Chemical Analysis of Single Cells

Light scattering imaging modal expansion cytometry for label-free single-cell analysis with deep learning

BACKGROUND AND OBJECTIVE

Single-cell imaging plays a key role in various fields, including drug development, disease diagnosis, and personalized medicine. To obtain multi-modal information from a single-cell image, especially for label-free cells, this study develops modal expansion cytometry for label-free single-cell analysis.

METHODS

The study utilizes a deep learning-based architecture to expand single-mode light scattering images into multi-modality images, including bright-field (non-fluorescent) and fluorescence images, for label-free single-cell analysis. By combining adversarial loss, L1 distance loss, and VGG perceptual loss, a new network optimization method is proposed. The effectiveness of this method is verified by experiments on simulated images, standard spheres of different sizes, and multiple cell types (such as cervical cancer and leukemia cells). Additionally, the capability of this method in single-cell analysis is assessed through multi-modal cell classification experiments, such as cervical cancer subtypes.

RESULTS

This is demonstrated by using both cervical cancer cells and leukemia cells. The expanded bright-field and fluorescence images derived from the light scattering images align closely with those obtained through conventional microscopy, showing a contour ratio near 1 for both the whole cell and its nucleus. Using machine learning, the subtyping of cervical cancer cells achieved 92.85 % accuracy with the modal expansion images, which represents an improvement of nearly 20 % over single-mode light scattering images.

CONCLUSIONS

This study demonstrates the light scattering imaging modal expansion cytometry with deep learning has the capability to expand the single-mode light scattering image into the artificial multimodal images of label-free single cells, which not only provides the visualization of cells but also helps for the cell classification, showing great potential in the field of single-cell analysis such as cancer cell diagnosis.

Application of a variational autoencoder for clustering and analyzing in situ articular cartilage cellular response to mechanical stimuli

In various biological systems, analyzing how cell behaviors are coordinated over time would enable a deeper understanding of tissue-scale response to physiologic or superphysiologic stimuli. Such data is necessary for establishing both normal tissue function and the sequence of events after injury that lead to chronic disease. However, collecting and analyzing these large datasets presents a challenge-such systems are time-consuming to process, and the overwhelming scale of data makes it difficult to parse overall behaviors. This problem calls for an analysis technique that can quickly provide an overview of the groups present in the entire system and also produce meaningful categorization of cell behaviors. Here, we demonstrate the application of an unsupervised method-the Variational Autoencoder (VAE)-to learn the features of cells in cartilage tissue after impact-induced injury and identify meaningful clusters of chondrocyte behavior. This technique quickly generated new insights into the spatial distribution of specific cell behavior phenotypes and connected specific peracute calcium signaling timeseries with long term cellular outcomes, demonstrating the value of the VAE technique.

Microarray-Based Electrochemical Biosensing

Microarrays are widely utilized in bioanalysis. Electrochemical biosensing techniques are often applied in microarray-based assays because of their simplicity, low cost, and high sensitivity. In such systems, the electrodes and sensing elements are arranged in arrays, and the target analytes are detected electrochemically. These sensors can be utilized for high-throughput bioanalysis and the electrochemical imaging of biosamples, including proteins, oligonucleotides, and cells. In this chapter, we summarize recent progress on these topics. We categorize electrochemical biosensing techniques for array detection into four groups: scanning electrochemical microscopy, electrode arrays, electrochemiluminescence, and bipolar electrodes. For each technique, we summarize the key principles and discuss the advantages, disadvantages, and bioanalysis applications. Finally, we present conclusions and perspectives about future directions in this field.

Recent developments in ionization techniques for single-cell mass spectrometry

The variation among individual cells plays a significant role in many biological functions. Single-cell analysis is advantageous for gaining insight into intricate biochemical mechanisms rarely accessible when studying tissues as a whole. However, measurement on a unicellular scale is still challenging due to unicellular complex composition, minute substance quantities, and considerable differences in compound concentrations. Mass spectrometry has recently gained extensive attention in unicellular analytical fields due to its exceptional sensitivity, throughput, and compound identification abilities. At present, single-cell mass spectrometry primarily concentrates on the enhancement of ionization methods. The principal ionization approaches encompass nanoelectrospray ionization (nano-ESI), laser desorption ionization (LDI), secondary ion mass spectrometry (SIMS), and inductively coupled plasma (ICP). This article summarizes the most recent advancements in ionization techniques and explores their potential directions within the field of single-cell mass spectrometry.

