450 results on '"Jinxing Lin"'
Search Results
2. Single-molecule analysis reveals the phosphorylation of FLS2 governs its spatiotemporal dynamics and immunity
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Yaning Cui, Hongping Qian, Jinhuan Yin, Changwen Xu, Pengyun Luo, Xi Zhang, Meng Yu, Bodan Su, Xiaojuan Li, and Jinxing Lin
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single-molecule analysis ,phosphorylation ,spatiotemporal dynamics ,AtRem1.3-associated nanodomains ,endocytosis ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
The Arabidopsis thaliana FLAGELLIN-SENSITIVE2 (FLS2), a typical receptor kinase, recognizes the conserved 22 amino acid sequence in the N-terminal region of flagellin (flg22) to initiate plant defense pathways, which was intensively studied in the past decades. However, the dynamic regulation of FLS2 phosphorylation at the plasma membrane after flg22 recognition needs further elucidation. Through single-particle tracking, we demonstrated that upon flg22 treatment the phosphorylation of Ser-938 in FLS2 impacts its spatiotemporal dynamics and lifetime. Following Förster resonance energy transfer-fluorescence lifetime imaging microscopy and protein proximity indexes assays revealed that flg22 treatment increased the co-localization of GFP-tagged FLS2/FLS2S938D but not FLS2S938A with AtRem1.3-mCherry, a sterol-rich lipid marker, indicating that the phosphorylation of FLS2S938 affects FLS2 sorting efficiency to AtRem1.3-associated nanodomains. Importantly, we found that the phosphorylation of Ser-938 enhanced flg22-induced FLS2 internalization and immune responses, demonstrating that the phosphorylation may activate flg22-triggered immunity through partitioning FLS2 into functional AtRem1.3-associated nanodomains, which fills the gap between the FLS2S938 phosphorylation and FLS2-mediated immunity.
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- 2024
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3. SSR1 and CKAP4 as potential biomarkers for intervertebral disc degeneration based on integrated bioinformatics analysis
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Danqing Guo, Min Zeng, Miao Yu, Jingjing Shang, Jinxing Lin, Lichu Liu, Kuangyang Yang, and Zhenglin Cao
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immune infiltration ,intervertebral disc degeneration ,single‐cell sequencing ,WGCNA ,Orthopedic surgery ,RD701-811 - Abstract
Abstract Background Intervertebral disc degeneration (IDD) is a significant cause of low back pain and poses a significant public health concern. Genetic factors play a crucial role in IDD, highlighting the need for a better understanding of the underlying mechanisms. Aim The aim of this study was to identify potential IDD‐related biomarkers using a comprehensive bioinformatics approach and validate them in vitro. Materials and Methods In this study, we employed several analytical approaches to identify the key genes involved in IDD. We utilized weighted gene coexpression network analysis (WGCNA), MCODE, LASSO algorithms, and ROC curves to identify the key genes. Additionally, immune infiltrating analysis and a single‐cell sequencing dataset were utilized to further explore the characteristics of the key genes. Finally, we conducted in vitro experiments on human disc tissues to validate the significance of these key genes in IDD. Results we obtained gene expression profiles from the GEO database (GSE23130 and GSE15227) and identified 1015 DEGs associated with IDD. Using WGCNA, we identified the blue module as significantly related to IDD. Among the DEGs, we identified 47 hub genes that overlapped with the genes in the blue module, based on criteria of |logFC| ≥ 2.0 and p.adj
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- 2024
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4. Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar
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Yayu Guo, Shufang Wang, Keji Yu, Hou-Ling Wang, Huimin Xu, Chengwei Song, Yuanyuan Zhao, Jialong Wen, Chunxiang Fu, Yu Li, Shuizhong Wang, Xi Zhang, Yan Zhang, Yuan Cao, Fenjuan Shao, Xiaohua Wang, Xin Deng, Tong Chen, Qiao Zhao, Lei Li, Guodong Wang, Paul Grünhofer, Lukas Schreiber, Yue Li, Guoyong Song, Richard A. Dixon, and Jinxing Lin
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Science - Abstract
Abstract The conversion of lignocellulosic feedstocks to fermentable sugar for biofuel production is inefficient, and most strategies to enhance efficiency directly target lignin biosynthesis, with associated negative growth impacts. Here we demonstrate, for both laboratory- and field-grown plants, that expression of Pag-miR408 in poplar (Populus alba × P. glandulosa) significantly enhances saccharification, with no requirement for acid-pretreatment, while promoting plant growth. The overexpression plants show increased accessibility of cell walls to cellulase and scaffoldin cellulose-binding modules. Conversely, Pag-miR408 loss-of-function poplar shows decreased cell wall accessibility. Overexpression of Pag-miR408 targets three Pag-LACCASES, delays lignification, and modestly reduces lignin content, S/G ratio and degree of lignin polymerization. Meanwhile, the LACCASE loss of function mutants exhibit significantly increased growth and cell wall accessibility in xylem. Our study shows how Pag-miR408 regulates lignification and secondary growth, and suggest an effective approach towards enhancing biomass yield and saccharification efficiency in a major bioenergy crop.
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- 2023
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5. Transcriptional Profiling of BpWRKY49 Reveals Its Role as a Master Regulator in Stress Signaling Pathways in Birch (Betula platyphylla)
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Sammar Abbas, Ruotong Jing, Manzar Abbas, Zijian Hu, Rabia Kalsoom, Syed Sarfaraz Hussain, Liang Du, Jinxing Lin, and Xi Zhang
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WRKY ,salt stress ,transcription activity ,Betula platyphylla ,DAP-seq ,Plant ecology ,QK900-989 - Abstract
The WRKY family of transcription factors (TFs) is one of the most diverse families in plants, playing crucial roles in various plant growth and stress response processes. Asian white birch (Betula platyphylla) is a globally distributed tree species that holds ecological, medical, and economic significance. However, the regulatory mechanisms of WRKY TFs in birch remain poorly understood. Herein, we cloned and characterized the BpWRKY49 gene from birch. Through bioinformatics analyses, we revealed the potential involvement of BpWRKY49 in both biotic and abiotic stress responses. In addition, BpWRKY49 was found to be localized in the nucleus and exhibited transcriptional activity in yeast. Transactivation assays further confirmed that BpWRKY49 exhibited transcriptional activity at its C-terminal end. Notably, our binding specificity assays demonstrated the specific interaction of BpWRKY49 with the W-box cis element in vitro. Furthermore, tissue-specific expression analysis demonstrated that BpWRKY49 exhibited the highest expression level in the roots. Real-time quantitative PCR (RT-qPCR) analysis of birch plants subjected to salt and drought treatments revealed that BpWRKY49 displayed significant 30-fold and 10-fold upregulations under salt and drought stress conditions, respectively. DAP-seq analysis of BpWRKY49 identified a total of 21,832 peaks, with 3477 occurring in the promoter region of genes. Gene ontology (GO) enrichment analysis highlighted prominent terms related to defense against biotic stress, followed by terms associated with abiotic stress and development. Y1H assays of three genes provided evidence for the binding ability of BpWRKY49 to the promoters of BpPUB21, BpBTL15, and BpHIP47 in vitro. Collectively, our findings strongly suggest that BpWRKY49 possesses diverse functions and may activate multiple genes to contribute to various biological processes, including salt stress tolerance, in birch.
