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  • 1
    Online Resource
    Online Resource
    3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
    Springer Science and Business Media LLC ; 2020
    In:  Genome Biology Vol. 21, No. 1 ( 2020-12)
    Details
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 21, No. 1 ( 2020-12)
    Abstract: Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown. Results We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated epigenetic modification and transcription factor binding to OCRs highlights the cis and trans regulation of differentially expressed genes in ear and tassel controlling inflorescence architecture. We further systematically map chromatin interactions at high-resolution in corresponding tissues using in situ digestion-ligation-only Hi-C (DLO Hi-C). The extensive chromatin loops connecting OCRs and genes provide a 3D view on cis- and trans -regulatory modules responsible for ear- and tassel-specific gene expression. We find that intergenic SNPs tend to locate in distal OCRs, and our chromatin interaction maps provide a potential mechanism for trait-associated intergenic SNPs that may contribute to phenotypic variation by influencing target gene expression through chromatin loops. Conclusions Our comprehensive epigenome annotations and 3D genome maps serve as valuable resource and provide a deep understanding of the complex regulatory mechanisms of genes underlying developmental and morphological diversities between maize ear and tassel.
    Type of Medium: Online Resource
    ISSN: 1474-760X
    URL: Article
    DOI: 10.1186/s13059-020-02063-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2040529-7
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  • 2
    Online Resource
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    A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize
    Springer Science and Business Media LLC ; 2023
    In:  Genome Biology Vol. 24, No. 1 ( 2023-03-29)
    Details
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 24, No. 1 ( 2023-03-29)
    Abstract: Maize ( Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-omics GRN connecting the translatome and transcriptome is lacking, hampering our understanding and exploration of the maize regulatome. Results We collect spatio-temporal translatome and transcriptome data and systematically explore the landscape of gene transcription and translation across 33 tissues or developmental stages of maize. Using this comprehensive transcriptome and translatome atlas, we construct a multi-omics GRN integrating mRNAs and translated mRNAs, demonstrating that translatome-related GRNs outperform GRNs solely using transcriptomic data and inter-omics GRNs outperform intra-omics GRNs in most cases. With the aid of the multi-omics GRN, we reconcile some known regulatory networks. We identify a novel transcription factor, ZmGRF6 , which is associated with growth. Furthermore, we characterize a function related to drought response for the classic transcription factor ZmMYB31 . Conclusions Our findings provide insights into spatio-temporal changes across maize development at both the transcriptome and translatome levels. Multi-omics GRNs represent a useful resource for dissection of the regulatory mechanisms underlying phenotypic variation.
    Type of Medium: Online Resource
    ISSN: 1474-760X
    URL: Article
    DOI: 10.1186/s13059-023-02890-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2040529-7
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  • 3
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    Ultrasmall iron‐gallic acid coordination polymer nanodots with antioxidative neuroprotection for PET/MR imaging‐guided ischemia stroke therapy
    Wiley ; 2023
    In:  Exploration Vol. 3, No. 1 ( 2023-02)
    Details
    In: Exploration, Wiley, Vol. 3, No. 1 ( 2023-02)
    Abstract: Oxidative stress from reactive oxygen species (ROS) is a reperfusion injury factor that can lead to cell damage and death. Here, ultrasmall iron‐gallic acid coordination polymer nanodots (Fe‐GA CPNs) were developed as antioxidative neuroprotectors for ischemia stroke therapy guided by PET/MR imaging. As proven by the electron spin resonance spectrum, the ultrasmall Fe‐GA CPNs with ultrasmall size, scavenged ROS efficiently. In vitro experiments revealed that Fe‐GA CPNs could protect cell viability after being treated with hydrogen peroxide (H 2 O 2 ) and displayed the effective elimination of ROS by Fe‐GA CPNs, which subsequently restores oxidation balance. When analyzing the middle cerebral artery occlusion model, the neurologic damage displayed by PET/MR imaging revealed a distinct recovery after treatment with Fe‐GA CPNs, which was proved by 2,3,5‐triphenyl tetrazolium chloride staining. Furthermore, immunohistochemistry staining indicated that Fe‐GA CPNs inhibited apoptosis through protein kinase B (Akt) restoration, whereas western blot and immunofluorescence indicated the activation of the nuclear factor erythroid 2‐related factor 2 (Nrf2) and heme oxygenase‐1 (HO‐1) pathway following Fe‐GA CPNs application. Therefore, Fe‐GA CPNs exhibit an impressive antioxidative and neuroprotective role via redox homeostasis recovery by Akt and Nrf2/HO‐1 pathway activation, revealing its potential for clinical ischemia stroke treatment.
