Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging

In vitro hyperspectral biomarkers of human chondrosarcoma cells in nanoparticle-mediated radiosensitization using carbon ions

New therapeutic approaches are needed for the management of the highly chemo- and radioresistant chondrosarcoma (CHS). In this work, we used polyethylene glycol-encapsulated iron oxide nanoparticles for the intracellular delivery of the chemotherapeutic doxorubicin (IONPDOX) to augment the cytotoxic effects of carbon ions in comparison to photon radiation therapy. The in vitro biological effects were investigated in SW1353 chondrosarcoma cells focusing on the following parameters: cell survival using clonogenic test, detection of micronuclei (MN) by cytokinesis blocked micronucleus assay and morphology together with spectral fingerprints of nuclei using enhanced dark-field microscopy (EDFM) assembled with a hyperspectral imaging (HI) module. The combination of IONPDOX with ion carbon or photon irradiation increased the lethal effects of irradiation alone in correlation with the induction of MN. Alterations in the hyperspectral images and spectral profiles of nuclei reflected the CHS cell biological modifications following the treatments, highlighting possible new spectroscopic markers of cancer therapy effects. These outcomes showed that the proposed combined treatment is promising in improving CHS radiotherapy.

Optical Methods for Label-Free Detection of Bacteria

Pathogenic bacteria are the leading causes of food-borne and water-borne infections, and one of the most serious public threats. Traditional bacterial detection techniques, including plate culture, polymerase chain reaction, and enzyme-linked immunosorbent assay are time-consuming, while hindering precise therapy initiation. Thus, rapid detection of bacteria is of vital clinical importance in reducing the misuse of antibiotics. Among the most recently developed methods, the label-free optical approach is one of the most promising methods that is able to address this challenge due to its rapidity, simplicity, and relatively low-cost. This paper reviews optical methods such as surface-enhanced Raman scattering spectroscopy, surface plasmon resonance, and dark-field microscopic imaging techniques for the rapid detection of pathogenic bacteria in a label-free manner. The advantages and disadvantages of these label-free technologies for bacterial detection are summarized in order to promote their application for rapid bacterial detection in source-limited environments and for drug resistance assessments.

Flexible hyperspectral surface plasmon resonance microscopy

Optical techniques for visualization and quantification of chemical and biological analytes are always highly desirable. Here we show a hyperspectral surface plasmon resonance microscopy (HSPRM) system that uses a hyperspectral microscope to analyze the selected area of SPR image produced by a prism-based spectral SPR sensor. The HSPRM system enables monochromatic and polychromatic SPR imaging and single-pixel spectral SPR sensing, as well as two-dimensional quantification of thin films with the measured resonance-wavelength images. We performed pixel-by-pixel calibration of the incident angle to remove pixel-to-pixel differences in SPR sensitivity, and demonstrated the HSPRM's capabilities by using it to quantify monolayer graphene thickness distribution, inhomogeneous protein adsorption and single-cell adhesion. The HSPRM system has a wide spectral range from 400 nm to 1000 nm, an optional field of view from 0.884 mm² to 0.003 mm² and a high lateral resolution of 1.2 μm, demonstrating an innovative breakthrough in SPR sensor technology.

Diagnostic Approaches For COVID-19: Lessons Learned and the Path Forward

Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID-19 pandemic has the highest rate of infection and has had high levels of social and economic repercussions. The current COVID-19 pandemic has highlighted the limitations of existing virological tests, which have failed to be adopted at a rate to properly slow the rapid spread of SARS-CoV-2. Pandemic preparedness has developed as a focus of many governments around the world in the event of a future outbreak. Despite the largely widespread availability of vaccines, the importance of testing has not diminished to monitor the evolution of the virus and the resulting stages of the pandemic. Therefore, developing diagnostic technology that serves as a line of defense has become imperative. In particular, that test should satisfy three criteria to be widely adopted: simplicity, economic feasibility, and accessibility. At the heart of it all, it must enable early diagnosis in the course of infection to reduce spread. However, diagnostic manufacturers need guidance on the optimal characteristics of a virological test to ensure pandemic preparedness and to aid in the effective treatment of viral infections. Nanomaterials are a decisive element in developing COVID-19 diagnostic kits as well as a key contributor to enhance the performance of existing tests. Our objective is to develop a profile of the criteria that should be available in a platform as the target product. In this work, virus detection tests were evaluated from the perspective of the COVID-19 pandemic, and then we generalized the requirements to develop a target product profile for a platform for virus detection.

