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Microbial resources and interactions across three-dimensional space for a freshwater ecosystem

Science of the Total Environment 2025年 980卷 179522页

作者： Chu, Dongliang Zhang, Haohong Wang, Zhi Ning, Kang Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Center of AI Biology Department of Bioinformatics and Systems Biology College of Life Science and Technology Huazhong University of Science and Technology Wuhan China Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences Wuhan430077 China

Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems. © 2025 The Authors

关键词： Metagenomic Three-dimensional space Genome and gene catalog Microbial refuge

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An automatic annotation tool and reference database for T cell subtypes and states at single-cell resolution

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Science Bulletin 2025年第10期70卷 1659-1672页

作者： Shen, Wen-Kang Zhang, Chu-Yu Gu, Yi-Min Luo, Tao Chen, Si-Yi Yue, Tao Xie, Gui-Yan Liao, Yu Yuan, Yong Lei, Qian Guo, An-Yuan Department of Thoracic Surgery West China Biomedical Big Data Center West China Hospital Sichuan University Chengdu610041 China Hubei Bioinformatics & Molecular Imaging Key Laboratory College of Life Science and Technology Huazhong University of Science and Technology Wuhan430074 China College of Life Sciences University of Chinese Academy of Sciences Beijing101408 China Department of Rheumatology & Immunology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan430074 China

T cells have various subtypes and states with different functions. However, a reference list and automated annotation tool for T cell subtypes and states are lacking, which is critical for analyzing and comparing T cells under various conditions. We constructed the largest human T cell reference, containing 1,348,268 T cells from 35 conditions and 16 tissues. We classified T cells into 33 subtypes and further stratified them into 68 categories according to subtype and state. Based on this reference, we developed a tool named STCAT to automatically annotate T cells from scRNA-seq data by hierarchical models and marker correction. The accuracy of STCAT was 28% higher than that of existing tools validated on six independent datasets, including cancer and healthy samples. Using STCAT, we consistently discovered that CD4+ Th17 cells were enriched in late-stage lung cancer patients in multiple datasets, whereas MAIT cells were prevalent in milder-stage COVID-19 patients. We also confirmed a decrease in Treg cytotoxicity in post-treatment ovarian cancer. Systematic landscape analyses of CD4+ and CD8+ T cell references revealed that CD4+ Treg cells were enriched in tumor samples and that CD8+ naive-related cells were abundant in healthy individuals. Finally, we deposited all the T cell references and annotations into a TCellAtlas (https://***/TCellAtlas) database, which allows users to browse T cell expression profiles and analyze customized scRNA-seq data by STCAT. In conclusion, comprehensive human T cell subtypes and states reference, automated annotation tool, and database will greatly facilitate research on T cell immunity and tumor immunology. © 2025 Science China Press

关键词： T-cells

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Microbiome catalog and dynamics of the Chinese liquor fermentation process

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Bioresource Technology 2025年 431卷 132620页

作者： Zhu, Xue Chen, Liangqiang Yang, Pengshuo Luo, Sha Teng, Mengjing Zhu, Wenjie Li, Yuxue Zhao, Dan Wang, Nan Chen, Xiaoke Cheng, Mingyue Tu, Huabin Huang, Weihua Yang, Fan Wang, Li Liu, Xin Ning, Kang Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Center of AI Biology Department of Bioinformatics and Systems Biology College of Life Science and Technology Huazhong University of Science and Technology Hubei Wuhan430074 China Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation Industry Kweichow Moutai Group Guizhou Renhuai564500 China Kweichow Moutai Distillery Co. Ltd. Zunyi564501 China College of Chemistry and Molecular Sciences Wuhan University Hubei Wuhan430072 China Moutai Institute Guizhou Renhuai564500 China

Fermented food remains poorly understood, largely due to the lack of knowledge about microbes in food fermentation. Here, this study constructed Moutai Fermented Grain Catalog (MTFGC), a representative liquor fermented by one of the most complex fermentations. MTFGC comprised 8,379,551 non-redundant genes and 5,159 metagenome-assembled genomes, with 20% species and 20% genes being novel. Additionally, 25,625 biosynthetic gene clusters (BGCs) and 28 BGC-enriched species were identified. Moreover, the microbial community assembly was deterministic, with significant species and gene changes in early fermentation stages, while stabilizing in later stages. Further BGC-knockout experiments verified Bacillus licheniformis, a BGC-enriched species, employed its BGCs for synthesizing the aroma-related lipopeptide lichenysin. This study has established the largest genetic resource for fermented food, uncovering its uniqueness and high metabolic potential. These findings facilitate the transition potential from traditional fermentation to precision-driven synthetic biology in food systems. © 2025 Elsevier Ltd

关键词： Biosynthetic gene clusters Fermented food Microbiome dynamics Microbiome resource Multistage solid-state fermentation process

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Three-dimensional traction technology and its application in mechanomedicine

