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| 1 | A group of SUVH methyl-DNA binding proteins regulate expression of the DNA demethylase ROS_1 in Arabidopsis显示文摘DNA methylation is typically regarded as a repressive epigenetic marker for gene expression.Genome-wide DNA methylation patterns in plants are dynamically regulated by the opposing activities of DNA methylation and demethylation reactions. In Arabidopsis, a DNA methylation monitoring sequence(MEMS) in the promoter of the DNA demethylase gene ROS_1 functions as a methylstat that senses these opposing activities and regulates genome DNA methylation levels by adjusting ROS_1 expression. How DNA methylation in the MEMS region promotes ROS_1 expression is not known. Here, we show that several Su(var)3-9 homologs(SUVHs) can sense DNA methylation levels at the MEMS region and function redundantly to promote ROS_1 expression. The SUVHs bind to the MEMS region, and the extent of binding is correlated with the methylation level of the MEMS.Mutations in the SUVHs lead to decreased ROS_1 expression, causing DNA hypermethylation at more than 1,000 genomic regions. Thus, the SUVHs function to mediate the activation of gene transcription by DNA methylation. | Xinlong Xiao Jieqiong Zhang Tao Li Xing Fu Viswanathan Satheesh Qingfeng Niu Zhaobo Lang Jian-Kang Zhu Mingguang Lei | 2019 | Journal of Integrative Plant Biology2019，61，2： | 11 |
| 2 | Machine learning in nuclear physics at low and intermediate energies显示文摘Machine learning(ML)is becoming a new paradigm for scientific research in various research fields due to its exciting and powerful capability of modeling tools used for big-data processing tasks.In this review,we first briefly introduce the different methodologies used in ML algorithms and techniques.As a snapshot of many applications by ML,some selected applications are presented,especially for low-and intermediate-energy nuclear physics,which include topics on theoretical applications in nuclear structure,nuclear reactions,properties of nuclear matter,and experimental applications in event identification/reconstruction,complex system control,and firmware performance.Finally,we present a summary and outlook on the possible directions of ML use in low-intermediate energy nuclear physics and possible improvements in ML algorithms. | Wanbing He Qingfeng Li Yugang Ma Zhongming Niu Junchen Pei Yingxun Zhang | 2023 | Science China(Physics,Mechanics & Astronomy)2023，66，8： | 3 |
| 3 | Novel nanoporous palladium catalyst for electroreduction of hydrogen peroxide显示文摘Titanium-supported nanoporous palladium catalyst(Pd/Ti) was prepared by a hydrothermal method using PdCl2 as a precursor,ethylenediamine tetraacetic acid(EDTA) as a ligand,and formaldehyde as a reduction agent.Complex Pd-EDTA2-is favorable for the formation of Pd particles with nanoscale sizes.The electroactivity of the Pd/Ti catalyst towards the electroreduction of hydrogen peroxide in 1 mol/L NaOH solution was evaluated by voltammetric techniques.Both linear scan voltammetric and chronoamperometric data present significantly large steady-state reduction current density of the hydrogen peroxide electroreduction on the prepared Pd/Ti catalyst.The results show that the prepared Pd/Ti catalyst is an effective electrocatalyst for the electroreduction of hydrogen peroxide in alkaline media. | YI Qingfeng NIU Fengjuan | 2011 | Rare Metals2011，30，4： | 2 |
| 4 | Fabrication of novel porous Pd particles and their electroactivity towards ethanol oxidation in alkaline media显示文摘 | Qingfeng Yi Fengjuan Niu Lizhi Sun | 2011 | Fuel2011，90，： | 1 |
| 5 | Fabrication of novel porous Pd particles and their electroactivity towards ethanol oxidation in alkaline media显示文摘 | Qingfeng Yi Fengjuan Niu Lizhi Sun | 2011 | Fuel2011，90，： | 1 |
| 6 | Fabrication of novel porous Pd particles and their electroactivity towards ethanol oxidation in alkaline media显示文摘 | Qingfeng Yi Fengjuan Niu Lizhi Sun | 2011 | Fuel2011，，8： | 1 |
| 7 | Fabrication of novel porous Pd particles and their electroactivity towards etha- nol oxidation in alkaline media 显示文摘 | Yi Qingfeng Niu Fengjuan Sun Lizhi | 2011 | Fuel2011，90，： | 1 |
| 8 | Fabrication of novel porous Pd particles and their electroactivity towards ethanol oxidation in alkaline media显示文摘 | Qingfeng Yi Fengjuan Niu Lizhi Sun | 2011 | Fuel2011，，8： | 1 |
| 9 | Expanding the scope of CRISPR/Cas9-mediated genome editing in plants using an xCas9 and Cas9-NG hybrid^FA显示文摘The widely used Streptococcus pyogenes Cas9(SpCas9)requires NGG as a protospacer adjacent motif(PAM)for genome editing.Although Sp Cas9 is a powerful genome-editing tool,its use has been limited on the targetable genomic locus lacking NGG PAM.The Sp Cas9 variants xCas9 and Cas9-NG have been developed to recognize NG,GAA,and GAT PAMs in human cel s.Here,we show that xCas9 cannot recognize NG PAMs in tomato,and Cas9-NG can recognize some of our tested NG PAMs in the tomato and Arabidopsis genomes.In addition,we engineered BrSp Cas9(XNG-Cas9)based on mutations from both xCas9 and Cas9-NG,and found that XNG-Cas9 can efficiently mutagenize endogenous target sites with NG,GAG,GAA,and GAT PAMs in the tomato or Arabidopsis genomes.The PAM compatibility of XNG-Cas9 is the broadest reported to date among Cas9 s(SpCas9 and Cas9-NG)active in plant. | Qingfeng Niu Siqun Wu Yansha Li Xiaoxuan Yang Ping Liu Yaping Xu Zhaobo Lang | 2020 | Journal of Integrative Plant Biology2020，62，4： | 1 |