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- 2024
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6. Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the Lauraceae
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Xue-Chan Tian, Jing-Fang Guo, Xue-Mei Yan, Tian-Le Shi, Shuai Nie, Shi-Wei Zhao, Yu-Tao Bao, Zhi-Chao Li, Lei Kong, Guang-Ju Su, Jian-Feng Mao, and Jinxing Lin
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Lauraceae ,Lindera megaphylla ,wood decay resistance (WDR) ,tandem and proximal duplications (TD/PD) ,gene microsynteny ,Plant culture ,SB1-1110 - Abstract
Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.
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- 2023
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7. Hydroponic cultivation conditions allowing the reproducible investigation of poplar root suberization and water transport
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Paul Grünhofer, Yayu Guo, Ruili Li, Jinxing Lin, and Lukas Schreiber
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Abiotic stress ,Cultivation conditions ,Casparian bands ,Suberin lamellae ,Root suberin ,Poplar ,Plant culture ,SB1-1110 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background With increasing joint research cooperation on national and international levels, there is a high need for harmonized and reproducible cultivation conditions and experimental protocols in order to ensure the best comparability and reliability of acquired data. As a result, not only comparisons of findings of different laboratories working with the same species but also of entirely different species would be facilitated. As Populus is becoming an increasingly important genus in modern science and agroforestry, the integration of findings with previously gained knowledge of other crop species is of high significance. Results To ease and ensure the comparability of investigations of root suberization and water transport, on a high degree of methodological reproducibility, we set up a hydroponics-based experimental pipeline. This includes plant cultivation, root histochemistry, analytical investigation, and root water transport measurement. A 5-week-long hydroponic cultivation period including an optional final week of stress application resulted in a highly consistent poplar root development. The poplar roots were of conical geometry and exhibited a typical Casparian band development with subsequent continuously increasing suberization of the endodermis. Poplar root suberin was composed of the most frequently described suberin substance classes, but also high amounts of benzoic acid derivatives could be identified. Root transport physiology experiments revealed that poplar roots in this developmental stage have a two- to tenfold higher hydrostatic than osmotic hydraulic conductivity. Lastly, the hydroponic cultivation allowed the application of gradually defined osmotic stress conditions illustrating the precise adjustability of hydroponic experiments as well as the previously reported sensitivity of poplar plants to water deficits. Conclusions By maintaining a high degree of harmonization, we were able to compare our results to previously published data on root suberization and water transport of barley and other crop species. Regarding hydroponic poplar cultivation, we enabled high reliability, reproducibility, and comparability for future experiments. In contrast to abiotic stress conditions applied during axenic tissue culture cultivation, this experimental pipeline offers great advantages including the growth of roots in the dark, easy access to root systems before, during, and after stress conditions, and the more accurate definition of the developmental stages of the roots.
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- 2021
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8. Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures
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Zhaogeng Lu, Jiawen Cui, Li Wang, Nianjun Teng, Shoudong Zhang, Hon-Ming Lam, Yingfang Zhu, Siwei Xiao, Wensi Ke, Jinxing Lin, Chenwu Xu, and Biao Jin
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Arabidopsis thaliana ,Heat ,Molecular evolution ,Mutation accumulation ,Mutation bias ,Mutation rate ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown. Results Multigenerational exposure of Arabidopsis MA (mutation accumulation) lines and MA populations to extreme heat and moderate warming results in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observe distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition and transversion frequencies. Mutation occurs more frequently in intergenic regions, coding regions, and transposable elements in plants grown under elevated temperatures. At elevated temperatures, more mutations accumulate in genes associated with defense responses, DNA repair, and signaling. Notably, the distribution patterns of mutations among all progeny differ between MA populations and MA lines, suggesting that stronger selection effects occurred in populations. Methylation is observed more frequently at mutation sites, indicating its contribution to the mutation process at elevated temperatures. Mutations occurring within the same genome under elevated temperatures are significantly biased toward low gene density regions, special trinucleotides, tandem repeats, and adjacent simple repeats. Additionally, mutations found in all progeny overlap significantly with genetic variations reported in 1001 Genomes, suggesting non-uniform distribution of de novo mutations through the genome. Conclusion Collectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.
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- 2021
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9. A label-free, fast and high-specificity technique for plant cell wall imaging and composition analysis
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Huimin Xu, Yuanyuan Zhao, Yuanzhen Suo, Yayu Guo, Yi Man, Yanping Jing, Xinqiang He, and Jinxing Lin
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Coherent Raman scattering ,Coherent anti-Stokes Raman scattering ,Stimulated Raman scattering ,Cell wall ,Label-free imaging ,Chemical composition ,Plant culture ,SB1-1110 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background New cell wall imaging tools permit direct visualization of the molecular architecture of cell walls and provide detailed chemical information on wall polymers, which will aid efforts to use these polymers in multiple applications; however, detailed imaging and quantification of the native composition and architecture in the cell wall remains challenging. Results Here, we describe a label-free imaging technology, coherent Raman scattering (CRS) microscopy, including coherent anti-Stokes Raman scattering (CARS) microscopy and stimulated Raman scattering (SRS) microscopy, which can be used to visualize the major structures and chemical composition of plant cell walls. We outline the major steps of the procedure, including sample preparation, setting the mapping parameters, analysis of spectral data, and image generation. Applying this rapid approach will help researchers understand the highly heterogeneous structures and organization of plant cell walls. Conclusions This method can potentially be incorporated into label-free microanalyses of plant cell wall chemical composition based on the in situ vibrations of molecules.
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- 2021
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10. The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements
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Ping-Li Liu, Xi Zhang, Jian-Feng Mao, Yan-Ming Hong, Ren-Gang Zhang, Yilan E, Shuai Nie, Kaihua Jia, Chen-Kun Jiang, Jian He, Weiwei Shen, Qizouhong He, Wenqing Zheng, Samar Abbas, Pawan Kumar Jewaria, Xuechan Tian, Chang-jun Liu, Xiaomei Jiang, Yafang Yin, Bo Liu, Li Wang, Biao Jin, Yongpeng Ma, Zongbo Qiu, František Baluška, Jozef Šamaj, Xinqiang He, Shihui Niu, Jianbo Xie, Lei Xie, Huimin Xu, Hongzhi Kong, Song Ge, Richard A. Dixon, Yuannian Jiao, and Jinxing Lin
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Tetracentron sinense ,Vessel ,Phylogenomic ,Whole genome duplication ,VND7 ,Resequencing ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.
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- 2020
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11. Environmental Cues Contribute to Dynamic Plasma Membrane Organization of Nanodomains Containing Flotillin-1 and Hypersensitive Induced Reaction-1 Proteins in Arabidopsis thaliana
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Changwen Xu, Sammar Abbas, Hongping Qian, Meng Yu, Xi Zhang, Xiaojuan Li, Yaning Cui, and Jinxing Lin
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VA-TIRFM ,nanodomain ,dynamics ,biotic and abiotic stresses ,flotillin-1 ,hypersensitive induced reaction-1 ,Plant culture ,SB1-1110 - Abstract
Plasma membranes are heterogeneous and contain multiple functional nanodomains. Although several signaling proteins have been shown to function by moving into or out of nanodomains, little is known regarding the effects of environmental cues on nanodomain organization. In this study, we investigated the heterogeneity and organization of distinct nanodomains, including those containing Arabidopsis thaliana flotillin-1 (AtFlot1) and hypersensitive induced reaction-1 proteins (AtHIR1), in response to biotic and abiotic stress. Variable-angle total internal reflection fluorescence microscopy coupled with single-particle tracking (SPT) revealed that AtFlot1 and AtHIR1 exhibit different lateral dynamics and inhabit different types of nanodomains. Furthermore, via SPT and fluorescence correlation spectroscopy, we observed lower density and intensity of AtFlot1 fluorescence in the plasma membrane after biotic stress. In contrast, the density and intensity of signal indicating AtHIR1 markedly increased in response to biotic stress. In response to abiotic stress, the density and intensity of both AtFlot1 and AtHIR1 signals decreased significantly. Importantly, SPT coupled with fluorescence recovery after photobleaching revealed that biotic and abiotic stress can regulate the dynamics of AtFlot1; however, only the abiotic stress can regulate AtHIR1 dynamics. Taken together, these findings suggest that a plethora of highly distinct nanodomains coexist in the plasma membrane (PM) and that different nanodomains may perform distinct functions in response to biotic and abiotic stresses. These phenomena may be explained by the spatial clustering of plasma membrane proteins with their associated signaling components within dedicated PM nanodomains.
