Label-Free SERS for Rapid Differentiation of SARS-CoV-2-Induced Serum Metabolic Profiles in Non-Hospitalized Adults.

COVID-19 represents a multi-system infectious disease with broad-spectrum manifestations, including changes in host metabolic processes connected to the disease pathogenesis. Understanding biochemical dysregulation patterns as a consequence of COVID-19 illness promises to be crucial for tracking disease course and clinical outcomes. Surface-enhanced Raman scattering (SERS) has attracted considerable interest in biomedical diagnostics for the sensitive detection of intrinsic profiles of unique fingerprints of serum biomolecules indicative of SARS-CoV-2 infection in a label-free format. Here, we applied label-free SERS and chemometrics for rapid interrogation of temporal metabolic dynamics in longitudinal sera of mildly infected non-hospitalized patients (n = 22), at 4 and 16 weeks post PCR-positive diagnosis, and compared them with negative controls (n = 8). SERS spectral markers revealed distinct metabolic profiles in patient sera that significantly deviated from the healthy metabolic state at the two sampling time intervals. Multivariate and univariate analyses of the spectral data identified abundance dynamics in amino acids, lipids, and protein vibrations as the key spectral features underlying the metabolic differences detected in convalescent samples and perhaps associated with patient recovery progression. A validation study performed using spontaneous Raman spectroscopy yielded spectral data results that corroborated SERS spectral findings and confirmed the detected disease-specific molecular phenotypes in clinical samples. Label-free SERS promises to be a valuable analytical technique for rapid screening of the metabolic phenotype induced by SARS-CoV-2 infection to allow appropriate healthcare intervention.

A glycan-based plasmonic sensor for prostate cancer diagnosis.

Prostate cancer affects thousands of men who undergo clinical screening tests every year. The main biomarker used for the diagnosis of prostate cancer, prostate specific antigen (PSA), presents limitations that justify investigating new biomarkers to improve reliability. Antibodies against the tumor-associated carbohydrate antigen (Tn), or TACA, develop early in carcinogenesis, making them an interesting alternative as a target for prostate cancer diagnostics. In this work, the Tn antigen was synthesized and immobilized on a surface plasmon resonance sensor coated with a polydopamine/polyethylene oxide mixed layer used both as an anchoring surface for Tn capture moieties and to minimize surface fouling. The sensor could be regenerated and reused at least 60 times without any significant loss in sensitivity. Anti-Tn antibodies were detected in the 0-10 nM concentration range with detection limits of 0.1 and 0.3 nM in spiked buffer solutions and diluted human blood serum samples, respectively. Finally, as a proof-of-concept, this carbohydrate-based sensor was used to successfully discriminate blood serum samples from prostate cancer-free and prostate cancer patients.

Real-time monitoring of bead-based DNA hybridization in a microfluidic system: study of amplicon hybridization behavior on solid supports.

DNA hybridization phenomena occurring on solid supports are not understood as clearly as aqueous phase hybridizations and mathematical models cannot predict some empirically obtained results. Ongoing research has identified important parameters but remains incomplete to accurately account for all interactions. It has previously been shown that the length of the overhanging (dangling) end of the target DNA strand following hybridization to the capture probe is correlated to interactions with the complementary strand in solution which can result in unbinding of the target and its release from the surface. We have developed an instrument for real-time monitoring of DNA hybridization on spherical particles functionalized with oligonucleotide capture probes and arranged in the form of a tightly packed monolayer bead bed inside a microfluidic cartridge. The instrument is equipped with a pneumatic module to mediate displacement of fluid on the cartridge. We compared this system to both conventional (passive) and centrifugally-driven (active) microfluidic microarray hybridization on glass slides to establish performance levels for the detection of single nucleotide polymorphisms. The system was also used to study the effect of the dangling end's length in real-time when the immobilized target DNA is exposed to the complementary strand in solution. Our findings indicate that increasing the length of the dangling end leads to desorption of target amplicons from bead-bound capture probes at a rate approaching that of the initial hybridization process. Finally, bead bed hybridization was performed with Streptococcus agalactiae cfb gene amplicons obtained from randomized clinical samples, which allowed for identification of group B streptococci within 5-15 min. The methodology presented here is useful for investigating competitive hybridization mechanisms on solid supports and to rapidly validate the suitability of microarray capture probes.

