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Hybrid Spectral Library Combining DIA-MS Data and a Targeted Virtual Library Substantially Deepens the Proteome Coverage

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ISCIENCE 2020年第3期23卷 100903-100903页

作者： Lou, Ronghui Tang, Pan Ding, Kang Li, Shanshan Tian, Cuiping Li, Yunxia zhao, suwen Zhang, Yaoyang Shui, Wenqing ShanghaiTech Univ iHuman Inst Shanghai 201210 Peoples R China ShanghaiTech Univ Sch Life Sci & Technol Shanghai 201210 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Chinese Acad Sci Interdisciplinary Res Ctr Biol & Chem Shanghai Inst Organ Chem Shanghai 201210 Peoples R China

Data-independent acquisition mass spectrometry (DIA-MS) is a powerful technique that enables relatively deep proteomic profiling with superior quantification reproducibility. DIA data mining predominantly relies on a spectral library of sufficient proteome coverage that, in most cases, is built on data-dependent acquisition-based analysis of the same sample. To expand the proteome coverage for a pre-determined protein family, we report herein on the construction of a hybrid spectral library that supplements a DIA experiment-derived library with a protein family-targeted virtual library predicted by deep learning. Leveraging this DIA hybrid library substantially deepens the coverage of three transmembrane protein families (G protein-coupled receptors, ion channels, and transporters) in mouse brain tissues with increases in protein identification of 37%-87% and peptide identification of 58%-161%. Moreover, of the 412 novel GPCR peptides exclusively identified with the DIA hybrid library strategy, 53.6% were validated as present in mouse brain tissues based on orthogonal experimental measurement.

关键词： Analytical Chemistry Biological Sciences Classification of Proteins Proteomics

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Examination of the Deubiquitylation Site Selectivity of USP51 by Using Chemically Synthesized Ubiquitylated Histones

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CHEMBIOCHEM 2019年第2期20卷 221-229页

作者： Ai, Huasong Guo, Yu Sun, Demeng Liu, Sanling Qi, Yunkun Guo, Jing Qu, Qian Gong, Qingyue zhao, suwen Li, Jiabin Liu, Lei Tsinghua Univ Dept Chem MOE Key Lab Bioorgan Phosphorus Chem & Chem Biol Tsinghua Peking Ctr Life Sci Beijing 100084 Peoples R China ShanghaiTech Univ iHuman Inst Sch Life Sci & Technol Shanghai 201210 Peoples R China Chinese Acad Sci Shanghai Inst Nutr & Hlth Shanghai 201210 Peoples R China Univ Sci & Technol China Sch Life Sci Hefei 230026 Anhui Peoples R China

Histone ubiquitylation and deubiquitylation processes and the mechanisms of their regulation are closely relevant to the field of epigenetics. Recently, the deubiquitylating enzyme USP51 was reported to selectively cleave ubiquitylation on histone H2A at K13 or K15 (i.e., H2AK13Ub and H2AK15Ub), but not at K119 (i.e., H2AK119Ub), in nucleosomes in vivo. To elucidate the mechanism for the selectivity of USP51, we constructed structurally well-defined in vitro protein systems with a ubiquitin modification at precise sites. A total chemical protein synthesis procedure was developed, wherein hydrazide-based native chemical ligation was used to efficiently generate five ubiquitylated histones (H2AK13Ub, H2AK15Ub, H2AK119Ub, H2BK34Ub, and H2BK120Ub). These synthetic ubiquitylated histones were assembled into nucleosomes and subjected to in vitro USP51 deubiquitylation assays. Surprisingly, USP51 did not show preference between H2AK13/15Ub and H2AK119Ub, in contrast to previous in vivo observations. Accordingly, an understanding of the selectivity of USP51 may require consideration of other factors, such as alternative pre-existing histone modifications, competitive reader proteins, or different nucleosome quality among the in vivo extraction nucleosome and the in vitro reconstitution one. Further experiments established that USP51 in vitro could deubiquitylate a nucleosome carrying H2BK120Ub, but not H2BK34Ub. Molecular dynamics simulations suggested that USP51-catalyzed hydrolysis of ubiquitylated nucleosomes was affected by steric hindrance of the isopeptide bond.