Non-Mass Spectrometric Targeted Single-Cell Metabolomics

Metabolic assays serve as pivotal tools in biomedical research, offering keen insights into cellular physiological and pathological states. While mass spectrometry (MS)-based metabolomics remains the gold standard for comprehensive, multiplexed analyses of cellular metabolites, innovative technologies are now emerging for the targeted, quantitative scrutiny of metabolites and metabolic pathways at the single-cell level. In this review, we elucidate an array of these advanced methodologies, spanning synthetic and surface chemistry techniques, imaging-based methods, and electrochemical approaches. We summarize the rationale, design principles, and practical applications for each method, and underscore the synergistic benefits of integrating single-cell metabolomics (scMet) with other single-cell omics technologies. Concluding, we identify prevailing challenges in the targeted scMet arena and offer a forward-looking commentary on future avenues and opportunities in this rapidly evolving field.

Prospects of single-cell nuclear magnetic resonance spectroscopy with quantum sensors

Single-cell analysis can unravel functional heterogeneity within cell populations otherwise obscured by ensemble measurements. However, noninvasive techniques that probe chemical entities and their dynamics are still lacking. This challenge could be overcome by novel sensors based on nitrogen-vacancy (NV) centers in diamond, which enable nuclear magnetic resonance (NMR) spectroscopy on unprecedented sample volumes. In this perspective, we briefly introduce NV-based quantum sensing and review the progress made in microscale NV-NMR spectroscopy. Last, we discuss approaches to enhance the sensitivity of NV ensemble magnetometers to detect biologically relevant concentrations and provide a roadmap toward their application in single-cell analysis.

Plant nanobionics: Fortifying food security via engineered plant productivity

The world's human population is increasing exponentially, increasing the demand for high-quality food sources. As a result, there is a major global concern over hunger and malnutrition in developing countries with limited food resources. To address this issue, researchers worldwide must focus on developing improved crop varieties with greater productivity to overcome hunger. However, conventional crop breeding methods require extensive periods to develop new varieties with desirable traits. To tackle this challenge, an innovative approach termed plant nanobionics introduces nanomaterials (NMs) into cell organelles to enhance or modify plant function and thus crop productivity and yield. A comprehensive review of nanomaterials affect crop yield is needed to guide nanotechnology research. This article critically reviews nanotechnology applications for engineering plant productivity, seed germination, crop growth, enhancing photosynthesis, and improving crop yield and quality, and discusses nanobionic approaches such as smart drug delivery systems and plant nanobiosensors. Moreover, the review describes NM classification and synthesis and human health-related and plant toxicity hazards. Our findings suggest that nanotechnology application in agricultural production could significantly increase crop yields to alleviate global hunger pressures. However, the environmental risks associated with NMs should be investigated thoroughly before their widespread adoption in agriculture.

Exploring the performance of quadrupole, time-of-flight, and multi-collector ICP-MS for dual-isotope detection on single nanoparticles and cells

To meet the demand for multi-element/isotope analysis at the single nanoparticle (NP) or cell level, different types of inductively coupled plasma mass spectroscopy (ICP-MS) have been used to simultaneously monitor multiple mass-to-charge ratios in single-particle/cell ICP-MS (SP/SC-ICP-MS) analysis. Systematic evaluation and comparison of the performance of these techniques are urgently required. Herein, three ICP-quadrupole (Q)-MS, two ICP-time of flight (TOF)-MS, and one multi-collector (MC)-ICP-MS instruments were employed to simultaneously detect ¹⁰⁷Ag and ¹⁰⁹Ag on single Ag NPs and Ag-exposed cyanobacteria cells. The evaluation was conducted by comparing the measured event-specific ¹⁰⁹Ag:¹⁰⁷Ag ratios with the natural ratio. Duration of NP or cell events and time resolution in the peak hopping mode were the main factors affecting the performance of ICP-Q-MS. Under the optimal condition (100 μs for both dwell time and settling time), less than 45% of the NP or cell events had a ¹⁰⁹Ag:¹⁰⁷Ag ratio deviating <30% from the natural ratio. Most events obtained via ICP-TOF-MS were paired events with both isotopes detected. For large-size NPs and cells with high exposure levels, nearly 80% of the events had a ratio deviation within ±30%. MC-ICP-MS performed particularly well in isotope determination with all the events having a ratio deviation within ±5%. For ICP-TOF-MS and MC-ICP-MS, the signal intensity of the events was the main factor affecting the accuracy of the measured ¹⁰⁹Ag:¹⁰⁷Ag ratios due to the counting statistics. The established methods and results provide insight on the analyses of two elements/isotopes or more on single NPs or cells. Based on the comparison of the advantages and limitations of these instruments, this study provides a critical reference for future multi-element/isotope SP/SC-ICP-MS analyses.

