Article
Multidisciplinary Sciences
Yanxin Zhang, Rongrong Wen, Jialing Hu, Daoming Guan, Xiaochen Qiu, Yunxiang Zhang, Daniel S. Kohane, Qian Liu
Summary: Manipulating topological arrangement can enhance upconversion luminescence in inorganic optical nanosystems. The outside-in architecture produces the maximum upconversion luminescence, around 6 times brighter than the inside-out architecture at the single-particle level. Monte Carlo simulation suggests that topology-dependent energy migration favors the upconversion luminescence of the outside-in structure.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Yi-Fan Tian, Yu-Peng Zhang, Qiu-Mei Wu, Dai-Wen Pang, Shu-Lin Liu, Zhi-Gang Wang
Summary: Translation is a critical cellular activity regulated by viruses, and studying its kinetics and subcellular localization requires real-time visualization techniques. This study presents a new method using the CRISPR/dCas13 system and specific complementary guide RNAs to dynamically image translation without altering the coding regions. This tool provides promising opportunities for further investigating translation mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Yi-Fan Tian, Yu-Peng Zhang, Qiu-Mei Wu, Dai-Wen Pang, Shu-Lin Liu, Zhi-Gang Wang
Summary: This article introduces a method for real-time dynamic translation imaging using the CRISPR/dCas13 system. The method labels the unmodified coding regions of target mRNA, enabling real-time visualization of the translation process, and is promising for further investigations into translation mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Shiori Iida, Soya Shinkai, Yuji Itoh, Sachiko Tamura, Masato T. Kanemaki, Shuichi Onami, Kazuhiro Maeshima
Summary: The study revealed that local chromatin motion remains steady in live human cells throughout the phases of G1, S, and G2, driven mainly by thermal fluctuations, with an increase in motion following a DNA damage response. These findings support the viscoelastic properties of chromatin and suggest that steady-state chromatin motion enables cells to perform housekeeping functions during interphase.
Article
Chemistry, Analytical
Ricardo Monge Neria, Lydia Kisley
Summary: We used HILO microscopy to determine the three-dimensional location of single-molecule analytes within commercial stationary phase materials. By immobilizing individual stationary phase particles and modifying the microscope, we achieved improved imaging depth and resolution. The data showed that the heterogeneity in separations is caused by nanoscale kinetic differences on distinct adsorption sites rather than microscale affinity differences.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
J. J. Erik Maris, Freddy T. Rabouw, Bert M. Weckhuysen, Florian Meirer
Summary: Single-particle tracking is a powerful method for studying the motion of individual molecules and particles. The DiffusionLab software package provides motion analysis tools for challenging data sets, allowing trajectory classification based on motion type and computation of diffusion constants.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Dominique Bourgeois
Summary: Single Molecule Imaging Simulator (SMIS) is a simulation software that models the photophysical behavior of fluorophores in single-molecule localization experiments. It can simulate a widefield microscope and incorporate fluorophores with their spectral and photophysical properties. SMIS allows the evaluation of advanced fluorophore characteristics, imaging conditions, and environmental parameters, facilitating the design of real experiments and their interpretation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Xiaolong Liu, Yifei Jiang, Yutong Cui, Jinghe Yuan, Xiaohong Fang
Summary: Single-molecule microscopy is advantageous for studying molecular dynamics, but faces challenges in bio-chemical studies. Deep learning networks show promise in automating single-molecule experiments and processing data.
Article
Optics
Jie Xu, Changjun Min, Yuquan Zhang, Jielei Ni, Gengwei Cao, Qianyi Wei, Jianjun Yang, Xiaocong Yuan
Summary: In this study, a wide-field single-probe structured light microscopy (SPSLM) is proposed and built to image the ultrafast three-dimensional topography evolution induced by femtosecond (fs) lasers. The SPSLM achieves high-resolution imaging in both spatial and temporal domains by utilizing a single imaging frame and a structured probe pulse. The technology is of great significance for studying ultrafast dynamics in fields such as fs laser ablation and material science.
