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| 1 | Evidence for a mouse origin of the SARS-CoV-2 Omicron variant显示文摘The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of hostjumping. The molecular spectrum of mutations(i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host,then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak. | Changshuo Wei Ke-Jia Shan Weiguang Wang Shuya Zhang Qing Huan Wenfeng Qian | 2021 | Journal of Genetics and Genomics2021，48，12： | 16 |
| 2 | The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice显示文摘The genetic improvement of nitrogen use efficiency(NUE)of crops is vital for grain productivity and sustainable agriculture.However,the regulatory mechanism of NUE remains largely elusive.Here,we report that the rice Grain number,plant height,and heading date7(Ghd7)gene genetically acts upstream of ABC1 REPRESSOR1(ARE1),a negative regulator of NUE,to positively regulate nitrogen utilization.As a transcriptional repressor,Ghd7 directly binds to two Evening Element-like motifs in the promoter and intron 1 of ARE1,likely in a cooperative manner,to repress its expression.Ghd7 and ARE1 display diurnal expression patterns in an inverse oscillation manner,mirroring a regulatory scheme based on these two loci.Analysis of a panel of 2656 rice varieties suggests that the elite alleles of Ghd7 and ARE1 have undergone diversifying selection during breeding.Moreover,the allelic distribution of Ghd7 and ARE1 is associated with the soil nitrogen deposition rate in East Asia and South Asia.Remarkably,the combination of the Ghd7 and ARE1 elite alleles substantially improves NUE and yield performance under nitrogen-limiting conditions.Collectively,these results define a Ghd7–ARE1-based regulatory mechanism of nitrogen utilization,providing useful targets for genetic improvement of rice NUE. | Qing Wang Qingmei Su Jinqiang Nian Jian Zhang Meng Guo Guojun Dong Jiang Hu Rongsheng Wang Changshuo Wei Guanwen Li Wan Wang Hui-Shan Guo Shaoyang Lin Wenfeng Qian XianzhiXie Qian Qian Fan Chen Jianru Zuo | 2021 | Molecular Plant2021，14，6： | 10 |
| 3 | Single-cell transcriptome atlas of the leaf and root of rice seedlings显示文摘As a multicellular organism,rice flourishes relying on gene expression diversity among cells of various functions.However,cellular-resolution transcriptome features are yet to be fully recognized,let alone cell-specific transcriptional responses to environmental stimuli.In this study,we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells.We identify 15 and 9 cell types in the leaf and root,respectively,and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer,except for endodermis or epidermis.Abiotic stress stimuli alter gene expression largely in a cell type-specific manner,but for a given cell type,different stresses often trigger transcriptional regulation of roughly the same set of genes.Besides,we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory.Collectively,our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology. | Yu Wang Qing Huan Ke Li Wenfeng Qian | 2021 | Journal of Genetics and Genomics2021，48，10： | 8 |
| 4 | Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process显示文摘The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in RNA.Although the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome,little attention has been paid to the possibility of using molecular spectra to infer the host origins of a virus.Here,we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines,enabled by the use of sporadic junctions formed during discontinuous transcription as molecular barcodes.We find that de novo mutations are generated in a replication-independent manner,typically on the genomic strand,and highly dependent on mutagenic mechanisms specific to the host cellular environment.De novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution,in an asymmetric manner favoring specific mutation types.Consequently,similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13,which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into humans.Collectively,our findings provide data-driven support for the natural origin of SARS-CoV-2. | Ke-Jia Shan Changshuo Wei Yu Wang Qing Huan Wenfeng Qian | 2021 | The Innovation2021，2，4： | 6 |
| 5 | Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells显示文摘Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica(93-11) and japonica(Nipponbare) inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By contrast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-oforigin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9ac/H3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells. | Yingying Han Xiao Chu Haopeng Yu Ying-Ke Ma Xiu-Jie Wang Wenfeng Qian Yuling Jiao | 2017 | Science Bulletin2017，62，19： | 5 |
