1
|
Zhao J, Li X, Ji D, Bae J. Extrusion-based 3D printing of soft active materials. Chem Commun (Camb) 2024. [PMID: 38894652 DOI: 10.1039/d4cc01889c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Active materials are capable of responding to external stimuli, as observed in both natural and synthetic systems, from sensitive plants to temperature-responsive hydrogels. Extrusion-based 3D printing of soft active materials facilitates the fabrication of intricate geometries with spatially programmed compositions and architectures at various scales, further enhancing the functionality of materials. This Feature Article summarizes recent advances in extrusion-based 3D printing of active materials in both non-living (i.e., synthetic) and living systems. It highlights emerging ink formulations and architectural designs that enable programmable properties, with a focus on complex shape morphing and controllable light-emitting patterns. The article also spotlights strategies for engineering living materials that can produce genetically encoded material responses and react to a variety of environmental stimuli. Lastly, it discusses the challenges and prospects for advancements in both synthetic and living composite materials from the perspectives of chemistry, modeling, and integration.
Collapse
Affiliation(s)
- Jiayu Zhao
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California San Diego, La Jolla, CA 92093, USA.
| | - Xiao Li
- Material Science and Engineering Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Donghwan Ji
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California San Diego, La Jolla, CA 92093, USA.
| | - Jinhye Bae
- Aiiso Yufeng Li Family Department of Chemical and Nano Engineering, University of California San Diego, La Jolla, CA 92093, USA.
- Material Science and Engineering Program, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
2
|
Rong Q, Deng Y, Chen F, Yin Z, Hu L, Su X, Zhou D. Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400142. [PMID: 38676334 DOI: 10.1002/smll.202400142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 100 to 102 min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.
Collapse
Affiliation(s)
- Qinze Rong
- State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yingnan Deng
- State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Sinopec Key Laboratory of Research and Application of Medical and Hygienic Materials, Sinopec (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing, 100013, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Xin Su
- State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| |
Collapse
|
3
|
Geffen R, Braun C. Effects of Geometric Sound on Brainwave Activity Patterns, Autonomic Nervous System Markers, Emotional Response, and Faraday Wave Pattern Morphology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2024; 2024:9844809. [PMID: 38586300 PMCID: PMC10997421 DOI: 10.1155/2024/9844809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/28/2023] [Accepted: 01/31/2024] [Indexed: 04/09/2024]
Abstract
This study introduces Geometric Sound as a subfield of spatial sound featuring audio stimuli which are sonic holograms of mathematically defined 3D shapes. The effects of Geometric Sound on human physiology were investigated through EEG, heart rate, blood pressure, and a combination of questionnaires monitoring 50 healthy participants in two separate experiments. The impact of Geometric Sound on Faraday wave pattern morphology was further studied. The shapes examined, pyramid, cube, and sphere, exhibited varying significant effects on autonomic nervous system markers, brainwave power amplitude, topology, and connectivity patterns, in comparison to both the control (traditional stereo), and recorded baseline where no sound was presented. Brain activity in the Alpha band exhibited the most significant results, additional noteworthy results were observed across analysis paradigms in all frequency bands. Geometric Sound was found to significantly reduce heart rate and blood pressure and enhance relaxation and general well-being. Changes in EEG, heart rate, and blood pressure were primarily shape-dependent, and to a lesser extent sex-dependent. Pyramid Geometric Sound yielded the most significant results in most analysis paradigms. Faraday Waves patterns morphology analysis indicated that identical frequencies result in patterns that correlate with the excitation Geometric Sound shape. We suggest that Geometric Sound shows promise as a noninvasive therapeutic approach for physical and psychological conditions, stress-related disorders, depression, anxiety, and neurotrauma. Further research is warranted to elucidate underlying mechanisms and expand its applications.
Collapse
Affiliation(s)
| | - Christoph Braun
- Tübingen University, MEG-Center, Tübingen 72074, Germany
- HIH Hertie Institute for Clinical Brain Research, Tübingen, Germany
- CIMeC Center for Mind/Brain Sciences, University of Trento, Trento, Italy
| |
Collapse
|
4
|
Camacho-Vidales LJ, Robledo A. A Nonlinear Dynamical View of Kleiber's Law on the Metabolism of Plants and Animals. ENTROPY (BASEL, SWITZERLAND) 2023; 26:32. [PMID: 38248158 PMCID: PMC11154355 DOI: 10.3390/e26010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024]
Abstract
Kleiber's empirical law, which describes that metabolism increases as the mass to the power 3/4, has arguably remained life sciences' enigma since its formal uncovering in 1930. Why is this behavior sustained over many orders of magnitude? There have been quantitative rationalizations put forward for both plants and animals based on realistic mechanisms. However, universality in scaling laws of this kind, like in critical phenomena, has not yet received substantiation. Here, we provide an account, with quantitative reproduction of the available data, of the metabolism for these two biology kingdoms by means of broad arguments based on statistical mechanics and nonlinear dynamics. We consider iterated renormalization group (RG) fixed-point maps that are associated with an extensive generalized (Tsallis) entropy. We find two unique universality classes that satisfy the 3/4 power law. One corresponds to preferential attachment processes-rich gets richer-and the other to critical processes that suppress the effort for motion. We discuss and generalize our findings to other empirical laws that exhibit similar situations, using data based on general but different concepts that form a conjugate pair that gives rise to the same power-law exponents.
Collapse
Affiliation(s)
| | - Alberto Robledo
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, Mexico City 01000, Mexico
| |
Collapse
|
5
|
Packard GC. What is complex allometry? Biol Open 2023; 12:bio060148. [PMID: 38126464 PMCID: PMC10751937 DOI: 10.1242/bio.060148] [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: 09/09/2023] [Accepted: 10/14/2023] [Indexed: 12/23/2023] Open
Abstract
Complex allometry describes a smooth, curvilinear relationship between logarithmic transformations of a biological variable and a corresponding measure for body size when the observations are displayed on a bivariate graph with linear scaling. The curvature in such a display is commonly captured by fitting a quadratic equation to the distribution; and the quadratic term is typically interpreted, in turn, to mean that the mathematically equivalent equation for describing the arithmetic distribution is a two-parameter power equation with an exponent that changes with body size. A power equation with an exponent that is itself a function of body size is virtually uninterpretable, yet numerous attempts have been made in recent years to incorporate such an exponent into theoretical models for the evolution of form and function in both plants and animals. However, the curvature that is described by a quadratic equation fitted to logarithms usually means that an explicit, non-zero intercept is required in the power equation describing the untransformed distribution - not that the exponent in the power equation varies with body size. Misperceptions that commonly accompany reports of complex allometry can be avoided by using nonlinear regression to examine untransformed data.
Collapse
Affiliation(s)
- Gary C. Packard
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
6
|
Glazier DS. The Relevance of Time in Biological Scaling. BIOLOGY 2023; 12:1084. [PMID: 37626969 PMCID: PMC10452035 DOI: 10.3390/biology12081084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/13/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
Various phenotypic traits relate to the size of a living system in regular but often disproportionate (allometric) ways. These "biological scaling" relationships have been studied by biologists for over a century, but their causes remain hotly debated. Here, I focus on the patterns and possible causes of the body-mass scaling of the rates/durations of various biological processes and life-history events, i.e., the "pace of life". Many biologists have regarded the rate of metabolism or energy use as the master driver of the "pace of life" and its scaling with body size. Although this "energy perspective" has provided valuable insight, here I argue that a "time perspective" may be equally or even more important. I evaluate various major ways that time may be relevant in biological scaling, including as (1) an independent "fourth dimension" in biological dimensional analyses, (2) a universal "biological clock" that synchronizes various biological rates/durations, (3) a scaling method that uses various biological time periods (allochrony) as scaling metrics, rather than various measures of physical size (allometry), as traditionally performed, (4) an ultimate body-size-related constraint on the rates/timing of biological processes/events that is set by the inevitability of death, and (5) a geological "deep time" approach for viewing the evolution of biological scaling patterns. Although previously proposed universal four-dimensional space-time and "biological clock" views of biological scaling are problematic, novel approaches using allochronic analyses and time perspectives based on size-related rates of individual mortality and species origination/extinction may provide new valuable insights.
Collapse
|
7
|
Price CA. Flow similarity model predicts the allometry and allometric covariation of petiole dimensions. PLANT DIRECT 2023; 7:e510. [PMID: 37426892 PMCID: PMC10323609 DOI: 10.1002/pld3.510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 06/04/2023] [Indexed: 07/11/2023]
Abstract
Allometric relationships for plants, plant organs and plant parts, have long generated interest among biologists. Several prominent theoretical models based on biomechanical and/or hydraulic arguments have been introduced with mixed support. Here, I test a more recent offering, flow similarity, which is based on the conservation of volumetric flow rate and velocity. Using dimensional data for 935 petioles from 43 angiosperm species, I show that both the intraspecific and interspecific petiole allometries are more closely aligned with the predictions of the flow similarity model than that of elastic or geometric similarity. Further, allometric covariation among empirical scaling exponents falls along predicted functions with clustering around the flow similarity predictions. This work adds to the body of literature highlighting the importance of hydraulics in understanding the physiological basis of plant allometries, identifies previously unknown central tendencies in petiole allometry, and helps to delineate the scope within which the flow similarity model may be applicable.