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- 2022
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12. High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants
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Xi Zhang, Zijian Hu, Yayu Guo, Xiaoyi Shan, Xiaojuan Li, and Jinxing Lin
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Large-scale imaging ,Plant multicellularity ,Morphogenesis ,Parameters ,Image processing ,Plant culture ,SB1-1110 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background The increasing number of novel approaches for large-scale, multi-dimensional imaging of cells has created an unprecedented opportunity to analyze plant morphogenesis. However, complex image processing, including identifying specific cells and quantitating parameters, and high running cost of some image analysis softwares remains challenging. Therefore, it is essential to develop an efficient method for identifying plant complex multicellularity in raw micrographs in plants. Results Here, we developed a high-efficiency procedure to characterize, segment, and quantify plant multicellularity in various raw images using the open-source software packages ImageJ and SR-Tesseler. This procedure allows for the rapid, accurate, automatic quantification of cell patterns and organization at different scales, from large tissues down to the cellular level. We validated our method using different images captured from Arabidopsis thaliana roots and seeds and Populus tremula stems, including fluorescently labeled images, Micro-CT scans, and dyed sections. Finally, we determined the area, centroid coordinate, perimeter, and Feret’s diameter of the cells and harvested the cell distribution patterns from Voronoï diagrams by setting the threshold at localization density, mean distance, or area. Conclusions This procedure can be used to determine the character and organization of multicellular plant tissues at high efficiency, including precise parameter identification and polygon-based segmentation of plant cells.
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- 2020
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13. The Cytoskeleton in Plant Immunity: Dynamics, Regulation, and Function
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Jingyi Wang, Na Lian, Yue Zhang, Yi Man, Lulu Chen, Haobo Yang, Jinxing Lin, and Yanping Jing
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actin filament ,microtubule ,plant immunity ,dynamics ,regulation ,function ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
The plant cytoskeleton, consisting of actin filaments and microtubules, is a highly dynamic filamentous framework involved in plant growth, development, and stress responses. Recently, research has demonstrated that the plant cytoskeleton undergoes rapid remodeling upon sensing pathogen attacks, coordinating the formation of microdomain immune complexes, the dynamic and turnover of pattern-recognizing receptors (PRRs), the movement and aggregation of organelles, and the transportation of defense compounds, thus serving as an important platform for responding to pathogen infections. Meanwhile, pathogens produce effectors targeting the cytoskeleton to achieve pathogenicity. Recent findings have uncovered several cytoskeleton-associated proteins mediating cytoskeletal remodeling and defense signaling. Furthermore, the reorganization of the actin cytoskeleton is revealed to further feedback-regulate reactive oxygen species (ROS) production and trigger salicylic acid (SA) signaling, suggesting an extremely complex role of the cytoskeleton in plant immunity. Here, we describe recent advances in understanding the host cytoskeleton dynamics upon sensing pathogens and summarize the effectors that target the cytoskeleton. We highlight advances in the regulation of cytoskeletal remodeling associated with the defense response and assess the important function of the rearrangement of the cytoskeleton in the immune response. Finally, we propose suggestions for future research in this area.
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- 2022
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14. Polyvinyl Chloride Nanoparticles Affect Cell Membrane Integrity by Disturbing the Properties of the Multicomponent Lipid Bilayer in Arabidopsis thaliana
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Mingyang Li, Yuan Zhang, Changyuan Li, Jinxing Lin, and Xiaojuan Li
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NPs ,molecular dynamics (MD) simulations ,plant development ,cell membrane integrity ,Organic chemistry ,QD241-441 - Abstract
The ubiquitous presence of nanoplastics (NPs) in natural ecosystems is a serious concern, as NPs are believed to threaten every life form on Earth. Micro- and nanoplastics enter living systems through multiple channels. Cell membranes function as the first barrier of entry to NPs, thus playing an important biological role. However, in-depth studies on the interactions of NPs with cell membranes have not been performed, and effective theoretical models of the underlying molecular details and physicochemical behaviors are lacking. In the present study, we investigated the uptake of polyvinyl chloride (PVC) nanoparticles by Arabidopsis thaliana root cells, which leads to cell membrane leakage and damage to membrane integrity. We performed all-atom molecular dynamics simulations to determine the effects of PVC NPs on the properties of the multicomponent lipid bilayer. These simulations revealed that PVCs easily permeate into model lipid membranes, resulting in significant changes to the membrane, including reduced density and changes in fluidity and membrane thickness. Our exploration of the interaction mechanisms between NPs and the cell membrane provided valuable insights into the effects of NPs on membrane structure and integrity.
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- 2022
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15. Stability and bifurcation analysis of a gene expression model with small RNAs and mixed delays
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Fan Qing, Min Xiao, Chengdai Huang, Guoping Jiang, Jianlong Qiu, Jinxing Lin, Zhengxin Wang, and Cong Zheng
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Hopf bifurcation ,Local stability ,Periodic oscillation ,Distributed delay ,Genetic expression model ,Mathematics ,QA1-939 - Abstract
Abstract This paper investigates a gene expression model, which is mediated by sRNAs (small RNAs) and includes discrete and distributed delays. We take both the strong and weak kernel forms of distributed delay into consideration. The discrete time delay is chosen as the bifurcation parameter. By analyzing the distribution of characteristic values, we obtain the sufficient conditions of stability and examine the existence of periodic oscillations. When the discrete time delay is small and not greater than the threshold, the equilibrium of the gene expression model is asymptotically stable. When the bifurcation parameter exceeds the critical value, the model can produce limit cycles. Finally, numerical simulations are implemented to verify the correctness of our theoretical results.
