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DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening

Journal of Integrative Plant Biology 2024年第8期66卷 1718-1734页

作者： yunfan sun Xiaofang Yang Rongrong Wu Shouzheng Lv Yunduan Li Haoran Jia Yuying Yang Baijun Li Wenbo Chen Andrew C.Allan Guihua Jiang Yan-Na Shi Kunsong Chen College of Agriculture&Biotechnology Zhejiang UniversityZijingang CampusHangzhou 310058China Institute of Horticulture Zhejiang Academy of Agricultural SciencesHangzhouZhejiang 310021China Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityZijingang CampusHangzhou 310058China The State Agriculture Ministry Laboratory of Horticultural Plant Growth Development and Quality ImprovementZhejiang UniversityZijingang CampusHangzhou 310058China New Zealand Institute for Plant&Food Research Limited Private Bag 92169AucklandNew Zealand School of Biological Sciences University of AucklandPrivate Bag 92019AucklandNew Zealand

Phytohormones,epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be *** this study,bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light,correlating with reduced abscisic acid(ABA) *** of the key ABA catabolism gene,ABA 8′-hydroxylase FaCYP707A4,was induced in bagged *** light exclusion whole genome DNA methylation levels were up-regulated,corresponding to a delayed ripening process,while DNA methylation levels in the promoter of FaCYP707A4 were suppressed,correlating with increases in transcript and decreased ABA *** indicated FaCRY1,a blue light receptor repressed in bagged fruit and FaAGO4,a key protein involved in RNA-directed DNA methylation,could bind to the promoter of *** interaction between FaCRY1 and FaAGO4,and an increased enrichment of FaAGO4 directed to the FaCYP707A4 promoter in fruit grown under light suggests FaCRY1 may influence FaAGO4 to modulate the DNA methylation status of the FaCYP707A4 ***,transient overexpression of FaCRY1,or an increase in FaCRY1 transcription by blue light treatment,increases the methylation level of the FaCYP707A4 promoter,while transient RNA interference of FaCRY1 displayed opposite *** findings reveal a mechanism by which DNA methylation influences ABA catabolism,and participates in light-mediated strawberry ripening.

关键词： ABA catabolism DNA methylation light ripening strawberry

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术中超声造影在肝脏恶性肿瘤手术中的应用价值

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中国普通外科杂志 2024年第7期33卷 1051-1058页

作者：杨兴广成剑文许阳孙云帆周俭杨欣荣复旦大学附属中山医院肝肿瘤外科上海200032 大理大学第一附属医院普通外科云南大理671013

背景与目的:目前手术治疗仍然是肝脏恶性肿瘤主要根治性治疗措施之一。但是有时由于肿瘤微小、位置深在、多发或继发性肝癌经药物治疗后形成“消失的肝转移灶”等原因,导致手术时无法准确定位肿瘤或遗漏。本研究探讨术中超声造影(CE-IO... 详细信息

背景与目的:目前手术治疗仍然是肝脏恶性肿瘤主要根治性治疗措施之一。但是有时由于肿瘤微小、位置深在、多发或继发性肝癌经药物治疗后形成“消失的肝转移灶”等原因,导致手术时无法准确定位肿瘤或遗漏。本研究探讨术中超声造影(CE-IOUS)在肝脏恶性肿瘤手术中的应用价值。方法:回顾分析复旦大学附属中山医院2022年9月—2023年2月期间收治且接受手术切除的56例肝恶性肿瘤患者,比较术前增强核磁共振成像(P-MRI),术前超声(P-US)、术中超声(IOUS)和CE-IOUS对肝脏病灶检出率、恶性肿瘤诊断准确率的差异。结果:56例患者共85个病灶,行P-MRI检测到的75个病灶,术后病理诊断为恶性病灶64个,良性病灶11个,遗漏10个;P-US检测到的46个病灶,术后病理诊断为恶性病灶30个,良性病灶16个,遗漏39个;IOUS检测到的64个病灶,术后病理诊断为恶性病灶44个,良性病灶20个,遗漏21个;行CE-IOUS诊断为恶性的78个病灶,术后病理检查为恶性病灶66个,良性病灶12个,遗漏7个。CE-IOUS较P-US及IOUS有较高的病灶检出率,差异有统计学意义(91.8%vs.54.1%,P<0.001;91.8%vs.75.3%,P<0.001);对于肝脏占位的恶性肿瘤诊断准确率,CE-IOUS比P-US及IOUS高(86.8%vs.65.2%,P<0.001;86.8%vs.68.7%,P<0.001)。对于病灶检出率、恶性肿瘤诊断准确率,CE-IOUS和P-MRI差异无统计学意义。结论:利用Sonazoid造影剂进行CE-IOUS较P-US和IOUS具有较高的肿瘤检出率及恶性肿瘤诊断准确率,可用于发现和定位术前无法显示的微小病灶,进而在其引导下进行肿瘤切除或射频消融,提高手术疗效。

