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  1. Article ; Online: RiceProteomeDB (RPDB): a user-friendly database for proteomics data storage, retrieval, and analysis.

    Woo, Dong U / Lee, Yejin / Min, Cheol Woo / Kim, Sun Tae / Kang, Yang Jae

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 3671

    Abstract: Rice, feeding a significant portion of the world, poses unique proteomic challenges critical to agricultural research and global food security. The complexity of the rice proteome, influenced by various genetic and environmental factors, demands ... ...

    Abstract Rice, feeding a significant portion of the world, poses unique proteomic challenges critical to agricultural research and global food security. The complexity of the rice proteome, influenced by various genetic and environmental factors, demands specialized analytical approaches for effective study. The central challenges in rice proteomics lie in developing custom methods suited to the unique aspects of rice biology. These include data preprocessing, method selection, and result validation, all of which are essential for advancing rice research. Our aim is to decode these proteomic intricacies to facilitate breakthroughs in strain improvement, disease resistance, and yield optimization, all vital for combating global food insecurity. To achieve this, we have created the RiceProteomeDB (RPDB), a React + Django database, offering a streamlined and comprehensive platform for the analysis of rice proteomics data. RiceProteomeDB (RPDB) simplifies proteomics data management and analysis. It offers features for data organization, preprocessing, method selection, result validation, and data sharing. Researchers can access processed rice proteomics data, conduct analyses, and explore experimental conditions. The user-friendly web interface enhances navigation and interaction. RPDB fosters collaboration by enabling data sharing and proper acknowledgment of sources, contributing to proteomics research and knowledge dissemination. Availability and implementation: Web application: http://riceproteome.plantprofile.net/ . The web application's source code, user's manual, and sample data: https://github.com/dongu7610/Riceproteome .
    MeSH term(s) Proteomics/methods ; Data Management ; Software ; Databases, Factual ; Information Storage and Retrieval ; Oryza
    Language English
    Publishing date 2024-02-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-54151-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Dataset on post-translational modifications proteome analysis of MSP1-overexpressing rice leaf proteins

    Lee, Gi Hyun / Min, Cheol Woo / Jang, Jeong Woo / Gupta, Ravi / Kim, Sun Tae

    Data in Brief. 2023 Sept. 13, p. 109573

    2023  , Page(s) 109573

    Abstract: The data reported here are associated with the article entitled “Analysis of Post-Translational Modification Dynamics Unveiled Novel Insights into Rice Responses to MSP1” [1]. pathogen-associated molecular pattern (PAMP) -triggered immunity (PTI) serves ... ...

    Abstract The data reported here are associated with the article entitled “Analysis of Post-Translational Modification Dynamics Unveiled Novel Insights into Rice Responses to MSP1” [1]. pathogen-associated molecular pattern (PAMP) -triggered immunity (PTI) serves as the fundamental defense mechanism in plants, providing innate protection against pathogen invasion. The fungus Magnaporthe oryzae (M. oryzae) secretes MSP1, a protein recognized as a PAMP that induces PTI responses in rice. However, the comprehensive characterization of MSP1-induced post-translational modifications (PTMs) and their contribution to PTI responses remains elusive thus far. In this manuscript, we report the analysis of the phosphoproteome, ubiquitinome, and acetylproteome to investigate the alterations in MSP1-induced changes in these PTMs in MSP1 overexpressed and wild-type rice, utilizing the QExactiveᵀᴹ Orbitrap High-Resolution Mass Spectrometer [1]. Our data primarily focuses on unraveling the PTMs of MSP1-overexpressing transgenic rice, with the goal of elucidating MSP1-induced signaling cascades and deciphering their regulatory mechanisms.
    Keywords Magnaporthe oryzae ; data collection ; fungi ; genetically modified organisms ; immunity ; leaves ; pathogen-associated molecular patterns ; pathogens ; phosphoproteome ; post-translational modification ; rice ; spectrometers ; Post-Translational Modifications ; Rice blast disease ; Plant-pathogen interaction ; Proteomics
    Language English
    Dates of publication 2023-0913
    Size p. 109573
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note Pre-press version
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2023.109573
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Label-free proteome data of susceptible and resistant rice cultivars in response to

    Gupta, Ravi / Min, Cheol Woo / Park, Sang-Ryeol / Kim, Sun Tae

    Data in brief

    2022  Volume 41, Page(s) 107890

    Abstract: Here we report the data associated with the article: "Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense ... ...

    Abstract Here we report the data associated with the article: "Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against
    Language English
    Publishing date 2022-02-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2022.107890
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Dataset on post-translational modifications proteome analysis of MSP1-overexpressing rice leaf proteins.

