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Prescreening of large-effect markers with multiple strategies improves the accuracy of genomic prediction

Journal of Integrative Agriculture 2024年第5期23卷 1634-1643页

作者： Keanning Li Bingxing An Mang Liang Tianpeng Chang Tianyu Deng lili du Sheng Cao Yueying du Hongyan Li Lingyang Xu Lupei Zhang Xue Gao Junya LI Huijiang Gao Laboratory of Molecular Biology and Bovine Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China College of Computer and Information Engineering Tianjin Agricultural UniversityTianjin 300384China College of Animal Science and Technology Qingdao Agricultural UniversityQingdao 266109China Tongliao Animal Agriculture Development Service Center Tongliao 028000China

Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)<0.01),where these loci were set as extra fixed effects(named GBLUP-Fix)and random effects(GFBLUP)to improve the prediction accuracy in the validation population,respectively.The results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle(LDM),water holding capacity(WHC),shear force(SF),and pH in Huaxi cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for SF.These methods also captured more genetic variance than GBLUP.Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.

关键词： multi-omics data features prescreening eQTL mapping Huaxi cattle genomic selection

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The DNA damage repair complex MoMMS21-MoSMC5 is required for infection-related development and pathogenicity of Magnaporthe oryzae

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Journal of Integrative Agriculture 2024年第6期23卷 1956-1966页

作者： Yue Jiang Rong Wang lili du Xueyu Wang Xi Zhang Pengfei Qi Qianfei Wu Baoyi Peng Zonghua Wang Mo Wang Ya Li State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Agriculture and Forestry UniversityFuzhou 350002China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan Agricultural UniversityKunming 650201China Fujian Universities Key Laboratory for Plant-Microbe Interaction Fujian Agriculture and Forestry UniversityFuzhou 350002China Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops Minjiang UniversityFuzhou 350108China Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests Fuzhou 350003China

The conserved DNA damage repair complex,MMS21-SMC5/6(Methyl methane sulfonate 21-Structural maintenance of chromosomes 5/6),has been extensively studied in yeast,animals,and plants.However,its role in phytopathogenic fungi,particularly in the highly destructive rice blast fungus Magnaporthe oryzae,remains unknown.In this study,we functionally characterized the homologues of this complex,MoMMS21 and MoSMC5,in M.oryzae.We first demonstrated the importance of DNA damage repair in M.oryzae by showing that the DNA damage inducer phleomycin inhibited vegetative growth,infection-related development and pathogenicity in this fungus.Additionally,we discovered that MoMMS21 and MoSMC5 interacted in the nuclei,suggesting that they also function as a complex in M.oryzae.Gene deletion experiments revealed that both MoMMS21 and MoSMC5 are required for infection-related development and pathogenicity in M.oryzae,while only MoMMS21 deletion affected growth and sensitivity to phleomycin,indicating its specific involvement in DNA damage repair.Overall,our results provide insights into the roles of MoMMS21 and MoSMC5 in M.oryzae,highlighting their functions beyond DNA damage repair.

关键词： Magnaporthe oryzae MMS21 SMC5 DNA damage repair pathogenicity

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Incorporating kernelized multi-omics data improves the accuracy of genomic prediction

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Journal of Animal Science and Biotechnology 2023年第1期14卷 88-97页

作者： Mang Liang Bingxing An Tianpeng Chang Tianyu Deng lili du Keanning Li Sheng Cao Yueying du Lingyang Xu Lupei Zhang Xue Gao Junya Li Huijiang Gao Laboratory of Molecular Biology and Bovine Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193People’s Republic of China

Background:Genomic selection(GS)has revolutionized animal and plant breeding after the first implementation via early selection before measuring phenotypes.Besides genome,transcriptome and metabolome information are increasingly considered new sources for GS.Difficulties in building the model with multi-omics data for GS and the limit of specimen availability have both delayed the progress of investigating multi-omics.Results:We utilized the Cosine kernel to map genomic and transcriptomic data as n×n symmetric matrix(G matrix and T matrix),combined with the best linear unbiased prediction(BLUP)for GS.Here,we defined five kernel-based prediction models:genomic BLUP(GBLUP),transcriptome-BLUP(TBLUP),multi-omics BLUP(MBLUP,M=ratio×G+(1-ratio)×T),multi-omics single-step BLUP(mss BLUP),and weighted multi-omics single-step BLUP(wmss BLUP)to integrate transcribed individuals and genotyped resource population.The predictive accuracy evaluations in four traits of the Chinese Simmental beef cattle population showed that(1)MBLUP was far preferred to GBLUP(ratio=1.0),(2)the prediction accuracy of wmss BLUP and mss BLUP had 4.18%and 3.37%average improvement over GBLUP,(3)We also found the accuracy of wmss BLUP increased with the growing proportion of transcribed cattle in the whole resource population.Conclusions:We concluded that the inclusion of transcriptome data in GS had the potential to improve accuracy.Moreover,wmss BLUP is accepted to be a promising alternative for the present situation in which plenty of individuals are genotyped when fewer are transcribed.

