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The RNA binding protein EHD6 recruits the m^(6)A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

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Molecular Plant 2024年第6期17卷 935-954页

作者： Song Cui Peizhe Song Chaolong Wang Saihua Chen Benyuan Hao Zhuang Xu Liang Cai Xu Chen Shanshan Zhu Xiangchao Gan Hui Dong Yuan Hu Liang zhou Haigang Hou Yunlu Tian Xi Liu Liangming Chen Shijia Liu Ling Jiang Haiyang Wang Guifang Jia shirong zhou Jianmin Wan State Key Laboratory for Crop Genetics&Germplasm Enhancement and Utilization Zhongshan Biological Breeding LaboratoryNational Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjing 210095China State Key Laboratory for Crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking-Tsinghua Center for Life SciencesBeijing Advanced Center of RNA BiologyPeking UniversityBeijingChina Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Max Planck Institute for Plant Breeding Research Carl-von-Linne´-Weg 1050829 KolnGermany

N6-Methyladenosine(m^(6)A)is one of the most abundant modifications of eukaryotic mRNA,but its comprehensive biological functionality remains further *** this study,we identified and characterized a new flowering-promoting gene,EARLY HEADING DATE6(EHD6),in ***6 encodes an RNA recognition motif(RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein(RNP)granules and can bind both m^(6)A-modified RNA and unmodified RNA *** found that EHD6 can physically interact with YTH07,a YTH(YT521-B homology)domain-containing m^(6)A *** showed that their interaction enhances the binding of an m^(6)A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated *** these condensates,the mRNA of a rice flowering repressor,CONSTANS-like 4(OsCOL4),becomes sequestered,leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 *** together,these results not only shed new light on the molecular mechanism of efficient m^(6)A recognition by the collaboration between an RNA binding protein and YTH family m^(6)A reader,but also uncover the potential for m^(6)A-mediated translation regulation through phaseseparated ribonucleoprotein condensation in rice.

关键词： N6-methyladenosine m^(6)A EHD6 YTH domain-containing protein phase separation heading date

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基于贝叶斯深度学习方法的上海新冠肺炎病例时空预测和不确定性量化

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应用概率统计 2024年第2期40卷 298-322页

作者：周世荣汤银才王平平庄亮亮徐嘉威华东师范大学统计学院统计与数据科学前沿理论及应用教育部重点实验室上海200062 温州大学数理学院温州325035 南京财经大学经济学院南京210023 浙江工商大学统计与数学学院杭州310018

2022年春季在上海爆发的新冠肺炎疫情对上海的社会、经济和居民的日常生活造成了严重影响.新冠肺炎的传播通常表现出复杂的非线性动力学,受环境、人口统计、医疗条件、核酸或抗原检测频率、流行病控制策略等影响.具有复杂网络结构和广... 详细信息

2022年春季在上海爆发的新冠肺炎疫情对上海的社会、经济和居民的日常生活造成了严重影响.新冠肺炎的传播通常表现出复杂的非线性动力学,受环境、人口统计、医疗条件、核酸或抗原检测频率、流行病控制策略等影响.具有复杂网络结构和广泛训练的长短期记忆(LSTM)模型被广泛用于学习和预测流行病的传播.然而,这种模型既没有解释数据的不确定性,也没有考虑各种协变量和异质性的影响.因此,本文提出了一个两阶段LSTM嵌套广义泊松回归模型来分析2022年春季上海爆发的新冠肺炎疫情数据.在第一阶段,训练一个多层LSTM网络来学习特定地区的感染数据,然后使用训练好的LSTM来拟合和预测有症状的新冠肺炎感染人数.在第二阶段,在分层贝叶斯框架下通过广义泊松回归模型对预测的病例数进行建模,其中相对风险的对数用带有协变量和时空异质性的随机效应的线性函数来建模.在深度学习方法的帮助下,时空广义泊松回归模型可以预测和量化每日新增症状感染数量的不确定性.此外,得益于从协变量和时空异质性的借力,基于贝叶斯深度学习方法的预测比基于LSTM方法的预测性能更好.

