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  • 1
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 19 ( 2012-05-08)
    Abstract: Overall, our study has revealed a potentially widely conserved mechanism, i.e., one maintained across a range of species (from rice to Arabidopsis ), by which flowering plants adjust growth rates, presumably to accommodate increased energy demand during defense against insect and pathogen attacks. Understanding this mechanism may lead to innovative methods to lessen the growth/defense conflict in crop plants so yields and defense against stresses can be augmented at the same time in agriculture. A recent report shows that several JAZ repressors physically interact with DELLA proteins in Arabidopsis ( 5 ). Hou et al. studied how gibberellin antagonizes JA signaling, providing evidence that gibberellin could inhibit JA signaling through DELLA-mediated interference with the JAZ–MYC2 interaction ( 5 ). We also observed multiple JAZ–DELLA interactions based on a number of plant- or yeast-based assays. Most strikingly, in our study, we found that the ability of JAZ overexpression (a procedure that mimics coi1 mutations) to confer gibberellin hypersensitivity-like phenotypes was correlated with the ability of specific JAZ proteins to physically interact with DELLA proteins. Because DELLA proteins physically interact and repress growth-promoting transcription factors, such as the PIF-family proteins in Arabidopsis ( 4 ), we investigated the possibility that JAZ repressors may impede the DELLA–PIF interaction. Indeed, we found that JAZ9 could effectively inhibit PIF3 interaction with RGA in yeast and plant cells. Furthermore, overexpression of PIF3 alone was sufficient to partially counter JA-induced inhibition of hypocotyl growth, whereas the pif quadruple mutant ( pifq ) was no longer able to respond to JA-mediated inhibition of hypocotyl growth. Thus, JAZ repressors interfere with one of the most important steps in gibberellin signaling: the DELLA–PIF interaction. How does removal of the JA receptor COI1 potentiate gibberellin signaling? Because the stability of DELLA repressors is the key to gibberellin signaling ( 4 ) ( Fig. P1 ), we investigated the level of the DELLA repressors (SLR1 in rice and RGA in Arabidopsis ) in coi1 mutants and/or in response to JA treatment. We found that, in rice, the SLR1 level was significantly lower in the absence of COI1. Conversely, JA treatment increased DELLA protein levels and slowed gibberellin-induced DELLA degradation. These results suggest that activation of JA signaling stabilizes DELLA repressors. Our study began with the observation that, when the two COI1 genes were silenced in rice (a model crop plant), the plants exhibited several hallmark phenotypes of gibberellin hypersensitivity, including increased height, elongated internodes, faster germination, and hypersensitivity to exogenous gibberellin. Furthermore, we found that the gibberellin receptor GID1 is required for the gibberellin hypersensitivity of COI1 -silenced rice plants. Similarly, coi1 mutants in Arabidopsis , another common experimental plant, exhibit several phenotypes that resemble gibberellin hypersensitivity, including elongated petioles (i.e., stalks attaching leaf blades to the stem) and hypocotyls (i.e., stems of germinating seedlings) and early flowering. Collectively, these results suggest that removal of the JA receptor COI1 enhances gibberellin signaling in both monocot (i.e., rice) and dicot (i.e., Arabidopsis ) plants. JA defense signaling requires the coronatine insensitive 1 (COI1)–JA ZIM domain (JAZ)–MYC core signaling module. The COI1 protein is a substrate-recognition component of an E3 ubiquitin ligase, which adds a ubiquitin molecule to specific substrate proteins. Ubiquitin-tagged proteins are subsequently degraded by the proteasome, a major protein-degradation nanomachine in eukaryotic cells. Recent studies show that COI1 is a principal component of a receptor for JA, and that the JAZ-family transcriptional repressor proteins are the substrate proteins of the COI-associated E3 ubiquitin ligase ( Fig. P1 ). At rest, JAZ proteins repress the transcription of JA-responsive genes through direct interaction with defense-associated transcription factors, such as MYC2 ( 1 , 2 ). Bioactive JA promotes physical interaction between the COI1 protein and JAZ proteins, which results in the degradation of JAZs, thereby initiating JA responses. In an analogous signaling cascade, active gibberellin binds to the GID1 receptor, which, in turn, interacts with the DELLA family transcriptional repressors ( 3 , 4 ). The DELLA repressors are recognized and ubiquitinated by the SLY1-associated E3 ubiquitin ligase, leading to degradation of DELLA proteins through the proteasome. Degradation of DELLA