Article
Chemistry, Analytical
Bing Li, Aleks Ponjavic, Wei-Hsin Chen, Lee Hopkins, Craig Hughes, Yu Ye, Clare Bryant, David Klenerman
Summary: The study combines light-sheet microscopy with local delivery to accurately deliver single proteins to specific locations within cells and achieve high-speed 3D detection. This method enables control over the position and quantity of protein delivery, providing a new approach for biological research.
ANALYTICAL CHEMISTRY
(2021)
Editorial Material
Biochemical Research Methods
Rita Strack
Summary: Single-objective light sheet fluorescence microscopes are significantly advancing volumetric imaging innovation.
Article
Multidisciplinary Sciences
Hotaka Kobayashi, Robert H. Singer
Summary: This study reports single-molecule methods to visualize each step of miRNA-mediated gene silencing inside cells. It is found that miRNAs preferentially bind to translated mRNAs and induce translational repression and mRNA decay after binding to mRNAs.
NATURE COMMUNICATIONS
(2022)
Article
Optics
N. R. Subedi, S. Yaraghi, P. S. Jung, G. Kukal, A. G. McDonald, D. N. Christodoulides, A. E. Vasdekis
Summary: Research shows that digitally scanned Airy beams can improve the throughput rates in Raman imaging by an order of magnitude compared to traditional diffraction-limited beams, achieving high contrast and 1 micron axial resolution for three-dimensional imaging of microparticles. This method also achieves orders of magnitude lower irradiation density than coherent Raman imaging schemes, with faster speed and lower phototoxicity.
Article
Chemistry, Analytical
Bin Li, Zihui Fan, Yanwei Lu, Binxiao Li, Xuedong Huang, Yixin Liu, Baohong Liu
Summary: In this study, a non-enzyme-assisted signal amplification sensing strategy was developed to achieve high-resolution imaging of microRNAs (miRNAs) in migrating cells. The spatial distribution of miRNA let-7a in single living cells was visualized and the differential expression of let-7a during migration was monitored. The results showed that fast migration modes exhibited lower let-7a expression. This work provides a new perspective for exploring regulatory mechanisms of key molecules in crowded intracellular environments.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Analytical
Yingying Cao, Seungah Lee, Kyungsoo Kim, Seong Ho Kang
Summary: In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to overcome optical illusions in cells. The system integrated total internal reflection fluorescence and a differential interference contrast microscope, and used a rotatable cuboid prism to change the direction of light and select the optimal illumination angle. The 4D CMLS imaging method enables in-depth 4D observation of samples, making it suitable for single-molecule and subcellular organelle observations in single cells.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Ai-Yu Guo, Ya-Mei Zhang, Liu Wang, Di Bai, Ya-Peng Xu, Wen-Qiang Wu
Summary: Single-molecule imaging is a revolutionary approach for studying fundamental questions in plants, but its application in plants is still underexplored compared to animals. This technique provides unprecedented quantitative details and faces challenges that require possible solutions to be addressed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Simona Machacova, Helena Chmelova, Anna Vavrova, Zbynek Kozmik, Iryna Kozmikova
Summary: Cephalochordates serve as representatives of the most basally divergent group of the chordate phylum, offering crucial insights into vertebrate evolution. In evolutionary developmental research, the combination of light sheet microscopy and tissue clearing methods allows for visualization of anatomical structures and individual cells of amphioxus in 3D space.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Kayvan Samimi, Danielle E. Desa, Wei Lin, Kurt Weiss, Joe Li, Jan Huisken, Veronika Miskolci, Anna Huttenlocher, Jenu V. Chacko, Andreas Velten, Jeremy D. Rogers, Kevin W. Eliceiri, Melissa C. Skala
Summary: This study developed a novel light-sheet microscope system for fluorescence lifetime imaging microscopy (FLIM) of NAD(P)H. The system demonstrated advantages in rapid imaging and limiting out-of-focus contributions, and successfully monitored metabolic perturbations in pancreas cancer cells and neutrophil imaging in a zebrafish tail wound. Compared to laser scanning, light-sheet FLIM showed significantly faster imaging speeds.
