Article
Chemistry, Multidisciplinary
Hao Luo, Chaodi Jiang, Yangdong Wen, Xiaoduo Wang, Feifei Wang, Lianqing Liu, Haibo Yu
Summary: The resolution of fluorescence imaging has been enhanced by the development of super-resolution techniques, but the resolution of bright-field imaging lags behind. This study uses microsphere superlenses to simultaneously enhance the resolution of both imaging techniques and achieves correlated super-resolution imaging. This allows for clear observation of the precise distribution of nanoparticles in cells and has the potential to capture ultrafast biological activity with high temporal resolutions.
Article
Multidisciplinary Sciences
Vytautas Navikas, Samuel M. Leitao, Kristin S. Grussmayer, Adrien Descloux, Barney Drake, Klaus Yserentant, Philipp Werther, Dirk-Peter Herten, Richard Wombacher, Aleksandra Radenovic, Georg E. Fantner
Summary: The combination of scanning ion conductance microscopy (SICM) and live-cell super-resolution optical fluctuation imaging (SOFI) is introduced for non-invasive topographical imaging of soft biological samples, preserving high axial resolution. This method allows for the visualization of cellular structures in 3D with high resolution while maintaining the integrity of fragile membrane samples.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Dokyung Jeong, Doory Kim
Summary: The combination of correlative super-resolution fluorescence microscopy (SRM) and electron microscopy (EM) is an effective hybrid technique that allows the simultaneous acquisition of spatial locations of specific molecules and the context of cellular ultrastructure. Although there are challenges in integrating these two microscopy techniques, extensive research has led to significant improvements and widespread applications.
MOLECULES AND CELLS
(2022)
Article
Chemistry, Multidisciplinary
Raveen K. G. Tank, Victoria A. Lund, Sandip Kumar, Robert D. Turner, Lucia Lafage, Laia Pasquina Lemonche, Per A. Bullough, Ashley Cadby, Simon J. Foster, Jamie K. Hobbs
Summary: This study combines STORMForce and SIMForce technologies to map the synthesis of peptidoglycan, a structural macromolecule of bacterial cell walls, during growth and division in Bacillus subtilis. It reveals a two-stage process of septal synthesis during division and bands of synthesis during growth. The combination of super-resolution optics and AFM provides insights into the synthesis processes of bacterial structural biopolymers.
Article
Chemistry, Analytical
Jelena Lovric, Neda Najafinobar, Michael E. Kurczy, Olivier De Castro, Antje Biesemeier, Lena von Sydow, Magnus Klarqvist, Tom Wirtz, Per Malmberg
Summary: This study developed correlative methodologies to investigate iron accumulation and subcellular localization in alveolar macrophages. By using nanoscale magnetic sector secondary ion mass spectrometry (SIMS) and various high-resolution imaging technologies, they found that iron accumulates in mitochondria and electrolucent compartments such as vacuoles, lysosomes, and lipid droplets.
ANALYTICAL CHEMISTRY
(2022)
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.
Review
Chemistry, Multidisciplinary
Adelaide Miranda, Ana I. Gomez-Varela, Andreas Stylianou, Liisa M. Hirvonen, Humberto Sanchez, Pieter A. A. De Beule
Summary: The invention of the Atomic Force Microscope (AFM) in 1986 allowed for the study of cellular specimens under nearly physiological conditions with nanometric resolution, and the application of AFM to biological research expanded with improvements in imaging modes. Advances in super-resolution fluorescence microscopy techniques have brought the resolution of light microscopy to a level comparable to that of AFM, leading to the combination of AFM with fluorescence based super-resolution microscopy modalities.
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
Multidisciplinary Sciences
Jing Wang, Steven Randolph, Qian Wu, Aurelien Botman, Jenna Schardt, Cedric Bouchet-Marquis, Xiaolin Nan, Chad Rue, Marcus Straw
Summary: A CLEM workflow based on a novel FIB/SEM technology using an OSSM process was proposed, which achieved high resolution and imaging efficiency while improving throughput. By combining with iPALM technique, successful 3D imaging of mitochondria was carried out, demonstrating the advantages of OSSM-SEM in CLEM applications.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
D. Lumkwana, C. Peddie, J. Kriel, L. L. Michie, N. Heathcote, L. Collinson, C. Kinnear, B. Loos
Summary: The study reveals that spermidine induces autophagic flux in a concentration-dependent manner, but the detectable change in the autophagy response critically depends on the specificity and sensitivity of the method employed.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
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
Biology
Ashley M. Rozario, Sam Duwe, Cade Elliott, Riley B. Hargreaves, Gregory W. Moseley, Peter Dedecker, Donna R. Whelan, Toby D. M. Bell
Summary: The study reveals that low concentrations of colcemid cause abnormal microtubule curvature, with a trend of increased curvature associated to higher doses, and curvatures greater than 2 rad/μm being linked to microtubule breakage. Higher doses (>100 nM) of colcemid result in microtubule fragmentation, while lower doses (<20 nM after 5 h) lead to subtle but significant microtubule architecture remodeling and suppression of microtubule dynamics.
