Article
Chemistry, Multidisciplinary
Shikha Dhiman, Teodora Andrian, Beatriz Santiago Gonzalez, Marrit M. E. Tholen, Yuyang Wang, Lorenzo Albertazzi
Summary: Characterization of newly synthesized materials is crucial in chemistry and nanotechnology, with standardized analytical techniques and novel technologies continually developing. The adoption of reporting standards like MIRIBEL aims to provide reproducible and reliable sample preparation for the scientific community. Super-resolution microscopy (SRM) shows potential to transition into a standard routine method for material characterization, but faces challenges in sample preparation, data analysis, and expensive instrumentation.
Article
Chemistry, Multidisciplinary
Bowen Wang, Michael Xiong, Josephine Susanto, Xue Li, Wai-Yee Leung, Ke Xu
Summary: We propose a strategy to optimize the photoswitching behavior of rhodamines for (d)STORM super-resolution microscopy. By replacing the benzene ring with a permanently charged 1,3-disubstituted imidazolium, the resulting dyes show enhanced photoswitching capability and exhibit excellent performance in (d)STORM with fast on-off switching, long-lasting blinking, and bright single-molecule emission. Our method achieves high-quality (d)STORM images under green excitation that are comparable to those obtained using ideal red-excited dyes, even for challenging structures like the mammalian actin cytoskeleton. We also demonstrate high-quality two-color three-dimensional (d)-STORM.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Chemistry, Multidisciplinary
Yanzi Xu, Ruohan Xu, Zhi Wang, Yu Zhou, Qifei Shen, Wenchen Ji, Dongfeng Dang, Lingjie Meng, Ben Zhong Tang
Summary: Recent progress on STED fluorophores for super-resolution imaging is outlined, including inorganic fluorophores, fluorescent proteins, organic luminescent materials, aggregation-induced emission (AIE) luminogens, and fluorescent nanoparticles. Characteristics of these aforementioned STED fluorophores are also included and compared to provide a deep understanding of the relationship between the properties in luminescent materials and their performance in STED imaging.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Chemistry, Multidisciplinary
Weijie Chi, Davin Tan, Qinglong Qiao, Zhaochao Xu, Xiaogang Liu
Summary: Single-molecule localization microscopy (SMLM) has been widely used in biology and chemistry. Fluorophores, as an essential component of SMLM, play a crucial role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores simplifies experimental setups and extends the imaging duration of SMLM. This review provides an overview of the development of spontaneously blinking rhodamines from 2014 to 2023 and the key mechanistic aspects of intramolecular spirocyclization reactions, aiming to accelerate the advancement of super-resolution imaging technologies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Daiki Hara, Shin-nosuke Uno, Takafumi Motoki, Yuji Kazuta, Yoshihiko Norimine, Masatoshi Suganuma, Shingo Fujiyama, Yuki Shimaoka, Kazuto Yamashita, Masaya Okada, Youichi Nishikawa, Hiroyuki Amino, Shigeki Iwanaga
Summary: This study introduces a novel silinane structure that lowers the ON/OFF ratio of Si-xanthene fluorophores, allowing for higher-density structure visualization in SMLM. The stabilizing effect of silinane on nonfluorescent spirocyclic forms expands the color palette of fluorophores and enables SMLM observation of microtubules in cells. The feasibility of extending SMLM probe design strategies based on Si-xanthenes by modifying substituents on the Si atom is demonstrated.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Yicong Wu, Xiaofei Han, Yijun Su, Melissa Glidewell, Jonathan S. Daniels, Jiamin Liu, Titas Sengupta, Ivan Rey-Suarez, Robert Fischer, Akshay Patel, Christian Combs, Junhui Sun, Xufeng Wu, Ryan Christensen, Corey Smith, Lingyu Bao, Yilun Sun, Leighton H. Duncan, Jiji Chen, Yves Pommier, Yun-Bo Shi, Elizabeth Murphy, Sougata Roy, Arpita Upadhyaya, Daniel Colon-Ramos, Patrick La Riviere, Hari Shroff
Summary: Researchers have enhanced the performance of confocal microscopy using four approaches: developing compact line scanners, combining multi-view imaging, adapting techniques from structured illumination microscopy, and utilizing deep learning. They successfully improved imaging resolution, reduced phototoxicity, and demonstrated these advancements on over 20 different samples.
