Review
Biochemical Research Methods
Jin Zhang, Jing Xue, Ningfeng Luo, Feng Chen, Badong Chen, Yongxi Zhao
Summary: Single-cell profiling is crucial for understanding cellular heterogeneity and cell fate. Microfluidics has emerged as an optimal tool for single-cell profiling due to its high throughput and automation advantages. Among different microfluidic platforms, microwell array chips offer simplicity and easy integration with in situ analysis, making them ideal for single-cell studies. This review summarizes recent advances in single-cell analysis based on microwell array chips, including chip design and preparation, cell capture and lysis strategies, as well as advanced analysis of single-cell proteins, nucleic acids, and metabolites. The challenges and opportunities in the development of microwell-based single-cell analysis are also discussed.
Article
Multidisciplinary Sciences
Ireneusz Roston, Aleksandre Japaridze, Stef Rodenhuis, Lieke Hamoen, Murali Krishna Ghatkesar, Peter Steeneken, Cees Dekker, Farbod Alijani
Summary: This article presents an optical testing method that can rapidly determine bacterial antibiotic susceptibility by measuring intensity fluctuations of a laser focused on a bacterium in reflective microwells. The method can achieve single-bacteria resolution within 1 hour.
Article
Chemistry, Multidisciplinary
Jialian Ding, Ping Zhou, Weiliang Guo, Bin Su
Summary: In this study, a gold-coated PDMS UMEA was successfully fabricated using an electroless deposition method for visualizing the ECL reaction process at the single microwell level, demonstrating the enhancement of ECL generation by the microwell gold walls. The ECL image of a single microwell appeared as a surface-confined ring, indicating the stronger ECL intensity generated inside the well compared to the top surface of UMEA. The ring-shaped ECL image was found to originate from the superposition effect of mass diffusion fields at both microwell wall and bottom surfaces, as revealed by theoretical simulation.
FRONTIERS IN CHEMISTRY
(2021)
Article
Genetics & Heredity
Marcos Kunihiro Masukawa, Yukiko Okuda, Masahiro Takinoue
Summary: DNA hydrogels are able to form single, uniform particles inside aqueous/aqueous two-phase systems, demonstrating potential for use in creating highly parallel models for artificial cells and membraneless organelles. By isolating dextran droplets containing DNA motifs and allowing them to undergo gelation within a microfluidic device, researchers observed the formation of an aqueous triple-phase system with uniform DNA hydrogel particles at the interface of the two-phase system of dextran and PEG.
FRONTIERS IN GENETICS
(2021)
Article
Nanoscience & Nanotechnology
Jolien Breukers, Sara Horta, Caroline Struyfs, Dragana Spasic, Hendrik B. Feys, Nick Geukens, Karin Thevissen, Bruno P. A. Cammue, Karen Vanhoorelbeke, Jeroen Lammertyn
Summary: This study focused on improving the surface chemistry of microwell arrays to enhance single cell manipulation using optical tweezers. The results showed that surfaces treated with PEG 2000 and PEG Mix yielded optimal outcomes in terms of cellular motion and lifting efficiency, with over 93% of cells displaying motion and over 96% lifting efficiency for both cell types. Integration of this optimized microwell surface with continuous microfluidics demonstrated a versatile platform for high-throughput single cell studies and retrieval of target cells for off-chip analysis.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Multidisciplinary
Kun Yin, Shanqing Huang, Weidong Ruan, Haopai Wei, He Dong, Dianyi Liang, Meijuan Zhao, Wei Qi, Chaoyong Yang, Zhi Zhu
Summary: Iso-seq is a rapid and uniform single-cell whole-genome sequencing method that uses a specially designed dual-well structure and a capillary-based centrifugal-driven droplet generator to isolate single cells and compartmentalize their genomes in droplets within 3 minutes. Iso-seq achieves high mapping ratio, broad coverage of the genome, and low coefficient of variation, making it promising for a wide variety of biological applications.
Article
Biochemical Research Methods
Jiande Zhou, Amaury Wei, Arnaud Bertsch, Philippe Renaud
Summary: The Poisson limit poses a major challenge for isolating single cells, but this article presents a passive microfluidic system that overcomes this limitation with high efficiency. It has a high throughput and low fault ratio, making it suitable for various cells and particles.
