Article
Multidisciplinary Sciences
Patricia A. Clow, Menghan Du, Nathaniel Jillette, Aziz Taghbalout, Jacqueline J. Zhu, Albert W. Cheng
Summary: The authors present a CRISPR-based approach to label nonrepetitive loci in the genome and image chromatin loops in living cells. This method allows for the visualization and tracking of dynamic interactions of DNA elements, revealing intercellular heterogeneity and interallelic asynchrony in chromatin interaction dynamics.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Nishkantha Arulkumaran, Conor Lanphere, Charlotte Gaupp, Jonathan R. Burns, Mervyn Singer, Stefan Howorka
Summary: DNA nanotechnology produces precision nanostructures of defined chemistry, which can function as vaccines by selectively binding with white blood immune cells via membrane anchors, showing potential advantages in serum stability and immune modulation.
Article
Biochemistry & Molecular Biology
Nadia Vezzio-Vie, Marie-Alice Kong-Hap, Eve Combes, Augusto Faria Andrade, Maguy Del Rio, Philippe Pasero, Charles Theillet, Celine Gongora, Philippe Pourquier
Summary: This study utilized Celigo(R) image cytometer to evaluate cell response to DNA-damaging agents and developed new multiplexed protocols to investigate qualitative and quantitative changes of multiple DDR markers. The results demonstrate the advantages of this method in providing valuable insights into the mechanism of action of investigational drugs inducing DNA damage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Engineering, Biomedical
Chrysafis Andreou, Ralph Weissleder, Moritz F. Kircher
Summary: In oncology, clinical molecular imaging technologies play an important role in diagnosing patients, assessing treatment efficacy, and monitoring disease recurrence. Multiplexed methods that detect multiple disease-specific biomarkers simultaneously can improve the accuracy and specificity of these technologies. This review discusses established and emerging multiplexed imaging techniques and highlights the advances in radiology made possible by multiplexed imaging.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Chemistry, Analytical
Dan Zhu, Yaqi Wei, Tao Sun, Chengwen Zhang, Lei Ang, Shao Su, Xiuhai Mao, Qian Li, Chunhai Fan, Xiaolei Zuo, Jie Chao, Lianhui Wang
Summary: This study developed a method using rationally designed one-pot assembled multicolor tetrahedral DNA frameworks (TDFs) encoded with multicomponent nucleic acid enzymes (MNAzymes) for signal-amplified multiple miRNAs imaging in living cells with high sensitivity and selectivity.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Youming Feng, Juanjuan Liu, Manli Tan, Lele Li, Ming Gao, Jian Zhao, Li Zheng
Summary: In this study, an enzyme-controlled DNA nanodevice was designed for the real-time monitoring of miRNA imaging during the epithelial-mesenchymal transition (EMT) process of tumor cells, achieving cancer cell-specific monitoring of EMT process. The integration of toehold-mediated strand displacement reactions and enzyme activatable modules allows for the generation of multiple signal outputs in response to different miRNA inputs. The system enables enzymatically activatable two-input and three-output imaging patterns in cancer cells, while lacking miRNA sensing functions in normal cells, resulting in enhanced sensitivity and cell specificity for the cancer-selective monitoring of EMT dynamics.
Article
Chemistry, Analytical
Gabriela Lomeli, Marc Bosse, Sean C. Bendall, Michael Angelo, Amy E. Herr
Summary: Improvements in single-cell protein analysis are necessary for studying the cell-to-cell variation seen in diseases like cancer. MIBI-TOF is a mass spectrometry imaging technology that allows for highly multiplexed protein detection at the single-cell level.
ANALYTICAL CHEMISTRY
(2021)
Article
Biophysics
William Teixeira, Yeray Pallas-Tamarit, Augusto Juste-Dolz, Amadeo Sena-Torralba, Roberto Gozalbo-Rovira, Jesus Rodriguez-Diaz, David Navarro, Javier Carrascosa, David Gimenez-Romero, Angel Maquieira, Sergi Morais
Summary: The COVID-19 pandemic has increased the demand for rapid and reliable point-of-care testing devices. This study presents an all-in-one POCT device that can perform parallel viral antigen and serological analysis. The biosensor demonstrates high diagnostic sensitivity and specificity for various respiratory viruses.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Multidisciplinary
Yuheng Lv, Qin Fu, Yi Xu, Peng Shi
Summary: In this study, sequentially-activated antibodies (SAAs) were developed using sequentially-activated DNA tags and signal enhancement strategies, enabling rapid, wash-free sequential imaging of different protein targets. This method successfully demonstrated sequential imaging of nine different protein targets within a few minutes.
