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| 1 | Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Brassica rapa comprises several important cultivated vegetables and oil crops.Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous,thereby limiting extensive genetic and genomic analyses.Here,we report an improved assembly of the B.rapa genome(v3.0)using single-molecule sequencing,optical mapping,and chromosome conformation capture technologies(Hi-C).Relative to the previous reference genomes,our assembly features a contig N50 size of 1.45 Mb,representing a~30-fold improvement.We also identified a new event that occurred in the B.rapa genome~1.2 million years ago,when a long terminal repeat retrotransposon(LTR-RT)expanded.Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B.rapa genome.The B.rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B.rapa.This resource will facilitate breeding efforts in B.rapa,as well as comparative genomic analysis with other Brassica species. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2018 | Horticulture Research2018，5，1： | 10 |
| 2 | Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway显示文摘Taxus,commonly known as yew,is a well-known gymnosperm with great ornamental and medicinal value.In this study,by assembling a chromosome-level genome of the Himalayan yew(Taxus wallichiana)with 10.9 Gb in 12 chromosomes,we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome,resulting in the main genes for paclitaxel biosynthesis,i.e.those encoding the taxadiene synthase,P450s,and transferases,being clustered on the same chromosome.The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization.Furthermore,we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway.The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodi-versity of taxoids in gymnosperms. | Jian Cheng Xiao Wang Xiaonan Liu Xiaoxi Zhu Zihe Li Huanyu Chu Qian Wang QianQian Lou Bijun Cai Yiqun Yang Xiaoyun Lu Kai Peng Dingyu Liu Yuwan Liu Lina Lu Huan Liu Ting Yang Qijin Ge Chengcheng Shi Guichun Liu Zhiwei Dong Xun Xu Wen Wang Huifeng Jiang Yanhe Ma | 2021 | Molecular Plant2021，14，7： | 6 |
| 3 | Brassica rapa Genome 2.0: A Reference Upgrade through Sequence Re-assembly and Gene Re-annotation显示文摘 | Chengcheng Cai Xiaobo Wang Bo Liu Jian Wu Jianli Liang Yinan Cui Feng Cheng Xiaowu Wang | 2017 | Molecular Plant2017，10，4： | 6 |
| 4 | Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage(Brassica rapa)显示文摘Chinese cabbage plants go through seedling and rosette stages before forming their leafy head.Chinese cabbage plants resemble pak-choi plants at their seedling stage,but in their rosette stage the leaves of Chinese cabbage differentiate,as they increase in size with shorter petioles.In order to understand the molecular pathways that play a role in leafy head formation,transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype.The two Chinese cabbages differed in many aspects,among others earliness,leaf size and shape,leaf numbers,and leafy head shape.Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi,from the later developmental stages of both Chinese cabbages(rosette,folding,and heading).Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi.Three clusters included genes with transcript abundance affected by both genotype and developmental stage,whereas two clusters showed only genotype effects.This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis,with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light.The other clusters contained many genes in the MapMan categories Cell,showing again differences between pak-choi and both Chinese cabbages.We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi,especially at the rosette stage.Overall,comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation. | XiaoXue Sun Ram Kumar Basnet Zhichun Yan Johan Bucher Chengcheng Cai Jianjun Zhao Guusje Bonnema | 2019 | Horticulture Research2019，6，1： | 4 |