Review about Powerful Combinations of Advanced and Hyphenated Sample Introduction Techniques with Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) for Elucidating Trace Element Species in Pathologic Conditions on a Molecular Level

Element analysis in clinical or biological samples is important due to the essential role in clinical diagnostics, drug development, and drug-effect monitoring. Particularly, the specific forms of element binding, actual redox state, or their spatial distribution in tissue or in single cells are of interest in medical research. This review summarized exciting combinations of sophisticated sample delivery systems hyphenated to inductively coupled plasma-mass spectrometry (ICP-MS), enabling a broadening of information beyond the well-established outstanding detection capability. Deeper insights into pathological disease processes or intracellular distribution of active substances were provided, enabling a better understanding of biological processes and their dynamics. Examples were presented from spatial elemental mapping in tissue, cells, or spheroids, also considering elemental tagging. The use of natural or artificial tags for drug monitoring was shown. In the context of oxidative stress and ferroptosis iron, redox speciation gained importance. Quantification methods for Fe2+, Fe3+, and ferritin-bound iron were introduced. In Wilson’s disease, free and exchangeable copper play decisive roles; the respective paragraph provided information about hyphenated Cu speciation techniques, which provide their fast and reliable quantification. Finally, single cell ICP-MS provides highly valuable information on cell-to-cell variance, insights into uptake of metal-containing drugs, and their accumulation and release on the single-cell level.

Capillary Electrophoresis Mass Spectrometry for Scalable Single-Cell Proteomics

Understanding the biochemistry of the cell requires measurement of all the molecules it produces. Single-cell proteomics recently became possible through advances in microanalytical sample preparation, separation by nano-flow liquid chromatography (nanoLC) and capillary electrophoresis (CE), and detection using electrospray ionization (ESI) high-resolution mass spectrometry (HRMS). Here, we demonstrate capillary microsampling CE-ESI-HRMS to be scalable to proteomics across broad cellular dimensions. This study established proof-of-principle using giant, ∼250-µm-diameter cells from embryos of the frog Xenopus laevis and small, ∼35-µm-diameter neurons in culture from the mouse hippocampus. From ∼18 ng, or ∼0.2% of the total cellular proteome, subcellular analysis of the ventral-animal midline (V11) and equatorial (V12) cells identified 1,133 different proteins in a 16-cell embryo. CE-HRMS achieved ∼20-times higher sensitivity and doubled the speed of instrumental measurements compared to nanoLC, the closest neighboring single-cell technology of choice. Microanalysis was scalable to 722 proteins groups from ∼5 ng of cellular protein digest from identified left dorsal-animal midline cell (D11), supporting sensitivity for smaller cells. Capillary microsampling enabled the isolation and transfer of individual neurons from the culture, identifying 37 proteins between three different cells. A total of 224 proteins were detected from 500 pg of neuronal protein digest, which estimates to a single neuron. Serial dilution returned 157 proteins from sample amounts estimating to about half a cell (250 pg protein) and 70 proteins from ca. a quarter of a neuron (125 pg protein), suggesting sufficient sensitivity for subcellular proteomics. CE-ESI-HRMS complements nanoLC proteomics with scalability, sensitivity, and speed across broad cellular dimensions.

Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry

Understanding of the relationship between cellular function and molecular composition holds a key to next-generation therapeutics but requires measurement of all types of molecules in cells. Developments in sequencing enabled semiroutine measurement of single-cell genomes and transcriptomes, but analytical tools are scarce for detecting diverse proteins in tissue-embedded cells. To bridge this gap for neuroscience research, we report the integration of patch-clamp electrophysiology with subcellular shot-gun proteomics by high-resolution mass spectrometry (HRMS). Recording of electrical activity permitted identification of dopaminergic neurons in the substantia nigra pars compacta. Ca. 20-50% of the neuronal soma content, containing an estimated 100 pg of total protein, was aspirated into the patch pipette filled with ammonium bicarbonate. About 1 pg of somal protein, or ∼0.25% of the total cellular proteome, was analyzed on a custom-built capillary electrophoresis (CE) electrospray ionization platform using orbitrap HRMS for detection. A series of experiments were conducted to systematically enhance detection sensitivity through refinements in sample processing and detection, allowing us to quantify ∼275 different proteins from somal aspirate-equivalent protein digests from cultured neurons. From single neurons, patch-clamp proteomics of the soma quantified 91, 80, and 95 different proteins from three different dopaminergic neurons or 157 proteins in total. Quantification revealed detectable proteomic differences between the somal protein samples. Analysis of canonical knowledge predicted rich interaction networks between the observed proteins. The integration of patch-clamp electrophysiology with subcellular CE-HRMS proteomics expands the analytical toolbox of neuroscience.

State-of-the-arts techniques and current evolving approaches in the separation and detection of circulating tumor cell

Circulating tumor cells (CTCs) are cancer cells that shed from the primary tumor and then enter the circulatory system, a small part of which may evolve into metastatic cancer under appropriate microenvironment conditions. The detection of CTCs is a truly noninvasive, dynamic monitor for disease changes, which has considerable clinical implications in the selection of targeted drugs. However, their inherent rarity and heterogeneity pose significant challenges to their isolation and detection. Even the "gold standard", CellSearch™, suffers from high expenses, low capture efficiency, and the consumption of time. With the advancement of CTCs analysis technologies in recent years, the yield and efficiency of CTCs enrichment have gradually been improved, as well as detection sensitivity. In this review, the isolation and detection strategies of CTCs have been completely described and the potential directions for future research and development have also been highlighted through analyzing the challenges faced by current strategies.

Multimodal imaging of drug and excipients in rat lungs following an inhaled administration of controlled-release drug laden PLGA microparticles

Controlled-release formulations, in the form of micro- or nanoparticles, are increasingly attractive to the pharmaceutical industry for drug delivery. For respiratory illnesses, controlled-release microparticle formulations provide an opportunity to deliver a higher percentage of an inhaled medicament dose to the lung, thus potentially reducing the therapeutic dose, frequency of dosing, and minimising side-effects. We describe the use of a multimodal approach consisting of MALDI MS imaging, 3D depth profiling TOF-SIMS analysis, and histopathology to monitor the distribution of drug and excipients in sections taken from excised rat lungs following an inhaled administration of drug-laden microparticles. Following a single dose, the administered drug was detected in the lung via both MALDI MS and TOF-SIMS over a range of time points. Both imaging techniques enabled the characterisation of the distribution and retention of drug particles and identified differences in the capabilities of both imaging modalities. Histochemical staining of consecutive sections was used to provide biological context to the findings and will also be discussed in this presentation. We demonstrate how this multimodal approach could be used to help increase our understanding of the use of controlled release microparticles.

Finite-size transitions in complex membranes

The lipid-raft hypothesis postulates that cell membranes possess some degree of lateral organization. The hypothesis has attracted much attention while remaining controversial, with an underlying mechanism that remains elusive. One idea that supports rafts relies on the membrane lying near a critical point. Although supported by experimental evidence, holding a many-component membrane at criticality requires a delicate tuning of all components-a daunting task. Here, we propose a coherent framework to reconcile critical behavior and lipid regulation. Using a lattice model, we show that lipid regulation of a complex membrane, i.e., allowing composition to fluctuate based on relative chemical potentials, can lead to critical behavior. The results are robust against specific values of the chemical potentials. Instead of a conventional transition point, criticality is observed over a large temperature range. This surprising behavior arises from finite-size effects, causing nonequivalent time and space averages. The instantaneous lipid distribution effectively develops a translational symmetry, which we relate to long-wavelength Goldstone modes. The framework is robust and reproduces important experimental trends; membrane-demixing temperature closely follows cell-growth temperature. It also ensures criticality of fixed-composition extracts, such as giant plasma membrane vesicles. Our clear picture provides a strong argument in favor of the critical-membrane hypothesis, without the need for specific sensing mechanisms.