关键词：肝肿瘤超声检查,术中造影剂肝切除术

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Single-cell RNA sequencing reveals spatial heterogeneity and immune evasion of circulating tumor cells

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Cancer Biology & Medicine 2021年第4期18卷 934-936页

作者： yunfan sun Jian Zhou Jia Fan Xinrong Yang Department of Liver Surgery&Transplantation Liver Cancer InstituteZhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer InvasionMinistry of EducationShanghai 200032China

Circulating tumor cells(CTCs),recognized as intermediaries between primary and distant lesions,are key to understanding the mechanisms of cancer *** the dissemination of tumor cells in the circulatory system is a spatially and temporally dynamic process,CTCs can logically be assumed to be a population of cells displaying both spatial and temporal heterogeneity^(1).Prior studies have revealed substantial temporal heterogeneity in CTC phenotypes during anti-cancer treatments^(2,3).However,current knowledge of CTCs is derived mostly from peripheral venous blood;thus,only a snapshot of the entire circulatory process has been determined,and much more remains to be understood.

关键词： cancer metastasis mostly

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多组学联合分析转移性肝细胞癌的时空演化

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肝癌电子杂志 2024年第2期11卷 72-88页

作者：张泽凡(翻译) 孙云帆赵宏(校对) 复旦大学附属中山医院肝肿瘤外科复旦大学肝癌研究所上海200032 国家癌症中心/国家肿瘤临床医学研究中心/中国医学科学院北京协和医学院肿瘤医院肝胆外科北京100021

目前,缺乏针对转移性肝细胞癌(hepatocellular carcinoma,HCC)的全面分子水平的分析。本研究对182例HCC患者的257个原发灶和176个转移灶开展了多组学分析。结果显示,富含缺氧特征的原发性肿瘤可促进多克隆播散。原发性肿瘤和转移性肿瘤... 详细信息

目前,缺乏针对转移性肝细胞癌(hepatocellular carcinoma,HCC)的全面分子水平的分析。本研究对182例HCC患者的257个原发灶和176个转移灶开展了多组学分析。结果显示,富含缺氧特征的原发性肿瘤可促进多克隆播散。原发性肿瘤和转移性肿瘤之间的基因组差异较大,早期播散较为普遍。由于新抗原呈递的障碍,转移瘤中存在显著的肿瘤内新抗原异质性,且与T细胞反应性降低有关。研究还发现,体细胞拷贝数的改变是驱动转移的高度选择性事件。原发瘤中,无Wnt突变的亚克隆比有Wnt突变的亚克隆显示出更强的转移选择性优势,并以微环境中丰富的活化成纤维细胞为特征,有利于转移的发生。而且,无Wnt突变的转移瘤中有更多的免疫抑制B细胞富集,通过人类白细胞抗原(human leukocyte antigen)-E:CD94-NKG2A检查点轴介导CD8+T细胞的终末耗竭。综上所述,本研究对复杂的转移进化过程进行了多维剖析。

关键词：原发性肿瘤高度选择性转移性肿瘤原发瘤人类白细胞抗原 NKG2A 转移瘤成纤维细胞

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One-shot Face Reenactment with Dense Correspondence Estimation

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Machine Intelligence Research 2024年第5期21卷 941-953页

作者： yunfan Liu Qi Li Zhenan sun School of Artificial Intelligence University of Chinese Academy of SciencesBeijing100049China Center for Research on Intelligent Perception and Computing Institute of AutomationChinese Academy of SciencesBeijing100190China

One-shot face reenactment is a challenging task due to the identity mismatch between source and driving *** existing methods fail to completely eliminate the interference of driving subjects’identity information,which may lead to face shape distortion and undermine the realism of reenactment *** solve this problem,in this paper,we propose using a 3D morphable model(3DMM)for explicit facial semantic decomposition and identity *** of using 3D coefficients alone for reenactment control,we take advantage of the generative ability of 3DMM to render textured face *** proxies contain abundant yet compact geometric and semantic information of human faces,which enables us to compute the face motion field between source and driving images by estimating the dense *** this way,we can approximate reenactment results by warping source images according to the motion field,and a generative adversarial network(GAN)is adopted to further improve the visual quality of warping *** experiments on various datasets demonstrate the advantages of the proposed method over existing state-of-the-art benchmarks in both identity preservation and reenactment fulfillment.