Multivariate Imaging for Fast Evaluation of In Situ Dark Field Microscopy Hyperspectral Data

Dark field scattering microscopy can create large hyperspectral data sets that contain a wealth of information on the properties and the molecular environment of noble metal nanoparticles. For a quick screening of samples of microscopic dimensions that contain many different types of plasmonic nanostructures, we propose a multivariate analysis of data sets of thousands to several hundreds of thousands of scattering spectra. By using non-negative matrix factorization for decomposing the spectra, components are identified that represent individual plasmon resonances and relative contributions of these resonances to particular microscopic focal volumes in the mapping data sets. Using data from silver and gold nanoparticles in the presence of different molecules, including gold nanoparticle-protein agglomerates or silver nanoparticles forming aggregates in the presence of acrylamide, plasmonic properties are observed that differ from those of the original nanoparticles. For the case of acrylamide, we show that the plasmon resonances of the silver nanoparticles are ideally suited to support surface enhanced Raman scattering (SERS) and the two-photon excited process of surface enhanced hyper Raman scattering (SEHRS). Both vibrational tools give complementary information on the in situ formed polyacrylamide and the molecular composition at the nanoparticle surface.

Advanced plasmonic technologies for multi-scale biomedical imaging

Plasmonic technologies are available for multi-scale biomedical imaging ranging from micrometre to angstrom level.

Rational Design of Surface-State Controlled Multicolor Cross-Linked Carbon Dots with Distinct Photoluminescence and Cellular Uptake Properties

We disclose for the first time a facile synthetic methodology for the preparation of multicolor carbon dots (CDs) from a single source barring any chromatographic separations. This was achieved via sequential intraparticle cross-linking of surface abundant carboxylic acid groups on the CDs synthesized from a precursor to control their photoluminescence (PL) spectra as well as affect their degree of cellular internalization in cancer cells. The change in PL spectra with sequential cross-linking was projected by theoretical density functional theory (DFT) studies and validated by multiple characterization tools such as X-ray photoelectron spectroscopy (XPS), PL spectroscopy, ninhydrin assay, etc. The variation in cellular internalization of these cross-linked CDs was demonstrated using inhibitor assays, confocal microscopy, and flow cytometry. We supplemented our findings with high-resolution dark-field imaging to visualize and confirm the colocalization of these CDs into distinct intracellular compartments. Finally, to prove the surface-state controlled PL mechanisms of these cross-linked CDs, we fabricated a triple-channel sensor array for the identification of different analytes including metal ions and biologically relevant proteins.

Safety Evaluation of Nanotechnology Products

Nanomaterials are now being used in a wide variety of biomedical applications. Medical and health-related issues, however, have raised major concerns, in view of the potential risks of these materials against tissue, cells, and/or organs and these are still poorly understood. These particles are able to interact with the body in countless ways, and they can cause unexpected and hazardous toxicities, especially at cellular levels. Therefore, undertaking in vitro and in vivo experiments is vital to establish their toxicity with natural tissues. In this review, we discuss the underlying mechanisms of nanotoxicity and provide an overview on in vitro characterizations and cytotoxicity assays, as well as in vivo studies that emphasize blood circulation and the in vivo fate of nanomaterials. Our focus is on understanding the role that the physicochemical properties of nanomaterials play in determining their toxicity.

Spatially Resolved Spectroscopic Characterization of Nanostructured Films by Hyperspectral Dark-Field Microscopy

Nanostructured films have been widely used for preparing various advanced thin-film devices because of their unique electrical, optical, and plasmonic characteristics associated with the nano-size effect. In situ, nondestructive and high-resolution characterization of nanostructured films is essential for optimizing thin-film device performance. In this work, such thin-film characterization was achieved using a hyperspectral dark-field microscope (HSDFM) that was constructed in our laboratory by integrating a hyperspectral imager with a commercial microscope. The HSDFM allows for high-resolution (Δλ = 0.4 nm) spectral analysis of nanostructured samples in the visible-near-infrared region with a spatial resolution as high as 45 nm × 45 nm (corresponding to a single pixel). Four typical samples were investigated with the HSDFM, including the gold nanoplate array, the self-assembled gold nanoparticle (GNP) sub-monolayer, the sol-gel nanoporous titanium dioxide (TiO₂) film, and the layer-stacked molybdenum disulfide (MoS₂) sheet. According to the experimental results, the plasmon resonance scattering bands for nanoplate clusters are identical with those for individual gold nanoplates, indicating that the gap between adjacent nanoplates is too large to allow plasmonic coupling between them. A different case was observed with the self-assembled GNP sub-monolayer in which the aggregated clusters with the internal plasmonic interaction show a considerable red-shift of the plasmon resonance band relative to the isolated single GNP. In addition, the protein adsorption on the nanoporous TiO₂ film was observed to be inhomogeneous on the microscale, and the stepped boundaries of the MoS₂ sheet were clearly observed. A quasi-linear dependence of the single-pixel light intensity on the step height was obtained by combining the HSDFM with atomic force microscopy. The minimum thickness detectable by the present HSDFM is 6.5 nm, corresponding to the 10-layer MoS₂ film. The work demonstrated the outstanding applicability of the HSDFM for nanostructured film characterization.