Antimalarial drugs impact chemical messenger secretion by blood platelets

Background

Advances in antimalarial drug development are important for combating malaria. Among the currently identified antimalarial drugs, it is suggested that some interact directly with the malarial parasites while others interact indirectly with the parasites. While this approach leads to parasite elimination, little is known about how these antimalarial drugs impact immune cells that are also critical in malarial response.

Methods

Herein, the effects of two common antimalarial drugs, chloroquine and quinine, on platelets were explored at both the bulk level, using high performance liquid chromatography, and the single cell level, using carbon-fiber microelectrode amperometry, to characterize any changes in chemical messenger secretion.

Results

The data reveal that both drugs cause platelet activation and reduce the number of platelet exocytosis events as well as delay fusion pore opening and closing.

Conclusions

This work demonstrates how chloroquine and quinine quantitatively and qualitatively impact in vitro platelet function.

General significance

Overall, the goal of this work is to promote understanding about how antimalarial drugs impact platelets as this may affect antimalarial drug development as well as therapeutic approaches to treat malarial infection.

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Antimalarial drugs impact platelet function by inducing activation.

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Single cell electrochemistry reveals changes in platelet function.

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It is important to consider platelet behaviors beyond aggregation to understand the side effects of antimalarial drugs.

Analysis of Lipids in Single Cells and Organelles Using Nanomanipulation-Coupled Mass Spectrometry

The ability to discriminately analyze the chemical constituents of single cells and organelles is highly sought after and necessary to establish true biomarkers. Some major challenges of individual cell analysis include requirement and expenditure of a large sample of cells as well as extensive extraction and separation techniques. Here, we describe methods to perform individual cell and organelle extractions of both tissues and cells in vitro using nanomanipulation coupled to mass spectrometry. Lipid profiles display heterogeneity from extracted adipocytes and lipid droplets, demonstrating the necessity for single cell analysis. The application of these techniques can be applied to other cell and organelle types for selective and thorough monitoring of disease progression and biomarker discovery.

Single-Cell Metabolomics by Mass Spectrometry

Single-cell level metabolomics gives a snapshot of small molecules, intermediates, and products of cellular metabolism within a biological system. These small molecules, typically less than 1 kDa in molecular weight, often provide the basis of biochemical heterogeneity within cells. The molecular differences between cells with a cell type are often attributed to random stochastic biochemical processes, cell cycle stages, environmental stress, and diseased states. In this chapter, current limitations and challenges in single-cell analysis by mass spectrometry will be discussed alongside the prospects of single-cell metabolomics in systems biology. A few selected example of the recent development in mass spectrometry tools to unravel single-cell metabolomics will be described as well.

Recent advances in single-cell analysis by mass spectrometry

Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.

Nanoscale tweezers for single-cell biopsies

Much of the functionality of multicellular systems arises from the spatial organization and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional 'snapshot' of individual cells. The real-time analysis and perturbation of living cells would generate a step change in single-cell analysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10-20 nm, which can be used for the dielectrophoretic trapping of DNA and proteins. Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells without affecting their viability. Finally, we report on the trapping and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.

High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis

We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.

True one cell chemical analysis: a review

The constantly growing field of True One Cell (TOC) analysis has provided important information on the direct chemical composition of various cells and cellular components.

