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Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits

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Plant Communications 2024年第6期5卷 173-192页

作者： Xue-Mei Lu Xiao-Fen Yu Guo-Qiang Li Ming-Hao Qu Huan wang Chuang Liu Yu-Ping Man Xiao-Han Jiang Mu-Zi Li Jian wang Qi-Qi Chen Rui Lei Cheng-Cheng Zhao Yun-Qiu Zhou Zheng-wang Jiang Zuo-Zhou Li Shang Zheng Chang Dong bai-lin wang Yan-Xiang Sun Hui-Qin Zhang Jie-Wei Li Quan-Hui Mo Ying Zhang Xin Lou Hai-Xu Peng Ya-Ting Yi He-Xin wang Xiu-Jun Zhang Yi-Bo wang Dan wang Li Li Qiong Zhang Wen-Xia wang Yongbo Liu Lei Gao Jin-Hu Wu Yan-Chang wang CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhanHubeiChina Key Laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhouGansuChina College of Life Sciences University of Chinese Academy of SciencesBeijingChina Wuhan Frasergen Bioinformatics Co. LtdWuhanHubeiChina Institute of Soil and Fertilizer Anhui Academy of Agricultural SciencesHefeiChina College of Agricultural Sciences Xichang UniversityXichangSichuanChina Department of Horticulture Heilongjiang Academy of Agricultural SciencesHarbinHeilongjiangChina College of Life Sciences Langfang Normal UniversityLangfangHebeiChina Institute of Horticulture Zhejiang Academy of Agricultural SciencesHangzhouZhejiangChina Guangxi Institute of Botany Chinese Academy of SciencesGuilinGuangxiChina Xi’an Botanical Garden of Shaanxi Province Institute of Botany of Shaanxi ProvinceXi’anShaanxiChina Institute of Modern Agricultural Research Dalian UniversityDalianLiaoningChina Bioinformatics Center College of Plant Science and TechnologyBeijing University of AgricultureBeijingChina College of Agriculture Eastern Liaoning UniversityDandongLiaoningChina Dalian Institute of Chemical Physics Chinese Academy of SciencesDalianLiaoningChina State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijingChina Hubei Hongshan Laboratory WuhanHubeiChina The New Zealand Institute for Plant and Food Research Limited AucklandNew Zealand

Actinidia arguta,the most widely distributed Actinidia species and the second cultivated species in the genus,can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit,rapid softening,and excellent cold *** evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still ***,we generated a chromosome-scale genome assembly of an autotetraploid male *** *** genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 *** and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups,Southern and Northern,which first diverged 12.9 million years *** underwent two prominent expansions and one demographic bottleneck from the midPleistocene climate transition to the late *** genomics studies using paleoclimate data enabled us to discern the evolution of the species’adaptation to different historical *** genes(AaCEL1,AaPME1,and AaDOF1)related to flesh softening were identified by multi-omics analysis,and their ability to accelerate flesh softening was verified through transient expression assays.A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome(Chr3)or autosomal chromosomes showed biased expression during stamen or carpel *** chromosome-level assembly of the autotetraploid *** genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of ***.

关键词： kiwiberry dioecism adaptive evolution paleoclimate GEA rapid softening

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Research progress of lncRNA and miRNA in hepatic ischemia-reperfusion injury

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Hepatobiliary & Pancreatic Diseases International 2023年第1期22卷 45-53页

作者： Shan-Fei Zhu Wei Yuan Yong-Liang Du bai-lin wang Department of Hepatobiliary Surgery Guangzhou Red Cross Hospital of Jinan UniversityGuangzhou 510220China

Background:Hepatic ischemia-reperfusion injury(HIRI)is a common complication of liver surgeries,such as hepatectomy and liver *** recent years,several non-coding RNAs(nc RNAs)including long non-coding RNAs(lnc RNAs)and micro RNAs(mi RNAs)have been identified as factors involved in the pathological progression of *** this review,we summarized the latest research on lnc RNAs,mi RNAs and the lnc RNA-mi RNA regulatory networks in *** sources:The Pub Med and Web of Science databases were searched for articles published up to December 2021 using the following keywords:“hepatic ischemia-reperfusion injury”,“lnc RNA”,“long noncoding RNA”,“mi RNA”and“micro RNA”.The bibliography of the selected articles was manually screened to identify additional ***:The mechanism of HIRI is complex,and involves multiple lnc RNAs and mi *** roles of lnc RNAs such as AK139328,CCAT1,MALAT1,TUG1 and NEAT1 have been established in *** addition,numerous mi RNAs are associated with apoptosis,autophagy,oxidative stress and cellular inflammation that accompany HIRI *** on the literature,we conclude that four lnc RNA-mi RNA regulatory networks mediate the pathological progression of ***,the expression levels of some lnc RNAs and mi RNAs undergo significant changes during the progression of HIRI,and thus are potential prognostic markers and therapeutic ***:Complex lnc RNA-mi RNA-m RNA networks regulate HIRI progression through mutual activation and *** is necessary to screen for more HIRI-associated lnc RNAs and mi RNAs in order to identify novel therapeutic targets.

