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The diverse roles of cytokinins in regulating leaf development

Horticulture Research 2021年第1期8卷 1753-1765页

作者： Wenqi Wu Kang Du Xiangyang Kang hairong wei Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry UniversityBeijingPR China National Engineering Laboratory for Tree Breeding Beijing Forestry UniversityBeijingChina Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMIUSA

Leaves provide energy for plants,and consequently for animals,through *** their important functions,plant leaf developmental processes and their underlying mechanisms have not been well ***,we provide a holistic description of leaf developmental processes that is centered on cytokinins and their signaling *** maintain the growth potential(pluripotency)of shoot apical meristems,which provide stem cells for the generation of leaf primordia during the initial stage of leaf formation;cytokinins and auxins,as well as their interaction,determine the phyllotaxis *** activities of cytokinins in various regions of the leaf,especially at the margins,collectively determine the final leaf morphology(e.g.,simple or compound).The area of a leaf is generally determined by the number and size of the cells in the *** promote cell division and increase cell expansion during the proliferation and expansion stages of leaf cell development,*** leaf senescence,cytokinins reduce sugar accumulation,increase chlorophyll synthesis,and prolong the leaf photosynthetic *** also briefly describe the roles of other hormones,including auxin and ethylene,during the whole leaf developmental *** this study,we review the regulatory roles of cytokinins in various leaf developmental stages,with a focus on cytokinin metabolism and signal transduction processes,in order to shed light on the molecular mechanisms underlying leaf development.

关键词： collective metabolism sugar

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Regulation of regeneration in Arabidopsis thaliana

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aBIOTECH 2023年第4期4卷 332-351页

作者： Md Khairul Islam Sai Teja Mummadi Sanzhen Liu hairong wei Computational Science and Engineering Program Michigan Technological UniversityHoughtonMI 49931USA Computer Science Michigan Technological UniversityHoughtonMI 49931USA Department of Plant Pathology Kansas State UniversityManhattanKS 66506USA College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931USA

We employed several algorithms with high efficacy to analyze the public transcriptomic data,aiming to identify key transcription factors(TFs)that regulate regeneration in Arabidopsis ***,we utilized CollaborativeNet,also known as TF-Cluster,to construct a collaborative network of all TFs,which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder(CoSE)*** analysis of these subnetworks led to the identification of nine subnetworks closely associated with *** further applied principal component analysis and gene ontology(GO)enrichment analysis to reduce the subnetworks from nine to three,namely subnetworks 1,12,and *** for TF-binding sites in the promoters of the co-expressed and co-regulated(CCGs)genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each ***,six potential candidate TFs-WOx9A,LEC2,PGA37,WIP5,PEI1,and AIL1 from subnetwork 1-were identified,and their roles in somatic embryogenesis(GO:0010262)and regeneration(GO:0031099)were discussed,so were the TFs in Subnetwork 12 and 17 associated with *** TFs identified were also assessed using the CIS-BP database and Expression *** analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to *** tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest.

关键词： Regeneration Pluripotency Transcription factor Collaborative network

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Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis

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Horticulture Research 2023年第7期10卷 265-279页

作者： Jiang Li Caili Li Yuxing Deng hairong wei Shanfa Lu Key Lab of Chinese Medicine Resources Conservation State Administration of Traditional Chinese Medicine of the People’s Republic of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Engineering Research Center of Chinese Medicine Resource Ministry of EducationBeijing 100193China College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931USA

Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal *** roots produce a group of diterpenoid lipophilic bioactive components,termed *** and regulation of tanshinones has attracted widespread ***,the methylome of *** has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely *** we report single-base resolution DNA methylomes from roots and *** analysis revealed differential methylation patterns for CG,CHG,and CHH contexts and the association between DNA methylation and the expression of genes and small *** methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in *** methylation variation analysis showed that CHH methylation contributed mostly to the *** enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_*** biosynthesis-related enzyme genes,such as DXS2,CMK,IDI1,HMGR2,DXR,MDS,CYP76AH1,2OGD25,and CYP71D373,were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in ***,gene expression was up-regulated in *** roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone *** suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in *** through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.

