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| 1 | Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice显示文摘Most of the important agronomic traits in crop plants,such as yield,quality and stress response,are quantitative and jointly controlled by many genomic loci or major genes.Improving these complex traits depends on the combination of beneficial alleles at the quantitative trait loci(QTLs).However,the conventional cross breeding method is extremely time-consuming and laborious for pyramiding multiple QTLs.In certain cases,this approach | Rongfang Xu Yachun Yang Ruiying Qin Hao Li Chunhong Qiu Li Li Pengcheng Wei Jianbo Yang | 2016 | Journal of Genetics and Genomics2016，43，8： | 47 |
| 2 | Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace显示文摘二十年后来过去了第一细菌的整个染色体的定序,它为微生物引起的染色体提供新机会。因而,可观的基因差异由细菌的染色体编码了,在在一样的种类之中,种类被揭示了。在最近的年里,染色体定序技术和生物信息学很快发展了,它导致了转变并且为在传染疾病流行病的解剖使用的细菌的染色体比较帮助了策略和方法论的应用程序。细菌的整个染色体的定序并且生物信息的计算允许 genotyping 在疾病控制满足流行病学的学习的要求。在这评论,我们构画出意义并且总结细菌的染色体在细菌的疾病控制和预防的上下文定序的角色。我们讨论细菌的染色体在爆发察觉,跟踪的来源,传播模式发现,和新流行克隆定序的应用程序鉴定。染色体在传染疾病监视网络定序并且数据分享的宽应用程序将更加支持爆发察觉和早警告阻止细菌的疾病的传播。 | Biao Kan Haijian Zhou Pengcheng Du Wen Zhang Xin Lu Tian Qin Jianguo Xu | 2018 | Frontiers of Medicine2018，12，1： | 11 |
| 3 | Direct differentiation of atrial and ventricular myocytes from human embryonic stem cells by alternating retinoid signals显示文摘尽管 myocyte 房间移植研究为心肌的梗塞建议了一个有希望的治疗学的潜力,到为心肌的修理的临床的治疗的发展的一个主要障碍是与为移植获得相对同类的室的 myocytes 联系的困难。人的胚胎的干细胞(hESCs ) 是 cardiomyocytes 的有希望的来源。这里,我们报导发信号的 retinoid 在 hESCs 的心脏的区别期间调整 atrial 对室的 myocytes 的命运说明。我们发现少量和 pan-retinoic 酸受体对手 BMS-189453 (RAi ) 显著地增加了 hESCs 的心脏的区别效率。为了调查 retinoid,工作,我们把对待 Noggin+RAi 的文化与对待 Noggin+RA 的文化作比较。我们的结果证明室特定的基因 IRX-4 的表示层次极端地在对待 Noggin+RAi 的文化被提高。MLC-2V,另一个室特定的标记,在对待 Noggin+RAi 的文化,然而并非在对待 Noggin+RA 的文化的 cardiomyocytes 在 cardiomyocytes 的多数被表示。流动 cytometry 分析和 electrophysiological 研究与 64.7 | Qiangzhe Zhang Junjie Jiang Pengcheng Han Qi Yuan Jing Zhang Xiaoqian Zhang Yanyan Xu Henghua Cao Qingzhang Meng Li Chen Tian Tian Xin Wang Pu Li Jurgen Hescheler Guangju Ji Yue Ma | 2011 | Cell Research2011，21，4： | 10 |
| 4 | Development of Plant Prime-Editing Systems for Precise Genome Editing显示文摘Prime-editing systems have the capability to perform efficient and precise genome editing in human cells.In this study,we first developed a plant prime editor 2(pPE2)system and test its activity by generating a targeted mutation on an HPT^(-ATG) reporter in rice.Our results showed that the pPE2 system could induce programmable editing at different genome sites.In transgenic T0 plants,pPE2-generated mutants occurred with 0%–31.3%frequency,suggesting that the efficiency of pPE2 varied greatly at different genomic sites and with prime-editing guide RNAs of diverse structures.To optimize editing efficiency,guide RNAs were introduced into the pPE2 system following the PE3 and PE3b strategy in human cells.However,at the genomic sites tested in this study,pPE3 systems generated only comparable or even lower editing frequencies.Furthemore,we developed a surrogate pPE2 system by incorporating the HPT^(-ATG) reporter to enrich the prime-edited cells.The nucleotide editing was easily detected in the resistant calli transformed with the surrogate pPE2 system,presumably due to the enhanced screening efficiency of edited cells.Taken together,our results indicate that plant prime-editing systems we developed could provide versatile and flexible editing in rice genome. | Rongfang Xu Juan Li Xiaoshuang Liu Tiaofeng Shan Ruiying Qin Pengcheng Wei | 2020 | Plant Communications2020，1，3： | 10 |
