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Advancing biological super-resolution microscopy through deep learning: a brief review

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Biophysics Reports 2021年第4期7卷 253-266页

作者： tianjie yang Yaoru Luo Wei Ji Ge yang Institute of Biophysics Chinese Academy of Sciences College of Life Sciences University of Chinese Academy of Sciences Laboratory of Computational Biology and Machine Intelligence School of Artificial IntelligenceUniversity of Chinese Academy of Sciences National Laboratory of Pattern Recognition Institute of AutomationChinese Academy of Sciences

Biological super-resolution microscopy is a new generation of imaging techniques that overcome the ～200 nm diffraction limit of conventional light microscopy in spatial resolution. By providing novel spatial or spatiotemporal information on biological processes at nanometer resolution with molecular specificity, it plays an increasingly important role in biomedical sciences. However, its technical constraints also require trade-offs to balance its spatial resolution, temporal resolution, and light exposure of samples. Recently, deep learning has achieved breakthrough performance in many image processing and computer vision tasks. It has also shown great promise in pushing the performance envelope of biological super-resolution microscopy. In this brief review, we survey recent advances in using deep learning to enhance the performance of biological super-resolution microscopy, focusing primarily on computational reconstruction of super-resolution images. Related key technical challenges are discussed. Despite the challenges, deep learning is expected to play an important role in the development of biological super-resolution microscopy. We conclude with an outlook into the future of this new research area.

关键词： Super-resolution microscopy Image super-resolution Deep learning Image reconstruction Fluorescence microscopy

连作根系分泌物加剧土传病害的机制和缓解措施研究进展

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土壤学报 2024年第5期61卷 1201-1211页

作者：游川杨天杰周新刚王孝芳徐阳春沈其荣韦中南京农业大学资源与环境科学学院/国家有机类肥料重点实验室/江苏省固体有机废弃物资源化高新技术研究重点实验室南京210095 东北农业大学园艺园林学院哈尔滨150030

基于植物-土壤反馈理论,连作体系中的根系分泌物必然在加剧土传病害发生中起重要作用,但相关研究证据尚缺少系统总结。本文梳理了连作加剧土传病害发生的现象以及连作累积典型根系分泌物组分的案例。从有利于土传病原菌由土体向根际迁... 详细信息

基于植物-土壤反馈理论,连作体系中的根系分泌物必然在加剧土传病害发生中起重要作用,但相关研究证据尚缺少系统总结。本文梳理了连作加剧土传病害发生的现象以及连作累积典型根系分泌物组分的案例。从有利于土传病原菌由土体向根际迁移、增殖和致病(“利病”)、破坏根际有益微生物群落防线(“压益”)和毒害根系免疫系统(“自毒”)等三个方面,阐述连作根系分泌物中某些物质促进土传病原菌入侵的机制。从根系分泌物的角度阐述轮作、间作、套作、伴生和嫁接等多样性种植方式缓解连作土传病害的发生机制。提出鉴定“利病”、“压益”和“自毒”物质以及构建对应的消减技术途径,可为土传病害绿色高效综合防控提供科学支撑。

关键词：连作障碍土传病原菌根系分泌物自毒物质根际微生物

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梨树枝条粉碎覆盖对梨园土壤养分和微生物组的影响

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土壤学报 2024年第2期61卷 549-561页

作者：杨天杰王孝芳胡红菊杨健藕继旺王晓祥郝宝锋王中华董彩霞徐阳春南京农业大学资源与环境科学学院/江苏省固体有机废弃物资源化高技术研究重点实验室/江苏省有机固体废弃物资源化协同创新中心/资源节约型肥料教育部工程研究中心/国家有机类肥料工程技术研究中心南京210095 湖北省农业科学院果树茶叶研究所武汉430209 中国农业科学院郑州果树研究所郑州450009 贵阳小河区金海农业科技开发有限公司贵阳550000 黑龙江省农业科学院园艺分院哈尔滨150069 河北省农林科学院昌黎果树研究所河北昌黎066600 江苏省农业科学院果树研究所/江苏省高效园艺作物遗传改良重点实验室南京210014

