Browsing by Author "Chen, Yirui"

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    Effect of slurry ice during storage on myofibrillar protein of Pseudosciaena crocea
    Guan, Feng; Chen, Yirui; Zhao, Simin; Chen, Zhuo; Yu, Chen; Yuan, Yongjun (2021-07)
    In order to explore the effect of slurry ice on myofibrillar protein of Pseudosciaena crocea, the changes in myofibrillar protein and muscle microstructure during storage were studied with crushed ice as a control. During the storage period, the rate of decrease in myofibrillar protein content, Ca2+-ATPase activity, and total sulfhydryl groups in the slurry ice group was lower than in the control group (p <.05). There was a significant linear correlation between the hydrophobicity and the storage time (R-crushed ice (4 degrees C) = 0.9881, R-slurry ice (4 degrees C) = 0.9878, Rslurry ice (-1 degrees C) = 0.9674), and trichloroacetic acid (TCA) soluble peptide content was lower than in the control group at the same time. Slurry ice (-1 degrees C) was optimal in maintaining protein content in P. crocea; the arrangement of myofibrils in P. crocea treated by slurry ice was compact and the gaps were small. Slurry ice can delay the denaturation and degradation of fish myofibrillar protein and maintain its quality.
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    Mathematical modeling of mechanosensitive reversal control in Myxococcus xanthus
    Chen, Yirui; Topo, Elias J.; Nan, Beiyan; Chen, Jing (Frontiers, 2024-01-08)
    Adjusting motility patterns according to environmental cues is important for bacterial survival. Myxococcus xanthus, a bacterium moving on surfaces by gliding and twitching mechanisms, modulates the reversal frequency of its front-back polarity in response to mechanical cues like substrate stiffness and cell-cell contact. In this study, we propose that M. xanthus’s gliding machinery senses environmental mechanical cues during force generation and modulates cell reversal accordingly. To examine our hypothesis, we expand an existing mathematical model for periodic polarity reversal in M. xanthus, incorporating the experimental data on the intracellular dynamics of the gliding machinery and the interaction between the gliding machinery and a key polarity regulator. The model successfully reproduces the dependence of cell reversal frequency on substrate stiffness observed in M. xanthus gliding. We further propose reversal control networks between the gliding and twitching motility machineries to explain the opposite reversal responses observed in wild type M. xanthus cells that possess both motility mechanisms. These results provide testable predictions for future experimental investigations. In conclusion, our model suggests that the gliding machinery in M. xanthus can function as a mechanosensor, which transduces mechanical cues into a cell reversal signal.
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    Mathematical modelling of motility regulation in Myxococcus xanthus
    Chen, Yirui (Virginia Tech, 2024-01-11)
    Myxococcus xanthus, referred to as a 'social bacterium', demonstrates unique behaviors such as coordinated motility, cooperative feeding, and multicellular structure formation. Its complex social behaviors and developmental processes make M. xanthus a model organism for studying bacterial social behaviors and their underlying mechanisms. Much of the social behavior of M. xanthus hinges on coordination of cell motility among bacteria in close proximity. M. xanthus moves on moist solid surfaces, using its Adventurous (A)-motility and Social (S)-motility systems. A striking feature of M. xanthus motility is the periodic reversal of its direction of movement. The reversal frequency is influenced by chemical and mechanical cues in the surrounding environment. The modulation of the reversal frequency upon physical contact between cells is believed to be a key factor in the bacterium's social behaviors, especially in the formation of complex patterns and structures within the cell population. Here I utilized mathematical modeling to study the motility regulation in M. xanthus, focusing on contact-dependent reversal control, mechanosensing response and impact of motility regulation in solitary (single-cell) predation. My goal is to provide experiment-guiding theories and hypotheses for M. xanthus motility regulation, which is essential to fully understand the social behaviors in this bacterium. In Chapter 2, I developed a single-cell model based on a hypothesis that the motility regulation in M. xanthus is mediated by the