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Effect of Preventive Measures and Heterogeneity of Sexual Contacts on Zika virus Transmission. 预防措施及性接触异质性对寨卡病毒传播的影响
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01622-6
Qiaojuan Jia, Ling Xue, Jichen Yang, Junyuan Yang, James M Hyman

The global spread of the Zika virus (ZIKV), compounded by the absence of effective antiviral drugs or widely available vaccines, highlights the importance of understanding its transmission dynamics to implement effective public health strategies. The transmission of the Zika virus is attributable to the heterogeneity of sexual contacts and the lack of miracle drugs or vaccines. We develop a degree-based mathematical network model which takes account of heterogeneity of sexual contacts and the adoption of preventive measures. We derive analytical expressions for the basic reproduction number for three scenarios: mosquito-borne transmission only, sexual transmission only, and a combined scenario where both transmission routes coexist. In particular, we demonstrate that the basic reproduction number is proportional to the degree of network heterogeneity when the Zika virus transmission is solely driven by sexual contacts. Our proposed model possesses infinitely many disease-free equilibrium points, and we prove that these collectively form a locally attracting set under specified conditions. Finally, we present numerical simulations, calibrated with Zika epidemic data from Brazil (2015-2016), which indicate that increasing the number of individuals who take comprehensive protective measures (using screens, mosquito nets, insect repellent, condoms, etc.) can significantly reduce the final epidemic size.

寨卡病毒(ZIKV)在全球的传播,加上缺乏有效的抗病毒药物或广泛获得的疫苗,凸显了了解其传播动态以实施有效公共卫生战略的重要性。寨卡病毒的传播可归因于性接触的异质性以及缺乏特效药物或疫苗。我们开发了一个基于程度的数学网络模型,该模型考虑了性接触的异质性和预防措施的采用。我们推导了三种情况下基本繁殖数的解析表达式:蚊媒传播、性传播和两种传播途径并存的组合情况。特别是,我们证明了当寨卡病毒传播仅由性接触驱动时,基本繁殖数与网络异质性程度成正比。我们所提出的模型具有无穷多个无病平衡点,并证明了这些平衡点在一定条件下共同形成一个局部吸引集。最后,我们以巴西2015-2016年的寨卡疫情数据进行了数值模拟,结果表明,采取综合防护措施(使用纱窗、蚊帐、驱蚊剂、避孕套等)的人数增加,可以显著减少最终的疫情规模。
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引用次数: 0
Counting Spinal Phylogenetic Networks. 计算脊柱系统发育网络。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01624-4
Andrew Francis, Michael Hendriksen

Phylogenetic networks are an important way to represent evolutionary histories that involve reticulate processes such as hybridisation or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain properties are very difficult. A new way to encode a large class of networks, using "expanding covers", may provide a way to approach such problems. Expanding covers encode a large class of phylogenetic networks, called labellable networks. This class does not include all networks, but does include many familiar classes, including orchard, normal, tree-child and tree-sibling networks. As expanding covers are a combinatorial structure, it is possible that they can be used as a tool for counting such classes for a fixed number of leaves and reticulations, for which, in many cases, a closed formula has not yet been found. More recently, a new class of networks was introduced, called spinal networks, which are analogous to caterpillar trees for phylogenetic trees and can be fully described using covers. In the present article, we describe a method for counting networks that are both spinal and belong to some more familiar class, with the hope that these form a base case from which to attack the more general classes.

系统发育网络是表示涉及网状过程(如杂交或水平基因转移)的进化史的重要方式,但诸如有多少网络满足某些特性之类的基本问题非常困难。一种对大型网络进行编码的新方法,即使用“扩展覆盖”,可能为解决这类问题提供了一种方法。扩展覆盖编码了一大类系统发育网络,称为可标记网络。这个类不包括所有的网络,但包括许多熟悉的类,包括果园、正常、树-子和树-兄弟网络。由于扩展盖是一种组合结构,它们可能被用作一种工具,用于计算固定数量的叶子和网状的这类,在许多情况下,还没有找到一个封闭的公式。最近,一种新的网络被引入,称为脊柱网络,它类似于系统发育树的毛虫树,可以用覆盖物完全描述。在本文中,我们描述了一种计算神经网络的方法,这些神经网络既属于脊椎神经网络,又属于一些更熟悉的类,希望这些神经网络能形成一个基础案例,从中攻击更一般的类。
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引用次数: 0
Vector Encoding of Phylogenetic Trees by Ordered Leaf Attachment. 基于有序叶片附着的系统发育树矢量编码。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01611-9
David Harry Richman, Cheng Zhang, Frederick A Matsen