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- 2019
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16. Non-Coding RNA Analyses of Seasonal Cambium Activity in Populus tomentosa
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Huimin Xu, Bo Chen, Yuanyuan Zhao, Yayu Guo, Guijun Liu, Ruili Li, Viktoria V. Zeisler-Diehl, Yanmei Chen, Xinqiang He, Lukas Schreiber, and Jinxing Lin
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lncRNA ,circRNA ,cambium activity periodicity ,Populus tomentosa ,Cytology ,QH573-671 - Abstract
Non-coding RNA, known as long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA), are taking part in the multiple developmental processes in plants. However, the roles of which played during the cambium activity periodicity of woody plants remain poorly understood. Here, lncRNA/circRNA-miRNA-mRNA regulatory networks of the cambium activity periodicity in Populus tomentosa was constructed, combined with morphologic observation and transcriptome profiling. Light microscopy and Periodic Acid Schiff (PAS) staining revealed that cell walls were much thicker and number of cell layers was increased during the active-dormant stage, accompanied by abundant change of polysaccharides. The novel lncRNAs and circRNAs were investigated, and we found that 2037 lncRNAs and 299 circRNAs were differentially expression during the vascular cambium period, respectively. Moreover, 1046 genes were identified as a target gene of 2037 novel lncRNAs, and 89 of which were the miRNA precursors or targets. By aligning miRNA precursors to the 7655 lncRNAs, 21 lncRNAs were identified as precursors tof 19 known miRNAs. Furthermore, the target mRNA of lncRNA/circRNA-miRNA network mainly participated in phytohormone, cell wall alteration and chlorophyll metabolism were analyzed by GO enrichment and KEGG pathway. Especially, circRNA33 and circRNA190 taking part in the phytohormone signal pathway were down-regulated during the active-dormant transition. Xyloglucan endotransglucosylase/hydrolase protein 24-like and UDP-glycosyltransferase 85A1 involved in the cell wall modification were the targets of lncRNA MSTRG.11198.1 and MSTRG.1050.1. Notably, circRNA103 and MSTRG.10851.1 regulate the cambium periodicity may interact with the miR482. These results give a new light into activity–dormancy regulation, associated with transcriptional dynamics and non-coding RNA networks of potential targets identification.
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- 2022
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17. Anatomical and chemical characteristics associated with lodging resistance in wheat
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Eryan Kong, Dongcheng Liu, Xiaoli Guo, Wenlong Yang, Jiazhu Sun, Xin Li, Kehui Zhan, Dangqun Cui, Jinxing Lin, and Aimin Zhang
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Molecular marker ,Solid stemmed wheat ,Lodging resistance ,Anatomical feature ,Agriculture ,Agriculture (General) ,S1-972 - Abstract
Anatomical and chemical characteristics of stems affect lodging in wheat (Triticum aestivum L.) cultivars. Traits associated with lodging resistance, such as plant height, stem strength, culm wall thickness, pith diameter, and stem diameter, were extensively investigated in earlier studies. However, the solid stem trait was rarely considered. In this study, we measured a range of anatomical and chemical characteristics on solid and hollow stemmed wheat cultivars. Significant correlations were detected between resistance to lodging and several anatomical features, including width of mechanical tissue, weight of low internodes, and width of stem walls. Morphological features that gave the best indication of improved lodging resistance were increased stem width, width of mechanical tissue layer, and stem density. Multiple linear regression analysis showed that 99% of the variation in lodging resistance could be explained by the width of the mechanical tissue layer, suggesting that solid stemmed wheat has several anatomical features for increasing resistance to lodging. In addition, microsatellite markers GWM247 and GWM340 were linked to a single solid stem QTL on chromosome 3BL in a population derived from the cross Xinongshixin (solid stem)/Line 3159 (hollow stem). These markers should be valuable in breeding wheat for solid stem.
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- 2013
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18. Exponential Estimates and Stabilization of Discrete-Time Singular Time-Delay Systems Subject to Actuator Saturation
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Jinxing Lin
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Mathematics ,QA1-939 - Abstract
This paper is concerned with exponential estimates and stabilization of a class of discrete-time singular systems with time-varying state delays and saturating actuators. By constructing a decay-rate-dependent Lyapunov-Krasovskii function and utilizing the slow-fast decomposition technique, an exponential admissibility condition, which not only guarantees the regularity, causality, and exponential stability of the unforced system but also gives the corresponding estimates of decay rate and decay coefficient, is derived in terms of linear matrix inequalities (LMIs). Under the proposed condition, the exponential stabilization problem of discrete-time singular time-delay systems subject actuator saturation is solved by designing a stabilizing state feedback controller and determining an associated set of safe initial conditions, for which the local exponential stability of the saturated closed-loop system is guaranteed. Two numerical examples are provided to illustrate the effectiveness of the proposed results.
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- 2012
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19. Mutation in SUMO E3 ligase, SIZ1, disrupts the mature female gametophyte in Arabidopsis.
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Yu Ling, Chunyu Zhang, Tong Chen, Huaiqing Hao, Peng Liu, Ray A Bressan, Paul M Hasegawa, Jing Bo Jin, and Jinxing Lin
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Medicine ,Science - Abstract
Female gametophyte is the multicellular haploid structure that can produce embryo and endosperm after fertilization, which has become an attractive model system for investigating molecular mechanisms in nuclei migration, cell specification, cell-to-cell communication and many other processes. Previous reports found that the small ubiquitin-like modifier (SUMO) E3 ligase, SIZ1, participated in many processes depending on particular target substrates and suppression of salicylic acid (SA) accumulation. Here, we report that SIZ1 mediates the reproductive process. SIZ1 showed enhanced expression in female organs, but was not detected in the anther or pollen. A defect in the siz1-2 maternal source resulted in reduced seed-set regardless of high SA concentration within the plant. Moreover, aniline blue staining and scanning electron microscopy revealed that funicular and micropylar pollen tube guidance was arrested in siz1-2 plants. Some of the embryo sacs of ovules in siz1-2 were also disrupted quickly after stage FG7. There was no significant affects of the siz1-2 mutation on expression of genes involved in female gametophyte development- or pollen tube guidance in ovaries. Together, our results suggest that SIZ1 sustains the stability and normal function of the mature female gametophyte which is necessary for pollen tube guidance.
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- 2012
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20. Exponential Admissibility and H∞ Control of Switched Singular Time-Delay Systems: An Average Dwell Time Approach
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Jinxing Lin and Zhifeng Gao
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Mathematics ,QA1-939 - Abstract
This paper deals with the problems of exponential admissibility and H∞ control for a class of continuous-time switched singular systems with time-varying delay. The H∞ controllers to be designed include both the state feedback (SF) and the static output feedback (SOF). First, by using the average dwell time scheme, the piecewise Lyapunov function, and the free-weighting matrix technique, an exponential admissibility criterion, which is not only delay-range-dependent but also decay-rate-dependent, is derived in terms of linear matrix inequalities (LMIs). A weighted H∞ performance criterion is also provided. Then, based on these, the solvability conditions for the desired SF and SOF controllers are established by employing the LMI technique, respectively. Finally, two numerical examples are given to illustrate the effectiveness of the proposed approach.
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- 2012
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21. Golgi apparatus-localized synaptotagmin 2 is required for unconventional secretion in Arabidopsis.