Using Single-Cell Amperometry and Intracellular Vesicle Impact Electrochemical Cytometry To Shed Light on the Biphasic Effects of Lidocaine on Exocytosis

Single cell amperometry and intracellular vesicle impact electrochemical cytometry were used to examine whether lidocaine can regulate neurotransmitter release or storage for PC12 cells to explain the biphasic effects whereby it can protect neurons and improve cognitive outcome at low concentration, but can cause neurotoxicity at high concentration. We show that lidocaine affects the behavior of PC12 cell exocytosis in a concentration dependent way, which exactly corresponds to its biphasic effects. At a relatively high concentration, it shows a much narrower pore size and a longer-duration fusion pore with less monoamine released than control cells. However, at a relatively low concentration, the fusion pore is open even longer than at high concentration, and with more monoamine released than control cells. Furthermore, intracellular vesicle impact electrochemical cytometry was used to confirm that lidocaine did not change the catecholamine content of the vesicles. These data provide a mechanism for the observed biphasic effects of the drug and suggest that lidocaine influences exocytosis through multiple mechanisms.

Biological imaging with scanning electrochemical microscopy

Scanning electrochemical microscopy (SECM) is a powerful and versatile technique for visualizing the local electrochemical activity of a surface as an ultramicroelectrode tip is moved towards or over a sample of interest using precise positioning systems. In comparison with other scanning probe techniques, SECM not only enables topographical surface mapping but also gathers chemical information with high spatial resolution. Considerable progress has been made in the analysis of biological samples, including living cells and immobilized biomacromolecules such as enzymes, antibodies and DNA fragments. Moreover, combinations of SECM with comple-mentary analytical tools broadened its applicability and facilitated multi-functional analysis with extended life science capabilities. The aim of this review is to present a brief topical overview on recent applications of biological SECM, with particular emphasis on important technical improvements of this surface imaging technique, recommended applications and future trends.

Design and Application of Sensors for Chemical Cytometry

The bulk cell population response to a stimulus, be it a growth factor or a cytotoxic agent, neglects the cell-to-cell variability that can serve as a friend or as a foe in human biology. Biochemical variations among closely related cells furnish the basis for the adaptability of the immune system but also act as the root cause of resistance to chemotherapy by tumors. Consequently, the ability to probe for the presence of key biochemical variables at the single-cell level is now recognized to be of significant biological and biomedical impact. Chemical cytometry has emerged as an ultrasensitive single-cell platform with the flexibility to measure an array of cellular components, ranging from metabolite concentrations to enzyme activities. We briefly review the various chemical cytometry strategies, including recent advances in reporter design, probe and metabolite separation, and detection instrumentation. We also describe strategies for improving intracellular delivery, biochemical specificity, metabolic stability, and detection sensitivity of probes. Recent applications of these strategies to small molecules, lipids, proteins, and other analytes are discussed. Finally, we assess the current scope and limitations of chemical cytometry and discuss areas for future development to meet the needs of single-cell research.

Emerging tools for studying single entity electrochemistry

Electrochemistry studies charge transfer and related processes at various microscopic structures (atomic steps, islands, pits and kinks on electrodes), and mesoscopic materials (nanoparticles, nanowires, viruses, vesicles and cells) made by nature and humans, involving ions and molecules. The traditional approach measures averaged electrochemical quantities of a large ensemble of these individual entities, including the microstructures, mesoscopic materials, ions and molecules. There is a need to develop tools to study single entities because a real system is usually heterogeneous, e.g., containing nanoparticles with different sizes and shapes. Even in the case of "homogeneous" molecules, they bind to different microscopic structures of an electrode, assume different conformations and fluctuate over time, leading to heterogeneous reactions. Here we highlight some emerging tools for studying single entity electrochemistry, discuss their strengths and weaknesses, and provide personal views on the need for tools with new capabilities for further advancing single entity electrochemistry.

Correlated mass spectrometry and confocal microscopy imaging verifies the dual-targeting action of an organoruthenium anticancer complex

An addressable single cell imaging strategy combining ToF-SIMS and confocal fluorescence microscopy imaging has been developed, and sucessfully applied to visualize the subcellular distribution of an organoruthenium anticancer complex, [(η⁶-benzene)Ru(N,N-L)Cl]⁺ (1; L: 4-anilinoquinazoline ligand), showing its accumulation in both cell membrane and nuclei, and verifying its dual-targeting feature.

Single-cell analysis by ICP-MS/MS as a fast tool for cellular bioavailability studies of arsenite

A fast and reliable single-cell ICP-MS/MS method is presented to determine the bioavailability of metal species as well as sulfur and phosphorus as internal control after re-suspension of cells in water.

Mass-spectrometry-based lipidomics

Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.

