Discretised flux balance analysis for reaction-diffusion simulation of single-cell metabolism DOI Creative Commons
Yin Hoon Chew,

Fabian Spill

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 3, 2023

Abstract Metabolites have to diffuse within the sub-cellular compartments they occupy specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used model metabolism, implicitly assumes all enzymatic are not diffusion-limited though may always be case. In this work, we developed spatial implements FBA grid-based system, enable exploration of diffusion effects metabolism. Specifically, discretises living cell into two-dimensional grid, represents metabolic in each grid element as well metabolites and from neighbouring elements, simulates system single problem. We varied number rows columns simulate different shapes, was able capture at shapes. then heterogeneous enzyme distribution, which suggested theoretical effect variability population level. propose use method, its future extensions, explore how spatiotemporal organisation molecules affect behaviour.

Language: Английский

Controlling the Spatiotemporal Self-Organization of Stimuli-Responsive Nanocrystals under Out-of-Equilibrium Conditions DOI
Patrick Damacet, Elissa O. Shehayeb, Katherine A. Mirica

et al.

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 3, 2025

Self-organization under out-of-equilibrium conditions is ubiquitous in natural systems for the generation of hierarchical solid-state patterns complex structures with intricate properties. Efforts applying this strategy to synthetic materials that mimic biological function have resulted remarkable demonstrations programmable self-healing and adaptive materials. However, extension these efforts multifunctional stimuli-responsive across defined spatial distributions remains an unrealized technological opportunity. This paper describes use a nonequilibrium reaction–diffusion process achieve synthesis electrically conductive metal–organic framework (cMOF) gelled medium control over particle size periodicity on macroscopic scale. Upon integration into chemiresistive devices, resulting cMOF particles exhibit size-dependent response toward hydrogen sulfide gas, as determined by their distinct surface-to-volume ratio, porosity, unique methodology, unusual microcrystallite morphology compared counterparts obtained through bulk solution phase synthesis. Taken altogether, achievements pave way gaining access functional nanomaterials well-defined chemical composition, dimensions, precisely tailored functions using far-from-equilibrium approaches.

Language: Английский

Citations

1
Genetically encoded protein oscillators for FM streaming of single-cell data DOI Creative Commons
Rohith Rajasekaran,

Thomas M. Galateo,

Zhejing Xu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 28, 2025

Radios and cellphones use frequency modulation (FM) of an oscillating carrier signal to reliably transmit multiplexed data while rejecting noise. Here, we establish a biochemical analogue this paradigm using genetically encoded protein oscillators (GEOs) as signals in circuits that enable continuous, real-time FM streaming single-cell data. GEOs are constructed from evolutionarily diverse MinDE-family ATPase activator modules generate fast synthetic oscillations when co-expressed human cells. These serve signal, with amplitude controlled by GEO component levels activity. We systematically characterize 169 ATPase/activator pairs engineer composite multiple competing activators develop comprehensive platform for waveform programming. Using these principles, design modulate response cellular activity decode their responses calibrated machine-learning model demonstrate sensitive, transcription proteasomal degradation dynamics single dynamically controllable unlocking noise-resistant data-encoding paradigms open new avenues dynamic analysis.

Language: Английский

Citations

0
Learning physics and biology from cytoskeletal and condensate interactions DOI Creative Commons

Julia F. Bourdeau,

Prashali Chauhan, Jennifer L. Ross

et al.

Current Opinion in Cell Biology, Journal Year: 2025, Volume and Issue: 94, P. 102506 - 102506

Published: April 6, 2025

Two important mechanisms for self-organization in cells include condensation of biomolecules, such as proteins and nucleic acids into phase-separated droplets to form membraneless organelles organization the cytoskeletal filaments larger-scale systems actin cortex microtubule-based mitotic spindle. Recent publications highlight that these two intracellular schemes are coordinated, with condensates controlling organizations cytoskeleton organizing condensates. Here, we focus on recent progress from past 2 years at interface between cytoskeleton. We split discussion physical biological principles can learn studies.

Language: Английский

Citations

0
The critical role of ion channels in kidney disease: perspective from AKI and CKD DOI Creative Commons
C. Li, Bing Yu, Qian Gao

et al.

