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Transcriptional, post-transcriptional and post-translational regulations of gene expression during leaf polarity formation

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Cell Research 2007年第6期17卷 512-519页

作者： Lin Xu Li YangHai Huang National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China National Laboratory of Plant Molecular Genetics Shanghai Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China present address: IBMP CNRS Universite Louis Pasteur 67084 Strasbourg France present address: department of Biology University of Pennsylvania Philadelphia PA 19104 USA

Leaf morphogenesis requires the establishment of adaxial-abaxial polarity after primordium initiation from the shootapical meristem (SAM). Several families of transcription factors are known to play critical roles in promoting adaxial orabaxial leaf fate. Recently, post-transcriptional gene silencing pathways have been shown to regulate the establishmentof leaf polarity, providing novel and exciting insights into leaf development. For example, microRNAs (miR165/166)and a trans-acting siRNA (TAS3-derived tasiR-ARF) have been shown to repress the expression of several key transcrip-tion factor genes. In addition, yet another level of regulation, post-translational regulation, has been revealed recently bystudies on the role of the 26S proteasome in leaf polarity. Although our understanding regarding the molecular mecha-nisms underlying establishment of adaxial-abaxial polarity has greatly improved, there is still much that remains elusive.This review aims to discuss recent progress, as well as the remaining questions, regarding the molecular mechanismsunderlying leaf polarity formation.

关键词： Arabidopsis leaf development polarity formation

Warming‑induced changes of broccoli head to cauliflower‑like curd in Brassica oleracea are regulated by DNA methylation as revealed by methylome and transcriptome co‑profiling

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Molecular Horticulture 2022年第1期2卷 318-332页

作者： Zilei Yao Lu Yuan Ke Liu Tingjin Wang Bin Liu Yan Zhao Susheng Gan Liping Chen department of Horticulture College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA present address:College of Agronomy and Biotechnology Yunnan Agricultural UniversityKunming 650201China

Increasingly warming temperature impacts on all aspects of growth and development in plants.Flower development is a complex process that is very sensitive to ambient temperature,and warming temperatures often lead to abnor-mal flower development and remarkably reduce the quality and yield of inflorescent vegetables and many other crops,which can be exemplified by Brassica oleracea cv.Green Harmony F1,a broccoli cultivar,whose floral develop-ment is ceased at inflorescence meristem(at 28℃)or floral primordium stage(at 22℃),forming a cauliflower-like curd(28℃)or intermediate curd(22℃)instead of normal broccoli head at 16℃.However,the underlying molecular regulatory mechanisms are not well understood.Here we report that warming temperature(28℃ or 22℃)induced hypermethylation of the genome,especially the promoter regions of such sets of genes as ribosome biogenesis-related and others,leading to the suppression of the apex-highly-expressed distinctive genes,subsequently resulting in the abnormal floral development,as revealed by methylome and transcriptome co-profiling.The regulation of warming-induced abnormal floral development in broccoli was further verified by the fact that the DNA methylation inhibitor 5-azacytidine(5-azaC)released the expression of genes from the warming temperature-induced suppres-sion,and restored the broccoli development to normalcy at warming temperature.The research provided new approaches to breeding broccoli and other crops for growing in wider or warmer temperature zones.

关键词： Brassica oleracea DNA methylation Floral development cessation Global warming Heat stress

Functional Cooperativity of Enzymes of Phosphoinositide Conversion According to Synergistic Effects on Pectin Secretion in Tobacco Pollen Tubes

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Molecular Plant 2010年第5期3卷 870-881页

作者： Till Ischebeck Linh Hai Vu Xu Jin Irene Stenzel Christian Lofke Ingo Heilmann department of Plant Biochemistry Albrecht-von-Haller-lnstitute for Plant Sciences Georg-August-University Gottingen Justus-von-Liebig-Weg 11 37077 Guttingen Germany present address: Center for Biochemistry Cologne University Joseph-Stelzmann-Straβe 52 50931 Cologne Germany present address: department of Forest Botany Georg-August-University Gottingen Busgenweg 2 37077 Gottingen Germany present address: department of Plant Cell Biology Albrecht-von-Haller-lnstitute for Plant Sciences Georg-August-University Gottingen Untere Karspule 2 37073 Gottingen Germany