关键词： ncRNA lncRNA miRNA Hepatic ischemia-reperfusion injury Research progress

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Cloning and Characterization of Largemouth Bass(Micropterus salmoides) Myostatin Encoding Gene and Its Promoter

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Journal of Ocean University of China 2008年第3期7卷 304-310页

作者： LI Shengjie bai Junjie wang lin Key Laboratory of Tropical and Subtropical Fish Breeding and Cultivation of CAFS Pearl RiverFisheries Research Institute CAFS Guangzhou 510380 P. R. China

Myostatin or GDF-8, a member of the transforming growth factor-β （TGF-β） superfamily, has been demonstrated to be a negative regulator of skeletal muscle mass in mammals. In the present study, we obtained a 5.64 kb sequence of myostatin encoding gene and its promoter from largemouth bass （Micropterus salmoides）. The myostatin encoding gene consisted of three exons （488bp, 371 bp and 1779bp, respectively） and two introns （390bp and 855 bp, respectively）. The intron-exon boundaries were conservative in comparison with those of mammalian myostatin encoding genes, whereas the size of introns was smaller than that of mammals. Sequence analysis of 1.569 kb of the largemouth bass myostatin gene promoter region revealed that it contained two TATA boxes, one CAAT box and nine putative E-boxes. Putative muscle growth response elements for myocyte enhancer factor 2 （MEF2）, serum response factor （SRF）, activator protein 1 （AP1）, etc., and muscle-specific Mt binding site （MTBF） were also detected. Some of the transcription factor binding sites were conserved among five teleost species. This infunnation will be useful for studying the tran- scriptional regulation of myostatin in fish.

关键词： myostatin encoding gene promoter largemouth bass E-box

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Digitalizing river aquatic ecosystems

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Journal of Environmental Sciences 2024年第3期137卷 677-680页

作者： Yaohui bai Hui lin Chenchen wang Qiaojuan wang Jiuhui Qu Key Laboratory of Drinking Water Science and Technology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China School of Environmental and Municipal Engineering Tianjin Chengjian UniversityTianjin 300384China Center for Water and Ecology Tsinghua UniversityBeijing 100084China

Traditional river health assessment relies on limited water quality indices and representative organism activity,but does not comprehensively obtain biotic and abiotic information of the ***,we propose a new approach to evaluate the ecological and health risks of river aquatic ***,detailed physicochemical and biological characterization of a river ecosystem can be obtained through pollutant determination(especially emerging pollutants)and DNA/RNA ***,supervised machine learning can be applied to perform classification analysis of characterization data and ascertain river ecosystem ecology and *** proposed methodology transforms river ecosystem health assessment and can be applied in river management.

关键词： Digitalizing River ecosystem health Emerging pollutants High throughput sequencing Machine learning

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Evaluating CMIP6 models in simulating the North Pacific decadal variability in sea surface salinity

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Science China Earth Sciences 2024年第8期67卷 2661-2680页

作者： Jian CHEN Hailong LIU Pengfei lin Wenrong bai Chengzu bai Lu wang Institute of Atmospheric Physics Chinese Academy of SciencesBeijing 100029China State Key Laboratory of Geo-Information Engineering Xi’an 710054China Beijing Municipal Climate Center Beijing Meteorological BureauBeijing 100089China Space System Department Equipment Department Beijing 100096China