repressors relieves the DELLA-imposed repression of downstream transcription factors, including phytochrome interacting factors (PIFs), thereby activating gibberellin responses ( 4 ). Organisms must effectively defend against biotic and abiotic stresses to survive in nature. However, this defense is costly, and, to efficiently allocate limited energy resources, organisms often slow down growth during defense activation. The coordination of this tradeoff is not well understood, however. In plants, hormones called gibberellin and jasmonate (JA) are essential for regulating growth and defense against stresses, respectively. Activation of JA defense signaling is associated with significant growth inhibition. In this study, we elucidated a potentially widespread molecular mechanism by which flowering plants prioritize JA-mediated defense over growth.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
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  • 2
    In: The Plant Journal, Wiley, Vol. 83, No. 4 ( 2015-08), p. 600-609
    Abstract: This study reports the genome of “Jiaobai”, a unique crop species domesticated from wild Zizania latifolia (Oryzeae) as a consequence of persistent infection by a fungal endophyte. Cultivated Z. latifolia (‘Jiaobai’) has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia , showing that continuous long‐standing endophyte association can have a major effect on the evolution of the host genome.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2015
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  • 3
    Online Resource
    Online Resource
    Georg Thieme Verlag KG ; 2009
    In:  Planta Medica Vol. 75, No. 04 ( 2009-3), p. 302-306
    In: Planta Medica, Georg Thieme Verlag KG, Vol. 75, No. 04 ( 2009-3), p. 302-306
    Type of Medium: Online Resource
    ISSN: 0032-0943 , 1439-0221
    Language: English
    Publisher: Georg Thieme Verlag KG
    Publication Date: 2009
    detail.hit.zdb_id: 2037089-1
    SSG: 15,3
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  • 4
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 44 ( 2014-11-04)
    Abstract: Antrodia cinnamomea , a polyporus mushroom of Taiwan, has long been used as a remedy for cancer, hypertension, and hangover, with an annual market of over $100 million (US) in Taiwan. We obtained a 32.15-Mb genome draft containing 9,254 genes. Genome ontology enrichment and pathway analyses shed light on sexual development and the biosynthesis of sesquiterpenoids, triterpenoids, ergostanes, antroquinonol, and antrocamphin. We identified genes differentially expressed between mycelium and fruiting body and 242 proteins in the mevalonate pathway, terpenoid pathways, cytochrome P450s, and polyketide synthases, which may contribute to the production of medicinal secondary metabolites. Genes of secondary metabolite biosynthetic pathways showed expression enrichment for tissue-specific compounds, including 14-α-demethylase (CYP51F1) in fruiting body for converting lanostane to ergostane triterpenoids, coenzymes Q (COQ) for antroquinonol biosynthesis in mycelium, and polyketide synthase for antrocamphin biosynthesis in fruiting body. Our data will be useful for developing a strategy to increase the production of useful metabolites.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 5
    In: New Phytologist, Wiley, Vol. 236, No. 4 ( 2022-11), p. 1422-1440
    Abstract: Rice false smut caused by Ustilaginoidea virens is becoming one of the most recalcitrant rice diseases worldwide. However, the molecular mechanisms underlying rice immunity against U. virens remain unknown. Using genetic, biochemical and disease resistance assays, we demonstrated that the xb24 knockout lines generated in non‐ Xa21 rice background exhibit an enhanced susceptibility to the fungal pathogens U. virens and Magnaporthe oryzae . Consistently, flg22‐ and chitin‐induced oxidative burst and expression of pathogenesis‐related genes in the xb24 knockout lines were greatly attenuated. As a central mediator of energy signaling, SnRK1A interacts with and phosphorylates XB24 at Thr83 residue to promote ATPase activity. SnRK1A is activated by pathogen‐associated molecular patterns and positively regulates plant immune responses and disease resistance. Furthermore, the virulence effector SCRE1 in U. virens targets host ATPase XB24. The interaction inhibits ATPase activity of XB24 by blocking ATP binding to XB24. Meanwhile, SCRE1 outcompetes SnRK1A for XB24 binding, and thereby suppresses SnRK1A‐mediated phosphorylation and ATPase activity of XB24. Our results indicate that the conserved SnRK1A‐XB24 module in multiple crop plants positively contributes to plant immunity and uncover an unidentified molecular strategy to promote infection in U. virens and a novel host target in fungal pathogenesis.