PHOTONICS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Esley Torres-Garcia, Raul Pinto-Camara, Alejandro Linares, Damian Martinez, Victor Abonza, Eduardo Brito-Alarcon, Carlos Calcines-Cruz, Gustavo Valdes-Galindo, David Torres, Martina Jablonski, Hector H. Torres-Martinez, Jose L. Martinez, Haydee O. Hernandez, Jose P. Ocelotl-Oviedo, Yasel Garces, Marco Barchi, Rocco D'Antuono, Ana Boskovic, Joseph G. Dubrovsky, Alberto Darszon, Mariano G. Buffone, Roberto Rodriguez Morales, Juan Manuel Rendon-Mancha, Christopher D. Wood, Armando Hernandez-Garcia, Diego Krapf, Alvaro H. Crevenna, Adan Guerrero
Summary: This study presents a new super-resolution microscopy algorithm called Mean-Shift Super Resolution (MSSR), which extends the spatial resolution of single fluorescence images beyond the diffraction limit. MSSR works on various fluorophore densities and optical setups, and has denoising capabilities.
NATURE COMMUNICATIONS
(2022)
Article
Mechanics
Eric Hedlund, Keith Hedlund, Adam Green, Ravin Chowdhury, Cheol S. Park, Joseph E. Maclennan, Noel A. Clark
Summary: Machine learning techniques have been used to identify inclusions on the surface of liquid crystal films. This method achieves higher accuracy than conventional tracking software, especially in non-uniform backgrounds or when target features are close to each other.
Article
Chemistry, Multidisciplinary
Shasha Liu, Mengqi Lv, Haoran Li, Sa Wang, Chengdong Feng, Xiaoliang Wang, Wenbing Hu, Wei Wang
Summary: This study proposes a thermal-optical imaging technique to determine the glass transition and rubber-fluid transition temperatures of single isolated polystyrene nanospheres for the first time. The experiments reveal the influence of the substrate on the glass transition temperature and the existence of a surface layer with enhanced molecular mobility.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Nesrine Aissaoui, Josephine Lai-Kee-Him, Allan Mills, Nathalie Declerck, Zakia Morichaud, Konstantin Brodolin, Sonia Baconnais, Eric Le Cam, Jean Baptiste Charbonnier, Remy Sounier, Sebastien Granier, Virginie Ropars, Patrick Bron, Gaetan Bellot
Summary: Technological breakthroughs in electron microscopy have made it possible to study biological macromolecular complexes with novel challenges, such as sample preparation and heterogeneous macromolecular assemblies. In this study, a V-shaped DNA origami template was used to position proteins, demonstrating a new approach for characterizing mechanosensitive proteins and expanding the range of potential targets for single-particle EM investigation. Validation with RNAP protein showed compatibility with cryo-EM sample preparation.
Article
Neurosciences
Jinwoo Hong, Hyuk Jin Yun, Gilsoon Park, Seonggyu Kim, Yangming Ou, Lana Vasung, Caitlin K. Rollins, Cynthia M. Ortinau, Emiko Takeoka, Shizuko Akiyama, Tomo Tarui, Judy A. Estroff, Patricia Ellen Grant, Jong-Min Lee, Kiho Im
Summary: The study successfully predicted fetal brain age accurately using a 2D single-channel CNN with multiplanar slices, significantly reducing prediction error and improving prediction accuracy.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Guangzhong Ma, Zijian Wan, Yunze Yang, Wenwen Jing, Shaopeng Wang
Summary: This study introduces a plasmonic imaging technique that enables precise 3D tracking of surface-tethered single particles in real time, with applications in studying DNA-enzyme interactions. The analysis of particle motion patterns allows for the identification of specific and nonspecific interactions in immunoassays, contributing to the understanding of molecular dynamics and interactions at the single-molecule level.
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
Education, Scientific Disciplines
Dogus Darici, Agnes Yueh-Dan Schneider, Markus Missler, Bettina Pfleiderer
Summary: This study investigated the presence of gender bias in anatomy e-learning platforms and found that they had a more balanced representation of gender compared to traditional textbooks. The results highlight the importance of electronic platforms in reducing stereotypical perceptions of human anatomy.