As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a binary, rooted phylogenetic tree topology as an integer vector. OLA encoding and decoding take linear time in the number of leaf nodes, and the set of vectors corresponding to trees is a simply-described subset of integer sequences. The OLA encoding is unique compared to other existing encodings in having these properties. The integer vector encoding induces a distance on the set of trees, and we investigate this distance in relation to the NNI and SPR distances.

作为将系统发育与机器学习联系起来的工作的一部分,最近对系统发育树的矢量编码产生了相当大的兴趣。我们提出了一种简单的新“有序叶连接”(OLA)方法,用于将二叉根系统发育树拓扑结构唯一地编码为整数向量。OLA的编码和解码在叶节点数量上占用线性时间,而树对应的向量集是整数序列的一个简单描述子集。与具有这些属性的其他现有编码相比,OLA编码是唯一的。整数向量编码在树的集合上产生一个距离,我们研究了这个距离与NNI和SPR距离的关系。
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引用次数: 0
Mono- and Polyauxic Growth Kinetics: A Semi-Mechanistic Framework for Complex Biological Dynamics. 单一和多元生长动力学:复杂生物动力学的半机械框架。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01621-7
Gustavo Mockaitis

Kinetic modeling of microbial growth is essential for the design, optimization, and scale-up of industrial bioprocesses. Classical empirical models often lack biologically interpretable parameters or fail to capture complex multiphasic (polyauxic) behaviors, while fully mechanistic models are impractical for systems involving complex substrates and mixed cultures. This study proposes a unified mathematical framework that reformulates the canonical Boltzmann and Gompertz equations into semi-mechanistic forms, explicitly defining the maximum specific reaction rate and lag phase duration. Polyauxic growth is represented as a weighted sum of sigmoidal phases, subject to stringent constraints that ensure parameter identifiability, temporal consistency, and biological plausibility. The methodology integrates a workflow to address nonlinear regression in high-dimensional parameter spaces. A two-stage optimization strategy using Differential Evolution for global search followed by L-BFGS-B for local refinement avoid bias and heuristic parameter initialization. A Charbonnier loss function and the Robust Regression and Outlier Removal procedure are employed to identify and mitigate experimental outliers. Model parsimony is enforced using Akaike (AIC, AICc) and Bayesian (BIC) information criteria to select the optimal number of growth phases and avoid overparameterization. The framework was evaluated using experimental anaerobic digestion datasets, demonstrating that conventional single-phase models can obscure relevant metabolic transitions in co-digestion systems.

微生物生长的动力学建模对于工业生物过程的设计、优化和规模化至关重要。经典的经验模型往往缺乏生物学上可解释的参数,或者无法捕捉复杂的多相(多源)行为,而完全机械的模型对于涉及复杂底物和混合培养的系统是不切实际的。本研究提出了一个统一的数学框架,将规范的玻尔兹曼和冈珀兹方程重新表述为半机械形式,明确定义了最大比反应速率和滞后相持续时间。复合生长被表示为s型相的加权和,受到严格的约束,以确保参数可识别性、时间一致性和生物合理性。该方法集成了一个工作流来解决高维参数空间中的非线性回归问题。采用差分进化进行全局搜索,L-BFGS-B进行局部优化,避免了偏差和启发式参数初始化。采用Charbonnier损失函数和鲁棒回归和异常值去除程序来识别和减轻实验异常值。采用Akaike (AIC, AICc)和Bayesian (BIC)信息准则来实现模型的简约性,以选择最优生长阶段数,避免过度参数化。使用实验厌氧消化数据集对该框架进行了评估,表明传统的单相模型可以模糊共消化系统中的相关代谢转变。
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引用次数: 0
Effects of Multi-Phase Control Mechanism on Fibroblast Dynamics: A Segmented Mathematical Modeling Approach. 多相调控机制对成纤维细胞动力学的影响:分段数学建模方法。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01607-5
Shuqi Fan, Yuhong Zhang, Jinzhi Lei