| 6 | HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation显示文摘DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing(BS-seq) data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http://qianlab.genetics.ac.cn/HeteroMeth. | Qing Huan Yuliang Zhang Shaohuan Wu Wenfeng Qian | 2018 | Genomics, Proteomics & Bioinformatics2018，16，4： | 2 |
| 7 | Simultaneous catalytic removal of NOx and soot particulates over CuMgAl hydrotalcites derived mixed metal oxides显示文摘 | Zhongpeng Wang Qian Li Liguo Wang Wenfeng Shangguan | 2011 | Applied Clay Science2011，，： | 1 |
| 8 | Partitioning of elements from coal by different solvents extraction显示文摘 | Wenfeng Wang Yong Qin Fuchang Qian Longfang Ye Weiduo Hao Li Yuan Fali Jin | 2014 | Fuel2014，，： | 1 |
| 9 | Experimental tests on reinforced concrete columns under biaxial quasi- static loading 显示文摘 | Fawei Qiu Wenfeng Li Peng Pan Jiaru Qian | 2002 | Engineering Structures2002，24，： | 1 |
| 10 | Neck-spinning quality analysis and optimization of process parameters for plunger components:Simulation and experimental study显示文摘The plunger component is a key part of the plunger pump in the aircraft hydraulic system.Neck-spinning process is commonly used to fabricate plunger components,of which the quality of the spinning process significantly affects the performance of plunger pumps.One of the bottlenecks faced by the industry in the spinning process is to choose a suitable neck-spinning process so as to ensure the quality of plunger components.It is necessary to propose a reliable method to optimize the process parameters which affect the neck-spinning quality of plunger components.In this study,a calculable finite element analysis(FEA)model is established to simulate the threeroller neck-spinning process of the plunger component,which includes six typical slipper structures,two roller structures,and two spinning parameters.The FEA model is then validated by comparing the simulated spinning forces with the corresponding experimental results.The influence of the process conditions on the neck-spinning quality is investigated.And the orthogonal simulation results are analyzed by a combination of range method and fuzzy mathematical analysis method to recommend a reasonable slipper structure,roller structure and neck-spinning parameters.This study provides a promising method to improve the manufacturing quality of the typical plunger components. | Yang WANG Honghua SU Ning QIAN Kui LIU Jianbo DAI Zhengcai ZHAO Wenfeng DING | 2021 | Chinese Journal of Aeronautics2021，34，4： | 1 |
| 11 | Variant rs8400 enhances ALKBH5 expression through disrupting miR-186 binding and promotes neuroblastoma progression显示文摘Objective:AlkB homolog 5(ALKBH5)has been proven to be closely related to tumors.However,the role and molecular mechanism of ALKBH5 in neuroblastomas have rarely been reported.Methods:The potential functional single-nucleotide polymorphisms(SNPs)in ALKBH5 were identified by National Center for Biotechnology Information(NCBI)dbSNP screening and SNPinfo software.TaqMan probes were used for genotyping.A multiple logistic regression model was used to evaluate the effects of different SNP loci on the risk of neuroblastoma.The expression of ALKBH5 in neuroblastoma was evaluated by Western blotting and immunohistochemistry(IHC).Cell counting kit-8(CCK-8),plate colony formation and 5-ethynyl-2'-deoxyuridine(EdU)incorporation assays were used to evaluate cell proliferation.Wound healing and Transwell assays were used to compare cell migration and invasion.Thermodynamic modelling was performed to predict the ability of miRNAs to bind to ALKBH5 with the rs8400 G/A polymorphism.RNA sequencing,N6-methyladenosine(mA)sequencing,mA methylated RNA immunoprecipitation(MeRIP)and a luciferase assay were used to identify the targeting effect of ALKBH5 on SPP1.Results:ALKBH5 was highly expressed in neuroblastoma.Knocking down ALKBH5 inhibited the proliferation,migration and invasion of cancer cells.miR-186-3p negatively regulates the expression of ALKBH5,and this ability is affected by the rs8400 polymorphism.When the G nucleotide was mutated to A,the ability of miR-186-3p to bind to the 3'-UTR of ALKBH5 decreased,resulting in upregulation of ALKBH5.SPPI is the downstream target gene of the ALKBH5 oncogene.Knocking down SPP1 partially restored the inhibitory effect of ALKBH5 downregulation on neuroblastoma.Downregulation of ALKBH5 can improve the therapeutic efficacy of carboplatin and etoposide in neuroblastoma.Conclusions:We first found that the rs8400 G>A polymorphism in the m6A demethylase-encoding gene ALKBH5 increases neuroblastoma susceptibility and determines the related mechanisms.The aberrant regulation of ALKBH5 by miR-186-3p caused by this genetic variation in ALKBH5 promotes the occurrence and development of neuroblastoma through the ALKBH5-SPP1 axis. | Qian Guan Huiran Lin Wenfeng Hua Lei Lin Jiabin Liu Linqing Deng Jiao Zhang Jiwen Cheng Zhonghua Yang Yong Li Jun Bian Haixia Zhou Suhong Li Li Li Lei Miao Huimin Xia Jing He Zhenjian Zhuo | 2023 | Chinese Journal of Cancer Research2023，35，2： | 0 |