关键词： deubiquitylation histones molecular dynamics proteins solid-phase synthesis

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Increased CD8⁺CD27⁺ perforin⁺ T cells and decreased CD8⁺CD70⁺ T cells may be immune biomarkers for aplastic anemia severity

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BLOOD CELLS MOLECULES AND DISEASES 2019年 77卷 34-42页

作者： zhao, suwen Zhang, Yuping Huang, Guixuan Luo, Weifeng Li, Yan Xiao, Yankai Zhou, Ming Li, Yumiao Lai, Jing Li, Yangqiu Li, Bo Jinan Univ Sch Med Inst Hematol Key Lab Regenerat MedMinist Educ Guangzhou Guangdong Peoples R China South China Univ Technol Affiliated Hosp 2 Guangzhou Municipal Peoples Hosp 1 Dept Hematol Guangzhou Guangdong Peoples R China Jinan Univ Sch Med Inst Hematol Guangzhou 510632 Guangdong Peoples R China Guangzhou Blood Ctr Guangzhou Guangdong Peoples R China Jinan Univ Affiliated Hosp 1 Dept Cardiol Guangzhou Guangdong Peoples R China Jinan Univ Affiliated Hosp 1 Dept Hematol Guangzhou Guangdong Peoples R China

Objectives: Aplastic anemia (AA) is T cell immune-mediated autoimmune disease. Aberrant T cell activation involves an imbalance in T cell homeostasis in AA. However, whether the T cell activation molecule CD27 and its ligand CD70 participate in the immune pathogenesis of AA remains ill defined. Methods: The frequencies of CD27/CD70 and perforin/granzyme B in different T cell subsets were detected in AA patients and healthy individuals by flow cytometry. Results: We first time demonstrate a significantly elevated proportion of CD27(+) and significantly decreased CD70(+) T cells from AA. Changed frequency of CD27(+) and CD70(+) in different T cell subsets appeared to be associated with AA severity. In very severe aplastic anemia (VSAA) and severe aplastic anemia (SAA), increased CD8(+) CD27(+) T cells present with a cytotoxic effector phenotype by elevating perforin proportion. Conclusions: Elevated proportion of CD27 in T cells may contribute to distinct immune pathogenesis for different severities of AA. The CD8(+) CD27(+) perforin(+) T cells combined with CD8(+) CD70(+) T cells may serve as an immune biomarker for AA severity estimation.

关键词： Aplastic anemia CD27 CD70 Perforin

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基于OrcaFlex的水下采油树钻杆下放影响因素敏感性分析

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石油矿场机械 2022年第2期51卷 22-31页

作者：黄熠王尔钧张崇孟文波同武军赵维青赵苏文段明付中海石油(中国)有限公司湛江分公司广东湛江524057 中海油能源发展股份有限公司工程技术深水钻采技术公司广东湛江524057

针对东方1-1气田的海况,基于OrcaFlex专业海工软件建立平台钻杆下放采油树的仿真模型,研究了水下采油树在下放过程中钻杆的受力情况,以及采油树的运动响应问题。研究结果表明:在钻杆受力方面,下放过程中所受到的Von Mises应力以及弯矩... 详细信息

针对东方1-1气田的海况,基于OrcaFlex专业海工软件建立平台钻杆下放采油树的仿真模型,研究了水下采油树在下放过程中钻杆的受力情况,以及采油树的运动响应问题。研究结果表明:在钻杆受力方面,下放过程中所受到的Von Mises应力以及弯矩都主要集中在钻杆上部靠近钻杆顶端处,在钻杆与采油树连接处有较小的应力集中和弯矩。在敏感性参数分析方面,风速对下放过程钻杆受力、弯矩以及水下采油树的运动响应影响很小;海流流速、浪高、海况的方向角度对其影响较大,其中海流流速和浪高都是正影响;不同的海况方向角度对钻杆的受力和采油树的运动响应有不同程度的影响。研究结果将对国内水下采油树的安装提供一定指导作用。

