Article
Biology
Nadia M. Huisjes, Thomas M. Retzer, Matthias J. Scherr, Rohit Agarwal, Lional Rajappa, Barbara Safaric, Anita Minnen, Karl E. Duderstadt
Summary: The rapid development of new imaging approaches has led to the generation of larger and more complex datasets, allowing us to uncover the time evolution of individual cells and biomolecules. However, there are currently few standards for processing these information-rich datasets, which poses challenges for wider dissemination. In this study, we introduce Mars, an open-source platform that stores and processes image-derived properties of biomolecules. Mars provides a flexible solution for reproducible analysis of image-derived properties and facilitates the discovery and quantitative classification of new biological phenomena.
Article
Cell Biology
Jozsef Meszaros, Peter Geggier, Jamie J. Manning, Wesley B. Asher, Jonathan A. Javitch
Summary: Single-molecule FRET (smFRET) is a powerful imaging platform for studying dynamic changes in biological molecules. Expanding smFRET imaging to living cells provides new research opportunities and challenges. Automating dataset curation is crucial for consistent and efficient analysis, allowing researchers to advance the technical boundaries of imaging living cells. Our automated approach addresses the problem of multiple particles entering a region of interest, increasing FRET data quantity and accuracy, and improving understanding of biological functions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biophysics
Ningning Wang, Hang Ao, Wencheng Xiao, Weiwei Chen, Guangming Li, Jie Wu, Huangxian Ju
Summary: In this work, a CEIM chip was designed for high-throughput quantification of cell-secreted dopamine. The chip was able to recognize the target DA secretion from cells and emit an ECL signal without the need for additional coreactants.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Biology
M. Shahid Mansuri, Kenneth Williams, Angus C. Nairn
Summary: Recent technological advances have enabled single-cell proteomics to unravel the role of protein expression, post-translational modifications, and protein interactions in determining cell state in both health and disease.
COMMUNICATIONS BIOLOGY
(2023)
Review
Cell Biology
Mengdi Zhang, Clayton Seitz, Garrick Chang, Fadil Iqbal, Hua Lin, Jing Liu
Summary: The emergence of labeling strategies and live cell imaging methods has revolutionized our understanding of chromatin structure, dynamics, and functions by enabling imaging at single digit nanometer resolution and milliseconds temporal resolution. This review summarizes the fluorescent labeling strategy of chromatin in live cells, compares live cell imaging instrumentation, and discusses image analysis pipelines to extract the biophysical properties of chromatin. Practical suggestions are also provided for selecting methods and linking them to models according to different investigation purposes.
CELL BIOLOGY INTERNATIONAL
(2022)
Review
Chemistry, Analytical
Fei Ma, Xinyi Zhang
Summary: MicroRNAs play a crucial role in regulating post-transcriptional gene expression and are involved in various cellular processes. Dysregulation of miRNAs can contribute to the development of human diseases, including cancer. Accurate and sensitive detection of miRNAs is essential for disease diagnosis, prognosis, and therapy. Single-molecule fluorescence detection is an advanced bioanalysis technology that offers simplicity, minimal sample consumption, ultrahigh sensitivity, and rapid assay time. This review summarizes the recent advances in single-molecule/particle counting for miRNA detection and imaging in vitro and in vivo, discussing their principles, features, and biomedical applications. The future directions in this field are also highlighted.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Zixuan Zhan, Yongcheng Dai, Qiuyan Li, Yi Lv
Summary: Small molecules-based bioluminescence and chemiluminescence probes have emerged as powerful tools for biomarkers imaging without requiring excitation light source, showing intriguing properties and fast development. However, probes for reactive species have not been reviewed comprehensively in the past decade. Recent research indicates the significant potential of these probes in the field of biomedical imaging.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Ece Bueber, Tim Schroeder, Michael Scheckenbach, Mihir Dass, Philip Tinnefeld, Henri G. Franquelim
Summary: Particle size is a crucial parameter that affects the physicochemical properties of materials. In the context of lipids and cellular membranes, particle size and surface curvature play a significant role, as the cell membrane undergoes conformational changes in various biological processes, resulting in different local curvature values. Hence, it is important to develop cost-effective and accurate systems capable of measuring surface curvature on the nanoscale and translating it to spherical particle size. This study presents a novel approach utilizing flexible DNA nanodevices as curvature sensors, which can adapt to the curvature of the structures they bind to. These sensors employ Fluorescence Resonance Energy Transfer (FRET) as a transduction mechanism at the single-molecule level. By connecting segmented DNA origami structures with flexible DNA linkers containing a FRET pair, the sensors were able to accurately measure the size of spherical silica beads and lipid vesicles within the range of 50-300 nm and the bending angle range of 50-180 degrees. This research contributes to the development of advanced modular-curvature sensing devices capable of accurately determining the sizes of nanoparticles and biological complexes.