| 12 | Synonymous somatic mutations that alter proximal out-of-frame downstream ATGs are associated with aberrant gene expression levels in cancer cells显示文摘Synonymous mutations are mutations that occur in the coding sequence of a gene but do not change the amino acid sequence of the encoded protein.It is now understood that synonymous mutations can have a variety of functional consequences by altering the expression of genetic information and are often non-neutral(Shen et al.,2022). | Jinhui Kong Shuo Zhang Wenfeng Qian Ke Li | 2023 | Journal of Genetics and Genomics2023，50，6： | 0 |
| 13 | Volatile organic chloramines formation during ClO2 treatment显示文摘Volatile organic chloramines are reported as the disinfection byproducts during chlorination or chloramination.However,ClO2,as an important alternative disinfectant for chlorine,was not considered to produce halogenated amines.In the present work,volatile organic chloramines including(CH3)2 NCl and CH3 NCl2 were found to be generated during the reaction of ClO2 and the dye pollutants.(CH3)2 NCl was the dominant volatile DBP to result from ClO2 treated all four dye pollutants including Methyl Orange,Methyl Red,Methylene Blue and Malachite Green,with molar yields ranging from 2.6%to 38.5%at a ClO2 to precursor(ClO2/P)molar ratio of 10.HOCl was identified and proved to be the reactive species for the formation of(CH3)2 NCl,which implied(CH3)2 NCl was transformed by a combined oxidation of ClO2 and hypochlorous acid.(CH3)2 NCl concentrations in the ppb range were observed when real water samples were treated by ClO2 in the presence of the dye pollutants.The results suggest that these azo dyes are one of the significant precursors for the formation of HOCl during ClO2 treatment and that organic chloramines should be considered in ClO2 disinfection chemistry and water treatment. | Yuanzhi Hu Qian Yang Yang Guo Jie Xu Wenfeng Zhou Jing Li Ernest R.Blatchley Ⅲ | 2020 | Journal of Environmental Sciences2020，32，6： | 0 |
| 14 | Facile synthesis of metal and alloy nanoparticles by ultrasound-assisted dealloying of metallic glasses显示文摘Metal and alloy nanoparticles synthesized by chemical reduction have attracted increasing attention due to their superior physical,chemical,and biological properties.However,most chemical synthesis processes rely on the use of harsh reducing agents and complicated chemical ingredients.Herein,we report a novel reduction-agent-free and surfactant(stabilizer)-free strategy to synthesize Cu,Ag,Au,Cu-Pt,Cu-Au,Cu-Au-Pt-Pd,and Au-Pt-Pd-Cu nanoparticles by ultrasound-assisted dealloying of Mgbased metallic glasses.The formation mechanism of the metal and alloy nanoparticles is revealed by a detailed investigation of sequential intermediate products.We demonstrate that the glass-liquid phase transition of the initially dealloying metallic glasses,together with the synergistic effect of dealloying and ultrasound-driven ligament-breakage of small enough nanoporous intermediates,play key roles in preparing the uniformly dispersed metal and alloy nanoparticles.This approach greatly simplifies the up-scaling synthesis of monometallic and bimetallic nanoparticles,and also provides a general strategy for synthesizing unprecedented multimetallic nanoparticles. | Yuan-Yun Zhao Feng Qian Wenfeng Shen Chengliang Zhao Jianguo Wang Chunxiao Xie Fengling Zhou Chuntao Chang Yanjun Li | 2021 | Journal of Materials Science & Technology2021，，23： | 0 |
| 15 | A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean显示文摘Although root nodules are essential for biological nitrogen fixation in legumes,the cell types and molecular regulatory mechanisms contributing to nodule development and nitrogen fixation in determinate nodule legumes,such as soybean(Glycine max),remain incompletely understood.Here,we generated a single-nucleus resolution transcriptomic atlas of soybean roots and nodules at 14 days post inoculation(dpi)and annotated 17 major cell types,including six that are specific to nodules.We identified the specific cell types responsible for each step in the ureides synthesis pathway,which enables spatial compartmentalization of biochemical reactions during soybean nitrogen fixation.By utilizing RNA velocity analysis,we reconstructed the differentiation dynamics of soybean nodules,which differs from those of indeterminate nodules in Medicago truncatula.Moreover,we identified several putative regulators