- Author
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Haiyan Zhang, Liang Zhang, Bin Gao, Hai Fan, Jingbo Jin, Miguel A Botella, Liwen Jiang, and Jinxing Lin
- Subjects
Medicine ,Science - Abstract
BACKGROUND: Most secretory proteins contain signal peptides that direct their sorting to the ER and secreted via the conventional ER/Golgi transport pathway, while some signal-peptide-lacking proteins have been shown to export through ER/Golgi independent secretory pathways. Hygromycin B is an aminoglycoside antibiotic produced by Streptomyces hygroscopicus that is active against both prokaryotic and eukaryotic cells. The hygromycin phosphotransferase (HYG(R)) can phosphorylate and inactivate the hygromycin B, and has been widely used as a positive selective marker in the construction of transgenic plants. However, the localization and trafficking of HYG(R) in plant cells remain unknown. Synaptotagmins (SYTs) are involved in controlling vesicle endocytosis and exocytosis as calcium sensors in animal cells, while their functions in plant cells are largely unclear. METHODOLOGY/PRINCIPAL FINDINGS: We found Arabidopsis synaptotagmin SYT2 was localized on the Golgi apparatus by immunofluorescence and immunogold labeling. Surprisingly, co-expression of SYT2 and HYG(R) caused hypersensitivity of the transgenic Arabidopsis plants to hygromycin B. HYG(R), which lacks a signal sequence, was present in the cytoplasm as well as in the extracellular space in HYG(R)-GFP transgenic Arabidopsis plants and its secretion is not sensitive to brefeldin A treatment, suggesting it is not secreted via the conventional secretory pathway. Furthermore, we found that HYG(R)-GFP was truncated at carboxyl terminus of HYG(R) shortly after its synthesis, and the cells deficient SYT2 failed to efficiently truncate HYG(R)-GFP,resulting in HYG(R)-GFP accumulated in prevacuoles/vacuoles, indicating that SYT2 was involved in HYG(R)-GFP trafficking and secretion. CONCLUSION/SIGNIFICANCE: These findings reveal for the first time that SYT2 is localized on the Golgi apparatus and regulates HYG(R)-GFP secretion via the unconventional protein transport from the cytosol to the extracelluar matrix in plant cells.
- Published
- 2011
- Full Text
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22. Arabidopsis R-SNARE proteins VAMP721 and VAMP722 are required for cell plate formation.
- Author
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Liang Zhang, Haiyan Zhang, Peng Liu, Huaiqing Hao, Jing Bo Jin, and Jinxing Lin
- Subjects
Medicine ,Science - Abstract
BACKGROUND: Cell plate formation during plant cytokinesis is facilitated by SNARE complex-mediated vesicle fusion at the cell-division plane. However, our knowledge regarding R-SNARE components of membrane fusion machinery for cell plate formation remains quite limited. METHODOLOGY/PRINCIPAL FINDINGS: We report the in vivo function of Arabidopsis VAMP721 and VAMP722, two closely sequence-related R-SNAREs, in cell plate formation. Double homozygous vamp721vamp722 mutant seedlings showed lethal dwarf phenotypes and were characterized by rudimentary roots, cotyledons and hypocotyls. Furthermore, cell wall stubs and incomplete cytokinesis were frequently observed in vamp721vamp722 seedlings. Confocal images revealed that green fluorescent protein-tagged VAMP721 and VAMP722 were preferentially localized to the expanding cell plates in dividing cells. Drug treatments and co-localization analyses demonstrated that punctuate organelles labeled with VAMP721 and VAMP722 represented early endosomes overlapped with VHA-a1-labeled TGN, which were distinct from Golgi stacks and prevacuolar compartments. In addition, protein traffic to the plasma membrane, but not to the vacuole, was severely disrupted in vamp721vamp722 seedlings by subcellular localization of marker proteins. CONCLUSION/SIGNIFICANCE: These observations suggest that VAMP721 and VAMP722 are involved in secretory trafficking to the plasma membrane via TGN/early endosomal compartment, which contributes substantially to cell plate formation during plant cytokinesis.
- Published
- 2011
- Full Text
- View/download PDF
23. No detectable maternal effects of elevated CO(2) on Arabidopsis thaliana over 15 generations.
- Author
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Nianjun Teng, Biao Jin, Qinli Wang, Huaiqing Hao, Reinhart Ceulemans, Tingyun Kuang, and Jinxing Lin
- Subjects
Medicine ,Science - Abstract
Maternal environment has been demonstrated to produce considerable impact on offspring growth. However, few studies have been carried out to investigate multi-generational maternal effects of elevated CO(2) on plant growth and development. Here we present the first report on the responses of plant reproductive, photosynthetic, and cellular characteristics to elevated CO(2) over 15 generations using Arabidopsis thaliana as a model system. We found that within an individual generation, elevated CO(2) significantly advanced plant flowering, increased photosynthetic rate, increased the size and number of starch grains per chloroplast, reduced stomatal density, stomatal conductance, and transpiration rate, and resulted in a higher reproductive mass. Elevated CO(2) did not significantly influence silique length and number of seeds per silique. Across 15 generations grown at elevated CO(2) concentrations, however, there were no significant differences in these traits. In addition, a reciprocal sowing experiment demonstrated that elevated CO(2) did not produce detectable maternal effects on the offspring after fifteen generations. Taken together, these results suggested that the maternal effects of elevated CO(2) failed to extend to the offspring due to the potential lack of genetic variation for CO(2) responsiveness, and future plants may not evolve specific adaptations to elevated CO(2) concentrations.
- Published
- 2009
- Full Text
- View/download PDF
24. Actin turnover is required for myosin-dependent mitochondrial movements in Arabidopsis root hairs.
- Author
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Maozhong Zheng, Martina Beck, Jens Müller, Tong Chen, Xiaohua Wang, Feng Wang, Qinli Wang, Yuqing Wang, Frantisek Baluska, David C Logan, Jozef Samaj, and Jinxing Lin
- Subjects
Medicine ,Science - Abstract
BACKGROUND:Previous studies have shown that plant mitochondrial movements are myosin-based along actin filaments, which undergo continuous turnover by the exchange of actin subunits from existing filaments. Although earlier studies revealed that actin filament dynamics are essential for many functions of the actin cytoskeleton, there are little data connecting actin dynamics and mitochondrial movements. METHODOLOGY/PRINCIPAL FINDINGS:We addressed the role of actin filament dynamics in the control of mitochondrial movements by treating cells with various pharmaceuticals that affect actin filament assembly and disassembly. Confocal microscopy of Arabidopsis thaliana root hairs expressing GFP-FABD2 as an actin filament reporter showed that mitochondrial distribution was in agreement with the arrangement of actin filaments in root hairs at different developmental stages. Analyses of mitochondrial trajectories and instantaneous velocities immediately following pharmacological perturbation of the cytoskeleton using variable-angle evanescent wave microscopy and/or spinning disk confocal microscopy revealed that mitochondrial velocities were regulated by myosin activity and actin filament dynamics. Furthermore, simultaneous visualization of mitochondria and actin filaments suggested that mitochondrial positioning might involve depolymerization of actin filaments on the surface of mitochondria. CONCLUSIONS/SIGNIFICANCE:Base on these results we propose a mechanism for the regulation of mitochondrial speed of movements, positioning, and direction of movements that combines the coordinated activity of myosin and the rate of actin turnover, together with microtubule dynamics, which directs the positioning of actin polymerization events.
