluorescence microscopy and supportive physical-chemical methods that the co-display of four antigens is indeed achieved in single nanoparticles. Additionally, we have determined percentages of multivalent (mosaic) nanoparticles with four, three, or two HA proteins. The integrated imaging and physicochemical methods we have developed for single nanoparticle multivalency will serve to further understand immunogenicity data from our current FluMos-v1 clinical trial.

Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy

Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.

Hot-Electron Dynamics Mediated Medical Diagnosis and Therapy

Surface plasmon resonance excitation significantly enhances the absorption of light and increases the generation of "hot" electrons, i.e., conducting electrons that are raised from their steady states to excited states. These excited electrons rapidly decay and equilibrate via radiative and nonradiative damping over several hundred femtoseconds. During the hot-electron dynamics, from their generation to the ultimate nonradiative decay, the electromagnetic field enhancement, hot electron density increase, and local heating effect are sequentially induced. Over the past decade, these physical phenomena have attracted considerable attention in the biomedical field, e.g., the rapid and accurate identification of biomolecules, precise synthesis and release of drugs, and elimination of tumors. This review highlights the recent developments in the application of hot-electron dynamics in medical diagnosis and therapy, particularly fully integrated device techniques with good application prospects. In addition, we discuss the latest experimental and theoretical studies of underlying mechanisms. From a practical standpoint, the pioneering modeling analyses and quantitative measurements in the extreme near field are summarized to illustrate the quantification of hot-electron dynamics. Finally, the prospects and remaining challenges associated with biomedical engineering based on hot-electron dynamics are presented.

Ambient Tip-Enhanced Two Photon Photoluminescence from CdSe/ZnS Quantum Dots

Nonlinear nano-optical measurements that combine ultrafast spectroscopy with tools of scanning probe microscopy are scarce. This is particularly the case when high spatial resolution on the order of a few nanometers is sought after in experiments performed under ambient laboratory conditions. In this work, we demonstrate the latter through measurements that track two-photon photoluminescence from aggregates of CdSe/ZnS quantum dots with sub-5 nm spatial resolution. Our proof-of-principle measurements that only take advantage of a plasmonic probe (as opposed to a gap mode) pave the way for nonlinear photoluminescence-based spectral nanoimaging of realistic/heterogeneous (bio) molecular and (bio) material systems.

Multimodal (Non)Linear Optical Nanoimaging and Nanospectroscopy

This Perspective highlights recent advances in linear and nonlinear spectral nanoimaging. The described developments are motivated by the need to characterize molecular and material systems noninvasively with nanometer spatial and femtosecond temporal resolution. Indeed, the ability to image and chemically characterize heterogeneous interfaces with joint nano-femto resolution is a prerequisite to advancing our fundamental understanding of processes as diverse as heterogeneous catalysis, microbial communication, and energy flow in pristine/defect-containing low-dimensional quantum materials, to name a few. We describe pioneering work and recent demonstrations of (non)linear optical nanoimaging and nanospectroscopy, with an emphasis on high spatial resolution measurements conducted under ambient laboratory conditions.

Imaging Techniques: Essential Tools for the Study of SARS-CoV-2 Infection

The world has seen the emergence of a new virus in 2019, SARS-CoV-2, causing the COVID-19 pandemic and millions of deaths worldwide. Microscopy can be much more informative than conventional detection methods such as RT-PCR. This review aims to present the up-to-date microscopy observations in patients, the in vitro studies of the virus and viral proteins and their interaction with their host, discuss the microscopy techniques for detection and study of SARS-CoV-2, and summarize the reagents used for SARS-CoV-2 detection. From basic fluorescence microscopy to high resolution techniques and combined technologies, this article shows the power and the potential of microscopy techniques, especially in the field of virology.

Progress of tip-enhanced Raman scattering for the last two decades and its challenges in very recent years

Tip-enhanced Raman scattering (TERS) has recently attracted remarkable attention as a novel nano-spectroscopy technique. TERS, which provides site-specific information, can be performed on any material surface regardless of morphology. Moreover, it can be applied in various environments, such as ambient air, ultrahigh vacuum (UHV), solutions, and electrochemical environments. This review reports on one hand progress of TERS for the last two decades, and on the other hand, its challenges in very recent years. Part of the progress of TERS starts with the prehistory and history of TERS, and then, the characteristics and advantages of TERS are described. Significant emphasis is put on the development of TERS instrumentation and equipment such as ultrahigh vacuum TERS, liquid TERS, electrochemical-TERS, and tip-preparations. Applications of TERS, particularly those with nanocarbons, biological materials, and surface and interface analysis, are mentioned in some detail. In the part on challenges, we focus on the very recent advances in TERS; progress in spatial resolution to the angstrom scale is the hottest topic. Recent TERS studies performed under UHV, for example chemical imaging at the angstrom scale and Raman detection of bond breaking and making of a chemisorbed up-standing single molecules at single-bond level, are reviewed. Of course, there is no clear border between the two parts. In the last part the perspective of TERS is discussed.

