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| 1 | WGDI:A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes显示文摘Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(http://gffzz188fe103f8f1460askk0f9nxf9cbq6ofc.ffgz.tsg.suse.edu.cn/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots. | Pengchuan Sun Beibei Jiao Yongzhi Yang Lanxing Shan Ting Li Xiaonan Li Zhenxiang Xi Xiyin Wang Jianquan Liu | 2022 | Molecular Plant2022，15，12： | 5 |
| 2 | Characteristics and risk assessment of agricultural meteorological disasters based on 30 years’disaster data from Heilongjiang Province of China显示文摘To determine the influence of agricultural meteorological disasters on agriculture in Heilongjiang Province,the disaster areas associated with different types of disasters and their variation characteristics were analyzed based on the statistical data of agricultural disasters from 1983 to 2013 in Heilongjiang Province,China.The moving average and the Mann-Kendall test were applied to identify the variation trends of drought,flooding,hailstorms and freezing(based on the disaster ratio and the disaster intensity index).Then,the Morlet wavelet analysis method was used to identify the periodicity of these four kinds of agricultural meteorological disasters.Finally,a fuzzy comprehensive evaluation method was adopted to analyze the degrees of agricultural loss induced by these disasters.The following results were obtained:1)The disaster ratio and disaster intensity index for drought exhibited increasing trends;the disaster ratio and disaster intensity index for flooding exhibited decreasing trends;for hailstorms,the disaster ratio exhibited no obvious trend of change,whereas the disaster intensity index exhibited an increasing trend;and for freezing,the disaster ratio also exhibited no obvious trend of change,whereas the disaster intensity index exhibited a decreasing trend.2)Mutation points were observed in the disaster ratio series for drought,flooding and hailstorms,whereas no mutation point was evident in the disaster ratio series for freezing.3)Multiple time-scale characteristics were observed in the disaster ratio series for all four types of agricultural meteorological disasters.Furthermore,the disaster ratio series for the different types of disasters had different main periodicities.4)From the perspective of the degree of agricultural loss induced by each type of disaster,drought was identified as the most severe type of agricultural meteorological disaster,followed by flooding,freezing,and hailstorms.The degree of agricultural loss caused by each type of disaster was different during different periods.Finally,based on the results,several strategies were identified for mitigating the effect of agricultural meteorological disasters in Heilongjiang Province. | Xing Zhenxiang Yang Zhaorui Fu Qiang Li Heng Gong Xinglong Wu Jingyan | 2017 | International Journal of Agricultural and Biological Engineering2017，10，6： | 4 |
| 3 | Targeted Gene Manipulation in Plants Using the CRISPR/Cas Technology显示文摘The CRISPR/Cas technology is emerging as a revolutionary genome editing tool in diverse organisms including plants,and has quickly evolved into a suite of versatile tools for sequence-specific gene manipulations beyond genome editing.Here,we review the most recent applications of the CRISPR/Cas toolkit in plants and also discuss key factors for improving CRISPR/Cas performance and strategies for reducing the off-target effects.Novel technical breakthroughs in mammalian research regarding the CRISPR/Cas toolkit will also be incorporated into this review in hope to stimulate prospective users from the plant research community to fully explore the potential of these technologies. | Dandan Zhang Zhenxiang Li Jian-Feng Li | 2016 | Journal of Genetics and Genomics2016，43，5： | 3 |
