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Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP

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Biophysics Reports 2022年第Z1期8卷 282-300页

作者： Jiechen Shen Zexuan Chen shisheng sun College of Life Sciences Northwest University

Protein glycosylation is of great importance in many biological processes. Glycosylation has been increasingly analyzed at the intact glycopeptide level using mass spectrometry to study site-specific glycosylation changes under different physiological and pathological conditions. StrucGP is a glycan database-independent search engine for the structural interpretation of N-glycoproteins at the site-specific level. To ensure the accuracy of results, two collision energies are implemented in instrument settings for each precursor to separate fragments of peptides and glycans. In addition, the false discovery rates(FDR) of peptides and glycans as well as probabilities of detailed structures are estimated. In this protocol, the use of StrucGP is demonstrated, including environment configuration,data preprocessing as well as result inspection and visualization using our in-house software“GlycoVisualTool ”. The described workflow should be able to be performed by anyone with basic proteomic knowledge.

关键词： Protein glycosylation Glycoproteomics Mass spectrometry StrucGP Glycan structure

Application of StrucGP in medical immunology:site-specific N-glycoproteomic analysis of macrophages

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Frontiers of Medicine 2023年第2期17卷 304-316页

作者： Pengfei Li Zexuan Chen Shanshan You Yintai Xu Zhifang Hao Didi Liu Jiechen Shen Bojing Zhu Wei Dan shisheng sun College of Life Sciences Northwest UniversityXi’an 710069China

The structure of N-glycans on specific proteins can regulate innate and adaptive immunity via sensing environmental ***,the structural diversity of N-glycans poses analytical challenges that limit the exploration of specific glycosylation *** this work,we used THP-1-derived macrophages as examples to show the vast potential of a N-glycan structural interpretation tool StrucGP in N-glycoproteomic *** intact glycopeptides of macrophages were enriched and analyzed using mass spectrometry(MS)-based glycoproteomic approaches,followed by the large-scale mapping of site-specific glycan structures via *** revealed that bisected GlcNAc,core fucosylated,and sialylated glycans(e.g.,HexNAc4Hex5Fuc1Neu5Ac1,N4H5F1S1)were increased in M1 and M2 macrophages,especially in the *** findings indicated that these structures may be closely related to macrophage *** addition,a high level of glycosylated PD-L1 was observed in M1 macrophages,and the LacNAc moiety was detected at Asn-192 and Asn-200 of PD-L1,and Asn-200 contained Lewis *** precision structural interpretation of site-specific glycans and subsequent intervention of target glycoproteins and related glycosyltransferases are of great value for the development of new diagnostic and therapeutic approaches for different diseases.

关键词： macrophage glycoproteome glycopeptides N-glycan structures PD-L1

Proteomic characterization of four subtypes of M2 macrophages derived from human THP-1 cells

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2022年第5期23卷 407-422页

作者： Pengfei LI Chen MA Jing LI Shanshan YOU Liuyi DANG Jingyu WU Zhifang HAO Jun LI Yuan ZHI Lin CHEN shisheng sun College of Life Science Northwest UniversityXi'an 710069China

Macrophages are widely distributed immune cells that contribute to tissue *** THP-1 cells have been widely used in various macrophage-associated studies,especially those involving pro-inflammatory M1 and anti-inflammatory M2 ***,the molecular characterization of four M2 subtypes(M2a,M2b,M2c,and M2d)derived from THP-1has not been fully *** this study,we systematically analyzed the protein expression profiles of human THP-1-derived macrophages(M0,M1,M2a,M2b,M2c,and M2d)using quantitative proteomics *** commonly and specially regulated proteins of the four M2 subtypes and their potential biological functions were further *** results showed that M2a and M2b,and M2c and M2d have very similar protein expression *** data could serve as an important resource for studies of macrophages using THP-1 cells,and provide a reference to distinguish different M2 subtypes in macrophage-associated diseases for subsequent clinical research.

关键词： Macrophage THP-1 cells M2 subtype Proteomics Biological function

Diverse foraging strategies of breeding Swinhoe's Storm-petrel in the productive marginal sea of the Northwest Pacific

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Avian Research 2024年第1期15卷 27-34页

作者： Yachang Cheng Lei Zhu Lin Xue shisheng Ma Nan Jia Shaoping Zang Zhihai Cao Jing Yuan Yang Liu State Key Laboratory of Biocontrol School of EcologySun Yat-sen UniversityShenzhen 518107China Guangxi Mangrove Research Center Guangxi Marine Academy of SciencesNanning 530021China Qingdao Bird Watch Society Qingdao 266121China Jiangsu Provincial Environmental Monitoring Center Nanjing 210019China Marine Science and Engineering Qingdao Agricultural UniversityQingdao 266109China Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering Fudan UniversityShanghai 200433China Qingdao Marine Management and Support Centre Qingdao 266555China Management Committee of Lingshan Island Provincial Nature Reserve Qingdao 266428China