梨树整形修剪枝条是一类重要的生物质资源,将其粉碎后覆盖于树下土壤是资源化利用的有效途径。为了科学评估梨树枝条粉碎覆盖对土壤理化性状及微生物群落结构的影响,采集了贵州毕节、河北昌黎、黑龙江哈尔滨、湖北枝江和河南许昌5个不... 详细信息

梨树整形修剪枝条是一类重要的生物质资源,将其粉碎后覆盖于树下土壤是资源化利用的有效途径。为了科学评估梨树枝条粉碎覆盖对土壤理化性状及微生物群落结构的影响,采集了贵州毕节、河北昌黎、黑龙江哈尔滨、湖北枝江和河南许昌5个不同纬度梨典型种植区梨园枝条覆盖1~2年后的土壤样品,检测了土壤基础理化特性及土壤细菌、真菌和原生生物群落。结果发现,与不覆盖枝条的对照相比,总体而言覆盖能有效提高土壤有机质和有效磷含量,土壤细菌、真菌和原生生物群落结构也发生了显著变化,但对群落多样性无显著影响;覆盖处理显著富集了土壤细菌中的变形菌门、酸杆菌门和真菌中的担子菌门以及原生生物中的孔虫界和囊泡虫类等类群的相对丰度。进一步利用随机森林模型挖掘了不同采样点枝条覆盖后的关键物种,模型预测准确率高达94.44%,关键物种以细菌为主,包括Acidibacter、Xanthobacteraceae、Nitrosomonadaceae等与有机残体降解有关的微生物,还发现土壤有效磷含量是土壤微生物群落结构差异的主要驱动因子。相关研究结果初步评估了梨树枝条覆盖对土壤养分和微生物组的影响,挖掘了潜在的关键微生物。

关键词：梨修剪枝条覆盖土壤理化性状微生物组关键物种

根际溶铁细菌与AM真菌协同提高石灰性土壤铁有效性的机制研究

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土壤学报 2024年第4期61卷 1111-1122页

作者：彭海英邵雅东栗晗李培根丁百玲杨天杰徐阳春沈其荣董彩霞南京农业大学资源与环境科学学院/江苏省固体有机废弃物资源化研究重点实验室/江苏省有机固体废弃物协同创新中心/教育部资源节约型肥料工程技术研究中心南京210095

石灰性土壤普遍存在铁有效性低导致的植物缺铁黄化现象,严重影响农业可持续发展。筛选高效溶铁细菌并探讨其与菌根真菌(AMF)协同提高土壤有效铁含量、改善植物铁营养机制具有重要意义。以石灰性土壤和番茄(Lycopersicon esculentum)为... 详细信息

石灰性土壤普遍存在铁有效性低导致的植物缺铁黄化现象,严重影响农业可持续发展。筛选高效溶铁细菌并探讨其与菌根真菌(AMF)协同提高土壤有效铁含量、改善植物铁营养机制具有重要意义。以石灰性土壤和番茄(Lycopersicon esculentum)为试材进行盆栽试验,分别接种Advenella kashmirensis(B1)、Arthrobacter cupressi(B2)、Klebsiellavariicola(B3)、Variovorax guangxiensis(B4)和Enterobacter ludwigii(B5)5株细菌,以不接菌处理为对照(CK),筛选出高效溶铁菌株B1、B2和B3。将其与纯培养得到的AM真菌孢子(Rhizoshagu irregularis,Ri)组合,设置单独接种AM真菌(Ri)、单菌与Ri(B1+Ri、B2+Ri和B3+Ri)、菌群与Ri(B1+B2+B3+Ri)共接种处理,进一步探究单菌及菌群与AMF协同促进石灰性土壤难溶性铁的活化和促进植物铁吸收的机制。结果表明:(1)与对照相比,接种B1、B2和B3能够显著促进番茄生长,根系和地上部全铁积累量分别提高6.48倍和2.61倍(B1)、4.11倍和2.03倍(B2)、4.37倍和2.25倍(B3);新叶活性铁含量分别提高74.21%、1.33倍和1.75倍。(2)与单接AMF相比,不同共接种组合显著增加番茄生物量,各部位平均全铁积累量显著提高58.32%~119.43%,其中B3+Ri处理、B1+B2+B3+Ri处理下番茄根系活性铁含量分别提高41.47%和44.30%、新叶活性铁含量分别提高12.61%和12.77%。不同共接种组合处理显著提高AM真菌的菌根侵染率,较单接AM真菌处理提高13.35%~30.99%;根系铁还原酶活性增加9.86%~22.07%,根系LeFIT1、LeFRO2和LeMYB72基因表达显著上调。与单接AM真菌相比,B3+Ri和B1+B2+B3+Ri处理下根际土壤pH分别降低0.21和0.09,土壤有效铁含量分别提高15.78%和55.23%。综上,AM真菌与3株高效溶铁细菌的协同作用可显著提高石灰性土壤铁有效性并改善植物铁营养,不同类型溶铁细菌与AMF的协同作用机制不同,为解决石灰性土壤铁有效性低的问题提供了微生物途径。