Article
Chemistry, Physical
D. Andersen, H. Chen, S. Pal, L. Cressa, O. De Castro, T. Wirtz, G. Schmitz, S. Eswara
Summary: In this study, high-resolution imaging of hydrogen and deuterium within Mg2Ni/Mg2NiH4 hydrogen storage thin films was achieved using a self-developed secondary ion mass spectrometer (SIMS) system attached to a commercially available dual-beam focused ion beam - scanning electron microscope (FIB-SEM) instrument. A novel approach using laser scanning confocal microscopy (LSCM) was demonstrated to measure the size, shape, and distribution of the hydride phase in partially transformed films. The combination of these techniques provides new insights on hydride nucleation and growth within the Mg2NiHx system. Additionally, the efficacy of tracking deuterium as a hydrogen analog for SIMS imaging in high-vacuum chambers was demonstrated.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Biochemistry & Molecular Biology
Dushyant Mehra, Santosh Adhikari, Chiranjib Banerjee, Elias M. Puchner
Summary: This study develops a correlative conventional fluorescence and PALM imaging approach to quantitatively map time-averaged chromatin structure and dynamics below the optical diffraction limit in living cells. The study finds that compacted telomeres move faster and have a higher density of bound dCas9 molecules, but the relative motion of those molecules is more restricted than in less compacted telomeres.
NUCLEIC ACIDS RESEARCH
(2022)
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
Biochemistry & Molecular Biology
Cecilia P. Sanchez, Pintu Patra, Shih-Ying Scott Chang, Christos Karathanasis, Lukas Hanebutte, Nicole Kilian, Marek Cyrklaff, Mike Heilemann, Ulrich S. Schwarz, Mikhail Kudryashev, Michael Lanzer
Summary: KAHRP plays a key role in Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, anchoring parasite-encoded adhesins to the membrane skeleton. Through super-resolution microscopy, it was found that KAHRP initially associates with various skeletal components before eventually colocalizing with remnant actin junctions under the spiral scaffold forming knobs. Additionally, a dynamic model of KAHRP organization and its function in attaching other factors to the spiral scaffold was proposed based on the findings.
MOLECULAR MICROBIOLOGY
(2022)
Article
Cell Biology
Sebastian Malkusch, Johanna Rahm, Marina S. Dietz, Mike Heilemann, Jean-Baptiste Sibarita, Jorn Lotsch
Summary: This study proposes a method that analyzes the differences in receptor mobility between internalin B-treated and -untreated cells. By using hidden Markov modeling and explainable artificial intelligence, the key differences in MET under different treatment conditions are learned from single-particle tracking data, allowing for inference of cellular information.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Multidisciplinary Sciences
Shivam Yadav, Martin Centola, Mathilda Glaesmann, Denys Pogoryelov, Roman Ladig, Mike Heilemann, L. C. Rai, Ozkan Yildiz, Enrico Schleiff
Summary: This study reveals the role of a cyanobacterial cyclophilin in stress responses and assembly of photosynthetic complexes, and presents its unique structural features.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Nicole Koller, Philipp Hoellthaler, Martina Barends, Marius Doering, Christoph Spahn, Veronica Duran, Bibiana Costa, Jennifer Becker, Mike Heilemann, Ulrich Kalinke, Robert Tampe
Summary: Dendritic cells (DCs) translate innate immune responses into adaptive immunity, but the spatial organization of underlying processes is not well understood. By studying human monocyte-derived DCs, we discovered a nanoscale organization of antigen-loading machinery and observed an increase in density during DC maturation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biology
Christoph Spahn, Estibaliz Gomez-de-Mariscal, Romain F. Laine, Pedro M. Pereira, Lucas von Chamier, Mia Conduit, Mariana G. Pinho, Guillaume Jacquemet, Seamus Holden, Mike Heilemann, Ricardo Henriques
Summary: This work demonstrates the use of state-of-the-art artificial neural networks in analyzing bacterial microscopy images. It provides strategies for data acquisition, curation, and model training, and showcases the capabilities of deep learning in tasks such as image segmentation, growth stage classification, phenotypic profiling, and image denoising. The creation of a purposefully-built database aids novice users in quickly exploring data analysis through deep learning.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Marius Glogger, Dongni Wang, Julian Kompa, Ashwin Balakrishnan, Julien Hiblot, Hans-Dieter Barth, Kai Johnsson, Mike Heilemann
Summary: Combining label exchange and the synergy of different types of exchangeable labels can increase the multiplexing capabilities in fluorescence microscopy and the information content of microscopy images.
