Review
Chemistry, Multidisciplinary
Weijie Chi, Davin Tan, Qinglong Qiao, Zhaochao Xu, Xiaogang Liu
Summary: Single-molecule localization microscopy (SMLM) has been widely used in biology and chemistry. Fluorophores, as an essential component of SMLM, play a crucial role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores simplifies experimental setups and extends the imaging duration of SMLM. This review provides an overview of the development of spontaneously blinking rhodamines from 2014 to 2023 and the key mechanistic aspects of intramolecular spirocyclization reactions, aiming to accelerate the advancement of super-resolution imaging technologies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biology
Adrien C. Descloux, Kristin S. Grussmayer, Aleksandra Radenovic
Summary: Descloux et al. introduce a parameter-free modified histogram rendering method for resolution estimation in localization microscopy datasets, accurately conveying localization information and depending on precision and density of localizations. Localization microscopy is a super-resolution imaging technique that relies on spatial and temporal separation of blinking fluorescent emitters, achieving sub-diffraction precision bounded by photon emission and sensor noise. The proposed bilinear histogram rendering pipeline avoids biases from Gaussian or standard rendering, demonstrating resolution estimation dependence on localization density and precision.
COMMUNICATIONS BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Jamal Ghanam, Venkatesh Kumar Chetty, Xingfu Zhu, Xiaomin Liu, Marton Gelleri, Lennart Barthel, Dirk Reinhardt, Christoph Cremer, Basant Kumar Thakur
Summary: sEVs are nanovesicles with a size of 30-200 nm enriched with unique cargoes of nucleic acids, lipids, and proteins. They play a critical role in cell-to-cell communication but the mechanism of sEVs biogenesis and uptake is still unknown due to the lack of suitable imaging technologies. This review highlights the application of single-molecule localization microscopy (SMLM) in sEV biology and discusses different labeling strategies to study sEV biogenesis and their biomolecular interaction with recipient cells.
Article
Nanoscience & Nanotechnology
Jiahui Wang, Jimmy Ching-Cheng Hsu, Ting-Jui Ben Chang, T. Tony Yang
Summary: This article proposes a simple approach to address the issue in single-molecule localization microscopy (SMLM) caused by overaccumulation of localizations from fluorophores. The proposed method successfully corrects localization artifacts and restores superresolution results of various cellular structures and organelles, allowing for precise interpretation of molecular clusters.
Article
Biotechnology & Applied Microbiology
Andrew E. S. Barentine, Yu Lin, Edward M. Courvan, Phylicia Kidd, Miao Liu, Leonhard Balduf, Timy Phan, Felix Rivera-Molina, Michael R. Grace, Zach Marin, Mark Lessard, Juliana Rios Chen, Siyuan Wang, Karla M. Neugebauer, Joerg Bewersdorf, David Baddeley
Summary: This study presents an integrated acquisition and analysis platform for single-molecule localization microscopy, which enables the imaging and analysis of 10,000 cells per day. The platform utilizes microscopy-specific data compression, distributed storage, and distributed analysis to increase throughput and allows for automated analysis initiation from the microscope. The platform also supports imaging of multiple cells in multi-well sample formats.
NATURE BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Yoonsuk Hyun, Doory Kim
Summary: With the development of super-resolution imaging techniques, understanding protein structure at the nanoscale in terms of clustering and organization in a cell is crucial. This review categorizes computational cluster analysis methods for single-molecule localization microscopy (SMLM) images into classical and machine learning-based methods, and discusses possible future directions for machine learning-based cluster analysis methods for SMLM data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Analytical
Jinxiu Wei, Siyao Zhang, Jiangnan Yuan, Zhuyuan Wang, Shenfei Zong, Yiping Cui
Summary: Tumor cell exosomes play a vital role in tumor cell proliferation and metastasis, but we still lack a comprehensive understanding of their appearance and biological characteristics due to their nanoscale size and high heterogeneity. We propose an imaging method called Expansion SMLM (ExSMLM) that combines Expansion Microscopy (ExM) and Single Molecule Localization Microscopy (SMLM) to achieve the expansion and super-resolution imaging of tumor cell exosomes.
