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Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

BioDesign Research 2024年第1期6卷 51-67页

作者： Md Torikul Islam yang Liu Md Mahmudul Hassan Paul E.Abraham Jean Merlet Alice Townsend Daniel Jacobson C.Robin Buell Gerald A.Tuskan xiaohan yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Genetics and Plant Breeding Patuakhali Science and Technology UniversityDumkiPatuakhali 8602Bangladesh Bredesen Center for Interdisciplinary Research and Graduate Education University of Tennessee KnoxvilleKnoxvilleTN 37996USA Center for Applied Genetic Technologies University of GeorgiaAthensGA 30602USA Department of Crop and Soil Sciences University of GeorgiaAthensGA 30602USA Institute of Plant Breeding Geneticsand GenomicsUniversity of GeorgiaAthensGA 30602USA

Plants are complex systems hierarchically organized and composed of various cell *** understand the molecular underpinnings of complex plant systems,single-cell RNA sequencing(scRNA-seq)has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type ***,scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology,which aims to modify plants genetically/epigenetically through genome editing,engineering,or re-writing based on rational design for increasing crop yield and quality,promoting the bioeconomy and enhancing environmental *** particular,data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side *** date,scRNA-seq has been demonstrated in a limited number of plant species,including model plants(e.g.,Arabidopsis thaliana),agricultural crops(e.g.,Oryza sativa),and bioenergy crops(e.g.,Populus spp.).It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in *** this review,we summarize current technical advancements in plant scRNA-seq,including sample preparation,sequencing,and data analysis,to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant *** then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology ***,we discuss the challenges and opportunities for the application of scRNA-seq in plants.

关键词： application biology systems plant advances single-cell synthetic transcriptomics

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Quantitative Evaluation of Sea-ice Disaster in Bohai Sea Based on GOCI and Sentinel-1

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Journal of Geodesy and Geoinformation Science 2021年第1期4卷 49-55页

作者： Meijie LIU Jin WANG Shilei ZHONG Hao YOU Qi LIANG Ting CHEN Wenbo LI xiaohan yang College of Physics Qingdao UniversityQingdao 266071China First Institute of Oceanography Ministry of Natural Resources of the People’s Republic of ChinaQingdao 266061China

The Circum-Bohai-Sea Region is an important economic zone of *** sea ice,which occurs at each winter,is the major marine hazard of the Bohai *** a result,it is very important to evaluate the damage effects quantitatively in this region,which is seldom studied and analyzed systematically using long-time-series *** this paper,the sea-ice disaster in the Bohai Sea is evaluated quantitatively based on the Sentinel-1 and *** different hazard-bearing bodies of the marine transportation and the offshore constructions,different sea-ice-hazard indexes are defined,which can be applied to analyze the sea-ice disaster quantitatively in the Bohai Sea,including the annual and inter-annual variations in the period from 2011 to *** analysis results can provide the reference of the sea-ice monitoring in the Bohai Sea.

关键词： the Bohai Sea sea-ice disaster the quantitative evaluation Sentinel-1 GOCI

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Plant Promoters and Terminators for High-Precision Bioengineering

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BioDesign Research 2023年第1期5卷 86-105页

作者： Emily G.Brooks Estefania Elorriaga yang Liu James R.Duduit Guoliang Yuan Chung-Jui Tsai Gerald A.Tuskan Thomas G.Ranney xiaohan yang Wusheng Liu Department of Horticultural Science North Carolina State UniversityRaleighNC 27607USA. Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA. The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA. Warnell School of Forestry and Natural Resource University of GeorgiaAthensGA 30602USA. Department of Plant Biology University of GeorgiaAthensGA 30602USA. Department of Genetics University of GeorgiaAthensGA 30602USA. Mountain Crop Improvement Lab Department of Horticultural ScienceMountain Horticultural Crops Research and Extension CenterNorth Carolina State UniversityMills RiverNC 28759USA.