Article
Biotechnology & Applied Microbiology
H. J. Geertsema, G. Aimola, V Fabricius, J. P. Fuerste, B. B. Kaufer, H. Ewers
Summary: Left-handed DNA probes improve super-resolution DNA-PAINT imaging in the nucleus by reducing background signal, maintaining the same specificity and multiplexing capabilities as right-handed DNA probes.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Chenxi Qian, Kun Miao, Li-En Lin, Xinhong Chen, Jiajun Du, Lu Wei
Summary: VISTA is a label-free superresolution method combining sample expansion and vibrational imaging, enabling high-resolution interrogation of protein-rich biological structures in cells and tissues, with a resolution down to 78 nm.
NATURE COMMUNICATIONS
(2021)
Review
Chemistry, Multidisciplinary
Sreejesh Sreedharan, Rajeshwari Tiwari, Deepak Tyde, Stephen O. Aderinto, Sumit Kumar Pramanik, Amitava Das, James A. Thomas
Summary: Super-resolution microscopy (SRM) has transformed the field of cell biology, allowing researchers to visualize cellular structures at nanometer resolution with single-molecule sensitivity. Luminescent nanocarriers (LNC) play a crucial role in controlling emissive states and organelle-specific delivery, enabling the development of novel optical-switched systems. Challenges related to molecular targeting in biological systems are discussed, providing practical guidance for super-resolution imaging in nanomedicine research.
MATERIALS CHEMISTRY FRONTIERS
(2021)
Review
Optics
Mingwei Tang, Yubing Han, Danchen Jia, Qing Yang, Ji-Xin Cheng
Summary: Far-field chemical microscopy, with molecular electronic or vibrational fingerprint information, offers a new perspective for studying three-dimensional biological, material, and chemical systems. Despite the limitation of optics, recent advances in super-resolution techniques have overcome this hurdle, pushing the boundaries of far-field chemical microscopy in terms of spatial resolution. This technique finds applications in various fields including biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Biochemical Research Methods
Linjing Fang, Fred Monroe, Sammy Weiser Novak, Lyndsey Kirk, Cara R. Schiavon, Seungyoon B. Yu, Tong Zhang, Melissa Wu, Kyle Kastner, Alaa Abdel Latif, Zijun Lin, Andrew Shaw, Yoshiyuki Kubota, John Mendenhall, Zhao Zhang, Gulcin Pekkurnaz, Kristen Harris, Jeremy Howard, Uri Manor
Summary: Point-scanning imaging systems are widely used for high-resolution cellular and tissue imaging, but optimizing resolution, speed, sample preservation, and signal-to-noise ratio simultaneously is challenging. The use of deep learning-based supersampling, known as point-scanning super-resolution (PSSR) imaging, can mitigate these limitations. PSSR facilitates high-resolution, fast, and sensitive image acquisition with otherwise unattainable resolution.
Review
Chemistry, Multidisciplinary
Soham Samanta, Kaitao Lai, Feihu Wu, Yingchao Liu, Songtao Cai, Xusan Yang, Junle Qu, Zhigang Yang
Summary: In the realm of biological research, super-resolution microscopy (SRM) has revolutionized the visualization of sub-cellular structures and their functions beyond the diffraction limit. The recent surge in the development of robust fluorophore systems for various SRM techniques, particularly using xanthene, cyanine, oxazine, and BODIPY cores as building blocks, has become crucial for advancing this field. This review article comprehensively discusses the recent advancements in designing fluorescence probes based on these four important fluorophore cores for SRM, with an emphasis on their integration into live cell imaging applications.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Materials Science, Multidisciplinary
Zhe Chen, Seong H. Kim
Summary: It has been discovered that nanoscale super-lubricity between amorphous silica tip and graphite basal plane can be tuned by physisorbing various molecules. This finding enables on-demand control of friction.
APPLIED MATERIALS TODAY
(2022)
Article
Chemistry, Multidisciplinary
Zengjin Liu, Ying Zheng, Ting Xie, Zihan Chen, Zhenlong Huang, Zhiwei Ye, Yi Xiao
Summary: Spontaneously blinking probes that do not require UV or external additives are highly attractive in super resolution imaging of live cells. A clickable rhodamine spirolactam probe, Atto565-Tet, was successfully applied to super resolution imaging of mitochondria and lysosomes after biorthogonal labelling.
