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Rahmani S, Jafree DJ, Lee PD, Tafforeau P, Jacob J, Bellier A, Ackermann M, Jonigk DD, Shipley RJ, Long DA, Walsh CL. Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.28.534566. [PMID: 37034801 PMCID: PMC10081185 DOI: 10.1101/2023.03.28.534566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The architecture of the kidney vasculature is essential for its function. Although structural profiling of the intact rodent kidney vasculature has been performed, it is challenging to map vascular architecture of larger human organs. We hypothesised that hierarchical phase-contrast tomography (HiP-CT) would enable quantitative analysis of the entire human kidney vasculature. Combining label-free HiP-CT imaging of an intact kidney from a 63-year-old male with topology network analysis, we quantitated vasculature architecture in the human kidney down to the scale of arterioles. Although human and rat kidney vascular topologies are comparable, vascular radius decreases at a significantly faster rate in humans as vessels branch from artery towards the cortex. At branching points of large vessels, radii are theoretically optimised to minimise flow resistance, an observation not found for smaller arterioles. Structural differences in the vasculature were found in different spatial zones of the kidney reflecting their unique functional roles. Overall, this represents the first time the entire arterial vasculature of a human kidney has been mapped providing essential inputs for computational models of kidney vascular flow and synthetic vascular architectures, with implications for understanding how the structure of individual blood vessels collectively scales to facilitate organ function.
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Affiliation(s)
- Shahrokh Rahmani
- Department of Mechanical Engineering, University College London, London, UK, WC1E 6BT
| | - Daniyal J. Jafree
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK, WC1N 1EH
- UCL MB/PhD Programme, Faculty of Medical Science, University College London, London, UK, WC1E 6BT
| | - Peter D. Lee
- Department of Mechanical Engineering, University College London, London, UK, WC1E 6BT
| | - Paul Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France, 38043
| | - Joseph Jacob
- Satsuma Lab, Centre for Medical Image Computing, UCL, London, UK
- Lungs for Living Research Centre, UCL, London, UK
| | - Alexandre Bellier
- Department of Anatomy (LADAF), Grenoble Alpes University, Grenoble, France, 38058
| | - Maximilian Ackermann
- Institute of Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Pathology and Department of Molecular Pathology, Helios University Clinic Wuppertal, University of Witten-Herdecke, Wuppertal, Germany
| | - Danny D. Jonigk
- Institute of Pathology, RWTH Aachen Medical University, Aachen, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Rebecca J. Shipley
- Department of Mechanical Engineering, University College London, London, UK, WC1E 6BT
| | - David A. Long
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK, WC1N 1EH
| | - Claire L. Walsh
- Department of Mechanical Engineering, University College London, London, UK, WC1E 6BT
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Desai-Chowdhry P, Brummer AB, Mallavarapu S, Savage VM. Neuronal branching is increasingly asymmetric near synapses, potentially enabling plasticity while minimizing energy dissipation and conduction time. J R Soc Interface 2023; 20:20230265. [PMID: 37669695 PMCID: PMC10480011 DOI: 10.1098/rsif.2023.0265] [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] [Received: 05/04/2023] [Accepted: 08/15/2023] [Indexed: 09/07/2023] Open
Abstract
Neurons' primary function is to encode and transmit information in the brain and body. The branching architecture of axons and dendrites must compute, respond and make decisions while obeying the rules of the substrate in which they are enmeshed. Thus, it is important to delineate and understand the principles that govern these branching patterns. Here, we present evidence that asymmetric branching is a key factor in understanding the functional properties of neurons. First, we derive novel predictions for asymmetric scaling exponents that encapsulate branching architecture associated with crucial principles such as conduction time, power minimization and material costs. We compare our predictions with extensive data extracted from images to associate specific principles with specific biophysical functions and cell types. Notably, we find that asymmetric branching models lead to predictions and empirical findings that correspond to different weightings of the importance of maximum, minimum or total path lengths from the soma to the synapses. These different path lengths quantitatively and qualitatively affect energy, time and materials. Moreover, we generally observe that higher degrees of asymmetric branching-potentially arising from extrinsic environmental cues and synaptic plasticity in response to activity-occur closer to the tips than the soma (cell body).
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Affiliation(s)
- Paheli Desai-Chowdhry
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Samhita Mallavarapu
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Van M. Savage
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- Santa Fe Institute, Santa Fe, NM, USA
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Desai-Chowdhry P, Brummer AB, Mallavarapu S, Savage VM. Neuronal Branching is Increasingly Asymmetric Near Synapses, Potentially Enabling Plasticity While Minimizing Energy Dissipation and Conduction Time. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541591. [PMID: 37292687 PMCID: PMC10245708 DOI: 10.1101/2023.05.20.541591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Neurons' primary function is to encode and transmit information in the brain and body. The branching architecture of axons and dendrites must compute, respond, and make decisions while obeying the rules of the substrate in which they are enmeshed. Thus, it is important to delineate and understand the principles that govern these branching patterns. Here, we present evidence that asymmetric branching is a key factor in understanding the functional properties of neurons. First, we derive novel predictions for asymmetric scaling exponents that encapsulate branching architecture associated with crucial principles such as conduction time, power minimization, and material costs. We compare our predictions with extensive data extracted from images to associate specific principles with specific biophysical functions and cell types. Notably, we find that asymmetric branching models lead to predictions and empirical findings that correspond to different weightings of the importance of maximum, minimum, or total path lengths from the soma to the synapses. These different path lengths quantitatively and qualitatively affect energy, time, and materials. Moreover, we generally observe that higher degrees of asymmetric branching- potentially arising from extrinsic environmental cues and synaptic plasticity in response to activity- occur closer to the tips than the soma (cell body).
