Review
Biochemical Research Methods
Kenneth F. Reardon
Summary: Precise control over bioreactor operation is crucial for optimal productivity and product quality, leading to an increased drive towards automation in biomanufacturing. Sensors are essential for monitoring parameters and substrate concentrations in order to achieve this automation in a wider array of bioreactors as the bioeconomy continues to grow.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Xuechen Li, Xing Liang, Junling Yin, Weiying Lin
Summary: Autophagy is a common degradation process in cells that plays crucial roles in biological activities, but its abnormalities are closely related to various diseases. Researchers have explored organic fluorescent probes in recent years for real-time monitoring of autophagy process, discussing design strategies, applications, and limitations of these probes.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Yuting Du, Hongliang Wang, Ting Zhang, Wen Wei, Minmin Guo
Summary: ONOO- is a reactive oxygen species that causes serious damage to living cells and leads to human diseases. A mitochondria-targeted ratiometric fluorescent probe, DMANI, has been designed to accurately detect ONOO- in cells, showing good selectivity, a large Stokes shift, and a low detection limit. DMANI can be used for ratiometric imaging and monitoring of mitochondrial ONOO- fluctuations in living cells, with great potential for applications in biological research.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Applied
Yong Zhang, Chengli Jia, Yuesong Wang, Haoli Yu, Min Ji
Summary: A unique turn-off probe N-1 containing OPD moiety with ICT mechanism was designed and synthesized in this study. N-1 showed excellent performance in NO detection with high selectivity, and also successfully imaged NO in living cells, demonstrating its practical significance in biology.
Article
Chemistry, Analytical
Xue Wu, Guanyu Fu, Ying Li, Sijin Li, Qiuyue Zhao, Fanpeng Kong, Lu Li, Bo Tang
Summary: In this study, three near-infrared fluorescent probes, named DHX-V-1-3, were developed for monitoring mitochondrial viscosity. DHX-V-3 showed the highest signal-to-noise ratio and excellent selectivity and targeting ability for mitochondria. It was successfully used to image mitochondrial viscosity in live cells and visualize increased viscosity in LPS-treated mice.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Dong Wang, Chunmeng Li, Ya Zhu, Yunxia Song, Sheng Lu, Huiyong Sun, Haiping Hao, Xiaowei Xu
Summary: In this study, a novel AIE probe TEPC466 was synthesized for selective detection of PKM2 protein, showing high selectivity and sensitivity. The probe was successfully used in imaging colorectal cancer cells and demonstrated better binding to PKM2 than TEPP-46, suggesting its potential as an agonist for PKM2. This bioprobe holds promise in selective PKM2 detection and could be a useful tool for cancer diagnosis and therapy.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Zefan Li, Jing Zhang, Hui-wang Ai
Summary: UDP-GlcNAc is a nucleotide sugar essential for synthesizing glycoproteins and plays a central role in connecting nutrition, metabolism, signaling, and disease. Researchers have developed genetically encoded fluorescent sensors for monitoring UDP-GlcNAc dynamics in live mammalian cells, as well as another biosensor responsive to UDP and UTP but not UDP-GlcNAc. These biosensors have been used to track UDP-GlcNAc levels in cultured mammalian cells under different conditions.