Amperometry methods for monitoring vesicular quantal size and regulation of exocytosis release

Chemical signaling strength during intercellular communication can be regulated by secretory cells through controlling the amount of signaling molecules that are released from a secretory vesicle during the exocytosis process. In addition, the chemical signal can also be influenced by the amount of neurotransmitters that is accumulated and stored inside the secretory vesicle compartment. Here, we present the development of analytical methodologies and cell model systems that have been applied in neuroscience research for gaining better insights into the biophysics and the molecular mechanisms, which are involved in the regulatory aspects of the exocytosis machinery affecting the output signal of chemical transmission at neuronal and neuroendocrine cells.

Tuning Selectivity of Fluorescent Carbon Nanotube-Based Neurotransmitter Sensors

Detection of neurotransmitters is an analytical challenge and essential to understand neuronal networks in the brain and associated diseases. However, most methods do not provide sufficient spatial, temporal, or chemical resolution. Near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) have been used as building blocks for sensors/probes that detect catecholamine neurotransmitters, including dopamine. This approach provides a high spatial and temporal resolution, but it is not understood if these sensors are able to distinguish dopamine from similar catecholamine neurotransmitters, such as epinephrine or norepinephrine. In this work, the organic phase (DNA sequence) around SWCNTs was varied to create sensors with different selectivity and sensitivity for catecholamine neurotransmitters. Most DNA-functionalized SWCNTs responded to catecholamine neurotransmitters, but both dissociation constants (K_d) and limits of detection were highly dependent on functionalization (sequence). K_d values span a range of 2.3 nM (SWCNT-(GC)₁₅ + norepinephrine) to 9.4 μM (SWCNT-(AT)₁₅ + dopamine) and limits of detection are mostly in the single-digit nM regime. Additionally, sensors of different SWCNT chirality show different fluorescence increases. Moreover, certain sensors (e.g., SWCNT-(GT)₁₀) distinguish between different catecholamines, such as dopamine and norepinephrine at low concentrations (50 nM). These results show that SWCNTs functionalized with certain DNA sequences are able to discriminate between catecholamine neurotransmitters or to detect them in the presence of interfering substances of similar structure. Such sensors will be useful to measure and study neurotransmitter signaling in complex biological settings.

Nanosensor Technology Applied to Living Plant Systems

An understanding of plant biology is essential to solving many long-standing global challenges, including sustainable and secure food production and the generation of renewable fuel sources. Nanosensor platforms, sensors with a characteristic dimension that is nanometer in scale, have emerged as important tools for monitoring plant signaling pathways and metabolism that are nondestructive, minimally invasive, and capable of real-time analysis. This review outlines the recent advances in nanotechnology that enable these platforms, including the measurement of chemical fluxes even at the single-molecule level. Applications of nanosensors to plant biology are discussed in the context of nutrient management, disease assessment, food production, detection of DNA proteins, and the regulation of plant hormones. Current trends and future needs are discussed with respect to the emerging trends of precision agriculture, urban farming, and plant nanobionics.

Facile Chip-Based Array Monolithic Microextraction System Online Coupled with ICPMS for Fast Analysis of Trace Heavy Metals in Biological Samples

Trace heavy metals have great impact on biological system; therefore, it is essential to develop suitable analytical methods for the determination of trace heavy metals in biological samples to elucidate their biochemical and physiological functions in organisms. Herein, we presented a chip-based array monolithic microextraction system and combined it with inductively coupled plasma mass spectrometry (ICPMS) for online analysis of trace Hg, Pb, and Bi in real-world biological samples. Six ethylenediamine modified poly(glycidyl methacrylate-co-ethylene glycol dimethacrylate) (poly(GMA-co-EDMA-NH₂)) capillary monolithic columns were embedded parallelly in microchannels of a microfluidic chip for array monolithic microextraction. Various parameters affecting the chip-based array monolithic microextraction of target metals were investigated. The sample throughput of the proposed method was 16 h^-1, with the limits of detection for Hg, Pb, and Bi of 23, 12, and 13 ng L^-1, respectively. The developed method was validated by the determination of trace Hg, Pb, and Bi in HepG2 cells and human urine samples, and the recoveries for the spiked samples were in the range of 90.4-102%. This chip-based array monolithic microextraction system is easy to prepare, and the proposed online analytical system provides a new platform for trace elements analysis in biological samples with the merits of high sample throughput, high sensitivity, and low sample/reagents consumption.