关键词： COVID-19 LSTM 泊松回归模型积分嵌套拉普拉斯近似(INLA)

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Research on three-step accelerated gradient algorithm in deep learning

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Statistical Theory and Related Fields 2022年第1期6卷 40-57页

作者： Yongqiang Lian Yincai Tang shirong zhou KLATASDS-MOE School of StatisticsEast China Normal UniversityShanghaiPeople's Republic of China

Gradient descent(GD)algorithm is the widely used optimisation method in training machine learning and deep learning *** this paper,based on GD,Polyak’s momentum(PM),and Nesterov accelerated gradient(NAG),we give the convergence of the algorithms from an ini-tial value to the optimal value of an objective function in simple quadratic *** on the convergence property of the quadratic function,two sister sequences of NAG’s iteration and par-allel tangent methods in neural networks,the three-step accelerated gradient(TAG)algorithm is proposed,which has three sequences other than two sister *** illustrate the perfor-mance of this algorithm,we compare the proposed algorithm with the three other algorithms in quadratic function,high-dimensional quadratic functions,and nonquadratic *** we consider to combine the TAG algorithm to the backpropagation algorithm and the stochastic gradient descent algorithm in deep *** conveniently facilitate the proposed algorithms,we rewite the R package‘neuralnet’and extend it to‘supneuralnet’.All kinds of deep learning algorithms in this paper are included in‘supneuralnet’***,we show our algorithms are superior to other algorithms in four case studies.

关键词： Accelerated algorithm backpropagation deep learning learning rate momentum stochastic gradient descent

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In-situ analysis and genetic investigation of Li-bearing minerals in McDermitt clay-type lithium deposit,Nevada,USA

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Acta Geochimica 2024年第3期43卷 478-488页

作者： Yi Cui Hanjie Wen Zhengbing zhou Kunyue Ling Lin Xu shirong Liu Fei Xu School of Earth Sciences East China University of TechnologyNanchang 330013China State Key Laboratory of Nuclear Resources and Environment East China University of TechnologyNanchang 330013China School of Earth Sciences and Resources Chang’an UniversityXi’an 710054China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Ore Deposit Geochemistry Institute of GeochemistryChinese Academy of SciencesGuiyang 550081China State Key Laboratory of Environmental Geochemistry Institute of GeochemistryChinese Academy of SciencesGuiyang 550081China

Clay-type Li deposits are poised to play a pivotal role in addressing the surging global demand for *** McDermitt clay-type Li deposit,located in Nevada,is the largest Li deposit in the United States,with Li hosted by a clay-rich sequence of smectite-dominated intervals and illite-dominated intervals,***,the occurrence of Li and the genesis of Li-bearing minerals within smectite-dominated intervals have not been thoroughly investigated in previous ***,we studied the mineralogy,the in-situ Li distribution,and the bonding environments of Li within the smectite intervals using a combination of instru-mental techniques including scanning electron microscope,transmission electron microscope,time-of-flight secondary ion mass spectrometry,and nuclear magnetic *** results indicate that the smectite exhibits low crystallinity characteristics of lacustrine clay authigenesis and is com-monly found tofill the interstices among volcanic minerals or envelop them;Li is mainly hosted by Mg-smectite rather than the volcanic *** the tuffaceous sediment samples,the volcanic glass has undergone a transformation,resulting in its complete disappearance and alteration into clay *** to the octahedral sites of Mg-smectite bounded in Li,it is referred to be *** interpret that the hectorite’s precipitation occurs in a high saline-alkaline water environment,a result of McDermitt *** conclusion can be supported by the coexistence of spherulitic calcite and ***,this study confirms hectorite as the main Li-bearing mineral and increases the understanding of the genetic model of hectorite formation in intracontinental caldera basins.

关键词： McDermitt caldera Lithium occurrence Tuffaceous sediments Mineralogy Hectorite neoformation

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Bayesian analysis of series system with dependent causes of failure

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Statistical Theory and Related Fields 2017年第1期1卷 128-140页

作者： Ancha Xu shirong zhou Department of Statistics College of Mathematics and Information ScienceWenzhou UniversityZhejiangChina

Most studies of series system assume the causes of failure are independent,which may not hold in *** this paper,dependent causes of failure are considered by using a Marshall-Olkin bivariateWeibull *** derived four reference priors based on several grouping *** sampling combined with the rejection sampling algorithm and Metropolis-Hastings algorithm is developed to obtain the estimates of the unknown *** proposed approach is compared with the maximum-likelihood method via *** find that the root-meansquared errors of the Bayesian estimates are much smaller for the case of small sample size,and that the coverage probabilities of the Bayesian estimates are much closer to the nominal ***,a real data-set is analysed for illustration.

关键词： Reference prior Bayesian analysis Weibull distribution Gibbs sampling Metropolis–Hastings algorithm

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Nuclear encoded elongation factor EF-Tu is required for chloroplast development in rice grown under low-temperature conditions

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Journal of Genetics and Genomics 2022年第5期49卷 502-505页

作者： Liang Cai Zongkai Liu Long Cai Xiaofeng Yan Yuan Hu Benyuan Hao Zhuang Xu Yunlu Tian Xi Liu Linglong Liu Ling Jiang shirong zhou Jianmin Wan State Key Laboratory for Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingJiangsu 210095China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

As a thermophilic crop that originated in tropical and subtropical areas, rice is sensitive to low temperatures, particularly during the early seedling stage. Cold stress at the seedling stage inhibits chlorophyll biosynthesis and causes oxidative damage, resulting in death(Zhao et al., 2020). Investigation of the mechanism of chloroplast development in rice seedlings under low-temperature conditions is important for breeding varieties with increased cold resistance.

