On‐Demand Droplet Collection for Capturing Single Cells

Droplet‐based microfluidic techniques are extensively used in efficient manipulation and genome‐wide analysis of individual cells, probing the heterogeneity among populations of individuals. However, the extraction and isolation of single cells from individual droplets remains difficult due to the inevitable sample loss during processing. Herein, an automated system for accurate collection of defined numbers of droplets containing single cells is presented. Based on alternate sorting and dispensing in three branch channels, the droplet number can be precisely controlled down to single‐droplet resolution. While encapsulating single cells and reserving one branch as a waste channel, sorting can be seamlessly integrated to enable on‐demand collection of single cells. Combined with a lossless recovery strategy, this technique achieves capture and culture of individual cells with a harvest rate of over 95%. The on‐demand droplet collection technique has great potential to realize quantitative processing and analysis of single cells for elucidating the role of cell‐to‐cell variations.     

A Microfabricated Sandwiching Assay for Nanoliter and High‐Throughput Biomarker Screening

Cells secrete substances that are essential to the understanding of numerous immunological phenomena and are extensively used in clinical diagnoses. Countless techniques for screening of biomarker secretion in living cells have generated valuable information on cell function and physiology, but low volume and real‐time analysis is a bottleneck for a range of approaches. Here, a simple, highly sensitive assay using a high‐throughput micropillar and microwell array chip (MIMIC) platform is presented for monitoring of biomarkers secreted by cancer cells. The sensing element is a micropillar array that uses the enzyme‐linked immunosorbent assay (ELISA) mechanism to detect captured biomolecules. When integrated with a microwell array where few cells are localized, interleukin 8 (IL‐8) secretion can be monitored with nanoliter volume using multiple micropillar arrays. The trend of cell secretions measured using MIMICs matches the results from conventional ELISA well while it requires orders of magnitude less cells and volumes. Moreover, the proposed MIMIC is examined to be used as a drug screening platform by delivering drugs using micropillar arrays in combination with a microfluidic system and then detecting biomolecules from cells as exposed to drugs.     

Biotinylated Photopolymers for 3D‐Printed Unibody Lab‐on‐a‐Chip Optical Platforms

The present work reports the first demonstration of straightforward fabrication of monolithic unibody lab‐on‐a‐chip (ULOCs) integrating bioactive micrometric 3D scaffolds by means of multimaterial stereolithography (SL). To this end, a novel biotin‐conjugated photopolymer is successfully synthesized and optimally formulated to achieve high‐performance SL‐printing resolution, as demonstrated by the SL‐fabrication of biotinylated structures smaller than 100 µm. By optimizing a multimaterial single‐run SL‐based 3D‐printing process, such biotinylated microstructures are incorporated within perfusion microchambers whose excellent optical transparency enables real‐time optical microscopy analyses. Standard biotin‐binding assays confirm the existence of biotin‐heads on the surfaces of the embedded 3D microstructures and allow to demonstrate that the biofunctionality of biotin is not altered during the SL‐printing, thus making it exploitable for further conjugation with other biomolecules. As a step forward, an in‐line optical detection system is designed, prototyped via SL‐printing and serially connected to the perfusion microchambers through customized world‐to‐chip connectors. Such detection system is successfully employed to optically analyze the solution flowing out of the microchambers, thus enabling indirect quantification of the concentration of target interacting biomolecules. The successful application of this novel biofunctional photopolymer as SL‐material enables to greatly extend the versatility of SL to directly fabricate ULOCs with intrinsic biofunctionality.     

Combining Whispering‐Gallery Mode Optical Biosensors with Microfluidics for Real‐Time Detection of Protein Secretion from Living Cells in Complex Media

The noninvasive monitoring of protein secretion of cells responding to drug treatment is an effective and essential tool in latest drug development and for cytotoxicity assays. In this work, a surface functionalization method is demonstrated for specific detection of protein released from cells and a platform that integrates highly sensitive optical devices, called whispering‐gallery mode biosensors, with precise microfluidics control to achieve label‐free and real‐time detection. Cell biomarker release is measured in real time and with nanomolar sensitivity. The surface functionalization method allows for antibodies to be immobilized on the surface for specific detection, while the microfluidics system enables detection in a continuous flow with a negligible compromise between sensitivity and flow control over stabilization and mixing. Cytochrome c detection is used to illustrate the merits of the system. Jurkat cells are treated with the toxin staurosporine to trigger cell apoptosis and cytochrome c released into the cell culture medium is monitored via the newly invented optical microfluidic platform.     