Hyperspectral-enhanced dark field analysis of individual and collective photo-responsive gold-copper sulfide nanoparticles

We used hyperspectral-enhanced dark field microscopy for studying physicochemical changes in biomaterials by tracking their unique spectral signatures along their pathway through different biological environments typically found in any biomedical application. We correlate these spectral signatures with discrete environmental features causing changes in nanoparticles' physicochemical properties. We use this correlation to track the nanoparticles intracellularly and to assess the impact of these changes on their functionality. We focus on one example of a photothermal nanocomposite, i.e., polymer-coated gold/copper sulfide nanoparticles, because their performance depends on their localized surface plasmon peak, which is highly sensitive to environmental changes. We found spectral differences both in the dependence of time and discrete environmental factors, affecting the range of illumination wavelengths that can be used to activate the functionality of these types of nanoparticles. The presence of proteins (protein corona) and the increase in ionic strength induce a spectral broadening towards the NIR region which we associated with nanoparticles' agglomeration. In acidic environments, such as that of the lysosome, a red shift was also observed in addition to a decrease in the scattering intensity probably associated with a destabilization of the proteins and/or the change in the net charge of the polymer around the nanoparticles. We observed a loss of the photo-excitation potential of those nanoparticles exposed to acidic conditions in the <600 nm spectral rage. In a similar manner, ageing induces a transitioning from a broad multipeak spectrum to a distinct shoulder with time (up to 8 months) with the loss of spectral contribution in the 450-600 nm range. Hence, a fresh preparation of nanoparticles before their application would be recommended for an optimal performance. We highlight the impact of ageing and the acidic environment on the responsiveness of this type of plasmonic nanoparticle. Regardless of the spectral differences found, polymer-coated gold/copper sulfide nanoparticles retained their photothermal response as demonstrated in vitro upon two-photon irradiation. This could be ascribed to their robust geometry provided by the polymer coating. These results should be useful to rationally design plasmonic photothermal probes.

e-MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation

The quantification of global 5-methylcytosine (5mC) content has emerged as a promising approach for the diagnosis and prognosis of cancers. However, conventional methods for the global 5mC analysis require large quantities of DNA and may not be useful for liquid biopsy applications, where the amount of DNA available is limited. Herein, we report magnetic nanoparticles-assisted methylated DNA immunoprecipitation (e-MagnetoMethyl IP) coupled with electrochemical quantification of global DNA methylation. Carboxyl (-COOH) group-functionalized iron oxide nanoparticles (C-IONPs) synthesized by a novel starch-assisted gel formation method were conjugated with anti-5mC antibodies through EDC/NHS coupling (anti-5mC/C-IONPs). Anti-5mC/C-IONPs were subsequently mixed with DNA samples, in which they acted as dispersible capture agents to selectively bind 5mC residues and capture the methylated fraction of genomic DNA. The target-bound Anti-5mC/C-IONPs were magnetically separated and directly adsorbed onto the gold electrode surface using gold-DNA affinity interaction. The amount of DNA adsorbed on the electrode surface, which corresponds to the DNA methylation level in the sample, was electrochemically estimated by differential pulse voltammetric (DPV) study of an electroactive indicator [Ru(NH₃)₆]³⁺ bound to the surface-adsorbed DNA. Using a 200 ng DNA sample, the assay could successfully detect differences as low as 5% in global DNA methylation levels with high reproducibility (relative standard deviation (% RSD) = <5% for n = 3). The method could also reproducibly analyze various levels of global DNA methylation in synthetic samples as well as in cell lines. The method avoids bisulfite treatment, does not rely on enzymes for signal generation, and can detect global DNA methylation using clinically relevant quantities of sample DNA without PCR amplification. We believe that this proof-of-concept method could potentially find applications for liquid biopsy-based global DNA methylation analysis in point-of-care settings.

Individual Plasmonic Nanoprobes for Biosensing and Bioimaging: Recent Advances and Perspectives

With the advent of nanofabrication techniques, plasmonic nanoparticles (PNPs) have been widely applied in various research fields ranging from photocatalysis to chemical and bio-sensing. PNPs efficiently convert chemical or physical stimuli in their local environment into optical signals. PNPs also have excellent properties, including good biocompatibility, large surfaces for the attachment of biomolecules, tunable optical properties, strong and stable scattering light, and good conductivity. Thus, single optical biosensors with plasmonic properties enable a broad range of uses of optical imaging techniques in biological sensing and imaging with high spatial and temporal resolution. This work provides a comprehensive overview on the optical properties of single PNPs, the description of five types of commonly used optical imaging techniques, including surface plasmon resonance (SPR) microscopy, surface-enhanced Raman scattering (SERS) technique, differential interference contrast (DIC) microscopy, total internal reflection scattering (TIRS) microscopy, and dark-field microscopy (DFM) technique, with an emphasis on their single plasmonic nanoprobes and mechanisms for applications in biological imaging and sensing, as well as the challenges and future trends of these fields.

