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Your search keyword '"Guan, Yichao"' showing total 10 results
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10 results on '"Guan, Yichao"'

1. Active random force promotes diffusion in bacterial cytoplasm

Author

Meng, Lingyu, Jin, Yiteng, Guan, Yichao, Xu, Jiayi, and Lin, Jie

Subjects
Physics - Biological Physics, 92C05
Abstract

Experiments have found that diffusion in metabolically active cells is much faster than in dormant cells, especially for large particles. However, the mechanism of this size-dependent diffusion enhancement in living cells is still unclear. In this work, we approximate the net effect of metabolic processes as a white-noise active force and simulate a model system of bacterial cytoplasm with a highly polydisperse particle size distribution. We find that diffusion enhancement in active cells relative to dormant cells can be more substantial for large particles. Our simulations agree quantitatively with the experimental data of Escherichia coli, suggesting an autocorrelation function of the active force proportional to the cube of particle radius. We demonstrate that such a white-noise active force is equivalent to an active force of about 0.57 pN with random orientation. Our work unveils an emergent simplicity of random processes inside living cells., Comment: 20 pages, 18 figures

Published
2022

3. RTCB deficiency triggers colitis in mice by influencing the NF-κB and Wnt/β-catenin signaling pathways

Author

Liu Peiyan, Zhang Ruitao, Song Xiaotong, Tian Xiaohua, Guan Yichao, Li Licheng, He Mei, He Chengqiang, and Ding Naizheng

Subjects
RTCB, colitis, NF-κB, Wnt/β-catenin, LGR5, Biochemistry, QD415-436, Genetics, QH426-470
Abstract

RNA terminal phosphorylase B (RTCB) has been shown to play a significant role in multiple physiological processes. However, the specific role of RTCB in the mouse colon remains unclear. In this study, we employ a conditional knockout mouse model to investigate the effects of RTCB depletion on the colon and the potential molecular mechanisms. We assess the efficiency and phenotype of Rtcb knockout using PCR, western blot analysis, histological staining, and immunohistochemistry. Compared with the control mice, the Rtcb-knockout mice exhibit compromised colonic barrier integrity and prominent inflammatory cell infiltration. In the colonic tissues of Rtcb-knockout mice, the protein levels of TNF-α, IL-8, and p-p65 are increased, whereas the levels of IKKβ and IκBα are decreased. Moreover, the level of GSK3β is increased, whereas the levels of Wnt3a, β-catenin, and LGR5 are decreased. Collectively, our findings unveil a close association between RTCB and colonic tissue homeostasis and demonstrate that RTCB deficiency can lead to dysregulation of both the NF-κB and Wnt/β-catenin signaling pathways in colonic cells.

Published
2024
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9. Cerium oxide nanoparticles modulating the Parkinson's disease conditions: From the alpha synuclein structural point of view and antioxidant properties of cerium oxide nanoparticles.

Author

Yao X, Guan Y, Wang J, and Wang D

Abstract

Parkinson's and Alzheimer's disease is the main cause of dementia, which is associated with the progressive deterioration of the intelligence and senses. Free radicals are created during oxidative stress in cells, which are considered one of the destructive factors in neurodegenerative diseases. In this study, the antifibrillar and antioxidant properties of cerium oxide nanoparticles (CeO 2 NPs) were investigated experimentally and theoretically. The CeO 2 NPs were synthesized and analyzed to reveal the physicochemical and biological properties. The results showed that the CeO 2 NPs have unique properties with potent antioxidant activities. The experimental and computational studies showed that the CeO 2 NPs interact with the active site of Alpha-synuclein. The existence of hydrogen bonding between O atoms of CeO 2 NPs and N-H of adjacent acid amines and the equilibrium distances were confirmed by 1.751 (Leu100), 1.786 (Gln99) and 2.213 Å (Lys97). The minimum free energy binding of L-DOPA drug (as positive control) and CeO 2 NPs were negative, resulting interaction between compounds and protein. As a result, these compounds inhibited Alpha-synuclein protein aggregation. In addition, that CeO 2 NPs strongly binds with receptor by relative binding energy as compared with L-DOPA drug. These findings revealed that CeO 2 NPs prevent Alpha-synuclein fibrillation and can be applied as nano-drug against the Parkinson's disease., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Authors.)

Published
2023
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10. Transcription-replication interactions reveal principles of bacterial genome regulation.

Author

Pountain AW, Jiang P, Yao T, Homaee E, Guan Y, Podkowik M, Shopsin B, Torres VJ, Golding I, and Yanai I

Abstract

Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome 1 . These modes interact with a changing cellular environment to yield highly dynamic expression patterns 2 . In bacteria, the relationship between a gene's regulatory architecture and its expression is well understood for individual model gene circuits 3,4 . However, a broader perspective of these dynamics at the genome-scale is lacking, in part because bacterial transcriptomics have hitherto captured only a static snapshot of expression averaged across millions of cells 5 . As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on each gene's transcriptional response to its own replication, which we term the Transcription-Replication Interaction Profile (TRIP). We found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal a gene's local regulatory context. While the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, including altered timing or amplitude of expression, and this is shaped by factors such as intra-operon position, repression state, or presence on mobile genetic elements. Our transcriptome analysis also simultaneously captures global properties, such as the rates of replication and transcription, as well as the nestedness of replication patterns. This work challenges previous notions of the drivers of expression heterogeneity within a population of cells, and unearths a previously unseen world of gene transcription dynamics., Competing Interests: Competing interests: The authors declare no competing interests.

Published
2023
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