Collapse
Affiliation(s)
- Charles A. Price
- National Institute for Mathematical and Biological SynthesisUniversity of TennesseeKnoxvilleTennesseeUSA
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| |
Collapse
|
8
|
Zhou X, Zheng Y, Zhang H, Yang L, Cui Y, Krishnan BP, Dong S, Aizenberg M, Xiong X, Hu Y, Aizenberg J, Cui J. Reversibly growing crosslinked polymers with programmable sizes and properties. Nat Commun 2023; 14:3302. [PMID: 37280214 DOI: 10.1038/s41467-023-38768-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
Growth constitutes a powerful method to post-modulate materials' structures and functions without compromising their mechanical performance for sustainable use, but the process is irreversible. To address this issue, we here report a growing-degrowing strategy that enables thermosetting materials to either absorb or release components for continuously changing their sizes, shapes, compositions, and a set of properties simultaneously. The strategy is based on the monomer-polymer equilibrium of networks in which supplying or removing small polymerizable components would drive the networks toward expansion or contraction. Using acid-catalyzed equilibration of siloxane as an example, we demonstrate that the size and mechanical properties of the resulting silicone materials can be significantly or finely tuned in both directions of growth and decomposition. The equilibration can be turned off to yield stable products or reactivated again. During the degrowing-growing circle, material structures are selectively varied either uniformly or heterogeneously, by the availability of fillers. Our strategy endows the materials with many appealing capabilities including environment adaptivity, self-healing, and switchability of surface morphologies, shapes, and optical properties. Since monomer-polymer equilibration exists in many polymers, we envision the expansion of the presented strategy to various systems for many applications.
Collapse
Affiliation(s)
- Xiaozhuang Zhou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Yijun Zheng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haohui Zhang
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, US
| | - Li Yang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Yubo Cui
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Baiju P Krishnan
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Shihua Dong
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Michael Aizenberg
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Xinhong Xiong
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China
| | - Yuhang Hu
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, US
- The School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, US
| | - Joanna Aizenberg
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Jiaxi Cui
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, China.
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany.
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
9
|
Sánchez-González JR, Nicieza AG. Declining metabolic scaling parallels an ontogenetic change from elongate to deep-bodied shapes in juvenile Brown trout. Curr Zool 2023; 69:294-303. [PMID: 37351295 PMCID: PMC10284058 DOI: 10.1093/cz/zoac042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 09/07/2023] Open
Abstract
Body shape and metabolic rate can be important determinants of animal performance, yet often their effects on influential traits are evaluated in a non-integrated way. This creates an important gap because the integration between shape and metabolism may be crucial to evaluate metabolic scaling theories. Here, we measured standard metabolic rate in 1- and 2-years old juvenile brown trout Salmo trutta, and used a geometric morphometrics approach to extricate the effects of ontogeny and size on the link between shape and metabolic scaling. We evidenced near-isometric ontogenetic scaling of metabolic rate with size, but also a biphasic pattern driven by a significant change in metabolic scaling, from positive to negative allometry. Moreover, the change in metabolic allometry parallels an ontogenetic change from elongate to deep-bodied shapes. This is consistent with the dynamic energy budget (DEB) and surface area (SA) theories, but not with the resource transport network theory which predicts increasing allometric exponents for trends towards more robust, three-dimensional bodies. In addition, we found a relationship between body shape and size independent metabolic rate, with a positive correlation between robustness and metabolic rate, which fits well within the view of Pace-of-Life Syndromes (POLS). Finally, our results align with previous studies that question the universality of metabolic scaling exponents and propose other mechanistic models explaining the diversity of metabolic scaling relationships or emphasizing the potential contribution of ecological factors.
Collapse
Affiliation(s)
- Jorge-Rubén Sánchez-González
- Department of Organisms and Systems Biology, University of Oviedo, 33006 Oviedo, Spain
- Department of Animal Science-Wildlife Section, University of Lleida, 25006 Lleida, Spain
| | - Alfredo G Nicieza
- Department of Organisms and Systems Biology, University of Oviedo, 33006 Oviedo, Spain
- Biodiversity Research Institute (IMIB), University of Oviedo-Principality of Asturias-CSIC, 33600 Mieres, Spain
| |
Collapse
|
10
|
Kurosawa Y, Mori S, Wang M, Pedro Ferrio J, Nishizono T, Yamaji K, Koyama K, Haruma T, Doyama K. Ontogenetic changes in root and shoot respiration, fresh mass and surface area of Fagus crenata. ANNALS OF BOTANY 2023; 131:313-322. [PMID: 36567503 PMCID: PMC9992930 DOI: 10.1093/aob/mcac143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS To date, studies on terrestrial plant ecology and evolution have focused primarily on the trade-off patterns in the allocation of metabolic production to roots and shoots in individual plants and the scaling of whole-plant respiration. However, few empirical studies have investigated the root : shoot ratio by considering scaling whole-plant respiration at various sizes throughout ontogeny. METHODS Here, using a whole-plant chamber system, we measured the respiration rates, fresh mass and surface area of entire roots and shoots from 377 Fagus crenata individuals, from germinating seeds to mature trees, collected from five different Japanese provenances. Non-linear regression analysis was performed for scaling of root and shoot respiration, fresh mass and surface area with body size. KEY RESULTS Whole-plant respiration increased rapidly in germinating seeds. In the seedling to mature tree size range, the scaling of whole-plant respiration to whole-plant fresh mass was expressed as a linear trend on the log-log coordinates (exponent slightly greater than 0.75). In the same body size range, root and shoot respiration vs. whole-plant fresh mass were modelled by upward-convex (exponent decreased from 2.35 to 0.638) and downward-convex trends (exponent increased from -0.918 to 0.864), respectively. The root fraction in whole-plant respiration, fresh mass and surface area shifted continuously throughout ontogeny, increasing in smaller seedlings during early growth stages and decreasing in larger trees. CONCLUSIONS Our results suggest a gradual shift in allocation priorities of metabolic energy from roots in seedlings to shoots in mature trees, providing insights into how roots contribute to shoot and whole-plant growth during ontogeny. The models of root : shoot ratio in relation to whole-plant physiology could be applied in tree growth modelling, and in linking the different levels of ecological phenomena, from individuals to ecosystems.
Collapse
Affiliation(s)
| | | | - Mofei Wang
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan
| | - Juan Pedro Ferrio
- Aragon Agency for Research and Development (ARAID), Zaragoza, Spain
- Department of Agricultural and Forest Systems and the Environment, Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
| | - Tomohiro Nishizono
- Department of Forest Management, Forestry and Forest Product Research Institute, Tsukuba, Ibaraki, Japan
| | - Keiko Yamaji
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Toshikatsu Haruma
- Division of Sustainable Resources Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kohei Doyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| |
Collapse
|
11
|
Summers HD, Wills JW, Rees P. Spatial statistics is a comprehensive tool for quantifying cell neighbor relationships and biological processes via tissue image analysis. CELL REPORTS METHODS 2022; 2:100348. [PMID: 36452868 PMCID: PMC9701617 DOI: 10.1016/j.crmeth.2022.100348] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Automated microscopy and computational image analysis has transformed cell biology, providing quantitative, spatially resolved information on cells and their constituent molecules from the sub-micron to the whole-organ scale. Here we explore the application of spatial statistics to the cellular relationships within tissue microscopy data and discuss how spatial statistics offers cytometry a powerful yet underused mathematical tool set for which the required data are readily captured using standard protocols and microscopy equipment. We also highlight the often-overlooked need to carefully consider the structural heterogeneity of tissues in terms of the applicability of different statistical measures and their accuracy and demonstrate how spatial analyses offer a great deal more than just basic quantification of biological variance. Ultimately, we highlight how statistical modeling can help reveal the hierarchical spatial processes that connect the properties of individual cells to the establishment of biological function.