Rapid, Ultrasensitive, and Quantitative Detection of SARS-CoV-2 Using Antisense Oligonucleotides Directed Electrochemical Biosensor Chip

A large-scale diagnosis of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is essential to downregulate its spread within as well as across communities and mitigate the current outbreak of the pandemic novel coronavirus disease 2019 (COVID-19). Herein, we report the development of a rapid (less than 5 min), low-cost, easy-to-implement, and quantitative paper-based electrochemical sensor chip to enable the digital detection of SARS-CoV-2 genetic material. The biosensor uses gold nanoparticles (AuNPs), capped with highly specific antisense oligonucleotides (ssDNA) targeting viral nucleocapsid phosphoprotein (N-gene). The sensing probes are immobilized on a paper-based electrochemical platform to yield a nucleic-acid-testing device with a readout that can be recorded with a simple hand-held reader. The biosensor chip has been tested using samples collected from Vero cells infected with SARS-CoV-2 virus and clinical samples. The sensor provides a significant improvement in output signal only in the presence of its target-SARS-CoV-2 RNA-within less than 5 min of incubation time, with a sensitivity of 231 (copies μL-1)-1 and limit of detection of 6.9 copies/μL without the need for any further amplification. The sensor chip performance has been tested using clinical samples from 22 COVID-19 positive patients and 26 healthy asymptomatic subjects confirmed using the FDA-approved RT-PCR COVID-19 diagnostic kit. The sensor successfully distinguishes the positive COVID-19 samples from the negative ones with almost 100% accuracy, sensitivity, and specificity and exhibits an insignificant change in output signal for the samples lacking a SARS-CoV-2 viral target segment (e.g., SARS-CoV, MERS-CoV, or negative COVID-19 samples collected from healthy subjects). The feasibility of the sensor even during the genomic mutation of the virus is also ensured from the design of the ssDNA-conjugated AuNPs that simultaneously target two separate regions of the same SARS-CoV-2 N-gene.

Epigenetic Modifications, and Alterations in Cell Cycle and Apoptosis Pathway in A549 Lung Carcinoma Cell Line upon Exposure to Perfluoroalkyl Substances

Per- and polyfluoroalkyl substances (PFAS) are a group of human-made compounds with strong C-F bonds, and have been used in various manufacturing industries for decades. PFAS have been reported to deleterious effect on human health, which has led to studies identifying the possible toxicity and toxicity routes of these compounds. We report that these compounds have the potential to cause epigenetic modifications, and to induce dysregulation in the cell proliferation cycle as well as apoptosis in A549 lung cancer cells when exposed to 10-, 200- and 400 μM concentrations of each compound. Our studies show that exposure to perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) may cause hypomethylation in the epigenome, but changes in the epigenetic makeup are not evident upon exposure to GenX. We establish that exposure to lower doses of these compounds causes the cells' balance to shift to cell proliferation, whereas exposure to higher concentrations shifts the balance more towards apoptosis. Furthermore, the apoptosis pathway upon exposure to GenX, PFOA, and PFOS has also been identified. Our findings suggest that exposure to any of these compounds may have profound effects in patients with pre-existing lung conditions or could trigger lung cancinogenesis.

Dark-field hyperspectral imaging for label free detection of nano-bio-materials

Nanomaterials are playing an increasingly important role in cancer diagnosis and treatment. Nanoparticle (NP)-based technologies have been utilized for targeted drug delivery during chemotherapies, photodynamic therapy, and immunotherapy. Another active area of research is the toxicity studies of these nanomaterials to understand the cellular uptake and transport of these materials in cells, tissues, and environment. Traditional techniques such as transmission electron microscopy, and mass spectrometry to analyze NP-based cellular transport or toxicity effect are expensive, require extensive sample preparation, and are low-throughput. Dark-field hyperspectral imaging (DF-HSI), an integration of spectroscopy and microscopy/imaging, provides the ability to investigate cellular transport of these NPs and to quantify the distribution of them within bio-materials. DF-HSI also offers versatility in non-invasively monitoring microorganisms, single cell, and proteins. DF-HSI is a low-cost, label-free technique that is minimally invasive and is a viable choice for obtaining high-throughput quantitative molecular analyses. Multimodal imaging modalities such as Fourier transform infrared and Raman spectroscopy are also being integrated with HSI systems to enable chemical imaging of the samples. HSI technology is being applied in surgeries to obtain molecular information about the tissues in real-time. This article provides brief overview of fundamental principles of DF-HSI and its application for nanomaterials, protein-detection, single-cell analysis, microbiology, surgical procedures along with technical challenges and future integrative approach with other imaging and measurement modalities. This article is categorized under: Diagnostic Tools > in vitro Nanoparticle-Based Sensing Diagnostic Tools > in vivo Nanodiagnostics and Imaging Implantable Materials and Surgical Technologies > Nanoscale Tools and Techniques in Surgery.

