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Effect of strawberry vein banding virus and strawberry mottle virus co-infection on the growth and development of strawberry

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BIOCELL 2022年第1期46卷 263-273页

作者： LINGJIAO FAN DAN SONG YINGWEI KHOO mengmeng wu TENGFEI XU XIAOLI ZHAO HONGQING WANG College of Horticulture China Agricultural UniversityBeijing100193China State Key Laboratory of Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193China

Strawberry mottle virus(SMoV)and strawberry vein banding virus(SVBV)cause diseases on strawberry plants,but the effect of coinfection of SMoV and SVBV on the growth,development,and defense system of strawberry(Fragaria×ananassa Duchesne)remains unknown.We investigated the effect of SMoV and SVBV coinfection on strawberry cultivar‘Benihope’.The results showed that stem diameter,leaf size,leaf number,relative chlorophyll content,total chlorophyll content,photosynthetic parameters,and stomatal aperture of SMoV and SVBV co-infected strawberry(VIS)plants were in a weaker level than uninfected control plants,indicating that viruses inhibited the growth and photosynthesis of strawberry plants.Furthermore,the initiation of flowering and fruiting stages of VIS plants were delayed by about three weeks compared with the controls,and the fruiting period was shortened,demonstrating that the reproduction of VIS plants was inhibited.Fruit quality was damaged in VIS plants due to a significant increase in fruit firmness and titratable acidity and decrease in total soluble solid content than control fruits.More dead cells and H_(2)O_(2) accumulated along the veins of VIS leaves,and the content of abscisic acid and catalase activity significantly increased,whereas anthocyanin content was lower than that of control plants.The results demonstrate that SVBV and SMoV coinfection inhibits the growth and development of‘Benihope’strawberry plants,and the plants respond to viruses by regulating stomatal aperture,the accumulation of ABA and antioxidants.To our knowledge,this study contributes information to understand how both viruses impair the strawberry growth and development for the first time.

关键词： Photosynthesis Flowering and fruiting period Antioxidants Plant defense

DEM study on effect of particle roundness on biaxial shearing of sand

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Underground Space 2021年第6期6卷 678-694页

作者： mengmeng wu Linghong Xiong Jianfeng Wang Department of Architecture and Civil Engineering City University of Hong KongHong KongChina Shenzhen Research Institute of City University of Hong Kong ShenzhenChina

In this study,discrete element method(DEM)simulations of a biaxial test were used to examine the effect of particle roundness on the mechanical behavior of sands at both the macro and micro scales.First,a stack of microcomputed tomography images were binarized,segmented,and labeled using advanced image processing and analysis techniques.Second,a spherical harmonic(SH)analysis,which involves a complete set of orthogonal functions,was implemented to rebuild the natural particle shape.Then,five templates of virtual particles were built in a DEM simulation,four of which were obtained from SH degrees of 3,8,12,and 15,and one template was an elementary sphere.A flexible membrane was numerically generated to allow the material to deform freely under a prescribed confining stress.Finally,the effect of particle roundness on the mechanical properties of granular materials was investigated and discussed.Two shear bands were found to intersect,forming an X shape in both the rotation and displacement fields.Moreover,a lower particle roundness results in higher deviatoric stress and stronger dilation in the volumetric change.A decrease in particle roundness leads to less rotation of particles despite a higher displacement value.In addition,a larger SH degree leads to smaller normalized contact forces of the particles.This implies that decreasing the roundness results in higher anisotropy of the contact forces.

关键词： Grain shape Roundness Flexible membrane Spherical harmonic analysis Discrete element method

Genome-wide analysis of microRNAs induced and regulated by colchicine in mulberry

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BIOCELL 2022年第8期46卷 1935-1945页

作者： mengmeng wu PENG GUO YISU SHI DANYAN ZHENG QIAONAN ZHANG XIN JIN YUHUA WANG QIANG LIN RONGJUN FANG WEIGUO ZHAO Key Laboratory of Silkworm and Mulberry Genetic Improvement Ministry of AgricultureSchool of Biology and TechnologyJiangsu University of Science and TechnologyZhenjiang212100China Sericultural Research Institute Nanning530007China