Article
Chemistry, Physical
Jennifer M. Urban, Wesley Chiang, Jennetta W. Hammond, Nicole M. B. Cogan, Angela Litzburg, Rebeckah Burke, Harry A. Stern, Harris A. Gelbard, Bradley L. Nilsson, Todd D. Krauss
Summary: Colloidal semiconductor quantum dots (QDs) have proven to be versatile and useful for visualizing biological interactions. QDs labeled neurons show significantly enhanced localization precision compared to neurons labeled with organic fluorophores, attributed to key photophysical parameters of QDs. These findings suggest the potential of QDs for super-resolution imaging applications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Ye Lin, Fatemeh Sharifi, Sean B. Andersson
Summary: The paper introduces a method based on SMC-EM technology that can simultaneously localize the position of biological macromolecules and estimate motion model parameters. The research results indicate that under low signal conditions, the SMC-EM method outperforms other methods, while at higher signal-to-background ratios, both SMC-EM and MLE-based methods perform equally well and are significantly better than fitting to the MSD.
BIOMEDICAL OPTICS EXPRESS
(2021)
Article
Biochemical Research Methods
Vincent Ebert, Patrick Eiring, Dominic A. Helmerich, Rick Seifert, Markus Sauer, Soren Doose
Summary: Characterizing the spatial fluorophore distribution using convex hull and related properties of localization clusters can be used for diagnostic purposes, as a parameter for cluster selection, or as a tool to determine localization precision.
Article
Biophysics
Dylan Kalisvaart, Jelmer Cnossen, Shih-Te Hung, Sjoerd Stallinga, Michel Verhaegen, Carlas S. Smith
Summary: Modulation enhanced single-molecule localization microscopy (meSMLM) methods improve localization precision by encoding additional position information. The use of iterative methods generates prior information on emitter positions, leading to improved precision. The Van Trees inequality (VTI) is used to bound the best achievable localization precision of meSMLM methods. Monte Carlo simulations evaluate different illumination pattern placement strategies. The results show that meSMLM can achieve significant improvement in localization precision under certain conditions, but traditional single-molecule localization microscopy methods outperform meSMLM when considering equal measurement time and illumination power per iteration.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Pierre Jouchet, Christian Pous, Emmanuel Fort, Sandrine Leveque-Fort
Summary: Structured illumination improves localization precision in single-molecule localization microscopy by providing new information on molecular positions. This study used time-shifted sinusoidal excitation and synchronous demodulation to modulate and recover the fluorescence signal. Flexible fast demodulation systems were designed to overcome camera acquisition frequency limitations. The ModLoc microscopy improved localization precision by a factor of 2.4 compared to classical Gaussian fitting methods.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Physics, Applied
Fabian Hinterer, Magdalena C. Schneider, Simon Hubmer, Montserrat Lopez-Martinez, Ronny Ramlau, Gerhard J. Schuetz
Summary: Single molecule localization microscopy relies on precise quantification of the positions of single dye emitters in a sample. The number of detected photons from each molecule determines the precision, which can be improved by recording at cryogenic temperatures to reduce photobleaching. However, long illuminations can cause image blur due to inevitable jitter or drift, which degrades localization precision. This paper demonstrates a method to largely eliminate drift effects by parallel recording fiducial marker beads and fitting the drift trajectory, applicable to drift magnitudes of several hundred nanometers per frame, and assuming fixed dipole orientations during each illumination.
APPLIED PHYSICS LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Hanna Manko, Yves Mely, Julien Godet
Summary: Spectrally-resolved single molecule localization microscopy (srSMLM) is enhanced by a deep-learning image processing routine called srUnet, which compensates for the resolution loss in simultaneously recording spectra and localization information. srUnet significantly improves both localization and spectral precision, especially for low-emitting species. It increases the fraction of localizations that can be characterized spatially and spectrally and preserves spectral shifts and linearity. srUnet greatly facilitates wavelength assignment in multicolor experiments and has the potential to make srSMLM the new standard for multicolor single molecule imaging.
Article
Optics
Zhiwei Zhou, Weibing Kuang, Zhengxia Wang, Zhen-Li Huang
Summary: Single molecule localization microscopy (SMLM) is a popular method in super-resolution fluorescence microscopy that can achieve high spatial resolution. However, it suffers from slow imaging speed. This study introduces a new image inpainting method called DI-STORM using ResNet generator, which improves the image artifact problem in current methods and demonstrates better performance compared to existing methods.