Multi and transgenerational epigenetic effects of di-(2-ethylhexyl) phthalate (DEHP) in liver

Di-(2-ethylhexyl) phthalate (DEHP), a ubiquitous industrial pollutant, is a known endocrine disrupter implicated in metabolic diseases. Prenatal DEHP exposure promotes epigenetic multi- and transgenerational inheritance of adult onset disease in subsequent generations (F1-F3). However, the epigenetic toxicity is less understood in the liver. In this study, CD-1 mice were prenatally exposed to 20 μg/kg/day, 200 μg/kg/day, 500 mg/kg/day, or 750 mg/kg/day DEHP from gestational day (GD) 10.5 until birth of pups. Following prenatal exposure, the multigenerational and transgenerational effects of mRNA expression of epigenetic regulators were evaluated in F1, F2, and F3 generation mouse livers at postnatal days (PNDs) 8 and 60. Results showed that DEHP exposed mice livers exhibited significant changes in global DNA methylation levels in all three generations, with the effect being different in F2 after high dosage exposure. Histopathology indicated that DEHP exposure could induce mild damage in F1 livers. The expression levels of DNA methyltransferase 1 (Dnmt1) were significantly changed in both the F1 and F2 generations at PND 8, suggesting that maintenance Dnmt1 plays a major role in the multigenerational effect that occur in the early developmental stages. Additionally, DEHP exposure caused significant changes in ten-eleven translocation methylcytosine (Tet) dioxygenases encoding Tet1 expression in all three generations and Tet2 expression in F3 at PND 60, implicating their contributions in inducing both multi- and transgenerational effects after DEHP exposure in mouse liver. Overall, our results establish that prenatal and ancestral DEHP exposure are critical for epigenetic regulation of DNA methylation in female mouse livers.

Real-Time Monitoring and Detection of Single-Cell Level Cytokine Secretion Using LSPR Technology

Cytokine secretion researches have been a main focus of studies among the scientists in the recent decades for its outstanding contribution to clinical diagnostics. Localized surface plasmon resonance (LSPR) technology is one of the conventional methods utilized to analyze these issues, as it could provide fast, label-free and real-time monitoring of biomolecule binding events. However, numerous LSPR-based biosensors in the past are usually utilized to monitor the average performance of cell groups rather than single cells. Meanwhile, the complicated sensor structures will lead to the fabrication and economic budget problems. Thus, in this paper, we report a simple synergistic integration of the cell trapping of microwell chip and gold-capped nanopillar-structured cyclo-olefin-polymer (COP) film for single cell level Interleukin 6 (IL-6) detection. Here, in-situ cytokine secreted from the trapped cell can be directly observed and analyzed through the peak red-shift in the transmittance spectrum. The fabricated device also shows the potential to conduct the real-time monitoring which would greatly help us identify the viability and biological variation of the tested single cell.

Optical Interrogation Techniques for Nanophotonic Biochemical Sensors

The manipulation of light via nanoengineered surfaces has excited the optical community in the past few decades. Among the many applications enabled by nanophotonic devices, sensing has stood out due to their capability of identifying miniscule refractive index changes. In particular, when free-space propagating light effectively couples into subwavelength volumes created by nanostructures, the strongly-localized near-fields can enhance light’s interaction with matter at the nanoscale. As a result, nanophotonic sensors can non-destructively detect chemical species in real-time without the need of exogenous labels. The impact of such nanophotonic devices on biochemical sensor development became evident as the ever-growing research efforts in the field started addressing many critical needs in biomedical sciences, such as low-cost analytical platforms, simple quantitative bioassays, time-resolved sensing, rapid and multiplexed detection, single-molecule analytics, among others. In this review, the optical transduction methods used to interrogate optical resonances of nanophotonic sensors will be highlighted. Specifically, the optical methodologies used thus far will be evaluated based on their capability of addressing key requirements of the future sensor technologies, including miniaturization, multiplexing, spatial and temporal resolution, cost and sensitivity.

Intracellular dark-field imaging of ATP and photothermal therapy using a colorimetric assay based on gold nanoparticle aggregation via tetrazine/trans-cyclooctene cycloaddition

In this study, we developed a colorimetric ATP assay based on the ATP-induced aggregation of Au nanoparticles (AuNPs). This aggregation modified the local surface plasmon resonance (LSPR) of the AuNPs, which was used to detect and localize ATP in cells via dark-field imaging. The AuNP aggregation process involved the reaction of two types of functionalized AuNPs with each other: tetrazine-modified AuNPs (Au₃-N₄) and asymmetrically functionalized trans-cyclooctene-modified AuNPs (Au₁-(E)-cyclooctene). This cycloaddition reaction occurs without the need for a catalyst such as the Cu ions that are used in the "click" reactions often employed in assays of this type. Initially, we asymmetrically functionalized both types of AuNPs and let them dimerize, which permitted us to explore the resulting wavelength shift in the LSPR of the AuNPs. Then, to facilitate the specific recognition of ATP, a designed DNA (DNA1) containing an ATP aptamer sequence was attached to carboxyl polystyrene microbeads (MBs). After attaching a different DNA (DNA2, which hybridizes with DNA1) to Au₁-(E)-cyclooctene, the assay probe MB/DNA1/DNA2/Au₁-(E)-cyclooctene (MB/Au₁) was generated. While bound to MB/DNA1, the DNA2/Au₁-(E)-cyclooctene cannot react with Au₃-N₄ due to steric hindrance from the MB. However, in the presence of ATP, the probe MB/Au₁ dissociates, and the resulting free DNA2/Au₁-(E)-cyclooctene can then react with the Au₃-N₄, leading to the formation of AuNP aggregates. Dark-field microscopy (DFM) images showed that the LSPR of the AuNPs shifted from the green region (AuNP monomers) to the orange-red region (AuNP aggregates) in the presence of intracellular ATP. Moreover, the AuNP aggregates were found to exhibit significant photothermal effects under 808-nm laser irradiation. Upon introducing the probe MB/Au₁ and Au₃-N₄ into HeLa cells in vitro and in vivo, and then irradiating the cells with a 808-nm NIR laser, the resulting AuNP aggregates showed promising photothermal cancer therapy performance. This assay therefore has the potential to be widely used for the identification and determination of nanoparticles in biological DFM and in tumor theranostics. Graphical abstract.