Collapse
Affiliation(s)
- Huw D. Summers
- Department of Biomedical Engineering, Swansea University, Swansea SA1 8QQ, UK
| | - John W. Wills
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Paul Rees
- Department of Biomedical Engineering, Swansea University, Swansea SA1 8QQ, UK
| |
Collapse
|
12
|
Price CA, Drake P, Veneklaas EJ, Renton M. Flow similarity, stochastic branching, and quarter-power scaling in plants. PLANT PHYSIOLOGY 2022; 190:1854-1865. [PMID: 35920766 PMCID: PMC9614476 DOI: 10.1093/plphys/kiac358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
The origin of allometric scaling patterns that are multiples of one-fourth has long fascinated biologists. While not universal, quarter-power scaling relationships are common and have been described in all major clades. Several models have been advanced to explain the origin of such patterns, but questions regarding the discordance between model predictions and empirical data have limited their widespread acceptance. Notable among these is a fractal branching model that predicts power-law scaling of both metabolism and physical dimensions. While a power law is a useful first approximation to some data sets, nonlinear data compilations suggest the possibility of alternative mechanisms. Here, we show that quarter-power scaling can be derived using only the preservation of volume flow rate and velocity as model constraints. Applying our model to land plants, we show that incorporating biomechanical principles and allowing different parts of plant branching networks to be optimized to serve different functions predicts nonlinearity in allometric relationships and helps explain why interspecific scaling exponents covary along a fractal continuum. We also demonstrate that while branching may be a stochastic process, due to the conservation of volume, data may still be consistent with the expectations for a fractal network when one examines sub-trees within a tree. Data from numerous sources at the level of plant shoots, stems, and petioles show strong agreement with our model predictions. This theoretical framework provides an easily testable alternative to current general models of plant metabolic allometry.
Collapse
Affiliation(s)
| | - Paul Drake
- School of Biological Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia 6009, Australia
- Centre of Excellence for Climate Change, Woodland and Forest Health, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Erik J Veneklaas
- School of Biological Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia 6009, Australia
- Centre of Excellence for Climate Change, Woodland and Forest Health, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Michael Renton
- School of Biological Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia 6009, Australia
- Centre of Excellence for Climate Change, Woodland and Forest Health, University of Western Australia, Perth, Western Australia 6009, Australia
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Koyama K, Smith DD. Scaling the leaf length-times-width equation to predict total leaf area of shoots. ANNALS OF BOTANY 2022; 130:215-230. [PMID: 35350072 PMCID: PMC9445601 DOI: 10.1093/aob/mcac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS An individual plant consists of different-sized shoots, each of which consists of different-sized leaves. To predict plant-level physiological responses from the responses of individual leaves, modelling this within-shoot leaf size variation is necessary. Within-plant leaf trait variation has been well investigated in canopy photosynthesis models but less so in plant allometry. Therefore, integration of these two different approaches is needed. METHODS We focused on an established leaf-level relationship that the area of an individual leaf lamina is proportional to the product of its length and width. The geometric interpretation of this equation is that different-sized leaf laminas from a single species share the same basic form. Based on this shared basic form, we synthesized a new length-times-width equation predicting total shoot leaf area from the collective dimensions of leaves that comprise a shoot. Furthermore, we showed that several previously established empirical relationships, including the allometric relationships between total shoot leaf area, maximum individual leaf length within the shoot and total leaf number of the shoot, can be unified under the same geometric argument. We tested the model predictions using five species, all of which have simple leaves, selected from diverse taxa (Magnoliids, monocots and eudicots) and from different growth forms (trees, erect herbs and rosette herbs). KEY RESULTS For all five species, the length-times-width equation explained within-species variation of total leaf area of a shoot with high accuracy (R2 > 0.994). These strong relationships existed despite leaf dimensions scaling very differently between species. We also found good support for all derived predictions from the model (R2 > 0.85). CONCLUSIONS Our model can be incorporated to improve previous models of allometry that do not consider within-shoot size variation of individual leaves, providing a cross-scale linkage between individual leaf-size variation and shoot-size variation.
Collapse
Affiliation(s)
| | - Duncan D Smith
- Department of Botany, University of Wisconsin—Madison, 430 Lincoln Dr., Madison, WI, USA
| |
Collapse
|
15
|
Volkov I, Tovo A, Anfodillo T, Rinaldo A, Maritan A, Banavar JR. Seeing the forest for the trees through metabolic scaling. PNAS NEXUS 2022; 1:pgac008. [PMID: 36712800 PMCID: PMC9802057 DOI: 10.1093/pnasnexus/pgac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2021] [Accepted: 02/01/2022] [Indexed: 02/01/2023]
Abstract
We demonstrate that when power scaling occurs for an individual tree and in a forest, there is great resulting simplicity notwithstanding the underlying complexity characterizing the system over many size scales. Our scaling framework unifies seemingly distinct trends in a forest and provides a simple yet promising approach to quantitatively understand a bewilderingly complex many-body system with imperfectly known interactions. We show that the effective dimension, D tree , of a tree is close to 3, whereas a mature forest has D forest approaching 1. We discuss the energy equivalence rule and show that the metabolic rate-mass relationship is a power law with an exponent D/(D + 1) in both cases leading to a Kleiber's exponent of 3/4 for a tree and 1/2 for a forest. Our work has implications for understanding carbon sequestration and for climate science.
Collapse
Affiliation(s)
- Igor Volkov
- Department of Physics, The George Washington University, 20052 Washington, DC, USA
| | - Anna Tovo
- Dipartimento di Fisica “G. Galilei”, Università di Padova, 35131 Padova, Italy
| | - Tommaso Anfodillo
- Dipartimento Territorio e Sistemi Agro-Forestali, Università di Padova, 35020 Agripolis, Legnaro (PD), Italy
| | - Andrea Rinaldo
- Laboratory of Ecohydrology, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland,Dipartimento di Ingegneria Civile, Edile e Ambientale, Università di Padova, 35131 Padova, Italy
| | | | | |
Collapse
|
16
|
Xiong X, Wang S, Xue L, Wang H, Cui J. Growing Strategy for Postmodifying Cross-Linked Polymers' Bulky Size, Shape, and Mechanical Properties. ACS APPLIED MATERIALS & INTERFACES 2022; 14:8473-8481. [PMID: 35129323 DOI: 10.1021/acsami.1c23954] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Living organisms are open systems that can incorporate externally provided nutrients to vary their appearances and properties, while synthetic materials normally have fixed sizes, shapes, and functions. Herein, we report a strategy for enabling cross-linked polymers to continuously grow with programmable bulky structures and properties. The growing strategy involves repeatable processes including swelling of polymerizable components into the cross-linked polymers, in situ polymerization of the components, and homogenization of the original and newborn polymer networks. Using acrylate-based polymers as an example, we demonstrate that homogenization allows the grown polymer materials to further integrate various polymerizable components to alternate their bulky properties. During the growth, the changes from elastomers to organogels and then to hydrogels with updated covalent-linked functions (i.e., photochromism and thermoresponsiveness) are shown. Since this growing strategy is applicable to different acrylate systems, we envision its great potential in the design of next-generation polymers, smartening systems, and postmodification of cross-linked polymer materials.
Collapse
Affiliation(s)
- Xinhong Xiong
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang 313001, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
- INM─Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Sheng Wang
- INM─Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lulu Xue
- INM─Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Hong Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
| | - Jiaxi Cui
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou, Zhejiang 313001, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
- INM─Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| |
Collapse
|
17
|
Gavrilov VM, Golubeva TB, Bushuev AV. Evolution of metabolic scaling among the tetrapod: Effect of phylogeny, the geologic time of class formation and uniformity of species within a class. Integr Zool 2021; 17:904-917. [PMID: 34751509 DOI: 10.1111/1749-4877.12611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The metabolic scaling in the animal has been discussed for over 90 years, but no consensus has been reached. Our analysis of 2,126 species of vertebrates reveals a significant allometric exponent heterogeneity. We show that classes of terrestrial vertebrates exhibit the evolution of metabolic scaling. Both the allometric coefficient "a" and the allometric exponent "b" change naturally, but differently depending on the geological time of group formation. The allometric coefficient "a" shows the measure of the evolutionary development of systems that forms resting metabolism in animals. Endothermic classes, such as birds and mammals, have a metabolic rate that is in an order of magnitude higher than that in ectothermic classes, including amphibians and reptiles. In the terrestrial vertebrate phylogeny, we find that the metabolic scaling is characterized by three main allometric exponent values: b = 3/4 (mammals), b > 3/4 (ectotherms, such as amphibians and reptiles), and b < 3/4 (birds). The heterogeneity of the allometric exponent is a natural phenomenon associated with the general evolution of vertebrates. The scaling factor decreases depending on both the external design and the size (birds vs mammals) of the animal. The metabolic rate and uniformity of species within a class increase as the geological start date of formation of the class approaches the present time. The higher the mass-specific standard metabolic rate in the class, the slower metabolic rate grows with increasing body size in this class. Our results lay the groundwork for further exploration of the evolutionary and ecological aspects of the development of metabolic scaling in animals. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Valery M Gavrilov
- Department of Vertebrate Zoology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Zvenigorod Biological Station, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana B Golubeva
- Department of Vertebrate Zoology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Andrey V Bushuev
- Department of Vertebrate Zoology, M.V. Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
18
|
Ghilardi M, Schiettekatte NMD, Casey JM, Brandl SJ, Degregori S, Mercière A, Morat F, Letourneur Y, Bejarano S, Parravicini V. Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes. Ecol Evol 2021; 11:13218-13231. [PMID: 34646464 PMCID: PMC8495780 DOI: 10.1002/ece3.8045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 01/24/2023] Open
Abstract
Trait-based approaches are increasingly used to study species assemblages and understand ecosystem functioning. The strength of these approaches lies in the appropriate choice of functional traits that relate to the functions of interest. However, trait-function relationships are often supported by weak empirical evidence.Processes related to digestion and nutrient assimilation are particularly challenging to integrate into trait-based approaches. In fishes, intestinal length is commonly used to describe these functions. Although there is broad consensus concerning the relationship between fish intestinal length and diet, evolutionary and environmental forces have shaped a diversity of intestinal morphologies that is not captured by length alone.Focusing on coral reef fishes, we investigate how evolutionary history and ecology shape intestinal morphology. Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area.We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles.Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.
