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Phylogenomics, divergence times and notes of orders in Basidiomycota

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  1. Article

    Open Access

    LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA

    Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, po...

    **ao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich in Genome Biology (2024)

  2. Article

    Open Access

    Revealing critical mechanisms in determining sorghum resistance to drought and salt using mRNA, small RNA and degradome sequencing

    Plant growth and development are severely threatened by drought and salt stresses. Compared with structural genes, transcription factors (TFs) play more pivotal roles in plant growth and stress adaptation. How...

    Qiong Li, Jibin Wang, Qian Liu, Junhan Zhang, **nlei Zhu, Yinpeng Hua in BMC Plant Biology (2024)

  3. Article

    Open Access

    DDRGK1-mediated ER-phagy attenuates acute kidney injury through ER-stress and apoptosis

    Acute kidney injury (AKI) constitutes a prevalent clinical syndrome characterized by elevated morbidity and mortality rates, emerging as a significant public health issue. This study investigates the interplay...

    Haijiao **, Yuanting Yang, Xuying Zhu, Yin Zhou, Yao Xu, Jialin Li in Cell Death & Disease (2024)

  4. Article

    Open Access

    Comprehensive analysis of the UDP-glucuronate decarboxylase (UXS) gene family in tobacco and functional characterization of NtUXS16 in Golgi apparatus in Arabidopsis

    UDP-glucuronate decarboxylase (also named UXS) converts UDP-glucuronic acid (UDP-GlcA) to UDP-xylose (UDP-Xyl) by decarboxylation of the C6-carboxylic acid of glucuronic acid. UDP-Xyl is an important sugar don...

    Zhimin Li, Run** Chen, Yufang Wen, Hanxiang Liu, Yangyang Chen in BMC Plant Biology (2023)

  5. Article

    Open Access

    Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes

    Lauraceae is well known for its significant phylogenetic position as well as important economic and ornamental value; however, most evergreen species in Lauraceae are restricted to tropical regions. In contras...

    Danqing Li, Han-Yang Lin, **uyun Wang, Bo Bi, Yuan Gao, Lingmei Shao in BMC Biology (2023)

  6. Article

    Open Access

    XrvB regulates the type III secretion system by directly repressing hrpG transcription in Xanthomonas oryzae pv. oryzicola

    Xrv proteins are a group of regulators in Xanthomonas spp., belonging to the histone-like nucleoid-structuring (H-NS) proteins of Gram-negative bacteria. The rice bacterial leaf streak pathogen Xanthomonas oryzae

    Jian-Ling Peng, Jia-Feng Shi, Zeng-Feng Ma, **ao-Long Zhou in Phytopathology Research (2023)

  7. Article

    Open Access

    Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere

    Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecos...

    Chenshuo Lin, Li-Juan Li, Kexin Ren, Shu-Yi-Dan Zhou, Alain Isabwe in ISME Communications (2023)

  8. Article

    Open Access

    SRSF3/AMOTL1 splicing axis promotes the tumorigenesis of nasopharyngeal carcinoma through regulating the nucleus translocation of YAP1

    Dysregulation of serine/arginine splicing factors (SRSFs) and abnormal alternative splicing (AS) have been widely implicated in various cancers but scarcely investigated in nasopharyngeal carcinoma (NPC). Here...

    **ao-Chen Xu, Jia-**n Jiang, Ya-Qing Zhou, Shuai He, Yang Liu in Cell Death & Disease (2023)

  9. Article

    Open Access

    Exosomal PGAM1 promotes prostate cancer angiogenesis and metastasis by interacting with ACTG1

    Tumor-derived exosomes and their contents promote cancer metastasis. Phosphoglycerate mutase 1 (PGAM1) is involved in various cancer-related processes. Nevertheless, the underlying mechanism of exosomal PGAM1 ...

