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| 1 | Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System显示文摘Transcription activator-like effector nucleases(TALENs) and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated(Cas) systems have emerged as powerful tools for genome editing in a variety of species. Here, we report, for the first time, targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. We designed five TALENs targeting 4 genes, namely ZmPDS, ZmIPK1A, ZmIPK, ZmMRP4, and obtained targeting efficiencies of up to 23.1% in protoplasts, and about 13.3% to 39.1% of the transgenic plants were somatic mutations. Also, we constructed two gRNAs targeting the ZmIPK gene in maize protoplasts, at frequencies of 16.4% and 19.1%, respectively. In addition, the CRISPR/Cas system induced targeted mutations in Z. mays protoplasts with efficiencies(13.1%) similar to those obtained with TALENs(9.1%). Our results show that both TALENs and the CRISPR/Cas system can be used for genome modification in maize. | Zhen Liang Kang Zhang Kunling Chen Caixia Gao | 2014 | Journal of Genetics and Genomics2014，41，2： | 136 |
| 2 | Mapping wetland changes in China between 1978 and 2008显示文摘Four wetland maps for all China have been produced,based on Landsat and CBERS-02B remote sensing data between 1978 and 2008 (1978,1990,2000 and 2008).These maps were mainly developed by manual interpretation and validated by substantial field investigation in 2009.Based on these maps,we analyzed the 2008 wetland distribution in China and discussed wetland changes and their drivers over the past 30 years.(i) There were about 324097 km 2 of wetlands in 2008,for which inland marshes or swamps were the most common wetland type (35%),with lakes (26%) second.Most of the wetlands were in Heilongjiang,Inner Mongolia,Qinghai and Tibet,occupying about 55% of the national wetland area.(ii) From 1978 to 2008,China's wetland area continually and significantly decreased,by about 33% based on changes in the wetland map.This was in sharp contrast to the increase in artificial wetlands,which increased by about 122%.Inland marshes accounted for the main loss of total wetlands from 1978 to 2000.From 2000 through 2008,riverine and lacustrine wetlands constituted the main wetland loss.Fortunately however,the rate of wetland loss decreased from 5523 to 831 km 2 /a.(iii) The change ratio of lost natural wetlands (including inland and coastal wetlands) to non-wetlands has decreased slightly over the past 30 years.From 1978 to 1990,nearly all natural wetlands (98%) lost were transformed into non-wetlands.However,the ratio declined to 86% from 1990 to 2000,and to 77% from 2000 to 2008.(iv) All Chinese provinces were divided into three groups according to patterns of wetland changes,which could relate to the driving forces of such changes.Tibet was completely different from other provinces,as it was one representative example in which there was a net wetland increase,because of global warming and decreased human activity since 1990.Increased economic development caused considerable wetland loss in most eastern provinces,and artificial wetlands increased. | NIU ZhenGuo ZHANG HaiYing WANG XianWei YAO WenBo ZHOU DeMin ZHAO KuiYi ZHAO Hui LI NaNa HUANG HuaBing LI CongCong YANG Jun LIU CaiXia LIU Shuang WANG Lin LI Zhan YANG ZhenZhong QIAO Fei ZHENG YaoMin CHEN YanLei SHENG YongWei GAO XiaoHong ZHU WeiHong WANG WenQing WANG Hong WENG YongLing ZHUANG DaFang LIU JiYuan LUO ZhiCai CHENG Xiao GUO ZiQi GONG Peng | 2012 | Chinese Science Bulletin2012，57，22： | 51 |
| 3 | Construction of a Genome-Wide Mutant Library in Rice Using CRISPR/Cas9显示文摘 | Meng, Xiangbing Yu, Hong Zhang, Yi Zhuang, Fengfeng Song, Xiaoguang Gao, Songsong Gao, Caixia Li, Jiayang | 2017 | Molecular Plant2017，10，9： | 46 |
| 4 | Rapid and Efficient Gene Modification in Rice and Brachypodium Using TALENs显示文摘 | Qiwei Shan Yanpeng Wang Kunling Chen Zhen Liang Jun Li Yi Zhang Kang Zhang Jinxing Liu Daniel F. Voytas Xuelian Zheng Yong Zhang Caixia Gao | 2013 | Molecular Plant2013，6，4： | 37 |
