📰 "Negative feedback and oscillations in a model for mRNA translation"
https://arxiv.org/abs/2504.12926 #Q-Bio.Qm
#Dynamics #Q-Bio.Mn
#Cell
Negative feedback and oscillations in a model for mRNA translation
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during translation. In this case, the particles model ribosomes and each site corresponds to a consecutive group of codons. Networks of interconnected RFMs have been used to model and analyze large-scale translation in the cell and, in particular, the effects of competition for shared resources. Here, we analyze the RFM with a negative feedback connection from the protein production rate to the initiation rate. This models, for example, the production of proteins that inhibit the translation of their own mRNA. Using tools from the theory of 2-cooperative dynamical systems, we provide a simple condition guaranteeing that the closed-loop system admits at least one non-trivial periodic solution. When this condition holds, we also explicitly characterize a large set of initial conditions such that any solution emanating from this set converges to a non-trivial periodic solution. Such a solution corresponds to a periodic pattern of ribosome densities along the mRNA, and to a periodic pattern of protein production.
📰 "The Dissipation Theory of Aging: A Quantitative Analysis Using a Cellular Aging Map"
https://arxiv.org/abs/2504.13044 #Physics.Bio-Ph
#Q-Bio.Qm
#Dynamics #Cs.Lg
#Cell
The Dissipation Theory of Aging: A Quantitative Analysis Using a Cellular Aging Map
We propose a new theory for aging based on dynamical systems and provide a data-driven computational method to quantify the changes at the cellular level. We use ergodic theory to decompose the dynamics of changes during aging and show that aging is fundamentally a dissipative process within biological systems, akin to dynamical systems where dissipation occurs due to non-conservative forces. To quantify the dissipation dynamics, we employ a transformer-based machine learning algorithm to analyze gene expression data, incorporating age as a token to assess how age-related dissipation is reflected in the embedding space. By evaluating the dynamics of gene and age embeddings, we provide a cellular aging map (CAM) and identify patterns indicative of divergence in gene embedding space, nonlinear transitions, and entropy variations during aging for various tissues and cell types. Our results provide a novel perspective on aging as a dissipative process and introduce a computational framework that enables measuring age-related changes with molecular resolution.
📰 "Boundary Effects in Biological Planar Networks: Pentagons Dominate Marginal Cells"
https://arxiv.org/abs/2503.18855 #CellDivision #Q-Bio.Ot
#Cell
Boundary Effects in Biological Planar Networks: Pentagons Dominate Marginal Cells
The topological and geometrical features at the boundary zone of planar polygonal networks remain poorly understood. Based on observations and mathematical proofs, we propose that marginal cells in Pyropia haitanensis thalli, a two-dimensional (2D) biological polygonal network, have an average edge number of exactly five. We demonstrate that this number is maintained by specific division patterns. Furthermore, we reveal significant limitations of Lewis law and Aboav-Weaire law by comparing the topological and geometrical parameters of marginal cells and inner cells. We find strong boundary effects that are manifested in the distinct distributions of interior angles and edge lengths in marginal cells. Similar to inner cells, cell division tend to occur in marginal cells with large sizes. Our findings suggest that inner cells should be strictly defined based on their positional relationship to the marginal cells.
📰 "Emergent microtubule properties in a model of filament turnover and nucleation"
https://arxiv.org/abs/2504.11466 #Physics.Bio-Ph
#Microtubule #Q-Bio.Sc
Emergent microtubule properties in a model of filament turnover and nucleation
Microtubules (MTs) are dynamic protein filaments essential for intracellular organization and transport, particularly in long-lived cells such as neurons. The plus and minus ends of neuronal MTs switch between growth and shrinking phases, and the nucleation of new filaments is believed to be regulated in both healthy and injury conditions. We propose stochastic and deterministic mathematical models to investigate the impact of filament nucleation and length-regulation mechanisms on emergent properties such as MT lengths and numbers in living cells. We expand our stochastic continuous-time Markov chain model of filament dynamics to incorporate MT nucleation and capture realistic stochastic fluctuations in MT numbers and tubulin availability. We also propose a simplified partial differential equation (PDE) model, which allows for tractable analytical investigation into steady-state MT distributions under different nucleation and length-regulating mechanisms. We find that the stochastic and PDE modeling approaches show good agreement in predicted MT length distributions, and that both MT nucleation and the catastrophe of large-length MTs regulate MT length distributions. In both frameworks, multiple mechanistic combinations achieve the same average MT length. The models proposed can predict parameter regimes where the system is scarce in tubulin, the building block of MTs, and suggest that low filament nucleation regimes are characterized by high variation in MT lengths, while high nucleation regimes drive high variation in MT numbers. These mathematical frameworks have the potential to improve our understanding of MT regulation in both healthy and injured neurons.
