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Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep

GENOMICS PROTEOMICS & BIOINFORMATICS 2024年第2期22卷 qzae030页

作者： Li, Chao Chen, Bingchun Langda, Suo Pu, Peng Zhu, Xiaojia Zhou, Shiwei Kalds, Peter Zhang, Ke Bhati, Meenu Leonard, Alexander Huang, Shuhong Li, Ran Cuoji, Awang Wang, Xiran Zhu, Haolin Wu, Yujiang Cuomu, Renqin Gui, Ba Li, Ming Wang, Yutao Li, Yan Fang, Wenwen Jia, Ting Pu, Tianchun pan, xiangyu Cai, Yudong He, Chong Jiang, Yu Han, Jian-Lin Chen, Yulin Zhou, Ping Pausch, Hubert Wang, Xiaolong Northwest A&F Univ Coll Anim Sci & Technol Int Joint Agr Res Ctr Anim Biobreeding Minist Agr & Rural AffairsKey Lab Anim Genet Bree Yangling 712100 Peoples R China Swiss Fed Inst Technol Anim Genom CH-8092 Zurich Switzerland Tibet Acad Agr & Anim Husb Sci Inst Anim Sci Lhasa 850009 Peoples R China Lanzhou Jiaotong Univ Sch Biol & Pharmaceut Engn Lanzhou 730070 Peoples R China Shaanxi Normal Univ Coll Life Sci Xian 710119 Peoples R China Univ Konstanz Dept Biol Zool & Evolutionary Biol D-78457 Constance Germany Kashi Univ Coll Life & Geog Sci Kashi 844000 Peoples R China Beijing Zoo Beijing Key Lab Capt Wildlife Technol Beijing 100044 Peoples R China Guangdong Acad Med Sci Guangdong Prov Peoples Hosp Dept Med Res Guangzhou Peoples R China Northwest A&F Univ Key Lab Agr Internet Things Minist Agr & Rural Affairs Shaanxi Key Lab Agr Informat Percept & Intelligent Yangling 712100 Peoples R China Xinjiang Acad Agr & Reclamat Sci Inst Anim Husb & Vet Med Shihezi 832000 Peoples R China Xinjiang Acad Agr & Reclamat Sci State Key Lab Sheep Genet Improvement & Healthy Pr Shihezi 832000 Peoples R China Chinese Acad Agr Sci Inst Anim Sci CAAS ILRI Joint Lab Livestock & Forage Genet Resou Beijing 100193 Peoples R China Int Livestock Res Inst Livestock Genet Program Nairobi 00100 Kenya

Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing similar to 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated beta-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

关键词： Environmental adaptation High altitude Hypoxia Selection signature Sheep PERMANENT HUMAN OCCUPATION POPULATION-STRUCTURE TIBETAN PLATEAU GENOME REVEALS ORIGIN DIFFERENTIATION HEMOGLOBINS SELECTION PROVIDES

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pigenetic reprogramming in small cell lung cancer

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Cancer Biology & Medicine 2022年第8期19卷 1111-1116页

作者： Jingyao Chen xiangyu pan Feifei Na Xuelan Chen Chong Chen State Key Laboratory of Biotherapy and Cancer Center West China HospitalSichuan UniversityChengdu 610044China Department of Thoracic Oncology West China HospitalSichuan UniversityChengdu 610044China

Small cell lung cancer(SCLC),a highly lethal lung cancer sub-type with distinct neuroendocrine-like features,accounts for 10%–15%of all lung *** overall 5-year survival rate remains less than 10%.SCLC is characterized by early metastasis,thus minimizing the potential patient benefits of *** recent decades,the first-line treatment for SCLC has remained chemotherapy combining etoposide and cisplatin(E/P).Despite high rates of response to E/P treatment,SCLC eventually relapses and is almost universally resistant to treatment at recurrence,thus making SCLC a recalcitrant ***,the limited knowledge regarding the molecular mechanisms underlying SCLC metastasis and resistance greatly hinders improvements in overall SCLC *** better understand the molecular mechanisms of SCLC and discover potential therapeutic targets,extensive efforts have continued for decades.