ACS CENTRAL SCIENCE
(2021)
Article
Biophysics
Guoliang Zheng, Liang Zhao, Deyu Yuan, Jia Li, Gang Yang, Danxia Song, Hui Miao, Linjuan Shu, Xianming Mo, Xiaoding Xu, Ling Li, Xu Song, Yongyun Zhao
Summary: A novel label-free fluorescent turn-on biosensor for monitoring ATP in living bacterias and mammalian cells was developed, utilizing heterobifunctional aptamers with high sensitivity. A tandem method combining Broc-ATPs with 3 x F30 three-way junction scaffold was established to construct an intracellular biosensor for sensitive and specific imaging of ATP dynamics in mammalian cells.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Biochemistry & Molecular Biology
Sellamuthu Anbu, Anup Paul, Kalpana Surendranath, Ahmed Sidali, Armando J. L. Pombeiro
Summary: The sensor NPP demonstrates a significant enhancement in fluorescence emission upon binding with Cu2+ and can be used for both fluorescent and colorimetric detection in an aqueous medium. It was also successfully applied as a fluorescent probe for detecting Cu2+ in live cancer cells, showing recovery of emission intensity upon complex formation and reversible response to Cu2+ and EDTA in solution.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2021)
Article
Chemistry, Analytical
Francisco Fueyo-Gonzalez, Rosario Herranz, Simona Plesselova, Maria D. Giron, Rafael Salto, Jose Manuel Paredes, Angel Orte, May C. Morris, Juan A. Gonzalez-Vera
Summary: CDK5 kinase is activated through interactions with different partners, playing a key role in neuronal functions and contributing to neurodegenerative diseases and human cancers. The design of fluorescently labeled peptides allowed for the detection of CDK5 partners, demonstrating the potential of the biosensor to report on the relative abundance of p25.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Chemistry, Analytical
Ying Hu, Shiman Guo, Junqian Peng, Yao Fan, Fang Wang, Lingmin Lu, Haiyan Fu, Xiaoqiang Chen, Yuanbin She
Summary: A ratiometric pyrene-based fluorescence sensor PN was developed for visual detection of formaldehyde (FA) by featuring homoallylamino group as specific recognition site. Sensor PN has high selectivity, fast response (< 100 s), low detection limit (18 mu M), wide quantitative detection range (0.018-4 mM) and large ratio enhancement (up to 10-fold), making it suitable for detecting FA in diverse food samples. It can also be used for fluorescence imaging of FA in living cells.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Analytical
Lei Jiang, Cai-Hong He, Hua-Ying Chen, Cheng-Ye Xi, Essy Kouadio Fodjo, Ze-Rui Zhou, Ruo-Can Qian, Da-Wei Li, Mahmoud Elsayed Hafez
Summary: A highly anti-interference ZIF-8-based SERS sensor was developed for detecting H2O2 released from living cells, with a low detection limit of 0.357 nM and a response time as short as 1 minute. The sensor also enables real-time monitoring of H2O2 secreted from cells under stimulation, showing promising potential for future applications.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Wangbo Qu, Bin Yang, Taiyu Guo, Ruowei Tian, Shuang Qiu, Xinyue Chen, Zhirong Geng, Zhilin Wang
Summary: In this study, a dual-response mitochondria-targeted fluorescent probe HBTN was developed for the quantitative detection of viscosity and HOCl. The probe showed promising results in both in vitro and in vivo experiments, providing a practical tool for monitoring viscosity and HOCl.
Article
Chemistry, Analytical
Robert Nissler, Julia Ackermann, Chen Ma, Sebastian Kruss
Summary: This article discusses the first examples of chirality-pure SWCNT-based fluorescent biosensors and introduces the method of using aqueous two-phase extraction for purification of SWCNTs. These new sensors can detect and image neurotransmitters, reactive oxygen species, lipids, bacterial motives, and plant metabolites in the near-infrared region, with enhanced bioanalytical performance.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Le Zhang, Yi-Fan Zhang, Ying-Feng Han
Summary: A fluorescent probe for OCl- detection in mitochondria was developed, showing high selectivity, ultra-fast response, and capability for cellular imaging.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Cell Biology
Xi Li, Yinan Zhang, Lingya Xu, Aoxue Wang, Yejun Zou, Ting Li, Li Huang, Weicai Chen, Shuning Liu, Kun Jiang, Xiuze Zhang, Dongmei Wang, Lijuan Zhang, Zhuo Zhang, Zeyi Zhang, Xianjun Chen, Wei Jia, Aihua Zhao, Xinfeng Yan, Haimeng Zhou, Linyong Zhu, Xinran Ma, Zhenyu Ju, Weiping Jia, Congrong Wang, Joseph Loscalzo, Yi Yang, Yuzheng Zhao
Summary: In this study, a highly sensitive lactate sensor called FiLa was developed, which allows for monitoring subtle lactate fluctuations in living cells and animals. It was found that lactate is highly enriched in mammalian mitochondria and functions as a key hub sensing various metabolic activities. The FiLa sensors also enable direct imaging of elevated lactate levels in diabetic mice and provide a simple, rapid, and sensitive lactate assay for clinical screening. Overall, the FiLa sensors are powerful and broadly applicable tools for studying lactate metabolism in health and disease.
