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Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

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Molecular Plant 2021年第10期14卷 1745-1756页

作者： Kui li Wenkai Jiang Yuanyuan Hui Mengjuan Kong li-Ying Feng li-zhi gao Pengfu li Shan Lu State Key Laboratory of Pharmaceutical Biotechnology School of Life SciencesNanjing UniversityNanjing 210023China Novogene Bioinformatics Institute Building 301Zone A10 Jiuxianqiao North RoadChaoyang DistrictBeijing 100083China Institution of Genomics and Bioinformatics South China Agricultural UniversityGuangzhou 510642China Shenzhen Research Institute of Nanjing University Shenzhen 518000China

The ultimate goal of genome assembly is a high-accuracy gapless ***,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui *** resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 *** chromosome is represented by a single contig and the genomic sequences of all chromosomes are *** evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice *** comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/*** insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these ***,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental ***,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.

关键词： evolution gapless genome rice segmental duplications transposable elements

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Columnar to Equiaxed Transition During Solidification of Small Ingot by Using Electric Current Pulse

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Journal of Iron and Steel Research International 2009年第6期16卷 7-12页

作者： li Jie MA Jian-hong SONG Chang-jiang li zhi-jun gao Yu-lai ZHAI Qi-jie Shanghai Key Laboratory of Modern Metallurgy and Materials Processing Shanghai University Shanghai 200072 China

A new approach to applying the electric current pulse （ECP） with parallel electrodes to the promotion of the transition from columnar crystal to equiaxed crystal and the improvement of macrosegregation was introduced. The ECP was applied to different stages of the solidification. The results showed that the application of the ECP in both the initial stage （the thickness of solidified shell reached 2 mm approximately） and the late stage （the thickness of solidified shell reached 14 mm approximately） of solidification can promote the columnar to equiaxed transition （CET）. The analysis showed that during solidification, a large number of nuclei around the upper surface fell off due to ECP, which subsequently showered on the melt and impinged the growth front of the columnar crystal. Therefore, the CEToccurred. In addition, this method was also employed to influence the solidification process of bearing steel, and the results showed that the structure was changed from columnar crystal to equiaxed crystal, indicating that ECP can enhance the homogeneity of structure and composition of bearing steel.

关键词： columnar to equiaxed transition solidification electric current pulse macrosegregation

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Regulation of Water Deficit-Induced Abscisic Acid Accumulation by Apoplastic Ascorbic Acid in Maize Seedlings

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Journal of Integrative Plant Biology 2005年第11期47卷 1335-1344页

作者： Jian-Fang HU Gui-Fen li zhi-Hui gao lin CHEN Hui-Bo REN Wen-Suo JIA College of Agronomy and Biotechnology State Key Laboratory of Plant Physiology and Biochemistry China Agricultural University Beijing 100094 China

Water deficit-induced abscisic acid （ABA） accumulation is one of the most important stress signaling pathways in plant cells. Redox regulation of cellular signaling has currently attracted particular attention, but much less is known about its roles and mechanisms in plant signaling. Herein, we report that water deficit-induced ABA accumulation could be regulated by ascorbic acid （AA）-controlled redox status in leave apoplast. The AA content in non-stressed leaves was approximately 3 umol/g FW, corresponding to a mean concentration of 3 mmol/L in a whole cell. Because AA is mainly localized in the cytosol and chloroplasts, the volume of which is much smaller than that of the whole cell, AA content in cytosolic and chloroplast compartments should be much higher than 3 mmol/L. Water deficit-induced ABA accumulation in both leaf and root tissues of maize seedlings was significantly inhibited by AA and reduced glutathione （GSH） at concentrations of 500 umol/L and was completely blocked by 50 mmol/L AA and GSH. These results suggest that the AA-induced inhibition of ABA accumulation should not occur at sites where AA exists in high concentrations. Although water deficit led to a small increase in the dehydroascorbic acid （DHA） content, no significant changes in AA content were observed in either leaf or root tissues. When compared with the whole leaf cell, the AA content in the apoplastic compartment was much lower （i.e. approximately 70 nmol/g FW, corresponding to 0.7 mmol/L）. Water deficit induced a significant decrease （approximately 2.5-fold） in the AA content and an increase （approximately 3.4-fold） in the DHA content in the apoplastic compartment, thus leading to a considerably decreased redox status there, which may have contributed to the relief of AA-induced inhibition of ABA accumulation, alternatively, promoting water deficit-induced ABA accumulation. Reactive oxygen species （ROS） could not mimic water deficit in inducing ABA accumulation, suggesting that the