Article
Chemistry, Multidisciplinary
M. Florencia Sanchez, Marina S. Dietz, Ulrike Mueller, Julian Weghuber, Karl Gatterdam, Ralph Wieneke, Mike Heilemann, Peter Lanzerstorfer, Robert Tampe
Summary: Membrane receptor clustering is important for cell-cell communication, but its physiological role in cell signaling is still unclear. In this study, the researchers developed a dynamic platform to induce cluster formation of neuropeptide Y2 hormone receptors (Y2R) and found that receptor clustering enhanced the cell's response to ligands and played a key role in cell signaling.
Article
Multidisciplinary Sciences
Kaarjel K. Narayanasamy, Johanna Rahm, Siddharth Tourani, Mike Heilemann
Summary: DNA-PAINT image acquisition speed is slow. The authors utilized the neural network DeepSTORM to predict fluorophore positions from high emitter density DNA-PAINT data in order to achieve image acquisition in one minute; they demonstrated multi-color and large-area imaging of semi-thin neuronal tissue.
NATURE COMMUNICATIONS
(2022)
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)
Review
Chemistry, Multidisciplinary
Lorenzo Albertazzi, Mike Heilemann
Summary: The exploitation of low-affinity molecular interactions in protein labeling is an emerging topic in optical microscopy, which allows for a constant renewal of fluorescence signals at target sites. It has versatile use across microscopy methods and has shown potential in 3D, live, and many-target applications. Although some progress has been made in developing low-affinity labels, this research field still has a lot of untapped potential.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Claudia Catapano, Johanna V. Rahm, Marjan Omer, Laura Teodori, Jorgen Kjems, Marina S. Dietz, Mike Heilemann
Summary: HER2 belongs to the ErbB sub-family of receptor tyrosine kinases and is activated through heterodimerization with other ErbB receptors. This study found that HER2 is strongly activated by EGFR-targeting ligands EGF and TGFa, with a distinguishable temporal fingerprint. HER4-targeting ligands EREG and NRG beta 1 showed weaker activation of HER2, with a preference for EREG and a delayed response to NRG beta 1.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Laurell F. F. Kessler, Ashwin Balakrishnan, Nina S. S. Deussner-Helfmann, Yunqing Li, Maximilian Mantel, Marius Glogger, Hans-Dieter Barth, Marina S. S. Dietz, Mike Heilemann
Summary: Super-resolution techniques such as SMLM and STED microscopy are enhanced by using weak affinity-based transient labelling systems, such as DNA-based hybrid systems. However, these techniques suffer from high background fluorescence signal caused by unbound fluorophore-labelled oligonucleotides. This study introduces short-distance self-quenching in fluorophore dimers as an efficient mechanism to reduce background fluorescence signal and increase photon budget in the bound state.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Alon Saguy, Onit Alalouf, Nadav Opatovski, Soohyen Jang, Mike Heilemann, Yoav Shechtman
Summary: Single-molecule localization microscopy (SMLM) has significantly improved spatial resolution in biological imaging, but has limitations in observing dynamics at high temporal resolution. In this study, we introduce DBlink, a deep-learning-based method that reconstructs super spatiotemporal resolution videos from SMLM data. DBlink utilizes a convolutional neural network combined with a bidirectional long short-term memory network to capture long-term dependencies between different frames. Experimental results demonstrate the effectiveness of DBlink in various scenarios, including simulated structures and live-cell dynamic SMLM. This advancement in super-resolution imaging of dynamic processes in living cells is crucial.
Article
Biophysics
Soohyen Jang, Kaarjel K. Narayanasamy, Johanna V. Rahm, Alon Saguy, Julian Kompa, Marina S. Dietz, Kai Johnsson, Yoav Shechtman, Mike Heilemann
Summary: Single-molecule localization microscopy achieves nanometer spatial resolution but faces challenges of long acquisition time and photobleaching. This study combines a neural network and a protein labeling method to improve acquisition speed and temporal resolution, enabling capturing of cellular structure dynamics in live cells.
BIOPHYSICAL REPORTS
(2023)
Proceedings Paper
Cell Biology
Johanna Rahm, Sebastian Malkusch, Ulrike Endesfelder, Marina S. Dietz, Mike Heilemann
Summary: This study presents a pipeline for the analysis of single-particle tracking data, allowing for the determination of biomolecule mobility and diffusion state transitions. The application of this pipeline to receptor trajectories revealed that activated receptors move slower and more confined, with more transitions from free to confined diffusion states. The analysis also identified three diffusion states, with increased transition probabilities towards the less mobile and immobile states upon ligand activation.
SINGLE MOLECULE SPECTROSCOP AND SUPERRESOLUTION IMAGING XV
(2022)