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| 1 | m6A promotes R-loop formation to facilitate transcription termination显示文摘R-loops are three-stranded nucleic acid structures consisting of a DNA:RNA heteroduplex and a displaced single DNA strand.They constitute a prevalent genomic feature with important functions in all kingdoms of eukaryotes.1,2,3 For example,R-loops have been found over unmethylated CpG island promoters,G-rich terminators,and many other regulatory chromosomal loci.2,3 Moreover,they are essential for diverse cellular processes,such as immunoglobulin class switching,mitotic chromosome segregation,4 DNA replication and repair,genome stability regulation,5 as well as in multiple steps during transcription.6,7 R-loops can be formed both in cis and in trans;cis R-loops are formed between a nascent RNA and its DNA template following transcribing RNA polymerases and exert co-transcriptional regulatory effects.3,8 Therefore,it is important to control their formation and resolution,and many external factors have already been identified for this process.7 However,it is still unknown whether the intrinsic properties of the RNA itself,such as various modifications,can modulate the formation of DNA:RNA hybrids. | Xin Yang Qian-Lan Liu Wei Xu Yi-Chang Zhang Ying Yang Lin-Fang Ju Jing Chen Yu-Sheng Chen Kuan Li Jie Ren Qianwen Sun Yun-Gui Yang | 2019 | Cell Research2019，29，12： | 5 |
| 2 | EARLY FLOWERING IN SHORT DAYS(EFS) regulates the seed size in Arabidopsis显示文摘Post-transcriptional modifications,including histone modifications and DNA methylation,alter the chromatin landscape to regulate gene expression,thus control various cellular processes in plants.EARLY FLOWERING IN SHORT DAYS(EFS)is the major contributor for H3K36 methylation in Arabidopsis and is important for plant development.Here,we find that EFS is expressed in different stages of embryo morphogenesis,and the efs mutant produces larger embryo that results in enlarged seeds.Further analysis reveals that an imprinted gene MOP9.5 is hypomethylated at the promoter region and its expression is derepressed in efs mutant.MOP9.5 promoter is marked by various epigenetic modifications,and we find that following the increase of H3K36me3,H3K27me3 and H3K9me2 levels are reduced in efs mutant.This data indicates an antagonistic regulation between H3K36me3 and DNA methylation,and/or H3K27me3 at MOP9.5.Our results further show that both maternal and paternal EFS alleles are responsible for the seed size regulation,which unraveled a novel function of EFS in plant development. | Lingling Cheng Sarfraz Shafiq Wei Xu Qianwen Sun | 2018 | Science China(Life Sciences)2018，61，2： | 4 |
| 3 | Selective partial salivary glands sparing during intensity-modulated radiation therapy for nasopharyngeal carcinoma显示文摘Objective This study evaluated the dosimetric consequences of selective partial salivary gland sparing during intensity-modulated radiotherapy(IMRT) for patients with nasopharyngeal carcinoma(NPC).Methods Ten patients with NPC were enrolled in the study.Two IMRT plans were produced for each patient:conventional(control) and partial salivary glands-sparing(treatment),with dose constraints to the entire parotid glands or partial salivary glands(including the parotid and submandibular glands,delineated with the adjacent distance of at least 0.5 cm between the glands and PTV,the planning target volume) in planning,respectively.Dosimetric parameters were compared between the two plans,including the V_(110%),V_(100%),V_(95%)(the volume covered by more than 110%,100%,or 95% of the prescribed dose),Dmin(the minimum dose) of PTV,homogeneity index(HI),conformity index(CI),and the mean dose and percentage of the volume receiving 30 Gy or more(V_(30)) for the parotid glands and submandibular glands.Results Treatment plans had significantly lower mean doses and V_(30) to both the entire parotid glands and partial parotid glands than those in control