| 5 | Mechanisms of ultraviolet disinfection and chlorination of Escherichia coli: Culturability, membrane permeability,metabolism, and genetic damage显示文摘Traditional culture methods may underestimate the tolerance of microorganisms to disinfectants because of the existence of viable but nonculturable or sublethally injured cells after disinfection.The selection of a strict method is crucial for the evaluation of disinfection performance.The actions of 2 typical disinfectants–ultraviolet(UV)and chlorine–on the fecal indicator Escherichia coli were investigated by the detection of culturability,membrane permeability,metabolic activity,deoxyribonucleic acid(DNA),and messenger ribonucleic acid(m RNA).During UV disinfection,the irreversible damages in the cell membrane and cellular adenosine triphosphate(ATP)were negligible at low UV doses(<80 m J/cm^2).However,membrane permeability was damaged at low doses of chlorine(<5 mg/L),leading to leakage of cellular ATP.Our study showed that a slight lesion in DNA was detected even at high doses of UV(400 m J/cm^2)and chlorine(>5 mg/L)treatments.The decay of m RNA was more rapid than that of DNA.The degradation level of m RNA depended on the choice of target genes.After exposure to 50 m J/cm^2UV dose or 5 mg/L chlorine for30 min,the DNA damage repair function(Rec A m RNA)was inhibited.The m RNA involved in the DNA damage repair function can be a potential indicator of bacterial viability. | Limei Xu Chongmiao Zhang Pengcheng Xu Xiaochang C.Wang | 2018 | Journal of Environmental Sciences2018，30，3： | 10 |
| 6 | Platelet-rich plasma accelerates skin wound healing by promoting re-epithelialization显示文摘Background:Autologous platelet-rich plasma(PRP)has been suggested to be effective for wound healing.However,evidence for its use in patients with acute and chronic wounds remains insufficient.The aims of this study were to comprehensively examine the effectiveness,synergy and possible mechanism of PRP-mediated improvement of acute skin wound repair.Methods:Full-thickness wounds were made on the back of C57/BL6 mice.PRP or saline solution as a control was administered to the wound area.Wound healing rate,local inflammation,angiogenesis,re-epithelialization and collagen deposition were measured at days 3,5,7 and 14 after skin injury.The biological character of epidermal stem cells(ESCs),which reflect the potential for re-epithelialization,was further evaluated in vitro and in vivo.Results:PRP strongly improved skin wound healing,which was associated with regulation of local inflammation,enhancement of angiogenesis and re-epithelialization.PRP treatment significantly reduced the production of inflammatory cytokines interleukin-17A and interleukin-1β.An increase in the local vessel intensity and enhancement of re-epithelialization were also observed in animals with PRP administration and were associated with enhanced secretion of growth factors such as vascular endothelial growth factor and insulin-like growth factor-1.Moreover,PRP treatment ameliorated the survival and activated the migration and proliferation of primary cultured ESCs,and these effects were accompanied by the differentiation of ESCs into adult cells following the changes of CD49f and keratin 10 and keratin 14.Conclusion:PRP improved skin wound healing by modulating inflammation and increasing angiogenesis and re-epithelialization.However,the underlying regulatory mechanism needs to be investigated in the future.Our data provide a preliminary theoretical foundation for the clinical administration of PRP in wound healing and skin regeneration. | Pengcheng Xu Yaguang Wu Lina Zhou Zengjun Yang Xiaorong Zhang Xiaohong Hu Jiacai Yang Mingying Wang Binjie Wang Gaoxing Luo Weifeng He Biao Cheng | 2020 | Burns & Trauma2020，8，1： | 8 |
| 7 | Multifunctional metasurfaces enabled by simultaneous and independent control of phase and amplitude for orthogonal polarization states显示文摘Monochromatic light can be characterized by its three fun dame ntal properties:amplitude,phase,and polarization.In this work,we propose a versatile,transmission-mode all-dielectric metasurface platform that can independently manipulate the phase and amplitude for two orthogonal states of polarization in the visible frequency range.For proof-o仁concept experimental demonstration,various single-layer metasurfaces composed of subwavelength-spaced titanium-dioxide nanopillars are designed,fabricated,and characterized to exhibit the ability of polarization-switchable multidimensional light-field manipulation,including polarization-switchable grayscale nanoprinting,nonuniform cylindrical lensing,and complex-amplitude holography.We envision the metasurface platform dem on strated here to open new possibilities toward creating compact multifunctional optical devices for applications in polarization optics,information encoding,optical data storage,and security. | Mingze Liu Wenqi Zhu Pengcheng Huo Lei Feng Maowen Song Cheng Zhang Lu Chen Henri JLezec Yanqing Lu Amit Agrawal Ting Xu | 2021 | Light(Science & Applications)2021，10，6： | 8 |
