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3D genome organization and its study in livestock breeding

Journal of Integrative Agriculture 2024年第1期23卷 39-58页

作者： Jie Cheng Xiukai Cao Shengxuan Wang Jiaqiang Zhang Binglin Yue Xiaoyan Zhang Yongzhen Huang Xianyong Lan Gang Ren Hong Chen Key laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Joint International Research laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China Yangzhou UniversityYangzhou 225009China College of Animal Science Xinjiang Agricultural UniversityUrumqi 830052China

Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene *** genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA *** identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer ***,there are relatively few studies about the 3D genome in livestock ***,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production *** this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock *** then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

关键词： 3D genome organization 3D genomic methodology regulatory mechanisms muscle development livestock breeding

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CCDC181 is required for sperm flagellum biogenesis and male fertility in mice

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Zoological Research 2024年第5期45卷 1061-1072页

作者： Xiang-Jun Zhang Xiao-Ning Hou Jian-Teng Zhou Bao-Lu Shi Jing-Wei Ye Meng-Lei Yang Xiao-Hua Jiang Bo Xu Li-Min Wu Qing-Hua Shi Division of reproduction and Genetics First Affiliated Hospital of University of Science and Technology of China(USTC)Hefei National Laboratory for Physical Sciences at MicroscaleSchool of Basic Medical SciencesDivision of Life Sciences and MedicineBiomedical Sciences and Health Laboratory of Anhui ProvinceInstitute of Health and MedicineHefei Comprehensive National Science CenterUniversity of Science and Technology of ChinaHefeiAnhui 230001China

The structural integrity of the sperm flagellum is essential for proper sperm *** defects can result in male infertility,yet the precise mechanisms underlying this relationship are not fully ***181,a coiled-coil domain-containing protein,is known to localize on sperm flagella and at the basal regions of motile *** this knowledge,the specific functions of CCDC181 in flagellum biogenesis remain *** this study,Ccdc181 knockout mice were *** absence of CCDC181 led to defective sperm head shaping and flagellum ***,the Ccdc181 knockout mice exhibited extremely low sperm counts,grossly aberrant sperm morphologies,markedly diminished sperm motility,and typical multiple morphological abnormalities of the flagella(MMAF).Additionally,an interaction between CCDC181 and the MMAF-related protein LRRC46 was identified,with CCDC181 regulating the localization of LRRC46 within sperm *** findings suggest that CCDC181 plays a crucial role in both manchette formation and sperm flagellum biogenesis.

关键词： Male infertility CCDC181 MMAF Spermiogenesis Flagellum biogenesis

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Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

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Journal of Genetics and Genomics 2024年第4期51卷 394-406页

作者： Xin Li Quan Liu Chong Fu Mengxun Li Changchun Li Xinyun Li Shuhong Zhao Zhuqing Zheng Key Lab of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China Institute of Agricultural Biotechnology Jingchu University of TechnologyJingmenHubei 448000China The Cooperative Innovation Center for Sustainable Pig Production WuhanHubei 430070China Hubei Hongshan laboratory WuhanHubei 430070China

structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic *** a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 *** results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local *** characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory *** identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in *** results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

关键词： Pigs structural variation Selection signatures Regulatory elements

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Network analysis reveals context-dependent structural complexity of social calls in serrate-legged small treefrogs

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Current Zoology 2024年第2期70卷 253-261页

作者： Ke Deng Qiao-Ling He Tong-Liang Wang Ji-Chao Wang Jian-Guo Cui CAS Key laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation Key laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengdu 610041China University of Chinese Academy of Science Beijing 100049China Ministry of Education Key laboratory for Ecology of Tropical lslands Key Laboratory of Tropical Animal and Plant Ecology of Hainan ProvinceCollege of Life SciencesHainan Normal UniversityHaikou 571158China

Vocal communication plays an important role in survival,reproduction,and animal social *** and mammals produce com-plex vocal sequence to convey context-dependent *** are conspicuous features of the behavior of most anuran species(frogs and toads),and males usually alter their calling strategies according to ecological context to improve the attractiveness/***,very few studies have focused on the variation of vocal sequence in *** the present study,we used both conventional method and network analysis to investigate the context-dependent vocal repertoire,vocal sequence,and call network structure in serrate-legged small treefrogs Kurixalus *** found that male *** modified their vocal sequence by switching to different call types and increasing repertoire size in the presence of a competitive ***,compared with before and after the playback of advertisement calls,males emited fewer advertisement calls,but more aggressive calls,encounter calls,and compound calls during the playback *** analysis revealed that the mean degree,mean closeness,and mean betweenness of the call networks significantly decreased during the playback period,which resulted in lower *** addition,the increased proportion of one-way motifs and average path length also indicated that the connectivity of the call network decreased in competitive ***,the vocal sequence of *** did not display a clear small-world network structure,regardless of *** study presents a paradigm to apply network analysis to vocal sequence in anurans and has important implications for understanding the evolution and function of sequence patterns.