| 5 | Two-step pyrolysis of ZIF-8 functionalized with ammonium ferric citrate for efficient oxygen reduction reaction显示文摘Zeolitic imidazolate frameworks(ZIFs) are widely employed in catalyst synthesis as parental materials for electrochemical energy storage and conversion. Herein, we have demonstrated a facile synthesis of highly efficient catalyst for oxygen reduction reaction in both alkaline and acidic medium, which is derived from ZIF-8 functionalized with ammonium ferric citrate via two-step pyrolysis in Ar and NH_3 atmosphere.The results reveal that the catalytic activity improvement after NH3 pyrolysis benefits from mesoporedominated morphology and high utilization of Fe-containing active sites. The optimum catalyst shows excellent performance in zinc-air battery and polymer electrolyte membrane fuel cell tests. | Yifan Ye Fan Cai Chengcheng Yan Yanshuo Li Guoxiong Wang Xinhe Bao | 2017 | Journal of Energy Chemistry2017，26，6： | 2 |
| 6 | Author Correction:Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Since the publication of this article,the authors have noticed that the total gene models(45,985),tandem arrays(2077),tandem genes(4963),redundancy removed(43,099),syntenic genes(39,858),nonsyntenic genes(3241),genes on chromosomes(45,411),genes on scaffolds(574)of B.rapa reference genome v3.0 were mistaken in the article. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2019 | Horticulture Research2019，6，1： | 2 |
| 7 | Interlayer gap widened TiS_(2) for highly efficient sodium-ion storage显示文摘As an alternative for lithium-ion batteries(LIBs),sodium-ion batteries(SIBs)have lately received tremendous interest due to their abundant reserves as well as low cost.Nevertheless,the lack of suitable anode materials severely hinders the application of sodium-ion batteries.TiS_(2)is elected as a representative material owing to its unique layered structure.But it always suffers from capacity fade due to poor electrochemical kinetics and structural stability.In this work,we fabricate a pre-potassiated TiS_(2)as a host material for sodium storage by an electrochemical pre-potassiation strategy.The intercalation/extraction mechanism,structural changes and reaction kinetics are completely investigated to reveal the outstanding electrochemical property of pre-potassiated TiS_(2)electrode.It turns out that the large interlayer space of pre-potassiated TiS_(2)is conducive to the diffusion of sodium ions,inducing the reduction of entropic barrier for the electrochemical reactions.In addition,the pre-potassiated host structure is still firmly maintained upon repeated cycles.Therefore,the pre-potassiated TiS_(2)presents superior rate capability(165.9 mA h g^(−1) at 1 C and 132.1 mA h g^(−1) at 20 C)and long-term cycling stability(85.3%capacity retention at 5 C after 500 cycles)for SIBs.This research provides an avenue to construct long-life sodium energy storage systems based on pre-potassiated TiS_(2). | Chengcheng Huang Yiwen Liu Runtian Zheng Zhengwei Yang Zhonghao Miao Junwei Zhang Xinhao Cai Haoxiang Yu Liyuan Zhang Jie Shu | 2022 | Journal of Materials Science & Technology2022，，12： | 1 |
| 8 | Circulating cell-free DNA for cancer early detection显示文摘Effective screening modalities are currently available for only a small subset of cancers,and they generally have suboptimal performance with complicated procedures.Therefore,there is an urgent need to develop simple,accurate,and non-invasive methods for early detection of cancers.Genetic and epigenetic alterations in plasma circulating cell-free DNA(cfDNA)have shown the potential to revolutionize methods of early detection of cancers and facilitate subsequent diagnosis to improve survival of patients.The medical interest in cfDNA assays has been inspired by emerging single-and multi-early detection of cancers studies.This review summarizes current technological and clinical advances,in the hopes of providing insights into the development and applications of cfDNA assays in various cancers and clinical scenarios.The key phases of clinical development of biomarkers are highlighted,and the future developments of cfDNA-based liquid biopsies in early detection of cancers are outlined.It is hoped that this study can boost the potential integration of cfDNA-based early detection of cancers into the current clinical workflow. | Qiang Gao Qiang Zeng Zhijie Wang Chengcheng Li Yu Xu Peng Cui Xin Zhu Huafei Lu Guoqiang Wang Shangli Cai Jie Wang Jia Fan | 2022 | The Innovation2022，3，4： | 1 |
