Review
Biochemistry & Molecular Biology
Carsten Alexander, Manuel Wolters, Martin Aepfelbacher
Summary: The development of super-resolution fluorescence microscopy technologies has significantly improved the resolution limit for fluorescently labeled molecules to the nanometer range. These technologies have great potential in studying bacterial structures, such as secretion systems, with high resolution on a millisecond time scale. This review focuses on recent applications of super-resolution fluorescence microscopy, including the use of MINFLUX fluorescence nanoscopy, which holds the promise of capturing molecular machines in action. The advancements in super-resolution fluorescence microscopy open up new opportunities in molecular and cellular bacteriology.
MOLECULAR MICROBIOLOGY
(2023)
Article
Optics
Prakash Joshi, Partha Pratim Mondal
Summary: Molecular assembly in cellular environments is crucial for understanding biological mechanisms. Biophysical parameters directly linked to cellular states require a multimodel approach for accurate estimation.
Article
Biotechnology & Applied Microbiology
Weisong Zhao, Shiqun Zhao, Liuju Li, Xiaoshuai Huang, Shijia Xing, Yulin Zhang, Guohua Qiu, Zhenqian Han, Yingxu Shang, De-En Sun, Chunyan Shan, Runlong Wu, Lusheng Gu, Shuwen Zhang, Riwang Chen, Jian Xiao, Yanquan Mo, Jianyong Wang, Wei Ji, Xing Chen, Baoquan Ding, Yanmei Liu, Heng Mao, Bao-Liang Song, Jiubin Tan, Jian Liu, Haoyu Li, Liangyi Chen
Summary: Sparse structured illumination microscopy (Sparse-SIM) achieves nearly twofold resolution enhancement by utilizing sparse deconvolution algorithm, enabling the resolution of intricate biological structures such as small fusion pores, nuclear pores, and relative movements of inner and outer mitochondrial membranes.
NATURE BIOTECHNOLOGY
(2022)
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
Optics
Zewei Luo, Ge Wu, Mengting Kong, Zhi Chen, Zhengfei Zhuang, Junchao Fan, Tongsheng Chen
Summary: Forster resonance energy transfer (FRET) microscopy is a valuable tool for studying biological systems, but super-resolution FRET imaging in living cells is challenging. In this study, we propose a SR FRET method called SIM-FRET that combines SR structured illumination microscopy (SIM) imaging and acceptor sensitized emission FRET imaging to achieve live-cell quantitative SR FRET imaging. Our method provides enhanced spatial resolution and maintains the advantages of quantitative FRET analysis. We validate the effectiveness of SIM-FRET through simulated models and live-cell samples, and demonstrate its ability to reveal the intricate structure of FRET signals.
PHOTONICS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Koen van den Dries, Jack Fransen, Alessandra Cambi
Summary: Correlative light and electron microscopy (CLEM) is a powerful imaging approach that combines light and electron microscopy, and has wide applications in biology. This review summarizes the important developments in CLEM for biological research, with a focus on the combination of fluorescence microscopy and electron microscopy.
Review
Biochemistry & Molecular Biology
Afonso Mendes, Hannah S. Heil, Simao Coelho, Christophe Leterrier, Ricardo Henriques
Summary: Understanding the structure of supramolecular complexes is important for studying their function and disease modulation. Super-resolution microscopy combined with single-particle analysis overcomes technical limitations and provides detailed structural information, broadening our knowledge.
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)
Article
Chemistry, Physical
Milan Vala, Lukasz Bujak, Antonio Garcia Marin, Kristyna Holanova, Verena Henrichs, Marcus Braun, Zdenek Lansky, Marek Piliarik
Summary: Research reveals that microtubule disassembly is a discrete process, suggesting a stochastic mechanism of switching from disassembly to assembly phase.
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.
Article
Multidisciplinary Sciences
Rajesh Ranjan, Xin Chen
Summary: This study presents a method for conducting super-resolution timelapse fluorescence live cell imaging in situ, compatible with low fluorescent intensity cells and capable of visualizing multiple subcellular structures. Special procedures in sample preparation and immobilizing specimens are necessary for this technique, but it is broadly applicable to various cell types.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Multidisciplinary
Ilya O. Aparin, Rui Yan, Remi Pelletier, Alexander A. Choi, Dmytro I. Danylchuk, Ke Xu, Andrey S. Klymchenko
Summary: This study proposes a concept of ON/OFF switchable probes for super-resolution fluorescence microscopy based on bright cyanine dyes. The new probes provide higher brightness and slower diffusion at the cell surface, improving the localization precision. The study validated the concept and demonstrated the observation of nanoscale cellular structures with enhanced dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Florian Levet, Guillaume Julien, Remi Galland, Corey Butler, Anne Beghin, Anael Chazeau, Philipp Hoess, Jonas Ries, Gregory Giannone, Jean-Baptiste Sibarita
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieslinski, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries
Article
Biochemical Research Methods
Maximilian Hoerner, Karl Gerhard, Pavel Salavei, Philipp Hoess, Daniel Haerrer, Johannes Kaiser, Jeffrey J. Tabor, Wilfried Weber
ACS SYNTHETIC BIOLOGY
(2019)
Correction
Biochemical Research Methods
Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieslinski, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries
Article
Multidisciplinary Sciences
Michelle S. Frei, Philipp Hoess, Marko Lampe, Bianca Nijmeijer, Moritz Kueblbeck, Jan Ellenberg, Hubert Wadepohl, Jonas Ries, Stefan Pitsch, Luc Reymond, Kai Johnsson
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
Klaus C. Gwosch, Jasmin K. Pape, Francisco Balzarotti, Philipp Hoess, Jan Ellenberg, Jonas Ries, Stefan W. Hell
Article
Cell Biology
Matthew E. Hurlock, Ivana Cavka, Lisa E. Kursel, Jocelyn Haversat, Matthew Wooten, Zehra Nizami, Rashi Turniansky, Philipp Hoess, Jonas Ries, Joseph G. Gall, Ofer Rog, Simone Koehler, Yumi Kim
JOURNAL OF CELL BIOLOGY
(2020)
Article
Biochemical Research Methods
Artur Speiser, Lucas-Raphael Mueller, Philipp Hoess, Ulf Matti, Christopher J. Obara, Wesley R. Legant, Anna Kreshuk, Jakob H. Macke, Jonas Ries, Srinivas C. Turaga
Summary: DECODE is a computational tool that uses deep learning to localize single emitters in high-density two-dimensional and three-dimensional single-molecule localization microscopy data. It outperforms available methods and enables fast live-cell SMLM of dynamic processes.
Correction
Biochemical Research Methods
Artur Speiser, Lucas-Raphael Muller, Philipp Hoess, Ulf Matti, Christopher J. Obara, Wesley R. Legant, Anna Kreshuk, Jakob H. Macke, Jonas Ries, Srinivas C. Turaga
Article
Materials Science, Biomaterials
Ramona Emig, Philipp Hoess, Hanyang Cai, Peter Kohl, Remi Peyronnet, Wilfried Weber, Maximilian Hoerner
Summary: In this study, bacterial phytochromes Cph1 and DrBphP were engineered and characterized for their switching properties to synthesize biohybrid hydrogels with increased light-responsive stiffness modulations. The R472A mutant of Cph1 was found to improve the dynamic range of storage modulus in the hydrogels, but showed a different light-response for the loss modulus compared to the original Cph1-based hydrogel. These findings highlight the importance of matrix viscoelasticity on cellular mechanotransduction.
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
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
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.