Article
Chemistry, Multidisciplinary
Puspam Keshri, Bin Zhao, Tianfa Xie, Yousef Bagheri, James Chambers, Yubing Sun, Mingxu You
Summary: Fluorescence lifetime-based imaging and quantification of intercellular molecular tensions offer a novel approach to simultaneously measure tensile forces among multiple ligand-receptor pairs. This method was validated and DNA tension probes were developed for imaging E-cadherin-mediated tension, which were further applied to quantify the correlations between E-cadherin and N-cadherin tensions during an epithelial-mesenchymal transition process. The modular design of these probes has the potential to study the mechanical features of various physiological and pathological processes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Analytical
Phi Hung Hoang, Islam Seder, Ana Isabel Ferrer Ramirez, Sung-Jin Kim
Summary: This study presents a fully automated and effective fluidic system for the isolation and detection of cfDNA from whole blood. The system utilizes disposable chambers and key components such as the sedimentation chamber and plunger chamber to achieve plasma separation and cfDNA capture, followed by detection using real-time PCR on a chip.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Immunology
John W. Hickey, Yuqi Tan, Garry P. Nolan, Yury Goltsev
Summary: This study introduces the method for generating single-cell multiplexed imaging datasets and discusses the impact of different normalization techniques and clustering algorithms on cell-type identification. The research found that finer cell-type granularity leads to lower labeling accuracy; unsupervised clustering is more accurate in identifying cell types than manual gating; Z-score normalization helps mitigate noise effects in single-cell multiplexed imaging.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Reto Eggenschwiler, Thomas Gschwendtberger, Christian Felski, Christopher Jahn, Florian Langer, Jared Sterneckert, Andreas Hermann, Jonathan Luehmann, Doris Steinemann, Alexandra Haase, Ulrich Martin, Susanne Petri, Tobias Cantz
Summary: CRISPR prime-editors are novel tools for genome editing, offering a versatile alternative to existing approaches. Proper expression levels and optimized transfection protocols are crucial for editing efficiency. The study demonstrates the effectiveness of piggyBac prime-editing in hiPSCs, showing over 50% editing efficiency and the ability to estimate pegRNA effectiveness quickly. Overall, the study presents a robust prime-editing toolbox for efficient genome editing in various cell lines.
SCIENTIFIC REPORTS
(2021)
Review
Biochemical Research Methods
Sabrina M. Lewis, Marie-Liesse Asselin-Labat, Quan Nguyen, Jean Berthelet, Xiao Tan, Verena C. Wimmer, Delphine Merino, Kelly L. Rogers, Shalin H. Naik
Summary: Understanding intratumoral heterogeneity through single-cell analyses has revealed new biomarkers, but lacks information on cellular location within the tumor microenvironment. New technologies enabling detection of cancer subclones in their native spatial context promise to drive the next generation of cancer research, diagnosis, and therapeutic strategies.
Article
Chemistry, Multidisciplinary
Baolei Liu, Jiayan Liao, Yiliao Song, Chaohao Chen, Lei Ding, Jie Lu, Jiajia Zhou, Fan Wang
Summary: The study introduces a method for multiplexed super-resolution imaging using lifetime-engineered upconversion nanoparticles, achieving a lateral resolution of 185 nm. By utilizing a deep learning algorithm, more accurate decoding compared to a numeric algorithm is achieved, with decoding accuracies above 93% for a three-channel super-resolution imaging.
