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Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition

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Journal of Integrative Plant Biology 2022年第9期64卷 1690-1705页

作者： Shuo Zhang Li Deng Lun Zhao Changyin Wu National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan430070 China

RICE INDETERMINATE 1(RID1)plays a critical role in controlling floral transition in rice(Oryza sativa).However,the molecular basis for this effect,particularly the target genes and regulatory specificity,remains largely unclear.Here,we performed chromatin immunoprecipitation followed by sequencing(ChIP-seq)in young leaves at the pre-floral-transition stage to identify the target genes of RID1,identifying 2,680 genes associated with RID1 binding sites genome-wide.RID1 binding peaks were highly enriched for TTTGTC,the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1.Interestingly,CACGTG and GTGGGCCC,two previously uncharacterized indirect binding motifs,were enriched through the interactions of RID1 with the novel floweringpromoting proteins OsPIL12 and OsTCP11,respectively.Moreover,the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes,such as HEADING DATE1(HD1)and FLAVIN-BINDING,KELCH REPEAT,F-BOX 1(OsFKF1).Notably,transcriptome sequencing(RNA-seq)analysis revealed roles of RID1 in diverse developmental pathways.Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136(a repressor of rice flowering)and negatively regulates its expression.Overall,our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.

关键词： ChIP-seq floral transition OsERF#136 rice(Oryza sativa) RID1 RNA-seq

Review on Metal-Acid Tandem Catalysis for Hydrogenative Rearrangement of Furfurals to C_(5) Cyclic Compounds

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Transactions of Tianjin University 2023年第5期29卷 347-359页

作者： Xiang li Qiang deng School of Chemistry and Chemical Engineering Nanchang UniversityNo.999 Xuefu AvenueNanchang 330031China College of Forestry Jiangxi Agricultural UniversityNo.1101 Zhimin AvenueNanchang 330045China

Hydrogenative rearrangement of biomas s-derived furfurals(furfural and 5-hydroxymethyl furfural) to C_(5) cyclic compounds(such as cyclopentanones and cyclopentanols) offers an expedient reaction route for acquiring O-containing value-added chemicals thereby replacing the traditional petroleum-based approaches.The scope for developing efficient bifunctional catalysts and establishing mild reaction conditions for upgrading furfurals to cyclic compounds has stimulated immense deliberation in recent years.Extensive efforts have been made toward developing catalysts for multiple tandem conversions,including those with various metals and supports.In this scientific review,we aim to summarize the research progress on the synergistic effect of the metal-acid sites,including simple metal-supported acidic supports,adjacent metal acid sites-supported catalysts,and in situ H_(2)-modified bifunctional catalysts.Distinctively,the catalytic performance,catalytic mechanism,and future challenges for the hydrogenative rearrangement are elaborated in detail.The methods highlighted in this review promote the development of C_(5) cyclic compound synthesis and provide insights to regulate bifunctional catalysis for other applications.

关键词： Bifunctional catalysts Furfurals Hydrogenative rearrangement C_(5)cyclic compounds Synergistic catalysis

Advances in plastid transformation for metabolic engineering in higher plants

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aBIOTECH 2022年第3期3卷 224-232页

作者： Sheng Yang Yi deng Shengchun li State Key Laboratory of Biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan430062China

The plastid(chloroplast)genome of higher plants is an appealing target for metabolic engineering via genetic transformation.Although the bacterial-type plastid genome is small compared with the nuclear genome,it can accommodate large quantities of foreign genes that precisely integrate through homologous recombination.Engineering complex metabolic pathways in plants often requires simultaneous and concerted expression of multiple transgenes,the possibility of stacking several transgenes in synthetic operons makes the transplastomic approach amazing.The potential for extraordinarily high-level transgene expression,absence of epigenetic gene silencing and transgene containment due to the exclusion of plastids from pollen transmission in most angiosperm species further add to the attractiveness of plastid transformation technology.This minireview describes recent advances in expanding the toolboxes for plastid genome engineering,and highlights selected high-value metabolites produced using transplastomic plants,including artemisinin,astaxanthin and paclitaxel.

关键词： Plastid transformation Metabolic engineering Multiple transgenes High-level expression

INVARIANTS-PRESERVING DU FORT-FRANKEL SCHEMES AND THEIR ANALYSES FOR NONliNEAR SCHRÖDINGER EQUATIONS WITH WAVE OPERATOR

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Journal of Computational Mathematics 2024年第3期42卷 814-850页

作者： Dingwen deng Zhijun li College of Mathematics and Information Science Nanchang Hangkong UniversityNanchang 330063China

