Article
Chemistry, Physical
Cecilia Zaza, German Chiarelli, Ludovit P. Zweifel, Mauricio Pilo-Pais, Evangelos Sisamakis, Fabio Barachati, Fernando D. Stefani, Guillermo P. Acuna
Summary: Fluorescence Resonance Energy Transfer (FRET)-based approaches are unique tools for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and Fluorescence Lifetime Imaging Microscopy (FLIM) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope is demonstrated. DNA Points Accumulation for Imaging in Nanoscale Topography with fluorogenic probes provides a suitable combination of background reduction and binding kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information.
Review
Cell Biology
Mark Tingey, Steven J. Schnell, Wenlan Yu, Jason Saredy, Samuel Junod, Dhrumil Patel, Abdullah A. Alkurdi, Weidong Yang
Summary: The transient nature of RNA and temporal constraints within cells make it difficult to image RNA, especially endogenous RNA in transfected cells. However, recent advances have provided researchers with the tools to image endogenous RNA at the cellular and single-molecule level.
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
Materials Science, Multidisciplinary
Zachary Hallenbeck, Esther A. Wertz
Summary: This work introduces a new technique that combines super-resolution microscopy with fluorescence lifetime imaging microscopy to study the enhancement of single-molecule decay rate by plasmonic nanoparticles. The technique provides high spatial resolution and temporal resolution, allowing for a better understanding of the mechanisms of plasmon-enhanced emission.
ADVANCED OPTICAL MATERIALS
(2022)
Review
Chemistry, Analytical
Yucheng Sun, Zengnan Wu, Yuting Shang, Seong Ho Kang, Jin-Ming Lin
Summary: This article provides a brief overview of the technical development, applications, challenges, and future directions in single-cell analysis using single-molecule detection-based super-resolution microscopy (SMDSRM), aiming to guide researchers in promoting the methodological development and exploring the potential of SMDSRM for single-cell analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Young-Joo Kim, Jaekyung Lim, Do-Nyun Kim
Summary: A systematic method combining data acquisition and preparation with deep-learning-based image super-resolution is proposed for rapid and accurate AFM characterization, achieving around a tenfold reduction in imaging time without significant loss of accuracy. Through a transfer learning strategy, it can be efficiently customized for a specific target sample on demand.
Review
Chemistry, Analytical
Hua Liu, Zhongju Ye, Yanan Deng, Jie Yuan, Lin Wei, Lehui Xiao
Summary: This review describes the basic principles of single-molecule localization microscopy (SMLM), factors affecting imaging quality, recent achievements in the development of fluorescent probes for SMLM, and challenges and future advances in SMLM for biological applications.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Mike Filius, Sung Hyun Kim, Ivo Severins, Chirlmin Joo
Summary: The research team introduced a new method that allows for determining multiple distances between FRET pairs in a single object by resolving the FRET efficiency of multiple fluorophore pairs through transient binding of short DNA strands. This FRET X technology is expected to be a tool for high-resolution analysis of biomolecules and nanostructures.
Review
Chemistry, Analytical
Shengnan Fu, Tengfang Zhang, Huanling Jiang, Yan Xu, Jing Chen, Linghao Zhang, Xin Su
Summary: Single-molecule tools, with the application of DNA nanotechnology, not only improve sensitivity and specificity, but also provide molecular receptors and rulers, helping to address the challenges hindering the development of single-molecule sensing and imaging.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Mark S. Schroeder, Marie-Lena I. E. Harwardt, Johanna Rahm, Yunqing Li, Petra Freund, Marina S. Dietz, Mike Heilemann
Summary: The study established an imaging and analysis pipeline for multiplexed single-molecule localization microscopy (SMLM) of the FGFR network at the plasma membrane. From the super-resolution imaging data, information on FGFR density, spatial distribution, and inner-subfamily colocalization was extracted.
Article
Chemistry, Multidisciplinary
Christopher M. Green, William L. Hughes, Elton Graugnard, Wan Kuang
Summary: The study utilized correlative microscopy techniques to investigate DNA nanostructures, finding that over 75% of defective docking sites were incorporated but inactive, with unincorporated strands playing a minor role in limiting the availability of addressable sites. Further exploration of the effects of strand purification, UV irradiation, and photooxidation on availability provided insights into potential sources of defects and pathways to improving the fidelity of DNA nanostructures.