NANOSCALE ADVANCES
(2021)
Article
Materials Science, Multidisciplinary
Shaokun Wang, Fan Zhang, Qing Yang, Minjing Li, Xun Hou, Feng Chen
Summary: This study proposes a method of fabricating glass infrared artificial compound eyes (ACE) using femtosecond laser wet etching and precision glass molding. The fabricated glass infrared ACE demonstrates high resolution, large field of view, and low aberration. Additionally, the proposed technology offers advantages of low cost and high efficiency.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Multidisciplinary
Yongqing Wang, Chengjun Zhang, Xianglin Meng, Qisheng Zhang, Haoyu Li, Feng Chen, Qing Yang, Weiqiang Zhang, Yuanjin Zheng, Sicheng Chen
Summary: This study proposes a compact and wireless sensing system for quantitatively assessing the pressure between a spatula and brain tissue, with high measurement accuracy and waterproof capabilities. By connecting the sensors to a server network or mobile client, brain damage alerts can be provided, and detailed pressure data on retracting operations can be collected, analyzed, and stored for medical assistance.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Chemistry, Physical
Tinglong Liu, Yu Wang, Huan Zhang, Feng Chen, Qiang Fu
Summary: This paper investigates the modification mechanism of silane coupling agent (SCA) and the role of free silane in improving the interfacial compatibility between fillers and matrix. The degree of hydrolysis, self-polymerization, and graft coupling can be controlled by regulating the reaction conditions. The study also shows that the degree of hydrolysis and self-polymerization of free silanes significantly affect the fluidity and store stability of the modified fillers.
APPLIED SURFACE SCIENCE
(2023)
Review
Biochemical Research Methods
Jin Zhang, Jing Xue, Ningfeng Luo, Feng Chen, Badong Chen, Yongxi Zhao
Summary: Single-cell profiling is crucial for understanding cellular heterogeneity and cell fate. Microfluidics has emerged as an optimal tool for single-cell profiling due to its high throughput and automation advantages. Among different microfluidic platforms, microwell array chips offer simplicity and easy integration with in situ analysis, making them ideal for single-cell studies. This review summarizes recent advances in single-cell analysis based on microwell array chips, including chip design and preparation, cell capture and lysis strategies, as well as advanced analysis of single-cell proteins, nucleic acids, and metabolites. The challenges and opportunities in the development of microwell-based single-cell analysis are also discussed.
Article
Biochemistry & Molecular Biology
Xiaowen Cao, Feng Chen, Jing Xue, Yue Zhao, Min Bai, Yongxi Zhao
Summary: Here, we present a hierarchical DNA branch assembly-encoded fluorescent nanoladders for denoised and highly multiplexed signal amplification of single-cell transcripts. Our method achieves independent RNA-primed rolling circle amplification without nonspecific amplification and allows for programmable DNA branch assembly to encode virtual signals for visualizing numbers of targets. We demonstrate accurate RNA profiling in different cancer cells and reveal diverse localization patterns for spatial regulation of transcripts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Materials Science, Multidisciplinary
Jie Liang, Hao Wang, Tao Hu, Chao Shan, Qing Yang, Chengjun Zhang, Tongzhen Yang, Zheng Fang, Xun Hou, Feng Chen
Summary: Fog can severely damage optical systems and reduce the imaging quality of optical components. Traditional methods have limitations, but a novel method using femtosecond lasers to fabricate anti-fogging surfaces on silica glass shows promise for durable and environment-friendly optical devices with real-time anti-fogging capabilities.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Thermodynamics
Guangqing Du, Fangrui Yu, Yu Lu, Lin Kai, Qing Yang, Xun Hou, Feng Chen
Summary: In this study, the ultrafast thermalization dynamics of temperature fields in Au/Ni film excited by a femtosecond laser double-pulse vortex beam were theoretically investigated. It was proposed that the energy deposition in the layered film can be significantly enhanced by applying the double-pulse vortex beam, leading to vortical thermalization in the Ni layer on a picosecond timescale. The intensified dynamics of the double-pulse vortex beam interacting with the excited state of the film and the energy competitive processes of electron diffusion and electron-phonon coupling were identified as the main causes for this phenomenon. The research also explored the relationship between the electron-phonon coupling period of the film and important laser parameters such as pulse separation and vortex beam fluence.