| 5 | Hi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems显示文摘The CRISPR/Cas system has been extensively applied to make precise genetic modifications in various organisms. Despite its importance and widespread use, large-scale mutation screening remains time-consuming, labour-intensive and costly. Here, we developed Hi-TOM(available at http://www.hi-tom.net/hi-tom/), an online tool to track the mutations with precise percentage for multiple samples and multiple target sites. We also described a corresponding next-generation sequencing(NGS) library construction strategy by fixing the bridge sequences and barcoding primers. Analysis of the samples from rice, hexaploid wheat and human cells reveals that the Hi-TOM tool has high reliability and sensitivity in tracking various mutations, especially complex chimeric mutations frequently induced by genome editing. Hi-TOM does not require special design of barcode primers,cumbersome parameter configuration or additional data analysis. Thus, the streamlined NGS library construction and comprehensive result output make Hi-TOM particularly suitable for high-throughput identification of all types of mutations induced by CRISPR/Cas systems. | Qing Liu Chun Wang Xiaozhen Jiao Huawei Zhang Lili Song Yanxin Li Caixia Gao Kejian Wang | 2019 | Science China(Life Sciences)2019，62，1： | 37 |
| 6 | Toward Wisdom-Evolutionary and Primitive-Concise 6G:A New Paradigm of Semantic Communication Networks显示文摘The sixth generation(6G)mobile networks will reshape the world by offering instant,efficient,and intelligent hyper-connectivity,as envisioned by the previously proposed Ubiquitous-X 6G networks.Such hyper-massive and global connectivity will introduce tremendous challenges into the operation and management of 6G networks,calling for revolutionary theories and technological innovations.To this end,we propose a new route to boost network capabilities toward a wisdom-evolutionary and primitive-concise network(WePCN)vision for the Ubiquitous-X 6G network.In particular,we aim to concretize the evolution path toward the WePCN by first conceiving a new semantic representation framework,namely semantic base,and then establishing an intelligent and efficient semantic communication(IE-SC)network architecture.In the IE-SC architecture,a semantic intelligence plane is employed to interconnect the semantic-empowered physical-bearing layer,network protocol layer,and application-intent layer via semantic information flows.The proposed architecture integrates artificial intelligence and network technologies to enable intelligent interactions among various communication objects in 6G.It features a lower bandwidth requirement,less redundancy,and more accurate intent identification.We also present a brief review of recent advances in semantic communications and highlight potential use cases,complemented by a range of open challenges for 6G. | Ping Zhang Wenjun Xu Hui Gao Kai Niu Xiaodong Xu Xiaoqi Qin Caixia Yuan Zhijin Qin Haitao Zhao Jibo Wei Fangwei Zhang | 2022 | Engineering2022，8，1： | 28 |
| 7 | TALENs:Customizable Molecular DNA Scissors for Genome Engineering of Plants显示文摘Precise genome modification with engineered nucleases is a powerful tool for studying basic biology and applied biotechnology. Transcription activator-like effector nucleases(TALENs),consisting of an engineered specific(TALE) DNA binding domain and a Fok I cleavage domain,are newly developed versatile reagents for genome engineering in different organisms.Because of the simplicity of the DNA recognition code and their modular assembly,TALENs can act as customizable molecular DNA scissors inducing double-strand breaks(DSBs) at given genomic location.Thus,they provide a valuable approach to targeted genome modifications such as mutations, insertions,replacements or chromosome rearrangements.In this article,we review the development of TALENs,and summarize the principles and tools for TALEN-mediated gene targeting in plant cells,as well as current and potential strategies for use in plant research and crop improvement. | Kunling Chen Caixia Gao | 2013 | Journal of Genetics and Genomics2013，40，6： | 18 |
