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Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

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Journal of Integrative Plant Biology 2022年第3期64卷 649-670页

作者： Yushan Zheng Deming Yang Jundong Rong Liguang Chen Qiang Zhu Tianyou He Lingyan Chen Jing Ye Lili Fan yubang gao Hangxiao Zhang Lianfeng Gu College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied PlantSystems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot *** genetic transformation and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing techniques are available for ***,enabling reverse genetic ***,*** has the potential to be a model bamboo ***,the genome sequence of *** has remained unreported due to its polyploidy and large genome ***,we sequenced the *** genome and assembled it into three allele-aware subgenomes(AABBCC),representingthe largest genome of a major bamboo *** assembled 70 allelic chromosomes(2,737 Mb)for hexaploid *** using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation capture sequencing(Hi-C).Repetitive sequences comprised 52.65%of the *** *** annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different *** sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing revealed highly differential alternative splicing(AS)between non-abortive and abortive shoots,suggesting that AS regulates the abortion rate of bamboo *** high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using *** as a model species.

关键词： alternative splicing bamboo shoots chromosome conformation capture sequencing D.latiflorus genome assembly single-molecular sequencing

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Genome-wide profiling of circular RNAs,alternative splicing,and R-loops in stem-differentiating xylem of Populus trichocarpa

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Journal of Integrative Plant Biology 2021年第7期63卷 1294-1308页

作者： Xuqing Liu yubang gao Jiakai Liao Miao Miao Kai Chen Feihu Xi Wentao Wei Huihui Wang Yongsheng Wang XiXu Anireddy S.N.Reddy Lianfeng Gu Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China Basic Forestry and Proteomics Research Center College of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology and Program in Cell and Molecular Biology Colorado State UniversityFort CollinsColorado 80523USA

Circular RNAs(circRNAs)are a recently dis-covered type of non‐coding RNA derived from pre‐mRNAs.R‐loops consist of a DNA:RNA hybrid andthe associated single‐stranded ***-dopsis thaliana,circRNA:DNA R‐loops regulatealternative splicing(AS)ofSEPALLATA3(SEP3).However,the occurrence and functions ofcircRNAs and R‐loops inPopulus trichocarpaarelargely ***,we performed circRNA‐enriched sequencing in the stem‐differentiatingxylem(SDX)*** identified 2,742distinct circRNAs,including circ‐CESA4,circ‐IRX7,and circ‐GUX1,which are generated from genesinvolved in cellulose,and hemicellulose biosyn-thesis,*** investigate the roles ofcircRNAs in modulating alternative splicing(AS),we detected 7,836 AS events using PacBio Iso‐Seq and identified 634 circRNAs that overlappedwith 699 AS ***,using DNA:RNAhybrid immunoprecipitation followed by se-quencing(DRIP‐seq),we identified 8,932 R‐looppeaks that overlapped with 181 circRNAs and 672AS ***,several SDX‐related circRNAsoverlapped with R‐loop peaks,pointing to theirpossible roles in modulating AS in ***,overexpressing circ‐IRX7increased the levels ofR‐loop structures and decreased the frequency ofintron retention in *** provides a valuable R‐loop atlas resourceand uncovers the interplay between circRNAs andAS in SDX ***.

关键词： alternative splicing circular RNA R‐loop Populustrichocarpa stem‐differentiating xylem

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Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo(Phyllostachys edulis)

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Genomics, Proteomics & Bioinformatics 2023年第4期21卷 866-885页

作者： Yongsheng Wang Huihui Wang Huiyuan Wang Ruifan Zhou Ji Wu Zekun Zhang Yandong Jin Tao Li Markus V.Kohnen Xuqing Liu Wentao Wei Kai Chen yubang gao Jiazhi Ding Hangxiao Zhang Bo Liu Chentao Lin Lianfeng Gu Basic Forestry and Proteomics Research Center College of ForestryFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China College of Forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Molecular Cell and Developmental BiologyUniversity of California at Los AngelesLos AngelesCA 90095USA

Circular RNAs(circRNAs)are endogenous non-coding RNAs with covalently closed structures,which have important functions in ***,their biogenesis,degradation,and function upon treatment with gibberellins(GAs)and auxins(1-naphthaleneacetic acid,NAA)remain ***,we systematically identified and characterized the expression patterns,evolutionary conservation,genomic features,and internal structures of circRNAs using RNase R-treated libraries from moso bamboo(Phyllostachys edulis)***,we investigated the biogenesis of circRNAs dependent on both cis-and *** explored the function of circRNAs,including their roles in regulating microRNA(miRNA)-related genes and modulating the alternative splicing of their linear ***,we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of ***,we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and ***,our study provides insights into the biogenesis,function,and miRNA-mediated degradation of circRNAs in moso bamboo.