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Peeples J, Xu W, Gloaguen R, Rowland D, Zare A, Brym Z. Spatial and Texture Analysis of Root System distribution with Earth mover's Distance (STARSEED). PLANT METHODS 2023; 19:2. [PMID: 36604751 PMCID: PMC9814335 DOI: 10.1186/s13007-022-00974-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
PURPOSE Root system architectures are complex and challenging to characterize effectively for agronomic and ecological discovery. METHODS We propose a new method, Spatial and Texture Analysis of Root SystEm distribution with Earth mover's Distance (STARSEED), for comparing root system distributions that incorporates spatial information through a novel application of the Earth Mover's Distance (EMD). RESULTS We illustrate that the approach captures the response of sesame root systems for different genotypes and soil moisture levels. STARSEED provides quantitative and visual insights into changes that occur in root architectures across experimental treatments. CONCLUSION STARSEED can be generalized to other plants and provides insight into root system architecture development and response to varying growth conditions not captured by existing root architecture metrics and models. The code and data for our experiments are publicly available: https://github.com/GatorSense/STARSEED .
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Affiliation(s)
- Joshua Peeples
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77845 USA
| | - Weihuang Xu
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, 32611 USA
| | | | - Diane Rowland
- College of Natural Sciences, Forestry, and Agriculture, University of Maine, Orono, 04469 USA
| | - Alina Zare
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, 32611 USA
| | - Zachary Brym
- Tropical Research and Education Center, University of Florida, Gainesville, 33031 USA
- Department of Agronomy, University of Florida, Gainesville, 32611 USA
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Aaryasree K, Yagnik A, Chordiya PK, Choudhury K, Kumar P. Nature-Inspired Vascularised Materials and Devices for Biomedical Engineering. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2022. [DOI: 10.1016/j.cobme.2022.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Chown SL. Macrophysiology for decision‐making. J Zool (1987) 2022. [DOI: 10.1111/jzo.13029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- S. L. Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences Monash University Melbourne Victoria Australia
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Glazier DS. Variable metabolic scaling breaks the law: from 'Newtonian' to 'Darwinian' approaches. Proc Biol Sci 2022; 289:20221605. [PMID: 36259209 PMCID: PMC9579773 DOI: 10.1098/rspb.2022.1605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Life's size and tempo are intimately linked. The rate of metabolism varies with body mass in remarkably regular ways that can often be described by a simple power function, where the scaling exponent (b, slope in a log-linear plot) is typically less than 1. Traditional theory based on physical constraints has assumed that b is 2/3 or 3/4, following natural law, but hundreds of studies have documented extensive, systematic variation in b. This overwhelming, law-breaking, empirical evidence is causing a paradigm shift in metabolic scaling theory and methodology from ‘Newtonian’ to ‘Darwinian’ approaches. A new wave of studies focuses on the adaptable regulation and evolution of metabolic scaling, as influenced by diverse intrinsic and extrinsic factors, according to multiple context-dependent mechanisms, and within boundary limits set by physical constraints.
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Abstract
Biological allometries, such as the scaling of metabolism to mass, are hypothesized to result from natural selection to maximize how vascular networks fill space yet minimize internal transport distances and resistance to blood flow. Metabolic scaling theory argues two guiding principles—conservation of fluid flow and space-filling fractal distributions—describe a diversity of biological networks and predict how the geometry of these networks influences organismal metabolism. Yet, mostly absent from past efforts are studies that directly, and independently, measure metabolic rate from respiration and vascular architecture for the same organ, organism, or tissue. Lack of these measures may lead to inconsistent results and conclusions about metabolism, growth, and allometric scaling. We present simultaneous and consistent measurements of metabolic scaling exponents from clinical images of lung cancer, serving as a first-of-its-kind test of metabolic scaling theory, and identifying potential quantitative imaging biomarkers indicative of tumor growth. We analyze data for 535 clinical PET-CT scans of patients with non-small cell lung carcinoma to establish the presence of metabolic scaling between tumor metabolism and tumor volume. Furthermore, we use computer vision and mathematical modeling to examine predictions of metabolic scaling based on the branching geometry of the tumor-supplying blood vessel networks in a subset of 56 patients diagnosed with stage II-IV lung cancer. Examination of the scaling of maximum standard uptake value with metabolic tumor volume, and metabolic tumor volume with gross tumor volume, yield metabolic scaling exponents of 0.64 (0.20) and 0.70 (0.17), respectively. We compare these to the value of 0.85 (0.06) derived from the geometric scaling of the tumor-supplying vasculature. These results: (1) inform energetic models of growth and development for tumor forecasting; (2) identify imaging biomarkers in vascular geometry related to blood volume and flow; and (3) highlight unique opportunities to develop and test the metabolic scaling theory of ecology in tumors transitioning from avascular to vascular geometries.
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