General C-H Arylation Strategy for the Synthesis of Tunable Visible Light-Emitting Benzo[a]imidazo[2,1,5-c,d]indolizine Fluorophores

Herein we report the discovery of the benzo[a]imidazo[2,1,5-c,d]indolizine motif displaying tunable emission covering most of the visible spectrum. The polycyclic core is obtained from readily available amides via a chemoselective process involving Tf₂O-mediated amide cyclodehydration, followed by intramolecular C-H arylation. Additionally, these fluorescent heterocycles are easily functionalized using electrophilic reagents, enabling divergent access to varied substitution. The effects of said substitution on the compounds' photophysical properties were rationalized by density functional theory calculations. For some compounds, emission wavelengths are directly correlated to the substituent's Hammett constants. Easily introduced nonconjugated reactive functional groups allow the labeling of biomolecules without modification of emissive properties. This work provides a straightforward platform for the synthesis of new moderately bright fluorescent dyes remarkable for their chemical stability, predictability, and unusually high excitation-emission differential.

DAPNe with micro-capillary separatory chemistry-coupled to MALDI-MS for the analysis of polar and non-polar lipid metabolism in one cell

The cellular metabolome is considered to be a representation of cellular phenotype and cellular response to changes to internal or external events. Methods to expand the coverage of the expansive physiochemical properties that makeup the metabolome currently utilize multi-step extractions and chromatographic separations prior to chemical detection, leading to lengthy analysis times. In this study, a single-step procedure for the extraction and separation of a sample using a micro-capillary as a separatory funnel to achieve analyte partitioning within an organic/aqueous immiscible solvent system is described. The separated analytes are then spotted for MALDI-MS imaging and distribution ratios are calculated. Initially, the method is applied to standard mixtures for proof of partitioning. The extraction of an individual cell is non-reproducible; therefore, a broad chemical analysis of metabolites is necessary and will be illustrated with the one-cell analysis of a single Snu-5 gastric cancer cell taken from a cellular suspension. The method presented here shows a broad partitioning dynamic range as a single-step method for lipid analysis demonstrating a decrease in ion suppression often present in MALDI analysis of lipids. Graphical Abstract ᅟ.

Bioapplications of Electrochemical Sensors and Biosensors

Recent progress in the electrochemical field enabled development of miniaturized sensing devices that can be used in biological settings to obtain fundamental and practical biochemically relevant information on physiology, metabolism, and disease states in living systems. Electrochemical sensors and biosensors have demonstrated potential for rapid, real-time measurements of biologically relevant molecules. This chapter provides an overview of the most recent advances in the development of miniaturized sensors for biological investigations in living systems, with focus on the detection of neurotransmitters and oxidative stress markers. The design of electrochemical (bio)sensors, including their detection mechanism and functionality in biological systems, is described as well as their advantages and limitations. Application of these sensors to studies in live cells, embryonic development, and rodent models is discussed.

Segmented flow sampling with push-pull theta pipettes

We report development of a mobile and easy-to-fabricate theta pipette microfluidic device for segmented flow sampling. The theta pipettes were also used as electrospray emitters for analysis of sub-nanoliter segments, which resulted in delivery of analyte to the vacuum inlet of the mass spectrometer without multiple transfer steps. Theta pipette probes enable sample collection with high spatial resolution due to micron or smaller sized probe inlets and can be used to manipulate aqueous segments in the range of 200 pL to tens of nanoliters. Optimized conditions can enable sampling with high spatial and temporal resolution, suitable for chemical monitoring in biological samples and studies of sample heterogeneity. Intercellular heterogeneity among Allium cepa cells was studied by collecting cytoplasm from multiple cells using a single probe. Extracted cytoplasm was analyzed in a fast and high throughput manner by direct electrospray mass spectrometry of segmented sample from the probe tip.

A simple metal staining procedure for identification and visualization of single cells by LA-ICP-MS

High lateral resolution of metal detection in single cells by use of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) demands powerful staining methods.