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Mechanobiology in Medicine 2025年第3期3卷

作者： Chen, Xinman Ji, Chenyang Liu, Xi Wang, Ning Wei, Fuxiang Chen, Junwei Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Bioinformatics and Molecular Imaging Key Laboratory Laboratory for Cellular Biomechanics and Regenerative Medicine Department of Biomedical Engineering College of Life Science and Technology Huazhong University of Science and Technology Hubei Wuhan 430074 China The Institute for Mechanobiology Northeastern University Boston 02115 MA United States Department of Bioengineering College of Engineering Northeastern University Boston 02115 MA United States

Endogenous forces generated by living cells are essential for biological processes and physiological functions of cells and tissues. Over the last several decades, numerous methods for detecting traction forces have been developed. Here we review these methods and discuss their respective strengths and limitations. Being able to reliably quantify tractions in living cells and tissues are critical in understanding how forces drive and regulate cell and tissue functions in physiology and diseases. © 2025 The Author(s)

关键词： 3D traction force Mechanomedicine Traction force microscopy Tumor microenvironment

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Deep Learning-Enhanced Hand-Driven Microfluidic Chip for Multiplexed Nucleic Acid Detection Based on RPA/CRISPR

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Advanced Science 2025年第0期 e2414918页

作者： Xu, Tao Zhang, Ying Li, Shunji Dai, Chenxi Wei, Hongguo Chen, Dongjuan Zhao, Yunjun Liu, He Li, Deliang Chen, Peng Liu, Bi-Feng Tian, Ye College of Medicine and Biological Information Engineering Northeastern University Shenyang110169 China The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme Department of Biomedical Engineering College of Life Science and Technology Huazhong University of Science and Technology Wuhan430074 China Department of Laboratory Medicine Maternal and Child Health Hospital of Hubei Province Tongji Medical College Huazhong University of Science and Technology Wuhan430070 China Foshan Graduate School of Innovation Northeastern University Foshan528300 China

The early detection of high-risk human papillomavirus (HR-HPV) is crucial for the assessment and improvement of prognosis in cervical cancer. However, existing PCR-based screening methods suffer from inadequate accessibility, which dampens the enthusiasm for screening among grassroots populations, especially in resource-limited areas, and contributes to the persistently high mortality rate of cervical cancer. Here, a portable system is proposed for multiplexed nucleic acid detection, termed R-CHIP, that integrates Recombinase polymerase amplification (RPA), CRISPR detection, Hand-driven microfluidics, and an artificial Intelligence Platform. The system can go from sample pre-processing to results readout in less than an hour with simple manual operation. Optimized for sensitivity of 10−17 M for HPV-16 and 10−18 M for HPV-18, R-CHIP has an accuracy of over 95% in 300 tests on clinical samples. In addition, a smartphone microimaging system combined with the ResNet-18 deep learning model is used to improve the readout efficiency and convenience of the detection system, with initial prediction accuracies of 96.0% and 98.0% for HPV-16 and HPV-18, respectively. R-CHIP, as a user-friendly and intelligent detection platform, has great potential for community-level HR-HPV screening in resource-constrained settings, and contributes to the prevention and early diagnosis of other diseases. © 2025 The Author(s). Advanced Science published by Wiley-VCH GmbH.

关键词： Risk assessment

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Stereotypes About Enterotype: the Old and New Ideas

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Genomics, Proteomics & bioinformatics 2019年第1期17卷 4-12页

作者： Mingyue Cheng Kang Ning Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imaging Department of Bioinformatics and Systems Biology College of Life Science and TechnologyHuazhong University of Science and Technology

In 2011, the term ‘‘enterotype" first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of *** firstly illustrated the definition of the enterotype and various factors influencing enterotypes,such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype ***, we showed that the concept of enterotype has been extended to other ecological *** on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.

关键词： Enterotype Gut microbiome Biomarker Continuity Computational methods

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ModuleNet:An R package on regulatory network building

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Chinese Science Bulletin 2010年第30期55卷 3430-3435页

作者： ZHOU Dao HE Dong LUO QingMing ZHOU YanHong Hubei Key Laboratory of Bioinformatics and Molecular Imaging Huazhong University of Science and Technology Wuhan 430074 China

Many researchers have used microarray gene expression data to investigate gene regulatory networks in specific life stages. In these analyses,Bayesian network was widely applied to regulatory network building from expression profiles because of its solid mathematical foundation and its robust analysis ability in noisy data. However,the building of Bayesian network is time consuming and the searching space is really large. Considering the biological feature of transcription factors (TFs) and targets (TGs),the regulatory network is possible to be separated into core TFs networks and the interactions from TFs to TGs. We developed an R package named ModuleNet which used Bayesian network model to the inner TFs network building and genetic algorithm on TF-TG interactions prediction. With determined number of transcription factors,the searching space and time requirements of ModuleNet is linear increasing according to the number of targets. After application to yeast cell-cycle expression profile,the results demonstrated the prediction accuracy of ModuleNet. Furthermore,significantly enriched Gene Ontology (GO) terms with similar expression behaviors were detected automatically by ModuleNet from expression profile,and the relationships from TFs to GO terms were figured out. The source code is available by asking for the author.