    Jun-qi Luo, Tao-wei Yang, Jun Wu, Hou-hua Lai, Li-bin Zou in Cell Death & Disease (2023)

  10. Article

    Open Access

    Large yellow croaker (Larimichthys crocea) mitofusin 2 inhibits type I IFN responses by degrading MAVS via enhanced K48-linked ubiquitination

    In mammals, mitofusin 2 (MFN2) is involved in mitochondrial fusion, and suppresses the virus-induced RIG-I-like receptor (RLR) signaling pathway. However, little is known about the function of MFN2 in non-mamm...

    Wen-**ng Li, **ao-Hong Wang, Yi-Jun Lin, Yuan-Yuan Zhou in Marine Life Science & Technology (2023)

  11. Article

    Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions

    Protein-biomolecule interactions play pivotal roles in almost all biological processes. For a biomolecule of interest, the identification of the interacting protein(s) is essential. For this need, although man...

    He-Wei Jiang, Hong Chen, Yun-**ao Zheng, Xue-Ning Wang in Science China Life Sciences (2023)

  12. Article

    Open Access

    P38-DAPK1 axis regulated LC3-associated phagocytosis (LAP) of microglia in an in vitro subarachnoid hemorrhage model

    The phagocytosis and homeostasis of microglia play an important role in promoting blood clearance and improving prognosis after subarachnoid hemorrhage (SAH). LC3-assocaited phagocytosis (LAP) contributes to t...

    **ang-**n Chen, Tao Tao, Xun-Zhi Liu, Wei Wu in Cell Communication and Signaling (2023)

  13. Article

    Open Access

    E-GWAS: an ensemble-like GWAS strategy that provides effective control over false positive rates without decreasing true positives

    Genome-wide association studies (GWAS) are an effective way to explore genotype–phenotype associations in humans, animals, and plants. Various GWAS methods have been developed based on different genetic or sta...

    Guang-Liang Zhou, Fang-Jun Xu, Jia-Kun Qiao, Zhao-Xuan Che in Genetics Selection Evolution (2023)

  14. Article

    Biomarkers of aging

    Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although ...

    Hainan Bao, Jiani Cao, Mengting Chen, Min Chen, Wei Chen in Science China Life Sciences (2023)

  15. Article

    Open Access

    Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice

    In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pat...

    Fu Guo, Hua Wang, Guiwei Lian, Gui Cai, Wu Liu, Haidao Zhang in Communications Biology (2023)

  16. Article

    Open Access

    Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation

    Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of...

    Chen Wang, Dong-Dong Wu, Yao-Hua Yuan, Meng-Cheng Yao, Jian-Lin Han in BMC Biology (2023)

  17. Article

    Open Access

    TM4SF1 upregulates MYH9 to activate the NOTCH pathway to promote cancer stemness and lenvatinib resistance in HCC

    TM4SF1, a member of the transmembrane 4 superfamily, is crucial for both healthy and malignant human tissues. The significant function of TM4SF1 in the incidence and progression of cancer has been widely recog...

    Si-bo Yang, Zi-han Zhou, ** Lei, **ao-wen Li, Qian Chen, Bo Li in Biology Direct (2023)

  18. Article

    Open Access

    Molecular and cellular evolution of the amygdala across species analyzed by single-nucleus transcriptome profiling

    The amygdala, or an amygdala-like structure, is found in the brains of all vertebrates and plays a critical role in survival and reproduction. However, the cellular architecture of the amygdala and how it has ...

    Bin Yu, Qianqian Zhang, Lin Lin, **n Zhou, Wenji Ma, Shaonan Wen in Cell Discovery (2023)

  19. Article

    Open Access

    Large-scale genomic and transcriptomic profiles of rice hybrids reveal a core mechanism underlying heterosis

    Heterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and...

    Jianyin **e, Wei** Wang, Tao Yang, Quan Zhang, Zhifang Zhang in Genome Biology (2022)

  20. Article

    Open Access

    A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein

    The emerging SARS-CoV-2 variants, commonly with many mutations in S1 subunit of spike (S) protein are weakening the efficacy of the current vaccines and antibody therapeutics. This calls for the variant-proof ...

    Wei Pang, Ying Lu, Yan-Bo Zhao, Fan Shen, Chang-Fa Fan, Qian Wang in Cell Research (2022)

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