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Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

Journal of Animal Science and Biotechnology 2024年第5期15卷 1866-1880页

作者： Zhen Wang Bangmin Song Jianyu Yao Xingzheng Li Yan Zhang Zhonglin Tang guoqiang yi Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Livestock and Poultry Multi‑Omics of MARAAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Kunpeng Institute of Modern Agriculture at Foshan Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesFoshan 528226China School of Life Sciences Henan UniversityKaifeng 475004China Shenzhen Research Institute of Henan University Shenzhen 518000China State Key Laboratory of Pharmaceutical Biotechnology The University of Hong KongHong Kong SARChina Key Laboratory of Tropical Animal Breeding and Disease Research Institute of Animal Science and Veterinary MedicineHainan Academy of Agricultural SciencesHaikou 571100China Bama Yao Autonomous County Rural Revitalization Research Institute Bama 547500China

Background Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological ***,the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain *** Here,we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical,high-altitude,and frigid *** genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig *** of selection signals revealed regions under selection for adaptation in tropical(55.5 Mb),high-altitude(43.6 Mb),and frigid(17.72 Mb)*** potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments,including fat coverage in frigid environments and blood indicators in tropical and high-altitude *** genes under selection were significantly enriched in biological pathways involved in environmental *** pathways included blood circulation,protein degradation,and inflammation for adaptation to tropical environments;heart and lung development,hypoxia response,and DNA damage repair for high-altitude adaptation;and thermogenesis,cold-induced vasodilation(CIVD),and the cell cycle for adaptation to frigid *** examining the chromatin state of the selection signatures,we identified the lung and ileum as two candidate functional tissues for environmental ***,we identified a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical *** In this study,we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical,high-altitude

关键词： Environmental adaptation Local Chinese breeds Pig Population genetics Selection signals Whole-genome resequencing

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The m6A methylation regulates gonadal sex differentiation in chicken embryo

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Journal of Animal Science and Biotechnology 2022年第6期13卷 1657-1670页

作者： Jianbo Li Xiuan Zhang Xiqiong Wang Congjiao Sun Jiangxia Zheng Junying Li guoqiang yi Ning Yang National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsChina Agricultural UniversityBeijingChina Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina

Background:As a ubiquitous reversible epigenetic RNA modification,N6-methyladenosine(m6A)plays crucial regulatory roles in multiple biological ***,its functional mechanisms in sex determination and differentiation during gonadal development of chicken embryos are not ***,we established a transcriptome-wide m6A map in the female and male chicken left gonads of embryonic day 7(E7)by methylated RNA immunoprecipitation sequencing(MeRIP-seq)to offer insight into the landscape of m6A methylation and investigate the post-transcriptional modification underlying gonadal ***:The chicken embryonic gonadal transcriptome was extensively *** found 15,191 and 16,111 m6A peaks in the female and male left gonads,respectively,which were mainly enriched in the coding sequence(CDS)and stop *** these m6A peaks,we identified that 1013 and 751 were hypermethylated in females and males,*** differential peaks covered 281 and 327 genes,such as BMP2,SMAD2,SOX9 and CYP19A1,which were primarily associated with development,morphogenesis and sex differentiation by functional *** analysis revealed that the m6A methylation level was positively correlated with gene expression ***,we found that YTHDC2 could regulate the expression of sex-related genes,especially HEMGN and SOX9,in male mesonephros/gonad mingle cells,which was verified by in vitro experiments,suggesting a regulatory role of m6A methylation in chicken gonad ***:This work provided a comprehensive m6A methylation profile of chicken embryonic gonads and revealed YTHDC2 as a key regulator responsible for sex *** results contribute to a better understanding of epigenetic factors involved in chicken sex determination and differentiation and to promoting the future development of sex manipulation in poultry industry.

关键词： Chicken Embryo Gonads m6A YTHDC2

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Microstructure Regulation and Combustion Performance Optimization of PVDF/Al Composite Powder by Non-covalent Functionalized Graphenes

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Journal of Wuhan University of Technology(Materials Science) 2024年第4期39卷 904-911页

作者：易卓然 DENG Haoyuan QIN Mei 孙一 LUO guoqiang State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of TechnologyWuhan 430070China

Graphene prepared by non-covalent modification of sulfonated poly(ether-ether-ketone)(SPG)was combined with polyvinylidene fluoride(PVDF)/Al to improve the PVDF/Al thermal conductivity while reducing the effect of the thermal resistance at the graphene-polymer *** regulation rule of SPG with different contents on the energy release of fluorine-containing system was *** the content of SPG is 4%,the peak pressure and rise rate of SPG/PVDF/Al composite powder during ignition reach the maximum of 4845.28 kPa and 8683.58 kPa/*** the content of SPG is 5%,the PVDF/Al composite powder is completely coated by SPG,and the calorific value of the material reachs the maximum of 29.094 kJ/*** the design and micro-control of the composite powder,the calorific value of the material can be effectively improved,but the improvement of the mass release rate still depends on the graphene content and surface modification state.