| 8 | Genome-wide variants of Eurasian facial shape differentiation and a prospective model of DNA based face prediction显示文摘It is a long-standing question as to which genes define the characteristic facial features among different ethnic groups. In this study, we use Uyghurs, an ancient admixed population to query the genetic bases why Europeans and Han Chinese look different. Facial traits were analyzed based on high-dense 3D facial images; numerous biometric spaces were examined for divergent facial features between European and Han Chinese, ranging from inter-landmark distances to dense shape geometrics. Genome-wide association studies(GWAS) were conducted on a discovery panel of Uyghurs. Six significant loci were identified, four of which, rs1868752, rs118078182, rs60159418 at or near UBASH3B, COL23A1, PCDH7 and rs17868256 were replicated in independent cohorts of Uyghurs or Southern Han Chinese. A prospective model was also developed to predict 3D faces based on top GWAS signals and tested in hypothetic forensic scenarios. | Lu Qiao Yajun Yang Pengcheng Fu Sile Hu Hang Zhou Shouneng Peng Jingze Tan Yan Lu Haiyi Lou Dongsheng Lu Sijie Wu Jing Guo Li Jin Yaqun Guan Sijia Wang Shuhua Xu Kun Tang | 2018 | Journal of Genetics and Genomics2018，45，8： | 7 |
| 9 | CRISPR/Cas9-Mediated Adenine Base Editing in Rice Genome显示文摘Precise base editing is highly desired in plant functional genomic research and crop molecular breeding. In this study, we constructed a rice-codon optimized adenine base editor(ABE)-nC as9 tool that induced targeted A·T to G·C point mutation of a key single nucleotide polymorphism site in an important agricultural gene. Combined with the modified single-guide RNA variant, our plant ABE tool can efficiently achieve adenine base editing in the rice genome. | LI Hao QIN Ruiying LIU Xiaoshuang LIAO Shengxiang XU Rongfang YANG Jianbo WEI Pengcheng | 2019 | Rice science2019，26，2： | 7 |
| 10 | Genetic mapping of quantitative trait loci in crops显示文摘Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists.Two complementary approaches for genetic mapping,linkage mapping and association mapping have led to successful dissection of complex traits in many crop species.Both of these methods detect quantitative trait loci(QTL) by identifying marker–trait associations,and the only fundamental difference between them is that between mapping populations,which directly determine mapping resolution and power.Based on this difference,we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association mapping.We then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in crops.In the era of next-generation sequencing,there has arisen an urgent need for proper population design,advanced statistical strategies,and precision phenotyping to fully exploit high-throughput genotyping. | Yang Xu Pengcheng Li Zefeng Yang Chenwu Xu | 2017 | The Crop Journal2017，5，2： | 7 |
