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| 1 | The willow genome and divergent evolution from poplar after the common genome duplication显示文摘 | Xiaogang Dai Quanjun Hu Qingle Cai Kai Feng Ning Ye Gerald A Tuskan Richard Milne Yingnan Chen Zhibing Wan Zefu Wang Wenchun Luo Kun Wang Dongshi Wan Mingxiu Wang Jun Wang Jianquan Liu Tongming Yin | 2014 | Cell Research2014，24，10： | 28 |
| 2 | Organellar genome assembly methods and comparative analysis of horticultural plants显示文摘Although organellar genomes(including chloroplast and mitochondrial genomes)are smaller than nuclear genomes in size and gene number,organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms.Few studies have focused on the organellar genomes of horticultural plants.Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information(NCBI),of which only 39 are from horticultural plants.In this paper,we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing(NGS)data.Sequencing reads were first assembled by Newbler,Amos,and Minimus software with default parameters.The remaining gaps were then filled through BLASTN search and PCR.The complete DNA sequence was corrected based on Illumina sequencing data using BWA(Burrows–Wheeler Alignment tool)software.The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation.Using this procedure,the complete mitochondrial and chloroplast genomes of an ornamental plant,Salix suchowensis,and a fruit tree,Ziziphus jujuba,were identified.This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants.Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome.In addition,a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA.Our study will provide an important reference for organellar genome assembly in other horticultural plants.Furthermore,phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants. | Xuelin Wang Feng Cheng Dekai Rohlsen Changwei Bi Chunyan Wang Yiqing Xu Suyun Wei Qiaolin Ye Tongming Yin Ning Ye | 2018 | Horticulture Research2018，5，1： | 4 |
| 3 | Status of the IHEP 1.3 GHz superconducting RF program显示文摘The 1.3 GHz superconducting radio-frequency (SRF) technology is one of the key technologies for the ILC and future XFEL and ERL projects in China. With the aim to develop 1.3 GHz SRF technology, IHEP has started a program to build an SRF Accelerating Unit. This unit contains a 9-cell 1.3 GHz superconducting cavity, a short cryomodule, a high power input coupler, a tuner and a low level RF system. This program also includes the SRF laboratory upgrade, which will permit the unit to be built and tested at IHEP. The unit will be used for the 1.3 GHz SRF system integration study, high power horizontal test and possible beam test in the future. In this paper, we report the recent R&D status of this program. The first large grain low-loss shape 9-cell superconducting RF cavity made by IHEP reached 20 MV/m in the first vertical test in July, 2010. The prototype tuner and low level RF (LLRF) system are under test. The high power input coupler and cryomodule are under fabrication. Several key SRF facilities for 9-cell cavity surface treatment and pre-tuning were successfully commissioned and are in operation. | GAO Jie ZHAI JiYuan PAN WeiMing LI ShaoPeng SUN Yi DAI JianPing CHI YunLong LI ZhongQuan ZHAO TongXian HUANG TongMing MA Qiang GE Rui LI ChunHua GUO HaiSheng WANG GuangWei QIU Feng LIN HaiYing HOU Mi WANG QunYao | 2011 | Science China(Physics,Mechanics & Astronomy)2011，54，S2： | 1 |
| 4 | Photo-catalytic Staphylococcus aureus inactivation and biofilm destruction with novel bis-tridentate iridium(Ⅲ) photocatalyst显示文摘Bacterial infection is currently a serious challenge globally, causing death of thousands of human beings. New antimicrobial agents with novel mechanism of action are urgently needed. Transition metal complexes have shown great potentials in photodynamic and photocatalytic therapy. Herein, we take full advantage of metal photocatalyst and successfully developed a novel cyclometalated iridium(Ⅲ) complex(Ir1) with higher biofilm damage efficiency than the clinical antibiotics. Ir1 synergistically generates reactive oxygen species and coenzyme photocatalytic activity with high efficiency under white light irradiation. Combined with these properties, Ir1 exhibited excellent photoinactivation of S. aureus and effectively damaged the biofilm. This work provides a new approach for the development of antibacterial photodynamic therapy. | Shihao Chen Zhishang Zhang Li Wei Zhongxian Fan Yue Li Xuezhi Wang Tongming Feng Huaiyi Huang | 2023 | Chinese Chemical Letters2023，34，11： | 0 |