A variety of plants were colchicine treated to double their chromosome number.Chromosomes are genetic carriers that determine the individual traits of organisms.The doubling of chromosomes will lead to modifications in plant morphology,physiology and genetics.To determine the response of mulberry trees induced by colchicine,using mulberry variety Yu-711 leaves as research materials,two small RNA libraries(control and experimental groups)were constructed.It was found that 45 known miRNA genes and 78 predicted novel miRNA genes in the sequence results.A comparison of data between the control group and the experimental group revealed 37 differentially expressed miRNA genes,19 genes of which were up-regulated and 18 genes of which were down-regulated.Eight miRNAs were selected from 37 differentially expressed miRNA genes.These miRNAs were verified by quantitative real-time PCR,and the expression levels of these miRNAs were found to be consistent with those obtained by sequencing,which proved the accuracy of sequencing results.The PsRNATarget software was used to predict the target genes of 8 miRNAs.The Gene Ontology and Kyoto Encycopedia of Genes and Genomes analysis were used to collect the functions of target genes and confirm that target genes are mainly involved in biological processes,cell components and molecular functions.novel-77 miRNA was selected from 37 differentially expressed miRNAs.What will serve as a fundamental data in understanding mulberry miRNAs function in molecular biology research and further provides the molecular mechanism of mulberry gene regulation as induced by colchicine is that the prediction of novel_77 precursor sequence and the target gene(XM_010104258.2),as well as the secondary structure analysis.

关键词： Chromosomes Novel_77 qRT-PCR Target genes Colchicine

Strength criterion effect of the translator and destabilization model of gas-bearing coal seam

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International Journal of Mining Science and Technology 2019年第2期29卷 327-333页

作者： Gang Wang Rui Wang mengmeng wu Cheng Fan Xiang Song Mine Disaster Prevention and Control-Ministry of State Key Laboratory Breeding Base Shandong University of Science & Technology College of Mining and Safety Engineering Shandong University of Science & Technology Department of Civil and Architectural Engineering City University of Hong Kong

Coal seam destabilization inflicts damage to equipment, causes property loss and personnel casualties,and severely threatens mining safety and efficient production. To further understand this destabilization based on the basic theory of Lippmann seam destabilization, a mathematical model was introduced for gas pressure distribution by considering intermediate principal stress and support resistance.Subsequently, we established a translation model suitable for the entire roadway coal seam with rocky roof and floor by applying the unified form of yield criterion in the state of plane strain. We also obtained the analytic expressions of coal seam stress distribution on both sides of the roadway and the widths of plastic and disturbance zones. Afterward, we analyzed several typical cases with different material yield criteria, obtained the plastic zone widths of the coal seam under different gas pressures, and assessed the effects of support resistance, roadway size, and coal strength on coal seam destabilization. Results showed that: the results obtained on the basis of Wilson and Mohr–Coulomb criteria are considerably conservative, and the use of Druker–Prager criteria to evaluate the rockburst-induced coal seam destabilization is safer than the use of the two other criteria; coal seam stability is correlated with gas pressure;and high-pressure gas accelerates the coal seam destabilization.

关键词： Coal seam destabilization Strength criterion effect Gas Stress distribution

Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks

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Journal of Molecular Cell Biology 2017年第6期9卷 436-452页

作者： mengmeng wu Zhixiang Lin Shining Ma Ting Chen Rui Jiang Wing Hung Wong Department of Computer Science Tsinghua University Beijing 100084 China Ministry of Education Key Laboratory of Bioinformatics and Bioinformatics Division Tsinghua National Laboratory for Information Science and Technology Beijing 100084 China Department of Statistics Stanford University CA 94305 USA Department of Automation Tsinghua University Beijing 100084 China

尽管染色体宽的协会研究( GWAS )成功地识别了几千 genomic ， loci 在过去的十年与几百个复杂特点联系了，关于象失踪的可遗传性和弱 interpretability 的如此的问题的争论一直在呼吁让有效计算方法便于存在的广阔体积的先进分析并且... 详细信息

