Article
Biology
Mingyu Luo, Yining Liu, Min Zhao
Summary: Blood-based detection of circulating cell-free DNA (cfDNA) is a non-invasive and easily accessible method for early cancer detection. However, there are challenges in developing clinical biomarkers, such as filtering out false-positive cfDNA mutations and detecting low-frequency genetic alterations.
Article
Microbiology
Fabien Rideau, Audrey Villa, Pauline Belzanne, Emeline Verdier, Eric Hosy, Yonathan Arfi
Summary: Mycoplasmas are important models in biology and problematic pathogens in medicine and veterinary fields. Their small size limits the usefulness of traditional fluorescence imaging methods, but recently developed superresolution imaging techniques can break this limit and offer new insights into the organization of these bacteria. This study describes an efficient protocol to perform superresolution microscopy imaging in Mycoplasma, showcasing the potential of these techniques to study subcellular structures at the nanometer scale.
MICROBIOLOGY SPECTRUM
(2022)
Article
Chemistry, Analytical
Junling Chen, Hongru Li, Qiang Wu, Qiuyan Yan, Jiayin Sun, Feng Liang, Yi Liu, Hongda Wang
Summary: The study revealed the unique distribution of Protein tyrosine kinase-7 (PTK7) on the cell membrane, which is possibly related to the assembly relationship with lipid rafts, actin cytoskeleton, and membrane carbohydrate chains.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Alice Sandmeyer, Lili Wang, Wolfgang Huebner, Marcel Mueller, Benjamin K. Chen, Thomas Huser
Summary: Cost-effective, highly portable, and easy to use high-resolution live-cell imaging systems can revolutionize research in challenging environments, enabling real-time tracking of virus particles and studying infection mechanisms.
Article
Biochemical Research Methods
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
Summary: We propose a deep-learning method for precise localization of spatially variant point emitters, covering the full chip of a modern sCMOS camera. By using a graphic processing unit-based vectorial point spread function fitter, we accurately model the spatially variant PSF of a high numerical aperture objective in the entire field of view. Combined with deformable mirror-based optimal PSF engineering, we demonstrate high-accuracy three-dimensional single-molecule localization microscopy over a large volume, enabling imaging of mitochondria and nuclear pore complexes in entire cells without hardware scanning, with a 100-fold increase in throughput compared to existing techniques.
Article
Chemistry, Analytical
Yan Peng, Linjuan Shu, Xiongfei Deng, Xin Huang, Xianming Mo, Feng Du, Zhuo Tang
Summary: We developed a genetically encoded sensor for sensitive imaging and tracking of endogenous RNA in living cells. This sensor can specifically recognize target RNAs and induce structural changes to enable fluorescence imaging. We successfully demonstrated its application in monitoring mRNA expression and confirming RNA distribution in cancer cells and zebrafish embryos, respectively. This study provides an effective molecular tool for RNA imaging and has potential applications in disease diagnosis and treatment evaluation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Danyang Wang, Ana Shalamberidze, Emilia Arguello, Byron W. Purse, Ralph E. Kleiner
Summary: The article introduces a platform for fluorescence imaging of bulk RNA dynamics in living cells and uses this platform to study RNA metabolism and localization during oxidative stress. The study found that bulk RNA turnover is accelerated upon oxidative stress treatment and identified new cytoplasmic RNA granules that co-localize with RNA helicase.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Dusan Mrdenovic, Wenjie Ge, Naresh Kumar, Renato Zenobi
Summary: Here, the researchers used tip-enhanced Raman spectroscopy (TERS) to visualize the molecular distribution in pancreatic cancer cell membranes without labeling. The study revealed various domains and mixed regions on the nanoscale of the cell membrane.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Nanoscience & Nanotechnology
Jing Liu, Juan Jiang, Mengyi He, Jiayi Chen, Shuang Huang, Zhengjie Liu, Chuanjie Yao, Hui-jiuan Chen, Xi Xie, Ji Wang
Summary: Cell transfection is crucial in gene function study and gene expression regulation. Nanopore-coupled electroporation is a promising technique for efficient cell membrane perforation and nucleic acid transfection. This study investigates the potential of nanopore electroporation for transfecting DNA plasmids into different cell types, and identifies its high efficiency in adherent cells but limited efficiency in weakly spreading cells. A COMSOL model is developed to gain insights into the underlying mechanism. These findings provide valuable references for advancing nanopore electroporation as a high-throughput, safe, and efficient gene transfection platform.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemical Research Methods
Michael Lawson, Johan Elf
Summary: Linking genetic perturbations to changes in phenotype is crucial in biological research. Advances in microscopy and the creation of genetically altered cell libraries have allowed for live-cell imaging of pool-generated strain libraries, enhancing biological discovery.