关键词：水下采油树钻杆受力分析 OrcaFlex 运动响应

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Disulfide-Containing Detergents (DCDs) for the Structural Biology of Membrane Proteins

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CHEMISTRY-A EUROPEAN JOURNAL 2019年第50期25卷 11635-11640页

作者： Xue, Dongxiang Xu, Tiandan Wang, Huixia Wu, Meng Yuan, Ya Wang, Wei Tan, Qiwen zhao, Fei Zhou, Fang Hu, Tao Jiang, Zhongxing Liu, Zhi-Jie zhao, suwen Liu, Dongsheng Wuthrich, Kurt Tao, Houchao ShanghaiTech Univ iHuman Inst Ren Bldg393 Middle Huaxia Rd Shanghai 201210 Peoples R China Chinese Acad Sci Shanghai Inst Mat Med 555 Zuchongzhi Rd Shanghai 201203 Peoples R China Univ Chinese Acad Sci 19A Yuquan Rd Beijing 100049 Peoples R China ShanghaiTech Univ Sch Life Sci & Technol Shanghai 201210 Peoples R China Chinese Acad Sci CAS Ctr Excellence Mol Cell Sci Shanghai Inst Biochem & Cell Biol Shanghai 200031 Peoples R China Wuhan Univ Hubei Prov Engn & Technol Res Ctr Fluorinated Pha Sch Pharmaceut Sci Wuhan 430071 Hubei Peoples R China

Disulfide-containing detergents (DCDs) are introduced, which contain a disulfide bond in the hydrophobic tail. DCDs form smaller micelles than corresponding detergents with linear hydrocarbon chains, while providing good solubilization and reconstitution of membrane proteins. The use of this new class of detergents in structural biology is illustrated with solution NMR spectra of the human G protein-coupled receptor A(2A)AR, which is an alpha-helical protein, and the beta-barrel protein OmpX from E. coli.

关键词： detergents disulfides membrane proteins micelle size NMR spectroscopy

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基于OrcaFlex水下采油树钢丝绳下放作业窗口研究

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石油矿场机械 2022年第1期51卷 20-28页

作者：张崇孟文波任冠龙唐咸弟赵苏文关清涛赵维青李新妍中海石油(中国)有限公司湛江分公司广东湛江524057 中海油能源发展股份有限公司工程技术深水钻采技术公司广东湛江524057

水下采油树的下放安装作业环境载荷非常复杂,下放作业窗口是我国南海水下采油树下放过程中亟待解决的关键问题。针对东方1-1气田73 m水下采油树钢丝缆绳下放安装方法,分析了水下采油树下放作业过程。利用OrcaFlex建立了工程船-钢丝缆绳... 详细信息

水下采油树的下放安装作业环境载荷非常复杂,下放作业窗口是我国南海水下采油树下放过程中亟待解决的关键问题。针对东方1-1气田73 m水下采油树钢丝缆绳下放安装方法,分析了水下采油树下放作业过程。利用OrcaFlex建立了工程船-钢丝缆绳-水下采油树系统的耦合模型,研究了不同浪高、流速、波浪方向角等关键因素对水下采油树安装过程的钢丝绳受力和采油树运动响应的影响。利用正交试验方法研究了各个影响因素的关键度排序,形成了水下采油树钢丝缆绳下放的作业窗口。研究结果表明:当浪高在[5.06 m,0 m],流速为[0 m/s,1.09 m/s]的封闭区域(安全作业区域)内,适合于东方1-1气田水下采油树下放安装作业。研究结果可为水下采油树钢丝绳下放安装过程提供一定的指导。

关键词：水下采油树 OrcaFlex 钢丝绳法下放安装下放作业窗口

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Microchannel structure affects fine particulate pollutant interception characteristics