CHINESE CHEMICAL LETTERS
(2021)
Article
Optics
Weisong Zhao, Shiqun Zhao, Zhenqian Han, Xiangyan Ding, Guangwei Hu, Liying Qu, Yuanyuan Huang, Xinwei Wang, Heng Mao, Yaming Jiu, Ying Hu, Jiubin Tan, Xumin Ding, Liangyi Chen, Changliang Guo, Haoyu Li
Summary: High-throughput super-resolution (SR) imaging is attractive for rapid and high-precision profiling in biomedical applications. The proposed SACD method reduces the number of frames required for SR imaging and enables four-dimensional imaging of live cells and events. SACD improves accessibility to SR imaging and facilitates high-throughput and low-cost biological studies.
Article
Chemistry, Multidisciplinary
Michael Holtmannspoetter, Eike Wienbeuker, Timo Dellmann, Isabelle Watrinet, Ana J. Garcia-Saez, Kai Johnsson, Rainer Kurre, Jacob Piehler
Summary: Self-labeling enzymes (SLE) like the HaloTag are valuable tools in high and super-resolution fluorescence microscopy. New fluorogenic substrates for SLE allow imaging with excess dye. Two engineered variants of HaloTag7 with restored dehalogenase activity, reHaloTagS (approx. 0.006 s(-1)) and reHaloTagF (approx. 0.055 s(-1)), showed different turnover kinetics in vitro. Imaging with reHaloTag labeling demonstrated 3-5 times enhanced photostability, and single molecule imaging enabled controlled and stable labeling density over extended periods. Combination with structured illumination allowed simultaneous visualization of single molecule diffusion and organellar dynamics. These applications showcase the potential of reHaloTag labeling in advancing fluorescence microscopy techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Cell Biology
Konstanty Cieslinski, Wu Yu-Le, Lisa Nechyporenko, Sarah Janice Hoerner, Duccio Conti, Michal Skruzny, Jonas Ries
Summary: In this study, the authors used single-molecule localization microscopy to visualize individual kinetochore complexes in budding yeast, and proposed a quantitative model of the budding yeast kinetochore based on their comprehensive dataset.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Cell Biology
Markus Mund, Aline Tschanz, Yu-Le Wu, Felix Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, Jonas Ries
Summary: The study reveals the three-dimensional shapes of clathrin coats during endocytosis and introduces a novel Cooperative Curvature Model that accurately describes the changes in shapes and dynamics. The findings provide insights into the mechanism of clathrin coat remodeling during endocytosis and offer a potential general model for clathrin coat remodeling on the plasma membrane.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Julian Kompa, Jorick Bruins, Marius Glogger, Jonas Wilhelm, Michelle S. Frei, Miroslaw Tarnawski, Elisa D'Este, Mike Heilemann, Julien Hiblot, Kai Johnsson
Summary: The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: Quantitative data analysis is crucial for extracting biological insights from the coordinates of single fluorophores in a single-molecule localization microscopy (SMLM) workflow. LocMoFit, an open-source framework, is introduced to fit an arbitrary model to localization coordinates, extract meaningful parameters, and select suitable models. It enables the analysis of complex, heterogeneous, and dynamic structures, and has been demonstrated in assembling multi-protein distribution maps, calculating single-particle averages, and performing time-resolved reconstruction of dynamic processes from static snapshots. Extensive simulation and visualization routines validate the robustness of LocMoFit, and tutorials are provided to enhance users' extraction of information from SMLM data.
Letter
Biochemical Research Methods
Klaus C. Gwosch, Francisco Balzarotti, Jasmin K. Pape, Philipp Hoess, Jan Ellenberg, Jonas Ries, Ulf Matti, Roman Schmidt, Steffen J. Sahl, Stefan W. Hell
Article
Optics
Jan Becker, Takahiro Deguchi, Alexander Juegler, Ronny Foerster, Uwe Huebner, Jonas Ries, Rainer Heintzmann
Summary: This paper proposes a method to improve the signal-to-noise ratio (SNR) of an imaging system by splitting the pupil and simultaneously acquiring and recombining two sub-images. This method achieves better SNR for transmitting high spatial frequency information without capturing more photons.