Stochastic Particle Barcoding for Single‐Cell Tracking and Multiparametric Analysis

This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co‐encapsulated within an enzymatically‐degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single‐cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re‐identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.     

Inertial Microfluidic Cell Stretcher (iMCS): Fully Automated,High‐Throughput,and Near Real‐Time Cell Mechanotyping

Mechanical biomarkers associated with cytoskeletal structures have been reported as powerful label‐free cell state identifiers. In order to measure cell mechanical properties, traditional biophysical (e.g., atomic force microscopy, micropipette aspiration, optical stretchers) and microfluidic approaches were mainly employed; however, they critically suffer from low‐throughput, low‐sensitivity, and/or time‐consuming and labor‐intensive processes, not allowing techniques to be practically used for cell biology research applications. Here, a novel inertial microfluidic cell stretcher (iMCS) capable of characterizing large populations of single‐cell deformability near real‐time is presented. The platform inertially controls cell positions in microchannels and deforms cells upon collision at a T‐junction with large strain. The cell elongation motions are recorded, and thousands of cell deformability information is visualized near real‐time similar to traditional flow cytometry. With a full automation, the entire cell mechanotyping process runs without any human intervention, realizing a user friendly and robust operation. Through iMCS, distinct cell stiffness changes in breast cancer progression and epithelial mesenchymal transition are reported, and the use of the platform for rapid cancer drug discovery is shown as well. The platform returns large populations of single‐cell quantitative mechanical properties (e.g., shear modulus) on‐the‐fly with high statistical significances, enabling actual usages in clinical and biophysical studies.     

Phenome–Genome Profiling of Single Bacterial Cell by Raman‐Activated Gravity‐Driven Encapsulation and Sequencing

The small size and low DNA amount of bacterial cells have hindered establishing phenome–genome links in a precisely indexed, one‐cell‐per‐reaction manner. Here, Raman‐Activated Gravity‐driven single‐cell Encapsulation and Sequencing (RAGE‐Seq) is presented, where individual cells are phenotypically screened via single‐cell Raman spectra (SCRS) in an aquatic, vitality‐preserving environment, then the cell with targeted SCRS is precisely packaged in a picoliter microdroplet and readily exported in a precisely indexed, “one‐cell‐one‐tube” manner. Such integration of microdroplet encapsulation to Raman‐activated sorting ensures high‐coverage one‐cell genome sequencing or cultivation that is directly linked to metabolic phenotype. For clinical Escherichia coli isolates, genome assemblies derived from precisely one cell via RAGE‐Seq consistently reach >95% coverage. Moreover, directly from a urine sample of urogenital tract infection, metabolic‐activity‐based antimicrobial susceptibility phenotypes and genome sequence of 99.5% coverage are obtained simultaneously from precisely one cell. This single‐cell global mutation map corroborates resistance phenotype and genotype, and unveils epidemiological features with high specificity and sensitivity. The ability to profile and correlate bacterial metabolic phenome and high‐quality genome sequences at one‐cell resolution suggests broad application of RAGE‐Seq.     

DNA Nanotweezers and Graphene Transistor Enable Label‐Free Genotyping

Electronic DNA‐biosensor with a single nucleotide resolution capability is highly desirable for personalized medicine. However, existing DNA‐biosensors, especially single nucleotide polymorphism (SNP) detection systems, have poor sensitivity and specificity and lack real‐time wireless data transmission. DNA‐tweezers with graphene field effect transistor (FET) are used for SNP detection and data are transmitted wirelessly for analysis. Picomolar sensitivity of quantitative SNP detection is achieved by observing changes in Dirac point shift and resistance change. The use of DNA‐tweezers probe with high‐quality graphene FET significantly improves analytical characteristics of SNP detection by enhancing the sensitivity more than 1000‐fold in comparison to previous work. The electrical signal resulting from resistance changes triggered by DNA strand‐displacement and related changes in the DNA geometry is recorded and transmitted remotely to personal electronics. Practical implementation of this enabling technology will provide cheaper, faster, and portable point‐of‐care molecular health status monitoring and diagnostic devices.     

