In situ mRNA isolation from a microfluidic single-cell array using an external AFM nanoprobe

Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation

With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.

Nanoscale Methods for Longitudinal Extraction of Intracellular Contents

Longitudinal analysis of intracellular contents including gene and protein expression is crucial for deciphering the fundamentally dynamic nature of cells. This offers invaluable insights into complex tissue composition and behavior, and drives progress in disease diagnosis, biomarker discovery, and drug development. Traditional longitudinal analysis workflows, involving the destruction of cells at various timepoints, limit insights to singular moments and fail to account for cellular heterogeneity. Current non-destructive approaches, like temporal modeling with single-cell ribonucleic acid sequencing (RNA-seq) and live-cell fluorescence imaging, either rely on biological assumptions or possess the risk of cellular perturbation. Recent advances in nanoscale technologies for non-destructive intracellular content extraction offer a promising solution to these challenges. These novel methods work at the nanoscale to non-destructively access cellular membranes and can be broadly classified into three mechanisms: tip-facilitated aspiration, membrane-based, and probe-based methods. This perspective focuses on these emerging nanotechnologies for repeated intracellular content extraction. Their potential in longitudinal analysis is discussed, the critical requirements for effective repeated sampling are addressed, and the suitability of each technique for various applications is explored. Furthermore, unresolved challenges in repeated sampling are highlighted to encourage further research in this growing field.

Massive and efficient encapsulation of single cells in monodisperse droplets and collagen-alginate microgels using a microfluidic device

Single-cell manipulation is the key foundation of life exploration at individual cell resolution. Constructing easy-to-use, high-throughput, and biomimetic manipulative tools for efficient single-cell operation is quite necessary. In this study, a facile and efficient encapsulation of single cells relying on the massive and controllable production of droplets and collagen-alginate microgels using a microfluidic device is presented. High monodispersity and geometric homogeneity of both droplet and microgel generation were experimentally demonstrated based on the well-investigated microfluidic fabricating procedure. The reliability of the microfluidic platform for controllable, high-throughput, and improved single-cell encapsulation in monodisperse droplets and microgels was also confirmed. A single-cell encapsulation rate of up to 33.6% was achieved based on the established microfluidic operation. The introduction of stromal material in droplets/microgels for encapsulation provided single cells an in vivo simulated microenvironment. The single-cell operation achievement offers a methodological approach for developing simple and miniaturized devices to perform single-cell manipulation and analysis in a high-throughput and microenvironment-biomimetic manner. We believe that it holds great potential for applications in precision medicine, cell microengineering, drug discovery, and biosensing.

Microinjection in C. elegans by direct penetration of elastomeric membranes

The nematode worm C. elegans is widely used in basic and translational research. The creation of transgenic strains by injecting DNA constructs into the worm's gonad is an essential step in many C. elegans research projects. This paper describes the fabrication and use of a minimalist microfluidic chip for performing microinjections. The worm is immobilized in a tight-fitting microchannel, one sidewall of which is a thin elastomeric membrane through which the injection pipet penetrates to reach the worm. The pipet is neither broken nor clogged by passing through the membrane, and the membrane reseals when the pipet is withdrawn. Rates of survival and transgenesis are similar to those in the conventional method. Novice users found injections using the device easier to learn than the conventional method. The principle of direct penetration of elastomeric membranes is adaptable to microinjections in a wide range of organisms including cells, embryos, and other small animal models. It could, therefore, lead to a new generation of microinjection systems for basic, translational, and industrial applications.