The North Pacific sea surface salinity(SSS)decadal variability(NPSDV)and its potential forcing were evaluated from 25 coupled models of the Coupled Model Intercomparison Project phase 6(CMIP6)considering the prospects for decadal climate *** results indicated that the CMIP6 models generally reproduced the spatial patterns of *** large standard deviation of the SSS anomaly over the strong current regions,such as the Kuroshio-Oyashio Extension(KOE),North Pacific Current(NPC),California Current System(CCS),and Alaskan Coastal Current(ACC),is reflected in the two leading modes of NPSDV:a dipole with out-of-phase loadings in the KOE-NPC versus CCS-ACC and a monopole with positive loading over the *** order of modes is sensitive to individual models that exhibit discrepancies,especially in temporal phases and power *** autoregressive model of order-1 was used to reconstruct the NPSDV with several forcing *** generally weaker influence of forcings in an autoregressive model of order-1 is partly related to the overestimated response time of NPSDV relative to *** NPSDV variances originate from the persistence of SSS anomalies,but the dominant forcing factors are diverse among *** model diversity for the NPSDV simulation mainly arises from the influence of the tropical El Ni?o-Southern Oscillation through teleconnection on the North Pacific Oscillation or Aleutian Low with timescale ***,models that can reproduce the NPSDV well are not dependent on those with larger impacts from the North Pacific oceanic processes.

关键词： North Pacific Sea surface salinity Decadal variability CMIP6 Leading mode

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Boundary Behaviors for a Continuous-state Nonlinear Neveu’s Branching Process

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Acta Mathematica Sinica,English Series 2024年第8期40卷 2005-2016页

作者： lin Yu bai Xu YANG School of Mathematics and Information Science North Minzu UniversityYinchuan 750021P.R.China

By generalizing a criterion of Mufa Chen for Markov jump processes,we establish the necessary and sufficient conditions for the extinction,explosion and coming down from infinity of a continuous-state nonlinear Neveu... 详细信息

关键词： Continuous-state branching process nonlinear branching Neveu’s branching extinction explosion coming down from infinity

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Jetting of a near-wall cavitation bubble induced by another tandem bubble

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Journal of Hydrodynamics 2024年第3期36卷 444-456页

作者： Hui Han Jing-zhu wang Jian-lin Huang Peng-bo bai Yong-gang Chen Yi-wei wang Key Laboratory for Mechanics in Fluid Solid Coupling Systems Institute of MechanicsChinese Academy of SciencesBeijing100190China School of Engineering Science University of Chinese Academy of SciencesBeijing100049China Guangdong Aerospace Research Academy Guangzhou511458China School of Future Technology University of Chinese Academy of SciencesBeijing100049China Jianghuai Advance Technology Center Hefei230088China

Double bubbles near a rigid wall surface collapse to produce a significant jet impact,with potential applications in surface cleaning and ultrasonic ***,the dynamic behaviors of near-wall bubbles remain *** this study,we investigate the jetting of a near-wall bubble induced by another tandem *** define two dimensionless standoff distances,γ_(1),γ_(2),to represent the distances from the center of the near-wall bubble to the rigid wall and the center of controlling bubble to the center of the near-wall bubble,*** observations reveal three distinct jetting regimes for the near-wall bubble:transferred jetting,double jetting,and directed *** further investigate the jetting mechanism,numerical simulations are conducted using the compressibleInterFoam solver in the open-source framework of OpenFOAM.A detailed analysis shows that the transferred jet flow is caused by the pinch-off resulting from the axial contraction velocity at the lower end of the near-wall bubble being greater than the vertical contraction velocity,leading to a maximum jet velocity of 682.58 m/*** the case of double jetting,intense stretching between the controlling bubble and the wall leads to a pinch-off and a double jetting with a maximum velocity of 1096.29 m/*** directed jet flow is caused by the downward movement of the high-pressure region generated by the premature collapse of the controlling bubble,with the maximum jet velocity reaching 444.62 m/s.

关键词： Jetting of near-wall bubble controlling bubble impact velocity

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Microfacies and diagenetic alteration in a semi-deep to deep lacustrine shale: The Yanchang Formation in the Ordos Basin, China

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Petroleum Science 2024年第3期21卷 1524-1538页

作者： Bin bai Jing-Yue Hao ling Fu Yu-Xi Liu Jian-Peng wang Lan wang Kevin GTaylor lin Ma PetroChina Research Institute of Petroleum Exploration and Development Beijing100083China Department of Earth and Environmental Sciences University of ManchesterM139PLUK College of Earth Sciences Jilin UniversityChangchun130061jilinChina Department of Chemical Engineering University of ManchesterM139PLUK