| 9 | Intrinsic magnetic topological materials显示文摘Topological states of matter possess bulk electronic structures categorized by topological invariants and edge/surface states due to the bulk-boundary correspondence. Topological materials hold great potential in the development of dissipationless spintronics, information storage and quantum computation, particularly if combined with magnetic order intrinsically or extrinsically. Here, we review the recent progress in the exploration of intrinsic magnetic topological materials, including but not limited to magnetic topological insulators, magnetic topological metals, and magnetic Weyl semimetals. We pay special attention to their characteristic band features such as the gap of topological surface state, gapped Dirac cone induced by magnetization (either bulk or surface), Weyl nodal point/line and Fermi arc, as well as the exotic transport responses resulting from such band features. We conclude with a brief envision for experimental explorations of new physics or effects by incorporating other orders in intrinsic magnetic topological materials. | Yuan Wang Fayuan Zhang Meng Zeng Hongyi Sun Zhanyang Hao Yongqing Cai Hongtao Rong Chengcheng Zhang Cai Liu Xiaoming Ma Le Wang Shu Guo Junhao Lin Qihang Liu Chang Liu Chaoyu Chen | 2023 | Frontiers of physics2023，18，2： | 0 |
| 10 | On the topological surface states of the intrinsic magnetic topological insulator Mn-Bi-Te family显示文摘We review recent progress in the electronic structure study of intrinsic magnetic topological insulators(MnBi_(2)Te_(4))·(Bi_(2)Te_(3))n(n=0,1,2,3)family.Specifically,we focus on the ubiquitously(nearly)gapless behavior of the topological Dirac surface state observed by photoemission spectroscopy,even though a large Dirac gap is expected because of surface ferromagnetic order.The dichotomy between experiment and theory concerning this gap behavior is perhaps the most critical and puzzling question in this frontier.We discuss various proposals accounting for the lack of magnetic effect on the topological Dirac surface state,which are mainly categorized into two pictures,magnetic reconfiguration and topological surface state redistribution.Band engineering towards opening a magnetic gap of topological surface states provides great opportunities to realize quantized topological transport and axion electrodynamics at higher temperatures. | Yuan Wang Xiao-Ming Ma Zhanyang Hao Yongqing Cai Hongtao Rong Fayuan Zhang Weizhao Chen Chengcheng Zhang Junhao Lin Yue Zhao Chang Liu Qihang Liu Chaoyu Chen | 2024 | National Science Review2024，11，2： | 0 |
| 11 | Seasonal Distribution of Observed Colored Dissolved Organic Matter(CDOM)in the Eastern Indian Ocean显示文摘Colored dissolved organic matter(CDOM)is a crucial constituent that affects the optical absorption properties of seawater.Owing to the relatively limited measured data on the spatial distribution characteristics of CDOM in the tropical eastern Indian Ocean,this study analyzes the optical absorption characteristics of CDOM in the southeast Indian Ocean using the data collected during four seasons from 2013 to 2017.This work also systematically describes the seasonal horizontal and vertical distribution characteristics of CDOM in this area and conducts a preliminary analysis of the relevant factors affecting CDOM absorption characteristics in this region.Results indicate that the CDOM ag(440)during summer was remarkably lower than that in the coastal waters of Europe and coastal waters of China but slightly higher than that in the western and southeast Pacific.The spatial distribution of surface CDOM shows remarkable seasonal differences,and the spatial distribution characteristics of CDOM in the 5°S,92°E region differ between spring/summer and autumn/winter.The values of ag(400)and ag(440)are weak/strong at a surface/subsurface level of 100 m,with differences found between summer and winter.The correlation of CDOM with temperature,salinity,and chlorophyll-a concentration is relatively low,indicating that CDOM is an independent driving mechanism influenced by phytoplankton degradation,photobleaching,and water mixing. | CAI Xiaoqing MENG Jie YUAN Chao LIU Rongjie HOU Erhu BI Dayong LI Yaoru QIAN Chengcheng ZHONG Shan | 2023 | Journal of Ocean University of China2023，22，4： | 0 |