关键词： energetic materials PVDF/Al composites graphene modification energy release combustion

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Anomalous bond lengthening in compressed magnetic doped semiconductor Ba(Zn_(0.95)Mn_(0.05))_(2)As_(2)

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Journal of Semiconductors 2024年第4期45卷 36-41页

作者： Fei Sun yi Peng guoqiang Zhao Xiancheng Wang Zheng Deng Changqing Jin Institute of Physics Chinese Academy of SciencesBeijing 100190China School of Physics University of Chinese Academy of SciencesBeijing 101408China Center for High Pressure Science and Technology Advanced Research Beijing 100094Chin

Applying pressure has been evidenced as an effective method to control the properties of semiconductors,owing to its capability to modify the band configuration around Fermi ***,structural evolutions under external pres-sures are required to analyze the *** high-pressure structure of a magnetic doped semiconductor Ba(Zn_(0.95)Mn_(0.05))_(2)As_(2)is studied with combination of in-situ synchrotron X-ray diffractions and diamond anvil *** materials become ferromagnetic with Curie temperature of 105 K after further 20%K *** title material undergoes an isostruc-tural phase transition at around 19 *** the transition pressure,it is remarkable to find lengthening of Zn/Mn-As bond within Zn/MnAs layers,since chemical bonds are generally shortened with applying *** with the bond stretch,interlayer As-As distances become shorter and the As-As dimers form after the phase *** further compres-sion,Zn/Mn-As bond becomes shortened due to the recovery of isotropic compression on the Zn/MnAs layers.

关键词： magnetic semiconductor high-pressure in-situ X-ray diffraction phase transition

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Single-cell analysis reveals the lncRNA-MEG3/miRNA-133a-3p/PRRT2 axis regulates skeletal muscle regeneration and myogenesis

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Genes & Diseases 2023年第2期10卷 359-362页

作者： yilong Yao Zishuai Wang Yun Chen Lei Liu Liyuan Wang guoqiang yi Yalan Yang Dazhi Wang Kui Li Zhonglin Tang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518000China Kunpeng Institute of Modern Agriculture at Foshan FoshanGuangdong 528226China Center for Regenerative Medicine University of South Florida Health Heart Institute Morsani College of MedicineUniversity of South FloridaFL 33602USA Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518000China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig BamaGuangxi 547500China State Key Laboratory of Animal Nutrition Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China

Skeletal muscle is the largest motor and metabolic organ of the body, which has a robust capacity for regeneration following injury or disease. Delayed regeneration after skeletal muscle injury reduces muscle contractility and leads to dysfunction of innervation. Therefore, identifying the regulation components in skeletal muscle regeneration and determining their molecular mechanisms are important to discover novel therapeutic markers for muscular diseases. Long non-coding RNA (LncRNA) has been implicated in skeletal muscle regeneration. Recent developed single-cell RNA sequencing (scRNA-seq) provides a higher resolution of cellular differences than bulk RNA-seq. Here, we re-analyzed single-cell transcriptomes data of skeletal muscle regeneration and identified lncRNA maternally expressed gene 3 (lncRNA-MEG3) was highly expressed in muscle satellite cells (MuSCs). Further study showed that lncRNA-MEG3 regulates skeletal muscle regeneration via sponging miR-133a-3p to regulate proline-rich transmembrane protein 2 (PRRT2) expression level. These results suggested that lncRNA-MEG3 might be a potential target for skeletal muscle diseases.