Collapse
Affiliation(s)
- Mattia Ghilardi
- Reef Systems Research GroupDepartment of EcologyLeibniz Centre for Tropical Marine Research (ZMT)BremenGermany
- Department of Marine EcologyFaculty of Biology and ChemistryUniversity of BremenBremenGermany
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
| | - Nina M. D. Schiettekatte
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
| | - Jordan M. Casey
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
- Department of Marine ScienceMarine Science InstituteUniversity of Texas at AustinPort AransasTXUSA
| | - Simon J. Brandl
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
- Department of Marine ScienceMarine Science InstituteUniversity of Texas at AustinPort AransasTXUSA
- CESABCentre for the Synthesis and Analysis of BiodiversityInstitut Bouisson BertrandMontpellierFrance
| | - Samuel Degregori
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | - Alexandre Mercière
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
| | - Fabien Morat
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
| | - Yves Letourneur
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
- UMR ENTROPIE (UR‐IRD‐CNRS‐IFREMER‐UNC)Université de la Nouvelle‐CalédonieNouméa CedexNew Caledonia
| | - Sonia Bejarano
- Reef Systems Research GroupDepartment of EcologyLeibniz Centre for Tropical Marine Research (ZMT)BremenGermany
| | - Valeriano Parravicini
- PSL Université Paris: EPHE‐UPVD‐CNRSUSR3278 CRIOBEPerpignanFrance
- Laboratoire d’Excellence “CORAIL”PerpignanFrance
- Institut Universitaire de FranceParisFrance
| |
Collapse
|
19
|
Pellizzoni E, Şologan M, Daka M, Pengo P, Marson D, Posel Z, Franchi S, Bignardi L, Franchi P, Lucarini M, Posocco P, Pasquato L. Thiolate end-group regulates ligand arrangement, hydration and affinity for small compounds in monolayer-protected gold nanoparticles. J Colloid Interface Sci 2021; 607:1373-1381. [PMID: 34583042 DOI: 10.1016/j.jcis.2021.09.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022]
Abstract
The ability to control the properties of monolayer protected gold nanoparticles (MPNPs) discloses unrevealed features stemming from collective properties of the ligands forming the monolayer and presents opportunities to design new materials. To date, the influence of ligand end-group size and capacity to form hydrogen bonds on structure and hydration of small MPNPs (<5 nm) has been poorly studied. Here, we show that both features determine ligands order, solvent accessibility, capacity to host hydrophobic compounds and interfacial properties of MPNPs. The polarity perceived by a radical probe and its binding constant with the monolayer investigated by electron spin resonance is rationalized by molecular dynamics simulations, which suggest that larger space-filling groups - trimethylammonium, zwitterionic and short polyethylene glycol - favor a radial organization of the thiolates, whereas smaller groups - as sulfonate - promote the formation of bundles. Zwitterionic ligands create a surface network of hydrogen bonds, which affects nanoparticle hydrophobicity and maximize the partition equilibrium constant of the probe. This study discloses the role of the chemistry of the end-group on monolayer features with effects that span from molecular- to nano-scale and opens the door to a shift in the conception of new MPNPs exploiting the end-group as a novel design motif.
Collapse
Affiliation(s)
- Elena Pellizzoni
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Maria Şologan
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Mario Daka
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy)
| | - Domenico Marson
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, (Italy)
| | - Zbyšek Posel
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, (Italy); Department of Informatics, Jan Evangelista Purkyně University, 400 96 Ústínad Labem, (Czech Republic)
| | - Stefano Franchi
- Elettra Sincrotrone Trieste S.C.p.A., 34149 Trieste, (Italy)
| | - Luca Bignardi
- Department of Physics, University of Trieste, 34127 Trieste, (Italy)
| | - Paola Franchi
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, (Italy)
| | - Marco Lucarini
- Department of Chemistry "G. Ciamician", University of Bologna, I-40126 Bologna, (Italy).
| | - Paola Posocco
- Department of Engineering and Architecture, University of Trieste, 34127 Trieste, (Italy).
| | - Lucia Pasquato
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Research Unit, University of Trieste, 34127 Trieste, (Italy).
| |
Collapse
|
20
|
Wang M, Mori S, Kurosawa Y, Ferrio JP, Yamaji K, Koyama K. Consistent scaling of whole-shoot respiration between Moso bamboo (Phyllostachys pubescens) and trees. JOURNAL OF PLANT RESEARCH 2021; 134:989-997. [PMID: 34115233 PMCID: PMC8364903 DOI: 10.1007/s10265-021-01320-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
Both Moso bamboo (Phyllostachys pubescens) and tree forests have a large biomass; they are considered to play an important role in ecosystem carbon budgets. The scaling relationship between individual whole-shoot (i.e., aboveground parts) respiration and whole-shoot mass provides a clue for comparing the carbon budgets of Moso bamboo and tree forests. However, nobody has empirically demonstrated whether there is a difference between these forest types in the whole-shoot scaling relationship. We developed whole-shoot chambers and measured the shoot respiration of 58 individual mature bamboo shoots from the smallest to the largest in a Moso bamboo forest, and then compared them with that of 254 tree shoots previously measured. For 30 bamboo shoots, we measured the respiration rate of leaves, branches, and culms. We found that the scaling exponent of whole-shoot respiration of bamboo fitted by a simple power function on a log-log scale was 0.843 (95 % CI 0.797-0.885), which was consistent with that of trees, 0.826 (95 % CI 0.799-0.851), but higher than 3/4, the value typifying the Kleiber's rule. The respiration rates of leaves, branches, and culms at the whole-shoot level were proportional to their mass, revealing a constant mean mass-specific respiration of 1.19, 0.224, and 0.0978 µmol CO2 kg- 1 s- 1, respectively. These constant values suggest common traits of organs among physiologically integrated ramets within a genet. Additionally, the larger the shoots, the smaller the allocation of organ mass to the metabolically active leaves, and the larger the allocation to the metabolically inactive culms. Therefore, these shifts in shoot-mass partitioning to leaves and culms caused a negative metabolic scaling of Moso bamboo shoots. The observed convergent metabolic scaling of Moso bamboo and trees may facilitate comparisons of the ecosystem carbon budgets of Moso bamboo and tree forests.
Collapse
Affiliation(s)
- Mofei Wang
- The United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate, 020-8550, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, 997-8555, Japan
| | - Shigeta Mori
- The United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate, 020-8550, Japan.
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, 997-8555, Japan.
| | - Yoko Kurosawa
- The United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate, 020-8550, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, 997-8555, Japan
| | - Juan Pedro Ferrio
- Aragon Agency for Research and Development (ARAID), 50018, Zaragoza, Spain
- Department of Forest Resources, Agrifood Research and Technology Centre of Aragon (CITA), 50059, Zaragoza, Spain
| | - Keiko Yamaji
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Kohei Koyama
- Department of Agro-environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, 080-8555, Japan
| |
Collapse
|
21
|
Nowak J, Eng RC, Matz T, Waack M, Persson S, Sampathkumar A, Nikoloski Z. A network-based framework for shape analysis enables accurate characterization of leaf epidermal cells. Nat Commun 2021; 12:458. [PMID: 33469016 PMCID: PMC7815848 DOI: 10.1038/s41467-020-20730-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023] Open
Abstract
Cell shape is crucial for the function and development of organisms. Yet, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Here, we introduce a visibility graph representation of shapes that facilitates network-driven characterization and analyses across shapes encountered in different domains. Using the example of complex shape of leaf pavement cells, we show that our framework accurately quantifies cell protrusions and invaginations and provides additional functionality in comparison to the contending approaches. We further show that structural properties of the visibility graphs can be used to quantify pavement cell shape complexity and allow for classification of plants into their respective phylogenetic clades. Therefore, the visibility graphs provide a robust and unique framework to accurately quantify and classify the shape of different objects.