Article
Biochemistry & Molecular Biology
Rong Pan, Xiaoyan Yang, Ke Ning, Yuanyuan Xie, Feng Chen, Ling Yu
Summary: This study used cell spheroids cultured in agarose micro-wells to investigate the movement of cells or spheroids towards other spheroids. The formation dynamics of tumor spheroids and the interactions of two batches of cells were studied. The results showed that the volume of the parental spheroids and the number of the second batch cells play a significant role in determining whether two generations of cell spheroids would fuse.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Xu Cui, Tianbao Hu, Qiang Chen, Qiang Zhao, Yin Wu, Tengbao Xie, Pengyong Liu, Xi Su, Gang Li
Summary: This study developed a rapid sample partitioning method for digital bioassays based on a detachable self-digitization (DSD) chip, which allows easy, fast, and large-scale sample partitioning. The chip can compartmentalize samples into more than 100,000 wells of picoliter volume with densities up to 14,000 wells/cm(2) in less than 30 s, demonstrating its utility in digital PCR and digital microbial assays.
Article
Optics
Xiaodan Gou, Jinglan Huo, Qing Yang, Yang Cheng, Xun Hou, Feng Chen
Summary: A new strategy of aerating micro bubbles by designing four different structures via laser ablation is proposed, which can produce nanoliter-sized bubbles and be applied in water treatment and gas detection. The designed micro bubble structure can also resist the damage of complex water environments and ultraviolet radiation.
OPTICS AND LASER TECHNOLOGY
(2023)
Article
Chemistry, Analytical
Misaki Hata, Masato Suzuki, Tomoyuki Yasukawa
Summary: The study introduced selective manipulation techniques based on dielectrophoresis for retrieving and retaining target cells in a microwell array. Negative dielectrophoresis was used to selectively retrieve and retain the target cells, allowing for the retrieval and recovery of single target cells after determining the function of cells trapped in each microwell.
ANALYTICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Hassan Rashidi, Yeh Chwan Leong, Kerrie Venner, Hema Pramod, Qi-Zhen Fei, Owen J. R. Jones, Dale Moulding, Jane C. Sowden
Summary: Retinal degenerative diseases are a major cause of blindness worldwide, but cell therapy shows promise in restoring and preserving sight. Researchers have successfully developed a large-scale retinal differentiation platform without the need for manual microdissection, and have generated retinal tissue using a stepwise differentiation protocol with small molecules.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Stefan H. Mueller, Lucy J. Fitschen, Afnan Shirbini, Samir M. Hamdan, Lisanne M. Spenkelink, Antoine M. van Oijen
Summary: Traditional enzyme characterization methods only provide population averages, while single-molecule methods can reveal kinetics and population heterogeneity but are often complex and time-consuming. We present a high-throughput single-molecule assay for rapidly characterizing DNA metabolism-related proteins by measuring changes in fluorescence intensity. Our method, combined with automated data analysis, can provide enzymatic activity data for thousands of molecules in less than an hour. We demonstrated three different enzyme activities and discovered a previously unknown activity of the UvrD helicase.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Min Zhang, LingJi Chen, Meihuan Chen, Yan Wang, Bin Liang, Na Lin, Xiaoqing Wu, Linshuo Wang, Liangpu Xu, Hailong Huang
Summary: The prenatal BoBs assay allows for rapid detection of chromosomal abnormalities and specific microdeletion syndromes. This study evaluated the effectiveness of prenatal BoBs in detecting sex chromosome mosaicism and found a sensitivity of 74.2%. These results provide valuable information for genetic counseling.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Optics
Miao Cai, Yanqing Lu, Min Xiao, Keyu Xia
Summary: The article introduces a machine learning algorithm for optimizing the control of a cavity-atom system to generate and store single photons, demonstrating high efficiency and accuracy. This machine learning-enhanced single-photon interface opens up new possibilities for building flexible and reliable quantum networks.