Article
Cell Biology
Hao Sun, Zhuo Zhang, Tianda Li, Ting Li, Weicai Chen, Tianshi Pan, Sen Fang, Chao Liu, Ying Zhang, Leyun Wang, Guihai Feng, Wei Li, Qi Zhou, Yuzheng Zhao
Summary: Metabolic programming is crucial in early embryonic development, and a noninvasive imaging technology is needed to track developmental metabolism. This study used genetically encoded fluorescent biosensors to characterize the regulation of energy metabolism and redox homeostasis during early zygotic cleavage. The results showed a decrease in NADH/NAD(+) levels and an increase in NADPH levels. Transcriptome profiling revealed changes in the expression of genes involved in glucose uptake, glycolysis, pyruvate metabolism, oxidative phosphorylation, and peroxiredoxin genes. Overall, this study provides insights into the programming of redox metabolism during ZGA.
JOURNAL OF CELLULAR PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Dan Huang, Changcheng Zhang, Ming Xiao, Xie Li, Weicai Chen, Yu Jiang, Yamin Yuan, Yaping Zhang, Yejun Zou, Lei Deng, Yang Wang, Yuying Sun, Wenping Dong, Zhuo Zhang, Li Xie, Zhuo Yu, Chiqi Chen, Ligen Liu, Jing Wang, Yi Yang, Jie Yang, Yuzheng Zhao, Junke Zheng
Summary: The rewiring of redox metabolism has a significant impact on tumor development, but the influence of cellular heterogeneity of redox balance on leukemogenesis remains unclear. This study developed a genetically encoded biosensor called HyPerion to track the redox state of leukemic cells in vivo. The findings revealed that a subset of acute myeloid leukemia (AML) cells with low levels of H2O2 (HyPerion-low) was enriched with leukemia-initiating cells, which exhibited high colony-forming ability, potent drug resistance, endosteal localization, and short survival. The high expression of malic enzymes, including ME1/3, accounted for NADPH production and the low abundance of H2O2. Deletion of malic enzymes reduced the population size of leukemia-initiating cells, impairing their leukemogenic capacity and drug resistance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Miaowei Mao, Yajie Qian, Wenyao Zhang, Siyu Zhou, Zefeng Wang, Xianjun Chen, Yi Yang
Summary: In this study, a stable monomeric tag (SULI) based on a single light-oxygen-voltage domain from Neurospora crassa was engineered for yeast and zebrafish. SULI allows control of protein stability by inducing degradation in dark conditions and provides spatiotemporal modulation of protein levels.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Yajie Qian, Ting Li, Siyu Zhou, Xianjun Chen, Yi Yang
Summary: The ltLightOn optogenetic Gal4-UAS system utilizes a single light-switchable transactivator to activate gene expression, eliminating the need for multiple protein components and extraneous light-sensitive cofactors. It offers quantitative, spatial, and temporal control of gene expression and has been successfully used in regulating zebrafish embryonic development.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Edward R. Pennington, Syed Masood, Steven O. Simmons, Lisa Dailey, Philip A. Bromberg, Rebecca L. Rice, Avram Gold, Zhenfa Zhang, Weidong Wu, Yi Yang, James M. Samet
Summary: This study investigates the effects of air pollutants on intracellular redox homeostasis in human airway cells. The results show that isoprene hydroxy hydroperoxide (ISOPOOH), an atmospheric oxidation product, can disrupt the redox balance in cells, but this imbalance can be restored by glucose. Additionally, glucose-6-phosphate dehydrogenase (G6PD) plays a regulatory role in this process.