Cell size is a fundamental determinant of cellular physiology, influencing processes such as growth, division, and function. In this study, we develop a segmented mathematical framework to investigate how different control mechanisms operating across multiple phases of the cell cycle affect fibroblast population dynamics. Building on our previous work modeling sizer, timer, and adder strategies, we extend the analysis by introducing phase-specific control schemes in the S and G2 phases, incorporating nonlinear growth dynamics and cell death. Using agent-based stochastic simulations, we examine how these mechanisms shape steady-state size distributions and respond to parameter variations. Our results reveal that the steady-state cell size distribution is primarily governed by division kernels and phase-specific control strategies, and appears remarkably robust to cell death modalities. We identify a fundamental trade-off between extrinsic and intrinsic growth feedbacks: while population-density-dependent regulation tightly limits total cell numbers, cell-size-dependent regulation acts as a proportional homeostatic mechanism, suppressing relative size variability. Furthermore, we demonstrate that population recovery is accelerated by the retention of proliferation-competent large cells. This study provides biologically relevant insights into the complex interplay between growth, division, and homeostasis, with implications for understanding tissue repair and disease progression.

细胞大小是细胞生理的基本决定因素,影响细胞生长、分裂和功能等过程。在这项研究中,我们开发了一个分段的数学框架来研究不同的控制机制如何在细胞周期的多个阶段影响成纤维细胞群体动力学。基于我们之前的工作建模大小器、计时器和加法器策略,我们通过在S和G2阶段引入相位特定控制方案来扩展分析,其中包含非线性生长动力学和细胞死亡。使用基于智能体的随机模拟,我们研究了这些机制如何形成稳态尺寸分布并响应参数变化。我们的研究结果表明,稳态细胞大小分布主要由分裂核和阶段特异性控制策略控制,并且对细胞死亡模式具有显著的鲁棒性。我们确定了外在和内在生长反馈之间的基本权衡:虽然种群密度依赖的调节严格限制了细胞总数,但细胞大小依赖的调节作为一种比例稳态机制,抑制了相对大小的可变性。此外,我们还证明,保留具有增殖能力的大细胞可以加速种群恢复。这项研究为生长、分裂和体内平衡之间复杂的相互作用提供了生物学相关的见解,对理解组织修复和疾病进展具有重要意义。
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引用次数: 0
Environmental Stochasticity Drives Adaptation to Cooler Thermal Optima in Competition. 环境随机性驱动竞争中对较冷热最优的适应。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01614-6
Abdulrahaman Lawal Suleiman, Pietro Landi, Cang Hui

Thermal reaction norms, or thermal performance curves (TPCs), describe how ectothermic organisms respond to temperature variation. Here, we investigate how stochastic environmental noise, by modulating competitive interactions among individuals with differing TPC shapes, can drive long-term evolutionary changes in thermal performance. We develop a Ricker competition model within the framework of adaptive dynamics to examine how environmental variability, corresponding to the joint effect of both periodic and stochastic temperature fluctuations, influences the evolution of competition TPCs. Growth, carrying capacity and competitive interactions are all temperature-dependent, with competition coefficients defined by the ratio of individuals' thermal performance curve at the prevailing temperature. Competition TPCs are modelled using a beta probability density function. Previous results from periodically (i.e., deterministically) fluctuating environments established that the thermal optimum converges to the mean environmental temperature, while performance breadth collapses under constant conditions. In contrast, we show that under stochastic environments, increasing thermal noise broadens competition TPCs and shifts the thermal optimum leftward, away from the environmental mean. This results in right-skewed competition TPCs and suggests an evolutionary bias towards cooler temperature optima for competition under moderate to high environmental noise. Alongside the broadening of competition TPCs to buffer against thermal fluctuations, the shift towards cooler optima reflects a more conservative thermal strategy for competition performance in the face of environmental uncertainty.

