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| 1 | A complete assembly of the rice Nipponbare reference genome显示文摘Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa ssp.japonica cv.Nipponbare)was initially released by the International Rice Genome Sequencing Project(International Rice Genome Sequencing Project,2005).Thereafter,the reference genome was further updated in 2013 with improved genome assembly(IRGSP-1.0)and gene annotations(MSU7,RAP-DB)(Kawahara et al.,2013;Sakai et al.,2013).In the past 10 years,this reference has been serving as one of the most important genetic resources for subsequent rice functional genomics efforts.As several rice genomes had been assembled into gapless chromosomes with only 2–5 telomeres absent(Li et al.,2021;Song et al.,2021;Zhang et al.,2022),the IRGSP1.0 and its annotations still performed as the most widely used reference.However,limitations of sequencing technology and intricate genomic organization led to an under-representation of complex regions in this reference,leaving a total of 72 major gaps(including 19 telomeres),167 minor gaps,and 779 unknown bases(Kawahara et al.,2013),with an estimated length of3%of the genome unsolved. | Lianguang Shang Wenchuang He Tianyi Wang Yingxue Yang Qiang Xu Xianjia Zhao Longbo Yang Hong Zhang Xiaoxia Li Yang Lv Wu Chen Shuo Cao Xianmeng Wang Bin Zhang Xiangpei Liu Xiaoman Yu Huiying He Hua Wei Yue Leng Chuanlin Shi Mingliang Guo Zhipeng Zhang Bintao Zhang Qiaoling Yuan Hongge Qian Xinglan Cao Yan Cui Qianqian Zhang Xiaofan Dai Congcong Liu Longbiao Guo Yongfeng Zhou Xiaoming Zheng Jue Ruan Zhukuan Cheng Weihua Pan Qian Qian | 2023 | Molecular Plant2023，16，8： | 1 |
| 2 | Kernel Optimization on Short-Range Potentials Computations in Molecular Dynamics Simulations显示文摘We present multi-threading and SIMD optimizations on short-range potential calculation kernel in Molecular Dynamics.For the multi-threading optimization,we design a partition-and-two-steps(PTS)method to avoid write conflicts caused by using Newton’s third law.Our method eliminates serialization bottle-neck without extra memory.We implement our PTS method using OpenMP.Afterwards,we discuss the influence of the cutoff if statement on the performance of vectorization in MD simulations.We propose a pre-searching neighbors method,which makes about 70%atoms meet the cutoff check,reducing a large amount of redundant calculation.The experiment results prove our PTS method is scalable and efficient.In double precision,our 256-bit SIMD implementation is about 3×faster than the scalar version. | Xianmeng Wang Jianjiang Li Jue Wang Xinfu He Ningming Nie | 2015 | 国际计算机前沿大会会议论文集2015，，B12： | 0 |
| 3 | A centromere map based on super pan-genome highlights the structure and function of rice centromeres显示文摘Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.Rice centromeres are crucial for chromosome segregation,and contain some unreported genes.Due to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is needed.We constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.We showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary patterns.We also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution.Furthermore,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 methods.By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement. | Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian Longbiao Guo Lianguang Shang | 2024 | Journal of Integrative Plant Biology2024，66，2： | 0 |
| 4 | HBXIP blocks myosin-ⅡA assembly by phosphorylating and interacting with NMHC-ⅡA in breast cancer metastasis显示文摘Tumor metastasis depends on the dynamic balance of the actomyosin cytoskeleton.As a key component of actomyosin filaments,non-muscle myosin-ⅡA disassembly contributes to tumor cell spreading and migration.However,its regulatory mechanism in tumor migration and invasion is poorly understood.Here,we found that oncoprotein hepatitis B X-interacting protein(HBXIP) blocked the myosin-ⅡA assemble state promoting breast cancer cell migration.Mechanistically,mass spectrometry analysis,co-immunoprecipitation assay and GST-pull down assay proved that HBXIP directly interacted with the assembly-competent domain(ACD) of non-muscle heavy chain myosin-ⅡA(NMHC-ⅡA).The interaction was enhanced by NMHC-ⅡA S1916 phosphorylation via HBXIP-recruited protein kinase PKCβⅡ.Moreover,HBXIP induced the transcription of PRKCB,encoding PKCβⅡ,by coactivating Sp1,and triggered PKCβⅡ kinase activity.Interestingly,RNA sequencing and mouse metastasis model indicated that the anti-hyperlipidemic drug bezafibrate(BZF) suppressed breast cancer metastasis via inhibiting PKCβⅡ-mediated NMHC-ⅡA phosphorylation in vitro and in vivo.We reveal a novel mechanism by which HBXIP promotes myosin-ⅡA disassembly via interacting and phosphorylating NMHC-ⅡA,and BZF can serve as an effective anti-metastatic drug in breast cancer. | Lu Zhang Xiaolei Zhou Bowen Liu Xuhe Shi Xianmeng Li Feifei Xu Xueli Fu Xue Wang Kai Ye Tianzhi Jin Huimin Sun Qianqian Li Weiying Zhang Lihong Ye | 2023 | Acta Pharmaceutica Sinica B2023，13，3： | 0 |
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