关键词： call network centrality Kurixalus odontotarsus vocal repertoire vocal sequence.

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Exploring the impact of pericentric inversion of chromosome 9 on fertility in sperm donors

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Asian Journal of Andrology 2024年第3期26卷 302-307页

作者： Qian Liu Wen-Jun Zhou Zeng-Hui Huang Xiu-Hai Huang Jian Wu Xi-Ren Ji Xue-Feng Luo Yu-Ling Tang Rui-Jun Wang Li-Qing Fan Chuan Huang Wen-Bing Zhu Institute of Reproductive and Stem Cell Engineering Basic Medicine CollegeCentral South UniversityChangsha 410013China Clinical Research Center for reproduction and Genetics in Hunan Province Reproductive and Genetic Hospital of CITIC-XiangyaChangsha 410005China

Pericentric inversion of chromosome 9(inv[9])is a common chromosomal structural variant,but its impact on clinical outcomesremains *** screening criteria of sperm banks are rarely mentioned to individuals with inv(9).In this study,we evaluatedthe fertility of sperm donors with inv(9)who met eligibility criteria for sperm banks(inv[9]-eligible donors).From March 2004 toMay 2022,chromosomal analysis of 16124 sperm donors at CITIC-Xiangya Human Sperm Bank in Hunan Province(Changsha,China)found that 251(1.6%)had chromosome variations,with inv(9)being the most prevalent at 1.1%.All 169 inv(9)-eligibledonors were contacted to collect fertility outcome data,along with 206 eligible donors without inv(9)as *** addition,semen samples from inv(9)-eligible donors and eligible donors underwent assessments of sperm fluorescence in situ hybridization(FISH),mitochondrial membrane potential,DNA fragmentation index,acrosome integrity,reactive oxygen species(ROS),andsperm *** showed that inv(9)did not significantly increase reproductive risks *** detecting ROSlevel differences,the clinical impact may be *** study provides new data on the inv(9)population that can serveas a valuable reference for decision-making by sperm banks as well as for genetic counseling and clinical guidance for individualscarrying inv(9)variant.

关键词： male fertility pericentric inversion of chromosome 9 sperm bank sperm functional parameters

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The role of botanical triterpenoids and steroids in bile acid metabolism,transport,and signaling:Pharmacological and toxicological implications

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3385-3415页

作者： Zichen Luo Wei Zhou Tong Xie Weichen Xu Chen Shi Zihan Xiao Yu Si Yan Ma Qingling Ren Liuqing Di Jinjun Shan Medical Metabolomics Center Institute of PediatricsJiangsu Key Laboratory of Children’s Health and Chinese MedicineNanjing University of Chinese MedicineNanjing 210023China State Key laboratory of Natural Medicines School of Traditional Chinese PharmacyChina Pharmaceutical UniversityNanjing 210009China Jiangsu CM Clinical Medicine Innovation Center for Obstetrics Gynecologyand ReproductionAffiliated Hospital of Nanjing University of Chinese MedicineNanjing 210001China National Institute of Biological Sciences Beijing 102206China Jiangsu Engineering Research Center for Efficient Delivery System of TCM School of PharmacyNanjing University of Chinese MedicineNanjing 210023China

Bile acids(BAs)are synthesized by the host liver from cholesterol and are delivered to the intestine,where they undergo further metabolism by gut microbes and circulate between the liver and intestines through various *** serve to emulsify dietary lipids and act as signaling molecules,regulating the host’s metabolism and immune homeostasis through specific ***,disruptions in BA metabolism,transport,and signaling are closely associated with cholestasis,metabolic disorders,autoimmune diseases,and *** triterpenoids and steroids share structural similarities with BAs,and they have been found to modulate BA metabolism,transport,and signaling,potentially exerting pharmacological ortoxicological ***,we have updated the research progress on BA,with a particular emphasis on new-found microbial ***,the latest advancements in targeting BA metabolism and signaling for disease treatment are ***,the roles of botanical triterpenoids in BA metabolism,transport,and signaling are examined,analyzing their potential pharmacological,toxicological,or drug interaction effects through these ***,a research paradigm is proposed that utilizes the gut microbiota as a link to interpret the role of these important natural products in BA signaling.