关键词：网络建设监管贝叶斯网络模型基因表达数据基因表达谱转录因子封装基因调控网络

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Microbial Dark Matter: from Discovery to Applications

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Genomics, Proteomics & bioinformatics 2022年第5期20卷 867-881页

作者： Yuguo Zha Hui Chong Pengshuo Yang Kang Ning MOE Key Laboratory of Molecular Biophysics Hubei Key Laboratory of Bioinformatics and Molecular-imagingCenter of Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China

With the rapid increase of the microbiome samples and sequencing data,more and more knowledge about microbial communities has been ***,there is still much more to learn about microbial communities,including billions of novel species and genes,as well as countless spatiotemporal dynamic patterns within the microbial communities,which together form the microbial dark *** this work,we summarized the dark matter in microbiome research and reviewed current data mining methods,especially artificial intelligence(AI)methods,for different types of knowledge discovery from microbial dark *** also provided case studies on using AI methods for microbiome data mining and knowledge *** summary,we view microbial dark matter not as a problem to be solved but as an opportunity for AI methods to explore,with the goal of advancing our understanding of microbial communities,as well as developing better solutions to global concerns about human health and the environment.

关键词： Microbiome Dark matter Artificial intelligence Knowledge discovery Application

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Characterization and Crystal Structure of a New Holmium(III) Complex with the Macrocyclic Ligand Derived from 2,6-Diformyl-4-methylphenol and Diethylenetriamine

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Chinese Journal of Structural Chemistry 2007年第12期26卷 1429-1434页

作者：胡学雷邱立赵元弟key laboratory of Biomedical Photonics of Ministry of Education - Wuhan National laboratory for Optoelectronics - Hubei bioinformatics and molecular imaging key laboratory - key laboratory of molecular Biophysics of the Ministry of Education Huazhong University of Science and Technology 潘志权 Key Laboratory of Biomedical Photonics of Ministry of Education - Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics and Molecular Imaging Key Laboratory - Key Laboratory of Molecular Biophysics of the Ministry of Education Huazhong University of Science and Technology Hubei Key Laboratory of Novel Chemical Reactor and Green Chemical Technology Wuhan Institute of Technology

The title compound （13,27-dimethyl-3,6,9,17,20,23-hexaazatricyclo-[23.3.1.1^11.15]- triaconta-l（29）,2,9,11,13,15（30）,16,23,25,27-decaene-29,30-diol-N^3,N^6,N^9,O^29,O^30）-bis（nitrato-O,O＇）- holmium（m） nitrate hydrate has been prepared and characterized by elemental analysis, infrared spectra, and electrospray mass spectra. Its crystal and molecular structures were determined by X-ray diffraction methods. The crystal crystallizes in the monoclinic system, space group C2/c with a = 23.737（12）, b = 14.237（7）, c = 19.801（10） A, β = 91.36（1）^o, Mr = 831.57, V = 6690（6） A^3, Z = 8, Dc = 1.651 g/cm^3, F（000） = 3344, R = 0.0482 and wR = 0.0923. The holmium ion is located in one of the compartments of the macrocyclic ligand and presents a distorted tricapped trigonal prismatic coordination geometry. The macrocycle is coordinated with two oxygen and three nitrogen atoms. Two nitrates are chelated in the opposite positions of the macrocycle, and the third one is ionic.

关键词： crystal structure lanthanide macrocycle

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Mechanosensitive nuclear checkpoint: nuclear envelope as a sensor of chromosomal instability and driver of cell fate

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Mechanobiology in Medicine 2025年第2期3卷

作者： Chenyang Ji Junwei Chen Fuxiang Wei Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Bioinformatics and Molecular Imaging Key Laboratory Laboratory for Cellular Biomechanics and Regenerative Medicine Department of Biomedical Engineering College of Life Science and Technology Huazhong University of Science and Technology Wuhan Hubei 430074 China

The nuclear envelope (NE) is a dynamic, mechanosensitive structure that functions as a protective barrier for the genome and serves as a checkpoint responding to external stimuli. It plays a critical role in maintaining genomic stability and regulating cell fate. This review synthesizes recent research highlighting the role of NE as a mechanical checkpoint in ensuring accurate chromosome segregation, regulating cell cycle progression, and contributing to cancer development. Chromosome mis-segregation during cell division is a major driver of aneuploidy, a condition closely associated with genomic instability and cellular transformation. The role of NE in chromatin organization and gene expression regulation is also discussed, underscoring its importance in cell differentiation and identity.

关键词： Nuclear envelope Mechanosensitive checkpoint Chromatin Gene expression Cell cycle

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