Article
Multidisciplinary Sciences
Mengshu Jia, Xiao Yue, Weixia Sun, Qianjun Zhou, Cheng Chang, Weihua Gong, Jian Feng, Xie Li, Ruonan Zhan, Kemin Mo, Lijuan Zhang, Yajie Qian, Yuying Sun, Aoxue Wang, Yejun Zou, Weicai Chen, Yan Li, Li Huang, Yi Yang, Yuzheng Zhao, Xiawei Cheng
Summary: In this study, it was found that lactate dehydrogenase A (LDHA) is activated upon UNC-51-like kinase 1 (ULK1) activation under nutrient deprivation, and promotes lactate production through Vps34 lactylation. These findings describe the interplay between autophagy and glycolysis.
Article
Cell Biology
Dasheng Zhang, Zhengda Chen, Zengmin Du, Bingkun Bao, Ni Su, Xianjun Chen, Yihui Ge, Qiuning Lin, Lipeng Yang, Yujie Hua, Shuo Wang, Xin Hua, Fangting Zuo, Ningfeng Li, Renmei Liu, Li Jiang, Chunyan Bao, Yuzheng Zhao, Joseph Loscalzo, Yi Yang, Linyong Zhu
Summary: Naturally occurring fluorescent proteins (FPs) have been widely used for tracking cellular proteins and sensing cellular events. Researchers have chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs), which exhibit bright, rapidly inducible fluorescence from cyan to infrared. These SmFPs are useful for real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and they outperform FPs like GFP in many important ways. Additionally, circularly permuted SmFPs exhibit fluorescence sensitivity to the conformational changes of their fusion partners, making them suitable for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.
Article
Biotechnology & Applied Microbiology
Hongguan Xing, Pingping Wang, Xing Yan, Yi Yang, Xinliang Li, Rui Liu, Zhihua Zhou
Summary: Directed evolution was used to enhance the thermostability of phytase, resulting in the generation of five mutants with higher residual activities and catalytic efficiencies. The substitution of C75 residue was identified as the main reason for the improved thermostability, indicating the crucial role of this amino acid in the stability and catalytic efficiency of phytase.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biophysics
Mengyue Fang, Huiwen Li, Xin Xie, Hui Wang, Ying Jiang, Tianyu Li, Bibi Zhang, Xin Jiang, Yueyang Cao, Rui Zhang, Dasheng Zhang, Yuzheng Zhao, Linyong Zhu, Xianjun Chen, Yi Yang
Summary: Engineered fluorescent RNA (FR)-based sensors have been used to detect essential metabolites in living systems, but their unfavorable characteristics limit their applications. Here, we demonstrate a strategy for converting Pepper fluorescent RNA into sensors with improved characteristics. These Pepper-based sensors showed expanded emission and improved brightness, allowing robust monitoring of intracellular changes and protein translocation in live cells. Furthermore, the use of Pepper-based sensors in the CRISPR-display strategy achieved signal amplification in fluorescence imaging. These results highlight the potential of Pepper as a high-performance FR-based sensor for detecting cellular targets.