| 4 | QTL analysis across multiple environments reveals promising chromosome regions associated with yield-related traits in maize under drought conditions显示文摘Drought is one of the most critical abiotic stresses influencing maize yield. Improving maize cultivars with drought tolerance using marker-assisted selection requires a better understanding of its genetic basis. In this study, a doubled haploid(DH) population consisting of 217 lines was created by crossing the inbred lines Han 21(drought-tolerant) and Ye 478(drought-sensitive). The population was genotyped with a 6 K SNP assay and 756 SNP(single nucleotide polymorphism) markers were used to construct a linkage map with a length of 1344 c M. Grain yield(GY), ear setting percentage(ESP), and anthesis–silking interval(ASI) were recorded in seven environments under well-watered(WW) and water-stressed(WS) regimes. High phenotypic variation was observed for all traits under both water regimes. Using the LSMEAN(least-squares mean) values from all environments for each trait, 18 QTL were detected, with 9 associated with the WW and 9 with the WS regime. Four chromosome regions,Chr. 3: 219.8–223.7 Mb, Chr. 5: 191.5–194.7 Mb, Chr. 7: 132.2–135.6 Mb, and Chr. 10: 88.2–89.4 Mb, harbored at least 2 QTL in each region, and QTL co-located in a region inherited favorable alleles from the same parent. A set of 64 drought-tolerant BC_3F_6 lines showed preferential accumulation of the favorable alleles in these four regions, supporting an association between the four regions and maize drought tolerance. QTL-by-environment interaction analysis revealed 28 ed QTL(environment-dependent QTL) associated with the WS regime and 22 associated with the WW regime for GY, ESP, and ASI. All WS QTL and55.6% of WW QTL were located in the ed QTL regions. The hotspot genomic regions identified in this work will support further fine mapping and marker-assisted breeding of drought-tolerant maize. | Xinmin Hu Guihua Wang Xuemei Du Hongwei Zhang Zhenxiang Xu Jie Wang Guo Chen Bo Wang Xuhui Li Xunji Chen Junjie Fu Jun Zheng Jianhua Wang Riliang Gu Guoying Wang | 2021 | The Crop Journal2021，9，4： | 3 |
| 5 | Effects of surface roughness on interfacial dynamic recrystallization and mechanical properties of Ti-6Al-3Nb-2Zr-1Mo alloy joints produced by hot-compression bonding显示文摘The influence of surface roughness on the interfacial dynamic recrystallization kinetics and mechanical properties of Ti-6 Al-3 Nb-2 Zr-1 Mo hot-compression bonding joints was systematically investigated.It is found that for the bonding interface of rough surfaces,elongated fine grains are formed at the bonding interface due to shear deformation of the interfacial area.As the surface roughness increases,the proportion of elongated grains drastically decreases as they further reorient to form equiaxed grains along the bonding interface of rougher surfaces resulting from severe incompatible deformation of the interface area.Meanwhile,high-density geometrically necessary dislocations accumulate around the interfacial recrystallization area to accommodate the incompatible strain and lattice rotation.A rotational dynamic recrystallization mechanism is thereby proposed to rationalize the formation of fine interfacial recrystallization grains during bonding of rough surfaces.In contrast to that of rough surfaces,bonding interface of polished surfaces exists in the form of straight interface grain boundaries without fine grains under the same deformation conditions.While with the increase of deformation strain,small grain nuclei form along the bonding interface,which is associated with discontinuous dynamic recrystallization assisted by strain-induced boundary migration of interface grain boundaries.Moreover,the bonding joints of rough surfaces show lower elongation compared with that of polished surfaces.This is because the formation of heterogeneous fine grains with low Schmid factor along the bonding interface of rough surfaces,leading to worse compatible deformation capability and thereby poor ductility of bonding joints. | Bijun Xie Zhenxiang Yu Haiyang Jiang Bin Xu Chunyang Wang Jianyang Zhang Mingyue Sun Dianzhong Li Yiyi Li | 2022 | Journal of Materials Science & Technology2022，，1： | 2 |
| 6 | Hyperbaric oxygen therapy for skin flap blood flow disorder: a case report显示文摘A female patient at the age of 17 received dilator implant on the right part of her face to prepare skin flap for her facial scar.The skin flap was in good conditions before scar cutting,but showed poor blood circulation after being transferred.Hyperbaric oxygen therapy was given at 0.2 MPa(2ATA) in double pure oxygen cabins for 90 min every day for 10 d.The skin flap showed in sound viability and sound blood circulation after the treatment.Hyperbaric oxygen therapy can be used to treat blood circulation disorder in transferred skin flap. | Chen Liang Wang Liang Wang Zhenxiang Guan Qing Li Shirong | 2012 | Journal of Medical Colleges of PLA(China)2012，27，3： | 2 |