Magnetic Focus Lateral Flow Sensor for Detection of Cervical Cancer Biomarkers

We report on a magnetic focus lateral flow biosensor (mLFS) for ultrasensitive detection of protein biomarkers in a practical format. With valosin-containing protein as a target protein, we show that the developed mLFS concept could detect as low as 25 fg/mL with magnetic focus to enhance target capture efficiency to deliver a 10⁶-fold improvement in sensitivity compared to that of conventional lateral flow (LF) systems. The conceptualized strategy utilizes a simple magnet placed beneath the three-dimensional printed LF device to concentrate the targets at the signal zone without any additional instrumentation. In addition, protein mixtures extracted from the tissue of cervical cancer patients was also utilized to validate the sensor. To investigate the effect of magnetic focus on sensitivity, surface-enhanced Raman spectroscopy and dark-field imaging was utilized to characterize the distribution and movement of Fe₃O₄ core-Au shell nanoprobes in a model LF strip. Our experiments show that the magnetic focus results in an increased interaction time between the magnetic probe-labeled targets and the capture antibody, yielding a higher capture efficiency, allowing for ultrasensitive detection of the target not possible before with LF. The proposed mLFS can be utilized to detect a range of trace protein biomarkers for early diagnosis and can be combined with diverse pretreatment and signal amplification steps to query complex samples.

Three-Dimensional Orientation of Anisotropic Plasmonic Aggregates at Intracellular Nuclear Indentation Sites by Integrated Light Sheet Super-Resolution Microscopy

Three-dimensional (3D) orientations of individual anisotropic plasmonic nanoparticles in aggregates were observed in real time by integrated light sheet super-resolution microscopy ( iLSRM). Asymmetric light scattering of a gold nanorod (AuNR) was used to trigger signals based on the polarizer angle. Controlled photoswitching was achieved by turning the polarizer and obtaining a series of images at different polarization directions. 3D subdiffraction-limited super-resolution images were obtained by superlocalization of scattering signals as a function of the anisotropic optical properties of AuNRs. Varying the polarizer angle allowed resolution of the orientation of individual AuNRs. 3D images of individual nanoparticles were resolved in aggregated regions, resulting in as low as 64 nm axial resolution and 28 nm spatial resolution. The proposed imaging setup and localization approach demonstrates a convenient method for imaging under a noisy environment where the majority of scattering noise comes from cellular components. This integrated 3D iLSRM and localization technique was shown to be reliable and useful in the field of 3D nonfluorescence super-resolution imaging.

Nanoplasmonic sensors for biointerfacial science

In recent years, nanoplasmonic sensors have become widely used for the label-free detection of biomolecules across medical, biotechnology, and environmental science applications. To date, many nanoplasmonic sensing strategies have been developed with outstanding measurement capabilities, enabling detection down to the single-molecule level. One of the most promising directions has been surface-based nanoplasmonic sensors, and the potential of such technologies is still emerging. Going beyond detection, surface-based nanoplasmonic sensors open the door to enhanced, quantitative measurement capabilities across the biointerfacial sciences by taking advantage of high surface sensitivity that pairs well with the size of medically important biomacromolecules and biological particulates such as viruses and exosomes. The goal of this review is to introduce the latest advances in nanoplasmonic sensors for the biointerfacial sciences, including ongoing development of nanoparticle and nanohole arrays for exploring different classes of biomacromolecules interacting at solid-liquid interfaces. The measurement principles for nanoplasmonic sensors based on utilizing the localized surface plasmon resonance (LSPR) and extraordinary optical transmission (EOT) phenomena are first introduced. The following sections are then categorized around different themes within the biointerfacial sciences, specifically protein binding and conformational changes, lipid membrane fabrication, membrane-protein interactions, exosome and virus detection and analysis, and probing nucleic acid conformations and binding interactions. Across these themes, we discuss the growing trend to utilize nanoplasmonic sensors for advanced measurement capabilities, including positional sensing, biomacromolecular conformation analysis, and real-time kinetic monitoring of complex biological interactions. Altogether, these advances highlight the rich potential of nanoplasmonic sensors and the future growth prospects of the community as a whole. With ongoing development of commercial nanoplasmonic sensors and analytical models to interpret corresponding measurement data in the context of biologically relevant interactions, there is significant opportunity to utilize nanoplasmonic sensing strategies for not only fundamental biointerfacial science, but also translational science applications related to clinical medicine and pharmaceutical drug development among countless possibilities.

