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Start Over Author "Wang Jin" Journal international journal of molecular sciences
234 results on '"Wang Jin"'

2. PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data.

Author

Wang, Jin, Song, Xiangrong, Wei, Meidan, Qin, Lexin, Zhu, Qingyun, Wang, Shujie, Liang, Tingting, Hu, Wentao, Zhu, Xinyu, and Li, Jianxiang

Subjects
*PROTEOMICS, *CANCER research, *MEDICAL research, *DATA analysis, *TRANSCRIPTOMES
Abstract

Proteomics offers a robust method for quantifying proteins and elucidating their roles in cellular functions, surpassing the insights provided by transcriptomics. The Clinical Proteomic Tumor Analysis Consortium database, enriched with comprehensive cancer proteomics data including phosphorylation and ubiquitination profiles, alongside transcriptomics data from the Genomic Data Commons, allow for integrative molecular studies of cancer. The ProteoCancer Analysis Suite (PCAS), our newly developed R package and Shinyapp, leverages these resources to facilitate in-depth analyses of proteomics, phosphoproteomics, and transcriptomics, enhancing our understanding of the tumor microenvironment through features like immune infiltration and drug sensitivity analysis. This tool aids in identifying critical signaling pathways and therapeutic targets, particularly through its detailed phosphoproteomic analysis. To demonstrate the functionality of the PCAS, we conducted an analysis of GAPDH across multiple cancer types, revealing a significant upregulation of protein levels, which is consistent with its important biological and clinical significance in tumors, as indicated in our prior research. Further experiments were used to validate the findings performed using the tool. In conclusion, the PCAS is a powerful and valuable tool for conducting comprehensive proteomic analyses, significantly enhancing our ability to uncover oncogenic mechanisms and identify potential therapeutic targets in cancer research. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Development and Regulation of the Extreme Biofilm Formation of Deinococcus radiodurans R1 under Extreme Environmental Conditions.

Author

Guo, Qiannan, Zhan, Yuhua, Zhang, Wei, Wang, Jin, Yan, Yongliang, Wang, Wenxiu, and Lin, Min

Subjects
DEINOCOCCUS radiodurans, QUORUM sensing, BIOFILMS, EXTREME environments, CARBOHYDRATE metabolism, ULTRAVIOLET radiation, STAPHYLOCOCCUS aureus
Abstract

To grow in various harsh environments, extremophiles have developed extraordinary strategies such as biofilm formation, which is an extremely complex and progressive process. However, the genetic elements and exact mechanisms underlying extreme biofilm formation remain enigmatic. Here, we characterized the biofilm-forming ability of Deinococcus radiodurans in vitro under extreme environmental conditions and found that extremely high concentrations of NaCl or sorbitol could induce biofilm formation. Meantime, the survival ability of biofilm cells was superior to that of planktonic cells in different extreme conditions, such as hydrogen peroxide stress, sorbitol stress, and high UV radiation. Transcriptome profiles of D. radiodurans in four different biofilm development stages further revealed that only 13 matched genes, which are involved in environmental information processing, carbohydrate metabolism, or stress responses, share sequence homology with genes related to the biofilm formation of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Overall, 64% of the differentially expressed genes are functionally unknown, indicating the specificity of the regulatory network of D. radiodurans. The mutation of the drRRA gene encoding a response regulator strongly impaired biofilm formation ability, implying that DrRRA is an essential component of the biofilm formation of D. radiodurans. Furthermore, transcripts from both the wild type and the drRRA mutant were compared, showing that the expression of drBON1 (Deinococcus radioduransBON domain-containing protein 1) significantly decreased in the drRRA mutant during biofilm development. Further analysis revealed that the drBON1 mutant lacked the ability to form biofilm and DrRRA, and as a facilitator of biofilm formation, could directly stimulate the transcription of the biofilm-related gene drBON1. Overall, our work highlights a molecular mechanism mediated by the response regulator DrRRA for controlling extreme biofilm formation and thus provides guidance for future studies to investigate novel mechanisms that are used by D. radiodurans to adapt to extreme environments. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Reprimo (RPRM) as a Potential Preventive and Therapeutic Target for Radiation-Induced Brain Injury via Multiple Mechanisms.