关键词： seedling breeding originated

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Clock component OsPRR59 delays heading date by repressing transcription of Ehd3 in rice

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The Crop Journal 2022年第6期10卷 1570-1579页

作者： Yupeng Wang Fuqing Wu shirong zhou Weiwei Chen Chenyan Li Erchao Duan Jiachang Wang Zhijun Cheng Xin Zhang Qibing Lin Yulong Ren Cailin Lei Xiuping Guo Ziming Wu Shanshan Zhu Jianmin Wan National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China National Key Laboratory for Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095JiangsuChina Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of EducationJiangxi Agricultural UniversityNanchang 330045JiangxiChina

Heading date(or flowering time),an important agronomic trait in crop species,is closely associated with regional adaptation and *** of the Pseudo-Response Regulator(PRR)family play key roles in regulating ***,their role and molecular mechanism controlling heading date in rice is not very ***,we identified rice OsPRR protein,OsPRR59,which delayed heading under longday ***59 positively regulates yield by affecting plant height,secondary branches number per panicle,grain number per panicle,seed setting rate,and grain weight per ***59 is expressed in most tissues and its protein is localized to the *** also found that OsPRR59 directly binds to the promoter of Ehd3 to inhibit its *** with the WT,osprr59 ehd3 showed a significantly delayed heading phenotype,as did the ehd3 *** was opposite to the phenotype of the osprr59 mutant,confirming that Ehd3 acted downstream of OsPRR59 in regulating rice *** results identified a direct regulator of Ehd3,and revealed a novel molecular mechanism of clock component OsPRR proteins in regulating heading date and provide a new genetic resource for fine-tuning heading date in rice.

关键词： Circadian clock Ehd3 Heading date Oryza sativa Pseudo-response regulator

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DNA methylation modification in heterosis initiation through analyzing rice hybrid contemporary seeds

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The Crop Journal 2021年第5期9卷 1179-1190页

作者： shirong zhou Meiqing Xing Zhilong Zhao Yincong Gu Yunping Xiao Qiaoquan Liu Hongwei Xue State Key Laboratory of Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095JiangsuChina Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Shanghai OEbiotech Shanghai 201210China Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009JiangsuChina

Heterosis is an important biological phenomenon and widely applied in *** many studies have been performed by using vegetative organs of F_(1) hybrid plants,how heterosis (or hybrid vigor) is initiated and formed,particularly the underlying molecular mechanism,remain *** contemporary seeds of rice indica varieties 9311 and PA64 were innovatively used and analysis of DNA methylome of embryo and endosperm at early developing stages revealed the globally decreased DNA ***,especially those relate to hormones function and transcriptional regulation present non-additive *** identified heterosis-related superior genes are non-additively methylated in early developing hybrid contemporary seeds,suggesting that key genes/loci responsible for heterosis are epigenetically modified even in early developing hybrid seeds and hypomethylation of hybrid seeds after cross-pollination finally result in the long-term transcriptional change of F_(1) hybrid vegetative tissues after germination,demonstrating that altered DNA methylation in hybrid seeds is essential for initiation regulation and maintenance of heterosis exhibiting in F_(1) hybrid ***,a large number of genes show non-additive methylation in the endosperm of reciprocal hybrids,suggesting that endosperm might also contribute to heterosis.

关键词： DNA methylome Heterosis Rice Reciprocally hybrid seeds Embryo Endosperm

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Ribonuclease H-like gene SMALL GRAIN2 regulates grain size in rice through brassinosteroid signaling pathway

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Journal of Integrative Plant Biology 2022年第10期64卷 1883-1900页