The mineralogical development and diagenetic sequence of lacustrine shales in the Chang 7 Member of the Yanchang Formation in the Ordos Basin are detailed studied.A model of their depositional system and a diagenetic diagram are proposed in this *** detailed petrographic,mineralogical,and elemental analyses,four distinct shale types are identified:argillaceous shale,siliceous shale,calcareous shale,and carbonate,clay,and silt-bearing *** main diagenetic process in argillaceous shale is the transformation of illite to smectite,negatively impacting shale *** shale undergoes carbonate cementation and quartz dissolution,contributing to increased porosity,particularly in *** shale experiences diagenesis characterised by carbonate formation and dissolution,with a prevalence of *** carbonate,clay,and silt-bearing shale,the dissolution of K-feldspar contributes to illitization of *** shale,characterised by more clay minerals and lower mesopore volume,is identified as a potential hydrocarbon *** shale,with the highest pore volume and abundant inter-mineral pores,emerges as a promising shale oil *** findings contribute to a comprehensive understanding of shale properties,aiding in the prediction of shale oil exploration potential in the studied area.

关键词： Ordos Basin Yanchang Formation Chang 7 Member Diagenesis Microfacies

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Responses of growth performance,antioxidant function,small intestinal morphology and mRNA expression of jejunal tight junction protein to dietary iron in yellow-feathered broilers

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Journal of Integrative Agriculture 2024年第4期23卷 1329-1337页

作者： Kaiwen Lei Hao Wu Jerry W Spears Xi lin Xi wang Xue bai Yanling Huang Key Laboratory of Animal Science of State Ethnic Affairs Commission Southwest Minzu UniversityChengdu 610041China Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Southwest Minzu UniversityChengdu 610041China Department of Animal Science North Carolina State UniversityRaleighNC 27695-7621USA

This study aimed to investigate the dose-effect of iron on growth performance,antioxidant *** morphology,and mRNA expression of jejunal tight junction protein in 1-to21-d-old yellow-feathered broilers.A total of 7201-d-old yellow-feathered maleb roilers were allocated to 9 treatments with 8 replicate cages of 10 birds per *** dietary treatments were consisted of a basal diet(contained 79.6 mg Fe kg^(-1))supplemented with 0,20,40,60,80,160,320,640,and 1,280 mg Fe kg^(-1)in the form of FeSO_(4)·7H_(2)*** with the birds in the control group,birds supplemented with 20mg Fe kg^(-1)had higher average daily gain(ADG)(Plinearly(Plinearly(Plinearly(P?0.05)as dietary *** dietary Fe increased,the jejunal relative mRNA abundance of claudin-1 decreased linearly(P=0.001),but the jejunal relative mRNA abundance of zona occludens-1(ZO-1)and occludin decreased linearly(P?0.05)or quadratically(P?0.05).Compared with the supplementation of 20 mg Fe kg^(-1),the supplementation of640 mg Fe kg^(-1)or higher increased(P?0.05)MDA concentrations in plasma,duodenum,and jejunum,decreased VH in the duodenum and jejunum,and the addition of 1,280 mg Fe kg^(-1)reduced(P?0.05)the jejunal tight junction protein(claudin-1,ZO-1,occludin)mRNA *** summary,640 mg of supplemental Fe kg^(-1)or greater was associated with decreased growth performance,increased oxidative stress,disrupted intestinal morphology,and reduced mRNA expression of jejunal tight junction protein.

关键词： iron yellow-feathered broiler antioxidant function intestinal morphology tight junction protein

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Variations of sediment organic phosphorus and organic carbon during the outbreak and decline of algal blooms in Lake Taihu,China

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Journal of Environmental Sciences 2024年第5期139卷 34-45页

作者： Jiehua wang Xiuling bai Wenchao Li Pingping Zhang Mengdi Zhang Haoran wang Yingge bai College of Geography and Environmental Science Henan UniversityKaifeng 475004China Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions(Henan University) Ministry of EducationKaifeng 475004China National Demonstration Center for Environment and Planning Henan UniversityKaifeng 475004China Surrey International Institute Dongbei University of Finance and EconomicsDalian 116000China

In this study,sediment organic phosphorus(OP)and organic carbon(OC)in Lake Taihu,China,as well as their relationships,were analyzed during the outbreak and decline of algal blooms(ABs)over a five-month field *** results showed synchronous temporal changes in the sediment OP and OC contents with the development of *** addition,there was a significant positive correlation between the sediment OP and OC(pline,*** active OC contents and proportions in the sediments in the ABs outbreak were significantly lower than those observed in the ABs decline period,demonstrating the significant impacts of the ABs outbreak and decline on the sediment OC and OP in Lake Taihu.

关键词： Algal blooms Organic phosphorus Organic carbon Sediment ^(31)P NMR Lake Taihu

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