JOURNAL OF BIOMEDICAL OPTICS
(2023)
Article
Multidisciplinary Sciences
Jinrun Dong, Yuxian Lu, Yang Xu, Fanfan Chen, Jinmei Yang, Yuang Chen, Jiandong Feng
Summary: Optical imaging of single-molecule electrochemical reactions in aqueous solution enables super-resolution electrochemiluminescence microscopy, providing high spatiotemporal resolution for monitoring adhesion dynamics of live cells. Single-molecule methods go beyond ensemble averages and reveal statistical distribution of reaction positions, pathways, and dynamics, advancing fundamental understanding of electrochemical reactions and proving useful for bioassays and cell-imaging applications.
Article
Biochemical Research Methods
Petra Paie, Gianmaria Calisesi, Alessia Candeo, Andrea Comi, Federico Sala, Francesco Ceccarelli, Ada De Luigi, Pietro Veglianese, Korbinian Muhlberger, Michael Fokine, Gianluca Valentini, Roberto Osellame, Mark Neil, Andrea Bassi, Francesca Bragheri
Summary: Heterogeneity investigation at the single-cell level is crucial in clinical research. The combination of light sheet fluorescence microscopy and structured illumination microscopy in an optofluidic platform enables high throughput super-resolution imaging, allowing comprehensive evaluation of cellular heterogeneity at high resolution.
Review
Chemistry, Multidisciplinary
Bin Dong, Nourhan Mansour, Teng-Xiang Huang, Wenyu Huang, Ning Fang
Summary: Recent progress has been made in using single molecule fluorescence microscopy imaging to study nanoconfinement in porous materials, revealing static and dynamic heterogeneities between seemingly equal molecules by removing ensemble averaging effects. These studies allow for the investigation of various physicochemical processes at nanometer spatial resolution and provide the ability to quantitatively measure the inhomogeneities of nanoconfinement effects.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Neurosciences
Gabriella Gagliano, Tyler Nelson, Nahima Saliba, Sofia Vargas-Hernandez, Anna-Karin Gustavsson
Summary: The function of the neuronal synapse relies on individual molecules at the nanoscale, making single-molecule super-resolution microscopy an essential tool for understanding molecular mechanisms. Light sheet illumination offers a promising approach for improving three-dimensional imaging of biological samples, particularly in thicker samples like mammalian cells and tissue.
FRONTIERS IN SYNAPTIC NEUROSCIENCE
(2021)
Article
Nanoscience & Nanotechnology
Yuan Luo, Ming Lun Tseng, Sunil Vyas, Ting-Yu Hsieh, Jui-Ching Wu, Shang-Yang Chen, Hsiao-Fang Peng, Vin-Cent Su, Tzu-Ting Huang, Hsin Yu Kuo, Cheng Hung Chu, Mu Ku Chen, Jia-Wern Chen, Yu-Chun Chen, Kuang-Yuh Huang, Chieh-Hsiung Kuan, Xu Shi, Hiroaki Misawa, Din Ping Tsai
Summary: Light-sheet fluorescent microscopy (LSFM) is the leading technique for in vivo imaging in the fields of disease, medicine, and cell biology research. This study demonstrates the successful integration of a nanophotonic meta-lens as the illumination component for LSFM, addressing the challenges of high image resolution and optical sectioning. With the meta-lens, the LSFM system complexity is significantly reduced, enabling multicolor fluorescent imaging of live biological specimens with cellular resolution.
Article
Multidisciplinary Sciences
Chih-Ping Mao, Shih-Chin Wang, Yu-Pin Su, Ssu-Hsueh Tseng, Liangmei He, Annie A. Wu, Richard B. S. Roden, Jie Xiao, Chien-Fu Hung
Summary: Characterizing individual biomarker protein molecules in patient blood samples using single-molecule imaging techniques holds promise for early disease diagnosis and effective treatment. However, current methods have detection limits that are orders of magnitude higher than needed, making them unsuitable for clinical use. The development of SMAC, with its ability to quantify and characterize protein molecules down to the subfemtomolar range, presents a new avenue for noninvasive disease profiling with single-molecule imaging.
