Review
Chemistry, Multidisciplinary
Alan M. Szalai, Cecilia Zaza, Fernando D. Stefani
Summary: The combination of super-resolution fluorescence microscopy and FRET has provided unique tools for studying biological systems and nanomaterials. The integration of these techniques has advanced super-resolution imaging and allowed for visualization of molecular interaction patterns with higher spatial resolution. Future perspectives include possible integration with next generation super-resolution techniques for true molecular-scale spatial resolution.
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.
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
Engineering, Electrical & Electronic
Miranda Parisi, Massimiliano Lucidi, Paolo Visca, Gabriella Cincotti
Summary: This article reviews various super-resolution microscopy techniques utilized by microbiologists to investigate bacterial cell morphology and functions. The achieved resolution is discussed, with a focus on fluorophore selection and other critical imaging requirements. Recent applications are described, which have provided novel insights into bacterial cellular structures. The pivotal role of super-resolution microscopy in addressing antimicrobial resistance is emphasized.
IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS
(2023)
Review
Biochemistry & Molecular Biology
Charles Bond, Adriana N. Santiago-Ruiz, Qing Tang, Melike Lakadamyali
Summary: Since its initial demonstration in 2000, there have been significant technological advancements in far-field super-resolution light microscopy. These developments have allowed for unprecedented visualization of the inner workings of cells. This review discusses the technical details of common implementations of super-resolution microscopy and highlights recent promising advances in the field.
Article
Biochemical Research Methods
Biagio Mandracchia, Jeonghwan Son, Shu Jia
Summary: The study introduced an optofluidic scanning microscopy (OSM) system for super-resolution, live-cell imaging, utilizing multi-focal excitation through the innate fluidic motion of specimens to achieve effective resolution doubling, optical sectioning, and contrast enhancement. The system features minimal instrumental complexity and full compatibility with various microfluidic configurations, offering a promising super-resolution optofluidic paradigm for miniaturization and different levels of integration at the chip scale.
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
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
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, Multidisciplinary
Jiwoong Kwon, Mohamed Saleh Elgawish, Sang-Hee Shim
Summary: Photobleaching is a major limitation in super-resolution microscopy, but it can be overcome by developing new probes, chemical environments, and utilizing the on-off transitions of fluorescence. These efforts have the potential to enhance resolution and extend the observation time in super-resolution microscopy.
Article
Optics
Yujun Tang, Gang Wen, Yong Liang, Linbo Wang, Jie Zhang, Hui LI
Summary: Deep learning is used to reconstruct super-resolution structured illumination microscopy (SR-SIM) images, effectively reducing photobleaching and phototoxicity. A proposed dynamic SIM imaging strategy records full raw images at the beginning and then only wide-field images, with a deep-learning-based reconstruction algorithm improving the quality of reconstructed SR images while reducing photobleaching and phototoxicity. This algorithm also has the capability to observe new structures not included during network training.
Article
Chemistry, Multidisciplinary
Anish R. Roy, Wei Zhang, Zeinab Jahed, Ching-Ting Tsai, Bianxiao Cui, W. E. Moerner
Summary: The topography of the plasma membrane has a strong influence on cellular processes. Recent studies have used 3D nanostructures to study the effects of membrane curvature on protein distribution. In this study, a method combining silicone-oil immersion objective and 3D double-helix point spread function microscopy is introduced to investigate the nanoscale distribution of proteins at the nano-bio interface.
Review
Food Science & Technology
Susana Dianey Gallegos-Cerda, Josue David Hernandez-Varela, Jose Jorge Chanona-Perez, Benjamin Arredondo Tamayo, Juan Vicente Mendez Mendez
Summary: Super-resolution microscopy has the potential to revolutionize food science by providing images beyond the diffraction limit of light microscopes. However, its application in this field is relatively unknown. This review provides a comprehensive overview of the techniques, advances, and challenges of super-resolution microscopy in food science.