📰 "Hemodynamic Markers: CFD-Based Prediction of Cerebral Aneurysm Rupture Risk"
https://arxiv.org/abs/2504.10524 #Physics.Med-Ph
#Physics.Bio-Ph
#Dynamics #Q-Bio.Qm
#Cell
Hemodynamic Markers: CFD-Based Prediction of Cerebral Aneurysm Rupture Risk
This study investigates the influence of aneurysm evolution on hemodynamic characteristics within the sac region. Using computational fluid dynamics (CFD), blood flow through the parent vessel and aneurysm sac was analyzed to assess the impact on wall shear stress (WSS), time-averaged wall shear stress (TAWSS), and the oscillatory shear index (OSI), key indicators of rupture risk. Additionally, Relative Residence Time (RRT) and Endothelial Cell Activation Potential (ECAP) were examined to provide a broader understanding of the aneurysm's hemodynamic environment. Six distinct cerebral aneurysm (CA) models, all from individuals of the same gender, were selected to minimize gender-related variability.
Results showed that unruptured cases exhibited higher WSS and TAWSS, along with lower OSI and RRT values patterns consistent with stable flow conditions supporting vascular integrity. In contrast, ruptured cases had lower WSS and TAWSS, coupled with elevated OSI and RRT, suggesting disturbed and oscillatory flow commonly linked to aneurysm wall weakening. ECAP was also higher in ruptured cases, indicating increased endothelial activation under unstable flow. Notably, areas with the highest OSI and RRT often aligned with vortex centers, reinforcing the association between disturbed flow and aneurysm instability.
These findings highlight the value of combining multiple hemodynamic parameters for rupture risk assessment. Including RRT and ECAP provides deeper insight into flow endothelium-interactions, offering a stronger basis for evaluating aneurysm stability and guiding treatment decisions.
#食物語 #TheTaleOfFood
書寫百壽，以成萬壽。終有一日，上天再也無法奪人算紀。
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#萬壽羹 #Q
ガザはパレスチナ人と支援者の「集団墓地」化＝国境なき医師団 | ロイター - WACOCA NEWS
国際医療援助団体「国境なき医師団（ＭＳＦ）」は１６日、パレスチナ自治区ガザは、パレスチナ人と彼らを助けようとする人々にとっての「集団墓地」と化しているとの見解を示した。
📰 "Hemodynamic Markers: CFD-Based Prediction of Cerebral Aneurysm Rupture Risk"
https://arxiv.org/abs/2504.10524 #Physics.Bio-Ph
#Physics.Med-Ph
#Dynamics #Q-Bio.Qm
#CellHemodynamic Markers: CFD-Based Prediction of Cerebral Aneurysm Rupture Risk
This study investigates the influence of aneurysm evolution on hemodynamic characteristics within the sac region. Using computational fluid dynamics (CFD), blood flow through the parent vessel and aneurysm sac was analyzed to assess the impact on wall shear stress (WSS), time-averaged wall shear stress (TAWSS), and the oscillatory shear index (OSI), key indicators of rupture risk. Additionally, Relative Residence Time (RRT) and Endothelial Cell Activation Potential (ECAP) were examined to provide a broader understanding of the aneurysm's hemodynamic environment. Six distinct cerebral aneurysm (CA) models, all from individuals of the same gender, were selected to minimize gender-related variability.
Results showed that unruptured cases exhibited higher WSS and TAWSS, along with lower OSI and RRT values patterns consistent with stable flow conditions supporting vascular integrity. In contrast, ruptured cases had lower WSS and TAWSS, coupled with elevated OSI and RRT, suggesting disturbed and oscillatory flow commonly linked to aneurysm wall weakening. ECAP was also higher in ruptured cases, indicating increased endothelial activation under unstable flow. Notably, areas with the highest OSI and RRT often aligned with vortex centers, reinforcing the association between disturbed flow and aneurysm instability.
These findings highlight the value of combining multiple hemodynamic parameters for rupture risk assessment. Including RRT and ECAP provides deeper insight into flow endothelium-interactions, offering a stronger basis for evaluating aneurysm stability and guiding treatment decisions.
📰 "Biomechanics of orientationally ordered epithelial tissue"
https://arxiv.org/abs/2504.10689 #Cond-Mat.Soft
#Cytoskeletal #Mechanical #Q-Bio.To
Biomechanics of orientationally ordered epithelial tissue
Organogenesis involves large deformations and complex shape changes that require elaborate mechanical regulation. Models of tissue biomechanics have been introduced to account for the coupling between mechanical response and biochemical processes. Recent experimental evidence indicates that the mechanical response of epithelial tissue is strongly anisotropic, with the degree of anisotropy being correlated with the existence of long range orientational order of cytoskeletal organization across the tissue. A theoretical framework is introduced that captures the dynamic feedback between tissue elastic response and cytoskeletal reorganization under stress. Within the linear regime for small and uniform applied strains, the shear modulus is effectively reduced by the nematic order in cytoskeletal alignment induced by the applied strain. This prediction agrees with experimental observations of epithelial response in lithographically patterned micro tissues.
Rxiv mechanobio
Rxiv cytoskeleton
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