ANATOMICAL SCIENCES EDUCATION
(2023)
Article
Biochemical Research Methods
Anne Beghin, Gianluca Grenci, Geetika Sahni, Su Guo, Harini Rajendiran, Tom Delaire, Saburnisha Binte Mohamad Raffi, Damien Blanc, Richard de Mets, Hui Ting Ong, Xareni Galindo, Anais Monet, Vidhyalakshmi Acharya, Victor Racine, Florian Levet, Remi Galland, Jean-Baptiste Sibarita, Virgile Viasnoff
Summary: In this study, an automated multi-scale 3D imaging platform was presented, which combines high-density organoid culture with rapid and live 3D imaging. The platform streamlines the process and achieves a throughput of 300 organoids per hour. Deep learning algorithms were used to quantify the morphogenetic organizations of organoids.
Article
Multidisciplinary Sciences
Premchand Rajeev, Nivedita Singh, Adel Kechkar, Cory Butler, Narendrakumar Ramanan, Jean-Baptiste Sibarita, Mini Jose, Deepak Nair
Summary: Synapse associated protein-97/Human Disk Large (SAP97/hDLG) is a conserved, alternatively spliced, modular, scaffolding protein critical in regulating the molecular organization of cell-cell junctions in vertebrates. The molecular determinants of first order phase transition of SAP97/hDLG is controlled by morpho-functional changes in its nanoscale organization. Additionally, the nanoscale molecular signatures of these signaling islands and phase transitions are altered in response to changes in cytosolic Ca2+, showing differential sensitivities to Ca2+ bound Calmodulin. SAP97/hDLG forms nanosized molecular domains in both heterologous cells and hippocampal pyramidal neurons, with molecular signatures and exchange kinetics being modulated by the availability of alternatively spliced isoforms.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Premchand Rajeev, Nivedita Singh, Adel Kechkar, Corey Butler, Narendrakumar Ramanan, Jean-Baptiste Sibarita, Mini Jose, Deepak Nair
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Pranesh Padmanabhan, Andrew Kneynsberg, Esteban Cruz, Rumelo Amor, Jean-Baptiste Sibarita, Jurgen Gotz
Summary: We found that Tau exhibits spatial and kinetic heterogeneity near the plasma membrane, forming nanometer-sized hot spots, which are longer-lasting than its interaction with microtubules. These hot spots are different from Tau condensation on microtubules and independent of cholesterol.
Article
Biochemistry & Molecular Biology
Ramon Martinez-Marmol, Christopher Small, Anmin Jiang, Tishila Palliyaguru, Tristan P. Wallis, Rachel S. Gormal, Jean-Baptiste Sibarita, Jurgen Gotz, Frederic A. Meunier
Summary: This study reveals the important role of Fyn kinase in learning and memory, and its involvement in dementias. The P301L mutant Tau promotes abnormal clustering of Fyn in dendrites, and inhibition of Fyn's auto-inhibitory closed conformation increases its clustering. The ability of P301L Tau to form biomolecular condensates enhances Fyn clustering and signaling.
MOLECULAR PSYCHIATRY
(2023)
Article
Multidisciplinary Sciences
Karen Perez de Arce, Adema Ribic, Dhrubajyoti Chowdhury, Katherine Watters, Garth J. J. Thompson, Basavaraju G. G. Sanganahalli, Elizabeth T. C. Lippard, Astrid Rohlmann, Stephen M. M. Strittmatter, Markus Missler, Fahmeed Hyder, Thomas Biederer
Summary: LRRTM1 is a post synaptic adhesion protein that promotes synaptic transmission. The authors found that LRRTM1 and SynCAM 1 work together to organize synapses in the prefrontal cortex, affecting cognitive function in mice. The study highlights the roles of LRRTM1 and SynCAM 1 in synaptic, network, and behavioral domains.