plans.The mean doses to the partial submandibular glands were also significantly lower in treatment plans than in control plans.The PTV coverage was comparable between the two plans,as indicated by V_(100%),V_(95%),Dmin,CI,and HI.The doses to critical structures,including brainstem and spinal cord,were slightly but not significantly higher in treatment plans than in control plans.Conclusion A selective partial salivary gland-sparing approach reduces the doses to parotid and submandibular glands during IMRT,which may decrease the risk of post-radiation xerostomia while not compromising target dose coverage in patients with NPC. | Guangjin Yuan Qianwen Li Shixian Chen Chengwei Zheng Jiang Tang Jiang Hu Ximing Xu | 2017 | Oncology and Translational Medicine2017，3，2： | 1 |
| 4 | DOCK2 regulates antifungal immunity by regulating RAC GTPase activity显示文摘Fungal infections cause~1.5 million deaths each year worldwide,and the mortality rate of disseminated candidiasis currently exceeds that of breast cancer and malaria.The major reasons for the high mortality of candidiasis are the limited number of antifungal drugs and the emergence of drug-resistant species.Therefore,a better understanding of antifungal host defense mechanisms is crucial for the development of effective preventive and therapeutic strategies.Here,we report that DOCK2(dedicator of cytokinesis 2)promotes indispensable antifungal innate immune signaling and proinflammatory gene expression in macrophages.DOCK2-deficient macrophages exhibit decreased RAC GTPase(Rac family small GTPase)activation and ROS(reactive oxygen species)production,which in turn attenuates the killing of intracellular fungi and the activation of downstream signaling pathways.Mechanistically,after fungal stimulation,activated SYK(spleen-associated tyrosine kinase)phosphorylates DOCK2 at tyrosine 985 and 1405,which promotes the recruitment and activation of RAC GTPases and then increases ROS production and downstream signaling activation.Importantly,nanoparticle-mediated delivery of in vitro transcribed(IVT)Rac1 mRNA promotes the activity of Rac1 and helps to eliminate fungal infection in vivo.Taken together,this study not only identifies a critical role of DOCK2 in antifungal immunity via regulation of RAC GTPase activity but also provides proof of concept for the treatment of invasive fungal infections by using IVT mRNA. | Xiaojian Ma Xi Tan Bingbing Yu Wanwei Sun Heping Wang Huijun Hu Yanyun Du Ruirui He Ru Gao Qianwen Peng Zhihui Cui Ting Pan Xiong Feng Junhan Wang Chengqi Xu Bin Zhu Wei Liu Chenhui Wang | 2022 | Cellular & Molecular Immunology2022，19，5： | 1 |
| 5 | 放疗诱导食管癌细胞上皮-间质转换与TGF-β信号活化及BMP信号抑制相关(英文)显示文摘Objective: Irradiation may enhance migration and/or invasiveness of cancer cells in vitro and in vivo, the mechanism of which may be associated with epithelial-mesenchymal transition (EMT). The present study explored the mechanisms of EMT induced by irradiation in esophageal cancer cells. Methods: Human esophageal cancer cell line EC109 was treated with increased doses of irradiation (0 Gy, 20 Gy, 40 Gy and 60 Gy). Cell morphology was observed. Expressions of E-cadherin and vimentin were determined by immunofluorescence assay or western blot. Secretion of transforming growth factor-β1 (TGF-β1) by cells was determined by enzyme-linked immunosorbent assay (ELISA), and the expressions of Smad2/3 and phosphorated Smad2 (p-Smad2) were also examined by Western blot. The mRNA expressions of BMP-4, a bone morphogenetic protein (BMP) ligand, and two secreted BMP antagonists (Chordin and Gremlin), were detected with reverse transcription-polymerase chain reaction (RT-PCR). Cell migratory capacity was evaluated. Results: Irradiation induced EMT in EC109 cells in a dose-dependent manner as evidenced by morphological changes, decreased expression of E-cadherin and increased expression of vimentin, and increased cell motility. The secretion of TGF-β1 and expression of p-Smad2 