Article
Nanoscience & Nanotechnology
Lianyu Lu, Huimin Zhang, Yang Wang, Peng Zhang, Zhi Zhu, Chaoyong Yang
Summary: The newly developed DEL-DMF immunoassay greatly improves the sensitivity and automation of protein bioassays. It utilizes a microfluidics platform and dissolution-enhanced luminescence to control sample transport, immunoreaction, and buffer washing, reducing sample consumption and enhancing binding efficiency. The use of NaEuF4 nanoprobes boosts fluorescence and increases the detection sensitivity. Overall, this novel immunoassay microsystem holds great potential in clinical and biological applications.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Yuqi Wu, Bingqian Lin, Yinzhu Lu, Liang Li, Kunyue Deng, Suhui Zhang, Huiming Zhang, Chaoyong Yang, Zhi Zhu
Summary: Recently, lysosome targeting chimeras (LYTACs) have been developed to degrade extracellular and membrane proteins through a lysosomal degradation pathway. To overcome the challenges of complex and time-consuming preparation of chimeras, the first aptamer-based LYTAC (Apt-LYTAC) was developed by conjugating aptamers to tri-GalNAc. The Apt-LYTACs efficiently and quickly degrade the extracellular protein PDGF and the membrane protein PTK7, expanding the usage of aptamers and providing a new dimension for targeted protein degradation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biophysics
Qian Lai, Juan Song, Jie Zha, Huijian Zheng, Manman Deng, Yilong Liu, Wei Lin, Zhi Zhu, Huimin Zhang, Bing Xu, Chaoyong Yang
Summary: The article introduces a novel non-invasive method for monitoring remission status and predicting prognosis in AML patients using the LSC-Chip. By capturing and releasing leukemic stem cells (LSCs), accurate counting of LSCs, subtype classification, and single-cell RNA sequencing analysis can be performed.
BIOSENSORS & BIOELECTRONICS
(2023)
Review
Biochemical Research Methods
Xing Xu, Linfeng Cai, Shanshan Liang, Qiannan Zhang, Shiyan Lin, Mingying Li, Qizheng Yang, Chong Li, Ziyan Han, Chaoyong Yang
Summary: Digital microfluidics (DMF) is an emerging liquid-handling technology that enables precise manipulation of discrete droplets using microelectrode arrays. It offers automation, addressability, integration, and dynamic configuration ability, making it suitable for lab-on-a-chip biological analysis. This review focuses on DMF bioassays actuated by electrowetting on dielectric (EWOD) force and provides an introduction to EWOD actuation theory, types of droplet motion, and comprehensive overview of DMF-based biological analysis and applications.
Article
Biochemical Research Methods
Bing Yang, Lu Shi, Qiaorong Tang, Wei Liu, Baoxin Li, Chaoyong Yang, Yan Jin
Summary: Automated manipulation of discrete droplets by digital microfluidics combined with chemiluminescence holds great potential for achieving automated and sensitive biosensing and bioanalysis. A DMF-CL device was built to study CL kinetics and biosensing of a glow-type CL reaction. The automated manipulation of droplets reduced reagent costs and manual errors, leading to real-time, automated, and reliable study of CL kinetics.
Article
Chemistry, Analytical
Lu Shi, Qiaorong Tang, Bing Yang, Wei Liu, Baoxin Li, Chaoyong Yang, Yan Jin
Summary: A dual-mode DNA logic gate based on gas pressure biosensing and lateral flow assay was developed for the intelligent detection of multiple microRNAs. The gate utilized platinum-coated gold nanoparticles as a signal reporter for dual-signal readout. The miRNAs initiated the cyclic strand displacement reaction to enrich a large amount of nanoparticles, which could be visually detected on a lateral flow strip. Additionally, the nanoparticles catalyzed the decomposition of H2O2 to generate gas pressure, which could be measured by a handheld gas pressure meter.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Lu Shi, Qiaorong Tang, Bing Yang, Chaoyong Yang, Yan Jin, Wei Liu, Baoxin Li
Summary: Researchers successfully developed a logic gate based on gas pressure for multiplex analysis of metal ions. The gate controlled DNA extension reaction by interacting with mismatched base pairs and enriched metal ions on platinum nanoparticles, which catalyzed the decomposition of hydrogen peroxide and generated gas pressure as an output for metal ion detection.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Yuqian Zhang, Qiuyue Wu, Yihao Huang, Wencheng Wang, Yinzhu Lu, Siyin Kang, Chaoyong Yang, Yanling Song