关键词： miltiorrhiza roots mechanism

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Breeding polyploid Populus:progress and perspective

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Forestry Research 2022年第1期2卷 25-34页

作者： Xiangyang Kang hairong wei Beijing Forestry Molecular Design and Breeding Advanced Innovation Center National Engineering Laboratory of Forestry BreedingKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of Education Beijing 100083China College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931USA

Populus is a genus of 25−30 species of deciduous flowering plants in the family Salicaceae,which are primarily planted in short-rotation planations for producing timber,pulpwood,wooden products as well as bioenergy feedstock;they are also widely planted in agricultural fields and along roadsides as shelter forest belts for windbreak,decoration,and reduction of pollutants and ***,their fast-growth and good adaptation to marginal lands enable them to provide some critical ecosystem services at various phytoremediation sites for land restoration and *** to their important roles,breeding for fast growing poplar trees has been one of the most important objectives for nearly a *** of the most demonstrated,documented achievements in this aspect is polyploid breeding,especially triploid *** paper critically reviews the various techniques used in inducing triploid plants,including natural 2n formation,artificial induction of 2n male and female gemmates through chemical or physical treatments,trait characterization of the triploid and tetraploid breeding populations,unveiling the molecular mechanisms underpinning the significantly improved traits,and identification and selection of the best triploid *** review also recapitulated the challenges and strategies facing the future of triploid breeding in Populus,including amelioration of 2n gamete induction techniques and efficiency,selection of the best parents and identification of the best progrenies,utilization of the huge amount of genomic,transcriptomic,proteomic,metabolomic,and other omics data for selecting parents for improving target traits.

关键词： traits breeding planted

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Determination of the Absolute Rate of Sea Level by Using GPS Reference Station and Tide Gauge Data

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Geo-Spatial Information Science 2005年第3期8卷 220-224页

作者： JIAO Wenhai GUO hairong FU Yang wei Ziqing Xi'an Institute of Surveying and Mapping 1 Middle Yanta Road Xi'an 710054 China

The absolute rate of mean sea level of Xiamen area is derived from the data of Xiamen tide gauge station and Xiamen GPS fiducial station of crustal movement observation network of China（CMONC）. The height variation is discussed deeply in this paper, h is shown that height has periodic variations. So the rate of vertical land movement can not be precisely obtained only from several GPS campaigns. It is pointed out that the vertical crustal movement of tide gauge station should be monitored by using long-term continuous GPS observations.

关键词： tide gauge station mean sea level GPS vertical crustal movement

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Telemetering system and its application for fruit cultivation in greenhouses

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International Journal of Agricultural and Biological Engineering 2013年第2期6卷 13-18页

作者： Zhang Daohui Wang Jiawei Zong Xiaojuan wei hairong Zhu Dongzi Liu Qingzhong Key Laboratory of Fruit Tree Biotechnology Breeding Shandong Institute of PomologyTaianShandong 271000China

Circuit of the temperature measurement equipment was improved in order to develop temperature telemetering system for cultivating fruit *** traditional temperature measuring equipments used in monitoring temperature changes in greenhouse include mercury column,merbromine column,kerosene column glass rod thermometer and mechanical inductive *** with the traditional method of temperature measurement the new system reduces the labor requirement and promotes precision monitoring and control of the *** addition,the temperature in the greenhouse was very accurate especially at night or in rainy and snowy *** new temperature telemetering system will promote the development of the fruit protection cultivation.

关键词： sweet cherry temperature wire telemetering universal instrument temperature measurement and control system

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Designing Microarray and RNA-Seq Experiments for Greater Systems Biology Discovery in Modern Plant Genomics

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Molecular Plant 2015年第2期8卷 196-206页

作者： Chuanping Yang hairong wei State Key Laboratory of Forest Tree Genetics and Breeding Northeast Forestry University Harbin Heilongjiang 150040 China Biotechnology Research Center School of Forest Resources and Environmental Science Michigan Technological University Houghton MI 49931 USA

Microarray and RNA-seq experiments have become an important part of modern genomics and systems biology. Obtaining meaningful biological data from these experiments is an arduous task that demands close attention to many details. Negligence at any step can lead to gene expression data containing inadequate or composite information that is recalcitrant for pattern extraction. Therefore, it is imperative to carefully consider experimental design before launching a time-consuming and costly experiment. Contemporarily, most genomics experiments have two objectives：（1） to generate two or more groups of comparable data for identifying differentially expressed genes, gene families, biological processes, or metabolic pathways under experimental conditions; （2） to build local gene regulatory networks and identify hierarchically important regulators governing biological processes and pathways of interest. Since the first objective aims to identify the active molecular identities and the second provides a basis for understanding the underlying molecular mechanisms through inferring causality relationships mediated by treatment, an optimal experiment is to produce biologically relevant and extractable data to meet both objectives without substantially increasing the cost. This review discusses the major issues that researchers commonly face when embarking on microarray or RNA-seq experiments and summarizes important aspects of experimental design, which aim to help researchers deliberate how to generate gene expression profiles with low background noise but with more interaction to facilitate novel biological discoveries in modern plant genomics.