Author

Ye, Zhujing, Wang, Jin, Shi, Wenyu, Zhou, Zhou, Zhang, Yarui, Wang, Jingdong, and Yang, Hongying

Subjects
*BRAIN injuries, *DNA damage, *DNA repair, *BRAIN tumors, *DNA mismatch repair, *TUMOR suppressor genes
Abstract

Patients receiving cranial radiotherapy for primary and metastatic brain tumors may experience radiation-induced brain injury (RIBI). Thus far, there has been a lack of effective preventive and therapeutic strategies for RIBI. Due to its complicated underlying pathogenic mechanisms, it is rather difficult to develop a single approach to target them simultaneously. We have recently reported that Reprimo (RPRM), a tumor suppressor gene, is a critical player in DNA damage repair, and RPRM deletion significantly confers radioresistance to mice. Herein, by using an RPRM knockout (KO) mouse model established in our laboratory, we found that RPRM deletion alleviated RIBI in mice via targeting its multiple underlying mechanisms. Specifically, RPRM knockout significantly reduced hippocampal DNA damage and apoptosis shortly after mice were exposed to whole-brain irradiation (WBI). For the late-delayed effect of WBI, RPRM knockout obviously ameliorated a radiation-induced decline in neurocognitive function and dramatically diminished WBI-induced neurogenesis inhibition. Moreover, RPRM KO mice exhibited a significantly lower level of acute and chronic inflammation response and microglial activation than wild-type (WT) mice post-WBI. Finally, we uncovered that RPRM knockout not only protected microglia against radiation-induced damage, thus preventing microglial activation, but also protected neurons and decreased the induction of CCL2 in neurons after irradiation, in turn attenuating the activation of microglial cells nearby through paracrine CCL2. Taken together, our results indicate that RPRM plays a crucial role in the occurrence of RIBI, suggesting that RPRM may serve as a novel potential target for the prevention and treatment of RIBI. [ABSTRACT FROM AUTHOR]

Published
2023
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13. Functional and Anatomical Outcomes of Anti-Vascular Endothelial Growth Factor Treatment for Exudative Age-Related Macular Degeneration with or without Obstructive Sleep Apnea

Author

Chen, Nan-Ni, primary, Chen, Chau-Yin, additional, Wang, Jin-Jhe, additional, Huang, Heng-Chiao, additional, Chen, Wei-Dar, additional, Chen, Ching-Lung, additional, Yang, Yao-Hsu, additional, Lin, Meng-Hung, additional, Kuo, Ting-Yu, additional, and Lai, Chien-Hsiung, additional

Published
2023
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19. Identification of a Putative SARS-CoV-2 Main Protease Inhibitor through In Silico Screening of Self-Designed Molecular Library.

Author

Liu, Nanxin, Yang, Zeyu, Liu, Yuying, Dang, Xintao, Zhang, Qingqing, Wang, Jin, Liu, Xueying, Zhang, Jie, and Pan, Xiaoyan

Subjects
PROTEASE inhibitors, MEDICAL screening, SARS-CoV-2, SECONDARY amines, DRUG target, VIRAL replication
Abstract

There have been outbreaks of SARS-CoV-2 around the world for over three years, and its variants continue to evolve. This has become a major global health threat. The main protease (Mpro, also called 3CLpro) plays a key role in viral replication and proliferation, making it an attractive drug target. Here, we have identified a novel potential inhibitor of Mpro, by applying the virtual screening of hundreds of nilotinib-structure-like compounds that we designed and synthesized. The screened compounds were assessed using SP docking, XP docking, MM-GBSA analysis, IFD docking, MD simulation, ADME/T prediction, and then an enzymatic assay in vitro. We finally identified the compound V291 as a potential SARS-CoV-2 Mpro inhibitor, with a high docking affinity and enzyme inhibitory activity. Moreover, the docking results indicate that His41 is a favorable amino acid for pi-pi interactions, while Glu166 can participate in salt-bridge formation with the protonated primary or secondary amines in the screened molecules. Thus, the compounds reported here are capable of engaging the key amino acids His41 and Glu166 in ligand-receptor interactions. A pharmacophore analysis further validates this assertion. [ABSTRACT FROM AUTHOR]

Published
2023
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23. Identification of TALE Transcription Factor Family and Expression Patterns Related to Fruit Chloroplast Development in Tomato (Solanum lycopersicum L.)

Author

Wang, Jin, primary, Zhao, Pan, additional, Cheng, Baohui, additional, Zhang, Yanhong, additional, Shen, Yuanbo, additional, Wang, Xinyu, additional, Zhang, Qinghua, additional, Lou, Qianqi, additional, Zhang, Shijie, additional, Wang, Bo, additional, Qi, Shiming, additional, Li, Yushun, additional, Islam, Md. Monirul, additional, Muhammad, Tayeb, additional, Zhang, Fei, additional, and Liang, Yan, additional

Published
2022
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27. Synergistic Effects of Organosilicon and Cu(OH) 2 in Controlling Sugarcane Leaf Scald Disease.