| 11 | Genomic selection: A breakthrough technology in rice breeding显示文摘Rice(Oryza sativa)provides a staple food source for more than half the world population.However,the current pace of rice breeding in yield growth is insufficient to meet the food demand of the everincreasing global population.Genomic selection(GS)holds a great potential to accelerate breeding progress and is cost-effective via early selection before phenotypes are measured.Previous simulation and experimental studies have demonstrated the usefulness of GS in rice breeding.However,several affecting factors and limitations require careful consideration when performing GS.In this review,we summarize the major genetics and statistical factors affecting predictive performance as well as current progress in the application of GS to rice breeding.We also highlight effective strategies to increase the predictive ability of various models,including GS models incorporating functional markers,genotype by environment interactions,multiple traits,selection index,and multiple omic data.Finally,we envision that integrating GS with other advanced breeding technologies such as unmanned aerial vehicles and open-source breeding platforms will further improve the efficiency and reduce the cost of breeding. | Yang Xu Kexin Ma Yue Zhao Xin Wang Kai Zhou Guangning Yu Cheng Li Pengcheng Li Zefeng Yang Chenwu Xu Shizhong Xu | 2021 | The Crop Journal2021，9，3： | 7 |
| 12 | Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants显示文摘Streptococcus pyogenes Cas9(SpCas9)is the most widely used genome editing tool in plants.The editing induced by SpCas9 strictly requires a canonical NGG protospacer-adjacent motif(PAM),significantly limiting its scope of application.Recently,five SpCas9 variants,SpCas9-NRRH,SpCas9-NRCH,SpCas9-NRTH,SpG,and SPRY,were developed to recognize non-canonical PAMs in human cells.In this study,these variants were engineered for plant genome editing,and their targeted mutagenesis capabilities were comprehensively examined at various canonical and non-canonical PAM sites in rice(Oryza sativa)by stable transformation.Moreover,both cytosine base editors using a rat APOBEC1 or a human APO-BEC3a and adenine base editors using a directly evolved highly compatible TadA*-8e deaminase were developed from these SpCas9 variants.Our results demonstrated that the developed SpCas9 variantsbased base editors readily generated conversions between C.G and T.A in the target sites with noncanonical PAMs in transgenic rice lines.Collectively,the toolbox developed in this study substantially expands the scope of SpCas9-mediated genome editing and will greatly facilitate gene disruption and precise editing in plants. | Juan Li Rongfang Xu Ruiying Qin Xiaoshuang Liu Fanna Kong Pengcheng Wei | 2021 | Molecular Plant2021，14，2： | 6 |
| 13 | A high-sensitivity H2S gas sensor based on optimized ZnO-ZnS nano-heterojunction sensing material显示文摘This paper reports a high-performance H2S gas sensing material that is made of ZnO nanowires(NWs)modified by an optimal amount of ZnS to form nano-hete rojunctions.Compared with the intrinsic ZnONWs,the three differently modified nano-heterostructure material ZnO-ZnS-x(x=5,10,15)shows significant improvement in sensing performance to H2S at the working temperatures of 100-400℃,especially in the low temperature range(<300℃).The chemiresistive sensor with ZnO-ZnS-10 sensingmaterial exhibits the largest response signal to H2S among all the other ZnO-ZnS-x(x=5,10,15,20)sensors.Its response signal to 5 ppm H2S at 150℃is about 2.7 times to that of the ZnO-NWs sensor.Besides,the ZnO-ZnS-10 sensor also features satisfactory selectivity and repeatability at 150℃.With the technical advantage attributed to the reduction of the redesigned band gap at the interface between ZnO and ZnS,the ZnO-ZnS hete ro structure sensor rather than the traditional ZnO-NWs sensor can be used for high-sensitivity application at low working temperature. | Pei Ding Dongsheng Xu Nan Dong Ying Chen Pengcheng Xu Dan Zheng Xinxin Li | 2020 | Chinese Chemical Letters2020，31，8： | 5 |