Cross-validation of ELISA and a portable surface plasmon resonance instrument for IgG antibody serology with SARS-CoV-2 positive individuals.

We report on the development of surface plasmon resonance (SPR) sensors and matching ELISAs for the detection of nucleocapsid and spike antibodies specific against the novel coronavirus 2019 (SARS-CoV-2) in human serum, plasma and dried blood spots (DBS). When exposed to SARS-CoV-2 or a vaccine against SARS-CoV-2, the immune system responds by expressing antibodies at levels that can be detected and monitored to identify the fraction of the population potentially immunized against SARS-CoV-2 and support efforts to deploy a vaccine strategically. A SPR sensor coated with a peptide monolayer and functionalized with various sources of SARS-CoV-2 recombinant proteins expressed in different cell lines detected human anti-SARS-CoV-2 IgG antibodies in clinical samples. Nucleocapsid expressed in different cell lines did not significantly change the sensitivity of the assays, whereas the use of a CHO cell line to express spike ectodomain led to excellent performance. This bioassay was performed on a portable SPR instrument capable of measuring 4 biological samples within 30 minutes of sample/sensor contact and the chip could be regenerated at least 9 times. Multi-site validation was then performed with in-house and commercial ELISA, which revealed excellent cross-correlations with Pearson's coefficients exceeding 0.85 in all cases, for measurements in DBS and plasma. This strategy paves the way to point-of-care and rapid testing for antibodies in the context of viral infection and vaccine efficacy monitoring.

Thinking outside the shell: novel sensors designed from plasmon-enhanced fluorescent concentric nanoparticles.

The alteration of photophysical properties of fluorophores in the vicinity of a metallic nanostructure, a phenomenon termed plasmon- or metal-enhanced fluorescence (MEF), has been investigated extensively and used in a variety of proof-of-concept demonstrations over the years. A particularly active area of development in this regard has been the design of nanostructures where fluorophore and metallic core are held in a stable geometry that imparts improved luminosity and photostability to a plethora of organic fluorophores. This minireview presents an overview of MEF-based concentric core-shell sensors developed in the past few years. These architectures expand the range of applications of nanoparticles (NPs) beyond the uses possible with fluorescent molecules. Design aspects that are being described include the influence of the nanocomposite structure on MEF, notably the dependence of fluorescence intensity and lifetime on the distance to the plasmonic core. The chemical composition of nanocomposites as a design feature is also discussed, taking as an example the use of non-noble plasmonic metals such as indium as core materials to enhance multiple fluorophores throughout the UV-Vis range and tune the sensitivity of halide-sensing fluorophores operating on the principle of collisional quenching. Finally, the paper describes how various solid substrates can be functionalized with MEF-based nanosensors to bestow them with intense and photostable pH-sensitive properties for use in fields such as medical therapy and diagnostics, dentistry, biochemistry and microfluidics.

The Fundamentals of Real-Time Surface Plasmon Resonance/Electrogenerated Chemiluminescence.

We report the integration of surface plasmon resonance (SPR), cyclic voltammetry and electrochemiluminescence (ECL) responses to survey the interfacial adsorption and energy transfer processes involved in ECL on a plasmonic substrate. It was observed that a Tween 80/tripropylamine nonionic layer formed on the gold electrode of the SPR sensor, while enhancing the ECL emission process, affects the electron transfer process to the luminophore, Ru(bpy)32+ , which in turn has an impact on the plasmon resonance. Concomitantly, the surface plasmon modulated the ECL intensity, which decreased by about 40 %, due to an interaction between the excited state of Ru(bpy)32+ and the plasmon. This occurred only when the plasmon was excited, demonstrating that the optically excited surface plasmon leads to lower plasmon-mediated luminescence and that the plasmon interacts with the excited state of Ru(bpy)32+ within a very thin layer.

Reversible Shape and Plasmon Tuning in Hollow AgAu Nanorods.