关键词： experimental design microarray RNA-seq treatment time course gene regulatory network

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A systems biology approach identifies a regulator,BplERF1,of cold tolerance in Betula platyphylla

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Forestry Research 2021年第1期1卷 96-105页

作者： Kaiwen Lv Wenqi Wu hairong wei Guifeng Liu State Key Laboratory of Tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040China Beijing Advanced Innovation Center for Tree Breeding by Molecular Design Beijing Forestry UniversityBeijing 100083China College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMI 49931United States of America

Cold is an abiotic stress that can greatly affect the growth and survival of ***,we reported that an AP2/ERF family gene,BplERF1,isolated from Betula platyphylla played a contributing role in cold stress *** of BplERF1 in *** transgenic lines enhanced cold stress tolerance by increasing the scavenging capability and reducing H_(2)O_(2) and malondialdehyde(MDA)content in transgenic *** of BplERF-mediated multilayered hierarchical gene regulatory network(ML-hGRN),using Top-down GGM algorithm and the transcriptomic data of BplERF1 overexpression lines,led to the identification of five candidate target genes of BplERF1 which include MPK20,ERF9,WRKY53,WRKY70,and *** of them were then verified to be the true target genes of BplERF1 by chromatin-immunoprecipitation PCR(ChIP-PCR)*** results indicate that BplERF1 is a positive regulator of cold tolerance and is capable of exerting regulation on the expression of cold signaling and regulatory genes,causing mitigation of reactive oxygen species.

关键词： tolerance platyphylla verified

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HB-PLS:A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression

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Forestry Research 2021年第1期1卷 43-55页

作者： Wenping Deng Kui Zhang Cheng He Sanzhen Liu hairong wei College of Forest Resources and Environmental Science Michigan Technological UniversityHoughtonMichigan 49931United States of America Department of Mathematical Science Michigan Technological UniversityHoughtonMichigan 49931United States of America Department of Plant Pathology Kansas State UniversityManhattanKansas 66506United States of America

Gene expression data features high dimensionality,multicollinearity,and non-Gaussian distribution noise,posing hurdles for identification of true regulatory genes controlling a biological process or *** this study,we integrated the Huber loss function and the Berhu penalty(HB)into partial least squares(PLS)framework to deal with the high dimension and multicollinearity property of gene expression data,and developed a new method called HB-PLS regression to model the relationships between regulatory genes and pathway *** solve the Huber-Berhu optimization problem,an accelerated proximal gradient descent algorithm with at least 10 times faster than the general convex optimization solver(CVX),was *** of HB-PLS to recognize pathway regulators of lignin biosynthesis and photosynthesis in Arabidopsis thaliana led to the identification of many known positive pathway regulators that had previously been experimentally *** compared to sparse partial least squares(SPLS)regression,an efficient method for variable selection and dimension reduction in handling multicollinearity,HB-PLS has higher efficacy in identifying more positive known regulators,a much higher but slightly less sensitivity/(1-specificity)in ranking the true positive known regulators to the top of the output regulatory gene lists for the two aforementioned *** addition,each method could identify some unique regulators that cannot be identified by the other *** results showed that the overall performance of HB-PLS slightly exceeds that of SPLS but both methods are instrumental for identifying real pathway regulators from high-throughput gene expression data,suggesting that integration of statistics,machine leaning and convex optimization can result in a method with high efficacy and is worth further exploration.

关键词： Huber penalty slightly

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Inaugural Editorial

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Forestry Research 2021年第1期1卷 1-2页

作者： hairong wei Michigan Technological University

Forests provide not only timber,pulp,biofuel,food,and various industrial biomaterials for humans,but also habitats,shelters and forages for *** also provide a wide range of ecosystem services,for example,provisioning services(*** water and fresh air),regulating services(*** and erosion control,water and air purification,ground water recharge,and climate abnormality control),cultural services(***,aesthetic,and spiritual benefits),and supporting services(*** formation),which are vital in restoring and maintaining biodiversity in terrestrial ***,forests play a leading role in the global cycling of energy,carbon,water and nutrients.

关键词： soil cycling flood

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