| 14 | Quasi-phase-matching-division multiplexing holography in a three-dimensional nonlinear photonic crystal显示文摘Nonlinear holography has recently emerged as a novel tool to reconstruct the encoded information at a new wavelength,which has important applications in optical display and optical encryption.However,this scheme still struggles with low conversion efficiency and ineffective multiplexing.In this work,we demonstrate a quasi-phasematching(QPM)-division multiplexing holography in a three-dimensional(3D)nonlinear photonic crystal(NPC).3D NPC works as a nonlinear hologram,in which multiple images are distributed into different Ewald spheres in reciprocal space.The reciprocal vectors locating in a given Ewald sphere are capable of fulfilling the complete QPM conditions for the high-efficiency reconstruction of the target image at the second-harmonic(SH)wave.One can easily switch the reconstructed SH images by changing the QPM condition.The multiplexing capacity is scalable with the period number of 3D NPC.Our work provides a promising strategy to achieve highly efficient nonlinear multiplexing holography for high-security and high-density storage of optical information. | Pengcheng Chen Chaowei Wang Dunzhao Wei Yanlei Hu Xiaoyi Xu Jiawen Li Dong Wu Jianan Ma Shengyun Ji Leran Zhang Liqun Xu Tianxin Wang Chuan Xu Jiaru Chu Shining Zhu Min Xiao Yong Zhang | 2021 | Light(Science & Applications)2021，10，8： | 5 |
| 15 | Cluster-formula-embedded machine learning for design of multicomponent β-Ti alloys with low Young’s modulus显示文摘The present work formulated a materials design approach,a cluster-formula-embedded machine learning(ML)model,to search for body-centered-cubic(BCC)β-Ti alloys with low Young’s modulus(E)in the Ti–Mo–Nb–Zr–Sn–Ta system.The characteristic parameters,including the Mo equivalence and the cluster-formula approach,are implemented into the ML to ensure the accuracy of prediction,in which the former parameter represents the BCC-βstructural stability,and the latter reflects the interactions among elements expressed with a composition formula.Both auxiliary gradient-boosting regression tree and genetic algorithm methods were adopted to deal with the optimization problem in the ML model. | Fei Yang Zhen Li Qing Wang Beibei Jiang Biaojie Yan Pengcheng Zhang Wei Xu Chuang Dong Peter K.Liaw | 2020 | npj Computational Materials2020，，1： | 5 |
| 16 | The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection显示文摘Epigenetic modifications to histones dictate the differentiation of naïve CD4^(+) T cells into different subsets of effector T helper(TH)cells.The histone methyltransferase enhancer of zeste homolog 2(EZH2)has been implicated in the mechanism regulating the differentiation of TH1,TH2 and regulatory T(Treg)cells.However,whether and how EZH2 regulates follicular helper T(TFH)cell differentiation remain unknown.Using a mouse model of acute lymphocytic choriomeningitis virus(LCMV)infection,we observed abundant EZH2 expression and associated H3K27me3 modifications preferentially in the early committed virus-specific TFH cells compared to those in TH1 cells.Ablation of EZH2 in LCMV-specific CD4^(+) T cells leads to a selective impairment of early TFH cell fate commitment,but not late TFH differentiation or memory TFH maintenance.Mechanistically,EZH2 specifically stabilizes the chromatin accessibility of a cluster of genes that are important for TFH fate commitment,particularly B cell lymphoma 6(Bcl6),and thus directs TFH cell commitment.Therefore,we identified the chromatin-modifying enzyme EZH2 as a novel regulator of early TFH differentiation during acute viral infection. | Xiangyu Chen Guoshuai Cao Jialin Wu Xinxin Wang Zhiwei Pan Jianbao Gao Qin Tian Lifan Xu Zhirong Li Yaxing Hao Qizhao Huang Pengcheng Wang Minglu Xiao Luoyingzi Xie Shupei Tang Zhenyu Liu Li Hu Jianfang Tang Ran He Li Wang Xinyuan Zhou Yuzhang Wu Mengjie Chen Beicheng Sun Bo Zhu Jun Huang Lilin Ye | 2020 | Cellular & Molecular Immunology2020，17，3： | 4 |
| 17 | Machine learning for perovskite materials design and discovery显示文摘The development of materials is one of the driving forces to accelerate modern scientific progress and technological innovation.Machine learning(ML)technology is rapidly developed in many fields and opening blueprints for the discovery and rational design of materials.In this review,we retrospected the latest applications of ML in assisting perovskites discovery.First,the development tendency of ML in perovskite materials publications in recent years was organized and analyzed.Second,the workflow of ML in perovskites discovery was introduced.Then the applications of ML in various properties of inorganic perovskites,hybrid organic–inorganic perovskites and double perovskites were briefly reviewed.In the end,we put forward suggestions on the future development prospects of ML in the field of perovskite materials. | Qiuling Tao Pengcheng Xu Minjie Li Wencong Lu | 2021 | npj Computational Materials2021，，1： | 4 |