关键词： Bile acid Triterpenoid Phytosterol Saponin Gut microbes Cholestasis Metabolic disorders Rheumatoid arthritis

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基因组结构变异研究的前瞻性及临床应用

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Science Bulletin 2024年第6期69卷 705-708页

作者：陈仲中 Richard H.Finnell 雷云平王红艳 Obstetrics and Gynecology Hospital State Key Laboratory of Genetic EngineeringInstitute of Reproduction and DevelopmentFudan UniversityShanghai 200011China Shanghai Children’s Hospital School of MedicineShanghai Jiao Tong UniversityShanghai 200062China Center for Precision Environmental Health Department of Molecular and Cellular BiologyBaylor College of MedicineHouston 77030USA Departments of Molecular and Human Genetics and Medicine Baylor College of MedicineOne Baylor PlazaHouston 77030USA Shanghai Key laboratory of Metabolic Remodelling and Health Institute of Metabolism and Integrative BiologyFudan UniversityShanghai 200438China Children’s Hospital of Fudan University Shanghai 201102China

The challenges and breakthroughs in human genetics can largely depend on the depth of exploring the missing heritability[1]and understanding of genetic variants,which enabled scientists to better elucidate the underlying causes of diseases and apply this knowledge in clinical *** genomes differ from one individual to another in the form of single nucleotide variants(SNVs),small insertions and deletions(indels)(structural variants(SVs)[2].

关键词： diseases breakthrough insertion

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Discovery of a potent and highly selective inhibitor of SIRT6 against pancreatic cancer metastasis in vivo

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1302-1316页

作者： Xinyuan Xu Qian Zhang Xufeng Wang Jing Jin Chengwei Wu Li Feng Xiuyan Yang Mingzhu Zhao Yingyi Chen Shaoyong Lu Zhen Zheng Xiaobing Lan Yi Wang Yan Zheng Xuefeng Lu Qiufen Zhang Jian Zhang State Key laboratory of Medical Genomics National Research Center for Translational Medicine at ShanghaiRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China Medicinal Chemistry and BioinformaticsCenter Shanghai Jiao Tong University School of MedicineShanghai 200025China Department of General Surgery Huashan HospitalCancer Metastasis InstituteFudan UniversityShanghai 200040China Institute of Immunology and the CAS Key laboratory of Innate Immunity and Chronic Disease School of Basic Medicine and Medical CenterUniversity of Science and Technology of ChinaHefei 230026China Department of Assisted reproduction Shanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai 200011China College of Pharmacy Ningxia Medical UniversityYinchuan 750004China Department of Pancreatic Surgery Shanghai General HospitalShanghai Key Laboratory of Pancreatic DiseaseInstitute of Pancreatic DiseaseShanghai Jiao Tong University School of MedicineShanghai 200080China

Pancreatic cancer,one of the most aggressive malignancies,has no effective treatment due to the lack of targets and drugs related to tumour ***6 can promote the migration of pancreatic cancer and could be a potential target for antimetastasis of pancreatic ***,highly selective and potency SIRT6 inhibitor that can be used in vivo is yet to be ***,we developed a noveSIRT6 allosteric inhibitor,compound 11e,with maximal inhibitory potency and an IC_(50) value of 0.98±0.13μmol/***,compound 11e exhibited significant selectivity against other histone deacetylases(HADC1-11 and SIRT1-3)at concentrations up to 100μmol/*** allosteric site and the molecular mechanism of inhibition were extensively elucidated by cocrystal complex structure and dynamic structural ***,we confirmed the antimetastatic function of such inhibitors in four pancreatic cancer cell lines as well as in two mouse models of pancreatic cancer liver *** our knowledge,this is the first study to reveal the in vivo effects of SIRT6 inhibitors on liver metastatic pancreatic *** not only provides a promising lead compound for subsequent inhibitor developmentargeting SIRT6 but also provides a potential approach to address the challenge of metastasis in pancreatic cancer.