Collapse
Affiliation(s)
- Jacqueline Nowak
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Ryan Christopher Eng
- Plant Cell Biology and Microscopy, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Timon Matz
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Matti Waack
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Department for Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Arun Sampathkumar
- Plant Cell Biology and Microscopy, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
| |
Collapse
|
22
|
Zhong M, Cerabolini BEL, Castro‐Díez P, Puyravaud J, Cornelissen JHC. Allometric co-variation of xylem and stomata across diverse woody seedlings. PLANT, CELL & ENVIRONMENT 2020; 43:2301-2310. [PMID: 32542660 PMCID: PMC7496827 DOI: 10.1111/pce.13826] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 06/08/2020] [Indexed: 05/14/2023]
Abstract
Leaf stomatal density is known to co-vary with leaf vein density. However, the functional underpinning of this relation, and how it scales to whole-plant water transport anatomy, is still unresolved. We hypothesized that the balance of water exchange between the vapour phase (in stomata) and liquid phase (in vessels) depends on the consistent scaling between the summed stomatal areas and xylem cross-sectional areas, both at the whole-plant and single-leaf level. This predicted size co-variation should be driven by the co-variation of numbers of stomata and terminal vessels. We examined the relationships of stomatal traits and xylem anatomical traits from the entire plant to individual leaves across seedlings of 53 European woody angiosperm species. There was strong and convergent scaling between total stomatal area and stem xylem area per plant and between leaf total stomatal area and midvein xylem area per leaf across all the species, irrespective of variation in leaf habit, growth-form or relative growth rate. Moreover, strong scaling was found between stomatal number and terminal vessel number, whereas not in their respective average areas. Our findings have broad implications for integrating xylem architecture and stomatal distribution and deepen our understanding of the design rules of plants' water transport network.
Collapse
Affiliation(s)
- Mengying Zhong
- Systems Ecology, Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
- Grassland Science Department, College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | | | - Pilar Castro‐Díez
- Departamento de Ciencias de la Vida, Facultad de CienciasUniversidad de Alcalá, Carretera Madrid‐BarcelonaMadridSpain
| | | | | |
Collapse
|
23
|
Comparison of natural and pharmacological hypothermia in animals: Determination of activation energy of metabolism. J Therm Biol 2020; 92:102658. [DOI: 10.1016/j.jtherbio.2020.102658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
|
24
|
Exploiting the role of nanoparticle shape in enhancing hydrogel adhesive and mechanical properties. Nat Commun 2020; 11:1420. [PMID: 32184392 PMCID: PMC7078206 DOI: 10.1038/s41467-020-15206-y] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/13/2020] [Indexed: 01/29/2023] Open
Abstract
The ability to control nanostructure shape and dimensions presents opportunities to design materials in which their macroscopic properties are dependent upon the nature of the nanoparticle. Although particle morphology has been recognized as a crucial parameter, the exploitation of the potential shape-dependent properties has, to date, been limited. Herein, we demonstrate that nanoparticle shape is a critical consideration in the determination of nanocomposite hydrogel properties. Using translationally relevant calcium-alginate hydrogels, we show that the use of poly(L-lactide)-based nanoparticles with platelet morphology as an adhesive results in a significant enhancement of adhesion over nanoparticle glues comprised of spherical or cylindrical micelles. Furthermore, gel nanocomposites containing platelets showed an enhanced resistance to breaking under strain compared to their spherical and cylindrical counterparts. This study opens the doors to a change in direction in the field of gel nanocomposites, where nanoparticle shape plays an important role in tuning mechanical properties. The ability to control nanostructure shape and dimensions presents opportunities to design materials in which their macroscopic properties are dependent upon the nature of the nanoparticle. Here the authors show nanoparticle shape is a critical consideration in the determination of nanocomposite hydrogel properties.
Collapse
|
25
|
Cepeda D, Álamo D, Sánchez N, Pardos F. Allometric growth in meiofaunal invertebrates: do all kinorhynchs show homogeneous trends? Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Allometry determines relevant modifications in metazoan morphology and biology and is affected by many different factors, such as ontogenetic constraints and natural selection. A linear mixed model approach and reduced major axis regression were used to explore evolutionary interspecific allometric trends between the total trunk length and the lengths of the segments and spines in the phylum Kinorhyncha at three taxonomic levels: the whole phylum, the class and the family. Statistically significant results were found in all the trunk segments, meaning that these body units grow proportionally correlated with the body, contrary to the results obtained for the spines. Developmental and morphophysiological constraints could lead to negative allometry in the first and last segments, because these body regions in kinorhynchs are essential to the implementation of some of the main biological functions, such as feeding and locomotion. The differential arrangement of cuticular appendages between the taxonomic groups considered seems to cause different evolutionary trends, because positive allometry may appear if a segment requires more space to accommodate a large number of organs and appendages, and vice versa. The presence of sexual dimorphism could also define positive allometry of a segment, owing to the need to harbour the sexually dimorphic appendages and their associated structures.
Collapse
Affiliation(s)
- Diego Cepeda
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University, Madrid, Spain
| | - David Álamo
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University, Madrid, Spain
| | - Nuria Sánchez
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University, Madrid, Spain
| | - Fernando Pardos
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University, Madrid, Spain
| |
Collapse
|
26
|
Generalized size scaling of metabolic rates based on single-cell measurements with freshwater phytoplankton. Proc Natl Acad Sci U S A 2019; 116:17323-17329. [PMID: 31409712 PMCID: PMC6717286 DOI: 10.1073/pnas.1906762116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kleiber's law describes the scaling of metabolic rate with body size across several orders of magnitude in size and across taxa and is widely regarded as a fundamental law in biology. The physiological origins of Kleiber's law are still debated and generalizations of the law accounting for deviations from the scaling behavior have been proposed. Most theoretical and experimental studies of Kleiber's law, however, have focused on the relationship between the average body size of a species and its mean metabolic rate, neglecting intraspecific variation of these 2 traits. Here, we propose a theoretical characterization of such variation and report on proof-of-concept experiments with freshwater phytoplankton supporting such framework. We performed joint measurements at the single-cell level of cell volume and nitrogen/carbon uptake rates, as proxies of metabolic rates, of 3 phytoplankton species using nanoscale secondary ion mass spectrometry (NanoSIMS) and stable isotope labeling. Common scaling features of the distribution of nutrient uptake rates and cell volume are found to hold across 3 orders of magnitude in cell size. Once individual measurements of cell volume and nutrient uptake rate within a species are appropriately rescaled by a function of the average cell volume within each species, we find that intraspecific distributions of cell volume and metabolic rates collapse onto a universal curve. Based on the experimental results, this work provides the building blocks for a generalized form of Kleiber's law incorporating intraspecific, correlated variations of nutrient-uptake rates and body sizes.
Collapse
|
27
|
Corliss BA, Mathews C, Doty R, Rohde G, Peirce SM. Methods to label, image, and analyze the complex structural architectures of microvascular networks. Microcirculation 2019; 26:e12520. [PMID: 30548558 PMCID: PMC6561846 DOI: 10.1111/micc.12520] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 11/26/2018] [Indexed: 12/30/2022]
Abstract
Microvascular networks play key roles in oxygen transport and nutrient delivery to meet the varied and dynamic metabolic needs of different tissues throughout the body, and their spatial architectures of interconnected blood vessel segments are highly complex. Moreover, functional adaptations of the microcirculation enabled by structural adaptations in microvascular network architecture are required for development, wound healing, and often invoked in disease conditions, including the top eight causes of death in the Unites States. Effective characterization of microvascular network architectures is not only limited by the available techniques to visualize microvessels but also reliant on the available quantitative metrics that accurately delineate between spatial patterns in altered networks. In this review, we survey models used for studying the microvasculature, methods to label and image microvessels, and the metrics and software packages used to quantify microvascular networks. These programs have provided researchers with invaluable tools, yet we estimate that they have collectively attained low adoption rates, possibly due to limitations with basic validation, segmentation performance, and nonstandard sets of quantification metrics. To address these existing constraints, we discuss opportunities to improve effectiveness, rigor, and reproducibility of microvascular network quantification to better serve the current and future needs of microvascular research.
Collapse
Affiliation(s)
- Bruce A Corliss
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Corbin Mathews
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Richard Doty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Gustavo Rohde
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Shayn M Peirce
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| |
Collapse
|
28
|
Thommen A, Werner S, Frank O, Philipp J, Knittelfelder O, Quek Y, Fahmy K, Shevchenko A, Friedrich BM, Jülicher F, Rink JC. Body size-dependent energy storage causes Kleiber's law scaling of the metabolic rate in planarians. eLife 2019; 8:e38187. [PMID: 30608231 PMCID: PMC6320072 DOI: 10.7554/elife.38187] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022] Open
Abstract
Kleiber's law, or the 3/4 -power law scaling of the metabolic rate with body mass, is considered one of the few quantitative laws in biology, yet its physiological basis remains unknown. Here, we report Kleiber's law scaling in the planarian Schmidtea mediterranea. Its reversible and life history-independent changes in adult body mass over 3 orders of magnitude reveal that Kleiber's law does not emerge from the size-dependent decrease in cellular metabolic rate, but from a size-dependent increase in mass per cell. Through a combination of experiment and theoretical analysis of the organismal energy balance, we further show that the mass allometry is caused by body size dependent energy storage. Our results reveal the physiological origins of Kleiber's law in planarians and have general implications for understanding a fundamental scaling law in biology.