| 12 | StSN2 interacts with the brassinosteroid signaling suppressor StBIN2 to maintain tuber dormancy显示文摘After harvest,potato tubers undergo an important period of dormancy,which significantly impacts potato quality and seed vigor.StSN2 has been reported as a key gene for maintaining tuber dormancy;in this study,we explored the molecular mechanism by which StSN2 maintains dormancy.StBIN2 was first identified as a candidate protein that interacts with StSN2 by co-immunoprecipitation/mass spectrometry,and both qPCR and enzyme activity experiments showed that StSN2 can promote the StBIN2 expression and activity.In addition,the interaction between StSN2 and StBIN2 was verified by yeast two-hybrid,luciferase complementation experiments and co-immunoprecipitation.Bioinformatics analysis and site-directed mutagenesis confirmed the critical role of cysteine residues of StBIN2 in its binding to StSN2.Similar to that of StSN2,overexpression of StBIN2 extended the dormancy of potato tuber.Interaction between StSN2 and StBIN2 increased the activity of the StBIN2 enzyme,inhibited the expression of StBZR1,and suppressed BR signaling.On the contrary,this interaction promoted the expression of StSnRK2.2/2.3/2.4/2.6 and StABI5,key genes of ABA signaling,and the phosphorylation of StSnRK2.3,thereby promoting ABA signaling.Altogether,our results indicate that StSN2 interacts with StBIN2 through key cysteine residues and StBIN2 maintains tuber dormancy by affecting ABA and BR signaling.Findings of this research offer new insights into the molecular mechanism by which StSN2 maintains potato tuber dormancy through interaction with StSIN2 and provide guidance for potato improvement. | Shifeng Liu Chengcheng Cai Luopin Li He Wen Jie Liu Liqin Li Qiang Wang Xiyao Wang | 2023 | Horticulture Research2023，10，12： | 0 |
| 13 | Analysis of Wellbore Flow in Shale Gas Horizontal Wells显示文摘Theflow behavior of shale gas horizontal wells is relatively complex,and this should be regarded as the main reason for which conventional pipeflow models are not suitable to describe the related dynamics.In this study,numerical simulations have been conducted to determine the gas-liquid distribution in these wells.In particular,using the measuredflow pressure data related to 97 groups of shale gas wells as a basis,9 distinct pipeflow models have been assessed,and the models displaying a high calculation accuracy for different water-gas ratio(WGR)ranges have been identified.The results show that:(1)The variation law of WGR in gas well satisfies a power function relation.(2)The well structure is the main factor affecting the gas-liquid distribution in the wellbore.(3)The Beggs&Brill,Hagedorn&Brown and Gray models exhibit a high calculation accuracy. | Linjuan Zeng Daogang Cai Yunhai Zhao Changqing Ye Chengcheng Luo | 2023 | Fluid Dynamics & Materials Processing2023，19，11： | 0 |
| 14 | Effects of enucleation method on in vitro and in vivo development rate of cloned pig embryos显示文摘Enucleation is a crucial procedure for mammalian somatic cell nuclear transfer(SCNT), especially for domestic animal cloning. Oocytes of domestic animals such as pigs and cattle contain dark lipid droplets that hinder localization and removal of the nucleus. Using an oocyte enucleation technique that can obtain a high enucleation rate but has minimal negative effects on the reprogramming potential of oocyte for cloning is bene?cial for enhancing the outcome of SCNT. In this study, we compared the pig cloning ef?ciency resulting from blind aspiration-based(BA-B) enucleation and spindle imaging system-assisted(SIS-A) enucleation, and compared the pig SCNT success rate associated with BA-B enucleation and blind aspiration plus post-enucleation staining-based(BAPPS-B) enucleation. SIS-A enucleation achieved a signi?cantly higher oocyte enucleation success rate and tended to obtain a higher in vivo full term development rate of SCNT embryos than BA-B enucleation. BAPPS-B enucleation also obtained signi?cantly higher in vitro as well as in vivo full term development ef?ciency of cloned porcine embryos than BA-B enucleation. These data indicate that SIS-A and BAPPS-B enucleation are better approaches for pig SCNT than BA-B enucleation. | Chengcheng ZHAO Junsong SHI Rong ZHOU Ranbiao MAI Lvhua LUO Xiaoyan HE Hongmei JI Gengyuan CAI Dewu LIU Enqin ZHENG Zhenfang WU Zicong LI | 2019 | Frontiers of Agricultural Science and Engineering2019，6，1： | 0 |