INTERNATIONAL JOURNAL OF THERMAL SCIENCES
(2023)
Article
Physics, Applied
Rui Wu, Feng Chen
Summary: Visualization experiments were conducted on microfluidic pore networks to understand the interactions between salt precipitation, corner liquid film flow, and gas-liquid displacement during evaporation. The study revealed two forms of salt precipitation - aggregated polycrystalline structures and large bulk crystals. It was found that gas bubbles could form due to liquid imbibition into aggregated polycrystalline structures. The length of a corner liquid film affected the growth direction of the aggregated polycrystalline structures.
JOURNAL OF APPLIED PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Wanchuan Ding, Xuan Yang, Huoyue Lin, Zixing Xu, Jun Wang, Jie Dai, Can Xu, Feng Chen, Xiaowei Wen, Weiran Chai, Gang Ruan
Summary: Hard-to-transfect cells, such as BMSCs, present challenges in intracellular delivery due to vesicle trapping. We found that coating nanoparticles with PDS1 can effectively avoid vesicle trapping in BMSCs and significantly enhance transfection efficiency and osteoblastic differentiation. Mechanistic studies suggest that higher cholesterol content in BMSCs' plasma membranes may contribute to the difficulty of vesicle escape.
Article
Chemistry, Physical
Shaobo Li, Fei Wang, Ze Zhang, Shuhao Zhao, Chengsheng Xia, Peirui Ji, Xiaomin Wang, Guofeng Zhang, Tao Liu, Feng Chen, Shuming Yang
Summary: Delivering light to the nanoscale using a flexible fiber platform has potential applications in quantum science and bioscience. A technique called broadband azimuthal plasmon interference nanofocusing on a fiber-coupled spiral tip is demonstrated for fiber-based near-field optical nanoimaging. This technique offers high optical resolution and easy incorporation with existing measurement platforms, making it promising for near-field optics, Raman spectroscopy, and quantum sensing.
Article
Multidisciplinary Sciences
Yanwu Chu, Yu Luo, Feng Chen, Chengwei Zhao, Tiancheng Gong, Yanqing Wang, Lianbo Guo, Minghui Hong
Summary: Deep learning method is applied to spectral detection without feature engineering. A DNN model is designed to mine data from LIBS spectra of ore. Compared with traditional methods, the DNN model achieves the highest recognition accuracy rate (75.92%). A training set update method based on DNN output is proposed, resulting in a recognition accuracy of 85.54%. The combination of LIBS and DNN model proves to be a valuable tool for accurate ore classification.
Article
Physics, Applied
Jialiang Zhang, Qing Yang, Qingyun Ma, Fangzheng Ren, Haoyu Li, Chengjun Zhang, Yang Cheng, Feng Chen
Summary: The study prepared a slippery surface with excellent self-cleaning, stability, and self-healing properties, inspired by the Nepenthes plant. The stretchability of the slippery surface is essential for application in flexible sensor surfaces. By using femtosecond laser, an interconnected porous structure was prepared on pre-stretched polydimethylsiloxane, and then infused with lubricant to create the slippery surface. This stretchable slippery surface maintained its performance even under tensile conditions and after multiple stretch cycles, demonstrating remarkable self-cleaning and chemical stability. The femtosecond laser direct writing technique holds promise for stable surfaces in various extreme environmental applications of flexible electronic devices.
APPLIED PHYSICS LETTERS
(2023)
Article
Optics
Xiaodan Gou, Jinglan Huo, Qing Yang, Yang Cheng, Xun Hou, Feng Chen
Summary: A new strategy of aerating micro bubbles by designing four different structures via laser ablation is proposed, which can produce nanoliter-sized bubbles and be applied in water treatment and gas detection. The designed micro bubble structure can also resist the damage of complex water environments and ultraviolet radiation.
OPTICS AND LASER TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Qingqing Liu, Wei Tang, Chen Yang, Wenlong Cai, Feng Chen, Qiang Fu
Summary: The aramid nanofibers form networks on micro silicon particles (ANF-SMPs) by cryofixation and acid-induced protonation, whose zongzi-like wrapping structure reduces volume expansion during (de)lithiation. The obtained ANF-SMP electrode achieves a high capacity retention of 90.7% after 100 cycles at 0.5C, mapping a promising future for anodes with a long lifespan.
CHEMICAL COMMUNICATIONS
(2023)