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巨桉GRF基因家族生物信息学分析及其在不同氮水平下的组织表达模式

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西北农林科技大学学报（自然科学版） 2024年第3期52卷 62-72页

作者：杨雪芮陈少雄王建忠何沙娥中国林业科学研究院速生树木研究所广东湛江524022 南京林业大学林学院江苏南京210037 广西国有东门林场广西崇左532108

【目的】从全基因组水平上鉴定巨桉生长调节因子(growth-regulating factor,GRF)基因家族成员,分析其在不同氮素水平下的组织表达模式,为巨桉GRF基因功能研究及氮高效利用桉树品种的培育奠定基础。【方法】在NCBI网站中选择巨桉基因组,... 详细信息

【目的】从全基因组水平上鉴定巨桉生长调节因子(growth-regulating factor,GRF)基因家族成员,分析其在不同氮素水平下的组织表达模式,为巨桉GRF基因功能研究及氮高效利用桉树品种的培育奠定基础。【方法】在NCBI网站中选择巨桉基因组,用拟南芥和毛果杨的GRF蛋白序列与巨桉基因组数据库进行BLAST蛋白序列同源比对,并通过InterPro和SMART数据库进行保守结构域分析,获得巨桉GRF基因。利用在线网站Ex-pasy protparam、SignalP-5.0、WoLF PSORT和SOPMA,对巨桉GRF蛋白进行基本理化性质分析、信号肽预测、亚细胞定位及二级结构预测。利用MEGA7.0软件构建系统进化树,使用MEME在线平台分析EgrGRF蛋白的保守结构域和基序,用Plant CARE预测基因上游的顺式作用元件,并使用TBtools软件将结果可视化。以2年生巨桉苗为供试材料,浇灌氮素浓度分别为45(高氮)、15(常规氮)和1.5(低氮)mmol/L的营养液,4 d后取样,采用实时荧光定量PCR技术检测EgrGRF基因在3种氮素水平下的叶片、茎和根中的表达情况。【结果】鉴定得到6个巨桉GRF基因家族成员(EgrGRF1~EgrGRF6),分布于4条染色体上;6个EgrGRF蛋白的氨基酸数目为296~605个,分子质量为33415.86~64630.89 u,理论等电点为7.29~8.85,脂溶指数为39.93~64.79,均为亲水性蛋白;无规则卷曲和α-螺旋为主要二级结构元件,均定位于细胞核上,未检测到信号肽存在。系统进化树分析表明,巨桉、毛果杨和拟南芥的GRF家族成员可分为4组,各组中EgrGRF蛋白数量分别为0,3,1和2个,多数EgrGRF成员与毛果杨亲缘关系较近。基因结构及蛋白基序分析结果显示,巨桉GRF基因家族成员具有2~4个内含子;6个EgrGRF蛋白均具有CX_(9)CX_(10)CX_(2)H和QX_(3)LX_(2)Q保守基序。顺式作用元件分析表明,EgrGRF基因启动子区含有茉莉酸甲酯、脱落酸、分生组织表达及低温等响应元件。实时荧光定量PCR结果显示,EgrGRF2和EgrGRF6基因在低氮处理的巨桉叶片中优势表达,EgrGRF2、EgrGRF3、EgrGRF5和EgrGRF6基因在低氮处理根中的表达量较高氮和常规氮处理显著升高,EgrGRF4基因在常规氮处理茎中的表达量最高。【结论】鉴定获得6个巨桉GRF基因家族成员,其中EgrGRF4基因可能参与茎生长发育的调控,EgrGRF2、EgrGRF3、EgrGRF5和EgrGRF6基因可能参与了巨桉对低氮胁迫的响应。

关键词：巨桉 GRF基因家族生物信息学分析基因表达氮响应

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Fluid Analysis and Structure Optimization of Impeller Based on Surrogate Model

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Computer Modeling in Engineering & Sciences 2022年第7期132卷 173-199页

作者： Huanwei Xu Wenzhang Wei Hanjin He xuerui yang School of Mechanical and Electrical Engineering University of Electronic Science and Technology of ChinaChengdu611731China