Article
Biochemical Research Methods
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
Summary: We propose a deep-learning method for precise localization of spatially variant point emitters, covering the full chip of a modern sCMOS camera. By using a graphic processing unit-based vectorial point spread function fitter, we accurately model the spatially variant PSF of a high numerical aperture objective in the entire field of view. Combined with deformable mirror-based optimal PSF engineering, we demonstrate high-accuracy three-dimensional single-molecule localization microscopy over a large volume, enabling imaging of mitochondria and nuclear pore complexes in entire cells without hardware scanning, with a 100-fold increase in throughput compared to existing techniques.
Article
Multidisciplinary Sciences
Takahiro Deguchi, Malina K. Iwanski, Eva-Maria Schentarra, Christopher Heidebrecht, Lisa Schmidt, Jennifer Heck, Tobias Weihs, Sebastian Schnorrenberg, Philipp Hoess, Sheng Liu, Veronika Chevyreva, Kyung-Min Noh, Lukas C. Kapitein, Jonas Ries
Summary: We developed a live-cell tracking method with nanometer spatial and millisecond temporal resolution using MINFLUX super-resolution technique. This method allowed us to resolve the precise stepping motion of motor protein kinesin-1 on microtubules in living cells. Tracking of motors on fixed cell microtubules also revealed the architecture of the microtubule cytoskeleton with protofilament resolution.
Article
Engineering, Electrical & Electronic
Joran Deschamps, Christian Kieser, Philipp Hoess, Takahiro Deguchi, Jonas Ries
Summary: Modern microscopy increasingly relies on microscope automation for improved throughput, reproducibility, and observation of rare events. Arduino microcontrollers are widely used for automation due to their low cost and accessibility, while field programmable gate arrays (FPGA) are capable of high-speed and parallel signal processing. However, configuring FPGA remains complex. In this work, an affordable FPGA called MicroFPGA with an open-source and user-friendly programming language is used to create a versatile microscope control platform.
Review
Chemistry, Multidisciplinary
Dongjuan Si, Quanlin Li, Yifan Bao, Jingye Zhang, Lu Wang
Summary: The advancement of fluorescence microscopy techniques has provided new possibilities for observing proteins and understanding their functions in living biological systems. However, traditional organic dyes face challenges in achieving high-contrast live-cell labeling due to their insufficient cell permeability and high background signal. In recent years, a new generation of fluorogenic and cell-permeable dyes has been developed, which significantly improve live-cell protein labeling by fine-tuning the reversible equilibrium between a cell-permeable, nonfluorescent state and a fluorescent state of rhodamines. This review presents the mechanism and design strategies of these fluorogenic and cell-permeable rhodamines, as well as their applications in bioimaging and biosensing.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Ewa Sitarska, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, Aline Tschanz, Christer Ejsing, Yannick Schwab, Jan Kosinski, Michael Sixt, Anna Kreshuk, Anna Erzberger, Alba Diz-Munoz
Summary: A curvature-sensing mechanism mediated by the BAR domain protein Snx33 is identified in immune-like cells for obstacle evasion. Actin polymerization at the leading edge of migrating cells is inhibited by Snx33 in regions with inward plasma membrane curvature. Genetic perturbation of this machinery reduces cells' ability to evade obstacles and increases their speed and persistence in obstacle-free environments. This study reveals how cells interpret their environment using actin and plasma membrane biophysics.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Aleksandar Salim, Philipp Werther, Georgios N. Hatzopoulos, Luc Reymond, Richard Wombacher, Pierre Goenczy, Kai Johnsson
Summary: Polo-like kinase (Plk4) is crucial for the biogenesis of centrioles, and a chemical probe called Cen-TCO based on the Plk4 inhibitor centrinone is introduced to visualize Plk4 and centrioles in live or fixed human cells. A bio-orthogonal two-step labeling system is established, allowing the direct labeling of Plk4 for STED super-resolution microscopy. Direct labeling of Plk4 improves the resolution of STED imaging compared to using anti-Plk4 antibodies, highlighting the significance of direct labeling strategies for super-resolution microscopy. Cen-TCO is expected to be an important tool for investigating the biology of Plk4 and centrioles.
Article
Biochemical Research Methods
Yu-Le Wu, Philipp Hoess, Aline Tschanz, Ulf Matti, Markus Mund, Jonas Ries
Summary: This paper presents an open-source framework called LocMoFit for fitting arbitrary models to localization coordinates. The framework has significant potential for analyzing complex, heterogeneous, and dynamic structures, and can be used for assembling protein distribution maps, calculating single-particle averages, and performing time-resolved analysis of highly dynamic processes.