Article
Cell Biology
Chi Wai Yip, Chung-Chau Hon, Kayoko Yasuzawa, Divya M. Sivaraman, Jordan A. Ramilowski, Youtaro Shibayama, Saumya Agrawal, Anika V. Prabhu, Callum Parr, Jessica Severin, Yan Jun Lan, Josee Dostie, Andreas Petri, Hiromi Nishiyori-Sueki, Michihira Tagami, Masayoshi Itoh, Fernando Lopez-Redondo, Tsukasa Kouno, Jen-Chien Chang, Joachim Luginbuhl, Masaki Kato, Mitsuyoshi Murata, Wing Hin Yip, Xufeng Shu, Imad Abugessaisa, Akira Hasegawa, Harukazu Suzuki, Sakari Kauppinen, Ken Yagi, Yasushi Okazaki, Takeya Kasukawa, Michiel de Hoon, Piero Carninci, Jay W. Shin
Summary: Within the FANTOM6 consortium, we conducted a large-scale knockdown of 200 lncRNAs in human iPSCs and explored their roles in self-renewal and pluripotency. We identified 36 lncRNAs that inhibit cell growth and 36 lncRNAs with molecular phenotypes, potentially affecting pluripotency.
Article
Biochemical Research Methods
Heejin Lim, Sun Young Lee, Yereum Park, Hyeonggyu Jin, Daeha Seo, Yun Hee Jang, Dae Won Moon
Summary: This study demonstrates a method for sputtering atomic and molecular secondary ions through single-layer graphene to enable SIMS imaging of untreated wet cell membranes at subcellular resolution. The findings show that the method allows observation of lipid distribution in cell membranes without labeling, and that cells remain intact during imaging. Additionally, molecular dynamics calculations and ion dose-dependence studies suggest that sputtering through graphene occurs through a transient hole in the graphene layer.
Article
Chemistry, Multidisciplinary
Ilya O. Aparin, Rui Yan, Remi Pelletier, Alexander A. Choi, Dmytro I. Danylchuk, Ke Xu, Andrey S. Klymchenko
Summary: This study proposes a concept of ON/OFF switchable probes for super-resolution fluorescence microscopy based on bright cyanine dyes. The new probes provide higher brightness and slower diffusion at the cell surface, improving the localization precision. The study validated the concept and demonstrated the observation of nanoscale cellular structures with enhanced dynamics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
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
Biology
Kelvin Yeung, Komal Kumar Bollepogu Raja, Yoon-Kyung Shim, Yumei Li, Rui Chen, Graeme Mardon
Summary: This study presents single cell transcriptomic data on the adult Drosophila eye, identifying cell type specific marker genes and revealing that the clustering of R7 and R8 photoreceptors is determined by the expression of specific Rhodopsin proteins. These transcriptomic data provide valuable insights into the mechanisms of the adult fly eye as a model system.
COMMUNICATIONS BIOLOGY
(2022)
Review
Chemistry, Analytical
Yan Shi, Mingjun Cai, Hongda Wang
Summary: This review presents various single-molecule force methods and their applications in cell force manipulation and measurement, highlighting the importance of mechanical properties in cell activities.