Ultrasound beam steering of oxygen nanobubbles for enhanced bladder cancer therapy

New intravesical treatment approaches for bladder cancer are needed as currently approved treatments show several side effects and high tumor recurrence rate. Our study used MB49 murine urothelial carcinoma model to evaluate oxygen encapsulated cellulosic nanobubbles as a novel agent for imaging and ultrasound guided drug delivery. In this study, we show that oxygen nanobubbles (ONB) can be propelled (up to 40 mm/s) and precisely guided in vivo to the tumor by an ultrasound beam. Nanobubble velocity can be controlled by altering the power of the ultrasound Doppler beam, while nanobubble direction can be adjusted to different desired angles by altering the angle of the beam. Precise ultrasound beam steering of oxygen nanobubbles was shown to enhance the efficacy of mitomycin-C, resulting in significantly lower tumor progression rates while using a 50% lower concentration of chemotherapeutic drug. Further, dark field imaging was utilized to visualize and quantify the ONB ex vivo. ONBs were found to localize up to 500 µm inside the tumor using beam steering. These results demonstrate the potential of an oxygen nanobubble drug encapsulated system to become a promising strategy for targeted drug delivery because of its multimodal (imaging and oxygen delivery) and multifunctional (targeting and hypoxia programming) properties.

Single-Cell Analysis Using Hyperspectral Imaging Modalities

Almost a decade ago, hyperspectral imaging (HSI) was employed by the NASA in satellite imaging applications such as remote sensing technology. This technology has since been extensively used in the exploration of minerals, agricultural purposes, water resources, and urban development needs. Due to recent advancements in optical re-construction and imaging, HSI can now be applied down to micro- and nanometer scales possibly allowing for exquisite control and analysis of single cell to complex biological systems. This short review provides a description of the working principle of the HSI technology and how HSI can be used to assist, substitute, and validate traditional imaging technologies. This is followed by a description of the use of HSI for biological analysis and medical diagnostics with emphasis on single-cell analysis using HSI.

Oxygen Nanobubble Tracking by Light Scattering in Single Cells and Tissues

Oxygen nanobubbles (ONBs) have significant potential in targeted imaging and treatment in cancer diagnosis and therapy. Precise localization and tracking of single ONBs is demonstrated based on hyperspectral dark-field microscope (HSDFM) to image and track single oxygen nanobubbles in single cells. ONBs were proposed as promising contrast-generating imaging agents due to their strong light scattering generated from nonuniformity of refractive index at the interface. With this powerful platform, we have revealed the trajectories and quantities of ONBs in cells, and demonstrated the relation between the size and diffusion coefficient. We have also evaluated the presence of ONBs in the nucleus with respect to an increase in incubation time and have quantified the uptake in single cells in ex vivo tumor tissues. Our results demonstrate that HSDFM can be a versatile platform to detect and measure cellulosic nanoparticles at the single-cell level and to assess the dynamics and trajectories of this delivery system.

Technical advances in global DNA methylation analysis in human cancers

Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types. Important breakthroughs in the recent years have uncovered further oxidized derivatives of 5mC - 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), thereby expanding our understanding of the DNA methylation dynamics. While the biological roles of these epigenetic derivatives are being extensively characterized, this review presents a perspective on the opportunity of innovation in the global methylation analysis platforms. While multiple methods for global analysis of 5mC in clinical samples exist and have been reviewed elsewhere, two of the established methods - Liquid Chromatography coupled with mass spectrometry (LC-MS/MS) and Immunoquantification have successfully evolved to include the quantitation of 5hmC, 5fC and 5caC. Although the analytical performance of LC-MS/MS is superior, the simplicity afforded by the experimental procedure of immunoquantitation ensures it’s near ubiquity in clinical applications. Recent developments in spectroscopy, nanotechnology and sequencing also provide immense promise for future evaluations and are discussed briefly. Finally, we provide a perspective on the current scenario of global DNA methylation analysis tools and present suggestions to develop the next generation toolset.

Photoinduced Electron Transfer Process Visualized on Single Silver Nanoparticles

Understanding the photoinduced electron transfer (PET) mechanism is vital to improving the photoelectric conversion efficiency for solar energy materials and photosensitization systems. Herein, we visually demonstrate the PET process by real-time monitoring the photoinduced chemical transformation of p-aminothiophenol (p-ATP), an important SERS signal molecule, to 4,4'-dimercaptoazobenzene on single silver nanoparticles (AgNPs) with a localized surface plasmon resonance (LSPR) spectroscopy coupled dark-field microscopy. The bidirectional LSPR scattering spectral shifts bathochromically at first and hypsochromically then, which are caused by the electron transfer delay of p-ATP, disclose the PET path from p-ATP to O₂ through AgNPs during the reaction, and enable us to digitalize the corresponding electron loss and gain on the surface of AgNP at different time periods. This visualized PET process could provide a simple and efficient approach to explore the nature of PET and help to interpret the SERS mechanism in terms of p-ATP.