were gradually increased in an irradiation dose-dependent manner, but the Smad2/3 protein levels remained stable. The mRNA expression of BMP-4 was gradually down-regulated, but the expressions of Chordin and Gremlin were gradually up-regulated in cells treated with increased doses of irradiation. Conclusion: Irradiation can induce EMT in esophageal cancer cells in a dose-dependent manner, and the mechanism may be associated with activation of TGF-β and restriction of BMP signaling. | Houyun Zhang Guangjin Yuan Shunlin Shan Qianwen Li Ximing Xu | 2013 | The Chinese-German Journal of Clinical Oncology2013，12，8： | 1 |
| 6 | Lanthanide-containing persistent luminescence materials with superbright red afterglow and excellent solution processability显示文摘Lanthanide-containing persistent luminescence materials are promising candidates for a wide range of applications by virtue of splendid superiorities in afterglow performance.However,it is a crucial challenge to achieve high-quality afterglow materials at the attractive nanoscale,with uniform size,controllable morphology,and satisfying brightness.Herein,a bottom-up approach was developed to construct the high-quality afterglow nanoparticles,incorporating luminescent lanthanide complex and organic molecular ingredients under mild conditions.These nanoparticles exhibited intrinsic lanthanide luminescence with superbright red afterglow(>10 cd m^(−2))in a homogeneous solution.The afterglow solution with excellent processability can serve as ideal building blocks for the on-demand fabrication of functional nanomaterials.Water-dispersible afterglow nanoparticles with state-of-the-art high brightness were uniformly constructed to perform whole-blood lateral flow assay of procalcitonin with a naked-eye detection limit of 0.5 ng mL^(−1),promoting the point-of-care testing development. | Ming Xu Jia Liu Xianlong Su Qianwen Zhou Hang Yuan Yue Wen Yihang Cheng Fuyou Li | 2021 | Science China Chemistry2021，64，12： | 0 |
| 7 | A likely autotetraploidization event shaped the Chinese mahogany(Toona sinensis)genome显示文摘Chinese mahogany(Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T.sinensis genome, we found evidence of a tetraploidization event(T. sinensis special tetraploidization, TST) that occurred approximately 15-17 million years ago(MYA) after the core eudicot-common hexaploidization(ECH or gamma) event. We characterized the synonymous nucleotide substitution rates(Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7chromosomal fusions that have shaped the T. sinensis genome;more information is available on a newly constructed karyotype platform(http://gffzze84c5b42976d4cd7hqqbb9bv0qpvu6pbq.ffgz.tsg.suse.edu.cn/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase(TPS) genes;conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond. | Jianyu Wang Ziyi Yang Tianyu Lei Yan Zhang Qimeng Xiao Zijian Yu Jiaqi Zhang Sangrong Sun Qiang Xu Shaoqi Shen Zimo Yan Mengnan Fang Yue Ding Zihan Liu Qianwen Zhu Ke Ren Yuxin Pan Haibin Liu Jinpeng Wang | 2023 | Horticultural Plant Journal2023，9，2： | 0 |
| 8 | R-loopAtlas:An integrated R-loop resource from 254 plant species sustained by a deep-learningbased tool显示文摘R-loops are chromatin structures consisting of anRNA:DNA hybrid and the other single-stranded DNA,which widely exist among genomes from bacteria to higher eukaryotes and participate in a variety of biological processes(Zhou et al.,2022).Currently,a variety of approaches to detect genome-wide R-loops have been developed,and ssDRIP-seq(single-strand DNA ligation-based library preparation from DNA:RNA hybrid immunoprecipitation,followed by sequencing)is one of the widely utilized methods(Xu et al.,2022).However,there are many limitations to genome-wide R-loop mapping based on high-throughput methods.For example,the activity of restriction enzymes for genomic DNA fragmentation. | Kuan Li Zhenzhen Wu Jincong Zhou Wei Xu Ling Li Chao Liu Wei Li Chengjun Zhang Qianwen Sun | 2023 | Molecular Plant2023，16，3： | 0 |
