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
Chemistry, Multidisciplinary
Marius Glogger, Christoph Spahn, Joerg Enderlein, Mike Heilemann
Summary: SOFI is a super-resolution microscopy technique that analyzes intensity fluctuations to overcome the diffraction limit, and can circumvent fluorophore photobleaching by using reversible and transient fluorophore labels that bind to a target.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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
Biochemistry & Molecular Biology
Yi-Fan Fang, Yi-Lan Li, Xiao-Ming Li, Ji-Long Liu
Summary: CTP synthase can form filamentous structures called cytoophidia in cells, which has dynamic and reticular properties and provides space for other components.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Ming-Hao Li, Daniel P. Raleigh, Erwin London
Summary: The natural asymmetry of cellular membranes affects their properties. Methods involving cyclodextrin have been developed for preparing asymmetric vesicles, enhancing their resistance to leakage and improving stability.
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
Paul Smith, Christian D. Lorenz
Summary: LiPyphilic is a fast, fully tested, and easy-to-install Python package for analyzing emergent phenomena in lipid membranes through molecular dynamics simulations. It offers various analysis tools and on-the-fly trajectory transformations to handle membranes with complex compositions effectively. Additionally, LiPyphilic addresses the issue of fluctuations in box volume under the NPT ensemble, which has been overlooked in most current implementations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
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
Nanoscience & Nanotechnology
Kyu Ri Choi, Shilong Li, Igor Ozerov, Frederic Bedu, Dong Hee Park, Bin Chan Joo, Jeong Weon Wu, Sile Nic Chormaic, Yeon Ui Lee
Summary: This study presents a systematic investigation of fluorescence engineering in metamaterial-assisted localization microscopy using cyclic group metasurfaces coated with a fluorescent film. The spatially varied Purcell effect near these metasurfaces leads to tailored variations in the photoluminescence intensity and photobleaching lifetime of fluorophores. The enhanced emissions and blinking dynamics of the fluorophores on these metasurfaces result in a super-resolution localization image with a localization accuracy of 0.9 nm.
Article
Chemistry, Multidisciplinary
Amandeep Kaur, Liam D. Adair, Sarah R. Ball, Elizabeth J. New, Margaret Sunde
Summary: In this study, the researchers developed a fluorescent amyloid sensor called AmyBlink-1 and used it for super-resolution imaging of amyloid structures. They were able to achieve nanoscale imaging of different types of amyloid fibrils and quantify their morphological features.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Optics
Sanduni I. Fernando, Jason T. Martineau, Robert J. Hobson, Thien N. Vu, Brian Baker, Brian D. Mueller, Rajesh Menon, Erik M. Jorgensen, Jordan M. Gerton
Summary: By engineering the point-spread function (PSF) of single molecules, different fluorophore species can be imaged simultaneously and distinguished by their unique PSF patterns. In this study, we inserted a silicon-dioxide phase plate at the Fourier plane of the detection path of a wide-field fluorescence microscope to generate distinguishable PSFs (X-PSFs) at different wavelengths. We demonstrated that the resulting PSFs can be localized spatially and spectrally using a maximum-likelihood estimation algorithm and can be used for hyper-spectral super-resolution microscopy of biological samples.
Article
Microscopy
Jafar H. Ghithan, Jennifer M. Noel, Thomas J. Roussel, Maureen A. McCall, Bruce W. Alphenaar, Sergio B. Mendes
Summary: The breakthroughs in far-field imaging techniques have led to the development of STED microscopy using a synchronous detection approach to reduce photobleaching effects. This approach allows for super-resolution imaging at lower power levels, which is particularly relevant for biological samples.
Article
Biochemistry & Molecular Biology
Nicole C. Robb
Summary: Diseases caused by viruses, such as the COVID-19 pandemic, pose significant challenges to human society. Super-resolution imaging technologies have enabled the direct visualization of virus structures at the nanoscale, providing new insights into their morphology and structure.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2022)
Article
Multidisciplinary Sciences
Jan Christoph Thiele, Marvin Jungblut, Dominic A. Helmerich, Roman Tsukanov, Anna Chizhik, Alexey Chizhik, Martin J. Schnermann, Markus Sauer, Oleksii Nevskyi, Joerg Enderlein
Summary: The MIET imaging method utilizes metal-induced energy transfer to achieve nanometer-level axial resolution, and combines it with the excellent lateral resolution of dSTORM to enable three-dimensional super-resolution imaging of subcellular structures.