- Published
- 2009
- Full Text
- View/download PDF
25. Fuel-Optimal Predictive Control of Satellite Formation Keeping Based on Genetic Algorithm.
- Author
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Nuo Xu, Jinxing Lin, Yuhang Miao, and Edmond Qi Wu
- Published
- 2019
- Full Text
- View/download PDF
26. Synchronization in Heterogeneous Networks Coupled of LC Oscillators Via Sampled-Data Control.
- Author
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Zhengxin Wang, Huihui Yang, Long-xia Qian, Min Xiao 0001, Guo-Ping Jiang, and Jinxing Lin
- Published
- 2019
- Full Text
- View/download PDF
27. PagUNE12 encodes a basic helix-loop-helix transcription factor that regulates the development of secondary vascular tissue in poplar
- Author
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Chengwei Song, Yayu Guo, Weiwei Shen, Xiaomin Yao, Huimin Xu, Yuanyuan Zhao, Ruili Li, and Jinxing Lin
- Subjects
Physiology ,Genetics ,Plant Science - Abstract
Secondary growth in woody plants generates new cells and tissues via the activity of the vascular cambium and drives the radial expansion of stems and roots. It is regulated by a series of endogenous factors, especially transcription factors. Here, we cloned the basic helix–loop–helix (bHLH) transcription factor gene UNFERTILIZED EMBRYO SAC12 (UNE12) from poplar (Populus alba × Populus glandulosa Uyeki) and used biochemical, molecular, and cytological assays to investigate the biological functions and regulatory mechanism of PagUNE12. PagUNE12 mainly localized in the nucleus and possessed transcriptional activation activity. It was widely expressed in vascular tissues, including primary phloem and xylem and secondary phloem and xylem. Poplar plants overexpressing PagUNE12 showed significantly reduced plant height, shorter internodes, and curled leaves compared with wild-type plants. Optical microscopy and transmission electron microscopy revealed that overexpressing PagUNE12 promoted secondary xylem development, with thicker secondary cell walls than wild-type poplar. Fourier transform infrared spectroscopy, confocal Raman microscopy, and 2D Heteronuclear Single Quantum Correlation analysis indicated that these plants also had increased lignin contents, with a lower relative abundance of syringyl lignin units and a higher relative abundance of guaiacyl lignin units. Therefore, overexpressing PagUNE12 promoted secondary xylem development and increased the lignin contents of secondary xylem in poplar, suggesting that this gene could be used to improve wood quality in the future.
- Published
- 2023
28. Endoplasmic reticulum membrane contact sites: cross-talk between membrane-bound organelles in plant cells
- Author
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Jiahui Bian, Xiao Su, Xiaoyan Yuan, Yuan Zhang, Jinxing Lin, and Xiaojuan Li
- Subjects
Physiology ,Plant Science - Abstract
Eukaryotic cells contain organelles surrounded by monolayer or bilayer membranes. Organelles take part in highly dynamic and organized interactions at membrane contact sites, which play vital roles during development and response to stress. The endoplasmic reticulum extends throughout the cell and acts as an architectural scaffold to maintain the spatial distribution of other membrane-bound organelles. In this review, we highlight the structural organization, dynamics, and physiological functions of membrane contact sites between the endoplasmic reticulum and various membrane-bound organelles, especially recent advances in plants. We briefly introduce how the combined use of dynamic and static imaging techniques can enable monitoring of the cross-talk between organelles via membrane contact sites. Finally, we discuss future directions for research fields related to membrane contact.
- Published
- 2023
29. Batch Bayesian Optimization via Maximizing Variance Change
- Author
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Zhao, Yongyao, primary, Wang, Ronghao, additional, Wang, Yuanzhen, additional, and Jinxing, Lin, additional
- Published
- 2023
- Full Text
- View/download PDF
30. Advances in vesicle trafficking of membrane proteins and their regulatory mechanisms
- Author
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Changwen Xu, Hongping Qian, Pengyun Luo, Meng Yu, Jingjing Xing, Liang Zhang, Xi Zhang, Yaning Cui, and Jinxing Lin
- Subjects
Multidisciplinary - Published
- 2022
31. The temptation from homogeneous linear catechyl lignin
- Author
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Shuizhong Wang, Qingru Shen, Shihao Su, Jinxing Lin, and Guoyong Song
- Subjects
General Chemistry - Published
- 2022
32. Event-triggered stabilisation of sampled-data singular systems: a hybrid control approach
- Author
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Jinxing Lin, Peng Shi, and Min Xiao
- Subjects
Control and Systems Engineering ,Computer Science Applications - Published
- 2022
33. Membrane microdomains: Structural and signaling platforms for establishing membrane polarity.
- Author
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Ruili Li, Ran Zhao, Mei Yang, Xi Zhang, and Jinxing Lin
- Published
- 2023
- Full Text
- View/download PDF
34. New results on admissibility and L2 gain property of discrete-time switched singular state-delayed systems.
- Author
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Jinxing Lin
- Published
- 2015
- Full Text
- View/download PDF
35. High-resolution genome mapping and functional dissection of chlorogenic acid production in Lonicera maackii
- Author
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Ruili Li, Jing Xu, Zengxing Qi, Shiwei Zhao, Ran Zhao, Yanrui Ge, Ruofan Li, Xiuya Kong, Zhenying Wu, Xi Zhang, Qizouhong He, Yan Zhang, Ping-Li Liu, Lei Zhu, Jian-Feng Mao, Chunxiang Fu, George Komis, Paul Grünhofer, Lukas Schreiber, and Jinxing Lin
- Subjects
Physiology ,Genetics ,Plant Science - Abstract
Amur honeysuckle (Lonicera maackii) is a widely used medicinal plant of the Caprifoliaceae family that produces chlorogenic acid. Research on this plant mainly focuses on its ornamental value and medicinal compounds, but a reference genome sequence and molecular resources for accelerated breeding are currently lacking. Herein, Nanopore sequencing and high-throughput chromosome conformation capture (Hi-C) allowed a chromosome-level genome assembly of Lonicera maackii (2n = 18). A global view of the gene regulatory network involved in the biosynthesis of chlorogenic acid and the dynamics of fruit coloration in L. maackii was established through metabolite profiling and transcriptome analyses. Moreover, we identified the genes encoding hydroxycinnamoyl-CoA quinate transferase (LmHQT) and hydroxycinnamoyl-CoA shikimic/quinate transferase (LmHCT), which localized to the cytosol and nucleus. Heterologous overexpression of these genes in Nicotiana benthamiana leaves resulted in elevated chlorogenic acid contents. Importantly, HPLC analyses revealed that LmHCT and LmHQTs recombinant proteins modulate the accumulation of chlorogenic acid (CGA) using quinic acid and caffeoyl CoA as substrates, highlighting the importance of LmHQT and LmHCT in chlorogenic acid biosynthesis. These results confirmed that LmHQTs and LmHCT catalyze the biosynthesis of CGA in vitro. The genomic data presented in this study will offer a valuable resource for the elucidation of CGA biosynthesis and facilitating selective molecular breeding.
- Published
- 2023
36. Plasmodesmal endoplasmic reticulum proteins regulate intercellular trafficking of Cucumber mosaic virus in Arabidopsis
- Author
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Byung-Kook Ham, Xiaohua Wang, Roberto Toscano-Morales, Jinxing Lin, and William J Lucas
- Subjects
Physiology ,Plant Science - Abstract
Plasmodesmata (PD) are plasma membrane (PM)-lined cytoplasmic nanochannels that mediate in cell-to-cell communication across the cell wall. A range of proteins are embedded in the PD PM and endoplasmic reticulum (ER) and function in regulating PD-mediated symplasmic trafficking. However, knowledge of the nature and function of the ER-embedded proteins, in the intercellular movement of non-cell-autonomous proteins, is limited. Here, we report the functional characterization of two ER luminal proteins, AtBiP1/2, and two ER integral membrane proteins, AtERdj2A/B, which are located within the PD. These PD proteins were identified as interacting proteins with Cucumber mosaic virus (CMV) movement protein (MP) in coimmunoprecipitation studies, using an Arabidopsis-derived plasmodesmal-enriched cell wall protein preparation (PECP). The AtBiP1/2 PD location was confirmed by transmission electron microscopy-based immunolocalization, and their AtBiP1/2 signal peptides (SPs) function in PD targeting. In vitro/in vivo pull-down assays revealed the association between AtBiP1/2 and CMV MP, mediated by AtERdj2A, through the formation of an AtBiP1/2-AtERdj2-CMV MP complex within PD. The role of this complex in CMV infection was established, as systemic infection was retarded in bip1/bip2w and erdj2b mutants. Our findings provide a model for a mechanism by which the CMV MP mediates in cell-to-cell trafficking of its viral ribonucleoprotein complex.