The surrogate model technology has a good performance in solving black-box optimization problems,which is widely used in multi-domain engineering optimization *** adaptive surrogate model is the mainstream research direction of surrogate model technology,which can realize model fitting and global optimization of engineering problems by infilling *** on the idea of the adaptive surrogate model,this paper proposes an efficient global optimization algorithm based on the local remodeling method(EGO-LR),which aims at improving the accuracy and optimization efficiency of the *** proposed algorithm firstly constructs the expectation improvement(EI)function in the local area and optimizes it to get the update ***,the obtained update points are added to the global region until the global accuracy of the model meets the *** the differential evolution algorithm is used for global *** benchmark functions are used to compare the EGO-LR algorithm with the existing *** results show that the EGO-LR algorithm can quickly converge to the accuracy requirements of the model and find the optimal value efficiently when facing complex problems with many local extrema and large variable *** proposed algorithm is applied to the optimization design of the structural parameter of the impeller,and the outflow field analysis of the impeller is realized through finite element *** optimization with the maximum fluid pressure(MP value)of the impeller as the objective function is completed,which effectively reduces the pressure value of the impeller under load.

关键词： The surrogate model EGO adaptive fluid analysis impeller

Oxygen dependent oxidation of trimethoprim by sulfate radical:Kinetic and mechanistic investigations

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Chinese Chemical Letters 2021年第10期32卷 3164-3168页

作者： xuerui yang Xi Ding Lei Zhou Yuefei Ji Guangli Xiu Shanghai Environmental Protection Key Laboratory for Environmental Standard and Risk Management of Chemical Pollutants School of Resources&Environmental EngineeringEast China University of Science and TechnologyShanghai 200237China State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes School of Resources&Environmental EngineeringEast China University of Science and TechnologyShanghai 200237China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China College of Resources and Environmental Sciences Nanjing Agricultural UniversityNanjing 210095China

Trimethoprim(TMP)is a typical antibiotic to treat infectious disease,which is among the most commonly detected antibacterial agents in natural waters and municipal *** the present study,the impacts of dissolved oxygen(DO)on the oxidation efficiency and pathways of TMP by reaction with sulfate radicals(SO_(4)^(-1))were *** results revealed that the presence of DO was favourable for TMP ***,TMP would react initially with SO_(4)^(-1)via electron-transfer process to form a carbon-centered *** the absence of oxygen,the carbon-centered radical could undergo hydrolysis to produceα-hydroxytrimethoprim(TMPàOH),followed by the further oxidation which generatedα-ketotrimethoprim(TMP=O).However,in the presence of oxygen,the carbon-centered radical would alternatively combine with oxygen,leading to a sequential reaction in which peroxyl radical and a tetroxide were formed,and finally generated TMPàOH and TMP=O *** proposed pathways were further confirmed by density functional theory(DFT)*** results obtained in this study would emphasize the significance of DO on the oxidation of organic micropollutants by SO_(4)^(-1).

关键词： Antibiotics Sulfate radicals Dissolved oxygen Hydroxylation DFT calculations

IDH1 fine-tunes cap-dependent translation initiation

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Journal of Molecular Cell Biology 2019年第10期11卷 816-828页

作者： Lichao Liu JYuyang Lu Fajin Li Xudong Xing Tong Li xuerui yang Xiaohua Shen Tsinghua-Peking Center for Life Sciences School of Medicine and School of Life SciencesTsinghua UniversityBeijing 100084China MOE Key Laboratory of Bioinformatics Center for Synthetic Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program School of Life SciencesTsinghua UniversityBeijing 100084China

The metabolic enzyme isocitrate dehydrogenase 1(IDH1)catalyzes the oxidative decarboxylation of isocitrate to a-ketoglutarate(a-KG).Its mutation often leads to aberrant gene expression in ***1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner;yet,the functional significance of this RNA-binding activity remains ***,we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation *** proteomic analysis in embryonic stem cells(ESCs)revealed strikingenrichmentof ribosomal proteins and translation regulators in IDH1-bound protein *** performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating ***,knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon,indicating inefficient translation initiation upon loss of *** IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation,independently of the catalytic activity of ***,IDH1 fails to enhance luciferase translation driven by an internal ribosome entry ***,these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.

