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Biology of Hippo signaling pathway:Skeletal muscle development and beyond

Journal of Integrative agriculture 2024年第6期23卷 1825-1838页

作者： Shuqi Qin Chaocheng Li Haiyan Lu Yulong Feng Tao Guo Yusong Han Yongsheng Zhang Zhonglin Tang Xinjiang Characteristic Livestock Breeding and Reproduction Team College of Animal Science and TechnologyShihezi UniversityShihezi 832003China Lanzhou Veterinary Research institute Chinese Academy of Agricultural SciencesLanzhou 730046China kunpeng institute of modern agriculture at foshan Foshan 528226China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Global demand for farm animals and their meat products i.e.,pork,chicken and other livestock meat,is steadily incresing.With the ongoing life science research and the rapid development of biotechnology,it is a great opportunity to develop advanced molecular breeding markers to efficiently improve animal meat production traits.Hippo is an important study subject because of its crucial role in the regulation of organ size.In recent years,with the increase of research on Hippo signaling pathway,the integrative application of multi-omics technologies such as genomics,transcriptomics,proteomics,and metabolomics can help promote the in-depth involvement of Hippo signaling pathway in skeletal muscle development research.The Hippo signaling pathway plays a key role in many biological events,including cell division,cell migration,cell proliferation,cell differentiation,cell apoptosis,as well as cell adhesion,cell polarity,homeostasis,maintenance of the face of mechanical overload,etc.Its influence on the development of skeletal muscle has important research value for enhancing the efficiency of animal husbandry production.In this study,we traced the origin of the Hippo pathway,comprehensively sorted out all the functional factors found in the pathway,deeply analyzed the molecular mechanism of its function,and classified it from a novel perspective based on its main functional domain and mode of action.Our aim is to systematically explore its regulatory role throughout skeletal muscle development.We specifically focus on the Hippo signaling pathway in embryonic stem cell development,muscle satellite cell fate determination,myogenesis,skeletal muscle meat production and organ size regulation,muscle hypertrophy and atrophy,muscle fiber formation and its transformation between different types,and cardiomyocytes.The roles in proliferation and regeneration are methodically summarized and analyzed comprehensively.The summary and prospect of the Hippo signaling pathway within this article will provide ideas for further improving

关键词： Hippo skeletal muscle organ size myogenesis C2C12 livestock animals

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Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

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Journal of Integrative agriculture 2024年第1期23卷 217-227页

作者： Mu Zeng Binhu Wang Lei Liu Yalan Yang Zhonglin Tang Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education institutes School of Life Science and EngineeringFoshan UniversityFoshan 528231China kunpeng institute of modern agriculture at foshan Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesFoshan 528200China Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture/Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in pigs.However,the available genetic markers for these traits are limited.To uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.We performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,respectively.Variant annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in pigs.Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle development.Overall,this study provides new candidate loci and genes for the genetic improvement of pigs.

关键词： GWAS pig growth trait QTL mapping skeletal muscle

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miR-378a-3p responds to physical activity by modulating insulin-mediated glucose uptake and tricarboxylic acid cycle in skeletal muscle

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Genes & Diseases 2024年第3期11卷 98-101页

作者： Zishuai Wang Yilong Yao Xinhua Hou Danyang Fan Yanwen Liu Adeyinka Abiola Adetula Yalan Yang kui Li Zhonglin Tang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong518000China kunpeng institute of modern Agriculiture at foshan Chinese Academy of Agricultural SciencesFoshanGuangdong528226China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig BamaGuangxi 547500China institute of Animal Science Chinese Academy of Agricultural SciencesBeijing100193China

Aerobic exercise training alters gene expression in skeletal muscle,and miRNAs significantly contribute to motion response.However,the molecular mechanisms by which miRNAs regulate the response to exercise training are not well understood.Here,we found that the abundance of miR-378a-3p in skeletal muscle significantly decreased after exercise training.miR-378a-3p knockout mice showed increased insulin sensitivity,insulin-mediated glucose uptake.

