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23. The enhancing effects of selenomethionine on harmine in attenuating pathological cardiac hypertrophy via glycolysis metabolism.

Author

Chen, Qi, Wang, Wen‐Yan, Xu, Qing‐Yang, Dai, Yan‐Fa, Zhu, Xing‐Yu, Chen, Zhao‐Yang, Sun, Ning, Leung, Chung‐Hang, Gao, Fei, and Wu, Ke‐Jia

Subjects
CARDIAC hypertrophy, ENERGY metabolism, CELLULAR signal transduction, GLYCOLYSIS, SELENOMETHIONINE, ANGIOTENSIN II
Abstract

Pathological cardiac hypertrophy, a common feature in various cardiovascular diseases, can be more effectively managed through combination therapies using natural compounds. Harmine, a β‐carboline alkaloid found in plants, possesses numerous pharmacological functions, including alleviating cardiac hypertrophy. Similarly, Selenomethionine (SE), a primary organic selenium source, has been shown to mitigate cardiac autophagy and alleviate injury. To explores the therapeutic potential of combining Harmine with SE to treat cardiac hypertrophy. The synergistic effects of SE and harmine against cardiac hypertrophy were assessed in vitro with angiotensin II (AngII)‐induced hypertrophy and in vivo using a Myh6R404Q mouse model. Co‐administration of SE and harmine significantly reduced hypertrophy‐related markers, outperforming monotherapies. Transcriptomic and metabolic profiling revealed substantial alterations in key metabolic and signalling pathways, particularly those involved in energy metabolism. Notably, the combination therapy led to a marked reduction in the activity of key glycolytic enzymes. Importantly, the addition of the glycolysis inhibitor 2‐deoxy‐D‐glucose (2‐DG) did not further potentiate these effects, suggesting that the antihypertrophic action is predominantly mediated through glycolytic inhibition. These findings highlight the potential of SE and harmine as a promising combination therapy for the treatment of cardiac hypertrophy. [ABSTRACT FROM AUTHOR]

Published
2024
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35. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

Author

Shi, Tian-Le, Jia, Kai-Hua, Bao, Yu-Tao, Nie, Shuai, Tian, Xue-Chan, Yan, Xue-Mei, Chen, Zhao-Yang, Li, Zhi-Chao, Zhao, Shi-Wei, Ma, Hai-Yao, Zhao, Ye, Li, Xiang, Zhang, Ren-Gang, Guo, Jing, Zhao, Wei, El-Kassaby, Yousry Aly, Müller, Niels, Van de Peer, Yves, Wang, Xiao-Ru, Street, Nathaniel Robert, Porth, Ilga, An, Xinmin, Mao, Jian-Feng, Shi, Tian-Le, Jia, Kai-Hua, Bao, Yu-Tao, Nie, Shuai, Tian, Xue-Chan, Yan, Xue-Mei, Chen, Zhao-Yang, Li, Zhi-Chao, Zhao, Shi-Wei, Ma, Hai-Yao, Zhao, Ye, Li, Xiang, Zhang, Ren-Gang, Guo, Jing, Zhao, Wei, El-Kassaby, Yousry Aly, Müller, Niels, Van de Peer, Yves, Wang, Xiao-Ru, Street, Nathaniel Robert, Porth, Ilga, An, Xinmin, and Mao, Jian-Feng

Abstract

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

Published
2024
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36. Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification

Author

Tian, Xue-Chan, Chen, Zhao-Yang, Nie, Shuai, Shi, Tian-Le, Yan, Xue-Mei, Bao, Yu-Tao, Li, Zhi-Chao, Ma, Hai-Yao, Jia, Kai-Hua, Zhao, Wei, Mao, Jian-Feng, Tian, Xue-Chan, Chen, Zhao-Yang, Nie, Shuai, Shi, Tian-Le, Yan, Xue-Mei, Bao, Yu-Tao, Li, Zhi-Chao, Ma, Hai-Yao, Jia, Kai-Hua, Zhao, Wei, and Mao, Jian-Feng

Abstract

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

Published
2024
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37. Advances in Strain‐Induced Noble Metal Nanohybrids for Electro‐Catalysis: From Theoretical Mechanisms to Practical Use.

Author

Chen, Zhao‐Yang, Li, Ling‐Tong, Zhao, Feng‐Ming, Zhu, Ying‐Hong, and Chu, You‐Qun

Subjects
PRECIOUS metals, CLIMATE change mitigation, CARBON offsetting, METAL catalysts, EPITAXY
Abstract

In response to the climate goal of achieving carbon neutrality by 2050, efficient electrochemical energy conversion devices are garnering increasing attention. However, the enhancement of electrochemical performance using noble metal electrocatalysts, along with cost reduction and electrode fabrication, remain significant challenges. Noble metal hybrid nanostructures, possessing multiple surface functionalities, lead to outstanding electrocatalytic performances and low‐cost potential. Strain effects can bolster the bonding strength between the noble metal layers and the substrate or core layers, while simultaneously affecting electrocatalytic performance through tuning the binding strength between catalytically active sites and reactants, including intermediates. This review encapsulates the research efforts directed towards improving the performance of noble metal electrocatalysts and provides an overview of the latest advancements in controlling the surface state of noble metals by incorporating a secondary component. We discuss systematic approaches to adjusting surface strain effects on noble metals, characterization techniques, and application case studies, while extracting key design indicators for readers to consider from a macroscopic perspective. Further, we outline the challenges encountered and current solutions when advancing noble metal catalysts from theoretical mechanisms to practical use. Finally, the perspectives on the future research of noble metal surface layer control techniques were also provided. [ABSTRACT FROM AUTHOR]

Published
2024
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40. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar

Author

Shi, Tian-Le, primary, Jia, Kai-Hua, additional, Bao, Yu-Tao, additional, Nie, Shuai, additional, Tian, Xue-Chan, additional, Yan, Xue-Mei, additional, Chen, Zhao-Yang, additional, Li, Zhi-Chao, additional, Zhao, Shi-Wei, additional, Ma, Hai-Yao, additional, Zhao, Ye, additional, Li, Xiang, additional, Zhang, Ren-Gang, additional, Guo, Jing, additional, Zhao, Wei, additional, El-Kassaby, Yousry Aly, additional, Müller, Niels, additional, Van de Peer, Yves, additional, Wang, Xiao-Ru, additional, Street, Nathaniel Robert, additional, Porth, Ilga, additional, An, Xinmin, additional, and Mao, Jian-Feng, additional

Published
2024
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43. Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values

Author

Shi, Tian-Le, primary, Ma, Hai-Yao, additional, Wang, Xinrui, additional, Liu, Hui, additional, Yan, Xue-Mei, additional, Tian, Xue-Chan, additional, Li, Zhi-Chao, additional, Bao, Yu-Tao, additional, Chen, Zhao-Yang, additional, Zhao, Shi-Wei, additional, Xiang, Qiuhong, additional, Jia, Kai-Hua, additional, Nie, Shuai, additional, Guan, Wenbin, additional, and Mao, Jian-Feng, additional

Published
2024
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