关键词： IDH1 proteomic interactome translation regulation RNA-binding protein

Ribosome Profiling Reveals Genome-wide Cellular Translational Regulation upon Heat Stress in Escherichia coli

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Genomics, Proteomics & Bioinformatics 2017年第5期15卷 324-330页

作者： yanqing zhang zhengtao xiao qin zou jianhuo fang qifan wang xuerui yang ning gao MOE Key Laboratory of Protein Sciences Beij'ing Advanced Innovation Center for Structural BiologyTsinghua—Peking Center for Lt Sciences School 0f LIfe SciencesTsinghua University.Beijing 100084 China MOE Key Laboratory of Bioinformatics.Tsinghua-Peking Joint Center for ife Sciences.Center for Synthetic and Systems Biology School of Lire SciencesTsinghua University Beijing 100084China State Key Laboratory ofMembrane Biology Peking—Tsinghua Centerfor Lire Sciences.School of Life Sciences.Peking University Beijing 100871Chin

Heat shock response is a classical stress-induced regulatory system in bacteria, character- ized by extensive transcriptional reprogramming. To compare the impact of heat stress on the tran- scriptome and translatome in Escherich＆ coli, we conducted ribosome profiling in parallel with RNA-Seq to investigate the alterations in transcription and translation efficiency when E. coli cells were exposed to a mild heat stress （from 30 ~C to 45 ~C）. While general changes in ribosome foot- prints correlate with the changes of mRNA transcripts upon heat stress, a number of genes show differential changes at the transcription and translation levels. Translation efficiency of a few genes that are related to environment stimulus response is up-regulated, and in contrast, some genes func- tioning in mRNA translation and amino acid biosynthesis are down-regulated at the translation level in response to heat stress. Moreover, our ribosome occupancy data suggest that in generalribosomes accumulate remarkably in the starting regions of ORFs upon heat stress. This study pro- vides additional insights into bacterial gene expression in response to heat stress, and suggests the presence of stress-induced but yet-to-be characterized cellular regulatory mechanisms of gene expression at translation level.

关键词： Ribosome profiling Translation regulation RNA-Seq Heat shock response Transcription regulation

A Multi-Stage Differential-Multifactorial Evolutionary Algorithm for Ingredient Optimization in the Copper Industry

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IEEE/CAA Journal of Automatica Sinica 2024年第10期11卷 2135-2153页

作者： xuerui Zhang Zhongyang Han Jun Zhao School of Control Science and Engineering Dalian University of TechnologyDalian 116024China IEEE

Ingredient optimization plays a pivotal role in the copper industry,for which it is closely related to the concentrate utilization rate,stability of furnace conditions,and the quality of copper *** acquire a practical ingredient plan,which should exhibit long duration time with sufficient utilization and feeding stability for real applications,an ingredient plan optimization model is proposed in this study to effectively guarantee continuous production and stable furnace *** address the complex challenges posed by this integer programming model,including multiple coupling feeding stages,intricate constraints,and significant non-linearity,a multi-stage differential-multifactorial evolution algorithm is *** the proposed algorithm,the differential evolutionary(DE)algorithm is improved in three aspects to efficiently tackle challenges when optimizing the proposed ***,unlike traditional time-consuming serial approaches,the multifactorial evolutionary algorithm is utilized to optimize multiple complex models contained in the population of evolutionary algorithm caused by the feeding stability in a parallel ***,a repair algorithm is employed to adjust infeasible ingredient lists in a timely *** addition,a local search strategy taking feedback from the current optima and considering the different positions of global optimum is developed to avoiding premature convergence of the differential evolutionary ***,the simulation experiments considering different planning horizons using real data from the copper industry in China are conducted,which demonstrates the superiority of the proposed method on feeding duration and stability compared with other commonly deployed *** is practically helpful for reducing material cost as well as increasing production profit for the copper industry.

关键词： Copper industry differential-multifactorial evolution ingredient optimization multi-stage optimization

加味真武汤联合西药治疗腹膜透析合并慢性心力衰竭临床研究

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新中医 2024年第16期56卷 1-5页

作者：彭玲孙致健刘兴正杨雪瑞莫锦莹宋高峰广州中医药大学第四临床医学院广东深圳518033 深圳市中医院广东深圳518033

目的:观察加味真武汤联合西药治疗腹膜透析(PD)合并慢性心力衰竭(CHF)阳虚水泛证的临床疗效。方法:选取54例PD合并CHF阳虚水泛证患者,采用随机数字表法分为对照组与观察组各27例。研究过程中对照组剔除2例、观察组剔除3例,最终纳入研究... 详细信息

