Review
Biochemistry & Molecular Biology
Nitesh Kumar Podh, Sheetal Paliwal, Partha Dey, Ayan Das, Shruti Morjaria, Gunjan Mehta
Summary: Single-molecule imaging in live yeast cells has become a powerful tool for researchers to quantitatively measure cellular activities in real time, with significant progress made in recent years to provide important references for studying biological processes. Different labs have tailored imaging setups and data analysis pipelines to estimate biophysical parameters for various biological processes, reflecting a rich variety of experimental experiences.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Analytical
Xinyu Zhou, Rui Wang, Zijian Wan, Pengfei Zhang, Shaopeng Wang
Summary: In this study, we demonstrate multiplexed protein detection and parallel protein interaction analysis through evanescent scattering microscopy (ESM). ESM allows label-free digital single-molecule counting for binding kinetics measurement, improving counting efficiency and accuracy. We show that digital single-molecule counting can differentiate proteins with different molecular weights, enabling real-time monitoring of protein binding processes in solution. Additionally, we show that this strategy can analyze the kinetics of two different protein interaction processes simultaneously, both on surfaces and in solution. This work may provide a way to investigate complex protein interactions, such as the competition between biomarker-antibody binding in biofluids and biomarker-protein binding on cellular membranes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xinyu Zhou, Rui Wang, Zijian Wan, Pengfei Zhang, Shaopeng Wang
Summary: Multiplexed protein detection and parallel protein interaction analysis are achieved using evanescent scattering microscopy (ESM), enabling label-free digital single-molecule counting with high temporal resolution. This strategy allows for real-time tracking of protein binding processes and simultaneous analysis of multiple protein interactions.
ANALYTICAL CHEMISTRY
(2023)
Review
Developmental Biology
Alan P. Boka, Apratim Mukherjee, Mustafa Mir
Summary: This article provides an accessible overview of the rapidly expanding family of technologies for single-molecule tracking (SMT), covering the basics, motivation, key technologies, and data analysis of SMT experiments. It aims to enable readers to critically analyze single-molecule studies and inspire the application of SMT to their own work by explaining the trade-offs involved in optimizing parameters.
Article
Biochemical Research Methods
Rasmus O. Thorsen, Christiaan N. Hulleman, Bernd Rieger, Sjoerd Stallinga
Summary: Combining localization microscopy with orientation estimation allows analysis of biomolecules' orientation on a nanoscale. The modulation of excitation polarization enhances the precision of orientation estimation. Theoretical and simulation studies demonstrate the high precision achievable under specific conditions.
BIOMEDICAL OPTICS EXPRESS
(2022)
Article
Chemistry, Analytical
Meng Liu, Nan Zhong, Xiaorui Tian, Li-juan Wang, Chun-yang Zhang
Summary: This study demonstrates the assembly of a single quantum-dot nanosensor for accurate monitoring of hSMUG1 at the single-cell level. The nanosensor shows a low detection limit, a wide dynamic range, and the ability to measure enzymatic kinetics. It can be used for hSMUG1-related biomedical studies and clinical diagnostics.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Multidisciplinary
Yoonjung Cho, Hyeong Jeon An, Taehoon Kim, Chulbom Lee, Nam Ki Lee
Summary: The article reports the mechanism of photoconversion of cyanine dyes under photoexcitation, indicating that the process can be achieved mainly through an intermolecular pathway involving bond cleavage and reconstitution. Additionally, the study shows that ketone products generated from singlet oxygen-mediated photooxidation undergo a series of carbon-carbon bond-breaking and -forming events, resulting in dye-to-dye transformation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biology
Jigmi Basumatary, Neptune Baro, Prakash Joshi, Partha Pratim Mondal