Collapse
Affiliation(s)
- Albert Thommen
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Steffen Werner
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- FOM Institute AMOLFAmsterdamThe Netherlands
| | - Olga Frank
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jenny Philipp
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource EcologyDresdenGermany
| | | | - Yihui Quek
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Massachusetts Institute of TechnologyCambridgeUnited States
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource EcologyDresdenGermany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Benjamin M Friedrich
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
- Center for Advancing Electronics DresdenTechnische Universität DresdenDresdenGermany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| |
Collapse
|
29
|
Harwig MC, Viana MP, Egner JM, Harwig JJ, Widlansky ME, Rafelski SM, Hill RB. Methods for imaging mammalian mitochondrial morphology: A prospective on MitoGraph. Anal Biochem 2018; 552:81-99. [PMID: 29505779 DOI: 10.1016/j.ab.2018.02.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/06/2018] [Accepted: 02/22/2018] [Indexed: 12/22/2022]
Abstract
Mitochondria are found in a variety of shapes, from small round punctate structures to a highly interconnected web. This morphological diversity is important for function, but complicates quantification. Consequently, early quantification efforts relied on various qualitative descriptors that understandably reduce the complexity of the network leading to challenges in consistency across the field. Recent application of state-of-the-art computational tools have resulted in more quantitative approaches. This prospective highlights the implementation of MitoGraph, an open-source image analysis platform for measuring mitochondrial morphology initially optimized for use with Saccharomyces cerevisiae. Here Mitograph was assessed on five different mammalian cells types, all of which were accurately segmented by MitoGraph analysis. MitoGraph also successfully differentiated between distinct mitochondrial morphologies that ranged from entirely fragmented to hyper-elongated. General recommendations are also provided for confocal imaging of labeled mitochondria (using mito-YFP, MitoTracker dyes and immunostaining parameters). Widespread adoption of MitoGraph will help achieve a long-sought goal of consistent and reproducible quantification of mitochondrial morphology.
Collapse
Affiliation(s)
- Megan C Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, United States
| | - Matheus P Viana
- Visual Analytics and Comprehension Group, IBM Research, Brazil; Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA, 92697, United States
| | - John M Egner
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, United States
| | | | - Michael E Widlansky
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, 53226, United States
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA, 92697, United States; Assay Development, Allen Institute for Cell Science, Seattle, WA, 98109, United States
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, United States.
| |
Collapse
|
30
|
Rediscovering and Reviving Old Observations and Explanations of Metabolic Scaling in Living Systems. SYSTEMS 2018. [DOI: 10.3390/systems6010004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
31
|
Ballesteros FJ, Martinez VJ, Luque B, Lacasa L, Valor E, Moya A. On the thermodynamic origin of metabolic scaling. Sci Rep 2018; 8:1448. [PMID: 29362491 PMCID: PMC5780499 DOI: 10.1038/s41598-018-19853-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023] Open
Abstract
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument predicts. The universality of exponent 3/4 -claimed in terms of the fractal properties of the nutrient network- has recently been challenged according to empirical evidence that observed a wealth of robust exponents deviating from 3/4. Here we present a conceptually simple thermodynamic framework, where the dependence of metabolic rate with body mass emerges from a trade-off between the energy dissipated as heat and the energy efficiently used by the organism to maintain its metabolism. This balance tunes the shape of an additive model from which different effective scalings can be recovered as particular cases, thereby reconciling previously inconsistent empirical evidence in mammals, birds, insects and even plants under a unified framework. This model is biologically motivated, fits remarkably well the data, and also explains additional features such as the relation between energy lost as heat and mass, the role and influence of different climatic environments or the difference found between endotherms and ectotherms.
Collapse
Affiliation(s)
- Fernando J Ballesteros
- Observatori Astronòmic, Universitat de València, Parque Científico de la Universitat de València, Paterna, Spain.
| | - Vicent J Martinez
- Observatori Astronòmic, Universitat de València, Parque Científico de la Universitat de València, Paterna, Spain
| | - Bartolo Luque
- Departamento de Matemática Aplicada y Estadística, ETSI Aeronauticos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Lucas Lacasa
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London, E14NS, UK
| | - Enric Valor
- Departament de Física de la Terra i Termodinàmica, Universitat de València, Valencia, Spain
| | - Andrés Moya
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Parque Científico de la Universitat de València, Paterna, Spain
| |
Collapse
|
32
|
Packard GC. Why allometric variation in mammalian metabolism is curvilinear on the logarithmic scale. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2018; 327:537-541. [DOI: 10.1002/jez.2129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/17/2017] [Accepted: 10/30/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Gary C. Packard
- Department of Biology; Colorado State University; Fort Collins Colorado USA
| |
Collapse
|
33
|
Covariations in ecological scaling laws fostered by community dynamics. Proc Natl Acad Sci U S A 2017; 114:10672-10677. [PMID: 28830995 DOI: 10.1073/pnas.1708376114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Scaling laws in ecology, intended both as functional relationships among ecologically relevant quantities and the probability distributions that characterize their occurrence, have long attracted the interest of empiricists and theoreticians. Empirical evidence exists of power laws associated with the number of species inhabiting an ecosystem, their abundances, and traits. Although their functional form appears to be ubiquitous, empirical scaling exponents vary with ecosystem type and resource supply rate. The idea that ecological scaling laws are linked has been entertained before, but the full extent of macroecological pattern covariations, the role of the constraints imposed by finite resource supply, and a comprehensive empirical verification are still unexplored. Here, we propose a theoretical scaling framework that predicts the linkages of several macroecological patterns related to species' abundances and body sizes. We show that such a framework is consistent with the stationary-state statistics of a broad class of resource-limited community dynamics models, regardless of parameterization and model assumptions. We verify predicted theoretical covariations by contrasting empirical data and provide testable hypotheses for yet unexplored patterns. We thus place the observed variability of ecological scaling exponents into a coherent statistical framework where patterns in ecology embed constrained fluctuations.
Collapse
|
34
|
Packard GC. Misconceptions about logarithmic transformation and the traditional allometric method. ZOOLOGY 2017; 123:115-120. [DOI: 10.1016/j.zool.2017.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 01/19/2023]
|
35
|
Harrison JF. Do Performance-Safety Tradeoffs Cause Hypometric Metabolic Scaling in Animals? Trends Ecol Evol 2017; 32:653-664. [PMID: 28760361 DOI: 10.1016/j.tree.2017.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/25/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Abstract
Hypometric scaling of aerobic metabolism in animals has been widely attributed to constraints on oxygen (O2) supply in larger animals, but recent findings demonstrate that O2 supply balances with need regardless of size. Larger animals also do not exhibit evidence of compensation for O2 supply limitation. Because declining metabolic rates (MRs) are tightly linked to fitness, this provides significant evidence against the hypothesis that constraints on supply drive hypometric scaling. As an alternative, ATP demand might decline in larger animals because of performance-safety tradeoffs. Larger animals, which typically reproduce later, exhibit risk-reducing strategies that lower MR. Conversely, smaller animals are more strongly selected for growth and costly neurolocomotory performance, elevating metabolism.
Collapse
Affiliation(s)
- Jon F Harrison
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA.
| |
Collapse
|
36
|
Sheldon spectrum and the plankton paradox: two sides of the same coin—a trait-based plankton size-spectrum model. J Math Biol 2017; 76:67-96. [PMID: 28547211 PMCID: PMC5754429 DOI: 10.1007/s00285-017-1132-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 04/18/2017] [Indexed: 01/25/2023]
|
37
|
Holló G. Demystification of animal symmetry: symmetry is a response to mechanical forces. Biol Direct 2017; 12:11. [PMID: 28514948 PMCID: PMC5436448 DOI: 10.1186/s13062-017-0182-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
ᅟ Symmetry is an eye-catching feature of animal body plans, yet its causes are not well enough understood. The evolution of animal form is mainly due to changes in gene regulatory networks (GRNs). Based on theoretical considerations regarding fundamental GRN properties, it has recently been proposed that the animal genome, on large time scales, should be regarded as a system which can construct both the main symmetries – radial and bilateral – simultaneously; and that the expression of any of these depends on functional constraints. Current theories explain biological symmetry as a pattern mostly determined by phylogenetic constraints, and more by chance than by necessity. In contrast to this conception, I suggest that physical effects, which in many cases act as proximate, direct, tissue-shaping factors during ontogenesis, are also the ultimate causes – i.e. the indirect factors which provide a selective advantage – of animal symmetry, from organs to body plan level patterns. In this respect, animal symmetry is a necessary product of evolution. This proposition offers a parsimonious view of symmetry as a basic feature of the animal body plan, suggesting that molecules and physical forces act in a beautiful harmony to create symmetrical structures, but that the concert itself is directed by the latter. Reviewers This article was reviewed by Eugene Koonin, Zoltán Varga and Michaël Manuel.