High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional *** transcription is tightly regulated by promoters and *** determine the timing,tissues and cells,and levels of the expression of *** mediate transcription termination of genes and affect mRNA levels posttranscriptionally,e.g.,the 3′-end processing,stability,translation efficiency,and nuclear to cytoplasmic export of *** promoter and terminator combination affects gene *** the present article,we review the function and features of plant core promoters,proximal and distal promoters,and terminators,and their effects on and benchmarking strategies for regulating gene expression.

关键词： expression Promoter proximal

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企业环境话语建构方式对公众态度的影响——基于两种绿色广告诉求的对比分析

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四川大学学报（哲学社会科学版） 2020年第2期 114-126页

作者：黄河杨小涵中国人民大学新闻学院北京100872

作为开展环境传播、践行环保责任的重要主体,越来越多的企业开始借助绿色广告这一方式与公众进行沟通,力求在唤醒公众环保意识、吸引公众更多地关注环境问题、促使公众积极展开环保行为的同时,提升企业品牌形象和产品销量。在环境话语... 详细信息

作为开展环境传播、践行环保责任的重要主体,越来越多的企业开始借助绿色广告这一方式与公众进行沟通,力求在唤醒公众环保意识、吸引公众更多地关注环境问题、促使公众积极展开环保行为的同时,提升企业品牌形象和产品销量。在环境话语建构中,绿色广告是企业使用最频繁、效果最显著的沟通方式。绿色广告通常会强调产品“环境友好”的特征,部分企业也开始尝试在广告中呼吁消费者“减少消费/减少消耗”。通过对比分析可以发现,消费者对前一类绿色广告的态度更积极,在广告中使用自然图片会改善广告传播的效果;在归因理论的视角下,当消费者对企业动机有较好评价时,他们更倾向于信任产品的环保效果、企业的环保行为,而这又能进一步增强企业环境传播的效果。

关键词：环境传播绿色广告归因理论结构方程模型

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差分侧信道密码分析中泄露模型的线性回归分析

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同济大学学报（自然科学版） 2014年第2期42卷 315-319页

作者：尹慧琳杨筱菡同济大学中德学院上海200092 同济大学数学系上海200092

从统计学线性回归模型的角度研究密码设备差分侧信道分析攻击中泄露模型的建模及估计,在不需对设备信息泄露有提前了解的情况下,得出线性回归泄露模型,克服了传统泄露模型的局限性.首先,分析能耗泄露的随机模型从而构建线性回归模型,然... 详细信息

从统计学线性回归模型的角度研究密码设备差分侧信道分析攻击中泄露模型的建模及估计,在不需对设备信息泄露有提前了解的情况下,得出线性回归泄露模型,克服了传统泄露模型的局限性.首先,分析能耗泄露的随机模型从而构建线性回归模型,然后用最小二乘估计和最小一乘估计两种方法求解线性回归模型的系数,最后基于八位控制器PayTV-AES智能卡平台实现能耗泄露的建模及系数估计.通过对两种求解方法结果的比较,提出最小二乘估计比最小一乘估计更适合用于泄露模型的线性回归分析;通过对被估模型系数曲线的分析,提出线性回归分析可以用于测量数据的预处理,以提高泄露模型建模效率.

关键词：智能卡安全差分侧信道密码分析差分能量攻击泄露模型线性回归分析

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The existence of a nonclassical TCA cycle in the nucleus that wires the metabolic-epigenetic circuitry

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Signal Transduction and Targeted Therapy 2021年第12期6卷 3666-3683页