| 8 | Manipulating mRNA splicing by base editing in plants显示文摘Precursor-mRNAs(pre-mRNA) can be processed into one or more mature m RNA isoforms through constitutive or alternative splicing pathways. Constitutive splicing of pre-mRNA plays critical roles in gene expressional regulation, such as intronmediated enhancement(IME), whereas alternative splicing(AS) dramatically increases the protein diversity and gene functional regulation. However, the unavailability of mutants for individual spliced isoforms in plants has been a major limitation in studying the function of mRNA splicing. Here, we describe an efficient tool for manipulating the splicing of plant genes. Using a Cas9-directed base editor, we converted the 5′ splice sites in four Arabidopsis genes from the activated GT form to the inactive AT form. Silencing the AS of HAB 1.1(encoding a type 2 C phosphatase) validated its function in abscisic acid signaling, while perturbing the AS of RS31 A revealed its functional involvement in plant response to genotoxic treatment for the first time. Lastly,altering the constitutive splicing of Act2 via base editing facilitated the analysis of IME. This strategy provides an efficient tool for investigating the function and regulation of gene splicing in plants and other eukaryotes. | Chenxiao Xue Huawei Zhang Qiupeng Lin Rong Fan Caixia Gao | 2018 | Science China(Life Sciences)2018，61，11： | 18 |
| 9 | Collagen type Ⅱ suppresses articular chondrocyte hypertrophy and osteoarthritis progression by promoting integrin β1-SMAD1 interaction显示文摘Hypertrophic differentiation is not only the terminal process of endochondral ossification in the growth plate but is also an important pathological change in osteoarthritic cartilage.Collagen type II(COL2A1)was previously considered to be only a structural component of the cartilage matrix,but recently,it has been revealed to be an extracellular signaling molecule that can significantly suppress chondrocyte hypertrophy.However,the mechanisms by which COL2A1 regulates hypertrophic differentiation remain unclear.In our study,a Col2a1 p.Gly1170Ser mutant mouse model was constructed,and Col2a1 loss was demonstrated in homozygotes.Loss of Col2a1 was found to accelerate chondrocyte hypertrophy through the bone morphogenetic protein(BMP)-SMAD1 pathway.Upon interacting with COL2A1,integrinβ1(ITGB1),the major receptor for COL2A1,competed with BMP receptors for binding to SMAD1 and then inhibited SMAD1 activation and nuclear import.COL2A1 could also activate ITGB1-induced ERK1/2 phosphorylation and,through ERK1/2-SMAD1 interaction,it further repressed SMAD1 activation,thus inhibiting BMP-SMAD1-mediated chondrocyte hypertrophy.Moreover,COL2A1 expression was downregulated,while chondrocyte hypertrophic markers and BMP-SMAD1 signaling activity were upregulated in degenerative human articular cartilage.Our study reveals novel mechanisms for the inhibition of chondrocyte hypertrophy by COL2A1 and suggests that the degradation and decrease in COL2A1 might initiate and promote osteoarthritis progression. | Chengjie Lian Xudong Wang Xianjian Qiu Zizhao Wu Bo Gao Lei Liu Guoyan Liang Hang Zhou Xiaoming Yang Yan Peng Anjing Liang Caixia Xu Dongsheng Huang Peiqiang Su | 2019 | Bone Research2019，7，1： | 17 |
| 10 | Current and future editing reagent delivery systems for plant genome editing显示文摘Many genome editing tools have been developed and new ones are anticipated; some have been extensively applied in plant genetics, biotechnology and breeding, especially the CRISPR/Cas9 system. These technologies have opened up a new era for crop improvement due to their precise editing of user-specified sequences related to agronomic traits. In this review, we will focus on an update of recent developments in the methodologies of editing reagent delivery, and consider the pros and cons of current delivery systems. Finally, we will reflect on possible future directions. | Yidong Ran Zhen Liang Caixia Gao | 2017 | Science China(Life Sciences)2017，60，5： | 16 |
