journal
https://read.qxmd.com/read/38452380/structural-maturation-of-myofilaments-in-engineered-3d-cardiac-microtissues-characterized-using-small-angle-x-ray-scattering
#1
JOURNAL ARTICLE
Geoffrey van Dover, Josh Javor, Jourdan K Ewoldt, Mikhail Zhernenkov, Patryk Wąsik, Guillaume Freychet, Josh Lee, Dana Brown, Christopher S Chen, David J Bishop
Understanding the structural and functional development of human-induced pluripotent stem-cell-derived cardiomyocytes is essential to engineering cardiac tissue that enables pharmaceutical testing, modeling diseases, and designing therapies. Here we use a method not commonly applied to biological materials, small angle X-ray scattering, to characterize the structural development of human-induced pluripotent stem-cell-derived cardiomyocytes within 3D engineered tissues during their preliminary stages of maturation...
March 7, 2024: Physical Biology
https://read.qxmd.com/read/38412523/dynamical-model-of-antibiotic-responses-linking-expression-of-resistance-genes-to-metabolism-explains-emergence-of-heterogeneity-during-drug-exposures
#2
JOURNAL ARTICLE
Mirjana Stevanovic, Joao Pedro Teuber Carvalho, Philip Bittihn, Daniel Schultz
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level...
February 27, 2024: Physical Biology
https://read.qxmd.com/read/38382117/coupled-action-potential-and-calcium-dynamics-underlie-robust-spontaneous-firing-in-dopaminergic-neurons
#3
JOURNAL ARTICLE
Hadeel Khamis, Ohad Cohen
Dopaminergic neurons are specialized cells in the substantia nigra, tasked with dopamine secretion. This secretion relies on intracellular calcium signaling coupled to neuronal electrical activity. These neurons are known to display spontaneous calcium oscillations in-vitro and in-vivo, even in synaptic isolation, controlling the basal dopamine levels. Here we outline a kinetic model for the ion exchange across the neuronal plasma membrane. Crucially, we relax the assumption of constant, cytoplasmic sodium and potassium concentration...
February 21, 2024: Physical Biology
https://read.qxmd.com/read/38330444/modeling-cancer-progression-an-integrated-workflow-extending-data-driven-kinetic-models-to-bio-mechanical-pde-models
#4
JOURNAL ARTICLE
Navid Mirzaei, Leili Shahriyari
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than ever. There are
many mathematical models which investigate cancer through different approaches, from sub-cellular to tissue scale, and from treatment to diagnostic points of view. In this study, we lay out a step-by-step methodology for a data-driven mechanistic model of the
tumor microenvironment...
February 8, 2024: Physical Biology
https://read.qxmd.com/read/38266294/an-effective-hydrodynamic-description-of-marching-locusts
#5
JOURNAL ARTICLE
Dan Gorbonos, Felix Oberhauser, Luke L Costello, Yannick Günzel, Einat Couzin-Fuchs, Benjamin Koger, Iain Couzin
A fundamental question in complex systems is how to relate interactions between individual components ("microscopic description") to the global properties of the system ("macroscopic description"). Furthermore, it is unclear whether such a macroscopic description exists and if such a description can capture large-scale properties. Here, we address the validity of a macroscopic description of a complex biological system using the collective motion of desert locusts as a canonical example. One of the world's most devastating insect plagues begins when flightless juvenile locusts form "marching bands"...
January 24, 2024: Physical Biology
https://read.qxmd.com/read/38266283/an-individual-based-model-to-explore-the-impact-of-psychological-stress-on-immune-infiltration-into-tumour-spheroids
#6
JOURNAL ARTICLE
Emma Leschiera, Gheed Al Hity, Melanie Flint, Chandrasekhar Venkataraman, Tommaso Lorenzi, Luis Almeida, Chloe Audebert
In recent in vitro experiments on co-culture between breast tumour spheroids and activated immune cells, it was observed that the introduction of the stress hormone cortisol resulted in a decreased immune cell infiltration into the spheroids. Moreover, the presence of cortisol deregulated the normal levels of the pro- and anti-inflammatory cytokines IFN-γ and IL-10. We present an individual-based model to explore the interaction dynamics between tumour and immune cells under psychological stress conditions...
January 24, 2024: Physical Biology
https://read.qxmd.com/read/38237200/structure-of-the-space-of-folding-protein-sequences-defined-by-large-language-models
#7
JOURNAL ARTICLE
A Zambon, R Zecchina, G Tiana
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently- developed structure prediction tools based on transformer models, we first examine the protein sequence landscape as defined by an effective energy that is a proxy of sequence foldability. This landscape shares characteristics with optimization challenges encountered in machine learning and constraint satisfaction problems. Our analysis reveals that natural proteins predominantly reside in wide, flat minima within this energy landscape...