关键词： MEG3 skeletal muscular

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Triplet-triplet annihilation upconversion materials as electrophoretic inks

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Chinese Chemical Letters 2024年第3期35卷 439-442页

作者： Qiaoyu Zhang Guiwen Luo Jinping Chen Tianjun Yu Rui Hu guoqiang Yang yi Zeng yi Li Key Laboratory of Photochemical Conversion and Optoelectronic Materials Technical Institute of Physics and ChemistryChinese Academy of SciencesBeijing 100190China Key Laboratory of Photochemistry Institute of ChemistryChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China

Luminescent materials that can be reversibly switched by electric field stimulation are attractive since the potential application for optoelectronic *** we report a triplet-triplet annihilation upconversion(TTA-UC)system with electrophoretic response which is developed as the electrophoretic *** TTA-UC system consists of an ionic derivative of 9,10-diphenyl anthracene(DPA)as the annihilator and Pt(II)octaethylporphyrin(PtOEP)as the *** applying an electric field,migration and enrichment of positively charged DPA derivatives towards the cathode results in a 20%enhancement of TTA-UC.A quasi-solid film for electrically writing is made using the electrophoretic TTA system as the ink and a platinum electrode as a *** prototype of TTA-UC ink demonstrates unique luminescence functions upon electrically writing and erasing,providing a promising strategy to develop electronic devices for display,information storage and encryption.

关键词： Triplet-triplet annihilation Photon upconversion Electrophoresis Electrophoretic ink Luminescence display

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MiR-743a-5p regulates differentiation of myoblast by targeting Mob1b in skeletal muscle development and regeneration

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Genes & Diseases 2022年第4期9卷 1038-1048页

作者： YongSheng Zhang yiLong Yao ZiShuai Wang Dan Lu YuanYuan Zhang Adeyinka Abiola Adetula SiYuan Liu Min Zhu YaLan Yang XinHao Fan MuYa Chen yiJie Tang Yun Chen YuWen Liu guoqiang yi ZhongLin Tang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124PR China Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124PR China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193PR China

The microRNAs (miRNAs) play an important role in regulating myogenesis by targeting mRNA. However, the understanding of miRNAs in skeletal muscle development and diseases is unclear. In this study, we firstly performed the transcriptome profiling in differentiating C2C12 myoblast cells. Totally, we identified 187 miRNAs and 4260 mRNAs significantly differentially expressed that were involved in myoblast differentiation. We carried out validation of microarray data based on 5 mRNAs and 5 miRNAs differentially expressed and got a consistent result. Then we constructed and validated the significantly up- and down-regulated mRNA-miRNA interaction networks. Four interaction pairs (miR-145a-5p-Fscn1, miR-200c-5p-Tmigd1, miR-27a-5p-Sln and miR-743a-5p-Mob1b) with targeted relationships in differentiated myoblast cells were demonstrated. They are all closely related to myoblast development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated cell cycle signals important for exploring skeletal muscle development and disease. Functionally, we discovered that miR-743a targeting gene Mps One Binder Kinase Activator-Like 1B (Mob1b) gene in differentiated C2C12. The up-regulated miR-743a can promote the differentiation of C2C12 myoblast. While the down-regulated Mob1b plays a negative role in differentiation. In addition, the expression profile of miR-743a and Mob1b are consistent with skeletal muscle recovery after Cardiotoxin (CTX) injury. Our study revealed that miR-743a-5p regulates myoblast differentiation by targeting Mob1b involved in skeletal muscle development and regeneration. Our findings made a further exploration for mechanisms in myogenesis and might provide potential possible miRNA-based target therapies for skeletal muscle regeneration and disease in the near future.

关键词： Differentiation miR 743a-5p Mob 1b Myoblast Skeletal muscle .Transcriptome

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Amelioration of habitat since the early Holocene contributed to the origin of agriculture in the farming-pastoral zone of northern China

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Science China Earth Sciences 2024年第8期67卷 2535-2546页

作者： Xin JIA Zhiping ZHANG Yonggang SUN Runqi JIANG Shuangwen yi Wei CHEN Jue SUN guoqiang LI Shuzhi WANG Enrui LI Xiaonong HU Qingchun BAO Harry F.LEE Huayu LU Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application Nanjing 210023China Schlool of History and Culture Chifeng UniversityChifeng 024000China School of Geography and Ocean Science Nanjing UniversityNanjing 210023China State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjing 210008China Key Laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China Institute of Archaeology Chinese Academy of Social SciencesBeijing 100710China Ulanqab Museum Ulanqab 012000China The Institute of Cultural Relics and Archaeology Hohhot 010011China Department of Geography and Resource Management The Chinese University of Hong KongHong Kong 999077China Key Laboratory of Virtual Geographic Environment(Ministry of Education of PRC) Nanjing Normal UniversityNanjing 210023China School of Geography Nanjing Normal UniversityNanjing 210023China Institute of Environmental Archaeology Nanjing Normal UniversityNanjing 210023China