    Lee, Gi Hyun / Min, Cheol Woo / Jang, Jeong Woo / Gupta, Ravi / Kim, Sun Tae

    Data in brief

    2023  Volume 50, Page(s) 109573

    Abstract: The data reported here are associated with the article entitled "Analysis of Post-Translational Modification Dynamics Unveiled Novel Insights into Rice Responses to MSP1" [1]. pathogen-associated molecular pattern (PAMP) -triggered immunity (PTI) serves ... ...

    Abstract The data reported here are associated with the article entitled "Analysis of Post-Translational Modification Dynamics Unveiled Novel Insights into Rice Responses to MSP1" [1]. pathogen-associated molecular pattern (PAMP) -triggered immunity (PTI) serves as the fundamental defense mechanism in plants, providing innate protection against pathogen invasion. The fungus
    Language English
    Publishing date 2023-09-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2023.109573
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Label-free proteome data of susceptible and resistant rice cultivars in response to Xanthomonas oryzae pv. oryzae inoculation

    Gupta, Ravi / Min, Cheol Woo / Park, Sang-Ryeol / Kim, Sun Tae

    Data in Brief. 2022 Apr., v. 41

    2022  

    Abstract: Here we report the data associated with the article: “Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against Xanthomonas oryzae pv. oryzae” [1]. Bacterial blight disease caused ... ...

    Abstract Here we report the data associated with the article: “Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against Xanthomonas oryzae pv. oryzae” [1]. Bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice across the globe; however, the underlying molecular mechanism of rice-Xoo interaction is currently not well understood. In this manuscript, we report the proteome profiles of rice leaves generated using a label-free quantitative proteomic analysis using QExactive™ Orbitrap High-Resolution Mass Spectrometer, MapMan, and rice interactome viewer [1].
    Keywords Xanthomonas oryzae pv. oryzae ; arginase ; blight ; cultivars ; proteome ; proteomics ; rice ; spectrometers
    Language English
    Dates of publication 2022-04
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 2786545-9
    ISSN 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2022.107890
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: TMT-based quantitative proteome data of MSP1 overexpressed rice.

    Min, Cheol Woo / Jang, Jeong Woo / Lee, Gi Hyun / Gupta, Ravi / Kim, Sun Tae

    Data in brief

    2022  Volume 46, Page(s) 108791

    Abstract: Data reported here is associated with the article entitled "TMT-based quantitative membrane proteomics identified pattern recognition receptors (PRRs) potentially involved in the perception of MSP1 in rice leaves" [1]. PAMP-triggered immunity (PTI) ... ...

    Abstract Data reported here is associated with the article entitled "TMT-based quantitative membrane proteomics identified pattern recognition receptors (PRRs) potentially involved in the perception of MSP1 in rice leaves" [1]. PAMP-triggered immunity (PTI) constitutes the first layer of plant innate immunity against pathogen infection.
    Language English
    Publishing date 2022-11-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2022.108791
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Examining the Effect of

    Shibato, Junko / Takenoya, Fumiko / Kimura, Ai / Min, Cheol Woo / Yamashita, Michio / Gupta, Ravi / Kim, Sun Tae / Rakwal, Randeep / Shioda, Seiji

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 4

    Abstract: The biological and psychological importance of hair is recognized worldwide. Molecules that can promote the activation of hair follicle stem cells and the initiation of the growth phase have been subjects of research. Clarifying how hair regeneration is ... ...

    Abstract The biological and psychological importance of hair is recognized worldwide. Molecules that can promote the activation of hair follicle stem cells and the initiation of the growth phase have been subjects of research. Clarifying how hair regeneration is regulated may help to provide hair loss treatments, including cosmetic and even psychological interventions. We examined the hair-growing effects of a cell extract (CE) obtained from cactus
    MeSH term(s) Mice ; Animals ; Cell Extracts/pharmacology ; Plant Extracts/chemistry ; Mice, Inbred C57BL ; Hair ; Hair Follicle/metabolism
    Chemical Substances Cell Extracts ; Plant Extracts
    Language English
    Publishing date 2023-02-06
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28041565
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.MO 81: Show issues

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  8. Article: Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development.

    Yoon, Jinmi / Min, Cheol Woo / Kim, Jiyoung / Baek, Gibeom / Kim, Dohyeon / Jang, Jeong Woo / Gupta, Ravi / Kim, Sun Tae / Cho, Lae-Hyeon

    Plants (Basel, Switzerland)

    2023  Volume 12, Issue 21

    Abstract: Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT ... ...

    Abstract Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and
    Language English
    Publishing date 2023-10-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants12213715
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The Phytophthora nucleolar effector Pi23226 targets host ribosome biogenesis to induce necrotrophic cell death.

    Lee, Soeui / Kim, Jaehwan / Kim, Myung-Shin / Min, Cheol Woo / Kim, Sun Tae / Choi, Sang-Bong / Lee, Joo Hyun / Choi, Doil

    Plant communications

    2023  Volume 4, Issue 5, Page(s) 100606

    Abstract: Pathogen effectors target diverse subcellular organelles to manipulate the plant immune system. Although the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus, the roles of nucleolar-targeted effectors remain ... ...

