Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Optics
Gwinky G. K. Yip, Michelle C. K. Lo, Wenwei Yan, Kelvin C. M. Lee, Queenie T. K. Lai, Kenneth K. Y. Wong, Kevin K. Tsia
Summary: The new high-speed quantitative phase imaging (QPI) technique presented in this study combines time-interleaved phase-gradient FACED image detection, enabling fast imaging and cell analysis. Integration with microfluidic technology allows for high-speed, high-resolution imaging of cell phenotypes.
Article
Chemistry, Multidisciplinary
Bowen Zhang, Taoran Tian, Dexuan Xiao, Shaojingya Gao, Xiaoxiao Cai, Yunfeng Lin
Summary: A DNA-enhanced HCR detection system (T-probe system) is introduced for the detection of cancer-related targets, demonstrating its versatility and efficiency by detecting miRNA-21 and nucleolin. The T-probe system shows high detection rate and rapid recognition of both membrane and intracellular cancer-related targets, and exhibits superior fluorescence for imaging tumor-related biomarkers in vitro and in vivo, indicating its great potential for clinical diagnosis and therapeutic applications.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Biochemical Research Methods
Chen Lin, Meng Jiang, Ling Liu, Xiaoyuan Chen, Yuancun Zhao, Lu Chen, Yujuan Hong, Xin Wang, Chengye Hong, Xihu Yao, Rongqin Ke
Summary: The asmFISH assay introduces a more efficient and specific method for highly specific imaging of individual transcripts in fixed cells and tissues, compared to the padlock probe assay. It can be applied not only to cultured cells, but also to fresh frozen and formalin-fixed, paraffin-embedded tissue sections.
Article
Chemistry, Analytical
Jidong Wang, Gaoxing Jing, Wenxuan Huang, Luhua Xin, Jihui Du, Xiaoqing Cai, Ying Xu, Xi Lu, Wenwen Chen
Summary: Rapid HPV screening method using hydrogel loop-mediated isothermal amplification (LAMP) has been developed, which can provide results in less than 30 minutes and detect HPV infection at the single-cell level in a large-scale parallel manner.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Junyun Cheng, Jie Liao, Xin Shao, Xiaoyan Lu, Xiaohui Fan
Summary: Barcoding technology has improved throughput in single-cell RNA sequencing studies by reducing processing time and costs. Focus on DNA-based barcoding methods for sample multiplexing, with guidelines for choosing appropriate techniques. Future applications include predicting severity of COVID-19 in patients of different demographics.
Article
Physics, Applied
Stephan Steinhauer, Samuel Gyger, Val Zwiller
Summary: The article outlines the advantages of superconducting nanowires in single-photon detection and discusses future directions for overcoming challenges related to up-scaling nanowire devices and detector systems for widespread applications. Additionally, it summarizes current readout and multiplexing schemes for multi-pixel detector arrays and discusses the implications of recently discovered microwire-based detector geometries.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Xueqin Yang, Lijiao Yang, Donglei Yang, Min Li, Pengfei Wang
Summary: Cell membrane proteins play a crucial role in regulating intracellular signal transductions and cell behaviors. By utilizing membrane-anchored DNA hybridization chain reaction, DNA self-assembly can be induced on the live cell surface, leading to the clustering of membrane proteins and modulation of cell behaviors.
Article
Chemistry, Multidisciplinary
Sylvie Egloff, Nina Melnychuk, Elisabete Cruz Da Silva, Andreas Reisch, Sophie Martin, Andrey S. Klymchenko
Summary: The study introduces a method named AmpliFISH for RNA imaging, utilizing small and ultrabright dye-loaded polymeric nanoparticles (NPs) functionalized with DNA. The optimized NPs enabled sequence-specific imaging of different mRNA targets and multiplexed detection of three mRNA targets simultaneously. AmpliFISH provided a stronger signal and shorter processing time compared to commercial locked nucleic acid (LNA)-based FISH technique.
Article
Multidisciplinary Sciences
Hongru Shen, Jilei Liu, Jiani Hu, Xilin Shen, Chao Zhang, Dan Wu, Mengyao Feng, Meng Yang, Yang Li, Yichen Yang, Wei Wang, Qiang Zhang, Jilong Yang, Kexin Chen, Xiangchun Li
Summary: tGPT is a method for learning feature representation of transcriptomes, which efficiently handles the exponential growth of single-cell transcriptome data. It shows good performance on tasks such as single-cell analysis and tumor tissue analysis.
Article
Biochemical Research Methods
Ziheng Zou, Kui Hua, Xuegong Zhang
Summary: HGC is a fast Hierarchical Graph-based Clustering tool that addresses the issues of fixed number of clusters and lack of hierarchical information in single-cell data clustering. Experiments demonstrate that HGC enables multiresolution exploration of biological hierarchy, achieves state-of-the-art accuracy on benchmark data, and is capable of scaling to large datasets.
Article
Marine & Freshwater Biology
Kathleen J. Pitz, Mindy L. Richlen, Evangeline Fachon, Tyler B. Smith, Michael L. Parsons, Donald M. Anderson
Summary: Ciguatera poisoning (CP) is caused by the accumulation of lipophilic ciguatoxins in coral reef fish and invertebrates, produced by Gambierdiscus spp. Recent studies have identified diverse species within the Gambierdiscus genus, prompting the development of new tools for species identification and enumeration. Fluorescence in situ hybridization (FISH) probes were designed for seven species, allowing for accurate determination of community composition and cell abundances. The application of species-specific FISH probes provides a powerful new tool to target individual Gambierdiscus species in field populations, aiding in understanding and managing the risks of CP worldwide.
Article
Biochemical Research Methods
Kehui Liu, Shanjun Deng, Chang Ye, Zeqi Yao, Jianguo Wang, Han Gong, Li Liu, Xionglei He
Summary: SMALT is a substitution mutation-aided lineage-tracing system that outperforms available cell barcoding methods in mapping cell phylogeny. Utilizing SMALT in Drosophila melanogaster enables high-quality cell phylogenetic trees to be obtained.
Article
Pathology
Pedro Horna, Kathryn E. Pearce, Rhett P. Ketterling, Min Shi, Jess F. Peterson
Summary: Chromosomal abnormalities are common in chronic lymphocytic leukemia/small lymphocytic lymphoma and are not associated with prominent proliferation centers.
AMERICAN JOURNAL OF CLINICAL PATHOLOGY
(2022)
Article
Biology
Haocheng Ye, Lin Cheng, Bin Ju, Gang Xu, Yang Liu, Shuye Zhang, Lifei Wang, Zheng Zhang
Summary: A specialized software SCIGA was developed for precise and quick analysis of 10X single-cell immunoglobulin repertoires, which helps researchers to interpret B-cell immunoglobulin repertoires with paired heavy and light chain. SCIGA successfully identified four neutralizing antibodies against SARS-CoV-2 in samples from patients with COVID-19.