interplay between the cell polarity regulation pathway and the A-motility machinery. The aim of this model is to elucidate the cellular mechanism governing contact-dependent motility coordination among cells and to understand how contact-dependent responses at the single-cell level contribute to population-level patterns. This model suggests that the A-motility machinery of M. xanthus potentially serves as a 'mechanosensor' that transduces mechanical cues in the environment into a reversal modulation signal. Chapter 3 addresses a puzzling observation: cells with A-motility alone (A+S−) show a dependence of reversal frequency on substrate stiffness that is opposite to what is observed in wild-type cells that possess both motility systems. Specifically, A+S− cells reverse less frequently on harder substrates, whereas wild-type cells reverse more frequently. To elucidate this perplexing phenomenon, I refined the single-cell model developed in Chapter 2 to study the mechanosensing behaviors with or without S-motility. The base model was sufficient to explain the mechanosensing response in A+S− cells. I then proposed possible interactions between the A-motility and S-motility systems that could explain the contrasting responses to substrate stiffness when S-motility is present or absent. This provides a testable prediction for future experimental investigations. The model suggests that the A-motility system in M. xanthus functions as a central hub of mechanosensing-based reversal control, modulating cell reversal in response to environmental mechanical cues. In Chapter 4, I constructed an agent-based model to investigate the optimal motility strategies for nutrient consumption by M. xanthus during its solitary predation. For different nutrient source types and their uptake latencies, the model identifies 'explore', 'inch', and 'fast explore' as the three most effective motility strategies. Variability in velocity and cell reversal period changes the optimal strategies from 'explore' mode to 'revisit' mode and to 'speed-controlled explore' mode, respectively, for massive remains of prey nutrient sources with moderate uptake latency. The experimental observation that solitary M. xanthus cells combined the 'revisit' and 'inch' mode—as predicted by the model for nutrient acquisition respectively from prey remains and macromolecules—suggests that some of the dead preys may not release its cellular contents immediately and that release of molecular nutrients may require multiple digestion cycles. This model provides insights into the functional role of complex motility regulation in M. xanthus during solitary predation.
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    The Regulation of Micro-Organisms' Extra-Cellular Polysaccharides on Immunity: A Meta-Analysis
    Zhang, Jin; Chen, Yirui; Zhang, Jiaqi; Wang, Yitong; Liu, Yanan (MDPI, 2022-06-30)
    Extra-cellular polysaccharides (EPSs) have excellent immunomodulatory functions. In order to further promote their application, we studied the ability of extra-cellular polysaccharides from different sources to regulate immunity. We studied the association of extra-cellular polysaccharides with immune factors (Interleukin (IL-2, IL-4, IL-10), Interferon γ (IFN-γ), tumor necrosis factor-α (TNF-α), Immunoglobulin A (IgA), and Immunoglobulin G (IgG)) and different concentrations of EPSs and interfering media on experimental results by using a forest plot under fixed-effect or random-effects models. Through Google, PubMed, Embase, ScienceDirect, and Medline, from 2000 to 2021, 12 articles were included. We found that exopolysaccharides (from bacteria or fungi) could significantly increase the immune index of spleen and thymus, spleen index (SMD: 2.11, ‘95%CI: [1.15, 3.08]’; p < 0.01), and thymus index (SMD: 1.62, ‘95%CI: [0.93, 2.32]’; p = 0.01 < 0.05). In addition, exopolysaccharides had a significant effect on TNF-α (SMD: 0.94, ‘95%CI: [0.29, 1.59]’; p = 0.01 < 0.05). For IL-4 (SMD: 0.49, ‘95%CI: [0.01, 0.98]’; p = 0.046 < 0.05), extra-cellular polysaccharides had a statistically significant effect on immunity. Although the data of other immune factors were not ideal, the comprehensive analysis showed that exopolysaccharides also had an effect on the release of these five immune factors. In the sub-group analysis, different concentrations of EPSs affected the results of experiments on the spleen and thymus, and the CY intervention had a relatively significant effect on immune regulation. Taken together, our study highlighted that EPSs have a significant impact on immune regulation.