    Type of Medium: Online Resource
    ISSN: 2766-2098 , 2766-2098
    URL: Issue
    URL: Article
    DOI: 10.1002/exp2.v3.1
    DOI: 10.1002/EXP.20220041
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 3103468-8
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  • 4
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    A novel authorization delegation scheme for multimedia social networks by using proxy re-encryption
    Springer Science and Business Media LLC ; 2016
    In:  Multimedia Tools and Applications Vol. 75, No. 21 ( 2016-11), p. 13995-14014
    Details
    In: Multimedia Tools and Applications, Springer Science and Business Media LLC, Vol. 75, No. 21 ( 2016-11), p. 13995-14014
    Type of Medium: Online Resource
    ISSN: 1380-7501 , 1573-7721
    URL: Article
    DOI: 10.1007/s11042-015-2929-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 1287642-2
    detail.hit.zdb_id: 1479928-5
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  • 5
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    Single‐molecule long‐read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte ( Zea mays ssp. parviglumis )
    Wiley ; 2022
    In:  Molecular Ecology Resources Vol. 22, No. 1 ( 2022-01), p. 272-282
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 22, No. 1 ( 2022-01), p. 272-282
    Abstract: Teosinte ( Zea mays ssp. parviglumis ), the wild progenitor of maize ( Zea mays L.), is an important germplasm resource for improvement of modern maize lines. However, we have limited genetic and genomic information about teosinte and lack state‐of‐the‐art tools to annotate transcriptomes assembled by single‐molecule long‐read sequencing without a reference genome. Here, we employed single‐molecule long‐read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 nonredundant transcript isoforms. We devised a state‐of‐the‐art, machine learning‐based bioinformatics pipeline DenovoAS_Finder to annotate the TIL11 transcriptome without a complete reference genome with an accuracy of up to 91%, providing a robust gene classifier of complex genomes. Additionally, we constructed a draft TIL11 genome with 16,633 high‐quality contigs and a N50 of 112 kb by Nanopore sequencing. Genes from families that expanded from teosinte to maize were significantly enriched in the gene ontology (GO) term “RNA modification pathway” and had more transcript isoforms in TIL11 than in the maize inbred line B73. Genes showed collinearity between TIL11 and B73, and intergenic regions were extensively altered by transposable elements. Our study furthers the understanding of maize domestication and provides a resource for the utilization of wild germplasm in maize breeding.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v22.1
    DOI: 10.1111/1755-0998.13454
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 6
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    Spatiotemporal distribution and prediction of chlorophyll-a in Ulansuhai lake from an arid area of China
    Frontiers Media SA ; 2023
    In:  Frontiers in Environmental Science Vol. 11 ( 2023-1-16)
    Details
    In: Frontiers in Environmental Science, Frontiers Media SA, Vol. 11 ( 2023-1-16)
    Abstract: Lake Ulansuhai, a typical shallow lake in an arid area that is economically and ecologically important along the Yellow River, is currently eutrophic. Long-term (2010–2020) data on chlorophyll-a, nutrient, and environmental factors were obtained from three Lake Ulansuhai monitoring stations. The temporal and spatial distribution characteristics of Chl-a were analyzed. Additionally, a hybrid evolutionary algorithm was established to simulate and predict Chl-a, and sensitivity analysis revealed the interaction between environmental factors and eutrophication. The results indicated that (1) the seasonal variation of eutrophication showed an obvious trend of spring & gt; summer & gt; autumn & gt; winter, and the concentration of Chl-a in the inlet was significantly higher than that in the outlet; (2) The inlet, center, and outlet of Ulansuhai Lake are satisfactorily affected by HEA in the best suited method. The fitting coefficients ( R 2 ) of the optimal models were 0.58, 0.59, and 0.62 for the three monitoring stations, and the root mean square errors (RMSE) were 3.89, 3.21, and 3.56, respectively; (3) under certain range and threshold conditions, Chl-a increased with the increase of permanganate index, water temperature, dissolved oxygen concentration, and ammonia nitrogen concentration, but decreased with the increase of water depth, Secchi disk depth, pH, and fluoride concentration. The results indicate that the HEA can simulate and predict the dynamics of Chl-a, and identify and quantify the relationships between eutrophication and the threshold data. The research results provide theoretical basis and technical support for the prediction and have great significance for the improvement of water quality and environmental protection in arid and semi-arid inland lakes.