Nanoscale chemical characterization of biomolecules using tip-enhanced Raman spectroscopy

Nanoscale chemical and structural characterization of single biomolecules and assemblies is of paramount importance for applications in biology and medicine. It aims to describe the molecular structure of biomolecules and their interaction with unprecedented spatial resolution to better comprehend underlying molecular mechanisms of biological processes involved in cell activity and diseases. Tip-enhanced Raman scattering (TERS) spectroscopy appears particularly appealing to reach these objectives. This state-of-the-art TERS technique is as versatile as it is ultrasensitive. To perform a successful TERS experiment, special care and a thorough methodology for the preparation of the TERS system, the TERS probe tip, and sample are needed. Intense efforts have been deployed to characterize nucleic acids, proteins and peptides, lipid membranes, and more complex systems such as cells and viruses using TERS. Although the vast majority of studies have first been performed in dry conditions, they have allowed for several scientific breakthroughs. These include DNA and RNA sequencing, and the determination of relationships between protein structure and biological function by the use of increasingly exploitative chemometric tools for spectral data analysis. The nanoscale determination of the secondary structure of amyloid fibrils, protofibrils and oligomers implicated in neurodegenerative diseases could, for instance, be connected with the toxicity of these species, amyloid formation pathways, and their interaction with phospholipids. Single particles of different viral strains could be distinguished from one another by comparison of their protein and lipid contents. In addition, TERS has allowed for the evermore accurate description of the molecular organization of lipid membranes. Very recent advances also demonstrated the possibility to carry out TERS in aqueous medium, which opens thrilling perspectives for the TERS technique in biological, biomedical, and potential clinical applications.

Raman Microspectroscopy Goes Viral: Infection Dynamics in the Cosmopolitan Microalga, Emiliania huxleyi

Emiliania huxleyi is a cosmopolitan member of the marine phytoplankton. This species’ capacities for carbon sequestration and sulfur mobilization make it a key player in oceanic biogeochemical cycles that influence climate on a planetary scale. Seasonal E. huxleyi blooms are abruptly terminated by viral epidemics caused by a clade of large DNA viruses collectively known as coccolithoviruses (EhVs). EhVs thereby mediate a significant part of material and energy fluxes associated with E. huxleyi population dynamics. In this study, we use spontaneous Raman microspectroscopy to perform label-free and non-invasive measurements of the macromolecular composition of individual virions and E. huxleyi host cells. Our novel autofluorescence suppression protocol enabled spectroscopic visualization of evolving macromolecular redistributions in individual E. huxleyi cells at different stages of EhV infection. Material transfer from E. huxleyi hosts to single EhV-163 virions was confirmed by combining stable isotope probing (SIP) experiments with Raman microspectroscopy. Inheritance of the host cells’ ¹³C-enriched isotopic signature was quantified based on red shifts of Raman peaks characteristic of phenylalanine’s phenyl ring. Two-dimensional Raman mapping of EhV-infected E. huxleyi cells revealed that the compact region producing an intense Raman DNA signal (i.e., the nucleus) in healthy E. huxleyi cells becomes diffuse during the first hours of infection. Raman DNA emissions integrated throughout individual cells decreased during the infection cycle. Our observations are consistent with EhV-163 degrading the host’s nuclear DNA, scavenging released nucleotides for its own genome replication, and shedding newly-produced virions prior to host lysis via budding.

A Nonclinical Spectroscopic Approach for Diagnosing Covid-19: A Concise Perspective

With the COVID-19 outbreak, many challenges are posed before the scientific world to curb this pandemic. The diagnostic testing, treatment, and vaccine development for this infection caught the scientific community's immediate attention. Currently, despite the global proliferation of COVID-19 vaccination, the specific treatment for this disease is yet unknown. Meanwhile, COVID-19 detection or diagnosis using polymerase chain reaction (PCR)-based me hods is expensive and less reliable. Moreover, this technique needs much time to furnish the results. Thus, the elaboration of a highly sensitive and fast method of COVID-19 diagnostics is of great importance. The spectroscopic approach is herein suggested as an efficient detection methodology for COVID-19 diagnosis, particularly Raman spectroscopy, infrared spectroscopy, and mass spectrometry.

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers' effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment.

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers' effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment.

Imaging Plasmons with Sub-2 nm Spatial Resolution via Tip-Enhanced Four-Wave Mixing

Four-wave mixing at plasmonic tip-sample nanojunctions may be used to visualize plasmonic fields with sub-2 nm spatial resolution under ambient laboratory conditions. We illustrate the latter using a gold-coated atomic force microscopy probe irradiated with a pair of near-infrared femtosecond laser pulses and used to image plasmonic gold nanoplates and silver nanocubes. Through diagnostic polarization-dependent tip-only measurements, we illustrate that the four-wave mixing signal is localized to the tip apex. The apex-bound signal is further enhanced when the tip is located at specific locations near plasmonic nanoparticles. Overall, this work paves the way for visualizing chemical transformations as well as coherent electronic and vibrational dynamics with joint femtosecond temporal and few-nanometer spatial resolution under ambient conditions.