作者： Xujun Liu Wenzhe Si Lin He Jianguo yang Yani Peng Jie Ren Xiaoping Liu Tong Jin Huajing Yu Zihan Zhang Xiao Cheng Wenting Zhang Lu Xia Yunchao Huang Yue Wang Shumeng Liu Lin Shan Yu Zhang xiaohan yang Haixia Li Jing Liang Luyang Sun Yongfeng Shang Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education) Department of Biochemistry and Molecular BiologyDepartment of Laboratory MedicinePeking University Third HospitalSchool of Basic Medical SciencesPeking University Health Science Center100191 BeijingChina Department of Clinical Laboratory Peking University First Hospital100034 BeijingChina Department of Biochemistry and Molecular Biology School of Basic Medical SciencesHangzhou Normal University311121 HangzhouChina Department of Biochemistry and Molecular Biology School of Basic Medical SciencesCapital Medical University100069 BeijingChina Department of Integration of Chinese and Western Medicine School of Basic Medical SciencesPeking University Health Science Center100191 BeijingChina

The scope and variety of the metabolic intermediates from the mitochondrial tricarboxylic acid(TCA)cycle that are engaged in epigenetic regulation of the chromatin function in the nucleus raise an outstanding question about how timely and precise supply/consumption of these metabolites is achieved in the *** report here the identification of a nonclassical TCA cycle in the nucleus(nTCA cycle).We found that all the TCA cycle-associated enzymes including citrate synthase(CS),aconitase 2(ACO2),isocitrate dehydrogenase 3(IDH3),oxoglutarate dehydrogenase(OGDH),succinyl-CoA synthetase(SCS),fumarate hydratase(FH),and malate dehydrogenase 2(MDH2),except for succinate dehydrogenase(SDH),a component of electron transport chain for generating ATP,exist in the *** showed that these nuclear enzymes catalyze an incomplete TCA cycle similar to that found in *** propose that the nTCA cycle is implemented mainly to generate/consume metabolic intermediates,not for energy *** demonstrated that the nTCA cycle is intrinsically linked to chromatin dynamics and transcription ***,our study uncovers the existence of a nonclassical TCA cycle in the nucleus that links the metabolic pathway to epigenetic regulation.

关键词： metabolic cycle Together

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Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis

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Plant Communications 2023年第5期4卷 208-222页

作者： Cheng Li Wenjie Huang Xiaoxu Han Guohua Zhao Wenyang Zhang Weijun He Bao Nie Xufeng Chen Taijie Zhang Wenhui Bai Xiaopeng Zhang Jingjing He Cheng Zhao Alisdair RFernie Timothy JTschaplinski xiaohan yang Shijuan Yan Li Wang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhouChina Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Max Planck Institute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Key Laboratory of Southern Subtropical Plant Diversity Fairy Lake Botanical GardenShenzhen&Chinese Academy of ScienceShenzhenChina Institute of Plant Protection Guangdong Academy of Agricultural SciencesKey Laboratory of Green Prevention and Control on Fruits and Vegetables in South ChinaMinistry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of High Technology for Plant ProtectionGuangzhouChina Kunpeng Institute of Modern Agriculture at Foshan Chinese Academy of Agricultural SciencesFoshanChina

Crassulacean acid metabolism(CAM)has high water-use efficiency(WUE)and is widely recognized to have evolved from C3 *** plant lineages have convergently evolved CAM,but the molecular mechanism that underlies C3-to-CAM evolution remains to be *** bifurcatum(elkhorn fern)provides an opportunity to study the molecular changes underlying the transition from C3 to CAM photosynthesis because both modes of photosynthesis occur in this species,with sporotrophophyll leaves(SLs)and cover leaves(CLs)performing C3 and weak CAM photosynthesis,***,we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs differed from those in strong CAM *** investigated the diel dynamics of the metabolome,proteome,and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental *** found that multi-omic diel dynamics in *** exhibit both tissue and diel *** analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway(TCA cycle),CAM pathway,and stomatal movement in CLs compared with *** also confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE(PPCK)exhibits convergence in gene expression among highly divergent CAM *** regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal *** together,our results provide new insights into weak CAM photosynthesis and new avenues for CAM bioengineering.