| 18 | Development of an efficient plant dual cytosine and adenine editor显示文摘An enhanced CDA-like(eCDAL)was established from Japanese lamprey CDA1-like 4 to achieve a high editing frequency in a broad region as a C-terminal cytosine base editors(CT-CBE).Then,a novel plant dual-base editor version1(pDuBE1)was developed by integrating TadA-8e into eCDAL.The editing efficiency of pDuBE1 could reach to 87.6%,with frequencies of concurrent A-to-G and C-to-T conversions as high as 49.7%in stably transformed plant cells.Our results showed that pDuBE1 could mediate robust dual editing in plant genome,providing a powerful manipulation tool for precise crop breeding and screening platforms for in planta direct evolution. | Rongfang Xu Fanna Kong Ruiying Qin Juan Li Xiaoshuang Liu Pengcheng Wei | 2021 | Journal of Integrative Plant Biology2021，63，9： | 4 |
| 19 | Progressive deterioration of the upper respiratory tract and the gut microbiomes in children during the early infection stages of COVID-19显示文摘Children are less susceptible to coronavirus disease 2019 (COVID-19), and they have manifested lower morbidity and mortality after infection, for which a multitude of mechanisms may be considered. Whether the normal development of the gut-airway microbiome in children is affected by COVID-19 has not been evaluated. Here, we demonstrate that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)infection alters the upper respiratory tract and the gut microbiomes in nine children. The alteration of the microbiome is dominated by the genus Pseudomonas, and it sustains for up to 25e58 days in different individuals. Moreover, the patterns of alternation are different between the upper respiratory tract and the gut. Longitudinal investigation shows that the upper respiratory tract and the gut microbiomes are extremely variable among children during the course of COVID-19. The dysbiosis of microbiome persists in7 of 8 children for at least 19e24 days after discharge from the hospital. Disturbed development of both the gut and the upper respiratory microbiomes and prolonged dysbiosis in these nine children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to the increased health risk in the post-COVID-19 era. | Rong Xu Pengcheng Liu Tao Zhang Qunfu Wu Mei Zeng Yingying Ma Xia Jin Jin Xu Zhigang Zhang Chiyu Zhang | 2021 | Journal of Genetics and Genomics2021，48，9： | 4 |
| 20 | A Novel Approach for QoS Prediction Based on Bayesian Combinational Model显示文摘As an important factor in evaluating service,QoS(Quality of Service) has drawn more and more concerns with the rapid increasing of Web services. However,due to the great volatility of services in Mobile Internet environments,such as internet of vehicles,Web services often do not work as announced and thus cause unacceptable problems. QoS prediction can avoid failure before it takes place,which is considered a more effective way to assure quality. However,Current QoS prediction approaches neither consider the highly dynamic of Web services,nor maintain good prediction performance all the time. Consequently we propose a novel Bayesian combinational model to predict QoS by continuously adjusting credit values of the basic models so as to keep good prediction accuracy. QoS attributes such as response time,throughput and reliability are used to validate the proposed model. Experimental results show that the model can provide stable prediction results in Mobile Internet environments. | Pengcheng Zhang Yingtao Sun Hareton Leung Meijun Xu Wenrui Li | 2016 | China Communications2016，13，11： | 3 |
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