Plasmonic‐Nanopore Biosensors for Superior Single‐Molecule Detection

Plasmonic and nanopore sensors have separately received much attention for achieving single‐molecule precision. A plasmonic “hotspot” confines and enhances optical excitation at the nanometer length scale sufficient to optically detect surface–analyte interactions. A nanopore biosensor actively funnels and threads analytes through a molecular‐scale aperture, wherein they are interrogated by electrical or optical means. Recently, solid‐state plasmonic and nanopore structures have been integrated within monolithic devices that address fundamental challenges in each of the individual sensing methods and offer complimentary improvements in overall single‐molecule sensitivity, detection rates, dwell time and scalability. Here, the physical phenomena and sensing principles of plasmonic and nanopore sensing are summarized to highlight the novel complementarity in dovetailing these techniques for vastly improved single‐molecule sensing. A literature review of recent plasmonic nanopore devices is then presented to delineate methods for solid‐state fabrication of a range of hybrid device formats, evaluate the progress and challenges in the detection of unlabeled and labeled analyte, and assess the impact and utility of localized plasmonic heating. Finally, future directions and applications inspired by the present state of the art are discussed.     

Single Upconversion Nanoparticle–Bacterium Cotrapping for Single‐Bacterium Labeling and Analysis

Detecting and analyzing pathogenic bacteria in an effective and reliable manner is crucial for the diagnosis of acute bacterial infection and initial antibiotic therapy. However, the precise labeling and analysis of bacteria at the single‐bacterium level are a technical challenge but very important to reveal important details about the heterogeneity of cells and responds to environment. This study demonstrates an optical strategy for single‐bacterium labeling and analysis by the cotrapping of single upconversion nanoparticles (UCNPs) and bacteria together. A single UCNP with an average size of ≈120 nm is first optically trapped. Both ends of a single bacterium are then trapped and labeled with single UCNPs emitting green light. The labeled bacterium can be flexibly moved to designated locations for further analysis. Signals from bacteria of different sizes are detected in real time for single‐bacterium analysis. This cotrapping method provides a new approach for single‐pathogenic‐bacterium labeling, detection, and real‐time analysis at the single‐particle and single‐bacterium level.     

A Single‐Cell Assay for Time Lapse Studies of Exosome Secretion and Cell Behaviors

To understand the inhomogeneity of cells in biological systems, there is a growing demand on the capability of characterizing the properties of individual single cells. Since single‐cell studies require continuous monitoring of the cell behaviors, an effective single‐cell assay that can support time lapsed studies in a high throughput manner is desired. Most currently available single‐cell technologies cannot provide proper environments to sustain cell growth and, proliferation of single cells and convenient, noninvasive tests of single‐cell behaviors from molecular markers. Here, a highly versatile single‐cell assay is presented that can accommodate different cellular types, enable easy and efficient single‐cell loading and culturing, and be suitable for the study of effects of in vitro environmental factors in combination with drug screening. One salient feature of the assay is the noninvasive collection and surveying of single‐cell secretions at different time points, producing unprecedented insight of single‐cell behaviors based on the biomarker signals from individual cells under given perturbations. Above all, the acquired information is quantitative, for example, measured by the number of exosomes each single‐cell secretes for a given time period. Therefore, our single‐cell assay provides a convenient, low‐cost, and enabling tool for quantitative, time lapsed studies of single‐cell properties.     

Real‐time ballistocardiographic artifact reduction using the k‐teager energy operator detector and multi‐channel referenced adaptive noise cancelling

The simultaneous electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) recording technique has recently received considerable attention and has been used in many studies on cognition and neurological disease. EEG‐fMRI simultaneous recording has the advantage of enabling the monitoring of brain activity with both high temporal resolution and high spatial resolution in real time. The successful removal of the ballistocardiographic (BCG) artifact from the EEG signal recorded during an MRI is an important prerequisite for real‐time EEG‐fMRI joint analysis. We have developed a new framework dedicated to BCG artifact removal in real‐time. This framework includes a new real‐time R‐peak detection method combining a k‐Teager energy operator, a thresholding detector, and a correlation detector, as well as a real‐time BCG artifact reduction procedure combining average artifact template subtraction and a new multi‐channel referenced adaptive noise cancelling method. Our results demonstrate that this new framework is efficient in the real‐time removal of the BCG artifact. The multi‐channel adaptive noise cancellation (mANC) method performs better than the traditional ANC method in eliminating the BCG residual artifact. In addition, the computational speed of the mANC method fulfills the requirements of real‐time EEG‐fMRI analysis. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 209–215, 2016     

Single‐Cell Detection of mRNA Expression Using Nanofountain‐Probe Electroporated Molecular Beacons