Renal Failure, Journal Year: 2025, Volume and Issue: 47(1)

Published: April 28, 2025

Ion channels, particularly those in the transient receptor potential (TRP) family, play key roles cellular stress responses like inflammation and apoptosis, significantly impacting renal disease progression. Some channels such as TRPV1, TRPM2, TRPC6 impact pathology by mediating detrimental calcium influx, exacerbating oxidative stress, promoting inflammatory pathways. Their activities are especially pronounced conditions ischemia nephrotoxicity, common acute kidney injury, persist into chronic influencing fibrosis nephron loss. Additionally, potassium sodium Kir4.1, KATP, ENaC critical maintaining electrolyte balance energy under conditions. Further exploration of ion channel functionality regulation is necessary to clarify their disease. This review summarizes involvement AKI CKD examines clinical value diagnosing treating

Language: Английский

Citations

0
Discretised Flux Balance Analysis for Reaction–Diffusion Simulation of Single-Cell Metabolism DOI Creative Commons
Yin Hoon Chew,

Fabian Spill

Bulletin of Mathematical Biology, Journal Year: 2024, Volume and Issue: 86(4)

Published: March 6, 2024

Abstract Metabolites have to diffuse within the sub-cellular compartments they occupy specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used model metabolism, implicitly assumes all enzymatic are not diffusion-limited though may always be case. In this work, we developed spatial implements FBA grid-based system, enable exploration of diffusion effects metabolism. Specifically, discretises living cell into two-dimensional grid, represents metabolic in each grid element as well metabolites and from neighbouring elements, simulates system single problem. We varied number rows columns simulate different shapes, was able capture at shapes. then heterogeneous enzyme distribution, which suggested theoretical effect variability population level. propose use method, its future extensions, explore how spatiotemporal organisation molecules affect behaviour.

Language: Английский

Citations

1
Integrating inverse reinforcement learning into data-driven mechanistic computational models: a novel paradigm to decode cancer cell heterogeneity DOI Creative Commons
Patrick C. Kinnunen, Kenneth K. Y. Ho, Siddhartha Srivastava

et al.

Frontiers in Systems Biology, Journal Year: 2024, Volume and Issue: 4

Published: March 8, 2024

Cellular heterogeneity is a ubiquitous aspect of biology and major obstacle to successful cancer treatment. Several techniques have emerged quantify in live cells along axes including cellular migration, morphology, growth, signaling. Crucially, these studies reveal that not result randomness or failure control systems, but instead predictable multicellular systems. We hypothesize individual complex tissues can behave as reward-maximizing agents differences reward perception explain heterogeneity. In this perspective, we introduce inverse reinforcement learning novel approach for analyzing briefly detail experimental approaches measuring over time how experiments generate datasets consisting states actions. Next, show be applied infer choose different actions based on heterogeneous states. Finally, potential applications three cell problems. Overall, expect why heterogeneously enable identification treatments new understanding.

Language: Английский

Citations

1
What can protein circuit design learn from DNA nanotechnology? DOI Creative Commons
Dingchen Yu,

Xinwen Fan,

Zibo Chen

et al.

Current Opinion in Biomedical Engineering, Journal Year: 2024, Volume and Issue: 32, P. 100556 - 100556

Published: Aug. 23, 2024

Protein circuit design is still in its infancy terms of programmability. DNA nanotechnology, however, excels at this property and community has created a myriad circuits assemblies following modular hierarchical rules. In mini-review, we reason that the rationales behind nanotechnology can nurture protein design, unique versatility orchestrated by groups proteins be further exploited to program cells. Community efforts develop databases algorithms for standardizing customizing modules could bring programmability level comparable ultimately empowering design. • achieve versatile functions both inside outside motivate forward-to-reverse paradigm shift

Language: Английский

Citations

1
Discretised flux balance analysis for reaction-diffusion simulation of single-cell metabolism DOI Creative Commons
Yin Hoon Chew,

Fabian Spill

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 3, 2023

Abstract Metabolites have to diffuse within the sub-cellular compartments they occupy specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used model metabolism, implicitly assumes all enzymatic are not diffusion-limited though may always be case. In this work, we developed spatial implements FBA grid-based system, enable exploration of diffusion effects metabolism. Specifically, discretises living cell into two-dimensional grid, represents metabolic in each grid element as well metabolites and from neighbouring elements, simulates system single problem. We varied number rows columns simulate different shapes, was able capture at shapes. then heterogeneous enzyme distribution, which suggested theoretical effect variability population level. propose use method, its future extensions, explore how spatiotemporal organisation molecules affect behaviour.

Language: Английский

Citations

0