Article
Chemistry, Multidisciplinary
Tonghui Wang, Jinbo Fei, Zhenzhen Dong, Xia Xu, Weiguang Dong, Junbai Li
Summary: In this study, a synthetic electrozyme was coupled with a supramolecule-assembled nanoarchitecture to mimic mitochondrial oxidative phosphorylation and achieve enhanced bioenergy transformation. The metal-free electrozyme, a semiconducting polymer deposited on an electrode, exhibited a well-matched electrocatalytic property that allowed the oxidation of reduced nicotinamide adenine dinucleotide (NADH) to release protons at a much lower electric potential. As a result, a proton gradient was generated and drove the rotary catalysis of adenosine 5'-triphosphate (ATP) synthase in a lipid membrane, resulting in the production of ATP. Significantly, the electrochemical bioenergy conversion of NADH to ATP in this bio-like system was much more efficient compared to natural mitochondria. This work integrates synthetic and natural catalytic chemistry, facilitating enhanced bioenergy transformation and greatly improving prospects in ATP-fueled bioapplications.
Review
Chemistry, Physical
Jinbo Fei, Junbai Li
Summary: Molecular assembly is a promising strategy for constructing active systems using biomolecules as building blocks. These assembled systems simulate or regulate important biological activities and have great potential in various bioapplications. This review focuses on recent progress in ATP-involved active self-assembled systems, which are constructed with hierarchical structures and generate ATP using external influences to create proton gradients. Additionally, active supermolecular systems driven by ATP as chemical fuel are highlighted. Finally, key challenges and future research perspectives are discussed.
CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Xianbao Li, Qi Li, Aoli Wu, Junbai Li
Summary: Symmetry of layered dipeptide crystals can be broken by utilizing CO2, which induces adjacent monomolecular layers to stack in the same direction. CO2 covers the interlayer interaction sites, forcing the dipeptides to adsorb asymmetrically. The dipeptide crystals exhibit enhanced piezoelectricity and the piezoelectric voltage generated from dipeptide-based generators is increased by more than 500% after symmetry breaking. This work provides a potential route to engineer structures and properties of layered materials, and offers insights into the control of non-covalent interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Aoli Wu, Yongxian Guo, Xianbao Li, Qi Li, Guixin Chen, Hengchang Zang, Junbai Li
Summary: The development of peptide-based supramolecular materials with hierarchical morphology and tunable guest loading shows great potential as a drug carrier due to their biocompatibility and biodegradability. In this study, a facile Schiff base nanoarchitectonic was reported for the supramolecular assembly of diphenylalanine (FF) metastable gel. The competitive assembly between FF-H2O and FF-GA oligomer resulted in the formation of FF nanoparticles and hierarchical beaded nanofibers. These assembled particles can easily load various guest molecules and release them under weak alkaline conditions, demonstrating their potential application as drug carriers.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Review
Multidisciplinary Sciences
Yamei Liu, Ruirui Xing, Junbai Li, Xuehai Yan
Summary: Covalently triggered peptide self-assembly has been developed for cancer theranostics, providing enhanced stability and functionality compared to noncovalent interactions. The review summarizes the design principles for constructing various peptide-based assemblies and discusses representative covalently assembled peptide-based nanodrugs, along with their challenges and potential in clinical applications for cancer diagnosis and therapeutics. This review offers new insights into the construction of peptide-based nanodrugs through covalent reaction and noncovalent self-assembly.