| 9 | Novel thieno[2,3-b]quinoline-procaine hybrid molecules:A new class of allosteric SHP-1 activators evolved from PTP1B inhibitors显示文摘Small molecule activators could equally provide powerful tools as inhibitors do for interrogating cellular signal transduction.However,targeted protein activation is chemically challenging.Developing activators against Src homology region 2 domain-containing phosphatase-1(SHP-1)to block STAT3 pathway represents a promising strategy for DLBCL therapy.Here we reported a new class of thieno[2,3-b]quinolineprocaine hybrid molecules as SHP-1 allosteric activators.The representative hybrid compound 3b displayed SHP-1 activating effect with EC50 of 5.48±0.28μmol/L.Further investigations confirmed that 3b allosterically interacted with SHP-1,switched it from close to open conformation,blocked SHP-1/p-STAT3 pathway,induced apoptosis and inhibited ABC-DLBCL cell proliferation in vitro,and delayed tumor growth in the xenograft model of SU-DHL-2.Overall,this work offered a novel paradigm to develop SHP-1 allosteric activators through chemical space evolution of PTPs inhibitors,and firstly validated the therapeutic strategy that directly activating SHP-1 alone could be a potential therapy against ABC-DLBCL via blocking STAT3 pathway. | Lei Xu Xuyang Mu Minmin Liu Zhijia Wang Chao Shen Qianwen Mu Bo Feng Yechun Xu Tingjun Hou Lixin Gao Haini Jiang Jia Li Yubo Zhou Wenlong Wang | 2023 | Chinese Chemical Letters2023，34，8： | 0 |
| 10 | DEtail-seq is an ultra-efficient and convenient method for meiotic DNA break profiling in multiple organisms显示文摘Programmed DNA double-strand break(DSB)formation is a crucial step in meiotic recombination,yet techniques for highefficiency and precise mapping of the 3’ends of DSBs are still in their infancy.Here,we report a novel technique,named DNA End tailing and sequencing(DEtail-seq),which can directly and ultra-efficiently characterize the 3’ends of meiotic DSBs with near single-nucleotide resolution in a variety of species,including yeast,mouse,and human.We find that the 3’ends of meiotic DSBs are stable without significant resection in budding yeast.Meiotic DSBs are strongly enriched in de novo H3K4me3 peaks in the mouse genome at leptotene stage.We also profile meiotic DSBs in human and find DSB hotspots are enriched near the common fragile sites during human meiosis,especially at CCCTC-binding factor(CTCF)-associated enhancers.Therefore,DEtail-seq provides a powerful method to detect DSB ends in various species,and our results provide new insights into the distribution and regulation of meiotic DSB hotspots. | Wei Xu Chao Liu Zhe Zhang Changbin Sun Qin Li Kuan Li Hui Jiang Wei Li Qianwen Sun | 2023 | Science China(Life Sciences)2023，66，6： | 0 |
| 11 | Comparison of 2-acetylfuran,2-ethylfuran,and 2-methylfuran spherically expanding flame intrinsic instabilities显示文摘The intrinsic instability of three furan derivatives, namely, 2-acetylfuran(AF), 2-ethylfuran(EF), and 2-methylfuran(MF), is experimentally and theoretically investigated and compared. A deep-learning-based end-to-end system is used to segment the cells and measure the crack length on the cellular flame front of the spherically expanding flame to quantitively investigate the flame morphology. Moreover, the flame front radius profile is quantitively investigated to shed light on the correlation between disturbance amplitude and flame radius. With the use of the linear stability model, the theoretical critical flame radius and Peclet number are obtained and compared to their corresponding experimental results to characterize the outset of cellularization and evaluate the flame instability propensity. Our analysis shows that compared with AF and EF, MF is prone to cellularization at a smaller flame radius and has a faster cell proliferation rate and crack length growth rate before reaching the hydrodynamic saturation limit. Meanwhile, the average area of saturated cells tends to be similar for the three furan derivatives. Furthermore,AF premixed flame does not exhibit cellularization before the flame radius is less than 45 mm in low initial pressure. | XU CangSu WANG QianWen LI XiaoLu OPPONG Francis LIU WeiNan | 2022 | Science China(Technological Sciences)2022，65，10： | 0 |
