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An Epigenetic Role for Disrupted Paternal Gene Expression in Postz.gotic Seed Abortion in Arabidopsis Interspecific Hybrids

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Molecular Plant 2015年第12期8卷 1766-1775页

作者： Ryan C. Kirkbride Helen Hong Yu Gyoungju Nah Changqing z.ang Xiaoli Shi z. jeffrey chen Department of Molecular Biosciences Center for Computational Biology and Bioinformatics and Institute for Cellular and Molecular Biology The University of Texas at Austin Austin TX 78712 USA These authors contributed equally to this article. present address: Department of Plant Science Research Institute of Agriculture and Life Sciences Seoul National University Seou1151-921 South Korea present address: Plants for Human Health Institute North Carolina State University 600 Laureate Way Kannapolis NC 28081 USA present address: Institute of Theoretical Physics Chinese Academy of Sciences PO Box 2735 Beijing 100080 China

Interspecific hybrids often increase the levels of heteroz.gosity and hybrid vigor, but some interspecific hybrid seeds are aborted shortly after fertiliz.tion. The mechanism behind this postz.gotic seed abortion is poorly understood. Here, we report genome-wide analysis of allelic expression changes in developing siliques and seeds in three F1 interspecific crosses between Arabidopsis thaliana （Col, Ler, or C24） and Arabidopsis arenosa. The majority of maternally expressed genes （MEGs） were shared among all three F1 interspecific crosses, whereas ~90% of 272 paternally expressed genes （PEGs） were found only in one or two F1 crosses, suggesting a role for disrupted paternal gene expression in seed abortion that varies in different crosses. Consistent with this notion, 12 PEGs in the infertile interspecific hybrids matched MEGs in fertile intraspecific hybrids. This disruption of PEGs in the interspecific hybrids was consistent with the upregulation of the genes in the paternal-excess interploidy cross （2X6） between a diploid mother and a hexaploid father, leading to the seed abortion. Moreover, a subset of PEGs in the interspecific crosses were also upregulated in the intraspecific hybrid metlXWT or meaXWT, in which the mutant of MET1 （DNA METHYL TRANSFERASE1） or MEDEA, a Polycomb Repressive Complex2 gene, was used as the maternal parent. These data suggest that maternal epigenetic factors and paternal gene expression play important roles in the postz.gotic seed abortion in interspecific hybrids or neo-allopolyploids.

关键词： epigenetics imprinting paternal gene expression polyploidy hybrid incompatibility seeddevelopment

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Rice Interploidy Crosses Disrupt Epigenetic Regulation, Gene Expression, and Seed Development

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Molecular Plant 2018年第2期11卷 300-314页

作者： Limei Wang Jingya Yuan Yujie Ma Wu Jiao Wenxue Ye Dong-Lei Yang Chuandeng Yi z. jeffrey chen State Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricultural University 1 Weigang Road Nanjing 210095 China Department of Molecular Biosciences Institute for Cellular and Molecular Biology Center for Computational Biology and Bioinformatics The University of Texasat Austin Austin TX 78712 USA Jiangsu Key Laboratory of Crop Genetics and Physiology Yangzhou University Yangzhou 225009 China

Seed development in angiosperms requires a 2：1 maternal-to-paternal genome ratio （2m：lp） in the endo- sperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5＇ and 3＇ flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylaUon-related genes including OsMETlb and OsCMT3a were upregulated in the 2x4 cross （polli- nating a diploid ＂mother＂ with a tetraploid ＂father＂） but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellulariz.tion during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4 ×2 crosses. WUSCHEL homeobox2 （WOX2）-Iike （WOX2L）, an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m：lp genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.

关键词： seed polyploidy small RNA gene expression endosperm epigenetics

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棉纤维发育的基因组分析和基因表达谱

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棉花学报 2002年第Z1期14卷 49-页

作者： z. jeffrey chen

　　The goals of our cotton research program are to understand fiber developmental biology and improve fiber production using molecular and genomic tools. In the genome mapping project,we have developed a cotton genetic map using a moderate set of AFLP, SSR, and RFLP markers. Polymorphism was detected in two polyploid cotton cultivars, G. hirsutum L. var.　　……

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Advances in Magnetic Resonance Imaging Technology Applied to Human Brain Glymphatic System

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Chinese General Practice 2024年第26期27卷 3314-3319页

作者： chen z. Huang M. z.ng L. Jin S. Yin H. School of Medical and Life Science Chengdu University of Traditional Chinese Medicine Chengdu 611137 China School of Acupuncture and Tuina Chengdu University of Traditional Chinese Medicine Chengdu 611137 China Department of Radiology Hospital of Chengdu University of Traditional Chinese Medicine Chengdu 610072 China Department of Neurology Hospital of Chengdu University of Traditional Chinese Medicine Chengdu 610072 China

The glial lymphatic system is a recently discovered anatomical structure in the field of neuroscience，with functions such as regulation of interstitial fluid movement，waste removal and potentially brain immunity，playing an important role in physiology and pathology of the central nervous system. With the development of imaging technology，more and more magnetic resonance imaging （MRI） techniques have been applied to the study of the glial lymphatic system of the human brain. Currently，the commonly used imaging techniques include dynamic contrast-enhanced MRI，diffusion tensor image analysis along the perivascular space，and novel multimodal ultra-fast magnetic resonance techniques，etc. This article summariz.s and reviews the application of these techniques in the brain glymphatic system，in order to provide a reference for the imaging study of the glymphatic system. © Editorial Office of Chinese General Practice.