New techniques for single‐cell analysis enable new discoveries in gene expression and systems biology. Time‐dependent measurements on individual cells are necessary, yet the common single‐cell analysis techniques used today require lysing the cell, suspending the cell, or long incubation times for transfection, thereby interfering with the ability to track an individual cell over time. Here a method for detecting mRNA expression in live single cells using molecular beacons that are transfected into single cells by means of nanofountain probe electroporation (NFP‐E) is presented. Molecular beacons are oligonucleotides that emit fluorescence upon binding to an mRNA target, rendering them useful for spatial and temporal studies of live cells. The NFP‐E is used to transfect a DNA‐based beacon that detects glyceraldehyde 3‐phosphate dehydrogenase and an RNA‐based beacon that detects a sequence cloned in the green fluorescence protein mRNA. It is shown that imaging analysis of transfection and mRNA detection can be performed within seconds after electroporation and without disturbing adhered cells. In addition, it is shown that time‐dependent detection of mRNA expression is feasible by transfecting the same single cell at different time points. This technique will be particularly useful for studies of cell differentiation, where several measurements of mRNA expression are required over time.     

Strategic Advances in Formation of Cell‐in‐Shell Structures: From Syntheses to Applications

Single‐cell nanoencapsulation, forming cell‐in‐shell structures, provides chemical tools for endowing living cells, in a programmed fashion, with exogenous properties that are neither innate nor naturally achievable, such as cascade organic‐catalysis, UV filtration, immunogenic shielding, and enhanced tolerance in vitro against lethal factors in real‐life settings. Recent advances in the field make it possible to further fine‐tune the physicochemical properties of the artificial shells encasing individual living cells, including on‐demand degradability and reconfigurability. Many different materials, other than polyelectrolytes, have been utilized as a cell‐coating material with proper choice of synthetic strategies to broaden the potential applications of cell‐in‐shell structures to whole‐cell catalysis and sensors, cell therapy, tissue engineering, probiotics packaging, and others. In addition to the conventional “one‐time‐only” chemical formation of cytoprotective, durable shells, an approach of autonomous, dynamic shellation has also recently been attempted to mimic the naturally occurring sporulation process and to make the artificial shell actively responsive and dynamic. Here, the recent development of synthetic strategies for formation of cell‐in‐shell structures along with the advanced shell properties acquired is reviewed. Demonstrated applications, such as whole‐cell biocatalysis and cell therapy, are discussed, followed by perspectives on the field of single‐cell nanoencapsulation.     

A Droplet‐Based High‐Throughput SERS Platform on a Droplet‐Guiding‐Track‐Engraved Superhydrophobic Substrate

A novel droplet‐based surface‐enhanced Raman scattering (SERS) sensor for high‐throughput real‐time SERS monitoring is presented. The developed sensors are based on a droplet‐guiding‐track‐engraved superhydrophobic substrate covered with hierarchical SERS‐active Ag dendrites. The droplet‐guiding track with a droplet stopper is designed to manipulate the movement of a droplet on the superhydrophobic substrate. The superhydrophobic Ag dendritic substrates are fabricated through a galvanic displacement reaction and subsequent self‐assembled monolayer coating. The optimal galvanic reaction time to fabricate a SERS‐active Ag dendritic substrate for effective SERS detection is determined, with the optimized substrate exhibiting an enhancement factor of 6.3 × 10⁵. The height of the droplet stopper is optimized to control droplet motion, including moving and stopping. Based on the manipulation of individual droplets, the optimized droplet‐based real‐time SERS sensor shows high resistance to surface contaminants, and droplets containing rhodamine 6G, Nile blue A, and malachite green are successively controlled and detected without spectral interference. This noble droplet‐based SERS sensor reduces sample preparation time to a few seconds and increased detection rate to 0.5 µ L s^?1 through the simple operation mechanism of the sensor. Accordingly, our sensor enables high‐throughput real‐time molecular detection of various target analytes for real‐time chemical and biological monitoring.     