关键词： BLUP Cosine kernel Genomic prediction Transcriptome

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Cellular and Molecular Atlas of Peripheral Blood Mononuclear Cells from a Pregnant Woman After Recovery from COVID-19

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Maternal-Fetal Medicine 2023年第2期5卷 88-96页

作者： lili du Yingyu Liang Xiaoyi Wang Lijun Huang Xingfei Pan Jingsi Chen dunjin Chen Department of Obstetrics and Gynecology Guangdong Provincial Clinical Research Center for Obstetrics and GynecologyGuangdong Engineering and Technology Research Center of Maternal-Fetal MedicineGuangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal MedicineGuangdong Provincial Key Laboratory of Major Obstetric DiseasesThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510150China Department of Infectious Diseases Guangdong Provincial Key Laboratory of Major Obstetric DiseasesThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510150China.

Objective:This study aimed to investigate the immune response of a pregnant woman who recovered from the coronavirus disease 2019(COVID_(R)S)by using single-cell transcriptomic profiling of peripheral blood mononuclear cells(PBMCs)and to analyze the properties of different immune cell subsets.Methods:PBMCs were collected from the COVID_(R)S patient at 28 weeks of gestation,before a cesarean section.The PBMCs were then analyzed using single-cell RNA sequencing.The transcriptional profiles of myeloid,T,and natural killer(NK)cell subsets were systematically analyzed and compared with those of healthy pregnant controls from a published single-cell RNA sequencing data set.Results:We identified major cell types such as T cells,B cells,NK cells,and myeloid cells in the PBMCs of our COVID_(R)S patient.The increase of myeloid and B cells and decrease of T cells and NK cells in the PBMCs in this patient were quite distinct compared with that in the control subjects.After reclustering and Augur analysis,we found that CD16 monocytes and mucosal-associated invariant T(MAIT)cells were mostly affected within different myeloid,T,and NK cell subtypes in our COVID_(R)S patient.The proportion of CD16 monocytes in the total myeloid population was increased,and the frequency of MAIT cells in the total T and NK cells was significantly decreased in the COVID-RS patient.We also observed significant enrichment of gene sets related to antigen processing and presentation,T-cell activation,T-cell differentiation,and tumor necrosis factor superfamily cytokine production in CD16 monocytes,and enrichment of gene sets related to antigen processing and presentation,response to type II interferon,and response to virus in MAIT cells.Conclusion:Our study provides a single-cell resolution atlas of the immune gene expression patterns in PBMCs from a COVID_(R)S patient.Our findings suggest that CD16-positive monocytes and MAIT cells likely play crucial roles in the maternal immune response against severe acute respiratory syndrome coronavirus 2 infect

关键词： Transcriptome Single-cell analysis Pregnancy Peripheral blood mononuclear cells Recovery COVID-19

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Co-optimization approach to post-storm recovery for interdependent power and transportation systems

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Journal of Modern Power Systems and Clean Energy 2019年第4期7卷 688-695页

作者： Yinyin GE lili du Hongxing YE Case Western Reserve University ClevelandUSA University of Florida GainesvilleUSA Cleveland State University ClevelandUSA

The power and transportation systems are urban interdependent critical infrastructures(CIs).during the post-disaster restoration process,transportation mobility and power restoration process are interdependent,and their functionalities significantly affect the well-beings of other urban CIs.Therefore,to enhance the resilience of urban CIs,successful recovery strategies should promote CI function cooperatively and synergistically to distribute goods and services efficiently.This paper develops an integrative framework that addresses the challenges of enhancing the recovery efficiency of urban power and transportation systems in short-term recovery period.Specifically,the post-storm recovery process is considered as a scheduling problem with the constraints representingcrew dispatch,equipment and fuel limit.We propose a new framework for co-optimizing the recovery scheduling of power and transportation systems,respecting precedency requirement and network constraints.The advantages and benefits of co-optimized recovery scheduling are validated in a testing system.