CURRENT ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yi-Feng Wang, Qingrong Zhang, Falin Tian, Hongda Wang, Yufei Wang, Xiaowei Ma, Qianqian Huang, Mingjun Cai, Yinglu Ji, Xiaochun Wu, Yaling Gan, Yan Yan, Kenneth A. Dawson, Shutao Guo, Jinchao Zhang, Xinghua Shi, Yuping Shan, Xing-Jie Liang
Summary: This study investigated the internalization behaviors of rod-shaped nanostructures with different aspect ratios using atomic force microscopy, transmission electron microscopy, and molecular dynamic simulation. It revealed that gold nanorods are endocytosed in an intermittent rotation manner and the internalization force and time are positively correlated with the aspect ratios. The study also found that internalization speed is negatively correlated with internalization time.
Article
Chemistry, Multidisciplinary
Mette Galsgaard Malle, Philipp M. G. Loeffler, Soren S-R Bohr, Magnus Berg Sletfjerding, Nikolaj Alexander Risgaard, Simon Bo Jensen, Min Zhang, Per Hedegard, Stefan Vogel, Nikos S. Hatzakis
Summary: In this study, a single-particle combinatorial multiplexed liposome fusion mediated by DNA is presented, enabling multistep and non-deterministic fusion of nanocontainers. Efficient and leakage-free stochastic fusion sequences were observed for arrays of target liposomes functionalized with individual DNA strands and labeled with distinct chromophores. The method allows high-throughput combinatorial multiplex screens using minimal material.
Article
Chemistry, Multidisciplinary
Lu Wang, Kim Jensen, Nikos Hatzakis, Min Zhang, Thomas Just Sorensen
Summary: This study aims to apply optical pH and dissolved oxygen (DO) optical chemosensors in industrial applications by exploring a many-sensors-in-one principle. The physical segregation of the optical sensor components in a single sensor polymer was tested to remove cross-talk and quenching. The results showed that incorporating an oxygen-responsive dye in polymer nanoparticles and a pH-responsive dye in an organically modified siloxane polymer resulted in a robust pH/O2 dual optical sensor.
Review
Medicine, Research & Experimental
Xiao Qi, Jing Gao, Zihao Li, Guangxin Zhang, Jialin Li, Yilin Fu, Mingjun Cai, Hongda Wang, Ti Tong
Summary: CDCP1 is overexpressed in various malignant tumors and plays important roles in tumorigenesis and progression. It is involved in multiple signaling pathways, prognosis, and drug resistance. It has the potential to be a therapeutic target and a biomarker for diagnosis.
Article
Chemistry, Analytical
Guanfang Zhao, Haijiao Xu, Hongru Li, Jinrui Zhang, Jing Gao, Mingjun Cai, Huili Wang, Yan Shi, Hongda Wang
Summary: This study investigated the effects of glucose on the subcellular localization and spatial distribution of t-SNAREs on the plasma membrane using live-cell confocal microscopy and single-molecule imaging. The results showed that increased glucose concentration increased the expression of t-SNAREs and induced larger clusters on the plasma membrane, while glucotoxicity inhibited t-SNAREs transport to the plasma membrane and caused fewer and smaller clusters. In addition, glucotoxicity also decreased the colocalization between t-SNAREs.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Haijiao Xu, Jinrui Zhang, Yijia Zhou, Guanfang Zhao, Mingjun Cai, Jing Gao, Lina Shao, Yan Shi, Hongru Li, Hongbin Ji, Yikai Zhao, Hongda Wang
Summary: This study visualized the entire process of EGFR from synthesis to secretion onto the plasma membrane, revealing the mechanisms of protein clustering and the role of actin in regulating this process.