关键词： Generative adversarial networks face image manipulation face image synthesis face reenactment 3D morphable model

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Mantle melting factors and amagmatic crustal accretion of the Gakkel ridge, Arctic Ocean

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Acta Oceanologica Sinica 2015年第6期34卷 42-48页

作者： ZHANG Tao GAO Jinyao CHEN Mei YANG Chunguo SHEN Zhongyan ZHOU Zhiyuan WU Zhaocai sun yunfan Key Laboratory of Submarine Geosciences State Oceanic Administration Second Institute of Oceanography State Oceanic Administration East China Construction Engineering Corporation of Zhejiang School of Ocean and Earth Science Tongji University

Spreading rate is a primary factor of mantle melting and tectonic behavior of the global mid-ocean ridges. The spreading rate of the Gakkel ridge decreases gradually from west to east. However, the Gakkel ridge can be divided into four thick-and-thin zones with varying crustal thicknesses along ridge axis. This phenomenon indicates that mantle melting of the Gakkel ridge is not a simple function of spreading rate. Mantle temperature, water content, mantle composition, and other factors are important in crustal accretion processes. Based on gravity-derived crustal thickness and wet melting model, we estimate that the mantle potential temperatures of the four zones are 1 270, 1 220, 1 280, and 1 280℃ （assuming that mantle water content equals to global average value）, with corresponding mantle water contents of 210, 0, 340, and 280 mg/kg （assuming that mantle potential temperature is 1 260℃）, respectivly. The western thinned crust zone is best modeled with low mantle temperature, whereas the other zones are mainly controlled by the enhanced conduction caused by the slower spreading rate. Along the Gakkel ridge, the crustal thickness is consistent with rock samples types. Predominated serpentinized peridotite and basalt are found in the area with crustal thickness 〈1.5 km and 〉2.5 km, respectively. The rock samples are including from basalt to peridotite in the area with crustal thickness between 1.5 and 2.5 km. Based on this consistency, the traditional magmatic accretion zone accounted for only 44% and amagmatic accretion accounted for 29% of the Gakkel ridge. The amagmatic accretion is a significant characteristic of the ultra-slow spreading ridge.

关键词： Gakkel ridge residual mantle bouguer anomaly crustal thickness wet melting amagmatic accretion

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scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 346-357页

作者： Liang Wu Miaomiao Jiang Yuzhou Wang Biaofeng Zhou yunfan sun Kaiqian Zhou Jiarui Xie Yu Zhong Zhikun Zhao Michael Dean Yong Hou Shiping Liu BGI Education Center University of Chinese Academy of SciencesShenzhen 518083China BGI-Shenzhen Beishan Industrial ZoneShenzhen 518083China Shenzhen Key Laboratory of Single-Cell Omics BGI-ShenzhenShenzhen 518100China Department of Liver Surgery&Transplantation Liver Cancer InstituteZhongshan HospitalFudan UniversityMOE Key Laboratory of Carcinogenesis and Cancer InvasionShanghai 200032China School of Biology and Biological Engineering South China University of TechnologyGuangzhou 510640China Laboratory of Translational Genomics Division of Cancer Epidemiology&GeneticsNational Cancer InstituteGaithersburgMD 20877USA

Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer ***,classical DNA amplification-based methods have low throughput and introduce coverage bias during sample *** developed a single-cell DNA library preparation method without preamplification in nanolitre scale(scDPN)to address these *** method achieved a throughput of up to 1800 cells per run for copy number variation(CNV)***,our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification(MDA)method and showed high sensitivity and accuracy for cell line and tumor tissue *** used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma(HCC).We identified three clonal subpopulations with a multitude of aneuploid alterations across the ***,we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q,10q,and 14q developed into the dominant clone in the recurrent tumor,indicating clonal selection during recurrence in ***,this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution.