关键词： Central nervous system Diffusion tensor imaging-analysis technique along the perivascular space Dynamic contrast-enhanced magnetic resonance imaging Glymphatic system Lymphatic system Magnetic resonance imaging Ultra-fast magnetic resonance imaging

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New insights on the high-corrosion resistance of UHP Mg-Ge alloys tested in a simulated physiological environment

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Journal of Magnesium and Alloys 2024年第3期12卷 1026-1044页

作者： Ting Liu Xingrui chen jeffrey Venez.ela Yuan Wang z.iming Shi Wenyi chen Matthew Dargusch Centre for Advanced Materials Processing and Manufacturing(AMPAM) School of Mechanical and Mining Engineeringthe University of QueenslandBrisbaneQLD 4072Australia CSIRO Mineral Resources 1 Technology CourtPullenvaleQLD 4069Australia

UHP Mg-Ge alloys was recently found to provide excellent corrosion resistance.This paper provides new insights on the mechanism of improved corrosion resistance of UHP Mg-Ge alloys in Hanks’solution.The studied UHP Mg-0.5Ge and UHP Mg-1Ge alloys showed superior corrosion resistance compared to UHP Mg and WE43,with the Mg-1Ge exhibiting the best corrosion performance.The exceptional corrosion resistance of the UHP alloy is attributed to(i)Mg_(2)Ge’s ability to suppress cathodic kinetics,(ii)Ge’s capability to accelerate the formation of a highly passive layer,and the(iii)low amounts of corrosion-accelerating impurities.

关键词： UHP Mg-Ge alloy Cathodic kinetics suppression Biodegradable metals In vitro corrosion Magnesium corrosion.

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Rational design of AgGaS/z.S/z.S quantum dots with a near-unity photoluminescence quantum yield via double shelling scheme

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Journal of Materials Science & Technology 2024年第2期169卷 235-242页

作者： H.X.Lu H.Liu z.z.Fu Y.Y.chen H.Q.Dai z.Hu W.L.z.ang R.Q.Guo Institute for Electric Light Sources School of Information Science and TechnologyFudan UniversityShanghai 200433China Institute of Future Lighting Academy for Engineering and TechnologyFudan UniversityShanghai 200433China Yiwu Research Institute of Fudan University YiwuZhejiang 322000China z.ongshan-Fudan Joint Innovation Center Zhongshan 528437China

In this study,a two-step method was used to synthesiz. highly luminescent AgGaS/z.S/z.S quantum dots(QDs).In the first step,an inner z.S shell was formed via a one-pot method,which resulted in a smaller lattice mismatch between the AgGaS core and the outer z.S shell,thereby facilitating the formation of a thick outer shell.After the two-step shelling process,the synthesiz.d AgGaS/z.S/z.S QDs showed an excellent photoluminescence quantum yield(PLQY)of 96.4%with a peak wavelength of 508 nm,repre-senting the highest PLQY reported thus far for AgGaS QDs.Furthermore,the effect of halogen ions in z. precursors on the shelling process was investigated.It was proposed that the capacity of halogen ions to coordinate with the QDs influenced the balance between z. cation diffusion and z.S shelling reaction.Specifically,the z.S shelling reaction was dominant when z.Cl_(2)was employed,while z. cation diffusion was the dominant process under the I^(−)-rich environment.This work provides insights into the interfacial restructuring during the z.S shelling and offers a clear map for the tailored synthesis of core/shell QDs.

关键词： AgGaS Quantum dots Photoluminescence Core/shell Alloyed core/shell interface

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Granger causal representation learning for groups of time series

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Science China(Information Sciences) 2024年第5期67卷 56-68页

作者： Ruichu CAI Yunjin WU Xiaokai HUANG Wei chen Tom z.J.FU z.ifeng HAO School of Computer Science Guangdong University of Technology Peng cheng Laboratory College of Science Shantou University

Discovering causality from multivariate time series is an important but challenging problem.Most existing methods focus on estimating the Granger causal structures among multivariate time series,while ignoring the prior knowledge of these time series, e.g., the group of the time series. Focusing on discovering the Granger causal structures among groups of time series, we propose a Granger causal representation learning method to solve this problem. First, we use the multiset canonical correlation analysis method to learn the Granger causal representation of each group of time series. Then, we model the Granger causal relationships among the learned Granger causal representations using a recurrent neural network with temporal information. Finally, we formulate the above two stages into one unified optimiz.tion problem, which is efficiently solved using the augmented Lagrangian method. We conduct extensive experiments on synthetic and real-world datasets to validate the correctness and effectiveness of the proposed method.

