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Identifying the dynamic behaviors in complete reconstruction of Co-based complex precatalysts during electrocatalytic oxygen evolution

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Journal of Energy Chemistry 2025年第1期100卷 226-233页

作者： Jingfang Zhang Danyang Wu Linke Cai Youluan Lu Fanpeng Cheng Lijuan Shi Qun Yi Yao Liu Yi Huang Key laboratory of Green Chemical Engineering Process of ministry of education Engineering Research Center of Phosphorus Resources Development and Utilization of Ministry of Education Hubei Key Laboratory of Novel Reactor and Green Chemical Technology School of Chemical Engineering & Pharmacy Wuhan Institute of Technology Key laboratory of Pesticide & Chemical biology of ministry of education Engineering Research Center of Photoenergy Utilization for Pollution Control and Carbon Reduction of Ministry of Education College of Chemistry Central China Normal University College of Materials Science and Engineering Fuzhou University

Transition metal-based nanomaterials have emerged as promising electrocatalysts for oxygen evolution reaction（OER）. Considerable research efforts have shown that self-reconstruction occurs on these nanomaterials under operating conditions of OER process. However, most of them undergo incomplete reconstruction with limited thickness of reconstruction layer, leading to low component utilization and arduous exploration of real catalytic mechanism. Herein, we identify the dynamic behaviors in complete reconstruction of Co-based complexes during OER. The hollow phytic acid（PA） cross-linked CoFe-based complex nanoboxes with porous nanowalls are designed because of their good electrolyte penetration and mass transport ability, in favor of the fast and complete reconstruction. A series of experiment characterizations demonstrate that the reconstruction process includes the fast substitution of PA by OH-to form Co（Fe）(OH)xand subsequent potential-driven oxidation to Co（Fe）OOH. The obtained CoFeOOH delivers a low overpotential of 290 mV at a current density of 10 mA cm-2and a long-term *** experiment results together with theory calculations reveal that the Fe incorporation can result in the electron rearrangement of reconstructed CoFeOOH and optimization of their electronic structure,accounting for the enhanced OER activity. The work provides new insights into complete reconstruction of metal-based complexes during OER and offers guidelines for rational design of high-performance electrocatalysts.

关键词： Complete reconstruction Co-based complex Precatalysts Oxygen evolution reaction

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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for bioinformatics and Computational biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Endoplasmic reticulum stress and autophagy in cerebral ischemia/reperfusion injury:PERK as a potential target for intervention

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Neural Regeneration Research 2025年第5期20卷 1455-1466页

作者： Ju Zheng Yixin Li Ting Zhang Yanlin Fu Peiyan Long Xiao Gao Zhengwei Wang Zhizhong Guan Xiaolan Qi Wei Hong Yan Xiao Key laboratory of Endemic and Ethnic Diseases Ministry of Education&Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyangGuizhou ProvinceChina Guizhou Center for Disease Control and Prevention GuiyangGuizhou ProvinceChina Department of Histology and Embryology Guizhou Medical UniversityGuiyangGuizhou ProvinceChina Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and ministry GuiyangGuizhou ProvinceChina

Several studies have shown that activation of unfolded protein response and endoplasmic reticulum(ER)stress plays a crucial role in severe cerebral ischemia/reperfusion *** occurs within hours after cerebral ischemia,but the relationship between ER stress and autophagy remains *** this study,we established experimental models using oxygen-glucose deprivation/reoxygenation in PC12 cells and primary neurons to simulate cerebral ischemia/reperfusion *** found that prolongation of oxygen-glucose deprivation activated the ER stress pathway protein kinase-like endoplasmic reticulum kinase(PERK)/eukaryotic translation initiation factor 2 subunit alpha(e IF2α)-activating transcription factor 4(ATF4)-C/EBP homologous protein(CHOP),increased neuronal apoptosis,and induced ***,inhibition of ER stress using inhibitors or by si RNA knockdown of the PERK gene significantly attenuated excessive autophagy and neuronal apoptosis,indicating an interaction between autophagy and ER stress and suggesting PERK as an essential target for regulating *** autophagy with chloroquine exacerbated ER stress-induced apoptosis,indicating that normal levels of autophagy play a protective role in neuronal injury following cerebral ischemia/reperfusion *** from this study indicate that cerebral ischemia/reperfusion injury can trigger neuronal ER stress and promote autophagy,and suggest that PERK is a possible target for inhibiting excessive autophagy in cerebral ischemia/reperfusion injury.

关键词： apoptosis ATF4 autophagy C/EBP homologous protein cerebral ischemia/reperfusion injury eIF2α endoplasmic reticulum stress PERK

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Machine learning driven rational design of dual atom catalysts on graphene for carbon dioxide electroreduction

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Nano Research 2025年第1期18卷 186-194页

作者： Dongxu Jiao Xinyi Li Mingzi Sun Lin Liu Jinchang Fan Jingxiang Zhao Bolong Huang Xiaoqiang Cui State Key laboratory of Automotive Simulation and Control School of Materials Science and Engineeringand Key Laboratory of Automobile Materials of MOEJilin UniversityChangchun 130012China Department of Applied biology and Chemical Technology The Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina College of Chemistry and Chemical Engineering and Key Laboratory of Photonic and Electronic Bandgap MaterialsMinistry of EducationHarbin Normal UniversityHarbin 150025China

The development of high-performance atomiccatalysts for the carbon dioxide reduction reaction(CO_(2)RR)is atime-consuming process due to the complexity of the reactionmechanism and the uncertainty of the active ***,wehave proposed combining density functional theory(DFT)andmachine learning(ML)to investigate the potential of topologicalgraphene-based dual-atom catalysts(DACs)as CO_(2)*** analyzing the ML results,we identify thenumber of d-orbital electrons in the active site as a key factorinfluencing the CO_(2)RR catalytic ***,wepropose a simple descriptor to measure the CO_(2)RR activity ofthese *** findings provide plausible explanations for thesynergistic interactions between bimetallic atoms in CO_(2)RR andallow us to screen the homogeneous Ni-Ni pair as the mostpromising dual-atom *** work offers a fast MLapproach based on limited DFT calculations to predict the mostelectroactive and stable DACs on carbon support for CO_(2)RR,facilitating rapid screening of high-performance dual-atomcatalysts.

