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| 1 | Insights into salvianolic acid B biosynthesis from chromosome-scale assembly of the Salvia bowleyana genome显示文摘Salvia bowleyanais a traditional Chinese medic-inal plant that is a source of nutritional supple-ments rich in salvianolic acid B and a potentialexperimental system for the exploration ofsalvianolic acid B biosynthesis in the Labiatae.Here,we report a high‐quality chromosome‐scalegenome assembly of S.bowleyana covering 462.44 Mb,with a scaffold N50 value of 57.96 Mband 44,044 annotated protein‐coding genes.Evolutionary analysis revealed an estimateddivergence time betweenS.bowleyanaand its close relativeS.miltiorrhiza of~3.94 millionyears.We also observed evidence of a whole‐genome duplication in theS.bowleyanagenome.Transcriptome analysis showed that SbPAL1(PHENYLALANINE AMMONIA‐LYASE1)ishighlyexpressed in roots relative to stem and leaves,paralleling the location of salvianolic acid Baccumulation.The laccase gene family in S.bowley anaoutnumbered their counterparts inbothS.miltiorrhiza and Arabidopsis thaliana,suggesting that the gene family has undergoneexpansion inS.bowleyana.Several laccasegenes were also highly expressed in roots,wheretheir encoded proteins may catalyze the oxida-tive reaction from rosmarinic acid to salvianolicacid B.Thesefindings provide an invaluable ge-nomic resource for understanding salvianolicacid B biosynthesis and its regulation,and will beuseful for exploring the evolution of the Labiatae. | Xuehai Zheng Duo Chen Binghua Chen Limin Liang Zhen Huang Wenfang Fan Jiannan Chen Wenjin He Huibin Chen Luqiang Huang Youqiang Chen Jinmao Zhu Ting Xue | 2021 | Journal of Integrative Plant Biology2021，63，7： | 2 |
| 2 | Dietary ellagic acid supplementation attenuates intestinal damage and oxidative stress by regulating gut microbiota in weanling piglets显示文摘Intestinal oxidative stress triggers gut microbiota dysbiosis,which is involved in the etiology of postweaning diarrhea and enteric infections.Ellagic acid(EA)can potentially serve as an antioxidant supplement to facilitate weaning transition by improving intestinal oxidative stress and gut microbiota dysbiosis.Therefore,we aimed to investigate the effects of dietary EA supplementation on the attenuation of intestinal damage,oxidative stress,and dysbiosis of gut microbiota in weanling piglets.A total of126 piglets were randomly assigned into 3 groups and treated with a basal diet and 2 m L saline orally(Ctrl group),or the basal diet supplemented with 0.1%EA and 2 m L saline orally(EA group),or the basal diet and 2 m L fecal microbiota suspension from the EA group orally(FEA group),respectively,for 14 d.Compared with the Ctrl group,EA group improved growth performance by increasing average daily feed intake and average daily weight gain(P<0.05)and decreasing fecal scores(P<0.05).EA group also alleviated intestinal damage by increasing the tight junction protein occludin(P<0.05),villus height,and villus height-to-crypt depth ratio(P<0.05),while decreasing intestinal epithelial apoptosis(P<0.05).Additionally,EA group enhanced the jejunum antioxidant capacity by increasing the total antioxidant capacity(P<0.01),catalase(P<0.05),and glutathione/oxidized glutathione(P<0.05),but decreased the oxidative metabolite malondialdehyde(P<0.05)compared to the Ctrl group.Compared with the Ctrl group,EA and FEA groups increased alpha diversity(P<0.05),enriched beneficial bacteria(Ruminococcaceae and Clostridium ramosum),and increased metabolites short-chain fatty acids(P<0.05).Correspondingly,FEA group gained effects comparable to those of EA group on growth performance,intestinal damage,and intestinal antioxidant capacity.In addition,the relative abundance of bacteria shifted in EA and FEA groups was significantly related to the examined indices(P<0.05).Overall,dietary EA supplementation could improve growth performance and attenuate intestinal damage and oxidative stress by regulating the gut microbiota in weanling piglets. | Wenxia Qin Baoyang Xu Yuwen Chen Wenbo Yang Yunzheng Xu Juncheng Huang Ting Duo Yihua Mao Guozong Zhou Xianghua Yan Libao Ma | 2022 | Animal Nutrition2022，，4： | 2 |