关键词： skeletal miR uptake

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Structural elucidation of mulberry leaf oligosaccharide and its selective promotion of gut microbiota to alleviate type 2 diabetes mellitus

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Food Science and Human Wellness 2024年第4期13卷 2161-2173页

作者： Tenggen Hu Yuanshan Yu Jijun Wu Yujuan Xu Gengsheng Xiao Kejing An Erna Li Sentai Liao Yuxiao Zou Sericultural&Agri-Food Research institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou 510610China Huagongliya(foshan)Technology Industry Co. Ltd.Foshan 528313China Heyuan Branch Guangdong Laboratory for Lingnan Modern AgricultureHeyuan 517001China Zhongkai University of agriculture and Engineering Guangzhou 510225China

Two oligosaccharide fractions(MLO 2-1 and 2-2)were purified from enzymatic hydrolysate of mulberry leaf polysaccharide.The results of simulated digestion showed that MLO 2-2 was a digestible oligosaccharide,which could be degraded by human digestive juice;while MLO 2-1 possessed the non-digestible property in the upper gastrointestinal tract and performed the function by regulating the gut microbiota.Hence,MLO 2-1 was selected for the further analysis.The structure of MLO 2-1 was elucidated as follow:α-T-Glcp-(1→3)-β-Glcp-(1→5)-α-Araf-(1→5)-α-Araf-1→5)-α-Araf-(1→3)-α-(2-OAc)-Glcp-1.The in vitro fecal fermentation results showed that MLO 2-1 could modulate the composition of gut microbiota.Meanwhile,MLO 2-1 was effectively metabolized by fecal bacteria to produce lactate and short chain fatty acids,especially acetate and butyrate.The specific metabolic pathways of MLO 2-1 by gut microbiota were further illuminated.Gut microbiota analysis revealed that MLO 2-1 selectively promoted the growth of Ligilactobacillus murinus,a commensal bacterium presented a reduced level in T2DM mice.Animal experiments indicated that MLO 2-1 and L.murinus exhibited hypoglycemic activities.These results demonstrated that MLO 2-1 might alleviate T2DM by selectively accelerating the proliferation of L.murinus.

关键词： Mulberry leaf oligosaccharide Characterization Gut microbiota Lactobacillus murinus Hypoglycemic activity

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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang 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 Sciences institute of Wetland agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle

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Journal of Animal Science and Biotechnology 2024年第2期15卷 733-748页

作者： Jianmin Chai Caleb P.Weiss Paul A.Beck Wei Zhao Ying Li Jiangchao Zhao Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding College of Life Science and EngineeringFoshan UniversityFoshanChina Division of agriculture Department of Animal ScienceUniversity of ArkansasFayettevilleARUSA Department of Animal and Food Sciences Oklahoma State UniversityStillwaterOKUSA institute of Feed Research of Chinese Academy of Agricultural Sciences Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural AffairsBeijing 100193China

Background Stocker cattle diet and management influence beef cattle performance during the finishing stage,but knowledge of the dynamics of the rumen microbiome associated with the host are lacking.A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota.During the stocker phase,either dry hay or wheat pasture were provided,and three levels of monensin were administrated.All calves were then transported to a feedlot and received similar finishing diets with or without monensin.Rumen microbial samples were collected on d 0,28,85 during the stocker stage(S0,S28 and S85)and d 0,14,28,56,30 d before slaughter and the end of the trial during the finishing stage(F0,F14,F28,F56,Pre-Ba,and Final).The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced.Results Higher alpha diversity,including the number of observed bacterial features and the Shannon index,was observed in the stocker phase compared to the finishing phase.The bacterial amplicon sequence variants(ASVs)differentiating different sampling time points were identified.Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota.For example,shared bacteria,including Bacteroidales(ASV19)and Streptococcus infantarius(ASV94),were significantly higher in hay rumen on S28,S85,and F0,while Bacteroidaceae(ASV11)and Limivicinus(ASV15)were more abundant in wheat.Monensin affected rumen microbial composition at a specific time.Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves.Bacterial taxa associated with body weight were classified,and core microbiotas interacted with each other during the trial.Conclusions In summary,the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy.Diet at the stocker phase may temporarily affect the microbial composition duri

关键词： Beef cattle Diet Feedlot phase Monensin Next-generation sequencing Rumen microbiota Stocker

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Three-Wave Mixing of Dipole Solitons in One-Dimensional Quasi-Phase-Matched Nonlinear Crystals

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Chinese Physics Letters 2024年第1期41卷 25-33页

作者：郭宇欣徐晓喜陈招拼周延桂刘彬和河向黎永耀谢嘉宁 School of Physics and Optoelectronic Engineering Foshan UniversityFoshan 528000China Physics Department and Solid-State institute TechnionHaifa 32000Israel Guangdong-Hong Kong-Macao Joint Laboratory for Intelligent Micro-Nano Optoelectronic Technology School of Physics and Optoelectronic EngineeringFoshan UniversityFoshan 528000China