热反应规范,或热性能曲线(TPCs),描述了恒温生物对温度变化的反应。在这里,我们研究了随机环境噪声如何通过调节具有不同TPC形状的个体之间的竞争相互作用,来驱动热性能的长期进化变化。我们在自适应动力学的框架内开发了一个Ricker竞争模型,以研究与周期性和随机温度波动的联合效应相对应的环境可变性如何影响竞争TPCs的进化。生长、承载能力和竞争相互作用都依赖于温度,竞争系数由个体在盛行温度下的热性能曲线之比定义。竞争tpc使用β概率密度函数建模。先前周期性(即确定性)波动环境的结果表明,热最佳收敛于平均环境温度,而性能宽度在恒定条件下崩溃。相反,我们发现在随机环境下,热噪声的增加扩大了竞争tpc,并使热最优向左移动,远离环境平均值。这导致竞争tpc右倾斜,并表明在中等到高环境噪声下,竞争的进化倾向于更低的温度。随着竞争tpc的扩大以缓冲热波动,向更冷的最佳状态的转变反映了面对环境不确定性时竞争表现的更保守的热策略。
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引用次数: 0
Characterising Epigenetic Tipping Points using a Spectral Dimension Reduction Approach. 表征表观遗传引爆点使用光谱降维方法。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01602-w
Tomás Alarcón, Javier A Menendez, Josep Sardanyés

Epigenetic landscapes (ELs) are defined by the pattern of epigenetic marks (acetylation, methylation, etc.) layed over large chromatin regions. The information contained in the ELs is essential to sustain the patterns of gene expression that shape cell fate and identity. EL maintenance requires the precise regulation of chromatin-modifying enzymes (ChME) and their metabolic cofactors (McF). Competition for ChME or dysregulation of McF abundance can lead to degradation of ELs, triggering large-scale changes in the cell fate information contained in EL. Thus, predicting impending epigenetic tipping points (ETPs) by identifying early warning signals (EWS) may help to anticipate the onset of cell identity loss during aging and cancer. Since ELs are formed (and maintained) by a systems of writer/eraser enzymes that interact both in cis (local) and trans (long-range) modes, their mathematical description involves a high-dimensional dynamical system, where identifying ETPs and characterising the biological mechanisms that control them remains challenging. Here, we develop a general mathematical framework that incorporates different connectivity patterns generated by the 3D chromatin folding structure to analyze competition-induced ETP in large EL. This framework allows us to measure the sensitivity and robustness of ETP to the availability of metabolic cofactors and to identify potential EWS. Using a dimension reduction method, we derived coarse-grained (CG) equations for the collective observables associated with chromatin modifications. Analysis of the CG system allows the prediction of global transitions that shape the large-scale features of EL, accurately reproduce the corresponding microscopic benchmarks, and reveal the existence of tipping points under conditions of ChME competition. We applied the CG method to predict ETP under different connectivity patterns, including heterogeneous profiles such as those found in Hi-C data. Although a robustness measure for stable EL was derived from the CG dynamics in bistable regimes, sensitivity analysis revealed that metabolic cofactors have the greatest impact on EL robustness. In particular, we identified the metabolic cofactors SAM and acetyl-CoA as potential EWS for the catastrophic loss of hyperacetylated EL induced by ChME competition. The ability to predict global ETP can facilitate the discovery of predictive biomarkers and inform metabolic interventions aimed at limiting and reversing pathological cell fate decisions.

表观遗传景观(el)是由表观遗传标记(乙酰化,甲基化等)分布在大染色质区域的模式所定义的。el中包含的信息对于维持塑造细胞命运和身份的基因表达模式至关重要。EL的维持需要染色质修饰酶(ChME)及其代谢辅助因子(McF)的精确调控。对ChME的竞争或McF丰度的失调可导致EL的降解,引发EL中包含的细胞命运信息的大规模变化。因此,通过识别早期预警信号(EWS)来预测即将到来的表观遗传引爆点(ETPs)可能有助于预测衰老和癌症期间细胞身份丧失的发生。由于etp是由书写/擦除酶系统形成(并维持)的,这些书写/擦除酶系统以顺式(局部)和反式(远程)模式相互作用,因此它们的数学描述涉及高维动态系统,其中识别etp并表征控制它们的生物机制仍然具有挑战性。在这里,我们开发了一个通用的数学框架,该框架包含了3D染色质折叠结构产生的不同连接模式,以分析大EL中竞争诱导的ETP。该框架使我们能够测量ETP对代谢辅助因子可用性的敏感性和稳健性,并识别潜在的EWS。使用降维方法,我们导出了与染色质修饰相关的集体可观察物的粗粒度(CG)方程。对CG系统的分析可以预测塑造EL大规模特征的全球转变,准确地再现相应的微观基准,并揭示在ChME竞争条件下临界点的存在。我们应用CG方法预测了不同连通性模式下的ETP,包括在Hi-C数据中发现的异质剖面。虽然稳定EL的稳健性度量来源于双稳态状态下的CG动力学,但敏感性分析显示,代谢辅助因子对EL稳健性的影响最大。特别是,我们确定了代谢辅助因子SAM和乙酰辅酶a是ChME竞争引起的高乙酰化EL灾难性损失的潜在EWS。预测全局ETP的能力可以促进预测性生物标志物的发现,并为旨在限制和逆转病理细胞命运决定的代谢干预提供信息。
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引用次数: 0
Transient and Asymptotic Dynamics of a Bioeconomic Fishery Model with Market Price Fluctuation and Effort Capacity Constraints. 具有市场价格波动和努力能力约束的生物经济渔业模型的瞬态和渐近动力学。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01623-5
Zhehao Liu, Wenjun Liu, Xuebing Zhang, Ali Moussaoui, Pierre Auger