Summary: Extracellular vesicle PD-L1 has great value in tumor diagnosis, prognosis, and monitoring of anti-PD-1/PD-L1 immunotherapy. A microfluidic differentiation method called DECLA was developed to detect extracellular PD-L1 without interference from soluble PD-L1.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Jianzhou Feng, Yun Shu, Yu An, Qi Niu, Qian Fan, Yanmei Lei, Yanli Gong, Xiaoya Hu, Peng Zhang, Yingbin Liu, Chaoyong Yang, Lingling Wu
Summary: This study proposes an encoded fusion strategy to profile miRNA signature in tumor-derived extracellular vesicles (tEVs) for pancreatic cancer diagnosis. By using encoded-targeted-fusion beads, tEVs can be selectively recognized and fused, and the turn-on fluorescence signals of molecule beacons are utilized for miRNA quantification and barcode signals for miRNA identification. This strategy shows great potential for multiplex profiling of miRNAs in tEVs and offers new avenues for cancer diagnosis and screening.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Xiyuan Yu, Wei Lin, Qian Lai, Juan Song, Yilong Liu, Rui Su, Qi Niu, Liu Yang, Chaoyong Yang, Huimin Zhang, Zhi Zhu
Summary: In this study, an Armor strategy was proposed to protect mammalian cell integrity from environmental changes. The Armor was created through dual-aptamer-based hybridization chain reaction (HCR) and Ca2+ assisted calcification for selective cell protection.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Shichao Lin, Kun Yin, Yingkun Zhang, Fanghe Lin, Xiaoyong Chen, Xi Zeng, Xiaoxu Guo, Huimin Zhang, Jia Song, Chaoyong Yang
Summary: In this study, a method called Well-TEMP-seq was developed, which is a high-throughput, cost-effective, accurate, and efficient approach for profiling the temporal dynamics of single-cell gene expression. By combining metabolic RNA labeling with single-cell RNA sequencing, Well-TEMP-seq can distinguish newly transcribed RNAs from pre-existing RNAs in thousands of single cells. The application of this method to colorectal cancer cells exposed to the DNA demethylating drug 5-AZA-CdR revealed its unbiased capturing of RNA dynamics and superior performance compared to splicing-based RNA velocity method.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Tian Wei, Kangxin Wang, Shuting Liu, Yunxuan Fang, Zixi Hong, Yingfu Liu, Huimin Zhang, Chaoyong Yang, Gaoliang Ouyang, Tiantian Wu
Summary: Periostin, a multifunctional extracellular protein, plays a crucial role in the immune microenvironment of colorectal cancer (CRC) by promoting the infiltration of PD-1+ tumor-associated macrophages (TAMs) and enhancing the expression of PD-1 on TAMs. This, in turn, leads to the production of IL-6 and IFN-g by PD-1+ TAMs, which induce the expression of PD-L1 on colorectal tumor cells. Combined inhibition of periostin and PD-1 shows significant efficacy in suppressing CRC progression.
Article
Chemistry, Analytical
Xi Zeng, Xiaoxu Guo, Shaowei Jiang, Xiaoping Yang, Zhixing Zhong, Siyu Liu, Zhi Zhu, Jia Song, Chaoyong Yang
Summary: This study presents a digital microfluidics-based single-cell reduced representation bisulfite sequencing (digital-scRRBS) technique, which is an automatic, effective, reproducible, and reagent-efficient method for dissecting the single-cell methylome. The digital-scRRBS allows for rapid isolation of single cells and construction of high-quality methylation sequencing libraries. This technology is valuable for distinguishing cell identity and tracking DNA methylation, and holds great significance for studying rare cells and populations with high levels of heterogeneity.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Qiuyue Wu, Wencheng Wang, Chi Zhang, Zhenlong You, Yinyan Zeng, Yinzhu Lu, Suhui Zhang, Xingrui Li, Chaoyong Yang, Yanling Song
Summary: This study developed a microfluidic-based strategy to selectively isolate newly-produced extracellular vesicles (EVs) by introducing azido groups as a timestamp during translation. The experimental results in mouse models of anti-PD-L1 immunotherapy showed a high positive correlation between the level of nascent PD-L1(+) EVs and tumor volume, suggesting the important role of nascent EVs in response to immunotherapy in cancer treatment.
NATURE COMMUNICATIONS
(2023)