| 3 | Molecular imaging of advanced atherosclerotic plaques with folate receptor-targeted 2D nanoprobes显示文摘Vulnerable atherosclerotic plaques are responsible for most cardiovascular diseases(CVDs).Folate receptor(FR)positive activated macrophages were thought to be a prominent component in the development of vulnerable plaque.The objective of this study is to develop folate conjugated two-dimensional(2D)Pd@Au nanomaterials(Pd@Au-PEG-FA)for targeted multimodal imaging of the FRs in advanced atherosclerotic plaques.Pharmacokinetic and imaging studies(single photon emission computed tomography(SPECT),computed tomography(CT)and photoacoustic(PA)imaging)were performed to confirm the prolonged blood half-life and enrichment of radioactivity in atherosclerotic plaques.Strong signals were detected in vivo with SPECT,CT and PA imaging in heavy atherosclerotic plaques,which were significantly higher than those of the normal aortas after injection of Pd@Au-PEG-FA.Blocking studies with preinjection of excess FA could effectively reduce the targeting ability of Pd@Au-PEG-FA in atherosclerotic plaques,further demonstrating the specific binding of Pd@Au-PEG-FA for plaque lesions.Histopathological characterization revealed that the signal of probe was in accordance with the high-risk plaques.In summary,the Pd@Au-PEG-FA has favorable pharmacokinetic properties and provides a valuable approach for detecting high-risk plaques in the presence of FRs in atherosclerotic plaques. | Zhide Guo Liu Yang Mei Chen Xuejun Wen Huanhuan Liu Jingchao Li Duo Xu Yuanyuan An Changrong Shi Jindian Li Xinhui Su Zijing Li Ting Liu Rongqiang Zhuang Nanfeng Zheng Haibo Zhu Xianzhong Zhang | 2020 | Nano Research2020，13，1： | 2 |
| 4 | A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis(Podostemaceae)显示文摘The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction.The taxonomic status of Podostemaceae has always been controversial.Here,we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae,obtained by incorporating Hi-C,Illumina and PacBio sequencing.We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes.The assembled genome size was close to the estimated size,and 659.42 Mb of the assembly was assigned to 29 superscaffolds(scaffold N5021.22 Mb).A total of 59.20%repetitive sequences were identified,among which long terminal repeats(LTRs)were the most abundant class(28.97%of the genome).Genome evolution analysis suggested that the divergence time of Cladopus chinensis(106 Mya)was earlier than that of Malpighiales(82 Mya)and that this taxon diverged into an independent branch of Podestemales.A recent whole-genome duplication(WGD)event occurred 4.43 million years ago.Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation,photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged species.Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses,including WUSCHEL(WUS),ASYMMETRIC LEAVES(ASL),SHOOT MERISTEMLESS(STM),NAC2,NAC8,NAC29,NAC47,NAC73,NAC83 and NAC102.These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae. | Ting Xue Xuehai Zheng Duo Chen Limin Liang Nan Chen Zhen Huang Wenfang Fan Jiannan Chen Wan Cen Shuai Chen Jinmao Zhu Binghua Chen Xingtan Zhang Youqiang Chen | 2020 | Horticulture Research2020，7，1： | 1 |
| 5 | Simulation of Heat Transfer Characteristics in Channel with Square Rib Under Uniform and Turbulent Inlet Conditions显示文摘The detailed flow structures and closely-related heat transfer characteristics are investigated along the wall of a cooling channel with rib tabulator by computation.Three typical Reynolds numbers defined by the rib height are set at 200,500,1300,and the Mach numbers is 0.2,respectively.Two inlet boundary conditions,including the uniform and the fully-developed turbulent conditions,are used to study the turbulence effects on the characteristics of heat transfer in the vicinity of rib and wall.Results show that the local Nusselt number increases when the Reynolds number rises from 