| 11 | An Uncanonical CCCH-Tandem Zinc-Finger Protein Represses Secondary Wall Synthesis and Controls Mechanical Strength in Rice显示文摘第二等的墙,代表生物资源的体积,在植物生长和改编上有大影响到环境。第二等的墙合成被一个复杂发信号 transduction 网络交换并且调整。然而,有这些规章的小径的有限理解。这里,我们报导(IIP4 )交往 ILA1 蛋白质 4 能镇压第二等的墙合成。IIP4 是象 Raf 一样 MAPKKK 的 phosphorylation 底层,但是它的功能是未知的。由产生 iip4 异种和相关转基因的植物,我们发现在 IIP4 的损害提高第二等的墙形成。基因表示和 transactivation 活动试金表明 IIP4 否定地调整 MYB61 和 CESA 的表示但是不绑 ? 他们的倡导者。IIP4 与 NAC29/NAC31 交往,第二等的墙合成的在上游的管理者,并且在植物压制下游地规章的小径。显示出的 Mutagenesis 分析那 phosphomimic IIP4 从原子核的蛋白质 translocate 到细胞质。而且,我们表明 IIP evolutionarily 被保存并且分享 unreported CCCH 主题,叫作 uncanonical CCCH 双人脚踏车锌手指蛋白质。一起,我们的学习提供机械学的卓见进第二等的墙合成的控制并且为在庄稼改进相关农学的特点介绍一个机会。 | Dongmei Zhang Zuopeng Xu Shaoxue Cao Kunling Chen Shance Li Xiangling Liu Caixia Gao Baocai Zhang Yihua Zhou | 2018 | Molecular Plant2018，11，1： | 14 |
| 12 | Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene显示文摘Maize(Zea mays L.)is one of the most important cereal crops,with a global production of 1.02 billion tons in 2013(Baldaufa et al.,2016).Heterosis is widely used to increase the productivity of maize,and the first commercial hybrid maize was introduced in the 1930s(Duvick,2001).The high-yield maize varieties used today are all hybrids,and the production of hybrid maize seed requires sterilization to prevent self-pollination.Conventional seed produc- | Jun Li Huawei Zhang Xiaomin Si Youhui Tian Kunling Chen Jinxing Liu Huabang Chen Caixia Gao | 2017 | Journal of Genetics and Genomics2017，44，9： | 14 |
| 13 | Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice显示文摘Dear Editor,The CRISPR-Cas9(clustered regularly interspaced short palindromic repeats/Cas9)system has been widely used for a variety of applications,including targeted gene knockout,gene insertion,gene replacement and base editing.Despite its wide use,the genome editing using CRISPR-Cas9 is performed almost exclusively at sites containing canonical NGG protospacer adjacent motifs(PAMs).To overcome the PAM constraint of the CRISPR-Cas9 system,many attempts have been made to develop various Cas9 orthologs | Xiangbing Meng Xixun Hu Qing Liu Xiaoguang Song Caixia Gao Jiayang Li Kejian Wang | 2018 | Science China(Life Sciences)2018，61，1： | 11 |
| 14 | Importance of Weighting for Multi-Variable Habitat Suitability Index Model: A Case Study of Winter- Spring Cohort of Ommastrephes bartramii in the Northwestern Pacific Ocean显示文摘Weighting values for different habitat variables used in multi-factor habitat suitability index (HSI) modeling reflect the relative influences of different variables on distribution of fish species. Using the winter-spring cohort of neon flying squid (Ommastrephes bartramii) in the Northwestern Pacific Ocean as an example, we evaluated the impact of different weighting schemes on the HSI models based on sea surface temperature, gradient of sea surface temperature and sea surface height. We compared differences in predicted fishing effort and HSI values resulting from different weighting. The weighting for different habitat variables could greatly influence HSI modeling and should be carefully done based on their relative importance in influencing the resource spatial distribution. Weighting in a multi-factor HSI model should be further studied and optimization methods should be developed to improve forecasting squid spatial distributions. | GONG Caixia CHEN Xinjun GAO Feng CHEN Yong | 2012 | Journal of Ocean University of China2012，11，2： | 11 |