关键词： metastasis chemotherapy treatment

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Urdnet:A Cryo-EM Particle Automatic Picking Method

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Computers, Materials & Continua 2022年第7期72卷 1593-1610页

作者： Jianquan Ouyang Yue Zhang Kun Fang Tianming Liu xiangyu pan School of Computer Science&School of Cyberspace Science Xiangtan UniversityXiangtan411105China Hunan Meteorological Information Center Hunan Meteorological BureauChangshaHunan410118China Department of Computer Science The University of GeorgiaAthensGeorgiaUSA

Cryo-Electron Microscopy(Cryo-EM)images are characterized by the low signal-to-noise ratio,low contrast,serious background noise,more impurities,less data,difficult data labeling,simpler image semantics,and relatively fixed structure,while U-Net obtains low resolution when downsampling rate information to complete object category recognition,obtains highresolution information during upsampling to complete precise segmentation and positioning,fills in the underlying information through skip connection to improve the accuracy of image segmentation,and has advantages in biological image processing like Cryo-EM *** article proposes A U-Net based residual intensive neural network(Urdnet),which combines point-level and pixel-level tags,used to accurately and automatically locate particles from cryo-electron microscopy images,and solve the bottleneck that cryo-EM Single-particle biologicalmacromolecule reconstruction requires tens of thousands of automatically picked *** 80S ribosome,HCN1 channel and TcdA1 toxin subunits,and other public protein datasets have been trained and tested on *** experimental results show that Urdnet could reach the same excellent particle picking performances as the mainstream methods of RELION,DeepPicker,and acquire the 3Dstructure of picked particleswith higher resolution.

关键词： Deep learning convolutional neural network particle picking cryo-electron microscopy single-particle reconstruction

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Nanophase precipitation and strengthening in a dual-phase Al_(0.5)CoCrFeNi high-entropy alloy

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Journal of Materials Science & Technology 2021年第13期72卷 1-7页

作者： Haoxue Yang Jinshan Li xiangyu pan William Yi Wang Hongchao Kou Jun Wang State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi’an 710072China

Precipitation-hardening in fcc-based high-entro py alloys(HEAs)have usually been realized by introducing complex intermetallic *** this study,enhanced strength is ascribed to the existence of L1_(2) precipitates and B2/bcc conjoint phases in the fcc *** nano-size particles in the Al_(0.5)CoCrFeNi HEA are produced by cold-rolling,followed by intermediate-temperature-annealing at 650℃.For L1_(2) ordering,the initial granular structure has transformed into lamella structure and then kept stable when the holding time prolonged to 200 *** formation of this conjoint B2/bcc driven by the concentration profiles takes place when the diffusion process of elements is sufficient after long-time *** on the microstructure analysis,changes in mechanical properties are associated with the shape,size scale and volume fraction of the *** peak ultimate tensile stress reaches 1221.5 MPa,1.97 times compared with the as-cast alloy,remaining plasticity of 21.3%.

关键词： High-entropy alloy L12 phase B2 phase Precipitation strengthening

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High temperature electrochemical discharge performance of LaFeO3 coated with C/Ni as anode material for NiMH batteries

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Progress in Natural Science:Materials International 2022年第6期32卷 684-692页

作者： Kailiang Ren Jiajia Miao Wenzhuo Shen Huanhuan Su Yunpeng pan Jiajin Zhao xiangyu pan Yuan Li Yaokun Fu Lu Zhang Shumin Han State Key Laboratory of Metastable Materials Science and Technology Yanshan University School of Environmental and Chemical Engineering Yanshan University