BIOSENSORS & BIOELECTRONICS
(2023)
Letter
Biochemistry & Molecular Biology
Jie Ren, Moshi Song, Weiqi Zhang, Jian-Ping Cai, Feng Cao, Zhongwei Cao, Piu Chan, Chang Chen, Guobing Chen, Hou-Zao Chen, Jun Chen, Xiao-Chun Chen, Weimin Ci, Bi-Sen Ding, Qiurong Ding, Feng Gao, Shaorong Gao, Jing-Dong J. Han, Qi-Yang He, Kai Huang, Zhenyu Ju, Qing-Peng Kong, Ji Li, Jian Li, Jingyi Li, Xin Li, Baohua Liu, Feng Liu, Jun-Ping Liu, Lin Liu, Qiang Liu, Qiang Liu, Xingguo Liu, Yong Liu, Xianghang Luo, Shuai Ma, Xinran Ma, Zhiyong Mao, Jing Nie, Yaojin Peng, Jing Qu, Ruibao Ren, Weihong Song, Zhou Songyang, Liang Sun, Yi Eve Sun, Yu Sun, Mei Tian, Xiao-Li Tian, Ye Tian, Jianwei Wang, Shusen Wang, Si Wang, Wengong Wang, Xia Wang, Xiaoning Wang, Yan-Jiang Wang, Yunfang Wang, Catherine C. L. Wong, Andy Peng Xiang, Yichuan Xiao, Zhi-Xiong Xiao, Zhengwei Xie, Wei Xiong, Daichao Xu, Ze Yang, Jing Ye, Wei Yu, Rui Yue, Cuntai Zhang, Hongbo Zhang, Liang Zhang, Xinchao Zhang, Yong Zhang, Yun-Wu Zhang, Zhuohua Zhang, Tongbiao Zhao, Yuzheng Zhao, Zhongjun Zhou, Dahai Zhu, Weiguo Zou, Gang Pei, Guang-Hui Liu
Article
Endocrinology & Metabolism
Xuefeng Dou, Qiang Fu, Qilai Long, Shuning Liu, Yejun Zou, Da Fu, Qixia Xu, Zhirui Jiang, Xiaohui Ren, Guilong Zhang, Xiaoling Wei, Qingfeng Li, Judith Campisi, Yuzheng Zhao, Yu Sun
Summary: This study reveals that senescent cells continue to have active metabolism and undergo metabolic reprogramming. Upregulation of PDK4 leads to aerobic glycolysis and increased lactate production, while mitochondrial respiration and redox activity are maintained. Lactate production promotes reactive oxygen species production and drives the senescence-associated secretory phenotype. Inhibition of PDK4 reduces the severity of DNA damage and restrains the senescence-associated secretory phenotype. In preclinical trials, PDK4 inhibition improves physical dysfunction and prevents age-associated frailty.
Review
Biochemistry & Molecular Biology
Zi-Heng Gao, Xuan Zou, Yi Zhou, Ting-Ting Xue, Xian-Jun Chen, Yi Yang
Summary: Nucleic acid metabolism is the fundamental metabolic process that maintains growth and development, metabolism, genetic variation, and aging. Enzyme activity related to nucleic acid metabolism is crucial for intracellular stability, and changes in activity can contribute to disease development. Enzymes involved in nucleic acid metabolism have become important targets for disease research and essential tools in biotechnology and bioengineering. Nucleic acid metabolism forms the basis for nucleic acid studies and other life science research.
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Chemistry, Physical
Renjie Zhou, Lipeng Yang, Zhengda Chen, Li Jiang, Tuan Liu, Zhiqiang Wang, Xinyi Huang, Qiuning Lin, Xueqing Gong, Yi Yang, Linyong Zhu
Summary: Photoactivated fluorophores (PAFs) have great potential as imaging tools for subcellular structures and dynamic biological processes. However, the current photoremovable protecting groups (PPGs) used in PAF construction have limitations in terms of excitation wavelength and efficiency. In this study, a new class of coumarin-based PPGs with electron-rich thiophene derived substitutions was developed to address these limitations. The modified PPGs showed redshifted absorption and increased photolysis efficiency, enabling efficient photolysis even under weak blue light. The resulting PAF exhibited fast photoactivation, low background signal, and high signal-to-noise ratio in fluorescence imaging. It is anticipated that these superior photolysis properties make the PPGs a novel platform for constructing photoresponsive systems in various applications.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemical Research Methods
Renmei Liu, Jing Yao, Siyu Zhou, Jing Yang, Yaqiang Zhang, Xiaoyan Yang, Leshi Li, Yunbin Zhang, Yingping Zhuang, Yi Yang, Xianjun Chen
Summary: This article introduces a strategy for engineering photoswitchable RNA-binding proteins (RBPs) to achieve spatiotemporal control of RNA metabolism. By using LicV, a synthetic RNA-binding protein that can bind to a specific RNA sequence in response to blue light irradiation, optogenetic control of RNA localization, splicing, translation, and stability has been achieved.