| 15 | Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture.显示文摘Genome editing provides novel strategies for improving plant traits,but relies on current genetic transformation and plant regeneration procedures,which can be inefficient.We have engineered a barley stripe mosaic virus(BSMV)-based sgRNA delivery vector(BSMV-sg)that is effective in performing heritable genome editing in Cas9-transgenic wheat plants.Mutated progenies were present in the next generation at frequencies ranging from 12.9%to 100%in three different wheat varieties,and 53.8%to 100%of mutants were virus-free.We also achieved multiplex mutagenesis in progeny using a pool of BSMV-sg vectors harboring different sgRNAs.Furthermore,we devised a virus-induced transgene-free editing procedure(VITF-Edit)to generate Cas9-free wheat mutants by crossing BSMV-infected Cas9-transgenic wheat pollen with wild-type wheat.Our study provides a robust,convenient and tissue culture-free approach for genome editing in wheat through virus infection. | Tingdong Li Jiacheng Hu Yu Sun Boshu Li Dingliang Zhang Wenli Li Jinxing Liu Dawei Li Caixia Gao Yongliang Zhang Yanpeng Wang | 2021 | Molecular Plant2021，14，11： | 10 |
| 16 | Sequence stratigraphy, paleogeography, and coal accumulation regularity of major coal-accumulating periods in China显示文摘There are 9 major coal-accumulating periods during geological history in China,including the Early Carboniferous,Late Carboniferous-Early Permian,Middle Permian,Late Permian,Late Triassic,Early-Middle Jurassic,Early Cretaceous,Paleogene and Neogene.The coal formed in these periods were developed in different coal-accumulating areas(CAA)including the North China,South China,Northwest China,Northeast China,the Qinghai–Tibet area,and China offshore area.In this paper,we investigated depositional environments,sequence stratigraphy,lithofacies paleogeography and coal accumulation pattern of five major coal-accumulating periods including the Late Carboniferous to Middle Permian of the North China CAA,the Late Permian of the South China CAA,the Late Triassic of the South China CAA,the Early-Middle Jurassic of the North and Northwest China CAA,and the Early Cretaceous in the Northeast China CAA.According to distribution of the coal-bearing strata and the regional tectonic outlines,we have identified distribution range of the coal-forming basins,sedimentary facies types and coal-accumulating models.The sequence stratigraphic frameworks of the major coal-accumulating periods were established based on recognition of a variety of sequence boundaries.The distribution of thick coals and migration patterns of the coal-accumulating centers in the sequence stratigraphic framework were analyzed.The lithofacies paleogeography maps based on third-order sequences were reconstructed and the distribution of coal accumulation centers and coal-rich belts were predicted. | Longyi Shao Xuetian Wang Dongdong Wang Mingpei Li Shuai Wang Yingjiao Li Kai Shao Chao Zhang Caixia Gao Daxiao Dong Aiguo Cheng Jing Lu Congwei Ji Di Gao | 2020 | International Journal of Coal Science & Technology2020，7，2： | 9 |
| 17 | The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat显示文摘Vernalization is a physiological process in which prolonged cold exposure establishes flowering competence in winter plants. In hexaploid wheat, TaVRN1 is a cold-induced key regulator that accelerates floral transition. However, the molecular mechanism underlying the gradual activation of TaVRN1 during the vernalization process remains unknown. In this study, we identified the novel transcript VAS (TaVRN1 alternative splicing) as a non-coding RNA derived from the sense strand of the TaVRN1 gene only in winter wheat, which regulates TaVRN1 transcription for flowering. VAS was induced during the early period of vernalization, and its overexpression promoted TaVRN1 expression to accelerate flowering in winter wheat. VAS physically associates with TaRF2b and facilitates docking of the TaRF2b-TaRF2a complex at the TaVRN1 promoter during the middle period of vernalization. TaRF2b recognizes the Sp1 motif within the TaVRN1 proximal promoter region, which is gradually exposed along with the disruption of a loop