Article
Biophysics
Anna H. Lippert, Ivan B. Dimov, Alexander K. Winkel, Jane Humphrey, James McColl, Kevin Y. Chen, Ana M. Santos, Edward Jenkins, Kristian Franze, Simon J. Davis, David Klenerman
Summary: Research suggests that the early stages of T cell activation may not be influenced by substrate rigidity, while later stages may be associated with substrate stiffness.
Exclusion of large receptor-type phosphatases was observed on soft bilayers.
This work lays the groundwork for exploring receptor signaling under physiological cell-cell contact conditions.
BIOPHYSICAL JOURNAL
(2021)
Review
Neurosciences
John S. H. Danial, David Klenerman
Summary: This review discusses the use of single molecule microscopy to study individual protein aggregates in neurodegenerative diseases, providing insights into important questions in neurobiology.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Chemistry, Multidisciplinary
Yufan Xu, Runzhang Qi, Hongjia Zhu, Bing Li, Yi Shen, Georg Krainer, David Klenerman, Tuomas P. J. Knowles
Summary: Liquid-liquid phase-separated biomolecular systems are key components in cellular organization, with reversible gelation processes potentially offering advantages for new soft materials. This study explores a thermoresponsive gel-sol transition of an extracellular protein in microgel form, resulting in a high homogeneity all-aqueous liquid-liquid phase-separated system. The transition process converts elongated gelatin microgels to a spherical geometry due to interfacial tension becoming the dominant energetic contribution.
ADVANCED MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Iztok Urbancic, Lisa Schiffelers, Edward Jenkins, Weijian Gong, Ana Mafalda Santos, Falk Schneider, Caitlin O'Brien-Ball, Mai Tuyet Vuong, Nicole Ashman, Erdinc Sezgin, Christian Eggeling
Summary: The partial immobilization of proteins can change their preference towards a more ordered lipid environment, affecting their localization and the frequency of protein interactions, providing new mechanistic insights into lipid-mediated signaling pathways.
Article
Multidisciplinary Sciences
Kevin Y. Chen, Edward Jenkins, Markus Korbel, Aleks Ponjavic, Anna H. Lippert, Ana Mafalda Santos, Nicole Ashman, Caitlin O'Brien-Ball, Jemma McBride, David Klenerman, Simon J. Davis
Summary: The study demonstrates that trapping TCRs in close contacts or simply slowing their diffusion in phosphatase-depleted regions of the cell surface is sufficient to initiate signaling. Ligands can act as receptor traps to trigger TCR signaling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
M. Rodrigues, P. Bhattacharjee, A. Brinkmalm, D. T. Do, C. M. Pearson, S. De, A. Ponjavic, J. A. Varela, K. Kulenkampff, I Baudrexel, D. Emin, F. S. Ruggeri, J. E. Lee, A. R. Carr, T. P. J. Knowles, H. Zetterberg, T. N. Snaddon, S. Gandhi, S. F. Lee, D. Klenerman
Summary: This study presents a method called "amyloid precipitation" to capture amyloid-containing aggregates in human biofluids in an unbiased way. By using a specific structure-specific chemical dimer, the researchers were able to target the amyloid structure of all protein aggregates present in human cerebrospinal fluid, isolate them for analysis, and characterize them using single-molecule fluorescence imaging and mass spectrometry.
Article
Multidisciplinary Sciences
Georg Meisl, Catherine K. Xu, Jonathan D. Taylor, Thomas C. T. Michaels, Aviad Levin, Daniel Otzen, David Klenerman, Steve Matthews, Sara Linse, Maria Andreasen, Tuomas P. J. Knowles
Summary: The study reveals that both disease-related proteins and proteins with functional roles in biology are capable of self-replication. However, the rate of self-replication is insignificant on the biologically relevant time scale for proteins fulfilling structural roles, while disease-related proteins can self-replicate quickly within the associated disease's time scale.