关键词： Alternative splicing Circular RNA Degradome Phyllostachys edulis Phytohormone

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陕南低山区排土场水土保持防洪排导措施配置模式

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中国水土保持 2023年第11期 50-52页

作者：靳宇蓉王琦高羽邦陕西环保集团生态建设管理有限公司陕西西安710043 北京新桥技术发展有限公司北京100088

为提出陕南低山区排土场防洪排导措施较为理想的配置模式,以陕西省镇安县东阳钨矿直沟排土场为例,应用汇水面积相关法和综合参数法分别对直沟排土场进行了水文计算,再根据计算结果对直沟排土场设计了三种不同的防洪排导措施配置方案,从... 详细信息

为提出陕南低山区排土场防洪排导措施较为理想的配置模式,以陕西省镇安县东阳钨矿直沟排土场为例,应用汇水面积相关法和综合参数法分别对直沟排土场进行了水文计算,再根据计算结果对直沟排土场设计了三种不同的防洪排导措施配置方案,从造价、优缺点及施工难易程度等方面对三种方案进行了比选,结果表明:(1)直沟流域内通过汇水面积相关法计算的洪峰流量大于通过综合参数法计算的;(2)直沟排土场配套的防洪建筑物种类越多,施工越复杂,造价越高,其配套的排洪沟尺寸虽小,但渣场安全性高;(3)实际工程应用中,应选取较大的洪峰流量作为设计标准,防洪排导设施采用上游拦洪溢流坝+场内截排水沟+下游拦渣坝+出口处消力池模式,不仅能确保排土场稳定安全,而且造价适中,可在陕南低山区排土场工程中推广应用。

关键词：排土场水土保持防洪排导水文计算措施配置陕南低山区

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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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环状RNA的产生、研究方法及功能

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遗传 2019年第6期41卷 469-485页

作者：刘旭庆高宇帮赵良真蔡宇晨王汇源苗苗顾连峰张航晓福建农林大学林学院基础林学与蛋白质组学中心福州350002 福建农林大学生命科学学院福州350002

随着高通量测序技术的发展,环状RNA(circular RNAs,circRNAs)逐渐成为非编码RNA研究领域的热点。本文系统综述了环状RNA侧翼内含子自身互补配对驱动、RNA结合蛋白驱动以及套索驱动这3种环状RNA形成模型,并从高通量文库构建、生物信息学... 详细信息

随着高通量测序技术的发展,环状RNA(circular RNAs,circRNAs)逐渐成为非编码RNA研究领域的热点。本文系统综述了环状RNA侧翼内含子自身互补配对驱动、RNA结合蛋白驱动以及套索驱动这3种环状RNA形成模型,并从高通量文库构建、生物信息学鉴别和常用的实验验证等3个方面对环状RNA的研究方法进行了介绍。同时,本文详细归纳了环状RNA作为microRNA(miRNA)或蛋白的海绵体、调控宿主基因的选择性剪接和表达、翻译成多肽等多种功能。最后通过系统综述植物环状RNA的特征及最新研究进展,为环状RNA在植物学中的进一步研究提供了新的视野。

关键词：环状RNA 反向剪接选择性剪接海绵体

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Investigating Müller glia reprogramming in mice: a retrospective of the last decade, and a look to the future

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Neural Regeneration Research 2025年第4期20卷 946-959页

作者： Zhiyuan Yin Jiahui Kang Xuan Cheng Hui gao Shujia Huo Haiwei Xu Key Lab of Visual Damage and Regeneration&Restoration of Chongqing Southwest Eye HospitalSouthwest HospitalThird Military Medical University(Army Medical University)ChongqingChina

Müller glia,as prominent glial cells within the retina,plays a significant role in maintaining retinal homeostasis in both healthy and diseased *** lower vertebrates like zebrafish,these cells assume responsibility for spontaneous retinal regeneration,wherein endogenous Müller glia undergo proliferation,transform into Müller glia-derived progenitor cells,and subsequently regenerate the entire retina with restored ***,Müller glia in the mouse and human retina exhibit limited neural reprogramming.Müller glia reprogramming is thus a promising strategy for treating neurodegenerative ocular disorders.Müller glia reprogramming in mice has been accomplished with remarkable success,through various *** in molecular,genetic,epigenetic,morphological,and physiological evaluations have made it easier to document and investigate the Müller glia programming process in ***,there remain issues that hinder improving reprogramming efficiency and ***,understanding the reprogramming mechanism is crucial toward exploring factors that will improve Müller glia reprogramming efficiency,and for developing novel Müller glia reprogramming *** review describes recent progress in relatively successful Müller glia reprogramming *** also provides a basis for developing new Müller glia reprogramming strategies in mice,including epigenetic remodeling,metabolic modulation,immune regulation,chemical small-molecules regulation,extracellular matrix remodeling,and cell-cell fusion,to achieve Müller glia reprogramming in mice.