尽管染色体宽的协会研究( GWAS )成功地识别了几千 genomic ， loci 在过去的十年与几百个复杂特点联系了，关于象失踪的可遗传性和弱 interpretability 的如此的问题的争论一直在呼吁让有效计算方法便于存在的广阔体积的先进分析并且期望基因数据。向这个目标，有与显型联系的基因趋于在生物基因集合或基因网络被充实的假设的基因级的综合 GWAS 分析最近吸引了许多注意，由于象越过研究的直接解释，不太多重的测试负担，和坚韧性的如此的优点。然而，存在在这个范畴的方法通常利用 non-tissue-specific 基因网络并且因此缺乏能力利用增进知识的织物特定的特征。克服这限制，我们建议一条贝叶斯的途径叫了图章(同时基因和纸巾的推理) 为联系显型的基因和相关纸巾的同时的推理集成 GWAS 数据和多重织物特定的基因网络。通过广泛的模拟研究，我们在为显型发现联系基因和相关纸巾显示出我们的方法的有效性。在到 14 复杂显型的真实 GWAS 数据的应用，我们在两个都译解表明了我们的方法的力量基因基础和显型的发现生物卓见。与这理解，我们期望为综合 GWAS 分析把图章看作一个珍贵工具，从而增加人的预防，诊断，和治疗继承了疾病和最后便于的精确药。

关键词：基因网络贝叶斯纸巾织物多重推理集成生物基因

糖尿病肾脏疾病患者血浆miR-34a表达水平及临床意义

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中国糖尿病杂志 2024年第5期32卷 361-363页

作者：胡文华吴蒙蒙杨凌示范区医院内分泌科咸阳712100

目的探讨DKD患者血浆miR-34a表达水平及临床意义。方法选取2019年6月至2020年6月于我院内分泌科治疗的T2DM患者189例。根据UACR分为正常蛋白尿组(Nor,UACR<30 mg/g,n=88)、微量蛋白尿组组(Mic,30≤UACR<300 mg/g,n=60)及大量蛋白尿组(... 详细信息

目的探讨DKD患者血浆miR-34a表达水平及临床意义。方法选取2019年6月至2020年6月于我院内分泌科治疗的T2DM患者189例。根据UACR分为正常蛋白尿组(Nor,UACR<30 mg/g,n=88)、微量蛋白尿组组(Mic,30≤UACR<300 mg/g,n=60)及大量蛋白尿组(Mac,UACR≥300 mg/g,n=41),同期选取体检健康者为正常对照组(NC,n=90)。采用ELISA法检测中性粒细胞明胶酶相关脂质运载蛋白(NGAL)、肾损伤分子1(KIM-1),受试者工作特征(ROC)曲线分析血浆miR-34a对DKD的诊断价值。结果 NC、Nor、Mic、Mac组FPG、HbA_(1)c、Scr、BUN、NGAL、UACR、KIM-1、miR-34a依次升高(P<0.05)。Pearson相关分析显示,miR-34a与FPG、HbA_(1)c、Scr、BUN、NGAL、UACR、KIM-1呈正相关(P<0.01)。ROC曲线下面积为0.824,敏感度、特异度为75.1%、86.7%。结论血浆miR-34a对DKD有一定诊断价值。

关键词：糖尿病肾脏疾病 miR-34a 受试者工作特征曲线

Whole genome sequencing and its applications in medical genetics

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Frontiers of Electrical and Electronic Engineering in China 2016年第2期4卷 115-128页

作者： Jiaxin wu mengmeng wu Ting Chen Rui Jiang MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic&Systems BiologyTNLIST Department of Automation Tsinghua UniversityBeijing 100084China

Fundamental improvement was made for genome sequencing since the next-generation sequencing （NGS） came out in the 2000s. The newer technologies make use of the power of massively-parallel short-read DNA sequencing, genome alignment and assembly methods to digitally and rapidly search the genomes on a revolutionary scale, which enable large-scale whole genome sequencing （WGS） accessible and practical for researchers. Nowadays, whole genome sequencing is more and more prevalent in detecting the genetics of diseases, studying causative relations with cancers, making genome-level comparative analysis, reconstruction of human population history, and giving clinical implications and instructions. In this review, we first give a typical pipeline of whole genome sequencing, including the lab template preparation, sequencing, genome assembling and quality control, variants calling and annotations. We compare the difference between whole genome and whole exome sequencing （WES）, and explore a wide range of applications of whole genome sequencing for both mendelian diseases and complex diseases in medical genetics. We highlight the impact of whole genome sequencing in cancer studies, regulatory variant analysis, predictive medicine and precision medicine, as well as discuss the challenges of the whole genome sequencing.