Article
Chemistry, Physical
Xin Zhou, Anders Wilgaard Sinkjaer, Min Zhang, Henrik Dahl Pinholt, Hanne Morck Nielsen, Nikos S. Hatzakis, Marco van de Weert, Vito Fodera
Summary: Amyloid aggregation is associated with diseases and therapeutic protein formulations. Co-solutes can modulate protein stability and work as inhibitors for drug design. This study uses insulin and polysorbate 80 to analyze the heterogeneous multicomponent system at a single aggregate level and reveals the inhibition mechanism depends on growth pathways. The method is a general tool for physicochemical characterization of self-assembly reactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Xiao Qi, Zihao Li, Jinrui Zhang, Hongru Li, Guangxin Zhang, Meng Li, Baofeng Li, Yilin Fu, Mingjun Cai, Hongda Wang, Ti Tong, Jing Gao
Summary: CDCP1 is a transmembrane protein involved in important biological processes and is upregulated in human solid malignancies. However, its spatial distribution and variation at the molecular level are unclear. This study analyzed CDCP1 expression and prognostic implications in lung cancer, and used super-resolution microscopy to reveal its spatial organization. The findings showed significant differences in CDCP1 clustering characteristics between cancer and normal cells, highlighting its potential as a target for lung cancer drugs.
Article
Multidisciplinary Sciences
Jing Gao, Hongru Li, Haijiao Xu, Yong Liu, Mingjun Cai, Yan Shi, Jingrui Zhang, Hongda Wang
Summary: Using dSTORM imaging, nanoscale GCGR clusters were observed on HepG2 cell membranes, and high glucose promoted GCGR expression and the formation of more and larger clusters. Glucagon stimulation under high glucose did not inhibit GCGR levels as significantly as that under low glucose, and did not increase the downstream cAMP-PKA signal, indicating high glucose-induced glucagon resistance. Furthermore, high glucose induced stronger glucagon resistance in hepatoma cells compared with hepatic cells.
Article
Biochemistry & Molecular Biology
Josephine F. F. Iversen, Soren S. -R. Bohr, Henrik D. D. Pinholt, Matias E. E. Moses, Lars Iversen, Sune M. M. Christensen, Nikos S. S. Hatzakis, Min Zhang
Summary: We investigated the diffusion behavior of Thermomyces lanuginosus lipase (TLL) variants with different lid structures in a laundry-like application condition using single-particle tracking (SPT). Our findings reveal that surface binding and lipase mobility when bound are crucial factors affecting the overall activity variation in the application condition. These mechanistic insights provide new perspectives on the development of enzyme-based detergents.
Correction
Multidisciplinary Sciences
Xiao Qi, Zihao Li, Jinrui Zhang, Hongru Li, Guangxin Zhang, Meng Li, Baofeng Li, Yilin Fu, Mingjun Cai, Hongda Wang, Ti Tong, Jing Gao
Article
Biology
Freja Bohr, Soren S. -R. Bohr, Narendra Kumar Mishra, Nicolas Sebastian Gonzalez-Foutel, Henrik Dahl Pinholt, Shunliang Wu, Emilie Milan Nielsen, Min Zhang, Magnus Kjaergaard, Knud J. Jensen, Nikos S. Hatzakis
Summary: Single-molecule studies reveal the pathway organization of insulin hexamers' self-assembly and disassembly, and how this is remodeled by regulatory cues and formulations. The abundance and kinetics of all oligomeric species are assessed. Insulin formulations with diverse oligomerization states play a crucial role in diabetes treatment interventions.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Analytical
Guan-Fang ZHAO, Ming-Jun CAI, Hong-Ru LI, Tian-Yi ZOU, Jing GAO, Hai-Jiao XU, Hong-Da WANG
Summary: Glucose concentration regulates insulin secretion; increased glucose concentration leads to elevated expression and clustering of STX-1A on cell membranes, while chronic high glucose stimulation reduces STX-1A expression and clustering. By linking the expression and spatial distribution of STX-1A to insulin secretion, the role of glucose in regulating the functional organization of STX-1A is revealed.
CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Hongru Li, Jinrui Zhang, Yan Shi, Guanfang Zhao, Haijiao Xu, Mingjun Cai, Jing Gao, Hongda Wang
Summary: This study uses super-resolution imaging to reveal the distribution changes of the insulin receptor during cell membrane activation. The findings show that insulin resistance inhibits receptor clustering and there is a highly co-localized relationship between the insulin receptor and the skeletal protein beta II-spectrin.