FOOD AND BIOPROCESS TECHNOLOGY
(2023)
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
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
Biochemistry & Molecular Biology
Yanan Zhu, Dapeng Sun, Andreas Schertel, Jiying Ning, Xiaofeng Fu, Pam Pam Gwo, Alan M. Watson, Laura C. Zanetti-Domingues, Marisa L. Martin-Fernandez, Zachary Freyberg, Peijun Zhang
Summary: The advancement of serial cryoFIB/SEM technology allows for the study of large volumes of near-native, fully hydrated frozen cells and tissues at voxel sizes of 10 nm and below. This capability was utilized to characterize the disruption of subcellular architecture in primary fibroblasts from a Leigh syndrome patient harboring a disease-causing mutation in USMG5 protein, responsible for impaired mitochondrial energy production.
Article
Biochemistry & Molecular Biology
Alia dos Santos, Alexander W. Cook, Rosemarie E. Gough, Martin Schilling, Nora A. Olszok, Ian Brown, Lin Wang, Jesse Aaron, Marisa L. Martin-Fernandez, Florian Rehfeldt, Christopher P. Toseland
Summary: DNA double-strand breaks lead to genomic instability, affecting the mechanical properties of the nucleus and potentially contributing to drug resistance. Investigation using Atomic Force Microscopy showed that reducing nuclear stiffness and tension can improve DNA repair efficiency and protect against further DNA damage accumulation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Nicole Rufo, Dimitris Korovesis, Sofie Van Eygen, Rita Derua, Abhishek D. Garg, Francesca Finotello, Monica Vara-Perez, Jan Rozanc, Michael Dewaele, Peter A. de Witte, Leonidas G. Alexopoulos, Sophie Janssens, Lasse Sinkkonen, Thomas Sauter, Steven H. L. Verhelst, Patrizia Agostinis
Summary: Immunogenic therapies engaging the unfolded protein response (UPR) following endoplasmic reticulum (ER) stress stimulate immunomodulatory/proinflammatory factors by stressed cancer cells, with NF-kappa B/AP-1 inflammatory stress response being a key mechanism. However, the anti-inflammatory effect of IRE1 alpha kinase inhibitor KIRA6 can impact inflammation responses, urging caution in interpreting its action.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Clinical Neurology
Mitra Forouhan, Wooi Fang Lim, Laura C. Zanetti-Domingues, Christopher J. Tynan, Thomas C. Roberts, Bilal Malik, Raquel Manzano, Alfina A. Speciale, Ruth Ellerington, Antonio Garcia-Guerra, Pietro Fratta, Gianni Soraru, Linda Greensmith, Maria Pennuto, Matthew J. A. Wood, Carlo Rinaldi
Summary: Androgens and androgen-related molecules can regulate muscle hypertrophy by forming a transcriptional complex with SMAD4, but an elongated polyQ tract impairs their cooperativity and leads to muscle atrophy in response to denervation. Delivery of BMP7 can rescue the muscle atrophy in SBMA mice, suggesting potential treatments targeting AR-SMAD4 transcriptional cooperativity for muscle loss.
ACTA NEUROPATHOLOGICA
(2022)
Article
Biochemistry & Molecular Biology
Verity Jackson, Julia Hermann, Christopher J. Tynan, Daniel J. Rolfe, Robin A. Corey, Anna L. Duncan, Maxime Noriega, Amy Chu, Antreas C. Kalli, E. Yvonne Jones, Mark S. P. Sansom, Marisa L. Martin-Fernandez, Elena Seiradake, Matthieu Chavent
Summary: FLRT proteins are broadly expressed single-spanning transmembrane receptors that play important roles in cell adhesion and guidance. This study reveals the dimerization motifs in the FLRT2 transmembrane helix and shows that FLRT2 receptors can associate and co-diffuse on the surface of the same cell, suggesting a competitive switching mechanism between in cis and in trans interactions, similar to classic adhesion molecules.