The internal structure of hollow AgAu nanorods created by partial galvanic replacement was manipulated reversibly, and its effect on optical properties was mapped with nanometer resolution. Using the electron beam in a scanning transmission electron microscope to create solvated electrons and reactive radicals in an encapsulated solution-filled cavity in the nanorods, Ag ions were reduced nearby the electron beam, reshaping the core of the nanoparticles without affecting the external shape. The changes in plasmon-induced near-field properties were then mapped with electron energy-loss spectroscopy without disturbing the internal structure, and the results are supported by finite-difference time-domain calculations. This reversible shape and near-field control in a hollow nanoparticle actuated by an external stimulus introduces possibilities for applications in reprogrammable sensors, responsive materials, and optical memory units. Moreover, the liquid-filled nanorod cavity offers new opportunities for in situ microscopy of chemical reactions.

Carbonic anhydrase XII in valve interstitial cells promotes the regression of calcific aortic valve stenosis.

AIMS: Calcific aortic valve stenosis (CAVS) is the most common heart valve disease. In the present work we sought to determine the reversibility of mineralization in the aortic valve. METHODS AND RESULTS: By using in vitro analyses we found that valve interstitial cells (VICs) have the ability to resorb minerals. We documented that agonist of P2Y2 receptor (P2Y2R) promoted the expression of carbonic anhydrase XII (CAXII) at the cell membrane of VICs, whereby minerals are resorbed. P2Y2R-mediated mineral resorption was corroborated by using mouse VICs isolated from wild type and P2Y2R(-/-) mice. Measurements of extracellular pH (pHe) by using core-shell nanosensors revealed that P2Y2R-mediated CAXII export to the cell membrane led to an acidification of extracellular space, whereby minerals are resorbed. In vivo, we next treated LDLR(-/-)/ApoB(100/100)/IGF2 mice, which had developed CAVS under a high-fat/high-sucrose diet for 8 months, with 2-thioUTP (a P2Y2R agonist) or saline for the next 2 months. The administration of 2-thioUTP (2mg/kg/day i.p.) reduced the mineral volume in the aortic valve measured with serial microCT analyses, which improved hemodynamics and reduced left ventricular hypertrophy (LVH). Examination of leaflets at necropsy confirmed a lower level of mineralization and fibrosis along with higher levels of CAXII in mice under 2-thioUTP. In another series of experiment, the administration of acetazolamide (a CA inhibitor) prevented the acidification of leaflets and the regression of CAVS induced by 2-thioUTP in LDLR(-/-)/ApoB(100/100)/IGF2 mice. CONCLUSION: P2Y2R-mediated expression of CAXII by VICs acidifies the extracellular space and promotes the regression of CAVS.

Plasmonic Properties of Self-Assembled Gold Nanocrescents: Implications for Chemical Sensing.

A bottom-up approach, the Langmuir-Blodgett technique, is used for the preparation of composite thin films of gold nanoparticles and polymers: poly(styrene-b-2-vinylpyridine), poly-2-vinylpyridine, and polystyrene. The self-assembly of poly(styrene-b-2-vinylpyridine) at the air-water interface leads to the formation of surface micelles, which serve as a template for the organization of gold nanoparticles into ring assemblies. By using poly-2-vinylpyridine in conjunction with low surface pressure, the distance between nanostructures can be increased, allowing for optical characterization of single nanostructures. Once deposited on a solid substrate, the preorganized gold nanoparticles are subjected to further growth by the reduction of additional gold, leading to a variety of nanostructures which can be divided into two categories: nanocrescents and circular arrays of nanoparticles. The optical properties of individual structures are investigated by optical dark-field spectroscopy and numerical calculations. The plasmonic behavior of the nanostructures is elucidated through the correlation of optical properties with structural features and the identification of dominant plasmon modes. Being based on a self-assembly approach, the reported method allows for the formation of interesting plasmonic materials under ambient conditions, at a relatively large scale, and at low cost. These attributes, in addition to the resonances located in the near-infrared region of the spectrum, make nanocrescents candidates for biological and chemical sensing.

Live virus neutralizing antibodies against pre and post Omicron strains in food and retail workers in Québec, Canada.