| 5 | Experimental study on workability and permeability of sandy soils conditioned with thickened foam显示文摘Water spewing and muck plugging often occur during earth pressure balance(EPB)shield machines tunnelling in water-rich sandy strata,even though the conventional foam has been employed to condition sandy soils.In this study,a novel thickened foaming agent suitable for EPB shield tunnelling in water-rich sandy strata is developed.In contrast to conventional foam-conditioned sands,the thickened foam-conditioned sand has a low permeability due to the consistent filling of soil pores with the thickened foam,and the initial permeability coefficient decreases by approximately two orders of magnitude.It also exhibits a suitable workability,which is attributed to the enhanced capability of the thickened foam to condition sandy soils.In addition,the effect of concentration on the stability of the foam is explained by the Gibbs-Marangoni effect,and conditioning mechanisms for the thickened foam on sands are discussed from the evolution of foam bubbles. | Zhiyao Feng Shuying Wang Tongming Qu Xiangcou Zheng Fanlin Ling | 2024 | Journal of Rock Mechanics and Geotechnical Engineering2024，16，2： | 0 |
| 6 | Applicability of discrete element method with spherical and clumped particles for constitutive study of granular materials显示文摘Discrete element method(DEM)has been intensively used to study the constitutive behaviour of granular materials.However,to what extent a real granular material can be reproduced by virtual DEM simulations remains unclear.This study attempts to answer this question by comparing DEM simulations with typical features of experimental granular materials.Three groups of models with spherical and clumped particles are investigated from four perspectives:(i)deviatoric stress and volumetric behaviour;(ii)critical state behaviour;(iii)stress-dilatancy relationship;and(iv)the evolution of principal stress ratio against axial strain.The results demonstrate that DEM with spherical or clumped particles is capable of qualitatively describing macroscopic deviatoric stress responses,volumetric behaviour,and critical state behaviour observed in experiments for granular materials.On the other hand,some qualitative deviations between experiments and the investigated DEM simulations are also observed,in terms of the stress-dilatancy behaviour and principal stress ratio against axial strain,which are proven to be critical for constitutive modelling.The results demonstrate that DEM with spherical or clumped particles may not necessarily fully capture experimental features of granular materials even from a qualitative perspective.It is thus encouraged to thoroughly validate DEM with experiments when developing constitutive models based on DEM observations. | Tongming Qu Min Wang Yuntian Feng | 2022 | Journal of Rock Mechanics and Geotechnical Engineering2022，14，1： | 0 |
| 7 | The Metasequoia genome and evolutionary relationships among redwoods显示文摘Redwood trees(Sequoioideae),including Metasequoia glyptostroboides(dawn redwood),Sequoiadendron giganteum(giant sequoia),and Sequoia sempervirens(coast redwood),are threatened and widely recognized iconic tree species.Genomic resources for redwood trees could provide clues to their evolutionary relationships.Here,we report the 8-Gb reference genome of M.glyptostroboides and a comparative analysis with two related species.More than 62%of the M.glyptostroboides genome is composed of repetitive sequences.Clade-specific bursts of long terminal repeat retrotransposons may have contributed to genomic differentiation in the three species.The chromosomal synteny between M.glyptostroboides and S.giganteum is extremely high,whereas there has been significant chromosome reorganization in S.sempervirens.Phylogenetic analysis of marker genes indicates that S.sempervirens is an autopolyploid,and more than 48%of the gene trees are incongruent with the species tree.Results of multiple analyses suggest that incomplete lineage sorting(ILS)rather than hybridization explains the inconsistent phylogeny,indicating that genetic variation among redwoods may be due to random retention of polymorphisms in ancestral populations.Functional analysis of ortholog groups indicates that gene families of ion channels,tannin biosynthesis enzymes,and transcription factors for meristem maintenance have expanded in S.giganteum and S.sempervirens,which is consistent with their extreme height.As a wetland-tolerant species,M.glyptostroboides shows a transcriptional response to flooding stress that is conserved with that of analyzed angiosperm species.Our study offers insights into redwood evolution and adaptation and provides genomic resources to aid in their conservation and management. | Fangfang Fu Chi Song Chengjin Wen Lulu Yang Ying Guo Xiaoming Yang Ziqiang Shu Xiaodong Li Yangfan Feng Bingshuang Liu Mingsheng Sun Yinxiao Zhong Li Chen Yan Niu Jie Chen Guibin Wang Tongming Yin Shilin Chen Liangjiao Xue Fuliang Cao | 2023 | Plant Communications2023，4，6： | 0 |
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