The origin of agriculture in the farming-pastoral zone of northern China remains in *** central region of the Inner Mongolia Plateau is located in the core area of the farming-pastoral zone;thus,it is a critical region for exploring the origin of the dryland farming system in northern *** study selected the Yumin Site and Banan Site,which belong to the Yumin Culture-the beginning of Neolithic culture in Inner Mongolia-as the research *** on the quartz optically stimulated luminescence(OSL)dating on the sedimentary sections from the Yumin site(YM)and Banan site(BN1 and BN2),the Holocene chronology framework of each section was *** that,by identifying carbonized grains in the Yumin site and the multi-proxy analysis of each section,we investigated the relationship between the origin of agriculture and climate change in this *** results revealed that the timing of the origin of agriculture recorded in the Yumin site lagged behind the timing of a significant increase of precipitation during the early Holocene but coincided with the timing of a significant increase of vegetation around 8.4 *** phenomenon was further confirmed by the published high-resolution paleoenvironmental records from the surrounding area of the Yumin *** propose that with the gradual amelioration of hydrothermal conditions since the beginning of the Holocene,the regional ecosystem had been improved,resulting in the gradual conversion of the land surface from infertile sand to organic-rich soil,providing an appropriate environmental foundation for the origin of dryland farming in northern China around 8.4 *** study highlighted that the“accumulative environmental effects”during the early Holocene played a vital role in the origin of agriculture in northern China and provided a reference for agricultural management in the context of future climate change.

关键词： Origin of agriculture Accumulative environmental effects Yumin Culture Northern China Holocene

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Identification of FOXO1 as a geroprotector in human synovium through single-nucleus transcriptomic profiling

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Protein & Cell 2024年第6期15卷 441-459页

作者： Feifei Liu yi Lu Xuebao Wang Shuhui Sun Huize Pan Min Wang Zehua Wang Weiqi Zhang Shuai Ma guoqiang Sun Qun Chu Si Wang Jing Qu Guang-Hui Liu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Sports Medicine Department Beijing Jishuitan HospitalCapital Medical UniversityBeijing 100035China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Division of Life Sciences and Medicine School of Life SciencesUniversity of Science and Technology of ChinaHefei 230001China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China The Fifth People’s Hospital of Chongqing Chongqing 400062China Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders Xuanwu Hospital Capital Medical UniversityBeijing 100053China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China

The synovium,a thin layer of tissue that is adjacent to the joints and secretes synovial fluid,undergoes changes in aging that contribute to intense shoulder pain and other joint ***,the mechanism underlying human synovial aging remains poorly ***,we generated a comprehensive transcriptomic profile of synovial cells present in the subacromial synovium from young and aged *** delineating aging-related transcriptomic changes across different cell types and their associated regulatory networks,we identified two subsets of mesenchymal stromal cells(MSCs)in human synovium,which are lining and sublining MSCs,and found that angiogenesis and fibrosis-associated genes were upregulated whereas genes associated with cell adhesion and cartilage development were downregulated in aged ***,the specific cell-cell communications in aged synovium mirrors that of aging-related inflammation and tissue remodeling,including vascular hyperplasia and tissue *** particular,we identified forkhead box O1(FOXO1)as one of the major regulons for aging differentially expressed genes(DEGs)in synovial MSCs,and validated its downregulation in both lining and sublining MSC populations of the aged *** human FOXO1-depleted MSCs derived from human embryonic stem cells,we recapitulated the senescent phenotype observed in the subacromial synovium of aged *** data indicate an important role of FOXO1 in the regulation of human synovial ***,our study improves our understanding of synovial aging during joint degeneration,thereby informing the development of novel intervention strategies aimed at rejuvenating the aged joint.

关键词： FOXO1 degeneration inflammation

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Shor's algorithm does not factor large integers in the presence of noise

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Science China(Information Sciences) 2024年第7期67卷 305-320页

作者： Jin-yi CAI College of Letters and Science University of Wisconsin

We consider Shor's quantum factoring algorithm in the setting of noisy quantum gates. Under a generic model of random noise for(controlled) rotation gates, we prove that the algorithm does not factor integers of the form pq when the noise exceeds a vanishingly small level in terms of n—the number of bits of the integer to be factored, where p and q are from a well-defined set of primes of positive density. We further prove that with probability 1-o(1) over random prime pairs(p, q), Shor's factoring algorithm does not factor numbers of the form pq, with the same level of random noise present.

关键词： random noise Shor's algorithm rotation gates quantum computing prime factorization

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