Semi-Implantable Bioelectronics

Developing techniques to effectively and real-time monitor and regulate the interior environment of biological objects is significantly important for many biomedical engineering and scientific applications, including drug delivery, electrophysiological recording and regulation of intracellular activities. Semi-implantable bioelectronics is currently a hot spot in biomedical engineering research area, because it not only meets the increasing technical demands for precise detection or regulation of biological activities, but also provides a desirable platform for externally incorporating complex functionalities and electronic integration. Although there is less definition and summary to distinguish it from the well-reviewed non-invasive bioelectronics and fully implantable bioelectronics, semi-implantable bioelectronics have emerged as highly unique technology to boost the development of biochips and smart wearable device. Here, we reviewed the recent progress in this field and raised the concept of "Semi-implantable bioelectronics", summarizing the principle and strategies of semi-implantable device for cell applications and in vivo applications, discussing the typical methodologies to access to intracellular environment or in vivo environment, biosafety aspects and typical applications. This review is meaningful for understanding in-depth the design principles, materials fabrication techniques, device integration processes, cell/tissue penetration methodologies, biosafety aspects, and applications strategies that are essential to the development of future minimally invasive bioelectronics.

Polarity-Specific Profiling of Metabolites in Single Cells by Probe Electrophoresis Mass Spectrometry

Sensitive analysis of metabolites in a single cell is of fundamental significance for the better understanding of biological variability, differential susceptibility in disease therapy, and cell-to-cell heterogeneity as well. Herein, polarity-specific profiling of metabolites in a single cell was implemented by probe electrophoresis mass spectrometry (PEMS), which combined electrophoresis sampling of metabolites from a single cell and nanoelectrospray ionization-mass spectrometry (nanoESI-MS) analysis of the sampled metabolites. Enhanced extraction of either negatively or positively charged metabolites from a single cell was achieved by applying a DC voltage offset of +2.0 and -2.0 V to the probe, respectively. The experimental data demonstrated that PEMS features high throughput (≥200 peaks) and high sensitivity (≥10-times signal enhancement for [Choline + H]⁺, [Glutamine + H]⁺, [Arginine + H]⁺, etc.) in comparison with direct nanoESI-MS analysis. The biological effects of CdSe quantum dots (QDs) and γ-radiation on Allium cepa cells were investigated by PEMS, which revealed that CdSe QDs lead to the increase of intracellular amines while γ-radiation causes the decrease of intracellular acids. Therefore, this work provides an alternative platform to probe novel insights of cells by sensitive analysis of polarity-specific metabolites in a single cell.

Microfluidics and surface-enhanced Raman spectroscopy, a win-win combination?

With the continuous development in nanoscience and nanotechnology, analytical techniques like surface-enhanced Raman spectroscopy (SERS) render structural and chemical information of a variety of analyte molecules in ultra-low concentration. Although this technique is making significant progress in various fields, the reproducibility of SERS measurements and sensitivity towards small molecules are still daunting challenges. In this regard, microfluidic surface-enhanced Raman spectroscopy (MF-SERS) is well on its way to join the toolbox of analytical chemists. This review article explains how MF-SERS is becoming a powerful tool in analytical chemistry. We critically present the developments in SERS substrates for microfluidic devices and how these substrates in microfluidic channels can improve the SERS sensitivity, reproducibility, and detection limit. We then introduce the building materials for microfluidic platforms and their types such as droplet, centrifugal, and digital microfluidics. Finally, we enumerate some challenges and future directions in microfluidic SERS. Overall, this article showcases the potential and versatility of microfluidic SERS in overcoming the inherent issues in the SERS technique and also discusses the advantage of adding SERS to the arsenal of microfluidics.

In Situ Single-Cell Surgery and Intracellular Organelle Manipulation Via Thermoplasmonics Combined Optical Trapping

Microsurgery and biopsies on individual cells in a cellular microenvironment are of great importance to better understand the fundamental cellular processes at subcellular and even single-molecular levels. However, it is still a big challenge for in situ surgery without interfering with neighboring living cells. Here, we report a thermoplasmonics combined optical trapping (TOT) technique for in situ single-cell surgery and intracellular organelle manipulation, without interfering with neighboring cells. A selective single-cell perforation was demonstrated via a localized thermoplasmonic effect, which facilitated further targeted gene delivery. Such a perforation was reversible, and the damaged membrane was capable of being repaired. Remarkably, a targeted extraction and precise manipulation of intracellular organelles were realized via the optical trapping. This TOT technique represents a new way for single-cell microsurgery, gene delivery, and intracellular organelle manipulation, and it provides a new insight for a deeper understanding of cellular processes as well as to reveal underlying causes of diseases associated with organelle malfunctions at a subcellular level.