January 18, 2024: Physical Biology
https://read.qxmd.com/read/38194907/fitness-effects-of-a-demography-dispersal-trade-off-in-expanding-saccharomyces-cerevisiae-mats
#8
JOURNAL ARTICLE
Rebekah Hall, Akila Bandara, Daniel Charlebois
Fungi expand in space and time to form complex multicellular communities. The mechanisms by which they do so can vary dramatically and determine the life-history and dispersal traits of expanding populations. These traits influence deterministic and stochastic components of evolution, resulting in complex eco-evolutionary dynamics during colony expansion. We perform experiments on budding yeast strains genetically-engineered to display rough-surface and smooth-surface phenotypes in colony-like structures called ``mats''...
January 9, 2024: Physical Biology
https://read.qxmd.com/read/38078366/a-thermodynamical-model-of-non-deterministic-computation-in-cortical-neural-networks
#9
JOURNAL ARTICLE
Elizabeth A Stoll
Neuronal populations in the cerebral cortex engage in probabilistic coding, effectively encoding the state of the surrounding environment with high accuracy and extraordinary energy efficiency. A new approach models the inherently probabilistic nature of cortical neuron signaling outcomes as a thermodynamic process of non-deterministic computation. A mean field approach is used, with the trial Hamiltonian maximizing available free energy and minimizing the net quantity of entropy, compared with a reference Hamiltonian...
December 11, 2023: Physical Biology
https://read.qxmd.com/read/37975194/calcium-regulates-cortex-contraction-in-physarum-polycephalum
#10
JOURNAL ARTICLE
Bjoern Kscheschinski, Mirna Kramar, Karen Alim
The tubular network-forming slime mold Physarum polycephalum is able to maintain long-scale contraction patterns driven by an actomyosin cortex. The resulting shuttle streaming in the network is crucial for the organism to respond to external stimuli and reorganize its body mass giving rise to complex behaviors. However, the chemical basis of the self-organized flow pattern is not fully understood. Here, we present ratiometric measurements of free intracellular calcium in simple morphologies of Physarum networks...
November 17, 2023: Physical Biology
https://read.qxmd.com/read/37963412/an-exploration-of-the-binding-prediction-of-anatoxin-a-and-atropine-to-acetylcholinesterase-enzyme-using-multi-level-computer-simulations
#11
JOURNAL ARTICLE
Showkat Ahmad Mir, Jamoliddin Razzokov, Vishwajeet Mukherjee, Iswar Baitharu, Binata Nayak
Acetylcholinesterase (AChE) is crucial for the breakdown of acetylcholine to acetate and choline, while the inhibition of AChE by Anatoxin-a (ATX-a) results in severe health complications. This study explores the structural characteristics of ATX-a and its interactions with AChE, comparing to the reference molecule Atropine for binding mechanisms. Molecular docking simulations reveal strong binding affinity of both ATX-a and Atropine to AChE, interacting effectively with specific amino acids in the binding site as potential inhibitors...
November 14, 2023: Physical Biology
https://read.qxmd.com/read/37899639/high-throughput-design-of-cultured-tissue-moulds-using-a-biophysical-model-optimising-cell-alignment
#12
JOURNAL ARTICLE
James P Hague, Allison E Andrews, Hugh Dickinson
The technique presented here identifies tethered mould designs, optimised for growing cultured tissue with very highly-aligned cells. It is based on a microscopic biophysical model for polarised cellular hydrogels. There is an unmet need for tools to assist mould and scaffold designs for the growth of cultured tissues with bespoke cell organisations, that can be used in applications such as regenerative medicine, drug screening and cultured meat. High-throughput biophysical calculations were made for a wide variety of computer-generated moulds, with cell-matrix interactions and tissue-scale forces simulated using a contractile network dipole orientation model...
October 30, 2023: Physical Biology
https://read.qxmd.com/read/37793414/rapid-prediction-of-lab-grown-tissue-properties-using-deep-learning
#13
JOURNAL ARTICLE
Allison Andrews, Hugh Dickinson, James Peter Hague
The interactions between cells and the extracellular matrix are vital for the self-organisation of tissues. In this paper we present proof-of-concept to use machine learning tools to predict the role of this mechanobiology in the self-organisation of cell-laden hydrogels grown in tethered moulds. We develop a process for the automated generation of mould designs with and without key symmetries. We create a large training set with $N=6400$ cases by running detailed biophysical simulations of cell-matrix interactions using the contractile network dipole orientation (CONDOR) model for the self-organisation of cellular hydrogels within these moulds...
