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10. A Course of Hands-On Nanopore Experiments for Undergraduates: Single-Molecule Detection with Portable Electrochemical Instruments

Author

Hu, Zheng-Li, Ying, Yi-Lun, Huo, Ming-Zhu, Kong, Xuan-Feng, Yu, Xiao-Dong, Zhang, Jian-Rong, and Long, Yi-Tao

Abstract

The prompt introduction of single-molecule science into undergraduates' curricula is an urgent but challenging task. However, the research experiments are often too complicated and the instruments are too expensive to be widely transferred into a compulsory course of undergraduate students. Herein, we introduce a recently developed nanopore technique into an accessible laboratory course for students with the advantages of simple operation, high repeatability, and low cost. The nanopore course serves to help undergraduates in practice to understand single-molecule behaviors, think at a single molecule level, and gradually develop single-molecule solutions for scientific issues. The learning activities for undergraduate students include setup of the instrument, fabrication of a biological nanopore on an artificial lipid bilayer membrane, detection of individual oligonucleotides, and data analysis. An experiment example is single-molecule detection of the model DNA sample poly(dA)[subscript n] (n = 4, 5) using the aerolysin nanopore. As our developed nanopore sensing system is simple, portable, and easy to handle, the experiment course could be implemented and popularized in undergraduates' laboratory education. For the undergraduate students who have taken general chemistry and/or biochemistry courses, this hands-on experience of nanopore experiments would benefit them with a better understanding of the chemical world at a single-molecule level and further using single-molecule tools in various applications including DNA and/or protein sequencing.

Published
2020
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14. HFM-Tracker: a cell tracking algorithm based on hybrid feature matching.

Author

Zhao, Yan, Chen, Ke-Le, Shen, Xin-Yu, Li, Ming-Kang, Wan, Yong-Jing, Yang, Cheng, Yu, Ru-Jia, Long, Yi-Tao, Yan, Feng, and Ying, Yi-Lun

Subjects
TRACKING algorithms, CELL migration, CELL morphology, CELL analysis, QUANTITATIVE research
Abstract

Cell migration is known to be a fundamental biological process, playing an essential role in development, homeostasis, and diseases. This paper introduces a cell tracking algorithm named HFM-Tracker (Hybrid Feature Matching Tracker) that automatically identifies cell migration behaviours in consecutive images. It combines Contour Attention (CA) and Adaptive Confusion Matrix (ACM) modules to accurately capture cell contours in each image and track the dynamic behaviors of migrating cells in the field of view. Cells are firstly located and identified via the CA module-based cell detection network, and then associated and tracked via a cell tracking algorithm employing a hybrid feature-matching strategy. This proposed HFM-Tracker exhibits superiorities in cell detection and tracking, achieving 75% in MOTA (Multiple Object Tracking Accuracy) and 65% in IDF1 (ID F1 score). It provides quantitative analysis of the cell morphology and migration features, which could further help in understanding the complicated and diverse cell migration processes. [ABSTRACT FROM AUTHOR]

Published
2024
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43. Single-entity electrochemistry at confined sensing interfaces

Author

Ying, Yi-Lun, Wang, Jiajun, Leach, Anna Rose, Jiang, Ying, Gao, Rui, Xu, Cong, Edwards, Martin A., Pendergast, Andrew D., Ren, Hang, Weatherly, Connor K. Terry, Wang, Wei, Actis, Paolo, Mao, Lanqun, White, Henry S., and Long, Yi-Tao

Abstract

Measurements at the single-entity level provide more precise diagnosis and understanding of basic biological and chemical processes. Recent advances in the chemical measurement provide a means for ultra-sensitive analysis. Confining the single analyte and electrons near the sensing interface can greatly enhance the sensitivity and selectivity. In this review, we summarize the recent progress in single-entity electrochemistry of single molecules, single particles, single cells and even brain analysis. The benefits of confining these entities to a compatible size sensing interface are exemplified. Finally, the opportunities and challenges of single entity electrochemistry are addressed.

Published
2024
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