Bioeconomic systems are inherently governed by fast-slow dynamics, arising from the interplay between rapid market adjustments and slower ecological processes. In this paper, we analyze a four-dimensional fishery model that couples predator-prey dynamics with fishing effort subject to capacity constraints and market-clearing prices. Using geometric singular perturbation theory, we show that the separation of timescales leads to a split critical manifold. The system's operational mode is determined by a single dimensionless bioeconomic parameter, which acts as a structural selector between an Internally-Regulated regime and a Capacity-Saturated regime. Beyond equilibrium stability, we focus on transient behaviors by deriving a closed-form approximation for the transient response time to external shocks. This analytical metric explicitly links recovery duration to the effective net growth budget. Our results demonstrate that while the Capacity-Saturated regime may sustain a stable equilibrium, it incurs significantly larger cumulative ecological deficits and slower recovery rates following perturbations. These findings quantify the trade-off between harvest intensity and system responsiveness, offering a dynamical basis for the vulnerability of high-effort fisheries.

生物经济系统本质上是由快速的市场调整和较慢的生态过程之间的相互作用而产生的快慢动态控制的。本文分析了一个受能力约束和市场出清价格约束的捕食者-猎物动态与渔获量耦合的四维渔业模型。利用几何奇异摄动理论,证明了时间尺度的分离导致临界流形的分裂。系统的运行模式由单一的无量纲生物经济参数决定,该参数在内部调节机制和容量饱和机制之间充当结构选择器。除了平衡稳定性之外,我们还通过推导对外部冲击的瞬态响应时间的封闭近似来关注瞬态行为。这一分析指标明确地将恢复持续时间与有效净增长预算联系起来。我们的研究结果表明,虽然容量饱和状态可以维持稳定的平衡,但它会导致更大的累积生态赤字和更慢的恢复速度。这些发现量化了捕捞强度和系统响应性之间的权衡,为高努力度渔业的脆弱性提供了动态基础。
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引用次数: 0
Identifies Tipping Points of cell Fate Transitions by Network Relative Entropy. 利用网络相对熵识别细胞命运转换的引爆点。
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-18 DOI: 10.1007/s11538-026-01625-3
Zhuozhen Xue, Xiaoqi Lu, Ruiqi Wang

Cell fate decisions typically occur at critical tipping points during development. Identifying these points offers valuable insights into the underlying mechanisms that govern cell fate determination. In this study, we introduce a novel approach called Network Relative Entropy (NRE), which is designed to detect crucial time points during development by analyzing variations in network structures between consecutive time points. After validating the NRE method using simulation data, we apply it to experimental datasets to discern the critical points of early embryonic development. Our findings indicate that the predictions made by the NRE method closely match experimental observations. Furthermore, by ranking the NREs, we identify distinct gene subsets, which we refer to as signaling genes. Statistical analysis reveals a notable divergence in the expression patterns of these signaling genes at the critical points compared to their preceding states. Additionally, we map the correlation coefficients of these signaling genes onto the known protein-protein interaction (PPI) networks. Notably, the correlations among signaling genes exhibit a significant increase at the critical points. These observations provide additional evidence for the reliability of the NRE method from an alternative perspective.

