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Patel RJS, Harlan CJ, Fuentes DT, Bankson JA. A Simulation of the Effects of Diffusion on Hyperpolarized [1- 13C]-Pyruvate Signal Evolution. IEEE Trans Biomed Eng 2023; 70:2905-2913. [PMID: 37097803 PMCID: PMC10538435 DOI: 10.1109/tbme.2023.3269665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
OBJECTIVE Hyperpolarized [1-13C]-pyruvate magnetic resonance imaging is an emerging metabolic imaging method that offers unprecedented spatiotemporal resolution for monitoring tumor metabolism in vivo. To establish robust imaging biomarkers of metabolism, we must characterize phenomena that may modulate the apparent pyruvate-to-lactate conversion rate (kPL). Here, we investigate the potential effect of diffusion on pyruvate-to-lactate conversion, as failure to account for diffusion in pharmacokinetic analysis may obscure true intracellular chemical conversion rates. METHODS Changes in hyperpolarized pyruvate and lactate signal were calculated using a finite-difference time domain simulation of a two-dimensional tissue model. Signal evolution curves with intracellular kPL values from 0.02 to 1.00 s-1 were analyzed using spatially invariant one-compartment and two-compartment pharmacokinetic models. A second spatially variant simulation incorporating compartmental instantaneous mixing was fit with the same one-compartment model. RESULTS When fitting with the one-compartment model, apparent kPL underestimated intracellular kPL by approximately 50% at an intracellular kPL of 0.02 s-1. This underestimation increased for larger kPL values. However, fitting the instantaneous mixing curves showed that diffusion accounted for only a small part of this underestimation. Fitting with the two-compartment model yielded more accurate intracellular kPL values. SIGNIFICANCE This work suggests diffusion is not a significant rate-limiting factor in pyruvate-to-lactate conversion given that our model assumptions hold true. In higher order models, diffusion effects may be accounted for by a term characterizing metabolite transport. Pharmacokinetic models used to analyze hyperpolarized pyruvate signal evolution should focus on carefully selecting the analytical model for fitting rather than accounting for diffusion effects.
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Cass JA, Williams CD, Irving TC, Lauga E, Malingen S, Daniel TL, Sponberg SN. A mechanism for sarcomere breathing: volume change and advective flow within the myofilament lattice. Biophys J 2021; 120:4079-4090. [PMID: 34384761 DOI: 10.1016/j.bpj.2021.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/19/2021] [Accepted: 08/04/2021] [Indexed: 11/28/2022] Open
Abstract
During muscle contraction, myosin motors anchored to thick filaments bind to and slide actin thin filaments. These motors rely on energy derived from ATP, supplied, in part, by diffusion from the sarcoplasm to the interior of the lattice of actin and myosin filaments. The radial spacing of filaments in this lattice may change or remain constant during contraction. If the lattice is isovolumetric, it must expand when the muscle shortens. If, however, the spacing is constant or has a different pattern of axial and radial motion, then the lattice changes volume during contraction, driving fluid motion and assisting in the transport of molecules between the contractile lattice and the surrounding intracellular space. We first create an advective-diffusive-reaction flow model and show that the flow into and out of the sarcomere lattice would be significant in the absence of lattice expansion. Advective transport coupled to diffusion has the potential to substantially enhance metabolite exchange within the crowded sarcomere. Using time-resolved x-ray diffraction of contracting muscle, we next show that the contractile lattice is neither isovolumetric nor constant in spacing. Instead, lattice spacing is time varying, depends on activation, and can manifest as an effective time-varying Poisson ratio. The resulting fluid flow in the sarcomere lattice of synchronous insect flight muscles is even greater than expected for constant lattice spacing conditions. Lattice spacing depends on a variety of factors that produce radial force, including cross-bridges, titin-like molecules, and other structural proteins. Volume change and advective transport varies with the phase of muscle stimulation during periodic contraction but remains significant at all conditions. Although varying in magnitude, advective transport will occur in all cases in which the sarcomere is not isovolumetric. Akin to "breathing," advective-diffusive transport in sarcomeres is sufficient to promote metabolite exchange and may play a role in the regulation of contraction itself.
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Affiliation(s)
- Julie A Cass
- Allen Institute for Cell Science, Seattle, Washington; Department of Biology, University of Washington, Seattle, Washington
| | - C David Williams
- Department of Biology, University of Washington, Seattle, Washington; Applied ML Group, Microsoft CSE, Redmond, Washington
| | - Thomas C Irving
- BioCAT and CSRRI, Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois
| | - Eric Lauga
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Sage Malingen
- Department of Biology, University of Washington, Seattle, Washington
| | - Thomas L Daniel
- Department of Biology, University of Washington, Seattle, Washington.
| | - Simon N Sponberg
- School of Physics & School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.
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Andrade SIE, Galvão RKH, Araujo MCU, Hadjiloucas S. Video-based fractional order identification of diffusion dynamics for the analysis of migration rates of polar and nonpolar liquids: Water and oil studies. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:035106. [PMID: 33819998 DOI: 10.1063/5.0010988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Diffusion dynamics of water and oil are observed in real-time using video images. Savitzky-Golay derivative filtering ensures accurate localization of the liquid front. System identification demonstrates that a fractional-order model with only two parameters may be used to describe the dynamics of the diffusion process. The method paves the way for video-based cellulose filter paper microfluidics and lateral flow assays, which are low cost and have broad diagnostic applications.