The Arabidopsis phosphoinositide kinases PI4Kβ1 and PIP5K5 have been implicated in the control of directional vesicle trafficking underlying polar tip growth in pollen tubes. PI4Kβ1 and PIP5K5 catalyze key consecutive steps of phosphoinositide conversion, and it appears obvious that phosphatidylinositol-4-phosphate formed by PI4Kβ1 might act as a substrate for phosphatidylinositol-4,5-bisphosphate formation by PIP5K5. However, this hypothesis has not been experimentally addressed and distinct localization patterns of PI4Kβ1, PIP5K5, and also PI-synthases （PIS） generating phosphatidylinositol suggest additional complexity. Here, the synergistic functionality of enzymes of phosphoinositide conversion was assessed. In tobacco and Arabidopsis pollen tubes, phosphoinositides influence the apical secretion of pectin, and increased pectin deposition results in characteristic morphological alterations. Catalytically active and dominant negative variants of PI4Kβ1 and PIP5K5 were systematically co-expressed in tobacco pollen tubes and the incidence of morphologies related to enhanced pectin secretion was evaluated. The data support a proposed functional interplay of PI4Kβ1 and PIP5K5 at the trans-Golgi network, mediating directional vesicle trafficking. Co-expression experiments additionally including PIS isoforms, PIS1 or PIS2, indicate that pectin secretion is synergistically mediated by PI4Kβ1 and PIPSK5 acting on Ptdlns formed by PIS2 rather than PIS1. Possible ramifications for the preferential channeling of phosphoinositide intermediates between particular isoforms of PI pathway enzymes are discussed.

关键词： Phosphatidylinositol synthase phosphatidylinositol 4-kinase phosphatidylinositol-4-phosphate 5-kinase cooperativity pectin secretion pollen tubes.

Enhancing Cybersecurity Competency in the Kingdom of Saudi Arabia:A Fuzzy Decision-Making Approach

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Computers, Materials & Continua 2024年第5期79卷 3211-3237页

作者： Wajdi Alhakami department of Information Technology College of Computers and Information TechnologyTaif UniversityTaif21944Saudi Arabia

The Kingdom of Saudi Arabia(KSA)has achieved significant milestones in cybersecurity.KSA has maintained solid regulatorymechanisms to prevent,trace,and punish offenders to protect the interests of both individual users and organizations from the online threats of data poaching and pilferage.The widespread usage of Information Technology(IT)and IT Enable Services(ITES)reinforces securitymeasures.The constantly evolving cyber threats are a topic that is generating a lot of discussion.In this league,the present article enlists a broad perspective on how cybercrime is developing in KSA at present and also takes a look at some of the most significant attacks that have taken place in the region.The existing legislative framework and measures in the KSA are geared toward deterring criminal activity online.Different competency models have been devised to address the necessary cybercrime competencies in this context.The research specialists in this domain can benefit more by developing a master competency level for achieving optimum security.To address this research query,the present assessment uses the Fuzzy Decision-Making Trial and Evaluation Laboratory(Fuzzy-DMTAEL),Fuzzy Analytic Hierarchy Process(F.AHP),and Fuzzy TOPSIS methodology to achieve segment-wise competency development in cyber security policy.The similarities and differences between the three methods are also discussed.This cybersecurity analysis determined that the National Cyber Security Centre got the highest priority.The study concludes by perusing the challenges that still need to be examined and resolved in effectuating more credible and efficacious online security mechanisms to offer amoreempowered ITES-driven economy for SaudiArabia.Moreover,cybersecurity specialists and policymakers need to collate their efforts to protect the country’s digital assets in the era of overt and covert cyber warfare.