目的:观察加味真武汤联合西药治疗腹膜透析(PD)合并慢性心力衰竭(CHF)阳虚水泛证的临床疗效。方法:选取54例PD合并CHF阳虚水泛证患者,采用随机数字表法分为对照组与观察组各27例。研究过程中对照组剔除2例、观察组剔除3例,最终纳入研究对照组25例、观察组24例。对照组给予常规西药治疗,观察组在对照组基础上给予加味真武汤治疗,2组均治疗24周。比较2组临床疗效、中医证候积分及心功能指标[脑钠肽(BNP)、半乳糖凝集素-3 (Galectin-3)]水平。结果:治疗24周后,观察组总有效率79.17%,高于对照组28.00%,差异有统计学意义(P0.05)。观察组血清BNP、Galectin-3水平均较治疗前降低,且均低于对照组,差异均有统计学意义(P0.05)。结论:加味真武汤联合西药治疗PD合并CHF阳虚水泛证临床疗效较好,可有效改善临床症状,降低血清BNP、Galectin-3水平。

关键词：慢性心力衰竭腹膜透析阳虚水泛证加味真武汤半乳糖凝集素-3 脑钠肽

Coupled multiphysical model for investigation of influence factors in the application of microbially induced calcite precipitation

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第6期16卷 2232-2249页

作者： xuerui Wang Pavan Kumar Bhukya Dali Naidu Arnepalli Shuang Chen Gesellschaft für Anlagen-und Reaktorsicherheit(GRS)GGmbH Braunschweig38122Germany Department of Civil Engineering Indian Institute of Technology MadrasChennai600036India Federal Institute for Geosciences and Natural Resources(BGR) Hannover30655Germany

The study presents a comprehensive coupled thermo-bio-chemo-hydraulic(T-BCH)modeling framework for stabilizing soils using microbially induced calcite precipitation(MICP).The numerical model considers relevant multiphysics involved in MICP,such as bacterial ureolytic activities,biochemical reactions,multiphase and multicomponent transport,and alteration of the porosity and *** model incorporates multiphysical coupling effects through well-established constitutive relations that connect parameters and variables from different physical *** was implemented in the open-source finite element code OpenGeoSys(OGS),and a semi-staggered solution strategy was designed to solve the couplings,allowing for flexible model ***,the developed model can be easily adapted to simulate MICP applications in different *** numerical model was employed to analyze the effect of various factors,including temperature,injection strategies,and application ***,a TBCH modeling study was conducted on the laboratory-scale domain to analyze the effects of temperature on urease activity and precipitated calcium *** understand the scale dependency of MICP treatment,a large-scale heterogeneous domain was subjected to variable biochemical injection *** simulations conducted at the field-scale guided the selection of an injection strategy to achieve the desired type and amount of ***,the study emphasized the potential of numerical models as reliable tools for optimizing future developments in field-scale MICP *** present study demonstrates the potential of this numerical framework for designing and optimizing the MICP applications in laboratory-,prototype-,and field-scale scenarios.

关键词： Multiphysics Microbially induced calcite precipitation(MICP) Coupled thermo-bio-chemo-hydraulic(TBCH) model OpenGeoSys(OGS) Influence factors

Modelling of the elastoplastic behaviour of the bio-cemented soils using an extended Modified Cam Clay model

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第6期16卷 2184-2197页

作者： xuerui Wang Christian B.Silbermann Thomas Nagel Udo Nackenhorst Institute of Mechanics and Computational Mechanics Leibniz UniversitätHannoverAppelstr.9aHannover30167Germany Gesellschaft für Anlagen-und Reaktorsicherheit(GRS)gGmbH Theodor-Heuss-Straße 4Braunschweig38122Germany Geotechnical Institute Technische Universität BergakademieFreibergGustav-Zeuner-Str.1Freiberg09599Germany

An elastoplastic constitutive model based on the Modified Cam Clay(MCC)model is developed to describe the mechanical behaviour of soils cemented via microbially induced calcite precipitation(MICP).It considers the increase of the elastic stiffness,the change of the yield surface due to MICP cementation and the degradation of calcium carbonate bonds during ***,to capture the typical contraction-dilation transition in MICP soils,the original volumetric hardening rule in the MCC model is modified to a combined deviatoric and volumetric hardening *** model could reproduce a series of drained triaxial tests on MICP-treated soils with different calcium carbonate ***,we carry out a parametric study and observe numerical instability in some *** combination with an analytical analysis,our numerical modelling has identified the benefits and limitations of using MCCbased models in the simulation of MICP-cemented soils,leading to suggestions for further model development.

关键词： Microbially induced calcite precipitation(MICP) Elastoplasticity Modified cam clay(MCC) OpenGeoSys MFront Contraction-dilation transition