Article
Optics
Sungyong You, Jerry Chao, Edward A. K. Cohen, E. Sally Ward, Raimund J. Ober
Summary: Single-molecule microscopy allows for high-resolution visualization of subcellular structures and investigation of individual molecular dynamics. Calibrating the microscope for multicolor imaging experiments at a nanometer scale is crucial for accurate results. This calibration method involves imaging a standard sample to detect and evaluate optical aberrations, including those caused by a dichroic filter and objective lens, to ensure high-quality imaging.
Article
Biochemistry & Molecular Biology
Alicja Kluczyk, Julita Ludwiczak, Maciej Modzel, Mariola Kuczer, Marek Cebrat, Monika Biernat, Remigiusz Bachor
Summary: Cosmetics containing Argireline are gaining public interest for their proven ability to reduce facial wrinkles. Argireline works by inhibiting neurotransmitter release at the neuromuscular junction, similar to the effects of botox. Analysis using RP-HPLC/MS and MS/MS confirmed the presence of Argireline and its oxidized form in various cosmetics, with the methionine residue identified as the oxidation point. The developed sample preparation strategy minimizes and monitors methionine oxidation, raising concerns about the impact of ingredients on cosmetic product stability.
CHEMISTRY & BIODIVERSITY
(2021)
Article
Chemistry, Organic
Emily M. Work, Guillermo Ferraudi, Luke Kiefer, Gang Liu, Michael Grigalunas, Atul Bhardwaj, Rasmin Kaur, Janel M. Dempsey, Daniel Wuestner, Paul Helquist, Olaf Wiest
Summary: The novel 15-azasterol has been designed and synthesized as a luminescent cholesterol mimic for monitoring cholesterol trafficking. It exhibits a brightness similar to 32-times greater than widely used probes, along with resistance to photobleaching and a large Stokes-like shift of approximately 150-200 nm. Experimental and computational studies have revealed the photophysical properties of the probe, indicating an intersystem crossing to the triplet excited state with subsequent phosphorescent decay. Additionally, molecular dynamics simulations demonstrate the structural similarity of the probe to cholesterol in its binding mode to NPC proteins.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Organic
Mick Hornum, Mads W. Mulberg, Maria Szomek, Peter Reinholdt, Jonathan R. Brewer, Daniel Wuestner, Jacob Kongsted, Poul Nielsen
Summary: Nile Red is a popular histological stain with unrivaled fluorescent properties for cellular membranes and lipid droplets, and has been utilized for chemical decoration to optimize its attributes. By synthesizing a series of monosubstituted Nile Red derivatives, researchers have found strong candidates for reporting the polarity of their local environment, with the spectroscopic features finely tuned by introducing substituents of distinct electronic character.
JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Maria Szomek, Peter Reinholdt, Daniel Petersen, Atenisa Caci, Jacob Kongsted, Daniel Wustner
Summary: Nystatin is a widely used antifungal drug that inhibits yeast infections and endocytic processes in mammalian cells. Through spectroscopic methods, its interaction with model membranes has been thoroughly investigated.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Chemistry, Physical
Salvatore Prioli, Daniel Wustner, Jacob Kongsted
Summary: In this study, the optical properties of cholestatrienol within the NPC2 binding pockets were simulated using response theory, and a change in CD signal was observed.
THEORETICAL CHEMISTRY ACCOUNTS
(2022)
Article
Physics, Multidisciplinary
Samudrajit Thapa, Seongyu Park, Yeongjin Kim, Jae-Hyung Jeon, Ralf Metzler, Michael A. Lomholt
Summary: We present a Bayesian inference scheme for scaled Brownian motion and investigate its performance on parameter estimation and model selection in a combined inference with fractional Brownian motion. The results show that the procedure is able to accurately resolve the true model and parameters for trajectories of a few hundred time points, and the approach using the prior of the synthetic data generation process is optimal based on decision theory.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Review
Cell Biology
Alice Dupont Juhl, Daniel Wustner
Summary: This review article discusses the complex mechanisms by which mammalian cells remove excess cholesterol, including reverse cholesterol transport, formation of high-density lipoprotein, and the role of ABC transporters and other sterol efflux proteins. It also explores the biophysical principles governing the efflux of sterols from cells and recent evidence for cholesterol efflux by the release of exosomes, microvesicles, and migrasomes. Additionally, it highlights the role of the endo-lysosomal network, lipophagy, lysosomal transporters, and oxysterols in cholesterol export from cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Daniel Wustner
Summary: A novel model-free approach is proposed in this study to analyze photobleaching of fluorescent probes in cells and tissues, using dynamic mode decomposition (DMD) to achieve image segmentation and denoising, as well as distinguishing probes from autofluorescence.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Irina Iachina, Michael A. Lomholt, Johannes H. Eriksen, Jonathan R. Brewer
Summary: In this study, Coherent anti-Stokes Raman Scattering microscopy was used to directly measure the spatial and temporal changes in water concentration in intact skin tissue. The diffusion coefficients at different depths were extracted using a multilayer diffusion model. The results revealed that the diffusion varied at different layers throughout the Stratum Corneum, indicating its heterogeneous structure. Additionally, treating the skin with acetone or tape stripping resulted in increased diffusion coefficients. The presented method and model have the potential for wide applications in measuring spatially resolved diffusion of different substances.