Author

Zhang, Ming-Yang, Hong, Ding-Kai, Chen, Yao-Hui, Gao, San-Ji, Fu, Hua-Ying, Zheng, Hua-Kun, Fang, Yong, and Wang, Jin-Da

Subjects
SUGARCANE, SUGARCANE growing, FEED additives, XANTHOMONAS diseases, BACTERICIDES, PATHOGENIC bacteria
Abstract

Sugarcane leaf scald is a systemic disease caused by Xanthomonas albilineans that limits sugarcane yield and quality. Previous research has shown that exogenous application of copper hydroxide to plants is effective in controlling this disease. However, long-term bactericide use causes serious "3R" problems: resistance, resurgence, and residue. It is therefore urgent to discover new methods for the improvement of bactericide efficiency and efficacy. In the present study, disease index values for leaf scald were measured in sugarcane seedlings over time to determine the effects of different concentrations of copper hydroxide, types of silicon additive, and treatment timing after inoculation with X. albilineans on controlling sugarcane leaf scald disease. Our results show copper hydroxide mixed with organosilicon additive could improve the bactericide efficiency and efficacy and reduce the growth of pathogenic bacteria, even at a reduced concentration in both laboratory and field conditions. This study provides an important practical model for controlling sugarcane leaf scald disease by reducing the concentration of bactericide and increasing its efficacy in sugarcane fields. [ABSTRACT FROM AUTHOR]

Published
2022
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29. The Ubiquitin E3 Ligase MaLUL2 is Involved in High Temperature-Induced Green Ripening in Banana Fruit

Author

Wei Wei, Ze-xiang Zeng, Wei Shan, Jian-fei Kuang, Wang-jin Lu, and Jian-ye Chen

Subjects
0106 biological sciences, 0301 basic medicine, Ubiquitin-Protein Ligases, banana fruit, green ripening, 01 natural sciences, Catalysis, Article, Inorganic Chemistry, high temperature, lcsh:Chemistry, 03 medical and health sciences, chemistry.chemical_compound, Ubiquitin, Protein Domains, Physical and Theoretical Chemistry, Molecular Biology, Gene, lcsh:QH301-705.5, Spectroscopy, Plant Proteins, chemistry.chemical_classification, biology, chlorophyll degradation, Organic Chemistry, food and beverages, Ripening, Musa, General Medicine, Subcellular localization, Computer Science Applications, Cell biology, Amino acid, Ubiquitin ligase, Protein Transport, 030104 developmental biology, chemistry, E3 ubiquitin ligase, lcsh:Biology (General), lcsh:QD1-999, Cytoplasm, Chlorophyll, Fruit, biology.protein, Heat-Shock Response, 010606 plant biology & botany
Abstract

Harvested banana fruit ripened under warm temperatures above 24 &deg, C remain green peel, leading to severe economic loss. E3 ubiquitin-ligases, as the major components in the ubiquitination pathway, have been implicated to play important roles in temperature-stress responses. However, the molecular mechanism underlying high temperature-triggered stay-green ripening bananas in association with E3 ubiquitin-ligases, remains largely unknown. In this study, a RING-type E3 ubiquitin ligase termed MaLUL2, was isolated and characterized from banana fruit. The MaLUL2 gene contains 1095 nucleotides and encodes a protein with 365 amino acids. The MaLUL2 protein contains a domain associated with RING2 (DAR2) and a RING domain, which are the typical characteristics of RING-type E3 ligases. MaLUL2 expression was up-regulated during high temperature-induced green ripening. Subcellular localization showed that MaLUL2 localized in the nucleus, cytoplasm, and plasma membrane. MaLUL2 displayed E3 ubiquitin ligase activity in vitro. More importantly, transient overexpression of MaLUL2 in banana fruit peel increased the level of ubiquitination in vivo and led to a stay-green phenotype, accompanying with decreased expression of chlorophyll catabolic genes. Collectively, these findings suggest that MaLUL2 might act as a negative regulator of chlorophyll degradation and provide novel insights into the regulatory mechanism of high temperature-induced green ripening bananas.

Published
2020

38. RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans

Author

Xue, Dong, primary, Liu, Wenzheng, additional, Chen, Yun, additional, Liu, Yingying, additional, Han, Jiahui, additional, Geng, Xiuxiu, additional, Li, Jiang, additional, Jiang, Shijie, additional, Zhou, Zhengfu, additional, Zhang, Wei, additional, Chen, Ming, additional, Lin, Min, additional, Ongena, Marc, additional, and Wang, Jin, additional

Published
2019
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40. Pitaya HpWRKY3 Is Associated with Fruit Sugar Accumulation by Transcriptionally Modulating Sucrose Metabolic Genes

Author

Wei, Wei, Mei-Nv, Cheng, Liang-Jie, Ba, Run-Xi, Zeng, Dong-Lan, Luo, Yong-Hua, Qin, Zong-Li, Liu, Jian-Fei, Kuang, Wang-Jin, Lu, Jian-Ye, Chen, Xin-Guo, Su, and Wei, Shan

Subjects
Cactaceae, Transcriptional Activation, Sucrose, Gene Expression Regulation, Plant, Fruit, Hydrolysis, fruit quality, sucrose-hydrolyzing enzyme genes, fruit maturation, Genes, Plant, Article, Plant Proteins, Transcription Factors
Abstract