Article
Nanoscience & Nanotechnology
Nathan Kimmitt, Esther A. Wertz
Summary: Metal nanoantennas can manipulate light emission and detection at the single photon level by confining light into small volumes. By using optical gradient forces, this study successfully traps single emitters into nanocavities, showing improved photostability and track lengths compared to emitters farther away from the structure, especially for resonant antennas. These results pave the way for reliable coupling of single emitters to single nanoantennas using plasmonic optical trapping.
Article
Chemistry, Multidisciplinary
Florian Schueder, Juanita Lara-Gutierrez, Daniel Haas, Kai Sandvold Beckwith, Peng Yin, Jan Ellenberg, Ralf Jungmann
Summary: The researchers introduced a new super-resolution microscopy technique called pPAINT, which can sensitively detect the spatial proximity of biomolecules and has broad applications in cellular research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(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)
Article
Optics
Miroslav Duris, Petr Bouchal, Radim Chmelik
Summary: Biomedical and metasurface researchers commonly use quantitative phase imaging (QPI) as their primary imaging technique due to its high-throughput, label-free, and quantitative nature. However, achieving super-resolution in QPI has been a challenge. In this study, a method for real-time super-resolution QPI is presented, achieved through shaping the coherence gate in the holographic microscope with partially coherent illumination. This method demonstrates resolution improvement on both simulated and experimental data, and shows practical feasibility in imaging biological specimens.
Article
Biochemical Research Methods
Eugenia Voytik, Isabell Bludau, Sander Willems, Fynn M. Hansen, Andreas-David Brunner, Maximilian T. Strauss, Matthias Mann
Summary: AlphaMap is a Python package for visual exploration of peptide-level proteomics data, mapping identified peptides and post-translational modifications to protein sequences with prior knowledge from UniProt. It provides an intuitive graphical user interface and flexibility as a Python package for integration into common analysis workflows for data visualization.
Article
Multidisciplinary Sciences
Adam C. O'Neill, Fatma Uzbas, Giulia Antognolli, Florencia Merino, Kalina Draganova, Alex Jaeck, Sirui Zhang, Giorgia Pedini, Julia P. Schessner, Kimberly Cramer, Aloys Schepers, Fabian Metzger, Miriam Esgleas, Pawel Smialowski, Renzo Guerrini, Sven Falk, Regina Feederle, Saskia Freytag, Zefeng Wang, Melanie Bahlo, Ralf Jungmann, Claudia Bagni, Georg H. H. Borner, Stephen P. Robertson, Stefanie M. Hauck, Magdalena Goetz
Summary: The centrosome serves as an anchor for the cytoskeleton and plays a crucial role in cell division, migration, and cilia formation. By using spatial proteomics, researchers have uncovered protein interaction networks specific to the centrosome in human induced pluripotent stem cell-derived neural stem cells and neurons. These cell type-specific centrosome interactomes explain how genetic variants in widespread proteins can lead to brain-specific phenotypes.
Editorial Material
Biochemistry & Molecular Biology
Florian Schueder, Joerg Bewersdorf
Summary: Spatial omics techniques provide comprehensive data about the identity and function of cells in tissues. Epigenetic multiplexing approaches like MERFISH allow researchers to study the epigenomic regulation of gene expression in tissue-specific regions.
Article
Chemistry, Multidisciplinary
Alexandra S. S. Eklund, Ralf Jungmann
Summary: Super-resolution microscopy has revolutionized sample characterization in the life sciences. DNA-PAINT is an easy-to-implement method that uses programmable binding of dye-labeled DNA to their respective docking strands. Peptide-PAINT, a new method, improves labeling by using short coiled-coil peptide sequences, but lacks multiplexing ability.
Article
Multidisciplinary Sciences
Mohamadreza Fazel, Michael J. Wester, David J. Schodt, Sebastian Restrepo Cruz, Sebastian Strauss, Florian Schueder, Thomas Schlichthaerle, Jennifer M. Gillette, Diane S. Lidke, Bernd Rieger, Ralf Jungmann, Keith A. Lidke
Summary: This study utilizes a Bayesian method to infer the positions of tagged molecules, improving localization precision and facilitating nanoscale structural insights by exploring the possible combinations of multiple blinking/binding events.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Wen-Feng Zeng, Xie-Xuan Zhou, Sander Willems, Constantin Ammar, Maria Wahle, Isabell Bludau, Eugenia Voytik, Maximillian T. Strauss, Matthias Mann
Summary: Machine learning and deep learning are becoming increasingly important in MS-based proteomics. AlphaPeptDeep is a modular Python framework built on PyTorch that can learn and predict peptide properties. It features a model shop that allows non-specialists to create models easily. AlphaPeptDeep can also predict sequence-based properties and performs well in predicting retention time, collisional cross sections, and fragment intensities.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Florian Schueder, Pierre Mangeol, Eunice HoYee Chan, Renate Rees, Juergen Schuenemann, Ralf Jungmann, Dirk Goerlich, Frank Schnorrer
Summary: Sarcomeres, the force-producing units of striated muscles, depend on the titin protein for their nanoarchitecture. This study used nanobodies and super-resolution microscopy to determine the location of two Drosophila titin homologs in flight muscles. The findings reveal the presence of these titin homologs and their role in muscle structure, providing insights into the organization of sarcomeres in non-vertebrates.