关键词： Cyber security fuzzy DMTAEL security policy cyber crime MCDM

Mitotic Spindle Organization by the Preprophase Band

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Molecular Plant 2008年第6期1卷 950-960页

作者： J. Christian Ambrose Richard Cyr The Pennsylvania State University Department of Biology The Huck Institutes of the Life Sciences Integrative Biosciences Graduate Degree Program PlantPhysiology Program University Park PA 16802 USA present address: department of Botany University of British Columbia Vancouver British Columbia V6T 1Z4 Canada

In higher plants, the preprophase band （PPB） of microtubules （MTs） forecasts the cell division site prior to mitosis and specifies the organization of MTs into a bipolar prophase spindle surrounding the nucleus. However, the mechanisms governing this PPB-dependent establishment of bipolarity are unclear. Here, we present evidence from live cell imaging studies that suggest a role for the MTs bridging the PPB and the prophase nucleus in mediating this function. Results from drug treatments, along with genetic evidence from null kinesin plants, suggest that these MTs contribute to the bipolarity, orientation, and position of the prophase spindle. Specifically, the absence of these bridge MTs is associated with lack of bipolarity, while non-uniform distributions of bridge MTs correlate with prophase spindle migration, deformation, and enhanced bipolarity toward the region of highest bridge MT density. This behavior does not require actomyosin-based forces, and is enhanced by suppressing MT dynamics with taxol. These observations occur during late prophase, and are coincident with the gradual closing of annular spindle poles. Based on these data, we describe a hypothetical mechanism for bridge MT-dependent organization of prophase spindles.

关键词： preprophase band mitosis acentrosomal spindle microtubule kinesin ATK5 cytokinesis.

Interactions of complement proteins C1q and factor H with lipid A and Escherichia coli:further evidence that factor H regulates the classical complement pathway

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Protein & Cell 2011年第4期2卷 320-332页

作者： Lee Aun Tan Andrew C.Yang Uday Kishore Robert B.Sim Medical Research Council Immunochemistry Unit Department of BiochemistryUniversity of OxfordSouth Parks RoadOxford OX13QUUK present address:department of Immunology Faculty of MedicineImperial College LondonHammersmith HospitalDu Cane RoadLondon W120NNUK St Peter’s College New Inn Hall St.Oxford OX12DLUK present address:SUNY Downstate College of Medicine 450 Clarkson Avenue BrooklynNY 11203USA Weatherall Institute of Molecular Medicine John Radcliffe HospitalUniversity of OxfordHeadingtonOxford OX39DSUK present address:Center for Infection Immunity and Disease MechanismsBiosciencesSchool of Health Sciences and Social CareBrunel UniversityUxbridge UB83PH West LondonUK present address:department of Pharmacology University of OxfordMansfield RoadOxford OX13QTUK

Proteins of the complement system are known to interact with many charged substances.We recently characterized binding of C1q and factor H to immobilized and liposomal anionic phospholipids.Factor H inhibited C1q binding to anionic phospholipids,suggesting a role for factor H in regulating activation of the complement classical pathway by anionic phospholipids.To extend this finding,we examined interactions of C1q and factor H with lipid A,a well-characterized activator of the classical pathway.We report that C1q and factor H both bind to immobilized lipid A,lipid A liposomes and intact Escherichia coli TG1.Factor H competes with C1q for binding to these targets.Furthermore,increasing the factor H:C1q molar ratio in serum diminished C4b fixation,indicating that factor H diminishes classical pathway activation.The recombinant forms of the Cterminal,globular heads of C1q A,B and C chains bound to lipid A and E.coli in a manner qualitatively similar to native C1q,confirming that C1q interacts with these targets via its globular head region.These observations reinforce our proposal that factor H has an additional complement regulatory role of down-regulating classical pathway activation in response to certain targets.This is distinct from its role as an alternative pathway downregulator.We suggest that under physiological conditions,factor H may serve as a downregulator of bacterially-driven inflammatory responses,thereby finetuning and balancing the inflammatory response in infections with Gram-negative bacteria.