    Abstract Pathogen effectors target diverse subcellular organelles to manipulate the plant immune system. Although the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus, the roles of nucleolar-targeted effectors remain elusive. In this study, we showed that Phytophthora infestans infection of Nicotiana benthamiana results in nucleolar inflation during the transition from the biotrophic to the necrotrophic phase. Multiple P. infestans effectors were localized in the nucleolus: Pi23226 induced cell death in N. benthamiana and nucleolar inflation similar to that observed in the necrotrophic stage of infection, whereas its homolog Pi23015 and a deletion mutant (Pi23226ΔC) did not induce cell death or affect nucleolar size. RNA immunoprecipitation and individual-nucleotide-resolution UV crosslinking and immunoprecipitation sequencing analysis indicated that Pi23226 bound to the 3' end of 25S rRNA precursors, resulting in accumulation of unprocessed 27S pre-rRNAs. The nucleolar stress marker NAC082 was strongly upregulated under Pi23226-expressing conditions. Pi23226 subsequently inhibited global protein translation in host cells by interacting with ribosomes. Pi23226 enhanced P. infestans pathogenicity, indicating that Pi23226-induced ribosome malfunction and cell death were beneficial for pathogenesis in the host. Our results provide evidence for the molecular mechanism underlying RNA-binding effector activity in host ribosome biogenesis and lead to new insights into the nucleolar action of effectors in pathogenesis.
    MeSH term(s) Cell Nucleolus/genetics ; Cell Nucleolus/metabolism ; Cell Death ; Ribosomes ; Nicotiana/genetics ; Nicotiana/metabolism ; Phytophthora infestans
    Language English
    Publishing date 2023-04-23
    Publishing country China
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2590-3462
    ISSN (online) 2590-3462
    DOI 10.1016/j.xplc.2023.100606
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Integrated "-omics" analysis highlights the role of brassinosteroid signaling and antioxidant machinery underlying improved rice seed longevity during artificial aging treatment.

    Gupta, Ravi / Min, Cheol Woo / Cho, Jun-Hyeon / Jung, Ju-Young / Jeon, Jong-Seong / Kim, Ye Jin / Kim, Jae Kwang / Kim, Sun Tae

    Plant physiology and biochemistry : PPB

    2023  Volume 206, Page(s) 108308

    Abstract: Seed longevity is a critical characteristic in agriculture, yet the specific genes/proteins responsible for this trait and the molecular mechanisms underlying reduced longevity during seed aging remain largely elusive. Here we report the comparative ... ...

    Abstract Seed longevity is a critical characteristic in agriculture, yet the specific genes/proteins responsible for this trait and the molecular mechanisms underlying reduced longevity during seed aging remain largely elusive. Here we report the comparative proteome and metabolome profiling of three rice cultivars exhibiting varying degrees of aging tolerance: Dharial, an aging-tolerant cultivar; Ilmi, an aging-sensitive cultivar; and A2, a moderately aging-tolerant cultivar developed from the crossbreeding of Dharial and Ilmi. Artificial aging treatment (AAT) markedly reduced the germination percentage and enhanced the activities of antioxidant enzymes in all the cultivars. Further, proteomics results showed a key role of the ubiquitin (Ub)-proteasome pathway in the degradation of damaged proteins during AAT while other proteases were majorly reduced. In addition, proteins associated with energy production and protein synthesis were strongly reduced in Ilmi while these were majorly increased in A2 and Dharial. These, along with metabolomics results, suggest that Ub-proteasome mediated protein degradation during AAT results in the accumulation of free amino acids in Ilmi while tolerant cultivars potentially utilize those for energy production and synthesis of stress-related proteins, especially hsp20/alpha-crystallin family protein. Additionally, both Dharial and A2 seem to activate brassinosteroid signaling and suppress jasmonate signaling which initiates a signaling cascade that allows accumulation of enzymatic and non-enzymatic antioxidants for efficient detoxification of aging-induced ROS. Taken together, these results provide an in-depth understanding of the aging-induced changes in rice seeds and highlight key pathways responsible for maintaining seed longevity during AAT.
    MeSH term(s) Antioxidants/metabolism ; Brassinosteroids/metabolism ; Germination ; Oryza/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Seeds/metabolism
    Chemical Substances Antioxidants ; Brassinosteroids ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2023-12-23
    Publishing country France
    Document type Journal Article
    ZDB-ID 742978-2
    ISSN 1873-2690 ; 0981-9428
    ISSN (online) 1873-2690
    ISSN 0981-9428
    DOI 10.1016/j.plaphy.2023.108308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 2696: Show issues
    Z 2005/727: Show issues

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