Understanding the foraging behavior is essential for investigating seabird ecology and conservation,as well as monitoring the well-being of the marine *** seabirds adopt diverse foraging strategies to maximize energy gains and cope with the intensified challenges of parenting and *** tradeoff may stem from the heterogeneity of food resources and the constraints of central place ***,abundant marine productivity could alleviate the energy limitation for seabirds,resulting in a consistent foraging ***,we investigated the foraging strategy during the breeding season of a cryptic small-sized seabird,Swinhoe’s Storm-petrel(Hydrobates monorhis),in the Yellow Sea,a productive marginal sea of the Northwest *** GPS tracking,we evaluated habitat preference,quantified the foraging strategy,and tested if environmental conditions and individual traits influence foraging *** found that Swinhoe’s Storm-petrels preferred nearshore areas with shallow water and engaged in primarily short foraging *** southeastward and southwestward strategies emerged when combining trip metrics,including foraging direction,duration,and maximum *** bathymetry,proximity to the coastline,and sea surface temperature differed in two foraging *** strategies exhibited flexibility between individuals,potentially explained by wing morphology,in which longer-winged birds are more likely to embark on longer-distance foraging *** findings highlight the impact of environmental factors and individual traits on seabirds’foraging decisions in productive marginal sea *** study also provides valuable insights into the foraging ecology of this Asian endemic storm-petrel.

关键词： Behavioral strategy Biologging Central place foraging Marine primary productivity Seabird Sea surface temperature

Divergent responses of runoff to climate change in the upper basins of the Third Pole dominated by westerlies and monsoon

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Science China Earth Sciences 2024年第8期67卷 2592-2614页

作者： Qikai sun Fengge SU He sun State Key Laboratory of Tibetan Plateau Earth System Environment and Resources(TPESER)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100101China

The diverse climates,distribution of snow and glaciers,and geographic locations directly affect the runoff response to climate change in the upper basins of the Third *** present,a comprehensive analysis of runoff variations and their distinct responses to climate change in the westerlies-and monsoon-dominated upper basins is still *** study comprehensively analyzed annual runoff variations in westerlies-dominated basins(the upper basins of the Aksu(UAKS),Syr Darya(USRD),Yarkant(UYK),Hotan(UHT),Amu Darya(UAMD),and Indus(UI))and monsoon-dominated basins(the upper basins of the Yangtze(UYA),Yellow(UYE),Lancang(ULC),Nujiang(UNJ),and Yarlung Zangbo(UYZ))of the Third Pole from 1961 *** multi-source meteorological data and large-scale circulation factors,this study investigated the divergent responses of runoff in the upper basins to climate change,and explored the large-scale circulation mechanisms underlying runoff variations in these upper *** results showed that:(1)The annual runoff in the majority of upper basins(except for the UYE and UYZ)exhibited an increasing trend,and the annual runoff in the UAKS,UYK,and UI showed a significant increasing trend from1961 to *** annual runoff in the upper basins of the Third Pole changed abruptly from decreasing to increasing between the 1980s and 2000s,with the exception of the UYE.(2)The runoff in the monsoon-dominated upper basins has been controlled primarily by changes in precipitation over the past 55 *** contrast,the runoff in the westerlies-dominated upper basins exhibited three distinct long-term responses to climate change:temperature-dominated(UYK and UHT),precipitation-dominated(USRD and UAMD),and the combined influence of precipitation and temperature(UAKS and UI).Since the 1960s,the sensitivity of runoff to warm season temperature changes in the most westerlies-dominated upper basins has decreased,while the response of runoff to precipitation changes has intensified.(3)The stud

关键词： Upper basins of the Third Pole Climate change Westerlies and monsoon Runoff variations Large-scale circulation factors

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Fossil Equidae in the Linxia Basin with Biostratigraphic and Paleozoogeographic Significance

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Acta Geologica Sinica(English Edition) 2024年第1期98卷 1-9页

作者： sun Boyang Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China

The Linxia Basin is characterized by an abundance of Cenozoic sediments,that contain exceptionally rich fossil *** are abundant in the Linxia Basin,the fossil record of equids in this region including 16 species that represent 10 *** comparison to other classic late Cenozoic areas in China,the Linxia Basin stands out,because the fauna and chronological data accompanying Linxia equids render them remarkably useful for *** anchitheriines in the region,such as Anchitherium and Sinohippus,represent early equids that appeared in the late stages of the middle and late Miocene,*** the equines,most species of Chinese hipparions have been identified in the Linxia Basin and some species of the genera Hipparion and Hippotherium have FAD records for ***,Equus eisenmannae is one of the earliest known species of Equus in the Old World and is well-represented at the Longdan *** species with precise geohistorical distributions can serve as standards for high-resolution chronological units within this *** at the eastern margin of the Tibetan Plateau and subject to considerable uplift,the Linxia Basin has served as a biogeographic transition area for equids throughout the late Cenozoic.