NATURE COMMUNICATIONS
(2023)
Letter
Biochemical Research Methods
Florian Levet, Jean-Baptiste Sibarita
Article
Biochemical Research Methods
Daniel J. Nieves, Jeremy A. Pike, Florian Levet, David J. Williamson, Mohammed Baragilly, Sandra Oloketuyi, Ario de Marco, Juliette Griffie, Daniel Sage, Edward A. K. Cohen, Jean-Baptiste Sibarita, Mike Heilemann, Dylan M. Owen
Summary: This study compares the performance of seven algorithms for cluster analysis of single-molecule localization microscopy data. The results provide a framework for comparing these methods and guide users to the best tools. Cluster analysis is an effective method for extracting meaningful information from single-molecule localization microscopy data, but there is no consensus framework for evaluating the performance of different algorithms. This study proposes a systematic approach and evaluation metrics based on simulated conditions to score the success of clustering algorithms.
Article
Neurosciences
Adekunle T. Bademosi, Marianna Decet, Sabine Kuenen, Carles Calatayud, Jef Swerts, Sandra F. Gallego, Nils Schoovaerts, Spyridoula Karamanou, Nikolaos Louros, Ella Martin, Jean-Baptiste Sibarita, Katlijn Vints, Natalia V. Gounko, Frederic A. Meunier, Anastassios Economou, Wim Versees, Frederic Rousseau, Joost Schymkowitz, Sandra-F. Soukup, Patrik Verstreken
Summary: Neuronal activity-induced calcium influx is connected to synaptic autophagy and neuronal survival through Endophilin-A in a Parkinson disease-relevant fashion. Mutations in the disordered loop of Endophilin-A render it insensitive to neuronal stimulation, affecting protein dynamics and autophagosome formation. Balanced stimulation-induced autophagy is critical for dopaminergic neuron survival, and a variant in the human ENDOA1 disordered loop conferring risk to Parkinson disease also blocks nanodomain protein mobility and autophagy in vivo and in human-induced dopaminergic neurons.
Article
Multidisciplinary Sciences
Tina Ghelani, Marc Escher, Ulrich Thomas, Klara Esch, Janine Luetzkendorf, Harald Depner, Marta Maglione, Pierre Parutto, Scott Gratz, Tanja Matkovic-Rachid, Stefanie Ryglewski, Alexander M. Walter, David Holcman, Kate O'Connor Giles, Martin Heine, Stephan J. Sigrist
Summary: In this study, dynamic intravital single-molecule imaging was used to investigate the interaction between scaffold proteins and voltage-gated calcium channels (VGCCs) during presynaptic homeostatic potentiation in Drosophila AZs. It was found that the interaction between the intracellular carboxyl terminus of the Cac channel and the amino-terminal region of the ELKS-family protein Bruchpilot played a crucial role in the sustained potentiation of AZs.
Article
Physiology
Barbora Schwarzova, Tim Stuedemann, Muhammed Soenmez, Judith Roessinger, Bangfen Pan, Thomas Eschenhagen, Justus Stenzig, J. Simon Wiegert, Torsten Christ, Florian Weinberger
Summary: Optogenetic actuators are advanced tools used to control physiological activity in excitable cells. They have been used in neuroscience to study the function of specific cell populations. In this study, researchers investigated the effects of BiPOLES activation in cardiomyocytes and found that both cation and anion channelrhodopsins can be used to either activate or silence these cells using pulsed photostimulation.
PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY
(2023)
Article
Biochemical Research Methods
Andrey Formozov, Alexander Dieter, J. Simon Wiegert
Summary: Fiber photometry is a popular technique in neuroscience for inferring brain activity by recording calcium dynamics. However, combining different biosensors and optogenetic actuators typically requires pre-configured assemblies of optical hardware. Therefore, a device that can flexibly combine molecular tools in different spectral ranges is highly desired.
CELL REPORTS METHODS
(2023)
Article
Mathematical & Computational Biology
Corey Butler, G. Ezequiel Saraceno, Adel Kechkar, Nathan Benac, Vincent Studer, Julien P. Dupuis, Laurent Groc, Remi Galland, Jean-Baptiste Sibarita
Summary: Single molecule localization and tracking techniques have provided unprecedented insight into the nanoscale molecular organization and dynamics in living cells. By simultaneously localizing and tracking multiple fluorescent emitters, important biological information can be obtained with high spatial and temporal resolution over large field of views.
FRONTIERS IN BIOINFORMATICS
(2022)