Single plasmonic nanoparticles as ultrasensitive sensors

In this mini review, we will provide a brief introduction focusing on the current applications of single plasmonic nanoparticle-based sensors using DFM, including the detection of molecules, the real-time monitoring of chemical/electrochemical reactions and the imaging of living cells.

Beyond quantification: in situ analysis of transcriptome and pre-mRNA alternative splicing at the nanoscale

In situ analysis offers a venue for dissecting the complex transcriptome in its natural context to tap into cellular processes that could explain the phenotypic physiology and pathology yet to be understood. Over the past decades, enormous progress has been made to improve the resolution, sensitivity, and specificity of single-cell technologies. The continued efforts in RNA research not only facilitates mechanistic studies of molecular biology but also provides state-of-the-art strategies for diagnostic purposes. The implementation of novel bio-imaging platforms has yielded valuable information for inspecting gene expression, mapping regulatory networks, and classifying cell types. In this article, we discuss the merits and technical challenges in single-molecule in situ RNA profiling. Advanced in situ hybridization methodologies developed for a variety of detection modalities are reviewed. Considering the fact that in mammalian cells the number of protein products immensely exceeds that of the actual coding genes due to pre-mRNA alternative splicing, tools capable of elucidating this process in intact cells are highlighted. To conclude, we point out future directions for in situ transcriptome analysis and expect a plethora of opportunities and discoveries in this field. WIREs Nanomed Nanobiotechnol 2017, 9:e1443. doi: 10.1002/wnan.1443 For further resources related to this article, please visit the WIREs website.

Plasmonically Engineered Nanoprobes for Biomedical Applications

The localized surface plasmon resonance of metal nanoparticles is the collective oscillation of electrons on particle surface, induced by incident light, and is a particle composition-, morphology-, and coupling-dependent property. Plasmonic engineering deals with highly precise formation of the targeted nanostructures with targeted plasmonic properties (e.g., electromagnetic field distribution and enhancement) via controlled synthetic, assembling, and atomic/molecular tuning strategies. These plasmonically engineered nanoprobes (PENs) have a variety of unique and beneficial physical, chemical, and biological properties, including optical signal enhancement, catalytic, and local temperature-tuning photothermal properties. In particular, for biomedical applications, there are many useful properties from PENs including LSPR-based sensing, surface-enhanced Raman scattering, metal-enhanced fluorescence, dark-field light-scattering, metal-mediated fluorescence resonance energy transfer, photothermal effect, photodynamic effect, photoacoustic effect, and plasmon-induced circular dichroism. These properties can be utilized for the development of new biotechnologies and biosensing, bioimaging, therapeutic, and theranostic applications in medicine. This Perspective introduces the concept of plasmonic engineering in designing and synthesizing PENs for biomedical applications, gives recent examples of biomedically functional PENs, and discusses the issues and future prospects of PENs for practical applications in bioscience, biotechnology, and medicine.

Optical Clearing Delivers Ultrasensitive Hyperspectral Dark-Field Imaging for Single-Cell Evaluation

A single-cell optical clearing methodology is developed and demonstrated in hyperspectral dark-field microscopy (HSDFM) and imaging of plasmonic nanoprobes. Our strategy relies on a combination of delipidation and refractive index (RI) matching with highly biocompatible and affordable agents. Before applying the RI-matching solution, the delipidation step by using a mild solvent effectively eliminates those high-density, lipid-enriched granular structures which emit strong scattering. Upon treatment, the background scattering from cellular organelles could be repressed to a negligible level while the scattering signals from plasmonic nanomaterials increase, leading to a significant improvement of the signal-to-noise ratio (SNR). With this method established, the versatility and applicability of HSDFM are greatly enhanced. In our demonstration, quantitative mapping of the dimerization-activated receptor kinase HER2 is achieved in a single cancer cell by a nonfluorescent approach. High-resolution imaging for oncogenic mRNAs, namely ER, PR, and HER2, is performed with single labeling. More importantly, in situ multiplex detection of mRNA and protein is made possible by HSDFM since it overcomes the difficulties of complex staining and signal imbalance suffered by the conventional optical imaging. Last, we show that with optical clearing, characterization of intracellularly grown gold particulates is accomplished at an unprecedented spatiotemporal resolution. Taken together, the uniqueness of optical clearing and HSDFM is expected to open ample avenues for single-cell studies and biomedical engineering.

Plasmonic nanohalo optical probes for highly sensitive imaging of survivin mRNA in living cells

A novel strategy for sensitive detection of survivin mRNA based on Rayleigh light scattering spectroscopy of AuNP nanohalo probes.