Article
Chemistry, Physical
Nan Sun, Yi Jia, Shiwei Bai, Qi Li, Luru Dai, Junbai Li
Summary: Super-resolution microscopy (SRM) technology has revolutionized the field of cell biology by breaking the diffraction limit, enabling researchers to visualize cellular structures with nanometric resolution, multiple colors, and single-molecule sensitivity. SRM has also extended its impact to other fields such as nanomedicine, material science, and nanotechnology, greatly contributing to breakthroughs in these areas.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Physical
Xin Li, Honglei Jian, Qingquan Han, Anhe Wang, Jieling Li, Ningyuan Man, Qi Li, Shuo Bai, Junbai Li
Summary: Short peptide self-assembled hydrogels have excellent biocompatibility and functional expansion, making them promising in cell culture and tissue engineering. However, the preparation of bio-inks with adjustable mechanical strength and controlled degradation for 3D bioprinting is challenging.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Physical
Zhenzhen Dong, Jinbo Fei, Tonghui Wang, Junbai Li
Summary: A strategy of matched spectral and temporal light management is developed to improve photosynthetic efficiency by co-assembling natural thylakoid membrane (TM) with artificial long afterglow particle (LAP). LAP with excellent stability and biocompatibility is optically-matched with the absorption of TM, serving as an additional light source for photosynthesis. Enhanced photosynthesis is achieved after co-assembly, with boosted electron transfer, oxygen yield, and ATP production due to down-conversion fluorescence emission from LAP. This proof-of-concept work opens a new route to augment the photosynthetic efficiency of green plants by utilizing precise light-managed materials.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Physical
Yilin Liu, Junbai Li
Summary: This study reports, for the first time, that Celastrol can self-assemble into size-controllable nanoparticles via the anti-solvent method using different solvents or varying Celastrol concentrations. In vitro experiments showed that the prepared nanoparticles can effectively kill MCF-7 cells. Furthermore, the nanoparticles can accumulate efficiently in tumors after intravenous injection. Administration of a lethal dosage of Celastrol resulted in significant tumor suppression with maintained activity in mice. These findings suggest that the anti-solvent method holds promise for fabricating Celastrol nano-drugs with controlled size and reduced systemic toxicity for clinical cancer treatment.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Review
Chemistry, Multidisciplinary
Jie Zhao, Xia Xu, Yang Yang, Junbai Li
Summary: Photodynamic therapy (PDT) is an efficient method for cancer treatment, but traditional photosensitizers (PSs) often have low bioavailability. This review discusses the use of molecular-assembly technique, adjusting the PS triplet state lifetime, and developing aggregation-induced emission (AIE) agents to improve the efficacy of PDT.
Article
Chemistry, Multidisciplinary
Yilin Liu, Jie Zhao, Xia Xu, Yang Xu, Wei Cui, Yang Yang, Junbai Li
Summary: The natural anthraquinone derivative emodin (Emo) is demonstrated to be a promising photosensitizer for two-photon-excited photodynamic therapy with a large two-photon absorption cross-section and high singlet oxygen quantum yield. The co-assembled Emo/HSA nanoparticles exhibit outstanding TPE-PDT properties against cancer cells. This work is beneficial for the use of natural extracts for high-efficiency TPE-PDT.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Zibo Li, Fanchen Yu, Xia Xu, Tonghui Wang, Jinbo Fei, Jingcheng Hao, Junbai Li
Summary: We demonstrate the realization of photozyme-catalyzed oxidative phosphorylation through the assembly of ATP synthase-reconstituted proteoliposome coatings on microcapsules. This is achieved through layer-by-layer deposition of semiconducting graphitic carbon nitride (g-C3N4) nanosheets and polyelectrolytes. The encapsulated g-C3N4 nanosheets act as the photozyme, accelerating the oxidation of glucose to yield protons under light illumination, establishing an outward transmembrane proton gradient to drive ATP synthesis. This artificial design enables higher energy conversion efficiency compared to conventional oxidative phosphorylation systems.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Materials Science, Multidisciplinary
Peng Zhou, Ruirui Xing, Qi Li, Junbai Li, Chengqian Yuan, Xuehai Yan
Summary: Controlling the morphology of supramolecular hydrogels is crucial in tuning their mechanical properties. This study investigates the evolution of fibrillar networks in hydrogels by modulating droplets formed via liquid-liquid phase separation. The size and amount of droplets, as well as the structural evolution and network development, can be finely tuned by varying the thermal history. The findings provide insights into the role of phase-separated droplets in self-assembling networks and contribute to the engineering of supramolecular hydrogels with adjustable mechanical properties.
Review
Chemistry, Multidisciplinary
Rui Chang, Luyang Zhao, Ruirui Xing, Junbai Li, Xuehai Yan
Summary: This review summarizes recent advances in chromopeptide nanoarchitectonics, focusing on the design strategy, assembly mechanism, and structure-function relationship. The effect of peptide sequences and the variation in photophysical performance are critically emphasized. Various applications, including biomedicine and artificial photosynthesis, are discussed, along with the future prospects of chromopeptide nanoarchitectonics.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Physical
Nan Sun, Yi Jia, Shiwei Bai, Yang Yang, Luru Dai, Junbai Li
Summary: This study demonstrates the direct observation and quantification of protein corona adsorbed onto PEGylated mesoporous silica particles using direct stochastic optical reconstruction microscopy. The effects of PEG molecular weights and incubation time on protein penetration depth are investigated for the first time.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2024)