Background: Measuring the ability of SARS-CoV-2 antibodies to neutralize live viruses remains an effective approach to quantify the level of protection of individuals. We assessed the neutralization activity against the ancestral SARS-CoV-2, Delta, Omicron BA.1, BA.2, BA.2.12.1, BA.4 and BA.5 strains, in 280 vaccinated restaurant/bar, grocery and hardware store workers in Québec, Canada. Methods: Participants were recruited during the emergence of Omicron BA.1 variant. The neutralizing activity of participant sera was assessed by microneutralization assay. Results: Serum neutralizing antibody (NtAb) titers of all participants against the ancestral SARS-CoV-2 strain were comparable with those against Delta variant (ranges of titers 10-2032 and 10-2560, respectively), however, their response was significantly reduced against Omicron BA.1, BA2, BA.2.12.1, BA.4 and BA.5 (10-1016, 10-1016, 10-320, 10-80 and 10-254, respectively). Individuals who received 2 doses of vaccine had significantly reduced NtAb titers against all SARS-CoV-2 strains compared to those infected and then vaccinated (≥1 dose), vaccinated (≥2 doses) and then infected, or those who received 3 doses of vaccine. Participants vaccinated with 2 or 3 doses of vaccine and then infected had the highest NtAb titers against all SARS-CoV-2 strains tested. Conclusion: We assessed for the first time the NtAb response in food and retail workers. We found that vaccination prior to the emergence of Omicron BA.1 was associated with higher neutralizing activity against pre-Omicron variants, suggesting the importance of updating vaccines to increase antibody response against new SARS-CoV-2 variants. Vaccination followed by infection was associated with higher neutralizing activity against all SARS-CoV-2 strains tested.

Acting as a Molecular Tailor: Dye Structural Modifications for Improved Sensitivity toward Lysophosphatidic Acids Sensing.

Lysophosphatidic acids (LPA) are key biomarkers for several physiological processes, the monitoring of which can provide insights into the host's health. Common lab-based techniques for their detection are cumbersome, expensive, and necessitate specialized personnel to operate. LPA-sensitive fluorescent probes have been described, albeit for nonaqueous conditions, which impedes their use in biological matrices. In this paper, we explore in detail the influence of structure on the extent of aggregation-induced fluorescence quenching using specially synthesized styrylpyridinium dyes bearing structural adaptations to bestow them enhanced affinity toward LPA in aqueous media. Spectroscopic investigations supported by time-resolved fluorimetry revealed the contribution of excimer formation to the fluorescence quenching mechanism displayed by the fluorescent probes. Experimental observations of the influence of structure on detection sensitivity were supported by DFT calculations.

Fall Decay Deceleration in Northern Latitudes: Merely a Matter of Cold?

The decomposition of cadavers and large vertebrate carcasses is the result of complex processes primarily influenced by ambient temperatures. Thus, low temperatures can alter decomposition by curtailing tissue autolysis and bacterial decomposition, and by limiting insect activity contributing to necromass removal. In this study, we tested whether carcass decomposition rate is modulated not only directly by temperature and insect occurrence, but also indirectly by the mediation of interactions among insects by ambient temperature. To test this, a comparative analysis of the decomposition of domestic pig carcasses in summer and fall was conducted in Atlantic Canada. The results indicated that carcass decomposition standardized to account for seasonal differences was significantly decelerated in the fall as opposed to the summer during the later decomposition stages and was sometimes incomplete. Moreover, the arrival, presence, and departure of insects from carcasses during ecological succession differed between summer and fall. Necrodes surinamensis (Fabricius) (Coleoptera: Silphidae) and Creophilus maxillosus (Linnaeus) (Coleoptera: Staphylinidae) maintained higher abundances late during succession in the fall than in the summer and their abundance was related to a decline in decomposition rates, probably because these species feed on dipteran larvae promoting necromass removal. These results demonstrate the variability in response to environmental parameters of insects of forensic importance and support the idea that slowed decomposition in the fall may be exacerbated by changes in interspecific interactions among insects. Furthermore, these results suggest that successional studies of insects carried out in the summer have little forensic utility for cadavers found in cold weather conditions.

Metal-Enhanced Hg2+-Responsive Fluorescent Nanoprobes: From Morphological Design to Application to Natural Waters.