Du Fort-Frankel finite difference method(FDM)was firstly proposed for linear diffusion equations with periodic boundary conditions by Du Fort and Frankel in 1953.It is an explicit and unconditionally von Neumann stable scheme.However,there has been no research work on numerical solutions of nonlinear Schrödinger equations with wave operator by using Du Fort-Frankel-type finite difference methods(FDMs).In this study,a class of invariants-preserving Du Fort-Frankel-type FDMs are firstly proposed for one-dimensional(1D)and two-dimensional(2D)nonlinear Schrödinger equations with wave operator.By using the discrete energy method,it is shown that their solutions possess the discrete energy and mass conservative laws,and conditionally converge to exact solutions with an order of for ofο(T^(2)+h_(x)^(2)+(T/h_(x))^(2))1D problem and an order ofο(T^(2)+h_(x)^(2)+h_(Y)^(2)+(T/h_(X))^(2)+(T/h_(y))^(2))for 2D problem in H1-norm.Here,τdenotes time-step size,while,hx and hy represent spatial meshsizes in x-and y-directions,respectively.Then,by introducing a stabilized term,a type of stabilized invariants-preserving Du Fort-Frankel-type FDMs are devised.They not only preserve the discrete energies and masses,but also own much better stability than original schemes.Finally,numerical results demonstrate the theoretical analyses.

关键词： Nonlinear Schrodinger equations with wave operator Du Fort-Frankel finite difference methods Discrete energy and mass conservative laws Numerical convergence

Diagnostic value of aldosterone to renin ratio calculated by plasma renin activity or plasma renin concentration in primary aldosteronism: a meta-analysis

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Chinese Medical Journal 2022年第6期135卷 639-647页

作者： Zhenjie liu Xiaohong deng li Luo Shaopeng li Man li Qinqin deng Weiguo Zhong Qiang Luo Department of Clinical Laboratory The Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdong 510120China Department of Clinical Laboratory Guangdong Provincial Hospital of Chinese MedicineGuangzhouGuangdong 510120China Guangzhou University of Chinese Medicine GuangzhouGuangdong 510120China

Background:Since the diagnostic value of aldosterone to renin ratio(ARR)calculated by plasma renin concentration(PRC)or plasma renin activity(PRA)is still inconclusive,we conducted a meta-analysis by systematically reviewing relevant literature to explore the difference in the diagnostic efficacy of ARR calculated by PRC or PRA,so as to provide guidance for clinical diagnosis.Methods:We searched PubMed,Embase,and Cochrane library from the establishment of the database to March 2021.We included studies that report the true positive,false positive,true negative,and false negative values for the diagnosis of primary aldosteronism,and we excluded duplicate publications,research without full text,incomplete information,or inability to conduct data extraction,animal experiments,reviews,and systematic reviews.STATA 15.1 was used to analyze the data.Results:The pooled results showed that ARR(plasma aldosterone concentration[PAC]/PRC)had a sensitivity of 0.82(95%confidence interval[CI]:0.78-0.86),a specificity of 0.94(95%CI:0.92-0.95),a positive-likelihood ratio(LR)of 12.77(95%CI:7.04-23.73),a negative LR of 0.11(95%CI:0.07-0.17),and symmetric area under the curve(SAUC)of 0.982,respectively.Furthermore,the diagnostic odds ratio(DOR)of ARR(PAC/PRC)was 180.21.Additionally,the pooled results showed that ARR(PAC/PRA)had a sensitivity of 0.91(95%CI:0.86-0.95),a specificity of 0.91(95%CI:0.90-0.93),a positive LR of 7.30(95%CI:2.99-17.99),a negative LR of 0.10(95%CI:0.04-0.26),and SAUC of 0.976,respectively.The DOR of ARR(PAC/PRA)was 155.52.Additionally,we conducted a subgroup analysis for the different thresholds(<35 or≥35)of PAC/PRC.The results showed that the DOR of the cut-off≥35 groups was higher than the cut-off<35 groups(DOR=340.15,95%CI:38.32-3019.66;DOR=116.40,95%CI=23.28-581.92).Conclusions:The research results suggest that the determination of ARR(PAC/PRC)and ARR(PAC/PRA)was all effective screening tools for PA.The diagnostic accuracy and diagnostic value of ARR(PAC/PRC)are higher than ARR(PAC/PRA).In addition,within

关键词： Primary aldosteronism Aldosterone to renin ratio Plasma renin activity Plasma renin concentration Diagnostic value Meta-analysis

Fe-bearing minerals and implications for gold mineralization for the Wangu deposit in Central Jiangnan Orogen

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Acta Geochimica 2023年第3期42卷 552-571页

作者： Teng deng Longyue Zhou Zenghua li State Key Laboratory of Nuclear Resources and Environment East China University of TechnologyNanchang 330013China School of Earth Sciences East China University of TechnologyNanchang 330013China