Collapse
Affiliation(s)
- Gábor Holló
- Institute of Psychology, University of Debrecen, H-4002, Debrecen, P.O. Box 400, Hungary.
| |
Collapse
|
38
|
Glazier DS, Paul DA. Ecology of ontogenetic body-mass scaling of gill surface area in a freshwater crustacean. ACTA ACUST UNITED AC 2017; 220:2120-2127. [PMID: 28373596 DOI: 10.1242/jeb.155242] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/24/2017] [Indexed: 01/03/2023]
Abstract
Several studies have documented ecological effects on intraspecific and interspecific body-size scaling of metabolic rate. However, little is known about how various ecological factors may affect the scaling of respiratory structures supporting oxygen uptake for metabolism. To our knowledge, our study is the first to provide evidence for ecological effects on the scaling of a respiratory structure among conspecific populations of any animal. We compared the body-mass scaling of gill surface area (SA) among eight spring-dwelling populations of the amphipod crustacean Gammarus minus Although gill SA scaling was not related to water temperature, conductivity or G. minus population density, it was significantly related to predation regime (and secondarily to pH). Body-mass scaling slopes for gill SA were significantly lower in four populations inhabiting springs with fish predators than for four populations in springs without fish (based on comparing means of the population slopes, or slopes calculated from pooled raw data for each comparison group). As a result, gill SA was proportionately smaller in adult amphipods from springs with versus without fish. This scaling difference paralleled similar differences in the scaling exponents for the rates of growth and resting metabolic rate. We hypothesized that gill SA scaling is shallower in fish-containing versus fishless spring populations of G. minus because of effects of size-selective predation on size-specific growth and activity that in turn affect the scaling of oxygen demand and concomitantly the gill capacity (SA) for oxygen uptake. Although influential theory claims that metabolic scaling is constrained by internal body design, our study builds on previous work to show that the scaling of both metabolism and the respiratory structures supporting it may be ecologically sensitive and evolutionarily malleable.
Collapse
Affiliation(s)
- Douglas S Glazier
- Department of Biology, Juniata College, 1700 Moore Street, Huntingdon, PA 16652, USA
| | - David A Paul
- Aqua Pennsylvania, 644 North Water Avenue, Sharon, PA 16146, USA
| |
Collapse
|
39
|
A general model for metabolic scaling in self-similar asymmetric networks. PLoS Comput Biol 2017; 13:e1005394. [PMID: 28319153 PMCID: PMC5378416 DOI: 10.1371/journal.pcbi.1005394] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 04/03/2017] [Accepted: 02/01/2017] [Indexed: 11/19/2022] Open
Abstract
How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE) model argues that these two principles (space-filling and energy minimization) are (i) general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii) can be used to predict how the resulting geometry of biological networks then governs their allometric scaling. Perhaps the most central biological allometry is how metabolic rate scales with body size. A core assumption of the WBE model is that networks are symmetric with respect to their geometric properties. That is, any two given branches within the same generation in the network are assumed to have identical lengths and radii. However, biological networks are rarely if ever symmetric. An open question is: Does incorporating asymmetric branching change or influence the predictions of the WBE model? We derive a general network model that relaxes the symmetric assumption and define two classes of asymmetrically bifurcating networks. We show that asymmetric branching can be incorporated into the WBE model. This asymmetric version of the WBE model results in several theoretical predictions for the structure, physiology, and metabolism of organisms, specifically in the case for the cardiovascular system. We show how network asymmetry can now be incorporated in the many allometric scaling relationships via total network volume. Most importantly, we show that the 3/4 metabolic scaling exponent from Kleiber’s Law can still be attained within many asymmetric networks. We present a model for incorporating geometrically asymmetric branching into biological resource distribution networks. Our work shows how space-filling and fluid flow principles constrain allowed branching morphologies within the context of our model. Simultaneously, we demonstrate that there is a wide range of asymmetrically branching network architectures that still give rise to 3/4 metabolic scaling exponents.
Collapse
|
40
|
Koyama K, Yamamoto K, Ushio M. A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees. Proc Biol Sci 2017; 284:20162395. [PMID: 28053062 PMCID: PMC5247503 DOI: 10.1098/rspb.2016.2395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/05/2016] [Indexed: 11/12/2022] Open
Abstract
Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees (Ulmus davidiana), the end products of a self-similar branching process, approaches a lognormal distribution. We measured the length of the stem segments of three elm branches and obtained the following results: (i) each occurrence of branching caused variations or errors in the lengths of the child stems relative to their parent stems; (ii) the branches showed statistical self-similarity; the observed error distributions were similar at all scales within each branch and (iii) the multiplicative effect of these errors generated variations of the lengths of terminal twigs that were well approximated by a lognormal distribution, although some statistically significant deviations from strict lognormality were observed for one branch. Our results provide the first empirical evidence that statistical self-similarity of an organismal form generates a lognormal distribution of organ sizes.
Collapse
Affiliation(s)
- Kohei Koyama
- Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro 080-8555, Japan
| | - Ken Yamamoto
- Department of Physics, Faculty of Science and Engineering, Chuo University, Bunkyo, Tokyo 112-8551, Japan
| | - Masayuki Ushio
- Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu 520-2194, Japan
- Joint Research Center for Science and Technology, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu 520-2194, Japan
| |
Collapse
|
41
|
Tekin E, Hunt D, Newberry MG, Savage VM. Do Vascular Networks Branch Optimally or Randomly across Spatial Scales? PLoS Comput Biol 2016; 12:e1005223. [PMID: 27902691 PMCID: PMC5130167 DOI: 10.1371/journal.pcbi.1005223] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/29/2016] [Indexed: 01/24/2023] Open
Abstract
Modern models that derive allometric relationships between metabolic rate and body mass are based on the architectural design of the cardiovascular system and presume sibling vessels are symmetric in terms of radius, length, flow rate, and pressure. Here, we study the cardiovascular structure of the human head and torso and of a mouse lung based on three-dimensional images processed via our software Angicart. In contrast to modern allometric theories, we find systematic patterns of asymmetry in vascular branching, potentially explaining previously documented mismatches between predictions (power-law or concave curvature) and observed empirical data (convex curvature) for the allometric scaling of metabolic rate. To examine why these systematic asymmetries in vascular branching might arise, we construct a mathematical framework to derive predictions based on local, junction-level optimality principles that have been proposed to be favored in the course of natural selection and development. The two most commonly used principles are material-cost optimizations (construction materials or blood volume) and optimization of efficient flow via minimization of power loss. We show that material-cost optimization solutions match with distributions for asymmetric branching across the whole network but do not match well for individual junctions. Consequently, we also explore random branching that is constrained at scales that range from local (junction-level) to global (whole network). We find that material-cost optimizations are the strongest predictor of vascular branching in the human head and torso, whereas locally or intermediately constrained random branching is comparable to material-cost optimizations for the mouse lung. These differences could be attributable to developmentally-programmed local branching for larger vessels and constrained random branching for smaller vessels. The architecture of vascular networks must balance complex demands to efficiently deliver oxygen and resources throughout the entire body. These demands constrain the possible forms of vasculature. Because of these constraints and the indispensable role of vasculature for much of life, scientists have sought to identify systematic patterns in the structural properties of vascular networks and whether these patterns can be predicted from models based on biological and physical principles. These studies have been limited by the lack of extensive, detailed data. Using high-quality vascular network data obtained via our software, Angicart, we identify novel, systematic patterns of asymmetry in sizes and branching angles among sibling vessels from mouse lung and human head and torso. To examine what constraints might underlie these patterns, we investigate several explanations, including various types of optimal branching as well as random branching. The optimal branchings were derived locally with respect to constraints on material costs or power loss. For random branching we allowed the degree of randomness to vary from local to global spatial scales. By comparing predictions with real data, our study suggests that a key component in determining vascular branching is material cost with some randomness at local to intermediate spatial scales.