Review
Chemistry, Multidisciplinary
Xin Guan, Haijuan Li, Limei Chen, Guohua Qi, Yongdong Jin
Summary: A glass capillary-based nanopore (G-nanopore) with tapered tip and flexible surface modifications provides a powerful sensing platform for diverse biological measurements. It enables noninvasive single molecule and subcellular single cell detections and shows potential for cancer diagnosis and treatment applications. However, current bottlenecks limit its widespread use in clinical applications.
Article
Multidisciplinary Sciences
Tobias F. Bartsch, Camila M. Villasante, Felicitas E. Hengel, Ahmed Toure, Daniel M. Firester, Aaron Oswald, A. J. Hudspeth
Summary: In high-speed single-molecule experiments, tethering proteins with force probes can avoid nonspecific interactions, but dissipate rapidly exerted forces through long linkers; due to the high frequency of mammalian hearing, short tethers are required for single-molecule experiments.
SCIENTIFIC REPORTS
(2021)
Article
Spectroscopy
Meng Zhao, Gang Zhang, Shan Huang, Jingmiao Zhang, Yingzhong Zhu, Xiaxia Zhu, Ruilong Zhang, Fei Li
Summary: In this study, two series of small-molecule compounds based on benzo[d] thiazole were developed with a donor-acceptor or donor pi-acceptor architecture. The optimized compound, BPM1, showed the highest binding affinity to A beta aggregates and could be activated with 10-fold fluorescence enhancement, enabling specific and sensitive detection of A beta aggregates.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Review
Chemistry, Multidisciplinary
Saisai Yuan, Qitao Zhang
Summary: The morphology of nanomaterials, particularly 1D nanomaterials, greatly influences their catalytic performance. Advanced characterization techniques are crucial in identifying catalytic active sites and understanding the mechanism of 1D nanomaterials. Future research should focus on addressing the challenges in catalysis of 1D nanomaterials.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Physical
Anders Kokkvoll Engdahl, Oleg Grauberger, Andreas Brockhinke, Mark Schuettpelz, Thomas Huser
Summary: Photoinduced off-switching of organic fluorophores is commonly used in super-resolution microscopy for single molecule imaging. This study suggests that the interactions between sodium sulfite and glycerol can also achieve efficient switching of organic fluorophores. The addition of glycerol to the imaging buffer allows tuning of the dye switching from intermittent fluorescence to the off-state.
Article
Chemistry, Analytical
Furui Jin, Danke Xu
Summary: The study utilized cascaded DNA circuits on a bead array platform for signal amplification of miRNA, achieving high sensitivity detection in single cells. This method allows accurate quantification and identification of single nucleotide differences, providing new possibilities for disease treatment strategies.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Boris I. Godoy, Nicholas A. Vickers, Sean B. Andersson
Summary: Single Particle Tracking (SPT) is a powerful method for studying biomolecular dynamics in living cells, revealing trajectories of individual particles and motion model parameters. However, existing algorithms assume constant parameters, while this study proposes an estimation algorithm to determine time-varying parameters in systems that switch between different linear models of motion.