Perovskite LaFeO3is considered as a promising new anode material for nickel/metal hydride batteries due to its low cost,environmental friendliness and high temperature ***,the poor conductivity of LaFeO3material restricts the discharge ability,which is problematic for its future widespread *** solve the above issue,in this study,we prepared C/Ni-coated LaFeO3composite in view of the excellent electrical conductivity of carbon and nickel *** show that the C/Ni-coated LaFeO3composite delivers remarkably increased discharge capacity of ～345 mAh g-1at 60℃ in contrast to ～267 mAh g-1for pure ***,the carbon and nickel not only increase the electrical conductivity of the LaFeO3but also reduces the agglomeration of the LaFeO3,therefore,the C/Ni-coated LaFeO3composite serves superior long cycle-life,which maintains 60.9% after 100 cycles(52.9% for the LaFeO3sample).In overall,the electrochemical behavior of the C/Ni-coated LaFeO3composite confirms its high potential as nickel/metal hydride batteries for energy storage applications.

关键词： Energy storage Perovskite-type oxide Nickel metal hydride batteries LaFeO 3 Electrochemical performance

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A Special Issue:“Artificial Intelligence Applied in New-Type Power System”for Global Energy Interconnection

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Global Energy Interconnection 2024年第3期7卷 I0002-I0003页

作者： Xueping pan xiangyu Kong School of Electrical and Power Engineering Hohai UniversityNanjingChina School of Electrical Engineering and Automation Tianjin University Intelligent Energy Use and Energy Saving Committee of China Electrical Engineering Society

In recent years,artificial intelligence(AI)has been widely used in the field of electricity,such as load prediction,fault diagnosis of the power equipment,intelligent scheduling of power ***,the application of latest AI technology still has many technical difficulties to be *** the process of upgrading from the traditional power system to the new-type power system,AC grids,DC grids and micro grids *** addition,there are huge amount of power equipment and electronic devices,and the coupling relationship is very ***,the high proportion of clean energy and flexible loads connected to the grid leads to the enhancement of the stochastic characteristics of the *** short-term and ultra-short-term forecasts are much more ***,the editorial office of Global Energy Interconnection has planned the special issue of“Artificial Intelligence Applied in New-Type Power System”.

关键词： artificial Power Type

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CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 632-648页

作者： xiangyu pan Zhaoxia Ma Xinqi Sun Hui Li Tingting Zhang Chen Zhao Nini Wang Rasmus Heller Wing Hung Wong Wen Wang Yu Jiang Yong Wang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Department of Medical Research Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Guangdong Cardiovascular Institute Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Academy of Mathematics and Systems Science Chinese Academy of SciencesBeijing 100190China School of Mathematics University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Animal Science and TechnologyGuangxi UniversityNanning 530005China Section for Computational and RNA Biology Department of BiologyUniversity of CopenhagenCopenhagen DK-2100Denmark Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford UniversityStanfordCA 94305USA Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China

The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in ***,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach *** generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during *** developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional ***,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the *** study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

关键词： Trait innovation Gene regulatory network Conserved non-coding element Toolkit transcription factor Ruminant

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Spontaneous apoptosis of cells in therapeutic stem cell preparation exert immunomodulatory effects through release of phosphatidylserine

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Signal Transduction and Targeted Therapy 2021年第8期6卷 2536-2549页

作者： Xuemei He Weiqi Hong Jingyun Yang Hong Lei Tianqi Lu Cai He Zhenfei Bi xiangyu pan Yu Liu Lunzhi Dai Wei Wang Canhua Huang Hongxin Deng Xiawei Wei Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanPeople’s Republic of China Experimental Medicine Center the Affiliated Hospital of Southwest Medical UniversityLuzhouSichuanPeople’s Republic of China