A quasi-phase-matched technique is introduced for soliton transmission in a quadratic[χ^((2))]nonlinear crystal to realize the stable transmission of dipole solitons in a one-dimensional space under three-wave mixing.We report four types of solitons as dipole solitons with distances between their bimodal peaks that can be laid out in different stripes.We study three cases of these solitons:spaced three stripes apart,one stripe apart,and confined to the same stripe.For the case of three stripes apart,all four types have stable results,but for the case of one stripe apart,stable solutions can only be found atω_(1)=ω_(2),and for the condition of dipole solitons confined to one stripe,stable solutions exist only for Type1 and Type3 atω_(1)=ω_(2).The stability of the soliton solution is solved and verified using the imaginary time propagation method and real-time transfer propagation,and soliton solutions are shown to exist in the multistability case.In addition,the relations of the transportation characteristics of the dipole soliton and the modulation parameters are numerically investigated.Finally,possible approaches for the experimental realization of the solitons are outlined.

关键词： soliton solitons dipole

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Precipitation of multi-type nano-quasicrystals in a Mg-Zn-Y alloy

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Journal of Magnesium and Alloys 2024年第3期12卷 997-1008页

作者： W.Z.Wang X.Z.Zhou L.F.Zhang H.Q.Ye Z.Q.Yang Shenyang National Laboratory for Materials Science Institute of Metal ResearchChinese Academy of ScienceShenyang 110016China Ji Hua Laboratory Foshan 528251China foshan University Foshan 528231China

Mg-6Zn-1Y(at.%)ribbons with strengthening precipitates of multi-type nanoquasicrystals were prepared by melt-spinning followed by aging treatments.Microstructural evolution of the rapidly solidified ribbons during isothermal aging was comprehensively studied using various electron microscopy techniques.Two new kinds of decagonal quasicrystals were formed in aged ribbons,in addition to precipitation of nanometer icosahedral quasicrystals.Atomic-resolution observations reveal that both decagonal quasicrystals can be modeled by quasiperiodic tiling with decagonal clusters of 2.5 nm in diameter,but overlap of neighboring clusters in both decagonal quasicrystals is different from the Gummelt model observed in other quasicrystals.A shell composed of complex Laves Mg-Zn domains was formed surrounding each decagonal quasicrystal precipitate upon prolonged aging.In addition,all kinds of nanoprecipitates exhibit excellent structure and size stability at 573 K.Our findings may have implications for not only fundamental studies about quasicrystals,but also microstructural manipulation of high-performance Mg alloys.

关键词： Quasicrystal Mg alloys Rapid solidification Scanning-transmission electron microscopy.

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Improving error-correcting capability in DNA digital storage via soft-decision decoding

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National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 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 Sciences Guangdong Provincial Key Laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

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Potential Secretory Transporters and Biosynthetic Precursors of Biological Nitrification Inhibitor 1,9-Decanediol in Rice as Revealed by Transcriptome and Metabolome Analyses

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Rice science 2024年第1期31卷 87-102页

作者： DI Dongwei MA Mingkun ZHANG Xiaoyang LU Yufang Herbert J.KRONZUCKER SHI Weiming State Key Laboratory of Soil and Sustainable agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China School of Food Science and Engineering Foshan UniversityFoshan 528000China School of BioSciences The University of MelbourneParkvilleVIC 3010Australia University of Chinese Academy of Sciences Beijing 100049China

Biological nitrification inhibitors(BNIs)are released from plant roots and inhibit the nitrification activity of microorganisms in soils,reducing NO_(3)^(‒)leaching and N2O emissions,and increasing nitrogenuse efficiency(NUE).Several recent studies have focused on the identification of new BNIs,yet little is known about the genetic loci that govern their biosynthesis and secretion.We applied a combined transcriptomic and metabolomic analysis to investigate possible biosynthetic pathways and transporters involved in the biosynthesis and release of BNI 1,9-decanediol(1,9-D),which was previously identified in rice root exudates.Our results linked four fatty acids,icosapentaenoic acid,linoleate,norlinolenic acid,and polyhydroxy-α,ω-divarboxylic acid,with 1,9-D biosynthesis and three transporter families,namely the ATP-binding cassette protein family,the multidrug and toxic compound extrusion family,and the major facilitator superfamily,with 1,9-D release from roots into the soil medium.Our finding provided candidates for further work on the genes implicated in the biosynthesis and secretion of 1,9-D and pinpoint genetic loci for crop breeding to improve NUE by enhancing 1,9-D secretion,with the potential to reduce NO_(3)^(‒)leaching and N2O emissions from agricultural soils.

关键词： 1,9-decanediol biological nitrification inhibitor metabolomic analysis nitrogen-use efficiency transcriptomic analysis

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