Article
Chemistry, Physical
Chengwu Qiu, Yaroslav Odarchenko, Qingwei Meng, Shaojun Xu, Ines Lezcano-Gonzalez, Paul Olalde-Velasco, Francesco Maccherozzi, Laura Zanetti-Domingues, Marisa Martin-Fernandez, Andrew M. Beale
Summary: The presence of surface oxygen vacancies (O-vac) on TiO2 can effectively reduce Co3O4 nanoparticles to CoO/Co-0. O-vac are particularly effective at reducing the edges of the nanoparticles, with smaller particles being more easily reduced than larger ones. During heating in H-2/syngas, further reduction and consumption of O-vac prevent the total reoxidation of Co nanoparticles, especially the smallest particles, thus maintaining the presence of metallic Co and potentially enhancing catalyst performance.
Article
Microscopy
M. L. Martin-Fernandez
Summary: EGFR is a key receptor involved in cell function and crucial for human health. Understanding the structure/function relationships of EGFR is important, particularly in relation to oncogenic mutant forms of EGFR that promote the development of lung and brain tumors. Traditional cell-free structural methods have limitations in capturing the complexity of EGFR states in physiological cellular environments, while quantitative fluorescence microscopy and super-resolution methods have proven useful in this regard.
JOURNAL OF MICROSCOPY
(2023)
Article
Multidisciplinary Sciences
Yanan Zhu, Christopher W. Koo, C. Keith Cassidy, Matthew C. Spink, Tao Ni, Laura C. Zanetti-Domingues, Benji Bateman, Marisa L. Martin-Fernandez, Juan Shen, Yuewen Sheng, Yun Song, Zhengyi Yang, Amy C. Rosenzweig, Peijun Zhang
Summary: The pMMO enzyme in methane-oxidizing bacteria forms a higher-order hexagonal array in the inner cell membrane, and its formation correlates with increased enzyme activity.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ellen Clancy, Siva Ramadurai, Sarah R. Needham, Karen Baker, Tara A. Eastwood, Julia A. Weinstein, Daniel P. Mulvihill, Stanley W. Botchway
Summary: Cytoplasmic viscosity plays a crucial role in diffusion-limited reactions, while nuclear viscosity determines gene integrity, regulation, and expression. This study investigates the impact of DNA damage on viscosity using a platinum complex, Pt[L]Cl, as a probe for nuclear viscosity. The results show that the phosphorescence lifetime of Pt[L]Cl is sensitive to viscosity, and fluorescence lifetime of green and red fluorescent proteins (FP) also exhibit sensitivity to cellular viscosity and refractive index changes. Moreover, DNA damage causes significant changes in the viscosity and refractive index of both nuclear and cytoplasmic regions, and a bystander effect is observed in adjacent un-irradiated cells.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Dimitris Korovesis, Teresa Rubio-Tomas, Nektarios Tavernarakis
Summary: Reactive oxygen species (ROS) play a dual role in physiological conditions, acting as signaling molecules but also causing oxidative stress when accumulated excessively. Ageing and neurodegenerative diseases are associated with oxidative stress and the accumulation of damaged proteins. This review discusses the role of oxidative stress in physiology and pathology, as well as state-of-the-art techniques for detecting and quantifying ROS and oxidized proteins in live cells and in vivo. It also explores the recent research findings on the involvement of oxidative stress in neurological disorders.
Article
Chemistry, Multidisciplinary
Bolong Zhang, Kieran D. Richards, Beatrice E. Jones, Abigail R. Collins, Rosie Sanders, Sarah R. Needham, Pu Qian, Amoghavarsha Mahadevegowda, Caterina Ducati, Stanley W. Botchway, Rachel C. Evans
Summary: This study demonstrates the first example of triplet-triplet annihilation upconversion (TTA-UC) based lifetime imaging microscopy. Ultra-small nanoparticle (NP) probes were used to overcome background autofluorescence and achieve excellent image contrast and oxygen mapping in living cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.