Mesenchymal stem cell(MSC)-mediated immunomodulation has been harnessed for the treatment of human diseases,but its underlying mechanism has not been fully *** cells,including apoptotic cells have immunomodulatory *** has been repeatedly reported that the proportion of nonviable MSCs in a MSC therapeutic preparation varied from 5-50%in the ongoing clinical *** is conceivable that the nonviable cells in a MSC therapeutic preparation may play a role in the therapeutic effects of *** found that the MSC therapeutic preparation in the present study had about 5%dead MSCs(DMSCs),characterized by apoptotic ***,1×10^(6) MSCs in the preparation contained about 5×10^(4) *** found that the treatment with even 5×10^(4) DMSCs alone had the equal therapeutic effects as with 1×10^(6) *** protective effect of the dead MSCs alone was confirmed in four mouse models,including concanavalin A(ConA)-and carbon tetrachloride(CCI4)-induced acute liver injury,LPS-induced lung injury and spinal cord *** also found that the infused MSCs died by apoptosis in ***,the therapeutic effect was attributed to the elevated level of phosphatidylserine(PS)upon the injection of MSCs or *** direct administration of PS liposomes(PSLs)mimic apoptotic cell fragments also exerted the protective effects as MSCs and *** Mer tyrosine kinase(MerTK)deficiency or the knockout of chemokine receptor C-C motif chemokine receptor 2(CCR2)reversed these protective effects of MSCs or *** results revealed that DMSCs alone in the therapeutic stem cell preparation or the apoptotic cells induced in vivo may exert the same immunomodulatory property as the'living MSCs preparation"through releasing PS,which was further recognized by MerTK and participated in modulating immune cells.

关键词： therapeutic protective preparation

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A Review of Contact Electrification at Diversified Interfaces and Related Applications on Triboelectric Nanogenerator

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Nano-Micro Letters 2024年第1期16卷 106-130页

作者： Jun Hu Mitsumasa Iwamoto xiangyu Chen CAS Center for Excellence in Nanoscience Beijing Institute of Nanoenergy and NanosystemsChinese Academy of SciencesBeijing 100083People’s Republic of China School of Nanoscience and Engineering University of Chinese Academy of SciencesBeijing 100049People’s Republic of China Department of Physical Electronics Tokyo Institute of Technology2‑12‑1 S3‑33 O‑OkayamaMeguro‑KuTokyo 152‑8552Japan

The triboelectric nanogenerator(TENG)can effectively collect energy based on contact electrification(CE)at diverse interfaces,including solid–solid,liquid–solid,liquid–liquid,gas–solid,and gas–*** enables energy harvesting from sources such as water,wind,and *** this review,we provide an overview of the coexistence of electron and ion transfer in the CE *** elucidate the diverse dominant mechanisms observed at different interfaces and emphasize the interconnectedness and complementary nature of interface *** review also offers a comprehensive summary of the factors influencing charge transfer and the advancements in interfacial modification ***,we highlight the wide range of applications stemming from the distinctive characteristics of charge transfer at various ***,this review elucidates the future opportunities and challenges that interface CE may *** anticipate that this review can offer valuable insights for future research on interface CE and facilitate the continued development and industrialization of TENG.

关键词： Contact electrification Interfaces Triboelectric nanogenerators Diversified applications

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GMAT:A Graph Modeling Method for Group Preference Prediction

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Journal of Systems Science and Systems Engineering 2024年第4期33卷 475-493页

作者： xiangyu Li Xunhua Guo Guoqing Chen International Business School Jinan UniversityZhuhai519070China School of Economics and Management Tsinghua UniversityBeijing100084China

Preference prediction is the building block of personalized services,and its implementation at the group level helps enterprises identify their target customers *** methods for preference prediction mainly focus on behavioral interactions to extract the associations between groups and products,ignoring the importance of other auxiliary records(e.g.,online reviews and social tags)in association *** paper proposes a novel method named GMAT for group preference prediction,aiming to collectively detect the sophisticated association patterns from user generated content(UGC)and behavioral *** doing so,we construct a tripartite graph to collaborate these two types of data,and design a deep-learning algorithm with mutual attention module for generating the contextualized representations of groups and *** experiments on two real-world datasets show that GMAT is superior to other baselines in terms of group preference ***,GMAT is able to improve prediction accuracy compared with its different variants,further verifying the proposed method’s effectiveness on association pattern detection.

关键词： Group preference UGC tripartite graph deep learning

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