| 10 | DNA cytosine methylation dynamics and functional roles in horticultural crops显示文摘Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases.In recent years,the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research.This review describes the regulatory mechanisms of DNA cytosine methylation in plants.It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening,development,senescence,plant height,organ size,and under biotic and abiotic stresses in horticultural crops.The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding,genetic improvement,research,innovation,and exploitation of new cultivars of horticultural crops. | Peipei Liu Ruie Liu Yaping Xu Caixi Zhang Qingfeng Niu Zhaobo Lang | 2023 | Horticulture Research2023，10，10： | 0 |
| 11 | Specific pupylation as IDEntity reporter(SPIDER)for the identification of protein-biomolecule interactions显示文摘Protein-biomolecule interactions play pivotal roles in almost all biological processes.For a biomolecule of interest,the identification of the interacting protein(s)is essential.For this need,although many assays are available,highly robust and reliable methods are always desired.By combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin(SA)-biotin system,we developed the Specific Pupylation as IDEntity Reporter(SPIDER)method for identifying protein-biomolecule interactions.Using SPIDER,we validated the interactions between the known binding proteins of protein,DNA,RNA,and small molecule.We successfully applied SPIDER to construct the global protein interactome for m^(6)A and m RNA,identified a variety of uncharacterized m^(6)A binding proteins,and validated SRSF7 as a potential m^(6)A reader.We globally identified the binding proteins for lenalidomide and Cob B.Moreover,we identified SARS-CoV-2-specific receptors on the cell membrane.Overall,SPIDER is powerful and highly accessible for the study of proteinbiomolecule interactions. | He-Wei Jiang Hong Chen Yun-Xiao Zheng Xue-Ning Wang Qingfeng Meng Jin Xie Jiong Zhang ChangSheng Zhang Zhao-Wei Xu Zi-Qing Chen Lei Wang Wei-Sha Kong Kuan Zhou Ming-Liang Ma Hai-Nan Zhang Shu-Juan Guo Jun-Biao Xue Jing-Li Hou Zhe-Yi Liu Wen-Xue Niu Fang-Jun Wang Tao Wang Wei Li Rui-Na Wang Yong-Jun Dang Daniel MCzajkowsky JianFeng Pei Jia-Jia Dong Sheng-Ce Tao | 2023 | Science China(Life Sciences)2023，66，8： | 0 |
| 12 | A novel protein complex that regulates active DNA demethylation in Arabidopsis显示文摘Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression.The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1000 s of genomic regions in Arabidopsis.How ROS1 is regulated and targeted to specific genomic regions is not well understood.Here,we report the discovery of an Arabidopsis protein complex that contains ROS1,regulates ROS1 gene expression,and likely targets the ROS1 protein to specific genomic regions.ROS1 physically interacts with a WD40 domain protein(RWD40),which in turn interacts with a methyl-DNA binding protein(RMB1)as well as with a zinc finger and homeobox domain protein(RHD1).RMB1 binds to DNA that is methylated in any sequence context,and this binding is necessary for its function in vivo.Loss-of-function mutations in RWD40,RMB1,or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1.Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter,plants mutated in RWD40,RMB1,or RHD1 show increased ROS1 expression.Importantly,ROS1 binding to the ROS1 promoter requires RWD40,RMB1,and RHD1,suggesting that this complex dictates ROS1 targeting to this locus.Our results demonstrate that ROS1 forms a protein complex with RWD40,RMB1,and RHD1,and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis. | Pan Liu Wen-Feng Nie Xiansong Xiong Yuhua Wang Yuwei Jiang Pei Huang Xueqiang Lin Guochen Qin Huan Huang Qingfeng Niu Jiamu Du Zhaobo Lang Rosa Lozano-Duran Jian-Kang Zhu | 2021 | Journal of Integrative Plant Biology2021，63，4： | 0 |
| 13 | Proteasome Inhibitors Sensitize Hepatocellular Carcinoma Cells to TRAIL显示文摘OBJECTIVE To investigate the effect of proteasome inhibition on the sensitivity of carcinoma cells to TRAIL-inducing apoptosis, and to study the mechanism of the response. METHODS Human hepatocellular carcinoma cells, pretreated with the proteasome inhibitor, MG132, were cotreated with TRAIL. Western blot assays, immunoprecipitation and RT-PCR were performed to test the expression of the Bcl-2 family proteins and Bax mRNA. RESULTS We found that (i) proteasome inhibition sensitized the human hepatocellular carcinoma cells to TRAIL; and (ii) resulted in Bax accumulation before release of cytochrome C and induction of apoptosis. These results were associated with the ability of proteasome inhibitors to overcome Bcl-2-mediated antiapoptotic function; (iii) Bax is regulated by an ubiquitin/proteasome-dependent degradation pathway. CONCLUSION Proteasome inhibition sensitized hepatocellular carcinoma cells to TRAIL by the inhibition of the ubiquitin/proteasome-mediated Bax degradation pathway. | Qingfeng Sheng Yurong Shi Qiang Li Jihui Hao Ruifang Niu Xiyin Wei Yi Yang Lin Zhang | 2006 | Chinese Journal of Clinical Oncology2006，3，6： | 0 |
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