200 to 1300.At lower Reynolds number,the turbulent inlet condition generates more tangible heat transfer enhancement.At higher Reynolds number,however,the uniform inlet condition contributes more to the convective heat transfer effects.The paper discovers that the high Nusselt number has a consistent correlation with the positive and negative sign alteration of the shear layer on the wall,which satisfactorily explains the mechanisms of heat transfer enhancement due to the flow. | LI Heng YU Ting WANG Duo ZU Yingqing XU Hongyi | 2019 | Transactions of Nanjing University of Aeronautics and Astronautics2019，36，5： | 1 |
| 6 | The noncanonical role of the protease cathepsin D as a cofilin phosphatase显示文摘Cathepsin D(cathD)is traditionally regarded as a lysosomal protease that degrades substrates in acidic compartments.Here we report cathD plays an unconventional role as a cofilin phosphatase orchestrating actin remodeling.In neutral pH environments,the cathD precursor directly dephosphorylates and activates the actin-severing protein cofilin independent of its proteolytic activity,whereas mature cathD degrades cofilin in acidic pH conditions.During development,cathD complements the canonical cofilin phosphatase slingshot and regulates the morphogenesis of actin-based structures.Moreover,suppression of cathD phosphatase activity leads to defective actin organization and cytokinesis failure.Our findings identify cathD as a dual-function molecule,whose functional switch is regulated by environmental pH and its maturation state,and reveal a novel regulatory role of cathD in actin-based cellular processes. | Yi-Jun Liu Ting Zhang Sicong Chen Daxiao Cheng Cunjin Wu Xingyue Wang Duo Duan Liya Zhu Huifang Lou Zhefeng Gong Xiao-Dong Wang Margaret S.Ho Shumin Duan | 2021 | Cell Research2021，31，7： | 0 |
| 7 | 建立具有体内胚内和胚外发育潜能的多能干细胞显示文摘文章简介在已知的体外培养的干细胞类型当中,多能干细胞具有最高的发育潜能,能够形成构成成年个体的所有细胞类型。但是,多能干细胞很难在体内发育过程中形成胚外的胎盘组织。 | Yang Yang Bei Liu Jun Xu Jinlin Wang Jun Wu Cheng Shi Yaxing Xu Jiebin Dong Chengyan Wang Weifeng Lai Jialiang Zhu Liang Xiong Dicong Zhu Xiang Li Weifeng Yang Takayoshi Yamauchi Atsushi Sugawara Zhongwei Li Fangyuan Sun Xiangyun Li Chen Li Aibin He Yaqin Du Ting Wang Chaoran Zhao Haibo Li Xiaochun Chi Hongquan Zhang Yifang Liu Cheng Li Shuguang Duo Ming Yin 沈浣 Juan Carlos Izpisua Belmonte 邓宏魁 | 2018 | 科学新闻2018，0，4： | 0 |
| 8 | Multi-omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis galbana显示文摘Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucoxanthin(Fx)content.However,multi-omics analysis of the regulatory networks for Fx biosynthesis in I.galbana has not been reported.In this study,we report a high-quality genome assembly of I.galbana LG007,which has a genome size of 92.73 Mb,with a contig N50 of 6.99 Mb and 14,900 protein-coding genes.Phylogenetic analysis confirmed the monophyly of Haptophyta,with I.galbana sister to Emiliania huxleyi and Chrysochromulina tobinii.Evolutionary analysis revealed an estimated divergence time between I.galbana and E.huxleyi of~133 million years ago.Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion,including IgPLMT,IgOAR1,and IgDEGS1.Metabolome analysis showed that the content of carotenoids in I.galbana cultured under green light for 7 days was higher than that under white light,andβ-carotene was the main carotenoid,accounting for 79.09%of the total carotenoids.Comprehensive multi-omics analysis revealed that the content ofβ-carotene,antheraxanthin,zeaxanthin,and Fx was increased by green light induction,which was significantly correlated with the expression of IgMYB98,IgZDS,IgPDS,IgLHCX2,IgZEP,IgLCYb,and IgNSY.These findings contribute to the understanding of Fx biosynthesis and its regulation,providing a valuable reference for food and pharmaceutical applications. | Duo Chen Xue Yuan Xuehai Zheng Jingping Fang Gang Lin Rongmao Li Jiannan Chen Wenjin He Zhen Huang Wenfang Fan Limin Liang Chentao Lin Jinmao Zhu Youqiang Chen Ting Xue | 2022 | Genomics, Proteomics & Bioinformatics2022，20，6： | 0 |
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