| 12 | Research on a fiber sensing system for metal ion detection based on SPF-PCF-SPF structure and coated LPFG显示文摘In order to provide a method for accurately detecting the concentration and types of heavy metal ions in water,a fluid ion detection system is designed.It consists of a side-polished fiber-assisted fluid structure and a long-period fiber grating(LPFG)coated with a metal chelating agent membrane.In this study,both theoretical and experimental investigations are conducted to examine the sensing characteristics of the system towards copper ion and iron ion solutions.The results demonstrate that under the premise of ensuring solution flow,the system can achieve specific identification of different types of heavy metal ions.Furthermore,it exhibits concentration sensing sensitivities of 9.23×10^(4) mL·nm/mol and 7.13×10^(4) mL·nm/mol for copper sulfate(CuSO_(4))and ferric chloride(FeCl_(3))solutions,respectively.Therefore,this sensing system offers the potential for real-time detection of metal ions. | GUO Junqi ZHOU Yanfang ZHENG Wenyue XU Qianwen LIU Yu LI Renpu | 2024 | Optoelectronics Letters2024，20，4： | 0 |
| 13 | CD19-targeted chimeric antigen receptor-modified T cells induce remission in patients with relapsed acute B lymphoblastic leukemia after umbilical cord blood transplantation显示文摘To the Editor:Umbilical cord blood transplant(UCBT)serves as an alternative option for treating patients with B cell acute lymphoblastic leukemia(ALL),in the absence of a compatible donor.However,disease recurrence presents a difficult challenge.Chimeric antigen receptor(CAR)-T cell therapy is a promising approach for treating patients with relapsed/refractory ALL.Among the intensive investigations of infusion of CAR-T cells after transplant,few focus on patients who were administered CAR-T therapy after they relapsed subsequently to UCBT.Here,we report the response rate,toxicity,and survival of CD19 CAR-T cells administered to 10 children and young adults with relapsed acute B lymphoblastic leukemia(B-ALL)after UCBT.Between April 2018 and September 2019,11 patients with relapsed B-ALL after UCBT were enrolled,including three females and eight males,the median age was 10 years(range 7-22 years)and median weight was 35.0 kg(range 21.0-72.0 kg).Patient 10 was excluded because of unsuccessful cell culture. | Qianwen Xu Hui Xu Lei Xue Min Wang Guiwang Pan Xuhan Zhang Kaidi Song Wen Yao Xiang Wan Juan Tong Huilan Liu Hanying Xu Xin Liu Xiaoyu Zhu Zimin Sun Lin Yang Xingbing Wang | 2022 | Chinese Medical Journal2022，，1： | 0 |
| 14 | MicrobiotaProcess:A comprehensive R package for deep mining microbiome显示文摘The data output from microbiome research is growing at an accelerating rate,yet mining the data quickly and efficiently remains difficult.There is still a lack of an effective data structure to represent and manage data,as well as flexible and composable analysis methods.In response to these two issues,we designed and developed the MicrobiotaProcess package.It provides a comprehensive data structure,MPSE,to better integrate the primary and intermediate data,which improves the integration and exploration of the downstream data.Around this data structure,the downstream analysis tasks are decomposed and a set of functions are designed under a tidy framework.These functions independently perform simple tasks and can be combined to perform complex tasks. | Shuangbin Xu Li Zhan Wenli Tang Qianwen Wang Zehan Dai Lang Zhou Tingze Feng Meijun Chen Tianzhi Wu Erqiang Hu Guangchuang Yu | 2023 | The Innovation2023，4，2： | 0 |
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