Sugar level is an important determinant of fruit taste and consumer preferences. However, upstream regulators that control sugar accumulation during fruit maturation are poorly understood. In the present work, we found that glucose is the main sugar in mature pitaya (Hylocereus) fruit, followed by fructose and sucrose. Expression levels of two sucrose-hydrolyzing enzyme genes HpINV2 and HpSuSy1 obviously increased during fruit maturation, which were correlated well with the elevated accumulation of glucose and fructose. A WRKY transcription factor HpWRKY3 was further identified as the putative binding protein of the HpINV2 and HpSuSy1 promoters by yeast one-hybrid and gel mobility shift assays. HpWRKY3 was localized exclusively in the nucleus and possessed trans-activation ability. HpWRKY3 exhibited the similar expression pattern with HpINV2 and HpSuSy1. Finally, transient expression assays in tobacco leaves showed that HpWRKY3 activated the expressions of HpINV2 and HpSuSy1. Taken together, we propose that HpWRKY3 is associated with pitaya fruit sugar accumulation by activating the transcriptions of sucrose metabolic genes. Our findings thus shed light on the transcriptional mechanism that regulates the sugar accumulation during pitaya fruit quality formation.

Published
2018

42. Pitaya HpWRKY3 Is Associated with Fruit Sugar Accumulation by Transcriptionally Modulating Sucrose Metabolic Genes HpINV2 and HpSuSy1

Author

Wei, Wei, primary, Cheng, Mei-nv, additional, Ba, Liang-jie, additional, Zeng, Run-xi, additional, Luo, Dong-lan, additional, Qin, Yong-hua, additional, Liu, Zong-li, additional, Kuang, Jian-fei, additional, Lu, Wang-jin, additional, Chen, Jian-ye, additional, Su, Xin-guo, additional, and Shan, Wei, additional

Published
2019
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48. Carbohydrate Stress Affecting Fruitlet Abscission and Expression of Genes Related to Auxin Signal Transduction Pathway in Litchi

Author

Jianguo Li, Caiqin Li, Wang-jin Lu, Jian-ye Chen, Hai-Ying Zhong, Jian-Yang Wu, and Jian-fei Kuang

Subjects
fruitlet abscission, Biology, auxin responsive genes, Catalysis, Article, Inorganic Chemistry, lcsh:Chemistry, Abscission, Litchi, Auxin, Gene Expression Regulation, Plant, Stress, Physiological, Gene expression, Transcriptional regulation, heterocyclic compounds, Physical and Theoretical Chemistry, Molecular Biology, Gene, lcsh:QH301-705.5, Spectroscopy, auxin response factor, Plant Proteins, chemistry.chemical_classification, Regulation of gene expression, clone, Litchi chinensis Sonn, gene expression, carbohydrate stress, Indoleacetic Acids, Organic Chemistry, food and beverages, General Medicine, biology.organism_classification, Computer Science Applications, chemistry, Biochemistry, Fruit abscission, lcsh:Biology (General), lcsh:QD1-999, Plant hormone, Signal Transduction
Abstract

Auxin, a vital plant hormone, regulates a variety of physiological and developmental processes. It is involved in fruit abscission through transcriptional regulation of many auxin-related genes, including early auxin responsive genes (i.e., auxin/indole-3-acetic acid (AUX/IAA), Gretchen Hagen3 (GH3) and small auxin upregulated (SAUR)) and auxin response factors (ARF), which have been well characterized in many plants. In this study, totally five auxin-related genes, including one AUX/IAA (LcAUX/IAA1), one GH3 (LcGH3.1), one SAUR (LcSAUR1) and two ARFs (LcARF1 and LcARF2), were isolated and characterized from litchi fruit. LcAUX/IAA1, LcGH3.1, LcSAUR1, LcARF1 and LcARF2 contain open reading frames (ORFs) encoding polypeptides of 203, 613, 142, 792 and 832 amino acids, respectively, with their corresponding molecular weights of 22.67, 69.20, 11.40, 88.20 and 93.16 kDa. Expression of these genes was investigated under the treatment of girdling plus defoliation which aggravated litchi fruitlet abscission due to the blockage of carbohydrates transport and the reduction of endogenous IAA content. Results showed that transcript levels of LcAUX/IAA1, LcGH3.1 and LcSAUR1 mRNAs were increased after the treatment in abscission zone (AZ) and other tissues, in contrast to the decreasing accumulation of LcARF1 mRNA, suggesting that LcAUX/IAA1, LcSAUR1 and LcARF1 may play more important roles in abscission. Our results provide new insight into the process of fruitlet abscission induced by carbohydrate stress and broaden our understanding of the auxin signal transduction pathway in this process at the molecular level.

Published
2012

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