of soybean nodulation and two of these genes,GmbHLH93 and GmSCL1,were as-yet uncharacterized in soybean.Overexpression of each gene in soybean hairy root systems validated their respective roles in nodulation.Notably,enrichment for cytokinin-related genes in soybean nodules led to identification of the cytokinin receptor,GmCRE1,as a prominent component of the nodulation pathway.GmCRE1 knockout in soybean resulted in a striking nodule phenotype with decreased nitrogen fixation zone and depletion of leghemoglobins,accompanied by downregulation of nodule-specific gene expression,as well as almost complete abrogation of biological nitrogen fixation.In summary,this study provides a comprehensive perspective of the cellular landscape during soybean nodulation,shedding light on the underlying metabolic and developmental mechanisms of soybean nodule formation. | Baocheng Sun Yu Wang Qun Yang Han Gao Haiyu Niu Yansong Li Qun Ma Qing Huan Wenfeng Qian Bo Ren | 2023 | Journal of Integrative Plant Biology2023，65，6： | 0 |
| 16 | Synergy of mesoporous SnO_(2)and RbF modification for high-efficiency and stable perovskite solar cells显示文摘Electron transport layer(ETL)is very critical to the performance of perovskite solar cells(PSCs),and optimization work on ETL has received extensive attentions especially on tin oxide(SnO_(2))since it is an excellent ETL material widely applied in high-efficiency PSCs.Thereinto,introducing mesoporous structure and surface modification are two important approaches which are commonly applied.Herein,based on the previous work in low-temperature fabrication process of mesoporous SnO_(2)(mSnO_(2)),we introduced a modification process with rubidium fuoride(Rb F)to the m-SnO_(2)ETL,and successfully achieved a synergy of the m-SnO_(2)and Rb F modification:not only the shortcoming of the m-SnO_(2)in interfacial traps was overcome,but also the carrier collection efficiency was further improved.The PSCs based on the m-SnO_(2)ETL with Rb F modification demonstrated outstanding performances:a champion power conversion efficiency(PCE)of 22.72%and a stability performance of maintaining 90%of the initial PCE after 300 h of MPP tracking were obtained without surface passivation of perovskite film.Hence,utilizing the abovementioned synergy is a cost-effective and feasible strategy for fabricating high-efficiency and stable PSCs since the fabrication process of the m-SnO_(2)ETL is a kind of low temperature process and RbF is cheap. | Qian Chen Changtao Peng Lin Du Tian Hou Wenjing Yu Dong Chen Hui Shu Dejun Huang Xiangqing Zhou Jinyang Zhang Wenfeng Zhang Haijin Li Jiale Xie Yuelong Huang | 2022 | Journal of Energy Chemistry2022，31，3： | 0 |
| 17 | Review of advanced road materials, structures, equipment, and detection technologies显示文摘As a vital and integral component of transportation infrastructure,pavement has a direct and tangible impact on socio-economic sustainability.In recent years,an influx of groundbreaking and state-of-the-art materials,structures,equipment,and detection technologies related to road engineering have continually and progressively emerged,reshaping the landscape of pavement systems.There is a pressing and growing need for a timely summarization of the current research status and a clear identification of future research directions in these advanced and evolving technologies.Therefore,Journal of Road Engineering has undertaken the significant initiative of introducing a comprehensive review paper with the overarching theme of“advanced road materials,structures,equipment,and detection technologies”.This extensive and insightful review meticulously gathers and synthesizes research findings from 39 distinguished scholars,all of whom are affiliated with 19 renowned universities or research institutions specializing in the diverse and multidimensional field of highway engineering.It covers the current state and anticipates future development directions in the four major and interconnected domains of road engineering:advanced road materials,advanced road structures and performance evaluation,advanced road construction equipment and technology,and advanced road detection and assessment technologies. | JRE Editorial Office Maria Chiara Cavalli De Chen Qian Chen Yu Chen Augusto Cannone Falchetto Mingjing Fang Hairong Gu Zhenqiang Han Zijian He Jing Hu Yue Huang Wei Jiang Xuan Li Chaochao Liu Pengfei Liu Quantao Liu Guoyang Lu Yuan Ma Lily Poulikakos Jinsong Qian Aimin Sha Liyan Shan Zheng Tong B.Shane Underwood Chao Wang Chaohui Wang Di Wang Haopeng Wang Xuebin Wang Chengwei Xing Xinxin Xu Min Ye Huanan Yu Huayang Yu Zhe Zeng You Zhan Fan Zhang Henglong Zhang Wenfeng Zhu | 2023 | Journal of Road Engineering2023，3，4： | 0 |
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