关键词： AM真菌溶铁细菌土壤有效铁土壤pH 活性铁铁营养

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POSITIVE CLASSICAL SOLUTIONS OF DIRICHLET PROBLEM FOR THE STEADY RELATIVISTIC HEAT EQUATION

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数学物理学报:B辑英文版 2023年第5期43卷 2279-2290页

作者：杨田洁袁光伟 Graduate School of China Academy of Engineering Physics Beijing 100088China Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing100088China

In this paper,for a bounded C2 domain,we prove the existence and uniqueness of positive classical solutions to the Dirichlet problem for the steady relativistic heat equation with a class of restricted positive C2 boundary *** have a non-existence result,which is the justification for taking into account the restricted boundary *** is a smooth positive boundary datum that precludes the existence of the positive classical solution.

关键词： Dirichlet problem steady relativistic heat equation classical solution

RIN enhances plant disease resistance via root exudate-mediated assembly of diseasesuppressive rhizosphere microbiota

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Molecular Plant 2023年第9期16卷 1379-1395页

作者： Keming yang Ruixin Fu Haichao Feng Gaofei Jiang Omri Finkel Tianyu Sun Mingchun Liu Baowen Huang Shan Li Xiaofang Wang tianjie yang Yikui Wang Shimei Wang yangchun Xu Qirong Shen Ville-Petri Friman Alexandre Jousset Zhong Wei Key Lab of Organic-based Fertilizers of China Jiangsu Provincial Key Lab of Solid Organic Waste UtilizationJiangsu Collaborative Innovation Center of Solid Organic WastesEducational Ministry Engineering Center of Resource-saving fertilizersNanjing Agricultural UniversityNanjingJiangsu 210095China College of Agro-grassland Science Nanjing Agricultural UniversityNanjingJiangsu 210095China School of Biology and Food Shangqiu Normal UniversityShangqiu 476000China College of Agriculture Henan UniversityZhengzhou 450046China Department of Plant and Environmental Sciences Institute of Life ScienceThe Hebrew University of JerusalemJerusalemIsrael Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China Key Laboratory of Plant Hormones and Development Regulation of Chongqing School of Life SciencesChongqing UniversityChongqingChina Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074China Institute of Vegetable Research Guangxi Academy of Agricultural SciencesNanningChina Department of Biology University of YorkYork YO105DDUK Department of Microbiology University of Helsinki00014 HelsinkiFinland

The RIPENING-INHIBITOR(RIN)transcriptional factor is a key regulator governing fruit *** RIN also affects other physiological processes,its potential roles in triggering interactions with the rhizosphere microbiome and plant health are *** we show that RIN affects microbiome-mediated disease resistance via root exudation,leading to recruitment of microbiota that suppress the soil-borne,phytopathogenic Ralstonia solanacearum *** with the wild-type(WT)plant,RIN mutants had different root exudate profiles,which were associated with distinct changes in microbiome composition and ***,the relative abundances of antibiosis-associated genes and pathogensuppressing Actinobacteria(Streptomyces)were clearly lower in the rhizosphere of rin *** composition,diversity,and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin,which were exuded in much lower concentrations by the rin ***,RIN-mediated effects on root exudates,Actinobacteria,and disease suppression were evident from the seedling stage,indicating that RIN plays a dual role in the early assembly of diseasesuppressive microbiota and late fruit ***,our work suggests that,while plant disease resistance is a complex trait driven by interactions between the plant,rhizosphere microbiome,and the pathogen,it can be indirectly manipulated using"prebiotic"compounds that promote the recruitment of disease-suppressive microbiota.