structure at the TaVRN1 locus during vernalization, to activate the transcription of TaVRN1. The tarf2b mutants exhibited delayed flowering, whereas transgenic wheat lines overexpressing TaRF2b showed earlier flowering. Taken together, our data reveal a distinct regulatory mechanism by which a long non-coding RNA facilitates the transcription factor targeting to regulate wheat flowering, providing novel insights into the vernalization process and a potential target for wheat genetic improvement. | Shujuan Xu Qi Dong Min Deng Dexing Lin Jun Xiao Peilei Cheng Lijing Xing Yuda Niu Caixia Gao Wenhao Zhang Yunyuan Xu Kang Chong | 2021 | Molecular Plant2021，14，9： | 7 |
| 18 | U-Pb Zircon Age, Geochemical, and Sr-Nd-Pb Isotopic Constraints on the Age and Origin of Mafic Dykes from Eastern Shandong Province, Eastern China显示文摘U-Pb 锆石年龄, geochemical,和从东方山东省的 mafic 女同性恋的 Sr-Nd-Pb 同位素的数据,东方中国此处被报导。激光脱离诱导地联合了从调查 mafic 女同性恋的二件样品的 U-Pb 锆石分析产出一致年龄从 121.9 妈的血浆团 spectrometry (LA-ICP-MS )?????? 猠潨桳湯瑩捩吗? | LIU Shen HU Ruizhong FENG Caixia GAO Shan FENG Guangying LAI Shaocong QI Youqiang Ian M. COULSON YANG Yuhong YANG Chaogui TANG Liang | 2013 | Acta Geologica Sinica(English Edition)2013，87，4： | 7 |
| 19 | CRISPR editing-mediated antiviral immunity: a versatile source of resistance to combat plant virus infections显示文摘Virus infection poses a constant threat on global crop productivity.It is estimated that virus diseases account for at least 10% of crop losses worldwide.Development of resistant crops using naturally evolved resistance genes has been a main measure for controlling plant virus epidemics.However,isolation of plant resistance genes is costly and time-consuming.Furthermore,most plant resistance genes are pathogen race-specific,with very few of them being broadly specific (Langner et al.,2018).Consequently,artificial immunity with engineered resistance to virus infections has received substantial research,which includes pathogenderived resistance,introducing single or stacked transgene into crops,and RNA interference (Shepherd et al.,2009).However,these strategies have so far achieved limited success due to narrow availability and/or fitness costs on host plants.Therefore,it is urgent to develop novel and more efficient strategies to combat plant virus infections.Recent breakthrough of CRISPR/Cas-based DNA and RNA editing tools provides a promising direction for engineering artificial immunity to plant viruses.There are now increasing reports demonstrating that CRISPR/Cas systems can be harnessed to develop antiviral immunity in plants with high efficiency and broad specificity (Table S1 in Supporting Information). | Xiang Ji Daowen Wang Caixia Gao | 2019 | Science China(Life Sciences)2019，62，9： | 6 |
| 20 | Fabrication of ultrafine ZnFe2O4 nanoparticles for efficient photocatalytic reduction CO2 under visible light illumination显示文摘A one-pot, solvent-thermal process was used to create the ultrafine ZnFe_2O_4 nanoparticles photocatalyst.During the solvent-thermal process, the in situ self-forming NaCl not only served as a 'cage' to confine the ion diffusion, but also acted as a microreactor for nanocrystallite growth. An average particle size of ~10 nm and a high-specific surface area of~112.9 m^2/g were observed for the ultrafine ZnFe_2O_4 nanoparticles Owing to the synergistic effect of ultrafine particle size, the full utilization of the visible light region and high conduction band(CB) position, ultrafine ZnFe_2O_4 photocatalyst displayed an efficient photocatalytic CO_2 reduction under visible light illumination. Besides, the ultrafine ZnFe_2 O_4 photocatalyst showed high production selectivity for CH_3CHO and C_2H_5OH generation in aqueous CO_2/NaHCO_3 solution. This work may provide a new idea for the synthesis of new high-efficiency photocatalysts. | Jun xiao Weiyi Yang Shuang Gao Caixia Sun Qi Li | 2018 | Journal of Materials Science & Technology2018，34，12： | 6 |
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