关键词： Single-cell sequencing Hepatocellular carcinoma Heterogeneity Clonal evolution Relapse

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DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry

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Horticulture Research 2023年第8期10卷 170-182页

作者： Yunduan Li Yanna Shi Yichen Li Jiao Lu yunfan sun Yuanyuan Zhang Wenbo Chen Xiaofang Yang Donald Grierson Zhaobo Lang Guihua Jiang Kunsong Chen College of Agriculture&Biotechnology Zhejiang UniversityZijingang CampusHangzhou 310058China Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityZijingang CampusHangzhou 310058China The State Agriculture Ministry Laboratory of Horticultural Plant Growth Development and Quality ImprovementZhejiang UniversityZijingang CampusHangzhou 310058China Institute of Horticulture Zhejiang Academy of Agricultural SciencesHangzhou 310021ZhejiangChina Division of Plant and Crop Sciences School of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough LE125RDUnited Kingdom Institute of Advanced Biotechnology and School of Life Sciences Southern University of Science and TechnologyShenzhen 518055China

Recently,increasing evidence suggests that DNA methylation plays a crucial role in fruit ***,the role of DNA methylation in regulating specific traits,such as flavor,remains ***,we report a role of DNA methylation in affecting furanone biosynthesis in *** quinone oxidoreductase(FaQR)is a key enzyme in furanone *** are four FaQR homologs in strawberry cultivar‘Yuexin’,and one of them,FaQR3,contributes∼50%of FaQR transcripts,indicating a major role of FaQR3 in furanone *** characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor,we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation,suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression,and responded to different temperatures *** addition,transient expression of a gene in the RNA-directed DNA methylation(RdDM)pathway,FaAGO4,and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM *** RNA interference(RNAi)of FaDML indicated that the demethylation pathway may be involved in regulating furanone *** findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening.

关键词： straw furan transient

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XRD Investigation of Phase Change in N-doped Diamond after High Energy Heavy Ion Irradiations

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近代物理研究所和兰州重离子加速器实验室年报：英文版 2002年第1期 48-49页

作者： Wang Zhiguang, Zhao Zhiming, Song Yin, Jin yunfan, Liu Jie, sun Youmei Zhang Chonghong and Duan Jinglai

We have proposed a novel technique, 'low energy ion implantation+swift heavy ion irradiation', for synthesizing new structures in atom mixed materials. The schematic procedure of this technique is shown in Fig.1. In detail, the original samples were prepared at first (1), and then they were implanted at room temperature (RT) with keV ions (2) after that irradiated at RT with high-energy heavy ions (3). After high-energy

关键词：高能重离子辐照掺氮金刚石相变 X射线分析重离子核物理低能离子植入技术金刚石薄膜化学气相沉积法

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The formation and stability of Si_(1-x)C_x alloys in Si implanted with carbon ions

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Chinese Science Bulletin 2001年第3期46卷 200-204页

作者： WANG Yinshu, LI Jinmin, JIN yunfan, WANG Yutian, sun Guosheng & LIN Lanying1. Department of Physics, Beijing Normal University, Beijing 100875, China 2. Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China 3. Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China Department of Physics Beijing Normal University Beijing China Institute of Semiconductors Chinese Academy of Sciences Beijing China Institute of Modern Physics Chinese Academy of Sciences Lanzhou China

Si1-xCx alloys of carbon (C) concentration between 0.6%-1.0% were grown in Si by ion implantation and high temperature annealing. The formation of Si1-xCx alloys under different ion doses and their stability during annealing were studied. If the implanted dose was less than that for amorphizing Si crystals, the implanted C atoms would like to combine with defects produced during implantation and it was difficult to form Si1-xCx alloys after being annealed at 850℃. With the increment of implanted C ion doses, the lattice damage increased and it was easier to form Si1-xCx alloys. But the lattice strain would become saturate and only part of implanted carbon atoms would occupy the substitutional positions to form Si1-xCx alloys as the implanted carbon dose increased to a certain degree. Once Si1-xCx alloys were formed, they were stable at 950℃, but part of their strain would release as the annealing temperature increased to 1 000℃. Stability of the alloys became worse with the increment of carbon

关键词： ion implantation Si1-xCx alloys stability of Si1-xCx alloys.

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