| 7 | User Association and Wireless Backhaul Bandwidth Allocation for 5G Heterogeneous Networks in the Millimeter-Wave Band显示文摘The user association and wireless backhaul bandwidth allocation for a two-tier heterogeneous network(Het Net) in the millimeter wave(mm Wave) band is proposed in this article. The two-tier Het Net is built up with a macro base station(MBS) and several small cell SBSs, where the MBS is assumed to be equipped with large-scale antenna arrays but the SBSs only have single-antenna capability and they rely on the wireless link to the MBS for backhaul. The sum of logarithmic user rate, which is established according to the result of multi-user Multiple Input Multiple Output(MIMO) downlink employing Zero-Force Beamforming(ZFBF), is chosen as the network utility for the objective function. And a distributed optimization algorithm based on primal and dual decomposition is used to jointly optimize the user association variable xj,i and the wireless backhaul bandwidth factor β. Simulation results reveal that the distributed optimization algorithm jointly optimizing two variables outperforms the conventional SINR-based user association strategies. | zhenxiang su bo ai yichuan lin danping he ke guan ning wang guoyu ma li niu | 2018 | China Communications2018，15，4： | 2 |
| 8 | A novel RNA-guided RNA-targeting CRISPR tool显示文摘Clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)technology has emerged as a programmable RNA-guided DNA-targeting tool for sequence-specific genome editing in diverse organisms.The most frequently used CRISPR/Cas system。 | Dandan Zhang Zhenxiang Li Bingyu Yan Jian-Feng Li | 2016 | Science China(Life Sciences)2016，59，8： | 2 |
| 9 | New cytosine base editor for plant genome editing显示文摘A large number of beneficial agronomic traits in crops are associated with single nucleotide polymorphisms(SNPs)or point mutations(Jiao et al.,2010;Li et al.,2017;Ma et al.,2015).In the past,site-specific point mutations in a target gene can only be achieved through the CRISPR/Cas9 mediated gene replacement via the homology-directed repair(HDR).However,the intrinsically low HDR activity in plant cells and the lack of efficient way to supply abundant HDR templates in plant nucleus have greatly limited the success rate of gene replacement in plants(Ran et al.,2017).In addition,DNA double-strand breaks(DSBs)generated by the Cas9 nuclease prior to HDR may lead to complicated and unexpected genome disturbance(Kosicki et al.,2018). | Zhenxiang Li Xiangyu Xiong Jian-Feng Li | 2018 | Science China(Life Sciences)2018，61，12： | 2 |
| 10 | Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China显示文摘Radiations are especially important for generating species biodiversity in mountainous ecosystems.The contribution of hybridization to such radiations has rarely been examined.Here,we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes,whose members show strong geographic isolation in the mountains of southwest China.We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera,and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene.Widespread hybridization events were inferred within and between the identified clades and subclades.This suggests that hybridization occurred both early and late during diversification of subgenus Hymenan thes,although the extent to which hybridization,speciation through mixing-isolation-mixing or hybrid speciation,accelerated the diversification needs further exploration.Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species.Similar radiation processes may apply to other montane floras in this region and elsewhere. | Yazhen Ma Xingxing Mao Ji Wang Lei Zhang Yuanzhong Jiang Yuying Geng Tao Ma Liming Cai Shuangquan Huang Pete Hollingsworth Kangshan Mao Minghui Kang Yiling Li Wenlu Yang Haolin Wu Yang Chen Charles C.Davis Nawal Shrestha Richard H.Ree Zhenxiang Xi Quanjun Hu Richard I.Milne Jianquan Liu | 2022 | National Science Review2022，9，12： | 1 |