    Type of Medium: Online Resource
    ISSN: 0028-646X , 1469-8137
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
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    detail.hit.zdb_id: 1472194-6
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  • 6
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2016
    In:  Proceedings of the National Academy of Sciences Vol. 113, No. 45 ( 2016-11-08), p. 12850-12855
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 113, No. 45 ( 2016-11-08), p. 12850-12855
    Abstract: Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most devastating insect pests of rice ( Oryza sativa L.). Currently, 30 BPH-resistance genes have been genetically defined, most of which are clustered on specific chromosome regions. Here, we describe molecular cloning and characterization of a BPH-resistance gene, BPH9 , mapped on the long arm of rice chromosome 12 (12L). BPH9 encodes a rare type of nucleotide-binding and leucine-rich repeat (NLR)-containing protein that localizes to the endomembrane system and causes a cell death phenotype. BPH9 activates salicylic acid- and jasmonic acid-signaling pathways in rice plants and confers both antixenosis and antibiosis to BPH. We further demonstrated that the eight BPH-resistance genes that are clustered on chromosome 12L, including the widely used BPH1 , are allelic with each other. To honor the priority in the literature, we thus designated this locus as BPH1/9 . These eight genes can be classified into four allelotypes, BPH1/9-1 , -2 , -7 , and -9 . These allelotypes confer varying levels of resistance to different biotypes of BPH. The coding region of BPH1/9 shows a high level of diversity in rice germplasm. Homologous fragments of the nucleotide-binding (NB) and leucine-rich repeat (LRR) domains exist, which might have served as a repository for generating allele diversity. Our findings reveal a rice plant strategy for modifying the genetic information to gain the upper hand in the struggle against insect herbivores. Further exploration of natural allelic variation and artificial shuffling within this gene may allow breeding to be tailored to control emerging biotypes of BPH.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2016
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    detail.hit.zdb_id: 1461794-8
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  • 7
    In: Journal of Natural Products, American Chemical Society (ACS), Vol. 77, No. 11 ( 2014-11-26), p. 2367-2374
    Type of Medium: Online Resource
    ISSN: 0163-3864 , 1520-6025
    RVK:
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2014
    detail.hit.zdb_id: 1491522-4
    SSG: 12
    SSG: 15,3
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  • 8
    In: Phytochemistry Letters, Elsevier BV, Vol. 6, No. 3 ( 2013-8), p. 379-382
    Type of Medium: Online Resource
    ISSN: 1874-3900
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2013
    detail.hit.zdb_id: 2425258-X
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    IOP Publishing ; 2023
    In:  Physics in Medicine & Biology Vol. 68, No. 18 ( 2023-09-21), p. 185025-
    In: Physics in Medicine & Biology, IOP Publishing, Vol. 68, No. 18 ( 2023-09-21), p. 185025-
    Abstract: Objective. To develop a deep ensemble learning (DEL) model with radiomics spatial encoding execution for improved glioma segmentation accuracy using multi-parametric magnetic resonance imaging (mp-MRI). Approach. This model was developed using 369 glioma patients with a four-modality mp-MRI protocol: T1, contrast-enhanced T1 (T1-Ce), T2, and FLAIR. In each modality volume, a 3D sliding kernel was implemented across the brain to capture image heterogeneity: 56 radiomic features were extracted within the kernel, resulting in a fourth-order tensor. Each radiomic feature can then be encoded as a 3D image volume, namely a radiomic feature map (RFM). For each patient, all RFMs extracted from all four modalities were processed using principal component analysis for dimension reduction, and the first four principal components (PCs) were selected. Next, a DEL model comprised of four U-Net sub-models was trained for the segmentation of a region-of-interest: each sub-model utilizes the mp-MRI and one of the four PCs as a five-channel input for 2D execution. Last, four softmax probability results given by the DEL model were superimposed and binarized using Otsu’s method as the segmentation results. Three DEL models were trained to segment the enhancing tumor (ET), tumor core (TC), and whole tumor (WT), respectively. The segmentation results given by the proposed ensemble were compared to the mp-MRI-only U-Net results. Main Results. All three radiomics-incorporated DEL models were successfully implemented: compared to the mp-MRI-only U-net results, the dice coefficients of ET (0.777 → 0.817), TC (0.742 → 0.757), and WT (0.823 → 0.854) demonstrated improvement. The accuracy, sensitivity, and specificity results demonstrated similar patterns. Significance. The adopted radiomics spatial encoding execution enriches the image heterogeneity information that leads to the successful demonstration of the proposed DEL model, which offers a new tool for mp-MRI-based medical image segmentation.
    Type of Medium: Online Resource
    ISSN: 0031-9155 , 1361-6560
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    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2023
    detail.hit.zdb_id: 1473501-5
    SSG: 12
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  • 10
    In: Gene, Elsevier BV, Vol. 816 ( 2022-03), p. 146172-
    Type of Medium: Online Resource
    ISSN: 0378-1119
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 1491012-3
    SSG: 12
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