关键词： whole genome sequencing whole exome sequencing next-generation sequencing non-coding regulatoryvariant

ASB3 knockdown promotes mitochondrial apoptosis via activating the interdependent cleavage of Beclin1 and caspase-8 in hepatocellular carcinoma

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Science China(Life Sciences) 2019年第12期62卷 1692-1702页

作者： Wenli Zhang Fuchen Liu Zhihui Che mengmeng wu Zihui Tang Jie Liu Dongqin Yang Department of Digestive Diseases of Huashan Hospital Fudan UniversityShanghai 200040China The Third Department of Hepatic Surgery Eastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai 200438China

Apoptosis and autophagy are distinct cellular processes that can be highly interconnected. The cross talk between the two processes is indispensable in determining the overall cell fate. Although the apoptosis-promoting effect of caspases has been demonstrated, the roles of autophagy-related proteins and even autophagy itself in regulating apoptosis remain poorly understood. In our present study, we found that downregulation of ubiquitin E3 ligase ASB3 led to enhanced mitochondrial apoptosis as well as autophagy, which synergistically promoted cell death in hepatocellular carcinoma(HCC). We observed the activation of caspase-8 and decrease of autophagy protein Beclin1 in apoptotic cells that were depleted of ASB3. Beclin1 was mainly cleaved by activated caspase-8 and active Beclin1 initiated mitochondrial apoptosis via locating its C-terminal fragment to mitochondria. In addition, knocking down of Beclin1 markedly blocked the apoptosis, indicating its essential role in the process.Notably, our study indicated that enhanced autophagy level might be involved in the activation of caspase-8 and promote the apoptosis. Taken together, our results demonstrated that ASB3 can regulate mitochondrial pathway of apoptosis by controlling caspase-8 mediated cleavage of Beclin1 in HCC. Therefore, ASB3 may potentially serve as a novel target for HCC therapy,especially when combined with autophagy agonist.

关键词： ASB3 apoptosis Beclinl caspase-8 autophagy liver cancer

A transition prediction method for flow over airfoils based on high-order dynamic mode decomposition

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Chinese Journal of Aeronautics 2019年第11期32卷 2408-2421页

作者： mengmeng wu Zhonghua HAN Han NIE Wenping SONG Soledad Le CLAINCHE Esteban FERRER School of Aeronautics Northwestern Poly technical UniversityX i’an 710072China ETSIAE-UPM School of AeronauticsUniversidad Politecnica de MadridPza Cardenal Cisneros 3Spain

This article presents a novel approach for predicting transition locations over airfoils,which are used to activate turbulence model in a Reynolds-averaged Navier-Stokes flow solver.This approach combines Dynamic Mode Decomposition(DMD)with e^Ncriterion.The core idea is to use a spatial DMD analysis to extract the modes of unstable perturbations from a steady flowfield and substitute the local Linear Stability Theory(LST)analysis to quantify the spatial growth of Tollmien–Schlichting(TS)waves.Transition is assumed to take place at the stream-wise location where the most amplified mode’s N-factor reaches a prescribed threshold and a turbulence model is activated thereafter.To improve robustness,the high-order version of DMD technique(known as HODMD)is employed.A theoretical derivation is conducted to interpret how a spatial highorder DMD analysis can extract the growth rate of the unsteady perturbations.The new method is validated by transition predictions of flows over a low-speed Natural-Laminar-Flow(NLF)airfoil NLF0416 at various angles of attack and a transonic NLF airfoil NPU-LSC-72613.The transition locations predicted by our HODMD/e^Nmethod agree well with experimental data and compare favorably to those obtained by some existing methods■.It is shown that the proposed method is able to predict transition locations for flows over different types of airfoils and offers the potential for application to 3D wings as well as more complex configurations.

关键词： Airfoil Dynamic mode decomposition(DMD) e^N criterion Navier-Stokes equations Transition prediction