Summary: Single-molecule localization microscopy (SMLM) is a powerful technique that improves spatial resolution beyond the diffraction limit and allows for the analysis of biological features at the nanoscale. This study introduces a single molecule-based scanning SMLM (scanSMLM) system that enables rapid volume imaging. By rapidly changing the aperture of an electrically-tunable lens, the system achieves selective imaging of the axial object plane, allowing for volume scanning. The technique is employed to visualize the architecture of actin-filaments, the distribution of Meos-Tom20 molecules on the mitochondrial membrane, and the clustering of Hemagglutinin (HA) protein single molecules for studying Influenza-A disease progression. The system enables 3D visualization of HA distribution, providing unprecedented insights into the disease progression at the single-molecule level.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell Biology
James H. Felce, Lucia Parolini, Erdinc Sezgin, Pablo F. Cespedes, Kseniya Korobchevskaya, Mathew Jones, Yanchun Peng, Tao Dong, Marco Fritzsche, Dirk Aarts, John Frater, Michael L. Dustin
Summary: The study reveals the spatiotemporal organization of GPCRs within the synapse of T cells, focusing on the contribution of CXCR4 in T cell activation. These GPCRs show a similar pattern of organization in the synapse to CXCR4, providing insights into how they contribute to T cell activation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Chemistry, Analytical
Hui Wang, Cuilin Zhu, Di Li
Summary: The emergence of single-molecule techniques has greatly advanced research in enzymology. Single-molecule enzymology studies the individual behavior of a single enzyme molecule, which is hidden under the overall average. This review summarizes the emerging developments of several single-molecule techniques, such as TIRFM, confocal microscopy, FCS, and magnetic/optical tweezers, in real-time monitoring of the catalytic process of single enzymes. It explores various enzymatic catalytic behaviors and mechanisms that differ from bulk experiments, providing a deeper understanding of enzymatic reaction mechanisms through the analysis of single-molecule enzymatic kinetics coupled with conformational changes. Additionally, this review critically discusses the future challenges of imaging and monitoring single enzymatic reactions in cellular environments.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Stefan Niekamp, Nico Stuurman, Nan Zhang, Ronald D. Vale
Summary: The study reveals that during motility, the motor protein dynein exhibits variability in the movement between its domains, with the AAA ring and MTBDs not always stepping simultaneously and taking differently sized steps. This variability results in a large number of unexpected conformational states of dynein during motility. The flexibility between major dynein domains is found to be critical for dynein motility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Antonio Garcia, Shannon J. Saluga, David J. Dibble, Pia A. Lopez, Nozomi Saito, Suzanne A. Blum
Summary: This study for the first time imaged the selectivity of individual molecular catalysts for two different reactions in real time at the single-catalyst level, revealing that catalyst selectivity may be unexpectedly spatially and time-variable in ruthenium-catalyzed polymerization.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biophysics
Soochul Shin, Sun Han, Juyoung Kim, Yumi Shin, Ji-Joon Song, Sungchul Hohng
Summary: SIMUL is a multiplexed ctDNA detection technique that can sensitively and specifically detect multiple single-nucleotide mutations in early cancer stages. It accurately measures mutant fractions and holds immense potential for clinical applications.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Alexandre Chappard, Craig Leighton, Rebecca S. S. Saleeb, Kiani Jeacock, Sarah R. R. Ball, Katie Morris, Owen Kantelberg, Ji-Eun Lee, Elsa Zacco, Annalisa Pastore, Margaret Sunde, David J. J. Clarke, Patrick Downey, Tilo Kunath, Mathew H. H. Horrocks
Summary: Protein misfolding and aggregation are common features of neurogenerative disorders. Single-molecule techniques have allowed the characterization of these protein aggregates, previously inaccessible with traditional methods. In this study, we employed a high affinity antibody labeled with orthogonal fluorophores, along with fast-flow microfluidics and single-molecule confocal microscopy, to specifically detect alpha-synuclein in biologically relevant samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Nizam Ud Din, Ji Yu
Summary: Traditional cell image segmentation methods require a large amount of manually labeled data, which is expensive and difficult to generalize. This study proposes an alternative strategy that trains CNN without human-labeled data, capable of producing accurate segmentation models applicable to both fluorescence and bright-field images, with little to no prior knowledge of signal characteristics needed.