关键词： abscisic acid (ABA) ascorbic acid (AA) maize (Zea mays) reactive oxygen species waterdeficit.

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Comparative genomics of AA-genome Oryza species provides novel insights into plant speciation

Comparative genomics of AA-genome Oryza species provides nov...

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2016年全国植物生物学大会

作者： li-zhi gao

Comparative and evolutionary genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome ***,we report five de novo-assembled AA-genome sequences for Oryza nivara,***,***,*** and *** analyses reveal massive levels of genomic structural variation,including segmental

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Position of increased signal intensity in the spinal cord on MR images： does it predict the outcome of cervical spondylotic myelopathy？

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Chinese Medical Journal 2009年第12期122卷 1418-1422页

作者： SHEN Hong-xing li ling YANG zhi-gao HOU Tie-sheng Department of Orthopaedics Changhai Hospital Second Military Medical University Shanghai 200433 China

Background Increased signal intensity （ISI） in the spinal cord on T2-weighted MR images has been reported in some previous researches, however no study focused on the position of the ISI in the spinal cord and its potential value. The aim of this study was to investigate the correlation between ISI position and the outcome of surgical treatment for cervical spondylotic myelopathy （CSM） patients. Methods A retrospective study was conducted. Pre- and post-operative clinical status was evaluated by modified Japanese Orthopaedic Association （JOA） score. ISI was evaluated according to the T2-weighted sequences. The JOA score and the recovery ratios among patients with ISI in gray matter （group A）, in both gray and white matter （group B）, and ISI-negative group were compared. Results Totally 64 patients were enrolled in this retrospective study. Preoperative JOA score of ISI positive and negative group had significant difference, but the recovery ratios had no significant difference （the recovery ratios of the two groups in week 1, week 26, and week 104 were （21.54±14.65）%, （50.56±14.76）%, （59.23±13.08）% and （20.25±14.32）%, （54.46±3.16）% and （61.26±29.4）%, respectively; P 〉0.05）. The recovery ratios of negative group and group A in week 104 were superior to group B （the recovery ratios of negative group, group A, and group B in week 104 were （61.26±29.49）%, （65.35±11.36）%, and （50.33±10.20）%, respectively; P 〈0.05）. Conclusions Patients with ISI in the gray matter alone on T2-weighted MR images did not have significantly different surgical outcomes compared with those without ISI. Patients with ISI in both gray and white matter had surgical outcomes that were worse than those without ISI.

关键词： cervical spondylotic myelopathy increased signal intensity Japanese Orthopaedic Association score prognosis recovery ratio

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The Medicinal Herb Panax notoginseng Genome Provides Insights into Ginsenoside Biosynthesis and Genome Evolution

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Molecular Plant 2017年第6期10卷 903-907页

作者： Dan Zhang Wei li En-hua Xia Qun-jie Zhang Yuan liu Yun Zhang Yan Tong Yuan Zhao Yong-chao Niu Jia-huan Xu li-zhi gao Institution of Genomics and Bioinformatics South China Agriculturar University Guangzhou 510642 China Plant Germplasm and Genomics Center Germplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China Agrobiological Gene Research Center Guangdong Academy of Agricultural Sciences Guangzhou 510640 China Yunnan Agricultural University Kunming 650201 China Genosys Inc. Shenzhen 518000 China

Dear Editor Panax notoginseng （Burk） F.H. Chen, belonging to the genus Panax （Araliaceae）, is one of the most highly valued medicinal plants in the world. The dried root of this plant, known as ＂Sanchi＂, is one of the most commonly used traditional Chinese medicines and has been used as a top-class tonic for more than 2000 years.