关键词： Equidae Cenozoic biostratigraphy paleozoogeography Linxia Basin

Achieving simultaneously high conversion and high selectivity for light olefins directly producing from syngas

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Science China Chemistry 2024年第3期67卷 753-754页

作者： Yuhan sun Shanxi Research Institute Huairou Research LaboratoryTaiyuan 030032China Institute of Carbon Neutrality ShanghaiTech UniversityShanghai 201210China

The activity and selectivity are two primary indexes of a successful catalyst for chemical reactions. However,achieving a high activity and a high selectivity simultaneously is a long-standing challenge in catalysis, the socalled activity-selectivity trade-off. In the article recently published in Science, a research team led by Prof.

关键词： selectivity simultaneous catalysis

ONE-PARAMETER FINITE DIFFERENCE METHODS AND THEIR ACCELERATED SCHEMES FOR SPACE-FRACTIONAL SINE-GORDON EQUATIONS WITH DISTRIBUTED DELAY

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Journal of Computational Mathematics 2024年第3期42卷 705-734页

作者： Tao sun Chengjian Zhang Haiwei sun School of Mathematics and Statistics Huazhong University of Science and TechnologyWuhan 430074China Hubei Key Laboratory of Engineering Modeling and Scientific Computing Huazhong University of Science and TechnologyWuhan 430074China Department of Mathematics University of MacaoMacaoChina

This paper deals with numerical methods for solving one-dimensional(1D)and twodimensional(2D)initial-boundary value problems(IBVPs)of space-fractional sine-Gordon equations(SGEs)with distributed *** 1D problems,we construct a kind of oneparameter finite difference(OPFD)*** is shown that,under a suitable condition,the proposed method is convergent with second order accuracy both in time and *** implementation,the preconditioned conjugate gradient(PCG)method with the Strang circulant preconditioner is carried out to improve the computational efficiency of the OPFD *** 2D problems,we develop another kind of OPFD *** such a method,two classes of accelerated schemes are suggested,one is alternative direction implicit(ADI)scheme and the other is ADI-PCG *** particular,we prove that ADI scheme can arrive at second-order accuracy in time and *** some numerical experiments,the computational effectiveness and accuracy of the methods are further ***,for the suggested methods,a numerical comparison in computational efficiency is presented.

关键词： Fractional sine-Gordon equation with distributed delay One-parameter finite difference methods Convergence analysis ADI scheme PCG method

Dominant woody plant species recognition with a hierarchical model based on multimodal geospatial data for subtropical forests

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Journal of Forestry Research 2024年第3期35卷 111-130页

作者： Xin Chen Yujun sun State Forestry&Grassland Administration Key Laboratory of Forest Resources&Environmental Management Beijing Forestry UniversityBeijing 100083People's Republic of China

Since the launch of the Google Earth Engine(GEE)cloud platform in 2010,it has been widely used,leading to a wealth of valuable ***,the potential of GEE for forest resource management has not been fully *** extract dominant woody plant species,GEE combined Sen-tinel-1(S1)and Sentinel-2(S2)data with the addition of the National Forest Resources Inventory(NFRI)and topographic data,resulting in a 10 m resolution multimodal geospatial dataset for subtropical forests in southeast *** and texture features,red-edge bands,and vegetation indices of S1 and S2 data were computed.A hierarchical model obtained information on forest distribution and area and the dominant woody plant *** results suggest that combining data sources from the S1 winter and S2 yearly ranges enhances accuracy in forest distribution and area extraction compared to using either data source ***,for dominant woody species recognition,using S1 winter and S2 data across all four seasons was *** terrain factors and removing spatial correlation from NFRI sample points further improved the recognition *** optimal forest extraction achieved an overall accuracy(OA)of 97.4%and a maplevel image classification efficacy(MICE)of 96.7%.OA and MICE were 83.6%and 80.7%for dominant species extraction,*** high accuracy and efficacy values indicate that the hierarchical recognition model based on multimodal remote sensing data performed extremely well for extracting information about dominant woody plant *** the results using the GEE application allows for an intuitive display of forest and species distribution,offering significant convenience for forest resource monitoring.

关键词： Google Earth Engine Sentinel Forest resource inventory data Dominant woody plant species Subtropics Model performance