关键词： CO_(2)reaction reduction dual-atom catalysts density functional theory machine learning

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Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration Research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz Computational biology and systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

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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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DIProT:A deep learning based interactive toolkit for efficient and effective Protein design

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Synthetic and systems Biotechnology 2024年第2期9卷 217-222页

作者： Jieling He Wenxu Wu Xiaowo Wang ministry of education Key laboratory of bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijingChina

The protein inverse folding problem,designing amino acid sequences that fold into desired protein structures,is a critical challenge in biological *** numerous data-driven and knowledge-driven methods,there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein *** this paper,we present DIProT,an interactive protein design *** leverages a non-autoregressive deep generative model to solve the inverse folding problem,combined with a protein structure prediction *** integration allows users to incorporate prior knowledge into the design process,evaluate designs in silico,and form a virtual design loop with human *** inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets,with promising sequence recovery and inference *** studies further illustrate how DIProT can facilitate user-guided protein design.

关键词： Computational Protein design Interactive design toolkit Protein inverse folding Non-autoregressive decoding

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Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction

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Genomics, Proteomics & bioinformatics 2021年第3期19卷 394-407页

作者： Tao Hu Lei Wei Shuailin Li Tianrun Cheng Xuegong Zhang Xiaowo Wang ministry of education Key laboratory of bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijing 100084China

Isogenic cells growing in identical environments show cell-to-cell variations because of the stochasticity in gene *** levels of variation or noise can disrupt robust gene expression and result in tremendous consequences for cell *** this work,we showed evidence from single-cell RNA sequencing data analysis that microRNAs(miRNAs)can reduce gene expression noise at the mRNA level in mouse *** identified that the miRNA expression level,number of targets,target pool abundance,and miRNA-target interaction strength are the key features contributing to noise *** tend to work together in cooperative subnetworks to repress target noise synergistically in a cell type-specific *** building a physical model of post-transcriptional regulation and observing in synthetic gene circuits,we demonstrated that accelerated degradation with elevated transcriptional activation of the miRNA target provides resistance to extrinsic ***,through the integrated analysis of single-cell RNA and miRNA expression profiles,we demonstrated that miRNAs are important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.

关键词： MicroRNA regulation Gene expression noise Competing RNA microRNA regulation network Singlecell RNA sequencing

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Refining biome labeling for large-scale microbial community samples:Leveraging neural networks and transfer learning

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Environmental Science and Ecotechnology 2024年第1期17卷 128-137页

作者： Nan Wang Teng Wang Kang Ning Key laboratory of Molecular Biophysics of the ministry of education Hubei Key Laboratory of Bioinformatics and Molecular-imagingCenter of AI BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074HubeiChina

Microbiome research has generated an extensive amount of data,resulting in a wealth of publicly accessible *** annotation of these samples is crucial for effectively utilizing microbiome data across scientific ***,a notable challenge arises from the lack of essential annotations,particularly regarding collection location and sample biome information,which significantly hinders environmental microbiome *** this study,we introduce Meta-Sorter,a novel approach utilizing neural networks and transfer learning,to enhance biome labeling for thousands of microbiome samples in the MGnify database that have incomplete *** findings demonstrate that Meta-Sorter achieved a remarkable accuracy rate of 96.7%in classifying samples among the 16,507 lacking detailed biome ***,Meta-Sorter provides precise classifications for representative environmental samples that were previously ambiguously labeled as“Marine”in MGnify,thereby elucidating their specific origins in benthic and water column ***,Meta-Sorter effectively distinguishes samples derived from human-environment interactions,enabling clear differentiation between environmental and human-related *** improving the completeness of biome label information for numerous microbial community samples,our research facilitates more accurate knowledge discovery across diverse disciplines,with particular implications for environmental research.

关键词： Microbial community Transfer learning Sample classification Environmental scientific research Novel knowledge discovery

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Exploring Traditional Chinese Medicine by A Novel Therapeutic Concept of Network Target

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Chinese Journal of Integrative Medicine 2016年第9期22卷 647-652页

作者：李梢 ministry of education Key laboratory of bioinformatics and bioinformatics Division Tsinghua National Laboratory for Information Science and Technology/Department of Automation Tsinghua University

Traditional Chinese medicine（TCM） holds a holistic theory, and specializes in balancing disordered human body using numerous natural products, particularly Chinese herbal formulae. TCM has certain treatment advantages for patients suffering from various complex diseases. However, due to the complex nature of TCM, it remains difficult to unveil such holistic medicine by the current reductionism research strategies, which treat both herbal ingredients and targets in isolation. Recently, an emerging network pharmacology approach has been introduced to tackle this bottleneck problem. A TCM-derived novel therapeutic concept, ＂network target＂, which is different from the Western medicine＇s ＂onetarget＂ concept, has been proposed from China. The network target strategy is able to illustrate the complex interactions among the biological systems, drugs, and complex diseases from a network perspective, and thus provides an innovative approach to access ancient remedies in a precision manner and at a systematic level, which also highlights TCM＇s potential in current medical systems.

关键词： traditional Chinese medicine network target network pharmacology herbal formula complex disease

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