细胞命运的决定通常发生在发育过程中的关键转折点。识别这些点为了解控制细胞命运决定的潜在机制提供了有价值的见解。在这项研究中,我们引入了一种称为网络相对熵(NRE)的新方法,该方法旨在通过分析连续时间点之间网络结构的变化来检测开发过程中的关键时间点。在使用模拟数据验证NRE方法后,我们将其应用于实验数据集,以识别早期胚胎发育的关键点。我们的研究结果表明,NRE方法的预测与实验观测结果非常吻合。此外,通过对NREs进行排序,我们确定了不同的基因子集,我们将其称为信号基因。统计分析显示,这些信号基因在临界点的表达模式与之前的状态相比有显著的差异。此外,我们将这些信号基因的相关系数映射到已知的蛋白质-蛋白质相互作用(PPI)网络上。值得注意的是,信号基因之间的相关性在临界点上表现出显著的增加。这些观测结果从另一个角度为NRE方法的可靠性提供了额外的证据。
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引用次数: 0
In Silico Comparison of Rifampicin and 25-desacetyl Rifampicin-Induced PXR-Mediated CYP450 Transcriptional Response in 3D Primary Human Hepatocytes. 利福平和25-去乙酰利福平诱导的pxr介导的CYP450转录反应在三维原代人肝细胞中的比较
IF 2.2 4区 数学 Q2 BIOLOGY Pub Date : 2026-03-06 DOI: 10.1007/s11538-026-01619-1
Ellen Tanaka Kahiya, Tomáš Smutný, Lucie Smutná, Jurjen Duintjer Tebbens, Petr Pávek, Veronika Bernhauerová

The pregnane X receptor (PXR) regulates the expression of cytochrome P450 (CYP) enzymes and plays a crucial role in the metabolism of various drugs. Rifampicin (RIF) is a PXR ligand that forms the primary metabolite, 25-desacetyl rifampicin (25-DRIF), which retains the antimicrobial activity of the original drug. In this study, we quantified PXR activation and its associated effects on CYP3A4, CYP2C9, and CYP2B6 enzymes in response to 25-DRIF treatment by combining mathematical modeling with long-term mRNA expression analysis of these enzymes in 3D primary human hepatocyte (3D PHH) spheroids. Our estimates suggest that 25-DRIF activates PXR at a rate 20 times lower than RIF. The PXR-dependent rate constant for CYP3A4 transcription was estimated to be higher in 3D PHHs treated with 25-DRIF than in those treated with RIF and also higher than that for CYP2B6 transcription in 3D PHHs treated with 25-DRIF. The rate constants driving PXR-dependent transcription of CYP2C9 were comparable in RIF- and 25-DRIF-treated 3D PHHs. These results demonstrate the ligand-specific nature of PXR activation and suggest that the transcription of PXR-controlled CYP enzymes is ligand- and CYP-specific in 3D PHHs. Finally, we showed that the half-maximal effective concentration ( EC 50 ) evaluated from our mathematical predictions was time-dependent, which was further validated by CYP3A4 gene reporter assays that measured RIF-induced PXR activity.

妊娠X受体(PXR)调节细胞色素P450 (CYP)酶的表达,在多种药物的代谢中起着至关重要的作用。利福平(RIF)是一种PXR配体,形成初级代谢物25-去乙酰利福平(25-DRIF),保留原药的抗菌活性。在这项研究中,我们量化了PXR的激活及其对25-DRIF治疗后CYP3A4、CYP2C9和CYP2B6酶的相关影响,方法是将数学建模与3D原代人肝细胞(3D PHH)球体中这些酶的长期mRNA表达分析相结合。我们的估计表明,25-DRIF激活PXR的速率比RIF低20倍。据估计,25-DRIF处理的3D phh中CYP3A4转录的pxr依赖速率常数高于RIF处理的3D phh,也高于25-DRIF处理的3D phh中CYP2B6转录的pxr依赖速率常数。在RIF和25- drif处理的3D phh中,驱动pxr依赖性CYP2C9转录的速率常数是相当的。这些结果证明了PXR激活的配体特异性,并表明PXR控制的CYP酶的转录在3D phh中具有配体特异性和CYP特异性。最后,我们发现根据我们的数学预测评估的半最大有效浓度(EC 50)是时间依赖性的,这一点通过测量rif诱导的PXR活性的CYP3A4基因报告基因试验进一步验证。
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引用次数: 0
期刊
Bulletin of Mathematical Biology
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