关键词： Granger causal discovery Granger causal representation learning time series data recurrent neural network multiset canonical correlation analysis

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Chemotherapy-induced small extracellular vesicles prime the pre-metastatic niche to accelerate neuroblastoma metastasis

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Genes & Diseases 2024年第4期11卷 65-68页

作者： Carson A.Wills Xiaoming Liu Longgui chen Yuanjun z.ao z.enqiu Liu Vladimir S.Spiegelman jeffrey Sundstrom Hong-Gang Wang Department of Pediatrics Division of Pediatric Hematology and OncologyThe Pennsylvania State University Collegeof MedicinePA 17033USA Department of Ophthalmology The Pennsylvania State University College of MedicinePA 17033USA Department of Public Health Sciences The Pennsylvania StateUniversityCollegeofMedicinePA 17033USA

Neuroblastoma is the most common extracranial solid tumor in children,accounting for more than 10%of cancerrelated deaths in this population.The standard of care for patients diagnosed with medium-to high-risk neurobl... 详细信息

关键词： neuroblastoma metastatic metastasis

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Arabidopsis thaliana histone deacetylase1(AtHD1)is localiz.d in euchromatic regions and demonstrates histone deacetylase activity in vitro

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Cell Research 2006年第5期16卷 479-488页

作者： Paulus M Fong z.jeffrey chen Department of Soil and Crop Sciences Texas A&M UniversityCollege StationTX 77843USA Molecular Cell and Developmental Biology University of Texas at AustinAustinTX78712USA

Arabidopsis thaliana histone deacetylase 1 (AtHD1 or AtHDA19),a homolog of yeast RPD3,is a global regulator ofmany physiological and developmental processes in plants.In spite of the genetic evidence for a role of AtHD1 in plantgene regulation and development,the biochemical and cellular properties of AtHD1 are poorly understood.Here we reportcellular localiz.tion patterns of AtHD1 in vivo and histone deacetylase activity in vitro.The transient and stable expres-sion of a green fluorescent protein (GFP)-tagged AtHD1 in onion cells and in roots,seeds and leaves of the transgenicArabidopsis,respectively,revealed that AtHD1 is localiz.d in the nucleus presumably in the euchromatic regions andexcluded from the nucleolus.The localiz.tion patterns of AtHD1 are different from those of AtHD2 and AtHDA6 thatare involved in nucleolus formation and silencing of transgenes and repeated DNA elements,respectively.In addition,a histone deacetylase activity assay showed that the recombinant AtHD1 produced in bacteria demonstrated a specifichistone deacetylase activity in vitro.The data suggest that AtHD1 is a nuclear protein and possesses histone deacetylaseactivities responsible for global transcriptional regulation important to plant growth and development.

关键词： Arabidopsis histone deacetylase RPD3 subcellular localiz.tion gene silencing chromatin

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High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals

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Molecular Plant 2024年第3期17卷 423-437页

作者： Jubin Wang Qingling z.ang jeffrey Tung Xi z.ang Dan Liu Yingtian Deng z.endong Tian Huilan chen Taotao Wang Weixiao Yin Bo Lij z.ibing Lai Savithramma P.Dinesh-Kumar Barbara Baker Feng Li National Key Laboratory for Germplasm Innovation and Utiliz.tion for Fruit and Vegetable Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubei 430070China Plant Gene Expression Center Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyBerkeleyCA 94706USA College of Plant Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China College of Life Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China Department of Plant Biology and The Genome Center College of Biological SciencesUniversity of CalforniaDavisDavisCA 95616USA The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi Province Institute of Biological ResourcesJiangxi Academy of SciencesNanchang 330299China institute of Vegetables and Flowers Jiangxi Academy of Agricultural SciencesNanchang 330200Chin Hubei Hongshan Laboratory WuhanHubei 430070China

Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research.However,genomic studies of these species have lagged.Here we report the chromosome-level reference genome assemblies for N.benthamiana and N.tabacum with an estimated 99.5%and 99.8%completeness,respec-tively.Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N.tabacum.Comparative analyses revealed evidence for the parental origins and chromosome structural changes,leading to hybrid genome formation of each species.Interestingly,theantiviral silencinggenesRDR1,RDR6,DCL2,DCL3,andAGO2were lost from one or both subgenomes in N.benthamiana,while both homeologs were kept in N.tabacum.Furthermore,the N.benthamiana genome encodes fewer immune receptors and signaling components than that of N.tabacum.These find-ings uncover possible reasons underlying the hypersusceptible nature of N.benthamiana.We developed the user-friendly Nicomics(http:/***/Nicomics/)web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.

关键词： Nicotiana tabacum Nicotiana benthamiana genomics evolution disease resistance NLR

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