- Published
- 2023
37. The ontogenetic ageing pattern and the molecular mechanism for prunning rejuvenation in Pinus elliottii × P . caribaea
- Author
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ShunYao YANG, GuiFang ZHANG, Xi ZHANG, ChangMing LIN, Ting HUANG, LePing DENG, ZhiLin ZHANG, FuMing LI, SuiYing ZHONG, XiaoYing PAN, QiZouHong HE, YingYing ZHANG, YiLan E, WeiWei SHEN, GuangChao WANG, Yang LI, YuanYuan ZHAO, XiaoJuan LI, ShaoWei HUANG, YingBai SHEN, ShiHui NIU, and JinXing LIN
- Subjects
Pharmacology (medical) - Published
- 2023
38. Stabilization of networked singular control systems under double-channel quantization and DoS attacks
- Author
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Jinxing Lin, Xiang Wu, Min Xiao, and Jie Ding
- Subjects
Computer Networks and Communications ,Control and Systems Engineering ,Applied Mathematics ,Signal Processing - Published
- 2022
39. Transcription factor dynamics in plants: Insights and technologies for in vivo imaging
- Author
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Yuan Zhang, Yuqing Lu, Hafez El Sayyed, Jiahui Bian, Jinxing Lin, and Xiaojuan Li
- Subjects
DNA-Binding Proteins ,Gene Expression Regulation ,Physiology ,Genetics ,DNA ,Plant Science ,Topical Review ,Protein Binding ,Transcription Factors - Abstract
Biochemical and genetic approaches have been extensively used to study transcription factor (TF) functions, but their dynamic behaviors and the complex ways in which they regulate transcription in plant cells remain unexplored, particularly behaviors such as translocation and binding to DNA. Recent developments in labeling and imaging techniques provide the necessary sensitivity and resolution to study these behaviors in living cells. In this review, we present an up-to-date portrait of the dynamics and regulation of TFs under physiologically relevant conditions and then summarize recent advances in fluorescent labeling strategies and imaging techniques. We then discuss future prospects and challenges associated with the application of these techniques to examine TFs’ intricate dance in living plants.
- Published
- 2022
40. H∞ Control In Finite Frequency Domain For Lipschitz Singular Nonlinear Systems
- Author
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Ziyan Zhu, Jinxing Lin, and Tian Tang
- Published
- 2022
41. Observer based fault-tolerant attitude control of a quadrotor UAV and an application
- Author
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Yingjiang Zhou, Shuo Chao, Jinxing Lin, Fengyu Xu, and Xin Shen
- Published
- 2022
42. CST-GANs: A Generative Adversarial Network Based on CST Parameterization for the Generation of Smooth Airfoils
- Author
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Jinxing Lin, Chenliang Zhang, Xiaoye Xie, Xingyu Shi, Xiaoyu Xu, and Yanhui Duan
- Published
- 2022
43. Populus × canescens root suberization in reaction to osmotic and salt stress is limited to the developing younger root tip region
- Author
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Paul Grünhofer, Tyll Stöcker, Yayu Guo, Ruili Li, Jinxing Lin, Kosala Ranathunge, Heiko Schoof, and Lukas Schreiber
- Subjects
Populus ,Physiology ,Meristem ,Genetics ,Water ,Cell Biology ,Plant Science ,General Medicine ,Sodium Chloride ,Plant Roots ,Salt Stress - Abstract
Populus is a valuable and fast-growing tree species commonly cultivated for economic and scientific purposes. But most of the poplar species are sensitive to drought and salt stress. Thus, we compared the physiological effects of osmotic stress (PEG8000) and salt treatment (NaCl) on poplar roots to identify potential strategies for future breeding or genetic engineering approaches. We investigated root anatomy using epifluorescence microscopy, changes in root suberin composition and amount using gas chromatography, transcriptional reprogramming using RNA sequencing, and modifications of root transport physiology using a pressure chamber. Poplar roots reacted to the imposed stress conditions, especially in the developing younger root tip region, with remarkable differences between both types of stress. Overall, the increase in suberin content was surprisingly small, but the expression of key suberin biosynthesis genes was strongly induced. Significant reductions of the radial water transport in roots were only observed for the osmotic and not the hydrostatic hydraulic conductivity. Our data indicate that the genetic enhancement of root suberization processes in poplar might be a promising target to convey increased tolerance, especially against toxic sodium chloride.
- Published
- 2022
44. Cross-talk between clathrin-dependent post-Golgi trafficking and clathrin-mediated endocytosis in Arabidopsis root cells
- Author
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Xu Yan, Chan Liu, Yutong Wang, Yan Zhang, Jianwei Pan, Jinxing Lin, Sebastian Y. Bednarek, Dana A Dahhan, and Mei Xu
- Subjects
0106 biological sciences ,AcademicSubjects/SCI01280 ,Endocytic cycle ,Arabidopsis ,Golgi Apparatus ,Plant Science ,Endocytosis ,Plant Roots ,01 natural sciences ,Clathrin ,Exocytosis ,03 medical and health sciences ,symbols.namesake ,Research Articles ,030304 developmental biology ,0303 health sciences ,AcademicSubjects/SCI01270 ,biology ,AcademicSubjects/SCI02288 ,Arabidopsis Proteins ,AcademicSubjects/SCI02287 ,AcademicSubjects/SCI02286 ,Signal transducing adaptor protein ,Cell Biology ,Receptor-mediated endocytosis ,Membrane transport ,Golgi apparatus ,Cell biology ,biology.protein ,symbols ,010606 plant biology & botany - Abstract
Clathrin-dependent endocytosis and exocytosis are coordinated to maintain cell homeostasis in Arabidopsis roots., Coupling of post-Golgi and endocytic membrane transport ensures that the flow of materials to/from the plasma membrane (PM) is properly balanced. The mechanisms underlying the coordinated trafficking of PM proteins in plants, however, are not well understood. In plant cells, clathrin and its adaptor protein complexes, AP-2 and the TPLATE complex (TPC) at the PM, and AP-1 at the trans-Golgi network/early endosome (TGN/EE), function in clathrin-mediated endocytosis (CME) and post-Golgi trafficking. Here, we utilized mutants with defects in clathrin-dependent post-Golgi trafficking and CME, in combination with other cytological and pharmacological approaches, to further investigate the machinery behind the coordination of protein delivery and recycling to/from the TGN/EE and PM in Arabidopsis (Arabidopsis thaliana) root cells. In mutants with defective AP-2-/TPC-dependent CME, we determined that clathrin and AP-1 recruitment to the TGN/EE as well as exocytosis are significantly impaired. Likewise, defects in AP-1-dependent post-Golgi trafficking and pharmacological inhibition of exocytosis resulted in the reduced association of clathrin and AP-2/TPC subunits with the PM and a reduction in the internalization of cargoes via CME. Together, these results suggest that post-Golgi trafficking and CME are coupled via modulation of clathrin and adaptor protein complex recruitment to the TGN/EE and PM.