A Review on SERS-Based Detection of Human Virus Infections: Influenza and Coronavirus

The diagnosis of respiratory viruses of zoonotic origin (RVsZO) such as influenza and coronaviruses in humans is crucial, because their spread and pandemic threat are the highest. Surface-enhanced Raman spectroscopy (SERS) is an analytical technique with promising impact for the point-of-care diagnosis of viruses. It has been applied to a variety of influenza A virus subtypes, such as the H1N1 and the novel coronavirus SARS-CoV-2. In this work, a review of the strategies used for the detection of RVsZO by SERS is presented. In addition, relevant information about the SERS technique, anthropozoonosis, and RVsZO is provided for a better understanding of the theme. The direct identification is based on trapping the viruses within the interstices of plasmonic nanoparticles and recording the SERS signal from gene fragments or membrane proteins. Quantitative mono- and multiplexed assays have been achieved following an indirect format through a SERS-based sandwich immunoassay. Based on this review, the development of multiplex assays that incorporate the detection of RVsZO together with their specific biomarkers and/or secondary disease biomarkers resulting from the infection progress would be desirable. These configurations could be used as a double confirmation or to evaluate the health condition of the patient.

Point of Care Diagnostic Devices for Rapid Detection of Novel Coronavirus (SARS-nCoV19) Pandemic: A Review

Coronaviruses are recognized as causative agents of human diseases worldwide. In Wuhan, China, an outbreak of Severe acute respiratory syndrome novel Coronavirus (SARS-nCoV-2) was reported at the end of December 2019, causing 63 million COVID cases and 1.3 million deaths globally by 2 December, 2020. The transmission risk forecasts and the SARS-nCoV-2 epidemic pattern are progressive. Unfortunately, there is no specific FDA approved drugs or vaccines available currently to treat SARS-nCoV-2. In response to nCoV-2 spread, the rapid detection is crucial for estimating the severity of the disease and treatment of patients. Currently, there are several RT-PCR based diagnostic kits available for SARS-nCoV-2 detection, which are time-consuming, expensive, need advanced equipment facilities and trained personnel. The cost of diagnosis and the unavailability of sufficient test kits may prevent to check community transmission. Furthermore, expanding the testing facilities in asymptomatic cases in hotspots require more Point of Care (PoC) devices. Therefore, fast, inexpensive, and reliable methods of detection of SARS-nCoV-2 virus infection in humans is urgently required. The rapid and easy-to-use devices will facilitate onsite testing. In this review, nucleic acid assays, serological assays, multiplex assays, and PoC devices are discussed to understand various diagnostic approaches to reduce the spread and mortality rate in the future. Aptamer based detection is most specific, inexpensive and rapid detection of SARS-nCoV-2 without laboratory tools. To the best of our knowledge more than 900 SARS-nCoV-2 test kits are in pipeline, among 395 test kits are molecular bested test kits and only few test kits are developed using Aptamer technology https://www.finddx.org/covid-19/pipeline/.

An Analysis Review of Detection Coronavirus Disease 2019 (COVID-19) Based on Biosensor Application

Timely detection and diagnosis are essentially needed to guide outbreak measures and infection control. It is vital to improve healthcare quality in public places, markets, schools and airports and provide useful insights into the technological environment and help researchers acknowledge the choices and gaps available in this field. In this narrative review, the detection of coronavirus disease 2019 (COVID-19) technologies is summarized and discussed with a comparison between them from several aspects to arrive at an accurate decision on the feasibility of applying the best of these techniques in the biosensors that operate using laser detection technology. The collection of data in this analysis was done by using six reliable academic databases, namely, Science Direct, IEEE Xplore, Scopus, Web of Science, Google Scholar and PubMed. This review includes an analysis review of three highlights: evaluating the hazard of pandemic COVID-19 transmission styles and comparing them with Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) to identify the main causes of the virus spreading, a critical analysis to diagnose coronavirus disease 2019 (COVID-19) based on artificial intelligence using CT scans and CXR images and types of biosensors. Finally, we select the best methods that can potentially stop the propagation of the coronavirus pandemic.

Rapid and label-free detection of COVID-19 using coherent anti-Stokes Raman scattering microscopy

From the 1918 influenza pandemic (H1N1) until the recent 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, no efficient diagnostic tools have been developed for sensitive identification of viral pathogens. Rigorous, early, and accurate detection of viral pathogens is not only linked to preventing transmission but also to timely treatment and monitoring of drug resistance. Reverse transcription-polymerase chain reaction (RT-PCR), the gold standard method for microbiology and virology testing, suffers from both false-negative and false-positive results arising from the detection limit, contamination of samples/templates, exponential DNA amplification, and variation of viral ribonucleic acid sequences within a single individual during the course of the infection. Rapid, sensitive, and label-free detection of SARS-CoV-2 can provide a first line of defense against the current pandemic. A promising technique is non-linear coherent anti-Stokes Raman scattering (CARS) microscopy, which has the ability to capture rich spatiotemporal structural and functional information at a high acquisition speed in a label-free manner from a biological system. Raman scattering is a process in which the distinctive spectral signatures associated with light-sample interaction provide information on the chemical composition of the sample. In this prospective, we briefly discuss the development and future prospects of CARS for real-time multiplexed label-free detection of SARS-CoV-2 pathogens.