Topography and Permeability Analyses of Vasculature-on-a-Chip Using Scanning Probe Microscopies

Microphysiological systems (MPS) or organs-on-chips (OoC) can emulate the physiological functions of organs in vitro and are effective tools for determining human drug responses in preclinical studies. However, the analysis of MPS has relied heavily on optical tools, resulting in difficulties in real-time and high spatial resolution imaging of the target cell functions. In this study, the role of scanning probe microscopy (SPM) as an analytical tool for MPS is evaluated. An access hole is made in a typical MPS system with stacked microchannels to insert SPM probes into the system. For the first study, a simple vascular model composed of only endothelial cells is prepared for SPM analysis. Changes in permeability and local chemical flux are quantitatively evaluated during the construction of the vascular system. The morphological changes in the endothelial cells after flow stimulation are imaged at the single-cell level for topographical analysis. Finally, the possibility of adapting the permeability and topographical analysis using SPM for the intestinal vascular system is further evaluated. It is believed that this study will pave the way for an in situ permeability assay and structural analysis of MPS using SPM.

Recent advances in dielectrophoresis toward biomarker detection: A summary of studies published between 2014 and 2021

Dielectrophoresis is a well-understood phenomenon that has been widely utilized in biomedical applications. Recent advancements in miniaturization have contributed to the development of dielectrophoretic-based devices for a wide variety of biomedical applications. In particular, the integration of dielectrophoresis with microfluidics, fluorescence, and electrical impedance has produced devices and techniques that are attractive for screening and diagnosing diseases. This review article summarizes the recent utility of dielectrophoresis in assays of biomarker detection. Common screening and diagnostic biomarkers, such as cellular, protein, and nucleic acid, are discussed. Finally, the potential use of recent developments in machine learning approaches toward improving biomarker detection performance is discussed. This review article will be useful for researchers interested in the recent utility of dielectrophoresis in the detection of biomarkers and for those developing new devices to address current gaps in dielectrophoretic biomarker detection.

Photo-assembly of plasmonic nanoparticles: methods and applications

In this review article, various methods for the light-induced manipulation of plasmonic nanoobjects are described, and some sample applications of this process are presented. The methods of the photo-induced nanomanipulation analyzed include methods based on: the light-induced isomerization of some compounds attached to the surface of the manipulated object causing formation of electrostatic, host-guest or covalent bonds or other structural changes, the photo-response of a thermo-responsive material attached to the surface of the manipulated nanoparticles, and the photo-catalytic process enhanced by the coupled plasmons in manipulated nanoobjects. Sample applications of the process of the photo-aggregation of plasmonic nanosystems are also presented, including applications in surface-enhanced vibrational spectroscopies, catalysis, chemical analysis, biomedicine, and more. A detailed comparative analysis of the methods that have been applied so far for the light-induced manipulation of nanostructures may be useful for researchers planning to enter this fascinating field.

Nanofountain Probe Electroporation Enables Versatile Single-Cell Intracellular Delivery and Investigation of Postpulse Electropore Dynamics

Introducing exogenous molecules into cells with high efficiency and dosage control is a crucial step in basic research as well as clinical applications. Here, the capability of the nanofountain probe electroporation (NFP-E) system to deliver proteins and plasmids in a variety of continuous and primary cell types with appropriate dosage control is reported. It is shown that the NFP-E can achieve fine control over the relative expression of two cotransfected plasmids. Finally, the dynamics of electropore closure after the pulsing ends with the NFP-E is investigated. Localized electroporation has recently been utilized to demonstrate the converse process of delivery (sampling), in which a small volume of the cytosol is retrieved during electroporation without causing cell lysis. Single-cell temporal sampling confers the benefit of monitoring the same cell over time and can provide valuable insights into the mechanisms underlying processes such as stem cell differentiation and disease progression. NFP-E parameters that maximize the membrane resealing time, which is essential for increasing the sampled volume and in meeting the challenge of monitoring low copy number biomarkers, are identified. Its application in CRISPR/Cas9 gene editing, stem cell reprogramming, and single-cell sampling studies is envisioned.