    Type of Medium: Online Resource
    ISSN: 2296-665X
    URL: Article
    DOI: 10.3389/fenvs.2023.1045464
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2741535-1
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  • 7
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    New lncRNA annotation reveals extensive functional divergence of the transcriptome in maize
    Wiley ; 2019
    In:  Journal of Integrative Plant Biology Vol. 61, No. 4 ( 2019-04), p. 394-405
    Details
    In: Journal of Integrative Plant Biology, Wiley, Vol. 61, No. 4 ( 2019-04), p. 394-405
    Abstract: Long non‐coding RNAs (lncRNAs), whose sequences are approximately 200 bp or longer and unlikely to encode proteins, may play an important role in eukaryotic gene regulation. Although the latest maize ( Zea mays L.) reference genome provides an essential genomic resource, genome‐wide annotations of maize lncRNAs have not been updated. Here, we report on a large transcriptomic dataset collected from 749 RNA sequencing experiments across different tissues and stages of the maize reference inbred B73 line and 60 from its wild relative teosinte. We identified 18,165 high‐confidence lncRNAs in maize, of which 6,873 are conserved between maize and teosinte. We uncovered distinct genomic characteristics of conserved lncRNAs, non‐conserved lncRNAs, and protein‐coding transcripts. Intriguingly, Shannon entropy analysis showed that conserved lncRNAs are likely to be expressed similarly to protein‐coding transcripts. Co‐expression network analysis revealed significant variation in the degree of co‐expression. Furthermore, selection analysis indicated that conserved lncRNAs are more likely than non‐conserved lncRNAs to be located in regions subject to recent selection, indicating evolutionary differentiation. Our results provide the latest genome‐wide annotation and analysis of maize lncRNAs and uncover potential functional divergence between protein‐coding, conserved lncRNA, and non‐conserved lncRNA genes, demonstrating the high complexity of the maize transcriptome.
    Type of Medium: Online Resource
    ISSN: 1672-9072 , 1744-7909
    URL: Issue
    URL: Article
    DOI: 10.1111/jipb.v61.4
    DOI: 10.1111/jipb.12708
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2130095-1
    SSG: 12
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  • 8
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    Next-generation bulked segregant analysis for Breeding 4.0
    Elsevier BV ; 2023
    In:  Cell Reports Vol. 42, No. 9 ( 2023-09), p. 113039-
    Details
    In: Cell Reports, Elsevier BV, Vol. 42, No. 9 ( 2023-09), p. 113039-
    Type of Medium: Online Resource
    ISSN: 2211-1247
    URL: Article
    DOI: 10.1016/j.celrep.2023.113039
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2649101-1
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  • 9
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    Online Resource
    IL-17A Promotes the Migration, Invasion and the EMT Process of Lung Cancer Accompanied by NLRP3 Activation
    Hindawi Limited ; 2022
    In:  BioMed Research International Vol. 2022 ( 2022-10-30), p. 1-14
    Details
    In: BioMed Research International, Hindawi Limited, Vol. 2022 ( 2022-10-30), p. 1-14
    Abstract: Background. Lung cancer is a deadly cancer worldwide, and its pathogenesis and treatment methods require continuous research and exploration. As a representative factor of adaptive immunity, the role of interleukin-17A (IL-17A) in lung cancer is still unclear. The purpose of the present study was to investigate the effect of IL-17A on the biological behaviour of lung cancer cells and the relative mechanism. Methods. The human lung adenocarcinoma A549 and H1299 cell lines were used for in vitro study. The effects of IL-17A on cell proliferation, migration and invasion were assessed by CCK-8 assay, wound-healing assay, transwell invasion assay and real-time cell analysis (RTCA). The expression levels of marker proteins in the process of epithelial-mesenchymal transition (EMT) were detected by western blot analysis. Caspase-1 activity and the concentration of IL-1β after NLRP3 inflammasome activation were measured by a Caspase-1 Activity Assay Kit and an IL-1β ELISA kit, respectively. Results. Compared to the control group, IL-17A treatment did not affect the proliferation of A549 and H1299 cells in vitro, but it promoted cell migration, invasion and the EMT process. IL-17A treatment increased NLRP3 expression, caspase-1 activity and IL-1β level. Blockade of NLRP3 alleviated the cell migration, invasion and the EMT process induced by IL-17A. Conclusions. In conclusion, these findings indicated that NLRP3 participates in the migration, invasion and the EMT process of IL-17A-stimulated lung cells in vitro.
    Type of Medium: Online Resource
    ISSN: 2314-6141 , 2314-6133
    URL: Article
    DOI: 10.1155/2022/7841279
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2022
    detail.hit.zdb_id: 2698540-8
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  • 10
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    QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples
    Elsevier BV ; 2019
    In:  Molecular Plant Vol. 12, No. 3 ( 2019-03), p. 426-437
    Details
    In: Molecular Plant, Elsevier BV, Vol. 12, No. 3 ( 2019-03), p. 426-437
    Type of Medium: Online Resource
    ISSN: 1674-2052
    URL: Article
    DOI: 10.1016/j.molp.2018.12.018
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
    detail.hit.zdb_id: 2393618-6
    SSG: 12
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