- Published
- 2021
45. Finite-time $H_{-}/H_{\infty}$ Fault Detection for Singular systems with Time-varying Delay
- Author
-
Jinchao Zhang, Jinxing Lin, and Ziyan Zhu
- Published
- 2022
46. Discrete fractional order PID controller design for nonlinear systems
- Author
-
Jinxing Lin, Jie Ding, Zhijie Li, and Min Wu
- Subjects
Nonlinear system ,Control and Systems Engineering ,Computer science ,Order (business) ,Control theory ,MathematicsofComputing_NUMERICALANALYSIS ,PID controller ,Model complexity ,Computer Science Applications ,Theoretical Computer Science - Abstract
In this study, a discrete fractional order PID controller for nonlinear systems is proposed. U-model is firstly employed to transform nonlinear systems into a linear-like model and model complexity...
- Published
- 2021
47. Age-dependent microRNAs in regulation of vascular cambium activity in Chinese fir (Cunninghamia lanceolata)
- Author
-
Jinxing Lin, Huimin Xu, Xian Xue, Guijun Liu, Dechang Cao, and Jinling Feng
- Subjects
0106 biological sciences ,0301 basic medicine ,Ecology ,Cell division ,Physiology ,fungi ,Xylem ,Forestry ,Plant Science ,Biology ,Meristem ,01 natural sciences ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,microRNA ,Vascular cambium ,Phloem ,Cambium ,Cell wall modification ,010606 plant biology & botany - Abstract
High-throughput sequencing and Degradome sequencing revealed that miRNAs play crucial roles during the juvenile-to-mature stages in Chinese fir. In woody plants, the vascular cambium is a continuous cylinder of meristematic cells in the stem that produces secondary xylem (wood) and secondary phloem via cell division, expansion, secondary wall formation, lignification, and programmed cell death. MicroRNAs (miRNAs) are endogenous single-stranded non-coding RNAs that play important roles in plant growth and development. However, little is known about the roles of miRNAs in age-related changes in the vascular cambium, especially in conifers. Here, we compared age-related miRNAs in the vascular cambium of 3-(juvenile), 13-(transition), and 35-year-old (mature) Chinese fir (Cunninghamia lanceolata) trees. Transmission electron microscopy revealed changes in the morphology and cell wall thickness of the vascular cambium during the juvenile-to-mature phase transition. In addition, high-throughput sequencing and subsequent analyses identified 700 miRNAs, including 651 known and 49 novel miRNAs. We identified 105, 120, and 94 differentially expressed miRNAs at the three stages of growth. These miRNAs included various differentially expressed development-related and phytohormone-related miRNAs involved in cambium activity, cell division, and cell wall modification. Degradome sequencing revealed 38 target genes that were cleaved by 88 known miRNAs and 16 target genes that were cleaved by seven novel miRNAs. Additionally, miR159, miR164, and miR166 were highly expressed in the 13-transition stage; these miRNAs are involved in the auxin-signaling pathway. Moreover, miR156 levels were abundant in VC13 along with miR172 levels decreased during the juvenile-to-mature stages. These results provide insight into the roles of age-specific miRNAs in the growth of C. lanceolata and shed light on vascular cambium development in conifers.
- Published
- 2021
48. Dynamic spatial reorganization of BSK1 complexes in the plasma membrane underpins signal-specific activation for growth and immunity
- Author
-
Jinxing Lin, Li Li, Xi Zhang, Xiaoyi Shan, Yaning Cui, Meng Yu, Inhwan Hwang, Sammar Abbas, Bodan Su, and František Baluška
- Subjects
0106 biological sciences ,0301 basic medicine ,Plant growth ,Cell Membrane ,fungi ,Arabidopsis ,Chromosomal translocation ,Plant Science ,Biology ,01 natural sciences ,Cell biology ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Membrane ,chemistry ,Gene Expression Regulation, Plant ,Immunity ,Brassinosteroid ,Molecular Biology ,Signal Transduction ,010606 plant biology & botany - Abstract
Growth and immunity are opposing processes that compete for cellular resources, and proper resource allocation is crucial for plant survival. BSK1 plays a key role in the regulation of both growth and immunity by associating with BRI1 and FLS2, respectively. However, it remains unclear how two antagonistic signals co-opt BSK1 to induce signal-specific activation. Here we show that the dynamic spatial reorganization of BSK1 within the plasma membrane underlies the mechanism of signal-specific activation for growth or immunity. Resting BSK1 localizes to membrane rafts as complexes. Unlike BSK1-associated FLS2 and BRI1, flg22 or exogenous brassinosteroid (BR) treatment did not decrease BSK1 levels at the plasma membrane (PM) but rather induced BSK1 multimerization and dissociation from FLS2/BSK1 or BRI1/BSK1, respectively. Moreover, flg22-activated BSK1 translocated from membrane rafts to non-membrane-raft regions, whereas BR-activated BSK1 remained in membrane rafts. When applied together with flg22, BR suppressed various flg22-induced BSK1 activities such as BSK1 dissociation from FLS2/BSK1, BSK1 interaction with MAPKKK5, and BSK translocation together with MAPKKK5. Taken together, this study provides a unique insight into how the precise control of BSK1 spatiotemporal organization regulates the signaling specificity to balance plant growth and immunity.
- Published
- 2021
49. Coordination of Phospholipid-Based Signaling and Membrane Trafficking in Plant Immunity
- Author
-
Jinxing Lin, Liang Zhang, Zhikun Duan, and Jingjing Xing
- Subjects
Cell Membrane ,Phospholipid ,Plant Immunity ,Plant Science ,Biology ,Endocytosis ,Exocytosis ,Cell biology ,Protein Transport ,chemistry.chemical_compound ,Membrane ,chemistry ,Extracellular ,lipids (amino acids, peptides, and proteins) ,Signal transduction ,Lipid bilayer ,Phospholipids ,Signal Transduction - Abstract
In plants, defense-associated signal transduction involves key membrane-related processes, such as phospholipid-based signaling and membrane trafficking. Coordination of these processes occurs in the lipid bilayer of plasma membrane (PM) and luminal/extracellular membranes. Deciphering the spatiotemporal organization of phospholipids and lipid-protein interactions provides crucial information on the mechanisms that link phospholipid-based signaling and membrane trafficking in plant immunity. In this review, we summarize recent advances in our understanding of these connections, including deployment of key enzymes and molecules in phospholipid pathways, and roles of lipid diversity in membrane trafficking. We highlight the mechanisms that mediate feedback between phospholipid-based signaling and membrane trafficking to regulate plant immunity, including their novel roles in balancing endocytosis and exocytosis.
- Published
- 2021
50. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques
- Author
-
Weiwei Shen, Jinxing Lin, Huimin Xu, Xiaohong Zhuang, Yuling Jiao, Shunyao Yang, Guangchao Wang, Xi Zhang, Yanping Jing, Yi Man, Xiaojuan Li, Ruili Li, Yi Zhang, Jinbo Shen, Yaning Cui, Jingjing Xing, Jiahui Bian, Sodmergen, Hu Zijian, Tonglin Mao, Lingyu Ma, Meng Yu, Na Lian, and Haiyun Ren
- Subjects
0301 basic medicine ,Computer science ,Systems biology ,Distributed computing ,Human Brain Project ,General Biochemistry, Genetics and Molecular Biology ,Field (geography) ,03 medical and health sciences ,Multicellular organism ,030104 developmental biology ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Connectome ,General Agricultural and Biological Sciences ,Organism ,Biological network ,General Environmental Science ,Network analysis - Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
- Published
- 2021
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