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PROCESS SAFETY AND ENVIRONMENTAL PROTECTION 2023年 179卷 421-429页

作者： Lv, Wenjie zhao, Jinchao Hu, Bin Zhang, Yanhong Yang, suwen Ding, Jun Huang, Yuan East China Univ Sci & Technol Natl Engn Res Ctr Ind Wastewater Detoxicat & Resou Shanghai 200237 Peoples R China Shanghai Univ Inst Environm Pollut & Hlth Sch Environm & Chem Engn Shanghai 200444 Peoples R China

Deep filtration is an important technology for the separation of fine particle pollutants in industrial wastewater. The theoretical core of microchannel separation is the interaction between channel interface and pollutants. Here, microchannels with different shapes and sizes were designed by microfluidic technology and the particle migration process in microchannels was visualized by high-speed camera. This paper studied the effects of apparent depth, inlet structure and channel angle of the interception channel on fluid flow and particle inter-ception. When apparent depth of the interception channel was equidistantly distributed, the flow rate in each channel was uniform, but interception efficiency gradually decreased with the increase of apparent depth. Interception efficiency of the first layer was 16.7 %, while for the 14th layer was only 0.4 %. Interception performance of the upper wall of the inlet of the interception channel was substantially higher than that of the lower wall. The smoother the angle between the interception channel and the mainstream channel was, the better the interception performance. When the angle between the upper and lower walls of the inlet and the mainstream channel was 30 degrees and 60 degrees, respectively, interception efficiency was the optimal, and cumulative interception efficiency of the three filtrations was 92.4 %. Additionally, flow rate and interception efficiency of the interception channel increased with decreasing channel angle. The total interception performance of the 30 degrees -45 degrees group was the optimal, and the total split ratio and total interception efficiency were 65.5 % and 85.5 %, respectively. This provides reference for the change of microchannel structure and the mechanism of particle migration and deposition.

关键词： Deep filtering Microchannel High-speed camera Particle migration

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Investigation of cell development and tissue structure network based on natural Language processing of scRNA-seq data

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JOURNAL OF TRANSLATIONAL MEDICINE 2025年第1期23卷 1-12页

作者： Wei, suwen Lu, Yuer Wang, Peng Li, Qichao Shuai, Jianwei zhao, Qi Lin, Hai Peng, Yuming Univ Chinese Acad Sci Wenzhou Inst Oujiang Lab Zhejiang Lab Regenerat Med Vis & Brain Hlth Wenzhou 325001 Zhejiang Peoples R China Wenzhou Med Univ Postgrad Training Base Alliance Wenzhou 325001 Zhejiang Peoples R China Univ Sci & Technol Liaoning Sch Comp Sci & Software Engn Anshan 114051 Peoples R China Cent Hosp Karamay Dept Gen Practice Karamay 834000 Xinjiang Peoples R China

BackgroundSingle-cell multi-omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have revolutionized our understanding of cellular heterogeneity and development by providing insights into gene expression at the single-cell level. Investigating the influence of genes on cellular behavior is crucial for elucidating cell fate determination and differentiation, cell development processes, and disease *** by NLP, we present a novel scRNA-seq analysis method that treats genes as analogous to words. Using word2vec to embed gene sequences derived from gene networks, we generate vector representations of genes, which are then used to represent cells by summing gene vectors and subsequently tissues by aggregating cell *** NLP-based approach analyzes scRNA-seq data by generating vector representations of genes, cells, and tissues. This multi-scale analysis includes mapping cell states in vector space to reveal developmental trajectories, quantifying cell similarity using Euclidean distance, and constructing inter-tissue relationship networks from aggregated cell *** method offers a computationally efficient approach for analyzing scRNA-seq data by constructing embedding representations similar to those used in large language model pre-training, but without requiring high-performance computing clusters. By generating gene embeddings that capture functional relationships, this method facilitates the study of cell development trajectories, the impact of gene perturbations, cell clustering, and the construction and analysis of tissue networks. This provides a valuable tool for single-cell data analysis.