关键词： Platycerium bifurcatum crassulacean acid metabolism multi-omics transcription factor PPCK convergent evolution

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Biodesign Research to Advance the Principles and Applications of Biosystems Design

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BioDesign Research 2019年第1期2019卷 1-4页

作者： xiaohan yang Lei S.Qi Alfonso Jaramillo Zong-Ming(Max)Cheng Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Bioengineering Stanford UniversityStanfordCA 94305USA Department of Chemical and Systems Biology Stanford UniversityStanfordCA 94305USA Stanford ChEM-H Stanford UniversityStanfordCA 94305USA Warwick Integrative Synthetic Biology Centre(WISB)and School of Life Sciences University of WarwickCV47AL CoventryUK ISSB CNRSUniv EvryCEAUniversitéParis-Saclay91025 EvryFrance Institute for Integrative Systems Biology(I2SysBio) University of Valencia-CSIC46980 PaternaSpain Department of Plant Sciences University of TennesseeKnoxvilleTN 37996USA Nanjing Agricultural University NanjingJiangsu ProvinceChina

Over the course of civilization,humans have increasingly expanded their freedom to live a better *** comparison with the primitive society,our modern society has many more choices of life-supporting resources,such as yearround food supply,permanent shelters,diverse energy sources,and effective preventive and curing ***,our society is currently still heavily relying on the resources provided by Mother Nature,which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth,natural resource reduction,and environmental *** example,the food sources originating from plants,animals,or microbes do not have the nutrition balance for optimal human health[1–3].Climate change and environmental deterioration threaten the food security[4–6].Increasingly,infectious diseases(e.g.,HIV/AIDS),genetic diseases(e.g.,cancer),and improper lifestyle-related disorders(e.g.,obesity)become more prevalent and remain challenging to be prevented,controlled,and *** medical technologies and modern medicine development are also meeting the ceiling.

关键词： expanded supporting deterioration

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基于随机效应模型的交叉口事故碰撞类型建模

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同济大学学报（自然科学版） 2016年第1期44卷 81-86页

作者：王雪松袁景辉杨筱菡同济大学道路与交通工程教育部重点试验室上海201804 同济大学数学系上海201804

考虑交叉口不同进口道之间的差异性,在进口道层面对不同碰撞类型事故分别建立随机效应模型,通过在负二项模型中引入随机效应项来考虑交叉口不同进口道之间的空间相关性.模型参数采用全贝叶斯方法进行估计.结果表明:不同碰撞类型事故的... 详细信息

考虑交叉口不同进口道之间的差异性,在进口道层面对不同碰撞类型事故分别建立随机效应模型,通过在负二项模型中引入随机效应项来考虑交叉口不同进口道之间的空间相关性.模型参数采用全贝叶斯方法进行估计.结果表明:不同碰撞类型事故的影响因素不同,且同一影响因素对不同碰撞类型事故的影响程度也存在显著差异,验证了区分碰撞类型进行事故建模的必要性.随机效应项在各模型中均显著,表明交叉口不同进口道之间事故频率存在显著的空间相关性.

关键词：信控交叉口事故碰撞类型交叉口进口道空间相关性随机效应模型

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不止于观看:社会史视角的时尚30年

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艺术设计研究 2023年第2期 5-7页

作者：杨晓涵北京服装学院时尚传播学院

我们对于时尚的认知应该具有多视角、多文化立场、跨知识领域的整体性。“不止于观看”展览的策展工作围绕中国国际青年设计师时装作品大赛30年(1993~2022)获奖作品及文献资料展开研究,以《新史学》(New History)主张的“总体历史(Total... 详细信息

我们对于时尚的认知应该具有多视角、多文化立场、跨知识领域的整体性。“不止于观看”展览的策展工作围绕中国国际青年设计师时装作品大赛30年(1993~2022)获奖作品及文献资料展开研究,以《新史学》(New History)主张的“总体历史(Total History)”观为理论基础,将获奖作品与同年的相关社会事件并置,形成社会史视角的30年时尚史。本文对“不止于观看”展览的策展思路进行简要的分析和讨论,其中包括策展思想、策展方法和混融性叙事方法。

关键词：社会史策展思想策展方法混融性叙事方法

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