关键词： Co-optimization Interdependent critical infrastructure(CI) Power system Resilience Transportation system

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Maternal high salt-diet increases offspring's blood pressure with dysfunction of NO/PKGI signaling pathway in heart tissue

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Gynecology and Obstetrics Clinical Medicine 2022年第2期2卷 69-75页

作者： Minshan Huang Xiuying Li Luwen Ren Lin Huang Jiahong Pan Jinlin Yao lili du dunjin Chen Jingsi Chen Department of Obstetrics and Gynecology The Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China Department of Fetal Medicine and Prenatal Diagnosis The Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China Obstetrics&Gynecology Institute of Guangzhou Guangzhou510150China Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes Guangzhou510150China Key Laboratories for Major Obstetric Diseases of Guangdong Province Guangzhou510150China Department of Obstetrics The First People's Hospital of FoshanFoshan528000China

Background:High salt-diets have become significant threats to human health,resulting in hypertension and cardiovascular diseases.Hypertensive disorders during pregnancy are complicated,since the maternal cardiovascular system undergoes extensive physiological changes during pregnancy.High-salt diets during pregnancy can disturb the intrauterine environment and negatively affect fetal development.Therefore,we explored how high-salt diets during pregnancy could affect the offspring.Methods:Rats were divided into three groups and fed with low,normal,and high salt diets.The offspring were separated into three groups after weaning based on dietary salt concentration.The blood pressure and urine protein content of both dams and offspring were measured.To evaluate cardiac function,we used Masson staining and immunodetection to confirm the fibrosis status.Finally,we extracted protein from cardiac tissue to test the expression levels of the Nitric Oxide(NO)/cGMP-dependent protein kinase I(PKGI)pathway and the angiotensin receptor.Results:High-salt diets increased blood pressure,and offspring previously exposed to high-salt environments were predisposed to hypertension.High-salt diets were also found to induce cardiac fibrosis and exacerbate fibrosis in offspring and alter the epithelial-mesenchymal transition(EMT).Under these conditions,the NO/PKGI pathway was activated in cardiac tissue and the type-1angiotensin II receptor(AT1R)was upregulated,though the type-2 angiotensin II receptor(AT2R)had the opposite effect.Conclusion:High-salt diets induce high blood pressure and increase predisposition to hypertension in offspring.They are accompanied by cardiac fibrosis,which could be caused by the activation of NO/PKGI and upregulation of AT1R.

关键词： High salt Hypertension Cardiac fibrosis Nitric oxide cGMP-dependent protein kinase I Fetal origins of adult disease

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论《从此以后》中的创伤、幽灵叙事和主体性重构

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吉林师范大学学报（人文社会科学版） 2024年第2期52卷 62-67页

作者：杜丽丽兰州大学外国语学院甘肃兰州730000

创伤与幽灵叙事存在密切联系,因为以幽灵的形式对现在造成侵扰的多是记忆中挥之不去的创伤,在这种意义上,历史书写即是对创伤的挖掘和治疗。文章通过对格雷厄姆·斯威夫特《从此以后》的文本细读,探讨小说所再现的个人和家族历史记忆中... 详细信息

创伤与幽灵叙事存在密切联系,因为以幽灵的形式对现在造成侵扰的多是记忆中挥之不去的创伤,在这种意义上,历史书写即是对创伤的挖掘和治疗。文章通过对格雷厄姆·斯威夫特《从此以后》的文本细读,探讨小说所再现的个人和家族历史记忆中的创伤,以及它所采用的幽灵叙事模式;借鉴列维纳斯的他者理论,分析在追寻的叙事框架下,当代主人公比尔·昂文艰难的自我主体性重构;进而论述以《从此以后》为代表的“新维多利亚小说”在创伤表征和创伤见证方面的伦理意义。

关键词：《从此以后》创伤幽灵他者主体性创伤表征

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Eplerenone inhibits atrial fibrosis in mutant TGF-β1 transgenic mice

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Science China(Life Sciences) 2016年第10期59卷 1042-1047页

作者： Xiaoqing Chen Wuchang Zhang Qian Wang lili du Yi Yi Yan Liu Xu Liu Shengzhong duan Department of Cardiology Shanghai Chest Hospital Shanghai Jiao tong University Key Laboratory of Nutrition and Metabolism Institute for Nutritional Sciences Shanghai Institutes for Biological Sciences Chinese Academy of Sciences University of the Chinese Academy of Sciences