关键词： cell fusion chemical small-molecules epigenetic extracellular matrix immune metabolic mice Müller glia neurodegenerative diseases reprogramming retina regeneration

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Observation of acoustic hybrid topological phases induced by the p-d orbital interactions

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 132-139页

作者： Xiao Xiang Feng gao Yu-Gui Peng Peng Wu Zong-Lin Li Xue-Feng Zhu School of Physics and Innovation Institute Huazhong University of Science and Technology

In spinless systems,growing attention has recently been attracted to synthetic gauge fields,which redefine the fundamental crystal symmetries by utilizing the projective algebraic ***,synthetic gauge fields have been commonly investigated in single orbital systems,and explorations on hybrid orbitals remain elusive in ***,we report the experimental observation of hybrid topological phases induced by hybrid synthetic gauge flux,which is formed by the interaction between p and d orbitals embedded in acoustic *** breaking the translation symmetries of Lxand/or Ly,we unambiguously demonstrate the first-order M?bius edge states and higher-order corner *** work establishes a platform for seeking exotic topological phases induced by hybrid-orbitals interactions and initializing the framework of hybrid-orbitalsrelated topological *** applications can be anticipated in scenarios such as high-quality sensing and robust wave trapping due to the stepwise energy distribution of the hybrid topological phase.

关键词： topological insulator synthetic gauge field projective symmetry corner states

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A mild, configurable, flexible CoNi-LDH（v）/Zn battery based on H-vacancy-induced reversible Zn2+ intercalation

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Journal of Energy Chemistry 2025年第1期100卷 498-508页

作者： Xinyue Cheng Dingsheng Wu Hao gao Qingqing Wang Pengfei Lv Sam S.Yoon Qufu Wei Key Laboratory of Eco-textiles Ministry of Education Jiangnan University School of Mechanical Engineering Korea University

Flexible Zn-based batteries have attracted increasing research interest as essential components of wearable energy storage ***,the advancement of flexible aqueous Zn-based batteries based on Co-Ni layered double hydroxide （CoNi-LDH） as the cathode material is hampered by their poor cycling stability and the corrosiveness of alkaline ***,CoNi-LDH nanosheets enriched with H vacancies (CoNi-LDH（v）) were constructed on a flexible carbon cloth （CC） substrate via electrochemical deposition and *** Zn-based battery comprising CoNi-LDH（v）@CC as the cathode exhibited highly reversible conversion reactions and stable operation in 3 M ZnSO4electrolyte （pH=4）.The battery delivered an excellent specific capacity (225 mA h g-1,0.26 mA h cm-2),acceptable cycling stability（53.9%,900 cycles）,and high discharging *** abundant H vacancies served as active sites for the reversible intercalation of Zn2+and the extravasation of NO3-generated channels and space for Zn2+transport and storage,together enabling an excellent Zn2+storage ***,a sandwich-structured solid-state CoNi-LDH（v）@CC//Zn@CC battery was fabricated and was found to exhibit a noteworthy electrochemical performance and mechanical *** a proof of concept,the unencapsulated battery powered a digital watch under various deformation conditions and operated stably for 80 ***,the flexible battery displayed outstanding customizability,maintaining an open-circuit voltage of 1.42 V even after being cut *** proposed engineering strategy contributes to the realization of textiles with truly wearable energy-storage devices.

关键词： CoNi/Zn battery H vacancies Mild aqueous electrolyte Tailorable battery Wearable energy storage device

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Low-cost and fluoride-free synthesis of MFI zeolite nanosheets with enhanced stability for benzene alkylation with ethanol

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Journal of Energy Chemistry 2025年第1期100卷 458-468页

作者： Peng Zhu Cun Liu Yiren Yu Guoshu gao Yumeng Zhao Xiongfu Zhang Guodong Liu Guohui Yang State Key Laboratory of Fine Chemicals School of Chemical Engineering Dalian University of Technology State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences

Zeolite nanosheets with a short b-axis thickness are highly desirable in lots of catalytic reactions due to their reduced diffusion resistance. Nevertheless, conventional synthesis methods usually require expensive structure-directing agents(SDAs), pricey raw materials, and eco-unfriendly fluorine-containing additives. Here, we contributed a cost-effective and fluoride-free synthesis method for synthesizing high-quality MFI zeolite nanosheets through a Silicalite-1(Sil-1) seed suspension and urea cooperative strategy, only with inexpensive colloidal silica as the Si source. Our approach was effective for synthesizing both Sil-1 and aluminum-containing ZSM-5 nanosheets. By optimizing key synthesis parameters,including seed aging time, seed quantity, and urea concentration, we achieved precise control over the crystal face aspect ratio and b-axis thickness. We also revealed a non-classical oriented nanosheet growth mechanism, where Sil-1 seeds induced the formation of quasi-ordered precursor particles, and the(010)crystal planes of these particles facilitated urea adsorption, thereby promoting c-axis-oriented *** obtained ZSM-5 nanosheets exhibited exceptional catalytic performance in the benzene alkylation with ethanol, maintaining stability for over 500 h, which is 5 times longer than traditional ZSM-5 catalysts. Furthermore, large-scale production of ZSM-5 nanosheets was successfully carried out in a 3 L highpressure autoclave, yielding samples consistent with those from laboratory-scale synthesis. This work marks a significant step forward in the sustainable and efficient production of MFI nanosheets using inexpensive and environmentally friendly raw materials, offering the broad applicability in catalysis.

关键词： MFI zeolite ZSM-5 Nanosheets Scale-up synthesis Aromatic alkylation

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