Advances in Microfluidics-Based Technologies for Single Cell Culture

Single cell culture has been considered one of the fundamental tools for single cell studies. Complex biological systems evolve from single cells, and the cells within biological systems are intrinsically heterogeneous. Therefore, culturing and understanding the behaviors of single cells are of great interest for both biological research and clinical studies. In recent years, advances in microfluidics-based technologies have demonstrated unprecedented capabilities for single cell studies, and they have made high-throughput single cell cultures possible. Microfluidic systems enable precise control of the microenvironment for single cell culture and monitoring of the behavior of single cells in real time. In addition, microfluidic devices can consist of upstream cell sorting and cell isolation, and they can also be seamlessly integrated with various downstream analysis methods. Therefore, microfluidic technologies can obtain data about the performance at the single-cell level, providing information that cannot be achieved by studying the ensemble behavior of cell colonies. In this review, the recent developments in droplet-based microfluidics, microwell-based microfluidics, trap-based microfluidics and SlipChip-based microfluidics for the study of single cell culture is focused on. Perspectives on future improvement regarding single cell culture and its related research opportunities are also provided.

Technological Advances in Multiscale Analysis of Single Cells in Biomedicine

Single-cell analysis has recently received significant attention in biomedicine. With the advances in super-resolution microscopy, fluorescence labeling, and nanoscale biosensing, new information may be obtained for the design of cancer diagnosis and therapeutic interventions. The discovery of cellular heterogeneity further stresses the importance of single-cell analysis to improve our understanding of disease mechanism and to develop new strategies for disease treatment. To this end, many studies are exploited at the single-cell level for high throughput, highly parallel, and quantitative analysis. Technically, microfluidics are also designed to facilitate single-cell isolation and enrichment for downstream detection and manipulation in a robust, sensitive, and automated manner. Further achievements are made possible by consolidating optically label-free, electrical, and molecular sensing techniques. Moreover, these technologies are coupled with computing algorithms for high throughput and automated quantitative analysis with a short turnaround time. To reflect on how the technological developments have advanced single-cell analysis, this mini-review is aimed to offer readers an introduction to single-cell analysis with a brief historical development and the recent progresses that have enabled multiscale analysis of single-cells in the last decade. The challenges and future trends are also discussed with the view to inspire forthcoming technical developments.

Lab-on-a-chip Dielectrophoretic Manipulation of Beta-2 Microglobulin for Toxin Removal in An Artificial Kidney

Background:

This paper presents a fundamental study of protein manipulation under the influence of dielectrophoretic (DEP) force for a lab-on-a-chip platform.

Objective:

Protein manipulation is dependent on the polarisation factor of protein when exposed to an electric field. Therefore the objective of this work is a microfluidic device and measurement system are used to characterise the human beta-2 microglobulin (β2M) protein via lateral attractive forces and vertical repulsive forces by means of DEP responses.

Method:

The manipulation of the β2M protein was conducted using a microfluidic platform with a tapered DEP microelectrode and the protein concentration was quantified based on a biochemical interaction using an Enzyme-Linked Immunosolvent Assay (ELISA). The protein distribution has been analysed based on the β2M concentration for each microfluidic outlet.

Results:

At 300 kHz, the protein experienced a negative DEP (nDEP) with of 83.3% protein distribution on the middle microchannel. In contrast, the protein experienced a positive DEP (pDEP) at 1.2 MHz with of 78.7% of protein on the left and right sides of the microchannel.