The purpose of the present study was to study the impacts of eplerenone(EPL), an antagonist of mineralocorticoid receptors(MR), on atrial fibrosis in a mouse model with selective fibrosis in the atrium, and to explore the possible mechanisms. Using mutant TGF-β1 transgenic(Tx) mice, we first demonstrated that EPL inhibited atrial fibrosis specifically and decreased macrophage accumulation in the atria of these mice. Results from immunohistochemistry and western blotting showed that EPL attenuated protein expression of fibrosis-related molecules such as connective tissue growth factor(CTGF) and fibronectin in the atria of Tx mice. In culture, EPL inhibited gene expression of fibrosis-related molecules such as fibronectin, α-SMA, and CTGF in TGF-β1-stimulated atrial fibroblasts. Finally, using a co-culture system, we showed that TGF-β1-stimulated atrial fibroblasts induced migration of macrophages and this was blocked by EPL. EPL also blocked TGF-β1-induced gene expression of intedeukin-6(IL-6) in atrial fibroblasts. Therefore, we conclude that EPL attenuated atrial fibrosis and macrophage infiltration in Tx mice. TGF-β1 and IL-6 were involved in the impacts of EPL on activation of atrial fibroblasts and interactions between fibroblasts and macrophages.

关键词： TGF-β1 转基因小鼠基因突变纤维化心房 Western印迹成纤维细胞结缔组织生长因子

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直齿行星传动罚函数修形优化及动力学分析

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华中科技大学学报(自然科学版) 2024年第6期52卷 80-86页

作者：张西金方宗德尹逊民贾海涛杜立立西北工业大学机电学院中国船舶集团有限公司第七〇三研究所

针对直齿行星传动齿轮修形问题，提出了减小齿轮副承载传动误差波动幅度的直齿行星轮系罚函数修形优化方法．研究了内外啮合直齿轮承载接触分析(LTCA)方法，并与Romax软件计算结果进行对比验证；基于承载接触分析方法计算承载传动误差... 详细信息

针对直齿行星传动齿轮修形问题，提出了减小齿轮副承载传动误差波动幅度的直齿行星轮系罚函数修形优化方法．研究了内外啮合直齿轮承载接触分析(LTCA)方法，并与Romax软件计算结果进行对比验证；基于承载接触分析方法计算承载传动误差，提出了直齿行星轮系内外啮合齿轮副的罚函数修形优化方法，进行了行星轮系内外啮合齿轮副修形优化设计．为了验证修形减振效果，将承载传动误差转换为啮合刚度，建立了直齿行星传动系统动力学模型，分析了内外修形优化对轴承支撑处振动加速度的影响．动力学分析表明：外啮合优化修形可以显著减小太阳轮支撑处振动加速度，内啮合修形优化可以减小内齿圈支撑处振动加速度，而且外啮合修形减振效果更好．

关键词：行星齿轮系统直齿轮承载传动误差修形优化动力学

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全球变暖背景下陕西省夏季极端降水及其大尺度环流特征

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高原气象 2024年第2期43卷 342-352页

作者：杜一博李双双冯典肖贻青陈小婷黄少妮杜莉丽陕西省气象台陕西西安710014

基于陕西省99个国家站1979-2021年夏季逐日降水资料和ERA5再分析数据,研究了陕西省夏季极端降水的时空变化以及相应的大尺度环流特征,并对全省典型地区进行水汽追踪分析。结果表明,陕西省夏季极端降水总体呈现出南多北少的空间分布,陕... 详细信息

基于陕西省99个国家站1979-2021年夏季逐日降水资料和ERA5再分析数据,研究了陕西省夏季极端降水的时空变化以及相应的大尺度环流特征,并对全省典型地区进行水汽追踪分析。结果表明,陕西省夏季极端降水总体呈现出南多北少的空间分布,陕北中部、关中中东部极端降水为增加的趋势,通过REOF分析并计算得到陕北、关中极端降水变化趋势分别为0.36 mm·a^(-1),0.35 mm·a^(-1),陕南极端降水变化趋势最小为0.11 mm·a^(-1)。夏季影响陕西省的水汽来源主要有三支路径,北支水汽来自欧亚中高纬地区,东支水汽主要来自内陆的江河流域,南支水汽主要来自南海和孟加拉湾。此外,陕西省夏季极端降水在2005年后增多是大气高、中、低层大气环流共同作用的结果,大气高层辐散增强有利于上升运动,大气中层西太平洋副热带高压(以下简称,西太副高)西伸北抬造成外围水汽更容易进入内陆,蒙古反气旋南侧的异常东风和低层的异常东南风更有利于水汽进一步向西北地区输送。

关键词：极端降水西太平洋副热带高压水汽追踪

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