| 11 | Phylotranscriptomics of Swertiinae(Gentianaceae)reveals that key floral traits are not phylogenetically correlated显示文摘Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth.Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups.The subtribe Swertiinae(Gentianaceae)comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries.Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu,representing the range of floral diversity,using data from the nuclear and plastid genomes.Extensive topological conflicts were present between the nuclear and plastome trees.Three of the 15 genera represented by multiple species are polyphyletic in both trees.Key floral traits including corolla type,absence or presence of lobe scales,nectary type,nectary position,and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation.We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits.These results highlight the complex evolutionary history of this subtribe.The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity. | Chunlin Chen Brad R.Ruhfel Jialiang Li Zefu Wang Lushui Zhang Lei Zhang Xingxing Mao Ji Wang Dashan He Yue Luo Quanjun Hu Yuanwen Duan Xiaoting Xu Zhenxiang Xi Jianquan Liu | 2023 | Journal of Integrative Plant Biology2023，65，6： | 1 |
| 12 | Administration of embryonic stem cells generates effective antitumor immunity in mice with minor and heavy tumor load显示文摘 | Wei Dong Jiajun Du Hongchang Shen Dongwei Gao Zhenxiang Li Guanghui Wang Xueru Mu Qi Liu | 2010 | Cancer Immunology, Immunotherapy2010，，： | 1 |
| 13 | Modified penis lengthening surgery: review of 52 cases 显示文摘 | Li Shirong Zhang Xuan Wang Zhenxiang | 2000 | Plast Reconstr Surg2000，105，2： | 1 |
| 14 | A highly efficient and selective turn-on fluorescent sensor for Cu2+ ion based oncalixarene bearing four iminoquinoline subunits on the upper rim显示文摘 | Li Guangke Xu Zhenxiang Chen Chuanfeng | 2008 | Chem Commun2008，，： | 1 |
| 15 | The working dead:repurposing inactive CRISPR-associated nucleases as programmable transcriptional regulators in plants显示文摘Targeted gene manipulation is highly desirable for fundamental plant research,plant synthetic biology,and molecular breeding.The clustered regularly interspaced short palindromic repeats-associated(Cas)nuclease is a revolutionary tool for genome editing,and has received snowballing popularity for gene knockout applications in diverse organisms including plants.Recently,the nuclease-dead Cas(dCas)proteins have been repurposed as programmable transcriptional regulators through translational fusion with portable transcriptional repression or activation domains,which has paved new ways for flexible and multiplex control over the activities of target genes of interest without the need to generate DNA lesions.Here,we review the most important breakthroughs of dCas transcriptional regulators in non-plant organisms and recent accomplishments of this growing field in plants.We also provide perspectives on future development directions of dCas transcriptional regulators in plant research in hope to stimulate their quick evolution and broad applications. | Zhenxiang Li Xiangyu Xiong Jian-Feng Li | 2020 | aBIOTECH2020，1，1： | 1 |
| 16 | Induction of matrix metalloproteinase-9 in alveolar macrophages by TNF-α through NF-κB signal pathway显示文摘Objective: To explore the effect of tumor necrosis factor (TNF)-α on matrix metalloproteinase-9 (MMP-9) expression and activity in alveolar macrophages (AM) from patients with chronic obstructive pulmonary disease (COPD) and study its associated signal pathway. Methods: AM were collected from bronchoalveolar lavage fluid in patients with COPD. The AM were incubated for 1.5 h with pyrrolidine dithiocarbamate(PDTC)at concentrations from 0 μmol/L to 50 μmol/L and then stimulated for 24 h by TNF-α at 10 ng/ml. MMP-9 expression and activity were respectively detected by semi- quantitative reverse transcription-polymerase chain reaction (RT-PCR), Western blotting and Zymography. NF-κB activity was investigated by electrophoretic mobility shift assay (EMSA). Results: Both the mRNA and protein levels of MMP-9 induced by TNF-α in AM were significantly elevated in a dose dependent manner (P<0.05). The level of MMP-9 activity was also correspondingly significantly elevated in the induction (P<0.05), which was possibly related with the over- expression of MMP-9. NF-κB activity was significantly increased when AM were stimulated by 10 ng/mL TNF-α (P<0.05). The expression of MMP-9 induced by TNF-α could be significantly inhibited by PDTC (P< 0.05). Conclusion: The expression and activity of MMP-9 from AM could be induced by TNF-α, and NF-κB signal pathway played an important role in the induction. | Yaqing Li Zhenxiang Zhang Yongjian Xu Wang Ni Shixin Chen | 2006 | Journal of Nanjing Medical University2006，20，1： | 1 |
| 17 | Multiplex and optimization of dCas9-TV-mediated gene activation in plants显示文摘Synthetic gene activators consisting of nucleasedead Cas9(dCas9)for single-guide RNA(sgRNA)-directed promoter binding and a transcriptional activation domain(TAD)represent new tools for gene activation from endogenous genomic locus in basic and applied plant research.However,multiplex gene coactivation by d Cas9-TADs has not been demonstrated in whole plants.There is also room to optimize the performance of these tools.Here,we report that our previously developed gene activator,dCas9-TV,could simultaneously upregulate OsGW7 and OsER1 in rice by up to 3,738 fold,with one sg RNA targeting to each promoter.The gene coactivation could persist to at least the fourth generation.Astonishingly,thepolycistronictRNA-sgRNAexpression under the maize ubiquitin promoter,a Pol II promoter,could cause enormous activation of these genes by up to>40,000-fold in rice.Moreover,the yeast GCN4 coiled coil-mediated dCas9-TV dimerization appeared to be promising for enhancing gene activation.Finally,we successfully introduced a self-amplification loop for dCas9-TV expression in Arabidopsis to promote the transcriptional upregulation of AtFLS2,a previously characterized dCas9-TV-refractory gene with considerable basal expression.Collectively,this work illustrates the robustness of dCas9-TV in multigene coactivation and provides broadly useful strategies for boosting transcriptional activation efficacy of dCas9-TADs in plants. | Xiangyu Xiong Jieping Liang Zhenxiang Li Ben-Qiang Gong Jian-Feng Li | 2021 | Journal of Integrative Plant Biology2021，63，4： | 1 |
| 18 | Formation of the 1300-km-wide intracontinental orogen and postorogenic magmatic province in Mesozoic South China: A flat-slab subduction model显示文摘 | Li Zhenxiang Li Xianhua | 2007 | Geology2007，35，2： | 1 |
| 19 | Aqueous Solution-Chemi- cal Derived Ni-A1203 Solar Selective Absorbing Coatings显示文摘 | LI Zhenxiang ZHAO Jianxi | 2012 | Solar Energy Materials & Solar Cells2012，，105： | 1 |
| 20 | Dysfunction of the oligodendrocytes in amyotrophic lateral sclerosis显示文摘Amyotrophic lateral sclerosis(ALS)is a fatal neurodegenerative disorder characterized by irreversible deterioration of upper and lower motor neurons(MNs).Previously,studies on the involvement of glial cells in the pathogenic process of ALS have mainly revolved around astrocytes and microglia.And oligodendrocytes(OLs)have only recently been highlighted.Grey matter demyelination within the motor cortex and proliferation of the oligodendrocyte precursor cells(OPCs)was observed in ALS patients.The selective ablation of mutant SOD1(the dysfunctional superoxide dismutase)from the oligodendrocyte progenitors after birth significantly delayed disease onset and prolonged the overall survival in ALS mice model(SOD1G37R).In this study,we review the several mechanisms of oligodendrocyte dysfunction involved in the pathological process of myelin damage and MNs death during ALS.Particularly,we examined the insufficient local energy supply from OLs to axons,impaired differentiation from OPCs into OLs mediated by oxidative stress damage,and inflammatory injury to the OLs.Since increasing evidence depicted that ALS is not a disease limited to MNs damage,exploring the mechanisms by which oligodendrocyte dysfunction is involved in MNs death would contribute to a more comprehensive understanding of ALS and identifying potential drug targets. | Zhenxiang Gong Li Ba Min Zhang | 2022 | The Journal of Biomedical Research2022，36，5： | 1 |
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