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Affiliation(s)
- Stefani I E Andrade
- Laboratório de Automação e Instrumentação em Química Analítica e Quimiometria (LAQA) Universidade Federal da Paraíba, CCEN, Departamento de Química, Caixa Postal 5093, 58051-970 João Pessoa, PB, Brazil
| | - Roberto K H Galvão
- Department of Electronics Engineering, Instituto Tecnológico de Aeronáutica, São José dos Campos, SP, Brazil
| | - Mario C U Araujo
- Laboratório de Automação e Instrumentação em Química Analítica e Quimiometria (LAQA) Universidade Federal da Paraíba, CCEN, Departamento de Química, Caixa Postal 5093, 58051-970 João Pessoa, PB, Brazil
| | - Sillas Hadjiloucas
- School of Biological Sciences, Department of Biomedical Engineering, The University of Reading, Reading RG6 6AY, United Kingdom
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Unrestrained ESCRT-III drives micronuclear catastrophe and chromosome fragmentation. Nat Cell Biol 2020; 22:856-867. [PMID: 32601372 DOI: 10.1038/s41556-020-0537-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/24/2020] [Indexed: 12/11/2022]
Abstract
The ESCRT-III membrane fission machinery maintains the integrity of the nuclear envelope. Although primary nuclei resealing takes minutes, micronuclear envelope ruptures seem to be irreversible. Instead, micronuclear ruptures result in catastrophic membrane collapse and are associated with chromosome fragmentation and chromothripsis, complex chromosome rearrangements thought to be a major driving force in cancer development. Here we use a combination of live microscopy and electron tomography, as well as computer simulations, to uncover the mechanism underlying micronuclear collapse. We show that, due to their small size, micronuclei inherently lack the capacity of primary nuclei to restrict the accumulation of CHMP7-LEMD2, a compartmentalization sensor that detects loss of nuclear integrity. This causes unrestrained ESCRT-III accumulation, which drives extensive membrane deformation, DNA damage and chromosome fragmentation. Thus, the nuclear-integrity surveillance machinery is a double-edged sword, as its sensitivity ensures rapid repair at primary nuclei while causing unrestrained activity at ruptured micronuclei, with catastrophic consequences for genome stability.
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Barredo WI, Bernido CC, Carpio-Bernido MV, Bornales JB. Modelling non-Markovian fluctuations in intracellular biomolecular transport. Math Biosci 2018; 297:27-31. [PMID: 29337131 DOI: 10.1016/j.mbs.2018.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 04/02/2017] [Accepted: 01/08/2018] [Indexed: 11/25/2022]
Abstract
To model non-Markovian fluctuations arising in biomolecular transport, we introduce a stochastic process with memory where Brownian motion is modulated sinusoidally. The probability density function and moments of this non-Markovian process are evaluated analytically as Hida stochastic functional integrals. Comparison of graphs of computed variance vis-á-vis empirical data for protein diffusion coefficients closely match with both exhibiting emergent superdiffusive then subdiffusive behavior for longer proteins.
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Affiliation(s)
- Wilson I Barredo
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines; Physics Department, Mindanao State University, Marawi City, 9700, Philippines
| | - Christopher C Bernido
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines; Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol, 6308, Philippines; Physics Department, University of San Carlos, Cebu City, 6000, Philippines.
| | - M Victoria Carpio-Bernido
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines; Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol, 6308, Philippines; Physics Department, University of San Carlos, Cebu City, 6000, Philippines
| | - Jinky B Bornales
- Physics Department, MSU-Iligan Institute of Technology, Tibanga, Iligan City, 9200, Philippines
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The structural and functional coordination of glycolytic enzymes in muscle: evidence of a metabolon? BIOLOGY 2014; 3:623-44. [PMID: 25247275 PMCID: PMC4192631 DOI: 10.3390/biology3030623] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/05/2014] [Accepted: 09/08/2014] [Indexed: 12/22/2022]
Abstract
Metabolism sustains life through enzyme-catalyzed chemical reactions within the cells of all organisms. The coupling of catalytic function to the structural organization of enzymes contributes to the kinetic optimization important to tissue-specific and whole-body function. This coupling is of paramount importance in the role that muscle plays in the success of Animalia. The structure and function of glycolytic enzyme complexes in anaerobic metabolism have long been regarded as a major regulatory element necessary for muscle activity and whole-body homeostasis. While the details of this complex remain to be elucidated through in vivo studies, this review will touch on recent studies that suggest the existence of such a complex and its structure. A potential model for glycolytic complexes and related subcomplexes is introduced.
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Discerning primary and secondary factors responsible for clinical fatigue in multisystem diseases. BIOLOGY 2014; 3:606-22. [PMID: 25247274 PMCID: PMC4192630 DOI: 10.3390/biology3030606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/21/2014] [Accepted: 09/01/2014] [Indexed: 01/03/2023]
Abstract
Fatigue is a common symptom of numerous acute and chronic diseases, including myalgic encephalomyelitis/chronic fatigue syndrome, multiple sclerosis, heart failure, cancer, and many others. In these multi-system diseases the physiological determinants of enhanced fatigue encompass a combination of metabolic, neurological, and myofibrillar adaptations. Previous research studies have focused on adaptations specific to skeletal muscle and their role in fatigue. However, most have neglected the contribution of physical inactivity in assessing disease syndromes, which, through deconditioning, likely contributes to symptomatic fatigue. In this commentary, we briefly review disease-related muscle phenotypes in the context of whether they relate to the primary disease or whether they develop secondary to reduced physical activity. Knowledge of the etiology of the skeletal muscle adaptations in these conditions and their contribution to fatigue symptoms is important for understanding the utility of exercise rehabilitation as an intervention to alleviate the physiological precipitants of fatigue.
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