| 15 | Organic interlayer engineering of TiS_(2) for enhanced aqueous Zn ions storage显示文摘Aqueous rechargeable zinc-ion batteries(ARZIBs)have a bright future for energy storage due to their high energy density and safety.However,for traditional ARZIBs,cathode materials always suffer from the limited space for large-sized zinc ions storage and transport,leading to low Coulombic efficiency and inferior cycling performance.To build a reliable host with large tunnel,1-butyl-1-methylpyrrolidinium ion(PY14^(+))pre-intercalated TiS_(2)(PY14^(+)-TiS_(2))is designed as an alternative intercalation-type electrode.As the insertion organic guest widens the interlayer space of TiS_(2)and buffers the lattice stress generated during the electrochemical cycles,the structural reversibility,cycling stability and kinetics properties of PY14^(+)-TiS_(2) are enhanced greatly.A specific capacity of 130.9 mAh g^(−1) with 84.3%capacity retention over 500 cycles can be achieved at 0.1 A g^(−1).Therefore,this study paves the way for enhancing the aqueous Zn ions storage capability by organic interlayer engineering. | Chengcheng Huang Yiwen Liu Jing Li Zhonghao Miao Xinhao Cai Zhouxiang Wu Haoxiang Yu Lei Yan Liyuan Zhang Jie Shu | 2023 | Journal of Materials Science & Technology2023，，9： | 0 |
| 16 | Integrated Photothermal Nanoreactors for Effi cient Hydrogenation of CO_(2)显示文摘To alleviate the energy crisis and global warming,photothermal catalysis is an attractive way to effi ciently convert CO_(2)and renewable H_(2) into value-added fuels and chemicals.However,the catalytic performance is usually restricted by the trade-off between the dispersity and light absorption property of metal catalysts.Here we demonstrate a simple SiO 2-protected metal-organic framework pyrolysis strategy to fabricate a new type of integrated photothermal nanoreactor with a comparatively high metal loading,dispersity,and stability.The core-satellite structured Co@SiO_(2)exhibits strong sunlight-absorptive abil-ity and excellent catalytic activity in CO_(2)hydrogenation,which is ascribed to the functional separation of diff erent sizes of Co nanoparticles.Large-sized plasmonic Co nanoparticles are mainly responsible for the light absorption and conversion to heat(nanoheaters),whereas small-sized Co nanoparticles with high intrinsic activities are responsible for the catalysis(nanoreactors).This study provides a new concept for designing effi cient photothermal catalytic materials. | Jiahui Shen Rui Tang Zhiyi Wu Xiao Wang Mingyu Chu Mujin Cai Chengcheng Zhang Liang Zhang Kui Yin Le He Chaoran Li | 2022 | Transactions of Tianjin University2022，28，4： | 0 |
| 17 | Combination of effective color information and machine learning for rapid prediction of soil water content显示文摘Soil water content(SWC)is one of the critical indicators in various fields such as geotechnical engineering and agriculture.To avoid the time-consuming,destructive,and laborious drawbacks of conventional SWC measurements,the image-based SWC prediction is considered based on recent advances in quantitative soil color analysis.In this study,a promising method based on the Gaussian-fitting gray histogram is proposed for extracting characteristic parameters by analyzing soil images,aiming to alleviate the interference of complex surface conditions with color information extraction.In addition,an identity matrix consisting of 32 characteristic parameters from eight color spaces is constituted to describe the multi-dimensional information of the soil images.Meanwhile,a subset of 10 parameters is identified through three variable analytical methods.Then,four machine learning models for SWC prediction based on partial least squares regression(PLSR),random forest(RF),support vector machines regression(SVMR),and Gaussian process regression(GPR),are established using 32 and 10 characteristic parameters,and their performance is compared.The results show that the characteristic parameters obtained by Gaussian-fitting can effectively reduce the interference from soil surface conditions.The RGB,CIEXYZ,and CIELCH color spaces and lightness parameters,as the inputs,are more suitable for the SWC prediction models.Furthermore,it is found that 10 parameters could also serve as optimal and generalizable predictors without considerably reducing prediction accuracy,and the GPR model has the best prediction performance(R^(2)≥0.95,RMSE≤2.01%,RPD≥4.95,and RPIQ≥6.37).The proposed image-based SWC predictive models combined with effective color information and machine learning can achieve a transient and highly precise SWC prediction,providing valuable insights for mapping soil moisture fields. | Guanshi Liu Shengkui Tian Guofang Xu Chengcheng Zhang Mingxuan Cai | 2023 | Journal of Rock Mechanics and Geotechnical Engineering2023，15，9： | 0 |
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