October 4, 2023: Physical Biology
https://read.qxmd.com/read/37769681/calcium-storage-in-multivesicular-endo-lysosome
#14
JOURNAL ARTICLE
Cameron C Scott, Vaibhav Wasnik, Paula Nunes-Hasler, Nicolas Demaurex, Karsten Kruse, Jean Gruenberg
It is now established that endo-lysosomes, also referred to as late endosomes, serve as intracellular calcium store, in addition to the endoplasmic reticulum. While abundant calcium-binding proteins provide the latter compartment with its calcium storage capacity, essentially nothing is known about the mechanism responsible for calcium storage in endo-lysosomes. In this paper, we propose that the structural organization of endo-lysosomal membranes drives the calcium storage capacity of the compartment. Indeed, endo-lysosomes exhibit a characteristic multivesicular ultrastructure, with intralumenal membranes providing a large amount of additional bilayer surface...
September 28, 2023: Physical Biology
https://read.qxmd.com/read/37769666/facilitating-cell-segmentation-with-the-projection-enhancement-network
#15
JOURNAL ARTICLE
Christopher Z Eddy, Austin Naylor, Christian T Cunningham, Bo Sun
Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly require recording sub-optimally sampled data that greatly reduces the utility of such 3D data, especially in crowded sample space with significant axial overlap between objects. In such regimes, 2D segmentations are both more reliable for cell morphology and easier to annotate...
September 28, 2023: Physical Biology
https://read.qxmd.com/read/37751749/seeking-and-sharing-information-in-collective-olfactory-search
#16
JOURNAL ARTICLE
Emanuele Panizon, Antonio Celani
Searching for a target is a task of fundamental importance for many living organisms. Long-distance search guided by olfactory cues is a prototypical example of such a process. The searcher receives signals that are sparse and very noisy, making the task extremely difficult. Information-seeking strategies have thus been proven to be effective for individual olfactory search and their extension to collective search has been the subject of some exploratory studies. Here, we study in detail how sharing information among members of a group affects the search behavior when agents adopt information-seeking strategies as Infotaxis and its recently introduced variant, Space-Aware Infotaxis...
September 26, 2023: Physical Biology
https://read.qxmd.com/read/37696269/universal-calcium-fluctuations-in-hydra-morphogenesis
#17
JOURNAL ARTICLE
Oded Agam, Erez Braun
Understanding the collective physical processes that drive robust morphological transitions in animal development necessitates the characterization of the relevant fields involved in morphogenesis. Calcium (Ca2+ ) is recognized as one such field. In this study, we demonstrate that the spatial fluctuations of Ca2+ during Hydra regeneration exhibit universal characteristics. To investigate this phenomenon, we employ two distinct controls, an external electric field and heptanol , a gap junction-blocking drug...
September 22, 2023: Physical Biology
https://read.qxmd.com/read/37678266/quantitative-insights-in-tissue-growth-and-morphogenesis-with-optogenetics
#18
JOURNAL ARTICLE
Mayesha Sahir Mim, Caroline Knight, Jeremiah Zartman
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics...
September 7, 2023: Physical Biology
https://read.qxmd.com/read/37652025/emt-induces-characteristic-changes-of-rho-gtpases-and-downstream-effectors-with-a-mitosis-specific-twist
#19
JOURNAL ARTICLE
Kamran Hosseini, Annika Frenzel, Elisabeth Fischer-Friedrich
Epithelial-mesenchymal transition (EMT) is a key cellular transformation for many physiological and pathological processes ranging from cancer over wound healing to embryogenesis. Changes in cell migration, cell morphology and cellular contractility were identified as hallmarks of EMT. These cellular properties are known to be tightly regulated by the actin cytoskeleton. EMT-induced changes of actin-cytoskeletal regulation were demonstrated by previous reports of changes of actin cortex mechanics in conjunction with modifications of cortex-associated f-actin and myosin...
August 31, 2023: Physical Biology
https://read.qxmd.com/read/37557188/phase-transitions-in-insect-swarms
#20
JOURNAL ARTICLE
Andy M Reynolds
In contrast with laboratory insect swarms, wild insect swarms display significant coordinated behaviour. It has been hypothesised that the presence of a fluctuating environment drives the formation of transient, local order (synchronized subgroups), and that this local order pushes the swarm into a new state that is robust to environmental perturbations. The hypothesis is supported by observations of swarming mosquitoes. Here I provide numerical evidence that the formation of transient, local order is an accidental by-product of the strengthening of short-range repulsion which is expected in the presence of environmental fluctuations...
August 9, 2023: Physical Biology
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