关键词： complement lipid A bacteria factor H C1q

Challenges and pitfalls of youth-onset type 2 diabetes

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World Journal of Diabetes 2024年第5期15卷 876-885页

作者： Lavinia La Grasta Sabolic Sanda Marusic Maja Cigrovski Berkovic department of Pediatric Endocrinology and Diabetology University Hospital Centre Sestre MilosrdniceZagreb 10000Croatia School of Medicine Catholic University of CroatiaZagreb 10000Croatia department for Sport and Exercise Medicine University of Zagreb Faculty of KinesiologyZagreb 10000Croatia

The incidence and prevalence of youth-onset type 2 diabetes mellitus(T2DM)are increasing.The rise in frequency and severity of childhood obesity,inclination to sedentary lifestyle,and epigenetic risks related to prenatal hyperglycemia exposure are important drivers of the youth-onset T2DM epidemic and might as well be responsible for the early onset of diabetes complications.Indeed,youth-onset T2DM has a more extreme metabolic phenotype than adult-onset T2DM,with greater insulin resistance and more rapid deterioration of beta cell function.Therefore,intermediate complications such as microalbuminuria develop in late childhood or early adulthood,while end-stage complications develop in mid-life.Due to the lack of efficacy and safety data,several drugs available for the treatment of adults with T2DM have not been approved in youth,reducing the pharmacological treatment options.In this mini review,we will try to address the present challenges and pitfalls related to youth-onset T2DM and summarize the available interventions to mitigate the risk of microvascular and macrovascular complications.

关键词： Youth-onset type 2 diabetes mellitus Insulin resistance Beta cell failure Risk factors Therapy Complications

Energy Management of Price-maker Community Energy Storage by Stochastic Dynamic Programming

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CSEE Journal of Power and Energy Systems 2024年第2期10卷 492-503页

作者： Lirong Deng Xuan Zhang Tianshu Yang Hongbin Sun Yang Fu Qinglai Guo Shmuel S.Oren department of Electrical Engineering Shanghai University of Electric PowerShanghai 200000China Tsinghua-Berkeley Shenzhen Institute Tsinghua UniversityShenzhen 518055China department of Industrial Engineering and Operations Research University of California BerkeleyBerkeleyCAUSA Risk Analytics and Optimization Chair EPFLSwitzerlandand also with Power Systems LaboratoryETH Zurich8092 ZurichSwitzerland State Key Laboratory of Power Systems Department of Electrical EngineeringTsinghua UniversityBeijing 100084China

In this paper,we propose an analytical stochastic dynamic programming(SDP)algorithm to address the optimal management problem of price-maker community energy storage.As a price-maker,energy storage smooths price differences,thus decreasing energy arbitrage value.However,this price-smoothing effect can result in significant external welfare changes by reduc-ing consumer costs and producer revenues,which is not negligible for the community with energy storage systems.As such,we formulate community storage management as an SDP that aims to maximize both energy arbitrage and community welfare.To incorporate market interaction into the SDP format,we propose a framework that derives partial but sufficient market information to approximate impact of storage operations on market prices.Then we present an analytical SDP algorithm that does not require state discretization.Apart from computational efficiency,another advantage of the analytical algorithm is to guide energy storage to charge/discharge by directly comparing its current marginal value with expected future marginal value.Case studies indicate community-owned energy storage that maximizes both arbitrage and welfare value gains more benefits than storage that maximizes only arbitrage.The proposed algorithm ensures optimality and largely reduces the computational complexity of the standard SDP.Index Terms-Analytical stochastic dynamic programming,energy management,energy storage,price-maker,social welfare.

关键词： Analytical stochastic dynamic programming energy management energy storage price-maker social welfare

An integrative protocol for one‑step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data

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Marine Life Science & Technology 2023年第4期5卷 564-572页

作者： Jiahao Ni Jiao Pan Yaohai Wang Tianhao Chen Xinshi Feng Yichen Li Tongtong Lin Michael Lynch Hongan Long Weiyi Li Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA department of Biology Indiana UniversityBloomingtonIN 47401USA present address:SLAC National Accelerator Laboratory Stanford UniversityStanford 94305USA

High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.

关键词： Amplicon library preparation Lab-made protocol Long-primer PCR Cost efficiency