关键词： Medicinal Herb Panax notoginseng Genome Provides Insights

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Real-world evidence on the efficacy and safety of vonoprazanamoxicillin dual therapy for Helicobacter pylori treatment in elderly patients

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World Journal of Gastroenterology 2025年第1期31卷 68-78页

作者： Wen gao Jing-Wen li Hui Ye Xue-zhi Zhang Jian-Xiang liu Hong Cheng Department of Gastroenterology Peking University First HospitalBeijing 100034China School of Medicine Tsinghua MedicineTsinghua UniversityBeijing 100034China Department of Traditional Chinese Medicine and Integrative Medicine Peking University First HospitalBeijing 100034China

BACKGROUND A dual therapy regimen containing amoxicillin is a common treatment option for the eradication of Helicobacter pylori(***).While substantial research supports the efficacy and safety of vonoprazan and amoxicillin(VA)dual therapy in the general population,there is still a lack of studies specifically focusing on its safety in elderly *** To evaluate efficacy and safety of VA dual therapy as first-line or rescue treatment for *** in elderly *** As a real-world retrospective study,data were collected from elderly patients aged 60 years and above who accepted VA dual therapy(vonoprazan 20 mg twice daily+amoxicillin 1000 mg thrice daily for 14 days)for *** eradication in the Department of Gastroenterology at Peking University First Hospital between June 2020 and January *** status was evaluated by^(13)C-urease breath test 6 weeks after *** adverse events(AEs)during treatment were *** In total,401 cases were ***-one cases were excluded due to loss to follow-up,lack of re-examination,or unwillingness to take *** total of 380 included cases comprised 250 who received VA dual therapy as first-line treatment and 130 who received VA dual therapy as rescue *** was successfully eradicated in 239 cases(95.6%)in the first-line treatment group and 116 cases(89.2%)in the rescue treatment *** overall incidence of AEs was 9.5%for both ***,9.2%of patients experienced an AE in the first-line treatment group and 10.0%in the rescue treatment *** patients discontinued treatment due to AE,with a discontinuation rate of 1.3%.No serious AE *** The VA dual therapy regimen as a first-line treatment and a rescue therapy was effective and safe for elderly patients aged 60 and older.

关键词： Helicobacter pylori Vonoprazan Amoxicillin Dual therapy Elderly

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Hepatocellular apoptosis after hepatectomy in obstructive jaundice in rats

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World Journal of Gastroenterology 2003年第12期9卷 2737-2741页

作者： De-Sheng Wang Ke-Feng Dou Kai-Zong li zhi-Qing gao Zhen-Shun Song Zheng-Cai liu Department of Hepatobiliary Surgery,Xijing Hospital,the Fourth Military Medical University,Xi’an 710032,Shannxi Province,China Department of Hepatobiliary Surgery Xijing Hospital the Fourth Military Medical University Xi'an 710032 Shannxi Province China. wangdesh@***

AIM: To investigate the hepatocellular apoptosis after hepatectomy in obstructive jaundice and biliary decompression ***: After bile duct ligation for 7 days, rats were randomly divided into OB group in which the rats undervvent 70 % hepatectorny, OB-CD group in which the rats underwent hepatectorny accompanied by choledochoduodenostomy, CDHx group in which the rats underwent choledochoduodenostomy and then received 70 % hepatectomy on the fifth day after biliary decompression. The control group (Hx group) only underwent ***: The level of total serum bilirubin and serum enzymes was significantly lower in CD-Hx group than in OB-CD and OB groups on day 1, 3 and 5 after hepatectorny. The apeptotic index was significantly lower in CD-Hx group than in OB-CD and OB groups on day 3 and 5. The oligonucleosomal DNA fragments and Caspase-3 activity were also lower in CD-Hx group than in OB-CD and OB groups 3 days after hepatectorny,without differences between CD-Hx and Hx ***. Hepatocellular apoptosis plays vital roles in jaundice rats, and biliary decompression is more effective in treatment of patients with severe jaundice before operation.