关键词： SIRT6 Inhibitor Allosteric Selectivity Cocrystal Pancreatic cancer metastasis

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Adenylate kinase phosphate energy shuttle underlies energetic communication in flagellar axonemes

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Science China(Life Sciences) 2024年第8期67卷 1697-1714页

作者： Huan Wu Yanman Zhang Yuqian Li Shuya Sun Jintao Zhang Qingsong Xie Yue Dong Shushu Zhou Xuan Sha Kuokuo Li Jinyi Chen Xin Zhang Yang Gao Qunshan Shen Guanxiong Wang Xiaomin Zha Zongliu Duan Dongdong Tang Chuan Xu Hao Geng Mingrong Lv Yuping Xu Ping Zhou Zhaolian Wei Rong Hua Yunxia Cao Mingxi Liu Xiaojin He Reproductive Medicine Center Department of Obstetrics and GynecologyThe First Affiliated Hospital of Anhui Medical UniversityHefei 230022China State Key laboratory of Reproductive Medicine and Offspring Health Department of Histology and EmbryologySchool of Basic Medical SciencesNanjing Medical UniversityNanjing 210029China State Key laboratory of Reproductive Medicine and Offspring Health The Affiliated Taizhou People’s Hospital of Nanjing Medical UniversityTaizhou School of Clinical MedicineNanjing Medical UniversityNanjing 211166China Reproductive Medicine Center Department of Obstetrics and GynecologyShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai 200080China State Key laboratory of Reproductive Medicine and Offspring Health Clinical Center of Reproductive MedicineThe First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029China NHC Key laboratory of Study on Abnormal Gametes and Reproductive Tract(Anhui Medical University) Hefei 230032China Key laboratory of Population Health Across Life Cycle(Anhui Medical University) Ministry of Education of the People’s Republic of ChinaHefei 230032China Anhui Province Key laboratory of Reproductive Health and Genetics Hefei 230032China Biopreservation and Artificial Organs Anhui Provincial Engineering Research CenterAnhui Medical UniversityHefei 230032China

The complexities of energy transfer mechanisms in the flagella of mammalian sperm flagella have been intensively investigated and demonstrate significant diversity across *** shuttles,particularly adenylate kinase(AK)and creatine kinase(CK),are pivotal in the efficient transfer of intracellular ATP,showing distinct tissue-and ***,the expression profiles of AK and CK were investigated in mice and found to fall into four subgroups,of which Subgroup III AKs were observed to be unique to the male reproductive system and conserved across *** AK8 and AK9 were found to be indispensable to male reproduction after analysis of an infertile male *** mouse models showed that AK8 and AK9 were central to promoting sperm *** combined with mass spectrometry revealed that AK8 and AK9 interact with the radial spoke(RS)of the *** of various human and mouse sperm samples with substructural damage,including the presence of multiple RS subunits,showed that the head of radial spoke 3 acts as an adapter for AK9 in the flagellar *** an ATP probe together with metabolomic analysis,it was found that AK8 and AK9 cooperatively regulated ATP transfer in the axoneme,and were concentrated at sites associated with energy consumption in the *** findings indicate a novel function for RS beyond its structural role,namely,the regulation of ATP *** conclusion,the results expand the functional spectrum of AK proteins and suggest a fresh model regarding ATP transfer within mammalian flagella.

关键词： adenylate kinase Subgroup III AKs AK8 AK9 male infertility ATP transfer radial spoke

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Temperature effect on the structural strains of an ancient Tibetan building based on long-term monitoring data

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Earthquake Engineering and Engineering Vibration 2018年第3期17卷 641-657页

作者： Bai Xiaobin Yang Na Yang Qingshan Beijing Key laboratory of structural Wind Engineering and Urban Wind Environment School of Civil EngineeringBeijing Jiaotong University

Many studies have indicated that structural strain will be significantly influenced by temperature variations,and a good understanding of the effect of temperature on structural strain is essential.A structural health monitoring system has been installed in a typical Tibetan timber building to measure the structural strains and ambient temperature since *** paper presents the correlation between temperature and strain data from the monitored structure.A method combining singular spectrum analysis and polynomial regression is proposed for modeling the temperature induced strains in the *** spectrum analysis is applied to smooth the temperature data,and the correlation between the resulting temperature time series and the measured strains is obtained by polynomial *** of the singular spectrum analysis and the regression model are selected to have the least regression *** show that the proposed method has both good reproduction and prediction capabilities for temperature induced strains,and that the method is accurate and effective for eliminating the effect of temperature from the measured strain.A standardized Novelty Index based on the residual strain is also used for the condition assessment of the structure.

关键词： temperature effect ancient Tibetan building strain singular spectrum analysis novelty detection

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