关键词： Single-cell RNA sequencing technology Natural Language processing Embedding Network structure

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Traceless specific fluorescence labeling of the smoothened receptor

Traceless specific fluorescence labeling of the smoothened r...

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第十一届全国化学生物学学术会议

作者： Dongxiang Xue Lintao Ye Yiran Wu suwen zhao Fei zhao Houchao Tao iHuman Institute ShanghaiTech University

The smoothened receptor（SMO） mediates the Hedgehog（Hh） signaling pathway and plays a vital role in embryonic development and *** visualization of SMO has the potential to provide new insights into its enigmatic mechanism and associated disease *** on recent progress in structural studies of SMO,we designed and characterized a group of affinity probes to facilitate the turn-on fluorescence labeling of SMO at the ε-amine of *** chemical probes were derived from a potent SMO antagonist skeleton by conjugation of a small non-fluorescent unit,O-nitrobenzoxadiazole（O-NBD）.Optimal probes were capable of efficient and selective lighting up SMO both in micelles and in native *** importantly,the resulting labeled SMO bears a very small fluorophore that allows the recovery of the unoccupied pocket after dissociation of the residual ligand *** probes could serve as a potential tool for monitoring SMO trafficking,understanding Hh activation,and the diagnosis of tumorigenesis in the future.

关键词： Smoothened receptor turn-on fluorescence probe selective labeling structure-guided design

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Theory-based interventions aimed at promoting physical activity in pregnant women: A systematic review and meta-analysis of randomized controlled trials

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INTERNATIONAL JOURNAL OF NURSING STUDIES 2024年 154卷 104761页

作者： Zhang, Wei zhao, Rujia Zhang, Le Xie, Fang Xu, Ping Guo, Pingping Mao, Minna Feng, suwen Zhejiang Univ Sch Med Hangzhou Peoples R China Zhejiang Univ Womens Hosp Sch Med Dept Nursing Hangzhou Peoples R China Zhejiang Univ Womens Hosp Sch Med Dept Obstet 1 Xueshi Rd Hangzhou Peoples R China

Objectives: The objectives were to assess (i) the quality of theory implementation, (ii) the application of behavior change techniques, and (iii) the effectiveness of theory-based interventions in promoting physical activity in pregnant women and improving maternal and neonatal outcomes. Methods: A systematic search was conducted across 8 databases (Cumulative Index to Nursing and Allied Health Literature, the Cochrane Library, EMBASE, MEDLINE, APA PsycINFO, PubMed, SPORTDiscus, and Web of Science) to identify randomized controlled trials published from database inception to 8 July 2023. The Cochrane risk-of-bias 2.0 tool was used to evaluate the quality of the included studies. The theory coding scheme was used to measure the quality of theory implementation, and behavior change techniques were coded according to behavior change taxonomy (version 1). The meta-analysis was performed using RevMan 5.3. The Grading of Recommendations, Assessment, Development, and Evaluation Approach was used to assess the certainty of evidence. Results: Eleven studies met the study criteria. Nine studies were based on one theory, while two studies were based on a combination of two theories. The quality of theory implementation was generally moderate. A total of 24 unique behavior change techniques were extracted. The most commonly used types of behavior change techniques were 'instruction on how to perform the behavior' (n = 9), 'goal setting' (behavior) (n = 8), 'action planning' (n = 7), and 'information about health consequences' (n = 7). Theory-based interventions significantly improved moderate-to-vigorous physical activity (standardized mean difference (SMD) = 0.17, 95 % confidence interval (CI) [0.04, 0.30], P = 0.01;moderate certainty of evidence), reduced the average gestational weight gain per week (mean difference (MD) = - 0.06, 95 % CI [- 0.11, - 0.01], P = 0.02;moderate certainty of evidence), and decreased the incidence of gestational diabetes mellitus (risk ratio (RR) =

关键词： Physical activity Pregnant women Interventions Behavior change techniques Theoretical frameworks

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