JOURNAL OF BIOPHOTONICS
(2022)
Article
Chemistry, Analytical
Daniel Wustner
Summary: The phase separation and aggregation of proteins in neurodegenerative diseases can be studied using a novel model-free method called dynamic-mode decomposition (DMD) of FLIP live-cell image sequences. The method allows for the discrimination of subcellular compartments and the analysis of different transport kinetics. Additionally, DMD-FLIP is efficient in denoising confocal time series data. This method has significant implications for studying protein dynamics and its role in disease formation.
Article
Biochemistry & Molecular Biology
Maria Szomek, Peter Reinholdt, Hanna-Loisa Walther, Holger A. Scheidt, Peter Mueller, Sebastian Obermaier, Bert Poolman, Jacob Kongsted, Daniel Wuestner
Summary: This study investigates the molecular interactions of natamycin and its antifungal activity. The results show that natamycin forms aggregates in aqueous solution and interacts with model membranes, leading to interference with the function of sterols in the membranes and membrane proteins. The study provides a mechanistic explanation for the selective action of natamycin.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Chemistry, Organic
Mads W. Mulberg, Mick Hornum, Peter Reinholdt, Brian Bjarke Jensen, Maria Szomek, Jonathan R. Brewer, Daniel Wuestner, Jacob Kongsted, Poul Nielsen
Summary: Fine-tuning of fluorophores is crucial for the development of next generation fluorescent dyes for microscopy. We report a robust and concise method for synthesizing 14 new Nile Red analogues with extended pi ring systems and diverse functionalities. These new fluorophores showed favorable two-photon excitation efficiency and general fluorescent properties. One derivative exhibited extreme solvent sensitivity and another showed significantly redshifted emission, large Stokes shift, and high two-photon brightness.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Kaustubh Wagh, Diana A. Stavreva, Rikke A. M. Jensen, Ville Paakinaho, Gregory Fettweis, R. Louis Schiltz, Daniel Wustner, Susanne Mandrup, Diego M. Presman, Arpita Upadhyaya, Gordon L. Hager
Summary: Using single-molecule tracking and machine learning, researchers found that histone H2B and multiple chromatin-bound transcriptional regulators have two distinct low-mobility states. Ligand activation increases the binding ability of steroid receptors in the lowest-mobility state. The results reveal common pathways for transcription activation in mammalian cells.
Article
Cell Biology
Jacob Marcus Egebjerg, Maria Szomek, Katja Thaysen, Alice Dupont Juhl, Suzana Kozakijevic, Stephan Werner, Christoph Pratsch, Gerd Schneider, Sergey Kapishnikov, Axel Ekman, Richard Rottger, Daniel Wustner
Summary: This study developed a novel method using soft X-ray tomography and deep learning computational approach to visualize and quantify vacuole fusion, droplet size, and lipophagy in yeast cells. The researchers found that cells lacking specific proteins showed reduced capacity for vacuole fusion and compromised droplet degradation.
Article
Cell Biology
Daniel Wustner, Alice Dupont Juhl, Jacob Marcus Egebjerg, Stephan Werner, James McNally, Gerd Schneider
Summary: In this study, we investigated the mechanism of cholesterol transport within cells by NPC2 using fluorescence microscopy and kinetic modeling. We found that NPC2 deficiency leads to trapped cholesterol in ILVs of LE/LYSs, causing delayed export and the presence of enlarged intraluminal vesicles in these cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Raja Narayanasamy, Dandamudi Usharani, Ram Rajasekharan
Summary: This study investigated the role of ABHD16B in lipid metabolism. The overexpression of ABHD16B was found to decrease cellular triacylglycerol levels and increase phospholipid synthesis in yeast cells. Additionally, ABHD16B overexpression led to a reduction in lipid droplets and significant modifications in fatty acid composition. These findings highlight the importance of ABHD16B in lipid homeostasis and provide insights into its regulatory function in cellular lipid metabolism.
CHEMISTRY AND PHYSICS OF LIPIDS
(2024)