关键词： rhizosphere microbiome plant-microbe interactions disease-suppressive microbiota rhizosphere immunity bacterial wilt tomato root exudates

Tetra-color superresolution microscopy based on excitation spectral demixing

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Light(Science & Applications) 2023年第1期12卷 99-108页

作者： Wanyan Wu Shihang Luo Chunyan Fan tianjie yang Shuwen Zhang Wenxiang Meng Tao Xu Wei Ji Lusheng Gu Institute of Biophysics Chinese Academy of SciencesBeijing 100101China College of Life Science University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China School of Future Technology University of Chinese Academy of SciencesBeijing 100049China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100049China Bioland Laboratory Guangzhou 510005China Guangzhou Laboratory Guangzhou 510030China

Multicolor imaging allows protein colocalizations and organelle interactions to be studied in biological research,which is especially important for single-molecule localization microscopy(SMLM).Here,we propose a multicolor method called excitation-resolved stochastic optical reconstruction microscopy(ExR-STORM).The method,which is based on the excitation spectrum of fluorescent dyes,successfully separated four spectrally very close far-red organic fluorophores utilizing three excitation lasers with cross-talk of less than 3%.Dyes that are only 5 nm apart in the emission spectrum were resolved,resulting in negligible chromatic *** method was extended to three-dimensional(3D)imaging by combining the astigmatic method,providing a powerful tool for resolving 3D morphologies at the nanoscale.

关键词： excitation spectral mixing

Community Residents' Heritage Preservation Intentions and Influencing Factors Based on the Extended Theory of Planned Behavior: A Case Study of Historic Districts in Tianjin

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China City Planning Review 2024年第3期33卷 40-50页

作者： Zhang tianjie Tang Shan School of Architecture Tianjin UniversityTianjinP.R.China

Community residents are important stakeholders in preserving historic districts. This paper introduces the extended theory of planned behavior to explore the intentions of residents to participate in heritage preservation, and further explains the influencing factors. Seven historic districts in Tianjin are selected as case studies. The results show that the residents' intentions to preserve heritage are positively influenced by three subjective perception factors of heritage preservation attitude, subjective norms, and perceived behavioral control, as well as two objective situational factors of environmental quality of historic district and policy guidance for heritage preservation. Furthermore, the objective situational factors indirectly influence heritage preservation intentions through the subjective perception factors. Based on these findings, this paper puts forward corresponding suggestions to enhance the heritage preservation intentions of community residents.

关键词： theory of planned behavior community residents heritage preservation intention historic districts in Tianjin

基于GARCH模型的人民币汇率形成机制研究

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中南财经政法大学学报 2019年第6期 113-120,160页

作者：杨甜婕邓富华西南财经大学金融学院四川成都611130 西南财经大学国际商学院四川成都611130

本文通过构建扩展的GARCH模型,探讨了人民币汇率中间价形成机制、宏观经济基本面及央行调控等因素对人民币汇率中间价变动的影响。研究结果表明:在岸和离岸市场人民币即期汇率、人民币汇率指数及逆周期因子对中间价波动均有显著影响。... 详细信息

本文通过构建扩展的GARCH模型,探讨了人民币汇率中间价形成机制、宏观经济基本面及央行调控等因素对人民币汇率中间价变动的影响。研究结果表明:在岸和离岸市场人民币即期汇率、人民币汇率指数及逆周期因子对中间价波动均有显著影响。宏观经济基本面上,通货膨胀率上升和中美两国利差收窄均会加剧中间价波动幅度,而外汇储备的回升和持续的贸易顺差对中间价形成有效支撑。央行调控方面对中间价变动的影响十分有限。此外,CFETS指数、美元指数以及VIX指数对人民币汇率中间价变动不存在非对称效应。

关键词：人民币汇率中间价汇率机制 GARCH模型汇率市场化