Article
Biology
Sebastian Strauss, Julia Acker, Guido Papa, Daniel Desiro, Florian Schueder, Alexander Borodavka, Ralf Jungmann
Summary: Rotaviruses form cytoplasmic protein-RNA granules called viroplasms during infection, which are important for segmented genome assembly and replication. Our study found that the distribution of viral RNA in viroplasms is different from the cytoplasmic RNA distribution, with the largest RNA being the most enriched. This suggests a selective RNA enrichment mechanism. The presence of 3' untranslated terminal regions and the localization of the viral polymerase VP1 in viroplasms are required for the accumulation of transcripts.
Article
Multidisciplinary Sciences
Susanne C. M. Reinhardt, Luciano A. Masullo, Isabelle Baudrexel, Philipp R. Steen, Rafal Kowalewski, Alexandra S. Eklund, Sebastian Strauss, Eduard M. Unterauer, Thomas Schlichthaerle, Maximilian T. Strauss, Christian Klein, Ralf Jungmann
Summary: Fluorescence microscopy is a major characterization method in the life sciences, but current super-resolution techniques do not achieve Angstrom resolution. This study introduces a DNA-barcoding method that greatly improves the resolution of fluorescence microscopy, allowing for single-protein resolution in intact cells. The method also demonstrates Angstrom resolution for DNA origami.
Article
Biochemical Research Methods
Florian A. Rosenberger, Marvin Thielert, Maximilian T. Strauss, Lisa Schweizer, Constantin Ammar, Sophia C. Maedler, Andreas Metousis, Patricia Skowronek, Maria Wahle, Katherine Madden, Janine Gote-Schniering, Anna Semenova, Herbert B. Schiller, Edwin Rodriguez, Thierry M. Nordmann, Andreas Mund, Matthias Mann
Summary: Single-cell proteomics by mass spectrometry is a powerful method for studying biological heterogeneity, and single-cell Deep Visual Proteomics (scDVP) is a technology that integrates high-content imaging, laser microdissection, and multiplexed mass spectrometry to analyze the spatial proteome of tissues. It can identify thousands of proteins and reveal differential regulation in spatially distinct regions.
Article
Multidisciplinary Sciences
Christian Niederauer, Chikim Nguyen, Miles Wang-Henderson, Johannes Stein, Sebastian Strauss, Alexander Cumberworth, Florian Stehr, Ralf Jungmann, Petra Schwille, Kristina A. Ganzinger
Summary: DNA-PAINT-SPT technique overcomes the limitations of fluorophore photobleaching and significantly improves observation times in in vitro SPT experiments. It is now extended to enable simultaneous dual-colour detection, allowing the quantification of protein dimerization and live cell membrane protein tracking. The technique demonstrates improved performance compared to single-dye SPT.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Elena Krismer, Isabell Bludau, Maximilian T. Strauss, Matthias Mann
Summary: AlphaPeptStats is a comprehensive Python package for normalization, imputation, visualization, and statistical analysis of label-free proteomics data. It provides a wide range of statistical algorithms and data visualization capabilities, allowing researchers to manually or automatically explore complex datasets and identify interesting patterns and outliers.
Meeting Abstract
Biochemical Research Methods
Andre C. Michaelis, Andreas-David Brunner, Maximilian Zwiebel, Florian Meier, Maximilian T. Strauss, Isabell Bludau, Matthias Mann
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Meeting Abstract
Gastroenterology & Hepatology
Lili Niu, Maja Thiele, Philipp Geyer, Ditlev Nytoft Rasmussen, Henry Emanuel Webel, Alberto Delgado, Rajat Gupta, Florian Meier, Maximilian Strauss, Maria Kjaergaard, Katrine Prier Lindvig, Mads Israelsen, Simon Rasmussen, Torben Hansen, Matthias Mann, Aleksander Krag
JOURNAL OF HEPATOLOGY
(2022)