Hydrothermal alteration with bleaching of host rocks is the most important prospecting indicator for gold deposits in the Jiangnan Orogen Belt.The alteration has been identified as pre-ore carbonate(siderite)-sericitization and the Fe of siderite in the alteration zone is derived from the host rocks rather than fluids.In addition,such alteration decreases in intensity and width with depth and gold mineralization also occur in the non-bleached rocks,casting doubt on the reliability of the prospecting indicator.Detailed petrographic work and SEM analysis on the Wangu deposit indicate that there are two types of siderites,i.e.,Sd1 and Sd2.Among them,Sd1 grains are relatively small and distributed along the planes of unaltered host rocks,while Sd2 grains,only occurring in the altered slates,are commonly larger.Both types of siderites were altered by auriferous fluids,producing porous cores and minerals such as pyrite,quartz,and ankerite.Compared with unaltered parts,the altered parts have lower Fe,but higher U,Pb,and REE.In addition,Sd1 and Sd2 are similar in Mn,Na,V,and Sr concentrations but different in Fe and Mg.The occurrence and geochemical compositions of both siderites indicate that Sd1 could be transformed into Sd2 by pre-mineralization alteration through dissolution-reprecipitation.Chlorite is another important Fe-bearing mineral in the host rocks,and EPMA analysis suggests that it is ripidolite with relatively high Fe contents.Consequently,chlorite can also provide Fe to form the pre-ore carbonate(siderite)-sericitization.Geochemical modeling demonstrates that both ripidolite and siderite can result in sulfidation and therefore gold precipitation.As a result,this study demonstrates that pre-ore alteration with characterized bleaching is not a prerequisite for gold mineralization despite of its prominent features.Due to the presence of Fe-bearing Sd1 and chlorite,gold mineralization could still occur through sulfidation in the unaltered rocks.

关键词： Jiangnan Orogen Gold precipitation Wangu deposit Hydrothermal alteration Fe-bearing minerals

Update on the role of noncoding RNAs in vitiligo

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Chinese Medical Journal 2022年第7期135卷 793-795页

作者： Ting Zhou Dong li Yunhua deng Department of Dermatology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubel 430030China

Vitiligo is a prevailing disfiguring skin disorder characterized by the selective absence of functional melanocytes,affecting 0.5%to 1%of the global population.^([1])Several hypotheses have been proposed for its pathogenesis,including autoimmunity,oxidative stress,genetic and environmental factors,and metabolic abnormalities.^([2])No individual factor can completely explain the complex progression of this disease.Most of the human genome encodes RNAs that are not translated into proteins,termed noncoding RNAs(ncRNAs).

关键词： Vit noncoding pathogenesis

A clustering based method to complete frame of discernment

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Chinese Journal of Aeronautics 2023年第4期36卷 400-408页

作者： Wenran YANG Xinde li Yong deng Institute of Fundamental and Frontier Science University of Electronic Science and Technology of ChinaChengdu 610054China Key Laboratory of Measurement and Control of CSE School of AutomationSoutheast UniversityNanjing 210096China School of Education Shannxi Normal UniversityXi’an 710062China School of Knowledge Science Japan Advanced Institute of Science and TechnologyNomiIshikawa 923-1211Japan Department of Management Technologyand EconomicsETH ZurichZurich 8092Switzerland

When the existing information does not contain all categories,the Generalized Evidence Theory(GET)can deal with information fusion.However,the question of how to determine the number of categories through GET is still intriguing.To address this question,a modified k-means clustering,named centers initialized clustering is proposed,filling the gap of identification and complement of the frame of discernment.Based on this clustering method,the number of cat-egories is determined.The initialized centers selected by center density keep the cluster results con-stant,enhancing the stability of clustering results.Besides,constructing Generalized basic Probability Assignment(GBPA)modules in a conservative way improves the reliability of the results.The mass of empty set in combined GBPAs is the indicator of the number of categories.Experiments on real and artificial data sets are conducted to show the effectiveness.

关键词： Dempster-Shafer evidence theory Generalized evidence theory Information fusion K-means clustering Open world assumption Target recognition

Web page classification based on heterogeneous features and a combination of multiple classifiers

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Frontiers of Information Technology & Electronic Engineering 2020年第7期21卷 995-1004页

作者： Li Deng Xin DU Ji-zhong SHEN College of Information Science&Electronic Engineering Zhejiang UniversityHangzhou 310027China

Precise web page classification can be achieved by evaluating features of web pages, and the structural features of web pages are effective complements to their textual features. Various classifiers have different characteristics, and multiple classifiers can be combined to allow classifiers to complement one another. In this study, a web page classification method based on heterogeneous features and a combination of multiple classifiers is proposed. Different from computing the frequency of HTML tags, we exploit the tree-like structure of HTML tags to characterize the structural features of a web page. Heterogeneous textual features and the proposed tree-like structural features are converted into vectors and fused. Confidence is proposed here as a criterion to compare the classification results of different classifiers by calculating the classification accuracy of a set of samples. Multiple classifiers are combined based on confidence with different decision strategies, such as voting, confidence comparison, and direct output, to give the final classification results. Experimental results demonstrate that on the Amazon dataset, 7-web-genres dataset, and DMOZ dataset, the accuracies are increased to 94.2%, 95.4%, and 95.7%, respectively. The fusion of the textual features with the proposed structural features is a comprehensive approach, and the accuracy is higher than that when using only textual features. At the same time, the accuracy of the web page classification is improved by combining multiple classifiers, and is higher than those of the related web page classification algorithms.

关键词： Web page classification Web page features Combined classifiers