Metal-enhanced fluorescence (MEF) is a powerful tool in the design of sensitive chemical sensors by improving brightness and photostability of target-responsive fluorophores. Compounding these advantages with the modest hardware requirements of fluorescence sensing compared to that of centralized elemental analysis instruments, thus expanding the use of MEF to the detection of low-level inorganic pollutants, is a compelling aspiration. Among the latter, monitoring mercury in the environment, where some of its species disseminate through the food chain and, in time, to humans, has elicited a broad research effort toward the development of Hg2+-responsive fluorescent sensors. Herein, a Hg2+-sensitive MEF-enabled probe was conceived by grafting a Hg2+-responsive fluorescein derivative to concentric Ag@SiO2 NPs, where the metallic core enhances fluorescence emission of molecular probes embedded in a surrounding silica shell. Time-resolved fluorescence measurements showed that the fluorophore's excited-state lifetime decreases from 3.9 ns in a solid, coreless silica sphere to 0.4 ns in the core-shell nanoprobe, granting the dye a better resistance to photobleaching. The Ag-core system showed a sizable improvement in the limit of detection at 2 nM (0.4 ppb) compared to 50 nM (10 ppb) in silica-only colloids, and its effectiveness for natural water analysis was demonstrated. Overall, the reported nanoarchitecture hints at the potential of MEF for heavy metal detection by fluorescence detection.

Pushing the Limits of Surface-Enhanced Raman Spectroscopy (SERS) with Deep Learning: Identification of Multiple Species with Closely Related Molecular Structures.

Raman spectroscopy is a non-destructive and label-free molecular identification technique capable of producing highly specific spectra with various bands correlated to molecular structure. Moreover, the enhanced detection sensitivity offered by surface-enhanced Raman spectroscopy (SERS) allows analyzing mixtures of related chemical species in a relatively short measurement time. Combining SERS with deep learning algorithms allows in some cases to increase detection and classification capabilities even further. The present study evaluates the potential of applying deep learning algorithms to SERS spectroscopy to differentiate and classify different species of bile acids, a large family of molecules with low Raman cross sections and molecular structures that often differ by a single hydroxyl group. Moreover, the study of these molecules is of interest for the medical community since they have distinct pathological roles and are currently viewed as potential markers of gut microbiome imbalances. A convolutional neural network model was developed and used to classify SERS spectra from five bile acid species. The model succeeded in identifying the five analytes despite very similar molecular structures and was found to be reliable even at low analyte concentrations.

Assessment of the longitudinal humoral response in non-hospitalized SARS-CoV-2-positive individuals at decentralized sites: Outcomes and concordance.

Introduction: Early in the COVID-19 pandemic, reagent availability was not uniform, and infrastructure had to be urgently adapted to undertake COVID-19 surveillance. Methods: Before the validation of centralized testing, two enzyme-linked immunosorbent assays (ELISA) were established independently at two decentralized sites using different reagents and instrumentation. We compared the results of these assays to assess the longitudinal humoral response of SARS-CoV-2-positive (i.e., PCR-confirmed), non-hospitalized individuals with mild to moderate symptoms, who had contracted SARSCoV-2 prior to the appearance of variants of concern in Québec, Canada. Results: The two assays exhibited a high degree of concordance to identify seropositive individuals, thus validating the robustness of the methods. The results also confirmed that serum immunoglobulins persist ≥ 6 months post-infection among non-hospitalized adults and that the antibodies elicited by infection cross-reacted with the antigens from P.1 (Gamma) and B.1.617.2 (Delta) variants of concern. Discussion: Together, these results demonstrate that immune surveillance assays can be rapidly and reliably established when centralized testing is not available or not yet validated, allowing for robust immune surveillance.

Is Forensic Entomology Lost in Space?

Spatial and scale effects have barely been considered in forensic entomology, despite their pervasive influence on most of the parameters affecting the development of insect larval stages and the progression of insect succession on cadavers. Here, we used smoothing/interpolation techniques and semivariograms to document the spatial dynamics of sarcosaprophageous Calliphoridae, an important forensic taxon, in the Greater Moncton area in New Brunswick, Canada. Results indicated that the spatial dynamics of Calliphoridae differed between species, some species showing strong patterns of regional aggregation while others did not. Multivariate spatial correlations indicated that interspecific relationships in space varied widely, ranging from local and large-scale aggregation to spatial anticorrelation between species. Overall, this study suggested that even within a restricted timescale, the spatial dynamics of Calliphoridae can operate at many scales, manifest in different patterns, and be attributed to multiple different causes. We stress that forensic entomology has much to benefit from the use of spatial analysis because many important forensic questions, both at the fundamental and practical levels, require a spatial solution.