Article
Biochemical Research Methods
John S. H. Danial, Jeff Y. L. Lam, Yunzhao Wu, Matthew Woolley, Eleni Dimou, Matthew R. Cheetham, Derya Emin, David Klenerman
Summary: This article presents an economic and easy-to-assemble single-molecule localization microscopy setup called NanoPro for high-throughput super-resolution imaging. It provides step-by-step instructions and illustrations to aid researchers in constructing and utilizing NanoPro, as well as assessing its performance.
Article
Multidisciplinary Sciences
Alyssa Miller, Jiapeng Wei, Sarah Meehan, Christopher M. Dobson, Mark E. Welland, David Klenerman, Michele Vendruscolo, Francesco Simone Ruggeri, Tuomas P. J. Knowles
Summary: Neurodegenerative diseases such as Alzheimer's disease are caused by protein misfolding and aggregation into amyloid fibrils. This study uses atomic force microscopy and statistical theory to characterize amyloid ring structures derived from the brains of AD patients and explains the diversity in the structures formed from protein aggregation. The results show that ex vivo protofibril chains possess greater flexibility than mature amyloid fibrils, allowing them to form end-to-end connections and shedding light on their role in disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Correction
Biochemical Research Methods
John S. H. Danial, Jeff Y. L. Lam, Yunzhao Wu, Matthew Woolley, Eleni Dimou, Matthew R. Cheetham, Derya Emin, David Klenerman
Article
Biochemistry & Molecular Biology
S. Basu, O. Shukron, D. Hall, P. Parutto, A. Ponjavic, D. Shah, W. Boucher, D. Lando, W. Zhang, N. Reynolds, L. H. Sober, A. Jartseva, R. Ragheb, X. Ma, J. Cramard, R. Floyd, J. Balmer, T. A. Drury, A. R. Carr, L. -m. Needham, A. Aubert, G. Communie, K. Gor, M. Steindel, L. Morey, E. Blanco, T. Bartke, L. Di Croce, I. Berger, C. Schaffitzel, S. F. Lee, T. J. Stevens, D. Klenerman, B. D. Hendrich, D. Holcman, E. D. Laue
Summary: This study presents an approach to extract key biophysical parameters from live-cell three-dimensional single-molecule imaging trajectories. It investigates the assembly of NuRD complex on chromatin and its regulation of enhancer dynamics. The study reveals that NuRD can decompact chromatin structure, increase enhancer dynamics, and restrict the time spent in a fast-diffusing state of enhancers. Hi-C and Cut&Run experiments demonstrate that NuRD modulates enhancer-promoter interactions in active chromatin, allowing longer distance contacts. A redistribution of CTCF and cohesin is also observed. The findings suggest that NuRD promotes a decondensed chromatin environment for stable and long-lived enhancer-promoter relationships.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Correction
Biochemistry & Molecular Biology
S. Basu, O. Shukron, D. Hall, P. Parutto, A. Ponjavic, D. Shah, W. Boucher, D. Lando, W. Zhang, N. Reynolds, L. H. Sober, A. Jartseva, R. Ragheb, X. Ma, J. Cramard, R. Floyd, J. Balmer, T. A. Drury, A. R. Carr, L. -m. Needham, A. Aubert, G. Communie, K. Gor, M. Steindel, L. Morey, E. Blanco, T. Bartke, L. Di Croce, I. Berger, C. Schaffitzel, S. F. Lee, T. J. Stevens, D. Klenerman, B. D. Hendrich, D. Holcman, E. D. Laue
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Meeting Abstract
Biophysics
Georg Krainer, Kadi Liis Saar, William E. Arter, Tuomas P. J. Knowles
BIOPHYSICAL JOURNAL
(2021)