A Bioresponsive Near‐Infrared Fluorescent Probe for Facile and Persistent Live‐Cell Tracking

Molecular imaging significantly transforms the field of biomedical science and facilitates the visualization, characterization, and quantification of biologic processes. However, it is still challenging to monitor cell localization in vivo, which is essential to the study of tumor metastasis and in the development of cell‐based therapies. While most conventional small‐molecule fluorescent probes cannot afford durable cell labeling, transfection of cells with fluorescent proteins is limited by their fixed fluorescence, poor tissue penetration, and interference of autofluorescence background. Here, a bioresponsive near‐infrared fluorescent probe is reported as facile and reliable tool for real‐time cell tracking in vivo. The design of this probe relies on a new phenomenon observed upon fluorobenzene‐conjugated fluorescent dyes, which can form complexes with cytosolic glutathione and actively translocates to lysosomes, exhibiting enhanced and stable cell labeling. Fluorobenzene‐coupled hemicyanine, a near‐infrared fluorophore manifests to efficiently staining tumor cells without affecting their invasive property and enables persistent monitoring of cell migration in metastatic tumor murine models at high resolution for one week. The method of fluorobenzene functionalization also provides a simple and universal “add‐on” strategy to render ordinary fluorescent probes suitable for long‐term live‐cell tracking, for which currently there is a deficit of suitable molecular tools.     

CMOS‐Compatible Silicon Nanowire Field‐Effect Transistors for Ultrasensitive and Label‐Free MicroRNAs Sensing

MicroRNAs (miRNAs) have been regarded as promising biomarkers for the diagnosis and prognosis of early‐stage cancer as their expression levels are associated with different types of human cancers. However, it is a challenge to produce low‐cost miRNA sensors, as well as retain a high sensitivity, both of which are essential factors that must be considered in fabricating nanoscale biosensors and in future biomedical applications. To address such challenges, we develop a complementary metal oxide semiconductor (CMOS)‐compatible SiNW‐FET biosensor fabricated by an anisotropic wet etching technology with self‐limitation which provides a much lower manufacturing cost and an ultrahigh sensitivity. This nanosensor shows a rapid (< 1 minute) detection of miR‐21 and miR‐205, with a low limit of detection (LOD) of 1 zeptomole (ca. 600 copies), as well as an excellent discrimination for single‐nucleotide mismatched sequences of tumor‐associated miRNAs. To investigate its applicability in real settings, we have detected miRNAs in total RNA extracted from lung cancer cells as well as human serum samples using the nanosensors, which demonstrates their potential use in identifying clinical samples for early diagnosis of cancer.     

Magnetic Tweezers‐Based 3D Microchannel Electroporation for High‐Throughput Gene Transfection in Living Cells

A novel high‐throughput magnetic tweezers‐based 3D microchannel electroporation system capable of transfecting 40 000 cells/cm² on a single chip for gene therapy, regenerative medicine, and intracellular detection of target mRNA for screening cellular heterogeneity is reported. A single cell or an ordered array of individual cells are remotely guided by programmable magnetic fields to poration sites with high (>90%) cell alignment efficiency to enable various transfection reagents to be delivered simultaneously into the cells. The present technique, in contrast to the conventional vacuum‐based approach, is significantly gentler on the cellular membrane yielding >90% cell viability and, moreover, allows transfected cells to be transported for further analysis. Illustrating the versatility of the system, the GATA2 molecular beacon is delivered into leukemia cells to detect the regulation level of the GATA2 gene that is associated with the initiation of leukemia. The uniform delivery and a sharp contrast of fluorescence intensity between GATA2 positive and negative cells demonstrate key aspects of the platform for gene transfer, screening and detection of targeted intracellular markers in living cells.     

Optofluidic Platform for Real‐Time Monitoring of Live Cell Secretory Activities Using Fano Resonance in Gold Nanoslits

An optofluidic platform for real‐time monitoring of live cell secretory activities is constructed via Fano resonance in a gold nanoslit array. Large‐area and highly sensitive gold nanoslits with a period of 500 nm are fabricated on polycarbonate films using the thermal‐annealed template‐stripping method. The coupling between gap plasmon resonance in the slits and surface plasmon polariton Bloch waves forms a sharp Fano resonance with intensity sensitivity greater than 11 000% per refractive index unit. The nanoslit array is integrated with a cell‐trapping microfluidic device to monitor dynamic secretion of matrix metalloproteinase 9 (MMP‐9) from human acute monocytic leukemia cells in situ. Upon continuous lipopolysaccharide (LPS) stimulation, MMP‐9 secretion is detected within 2 h due to ultrahigh surface sensitivity and close proximity of the sensor to the target cells. In addition to the advantage of detecting early cell responses, the sensor also allows interrogation of cell secretion dynamics. Furthermore, the average secretion per cell measured using our system well matches previous reports while it requires orders of magnitude less cells. The optofluidic platform may find applications in fundamental studies of cell functions and diagnostics based on secretion signals.