Small Bait Traps May Not Accurately Reflect the Composition of Necrophagous Diptera Associated to Remains.

Small bait traps are beginning to emerge in forensic entomology as a new approach to sample early-colonizing necrophagous Diptera species while reducing the investment in time and energy in obtaining information. To test the hypothesis conveyed by the literature that these traps can be a substitute for whole carcasses, we simultaneously documented the Diptera assemblages visiting and colonizing domestic pig carcasses and small traps baited with pork liver. Results indicated that Diptera species occurrence and assemblage composition in the small bait traps and on the carcasses differed, while they were similar when comparing only the pig carcasses. These results are in agreement with the literature that examined insect colonization of other decaying substrates. Although small bait traps can be useful tools to document the communities of necrophagous Diptera in a given area, we stress that caution must be exercised when extending the data obtained by these traps to courtroom proceedings.

Nucleation Points: The Forgotten Parameter in the Synthesis of Hydrogel-Coated Gold Nanoparticles.

The implementation of gold-hydrogel core-shell nanomaterials in novel light-driven technologies requires the development of well-controlled and scalable synthesis protocols with precisely tunable properties. Herein, new insights are presented concerning the importance of using the concentration of gold cores as a control parameter in the seeded precipitation polymerization process to modulate-regardless of core size-relevant fabrication parameters such as encapsulation yield, particle size and shrinkage capacity. Controlling the number of nucleation points results in the facile tuning of the encapsulation process, with yields reaching 99% of gold cores even when using different core sizes at a given particle concentration. This demonstration is extended to the encapsulation of bimodal gold core mixtures with equally precise control on the encapsulation yield, suggesting that this principle could be extended to encapsulating cores composed of other materials. These findings could have a significant impact on the development of stimuli-responsive smart materials.

Cross-reactivity of antibodies from non-hospitalized COVID-19 positive individuals against the native, B.1.351, B.1.617.2, and P.1 SARS-CoV-2 spike proteins.

SARS-CoV-2 variants of concern (VOCs) have emerged worldwide, with implications on the spread of the pandemic. Characterizing the cross-reactivity of antibodies against these VOCs is necessary to understand the humoral response of non-hospitalized individuals previously infected with SARS-CoV-2, a population that remains understudied. Thirty-two SARS-CoV-2-positive (PCR-confirmed) and non-hospitalized Canadian adults were enrolled 14-21 days post-diagnosis in 2020, before the emergence of the B.1.351 (also known as Beta), B.1.617.2 (Delta) and P.1 (Gamma) VOCs. Sera were collected 4 and 16 weeks post-diagnosis. Antibody levels and pseudo-neutralization of the ectodomain of SARS-CoV-2 spike protein/human ACE-2 receptor interaction were analyzed with native, B.1.351, B.1.617.2 and P.1 variant spike proteins. Despite a lower response observed for the variant spike proteins, we report evidence of a sustained humoral response against native, B.1.351, B.1.617.2 and P.1 variant spike proteins among non-hospitalized Canadian adults. Furthermore, this response inhibited the interaction between the spike proteins from the different VOCs and ACE-2 receptor for ≥ 16 weeks post-diagnosis, except for individuals aged 18-49 years who showed no inhibition of the interaction between B.1.617.1 or B.1.617.2 spike and ACE-2. Interestingly, the affinity (KD) measured between the spike proteins (native, B.1.351, B.1.617.2 and P.1) and antibodies elicited in sera of infected and vaccinated (BNT162b2 and ChAdOx1 nCoV-19) individuals was invariant. Relative to sera from vaccine-naïve (and previously infected) individuals, sera from vaccinated individuals had higher antibody levels (as measured with label-free SPR) and more efficiently inhibited the spike-ACE-2 interactions, even among individuals aged 18-49 years, showing the effectiveness of vaccination.

FRET enhancement in multilayer core-shell nanoparticles.

This study describes the preparation and characterization of novel multilayer core-shell nanoparticles displaying metal-enhanced Forster resonant energy transfer. The increase in range and efficiency of Forster resonant energy transfer in these fluorescent nanocomposites and their vastly improved luminosity make them promising optical probes for a variety of applications such as cell imaging and biosensing.