关键词：梗塞性黄疸肝切除术动物实验肝细胞细胞凋亡

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<i>In Situ</i>Conservation of Wild Rice Populations: A Targeted Study of Common Wild Rice <i>Oryza rufipogon</i>from China

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American Journal of Plant Sciences 2012年第7期3卷 854-868页

作者： li-zhi gao Dao-Yuan li Xian-Qiang Wu Wen Chen Zhen-Man Huang Xiao-Mei Wei Guangxi Agricultural School Nanning 530007 China Institute of Crop Germplasm Resources Guangxi Academy of Agricultural Sciences Nanning 530007 China liaozhou Prefecture Institute of Agricultural Sciences Liaozhou 545000 China. Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sci-ences Kunming China Rice Research Institute Hainan Academy of Agriculture Sciences Haikou 570000 China

Although great accomplishments of in situ conservation have been made during the last decade throughout the world, there is an urgent need to conduct more targeted research to explore many basic questions about crop wild relatives (CWR) in situ conservation such as how to better identify and manage the target in situ conservation populations of CWR. In this study, we performed an extensive field investigation of 201 natural populations or habitats of O. rufipogon, a seriously endangered wild progenitor of cultivated rice in China. Our updated information suggests that: 1) the majority of the natural populations have been extinct throughout China, which leads to serious fragmentation of the population system as a whole;and 2) the survived populations have become small in size and thus fragmented within the population as a result of the loss of subpopulations. To assess the relationships between the biodiversity education and conservation of wild rice, we employed participatory approaches in the field investigation. Our data indicate that the continuous rapid decline of biodiversity education seemed closely related to the extinction of wild rice germplasm. These findings imply the potential necessity and huge challenge for making in situ conservation plans in the future. By means of our understanding of ecogeography, sociology and culture, and population genetics of the species, we propose a strategy for selecting in situ conservation locations as well as priority sites for establishing in situ conservation practices in China.

关键词： In Situ Conservation Wild Rice Oryza rufipogon China

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Local magnetic moment oscillation around an Anderson impurity on graphene

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 192-201页

作者： Shuai li Zhen Ma Jin-Hua gao School of Science Hebei University of Science and Technology School of Electronics and Information Zhengzhou University of Light Industry School of Physics and Wuhan National High Magnetic Field Center Huazhong University of Science and Technology

We theoretically investigate the spin resolved Friedel oscillation （FO） and quasiparticle interference （QPI） in graphene induced by an Anderson *** the impurity becomes magnetic,the resulted FO becomes spin dependent,which gives rise to a local magnetic moment oscillation with an envelop decaying as r-2in real space in the doping ***,at half filling,the electron density and local magnetic moment will not oscillate but decay as *** spin resolved FO has both sublattice and spin ***,the local magnetic moment decay at half filling only occurs at one sublattice of graphene,which is quite like the phenomenon observed in the STM experiment (***ález-Herrero et al.,Science 352,437 （2016）).We further give an analytic formula about such spin dependent FO based on the stationary phase ***,we study the interference of quasiparticles around the magnetic impurity by calculating the spin dependent Fourier-transformed local density of states （FT-LDOS）.Our work gives a comprehensive understanding about the local magnetic moment oscillation around an Anderson impurity on graphene.

关键词： Friedel oscillation local magnetic moment graphene Anderson impurity

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