Conclusion:

This is concept proved that the tapered DEP microelectrode is capable of manipulating a β2M via particle polarisation, hence making it suitable to be utilised for purifying proteins in biomedical application.

Dielectrophoresis velocities response on tapered electrode profile: simulation and experimental

Purpose

The purpose of this paper is to use a particle velocity measurement technique on a tapered microelectrode device via changes of an applied voltage, which is an enhancement of the electric field density in influencing the dipole moment particles. Polystyrene microbeads (PM) have used to determine the responses of the dielectrophoresis (DEP) voltage based on the particle velocity technique.

Design/methodology/approach

Analytical modelling was used to simulate the particles’ polarization and their velocity based on the Clausius–Mossotti Factor (CMF) equation. The electric field intensity and DEP forces were simulated through the COMSOL numerical study of the variation of applied voltages such as 5 V p-p, 7 V p-p and 10 V p-p. Experimentally, the particle velocity on a tapered DEP response was quantified via the particle travelling distance over a time interval through a high-speed camera adapted to a high-precision non-contact depth measuring microscope.

Findings

The result of the particle velocity was found to increase, and the applied voltage has enhanced the particle trajectory on the tapered microelectrode, which confirmed its dependency on the electric field intensity at the top and bottom edges of the electrode. A higher magnitude of particle levitation was recorded with the highest particle velocity of 11.19 ± 4.43 µm/s at 1 MHz on 10 V p-p, compared to the lowest particle velocity with 0.62 ± 0.11 µm/s at 10 kHz on 7 V p-p.

Practical implications

This research can be applied for high throughout sensitivity and selectivity of particle manipulation in isolating and concentrating biological fluid for biomedical implications.

Originality/value

The comprehensive manipulation method based on the changes of the electrical potential of the tapered electrode was able to quantify the magnitude of the particle trajectory in accordance with the strong electric field density.

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 microfluidic single-cell trapping arrays for biomolecular and imaging analysis

Single-cell analysis is of critical importance in revealing population heterogeneity, identifying minority sub-populations of interest, as well as discovering unique characteristics of individual cells. Microfluidic platforms work at the scale comparable to cell diameter and is suitable for single-cell manipulation. Here we present a microfluidic trapping array which is able to rapidly and deterministically trap single-cells in highly-packed microwells. This chapter first describes the design and fabrication protocols of the trapping array, and then presents its two representative applications: single-cell mRNA probing when integrated with a dielectrophoretic nanotweezer (DENT), and live-cell real-time imaging when combined with fluorescence lifetime imaging microscopy (FLIM). As the single-cell trapping efficiency is determined by the channel design instead of the flow rate, this trapping array can be coupled with different microfluidic sample processing units with different flow rates for various single-cell analyses.

An integrated microfluidic platform for size-selective single-cell trapping of monocytes from blood

Reliable separation and isolation of target single cells from bodily fluids with high purity is of great significance for an accurate and quantitative understanding of the cellular heterogeneity. Here, we describe a fully integrated single-blood-cell analysis platform capable of size-selective cell separation from a population containing a wide distribution of sizes such as diluted blood sample and highly efficient entrapment of single monocytes. The spiked single U937 cells (human monocyte cell line) are separated in sequence by two different-sized microfilters for removing large cell clumps, white blood cells, and red blood cells and then discriminated by dielectrophoretic force and isolated individually by downstream single-cell trapping arrays. When 2% hematocrit blood cells with a final ratio of 1:1000 U937 cells were introduced under the flow rate of 0.2 ml/h, 400 U937 cells were trapped sequentially and deterministically within 40 s with single-cell occupancy of up to 85%. As a proof-of-concept, we also demonstrated single monocyte isolation from diluted blood using the integrated microfluidic device. This size-selective, label-free, and live-cell enrichment microfluidic single blood-cell isolation platform for the processing of cancer and blood cells has a myriad of applications in areas such as single-cell genetic analysis, stem cell biology, point-of-care diagnostics, and cancer diagnostics.

Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology

Examining the behavior of a single cell within its natural environment is valuable for understanding both the biological processes that control the function of cells and how injury or disease lead to pathological change of their function. Single-cell analysis can reveal information regarding the causes of genetic changes, and it can contribute to studies on the molecular basis of cell transformation and proliferation. By contrast, whole tissue biopsies can only yield information on a statistical average of several processes occurring in a population of different cells. Electrowetting within a nanopipette provides a nanobiopsy platform for the extraction of cellular material from single living cells. Additionally, functionalized nanopipette sensing probes can differentiate analytes based on their size, shape or charge density, making the technology uniquely suited to sensing changes in single-cell dynamics. In this review, we highlight the potential of nanopipette technology as a non-destructive analytical tool to monitor single living cells, with particular attention to integration into applications in molecular biology.

Progress of Inertial Microfluidics in Principle and Application

Inertial microfluidics has become a popular topic in microfluidics research for its good performance in particle manipulation and its advantages of simple structure, high throughput, and freedom from an external field. Compared with traditional microfluidic devices, the flow field in inertial microfluidics is between Stokes state and turbulence, whereas the flow is still regarded as laminar. However, many mechanical effects induced by the inertial effect are difficult to observe in traditional microfluidics, making particle motion analysis in inertial microfluidics more complicated. In recent years, the inertial migration effect in straight and curved channels has been explored theoretically and experimentally to realize on-chip manipulation with extensive applications from the ordinary manipulation of particles to biochemical analysis. In this review, the latest theoretical achievements and force analyses of inertial microfluidics and its development process are introduced, and its applications in circulating tumor cells, exosomes, DNA, and other biological particles are summarized. Finally, the future development of inertial microfluidics is discussed. Owing to its special advantages in particle manipulation, inertial microfluidics will play a more important role in integrated biochips and biomolecule analysis.

Rapid and label-free identification of single leukemia cells from blood in a high-density microfluidic trapping array by fluorescence lifetime imaging microscopy

The rapid screening and isolation of single leukemia cells from blood has become critical for early leukemia detection and tumor heterogeneity interrogation. However, due to the size overlap between leukemia cells and the more abundant white blood cells (WBCs), the isolation and identification of leukemia cells individually from peripheral blood is extremely challenging and often requires immunolabeling or cytogenetic assays. Here we present a rapid and label-free single leukemia cell identification platform that combines: (1) high-throughput size-based separation of hemocytes via a single-cell trapping array, and (2) leukemia cell identification through phasor approach and fluorescence lifetime imaging microscopy (phasor-FLIM), to quantify changes between free/bound nicotinamide adenine dinucleotide (NADH) as an indirect measurement of metabolic alteration in living cells. The microfluidic trapping array designed with 1600 highly-packed addressable single-cell traps can simultaneously filter out red blood cells (RBCs) and trap WBCs/leukemia cells, and is compatible with low-magnification imaging and fast-speed fluorescence screening. The trapped single leukemia cells, e.g., THP-1, Jurkat and K562 cells, are distinguished from WBCs in the phasor-FLIM lifetime map, as they exhibit significant shift towards shorter fluorescence lifetime and a higher ratio of free/bound NADH compared to WBCs, because of their glycolysis-dominant metabolism for rapid proliferation. Based on a multiparametric scheme comparing the eight parameter-spectra of the phasor-FLIM signatures, spiked leukemia cells are quantitatively distinguished from normal WBCs with an area-under-the-curve (AUC) value of 1.00. Different leukemia cell lines are also quantitatively distinguished from each other with AUC values higher than 0.95, demonstrating high sensitivity and specificity for single cell analysis. The presented platform is the first to enable high-density size-based single-cell trapping simultaneously with RBC filtering and rapid label-free individual-leukemia-cell screening through non-invasive metabolic imaging. Compared to conventional biomolecular diagnostics techniques, phasor-FLIM based single-cell screening is label-free, cell-friendly, robust, and has the potential to screen blood in clinical volumes through parallelization.