作者： Yunshuai Huang Hui Dong Changling Mou Ping Wang Qixian Hao Min Zhang Hongmin Wu Fulin Zhang Tengfei Ma Rong Miao Kai Fu Yaping Chen Ziyan Zhu Cheng Chen Qikai Tong Zhuoran Wang shirong zhou Xi Liu Shijia Liu Yunlu Tian Ling Jiang Jianmin Wan State Key Laboratory for Crop Genetics and Germplasm Enhancement Jiangsu Nanjing National Field Scientific Observation and Research Station for Rice GermplasmNanjing Agricultural UniversityNanjing 210095China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Grain size is a key agronomic trait that determines the yield in *** of grain size by brassinosteroids(BRs)in rice has been widely ***,the relationship between the BR signaling pathway and grain size still requires further ***,we isolated a rice mutant,named small grain2(sg2),which displayed smaller grain and a semi-dwarf *** decreased grain size was caused by repressed cell expansion in spikelet hulls of the sg2 *** map-based cloning combined with a Mut Map approach,we cloned SG2,which encodes a plant-specific protein with a ribonuclease H-like ***2 is a positive regulator downstream of GLYCOGEN SYNTHASE KINASE2(GSK2)in response to BR signaling,and its mutation causes insensitivity to exogenous BR *** and biochemical analysis showed that GSK2 interacts with and phosphorylates *** further found that BRs enhance the accumulation of SG2 in the nucleus,and subcellular distribution of SG2 is regulated by GSK2 kinase *** addition,Oryza sativa OVATE family protein 19(OsOFP19),a negative regulator of grain shape,interacts with SG2 and plays an antagonistic role with SG2 in controlling gene expression and grain *** results indicated that SG2 is a new component of GSK2-related BR signaling response and regulates grain size by interacting with Os OFP19.

关键词： BR signaling grain size GSK2 Oryza sativa OsOFP19 SG2

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Modulating p-type doping of two-dimensional material palladium diselenide

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Nano Research 2024年第4期17卷 3232-3244页

作者： Jiali Yang Yu Liu En-Yang Wang Jinbo Pang shirong Huang Thomas Gemming Jinshun Bi Alicja Bachmatiuk Hao Jia Shu-Xian Hu Chongyun Jiang Hong Liu Gianaurelio Cuniberti Weijia zhou Mark H Rümmeli Institute for Advanced Interdisciplinary Research(iAIR) University of JinanJinan 250022China Institute for Materials Chemistry Leibniz Institute for Solid State and Materials Research Dresden(IFW Dresden)20 Helmholtz StrasseDresden 01069Germany State Key Lab of Transducer Technology Shanghai Institute of Microsystem and Information TechnologyChinese Academy of SciencesShanghai 200050China College of Energy Soochow Institute for Energy and Materials Innovations Soochow UniversitySuzhou 215006China Key Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu Province Soochow UniversitySuzhou 215006China School of Integrated Circuits University of Chinese Academy of SciencesBeijing 101408China Institute of Microelectronics of Tianjin Binhai New Area Tianjin 300451China Institute of Microelectronics Chinese Academy of SciencesBeijing 100029China Lukasiewicz Research Network PORT Polish Center for Technology DevelopmentStablowicka 147Wroclaw 54-066Poland School of Mathematics and Physics University of Science and Technology BeijingBeijing 100083China College of electronic information and optical engineering Nankai UniversityTianjin 300350China Centre of Polymer and Carbon Materials Polish Academy of SciencesM.Curie Sklodowskiej 34Zabrze 41-819Poland Center for Energy and Environmental Technologies VŠB-Technical University of Ostrava17.Listopadu 15Ostrava 70833Czech Republic State Key Laboratory of Crystal Materials Center of Bio&Micro/Nano Functional MaterialsShandong UniversityJinan 250100China Dresden Center for Computational Materials Science Technische Universität DresdenDresden 01062Germany Dresden Center for Intelligent Materials(GCL DCIM) Technische Universität DresdenDresden 01062Germany Institute for Materials Science and Max Bergmann Center of Biomaterials Technische Universität DresdenDresden 01069Germany Center for Advancing Electronics Dresden Technische Universität DresdenDresden 01069Germany

The van der Waals heterostructures have evolved as novel materials for complementing the Si-based semiconductor ***-10 noble metal dichalcogenides(e.g.,PtS_(2),PtSe_(2),PdS_(2),and PdSe_(2))have been listed into two-dimensional(2D)materials toolkit to assemble van der Waals *** them,PdSe_(2) demonstrates advantages of high stability in air,high mobility,and wide tunable ***,the regulation of p-type doping of PdSe_(2) remains unsolved problem prior to fabricating p–n junction as a fundamental platform of semiconductor ***,a quantitative method for the controllable doping of PdSe_(2) is yet to be *** this study,the doping level of PdSe_(2) was correlated with the concentration of Lewis acids,for example,SnCl_(4),used for *** the transfer characteristics,the threshold voltage(the gate voltage corresponding to the minimum drain current)increased after SnCl_(4) soaking ***_(2) transistors were soaked in SnCl_(4) solutions with five different *** threshold voltages from the as-obtained transfer curves were extracted for linear fitting to the threshold voltage versus doping concentration correlation *** study provides in-depth insights into the controllable p-type doping of PdSe_(2).It may also push forward the research of the regulation of conductivity behaviors of 2D materials.

关键词： two-dimensional(2D)materials Lewis acid treatment p-type doping field-effect transistors transfer characteristic

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