SCIENTIFIC REPORTS
(2021)
Article
Instruments & Instrumentation
M. S. DeVore, D. G. Stich, A. M. Keller, C. Cleyrat, M. E. Phipps, J. A. Hollingsworth, D. S. Lidke, B. S. Wilson, P. M. Goodwin, J. H. Werner
REVIEW OF SCIENTIFIC INSTRUMENTS
(2015)
Article
Biochemical Research Methods
Pengfei Zhang, Mary E. Phipps, Peter M. Goodwin, James H. Werner
JOURNAL OF BIOMEDICAL OPTICS
(2016)
Article
Chemistry, Analytical
Aaron M. Keller, Matthew S. DeVore, Dominik G. Stich, Dung M. Vu, Timothy Causgrove, James H. Werner
ANALYTICAL CHEMISTRY
(2018)
Article
Optics
P. Zhang, M. E. Phipps, P. M. Goodwin, J. H. Werner
Review
Chemistry, Multidisciplinary
Yuxiang Chen, M. Lisa Phipps, James H. Werner, Saumen Chakraborty, Jennifer S. Martinez
ACCOUNTS OF CHEMICAL RESEARCH
(2018)
Article
Immunology
Sofiya N. Micheva-Viteva, Brittany N. Ross, Jun Gao, Samantha Adikari, Pengfei Zhang, Judith R. Mourant, Terry H. Wu, James H. Werner, Alfredo G. Torres, Elizabeth Hong-Geller
INFECTION AND IMMUNITY
(2019)
Article
Multidisciplinary Sciences
Daniel M. Kalb, Samantha H. Adikari, Elizabeth Hong-Geller, James H. Werner
Article
Physics, Applied
Megan K. Dunlap, Duncan P. Ryan, Peter M. Goodwin, James H. Werner, Somak Majumder, Jennifer A. Hollingsworth, Martin P. Gelfand, Alan Van Orden
APPLIED PHYSICS LETTERS
(2020)
Article
Physics, Applied
Duncan P. Ryan, Megan K. Dunlap, Somak Majumder, James H. Werner, Jennifer A. Hollingsworth, Martin P. Gelfand, Alan Van Orden, Peter M. Goodwin
APPLIED PHYSICS LETTERS
(2020)
Article
Multidisciplinary Sciences
Duncan P. Ryan, Yu Chen, Phong Nguyen, Peter M. Goodwin, J. William Carey, Qinjun Kang, James H. Werner, Hari S. Viswanathan
SCIENTIFIC REPORTS
(2020)
Proceedings Paper
Nanoscience & Nanotechnology
Duncan P. Ryan, Megan K. Dunlap, Somak Majumder, Chris J. Sheehan, James H. Werner, Jennifer Hollingsworth, Martin P. Gelfand, Alan K. Van Orden, Peter M. Goodwin
SINGLE MOLECULE SPECTROSCOPY AND SUPERRESOLUTION IMAGING XIII
(2020)
Proceedings Paper
Nanoscience & Nanotechnology
Megan K. Dunlap, Duncan P. Ryan, Peter M. Goodwin, James H. Werner, Somak Majumder, Jennifer A. Hollingsworth, Martin P. Gelfand, Alan K. Van Orden
SINGLE MOLECULE SPECTROSCOPY AND SUPERRESOLUTION IMAGING XIII
(2020)
Proceedings Paper
Engineering, Biomedical
Matthew S. DeVore, Dominik G. Stich, Aaron M. Keller, Yagnaseni Ghosh, Peter M. Goodwin, Mary E. Phipps, Michael H. Stewart, Cedric Cleyrat, Bridget S. Wilson, Diane S. Lidke, Jennifer A. Hollingsworth, James H. Werner
COLLOIDAL NANOPARTICLES FOR BIOMEDICAL APPLICATIONS X
(2015)
Proceedings Paper
Instruments & Instrumentation
Evan P. Perillo, Leyma De Haro, Mary E. Phipps, Jennifer S. Martinez, Hsin-Chih Yeh, Andrew K. Dunn, Douglas P. Shepherd, James H. Werner
SINGLE MOLECULE SPECTROSCOPY AND SUPERRESOLUTION IMAGING VII
(2014)
Proceedings Paper
Cell & Tissue Engineering
Pengfei Zhang, Peter M. Goodwin, James H. Werner
IMAGING, MANIPULATION, AND ANALYSIS OF BIOMOLECULES, CELLS, AND TISSUES XII
(2014)