Collapse
Affiliation(s)
- Elif Tekin
- Department of Biomathematics, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
| | - David Hunt
- Department of Biomathematics, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
| | - Mitchell G. Newberry
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Van M. Savage
- Department of Biomathematics, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
| |
Collapse
|
42
|
Shestopaloff YK. Metabolic allometric scaling model. Combining cellular transportation and heat dissipation constraints. J Exp Biol 2016; 219:2481-9. [DOI: 10.1242/jeb.138305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/01/2016] [Indexed: 11/20/2022]
Abstract
Living organisms need energy to be "alive". Energy is produced by biochemical processing of nutrients. The rate of energy production is called metabolic rate. Metabolism is very important from evolutionary, ecological perspectives, and for organisms' development and functioning. It depends on different parameters, of which organisms' mass is considered as one of the most important. Simple relationships between the mass of organisms and their metabolic rates were empirically discovered a while ago. Such dependence is described by a power function, whose exponent is called allometric scaling coefficient. With the increase of mass the metabolic rate usually increases slower; if mass increases by two times, the metabolic rate increases less than two times. This fact has far reaching implications for organization of life. The fundamental biological and biophysical mechanisms underlying this phenomenon are still not well understood. Here, we show that one of such primary mechanisms relates to transportation of substances, like nutrients and waste, at a cellular level. We show how variations in cell size and associated cellular transportation costs explain the known variance of allometric exponent. The introduced model also includes heat dissipation constraints. The model agrees with experimental observations and reconciles experimental results across different taxa. It ties metabolic scaling to organismal and environmental characteristics; helps defining perspective directions of future researches; allows predicting allometric exponents based on characteristics of organisms and environments they live in.
Collapse
|
43
|
Anfodillo T, Petit G, Sterck F, Lechthaler S, Olson ME. Allometric Trajectories and "Stress": A Quantitative Approach. FRONTIERS IN PLANT SCIENCE 2016; 7:1681. [PMID: 27881990 PMCID: PMC5101416 DOI: 10.3389/fpls.2016.01681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 10/25/2016] [Indexed: 05/18/2023]
Abstract
The term "stress" is an important but vague term in plant biology. We show situations in which thinking in terms of "stress" is profitably replaced by quantifying distance from functionally optimal scaling relationships between plant parts. These relationships include, for example, the often-cited one between leaf area and sapwood area, which presumably reflects mutual dependence between sources and sink tissues and which scales positively within individuals and across species. These relationships seem to be so basic to plant functioning that they are favored by selection across nearly all plant lineages. Within a species or population, individuals that are far from the common scaling patterns are thus expected to perform negatively. For instance, "too little" leaf area (e.g., due to herbivory or disease) per unit of active stem mass would be expected to incur to low carbon income per respiratory cost and thus lead to lower growth. We present a framework that allows quantitative study of phenomena traditionally assigned to "stress," without need for recourse to this term. Our approach contrasts with traditional approaches for studying "stress," e.g., revealing that small "stressed" plants likely are in fact well suited to local conditions. We thus offer a quantitative perspective to the study of phenomena often referred to under such terms as "stress," plasticity, adaptation, and acclimation.
Collapse
Affiliation(s)
- Tommaso Anfodillo
- Dipartimento Territorio e Sistemi Agro-Forestali, Università degli Studi di PadovaLegnaro, Italy
| | - Giai Petit
- Dipartimento Territorio e Sistemi Agro-Forestali, Università degli Studi di PadovaLegnaro, Italy
- *Correspondence: Giai Petit,
| | - Frank Sterck
- Forest Ecology and Forest Management Group, Wageningen UniversityWageningen, Netherlands
| | - Silvia Lechthaler
- Dipartimento Territorio e Sistemi Agro-Forestali, Università degli Studi di PadovaLegnaro, Italy
| | - Mark E. Olson
- Instituto de Biologia, Universidad Nacional Autonoma de MexicoMéxico, México
| |
Collapse
|
44
|
Yigit B, Pekkan K. Non-dimensional physics of pulsatile cardiovascular networks and energy efficiency. J R Soc Interface 2016; 13:20151019. [PMID: 26819334 PMCID: PMC4759807 DOI: 10.1098/rsif.2015.1019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/04/2016] [Indexed: 11/12/2022] Open
Abstract
In Nature, there exist a variety of cardiovascular circulation networks in which the energetic ventricular load has both steady and pulsatile components. Steady load is related to the mean cardiac output (CO) and the haemodynamic resistance of the peripheral vascular system. On the other hand, the pulsatile load is determined by the simultaneous pressure and flow waveforms at the ventricular outlet, which in turn are governed through arterial wave dynamics (transmission) and pulse decay characteristics (windkessel effect). Both the steady and pulsatile contributions of the haemodynamic power load are critical for characterizing/comparing disease states and for predicting the performance of cardiovascular devices. However, haemodynamic performance parameters vary significantly from subject to subject because of body size, heart rate and subject-specific CO. Therefore, a 'normalized' energy dissipation index, as a function of the 'non-dimensional' physical parameters that govern the circulation networks, is needed for comparative/integrative biological studies and clinical decision-making. In this paper, a complete network-independent non-dimensional formulation that incorporates pulsatile flow regimes is developed. Mechanical design variables of cardiovascular flow systems are identified and the Buckingham Pi theorem is formally applied to obtain the corresponding non-dimensional scaling parameter sets. Two scaling approaches are considered to address both the lumped parameter networks and the distributed circulation components. The validity of these non-dimensional number sets is tested extensively through the existing empirical allometric scaling laws of circulation systems. Additional validation studies are performed using a parametric numerical arterial model that represents the transmission and windkessel characteristics, which are adjusted to represent different body sizes and non-dimensional haemodynamic states. Simulations demonstrate that the proposed non-dimensional indices are independent of body size for healthy conditions, but are sensitive to deviations caused by off-design disease states that alter the energetic load. Sensitivity simulations are used to identify the relationship between pulsatile power loss and non-dimensional characteristics, and optimal operational states are computed.
Collapse
Affiliation(s)
- Berk Yigit
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kerem Pekkan
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA Department of Mechanical Engineering, Koç University, Istanbul, Turkey
| |
Collapse
|
45
|
Taguchi M, Schwalb N, Rong Y, Vanegas DC, Garland N, Tan M, Yamaguchi H, Claussen JC, McLamore ES. pulSED: pulsed sonoelectrodeposition of fractal nanoplatinum for enhancing amperometric biosensor performance. Analyst 2016; 141:3367-78. [DOI: 10.1039/c6an00069j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A technique for deposition of fractal nanometal as a transducer in electrochemical sensing is described. The effect(s) of duty cycle and deposition time were explored, and two sensors are demonstrated.
Collapse
Affiliation(s)
- M. Taguchi
- Department of Agricultural & Biological Engineering
- Institute of Food & Agricultural Sciences
- University of Florida
- USA
| | - N. Schwalb
- Department of Agricultural & Biological Engineering
- Institute of Food & Agricultural Sciences
- University of Florida
- USA
| | - Y. Rong
- Department of Agricultural & Biological Engineering
- Institute of Food & Agricultural Sciences
- University of Florida
- USA
| | - D. C. Vanegas
- Department of Agricultural & Biological Engineering
- Institute of Food & Agricultural Sciences
- University of Florida
- USA
- Department of Food Engineering
| | - N. Garland
- Department of Mechanical Engineering
- Iowa State University
- USA
| | - M. Tan
- Department of Mechanical and Aerospace Engineering
- University of Florida
- USA
| | - H. Yamaguchi
- Department of Mechanical and Aerospace Engineering
- University of Florida
- USA
| | - J. C. Claussen
- Department of Mechanical Engineering
- Iowa State University
- USA
| | - E. S. McLamore
- Department of Agricultural & Biological Engineering
- Institute of Food & Agricultural Sciences
- University of Florida
- USA
| |
Collapse
|
46
|
Ton R, Martin TE. Metabolism correlates with variation in post‐natal growth rate among songbirds at three latitudes. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12548] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Riccardo Ton
- Montana Cooperative Wildlife Research Unit University of Montana Missoula MT 59812 USA
| | - Thomas E. Martin
- U. S. Geological Survey Montana Cooperative Wildlife Research Unit University of Montana Missoula MT59812 USA
| |
Collapse
|
47
|
Newberry MG, Ennis DB, Savage VM. Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks. PLoS Comput Biol 2015; 11:e1004455. [PMID: 26317654 PMCID: PMC4552567 DOI: 10.1371/journal.pcbi.1004455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 07/06/2015] [Indexed: 02/03/2023] Open
Abstract
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to capillaries and uses scaling exponents to quantify these changes. Prominent scaling theories predict that combinations of these exponents explain how metabolic, growth, and other biological rates vary with body size. Nevertheless, direct measurements of individual vessel segments have been limited because existing techniques for measuring vasculature are invasive, time consuming, and technically difficult. We developed software that extracts the length, radius, and connectivity of in vivo vessels from contrast-enhanced 3D Magnetic Resonance Angiography. Using data from 20 human subjects, we calculated scaling exponents by four methods—two derived from local properties of branching junctions and two from whole-network properties. Although these methods are often used interchangeably in the literature, we do not find general agreement between these methods, particularly for vessel lengths. Measurements for length of vessels also diverge from theoretical values, but those for radius show stronger agreement. Our results demonstrate that vascular network models cannot ignore certain complexities of real vascular systems and indicate the need to discover new principles regarding vessel lengths. Vascular networks distribute resources and constrain metabolic rate. Founded on a few key principles, biological scaling theories predict characteristic patterns for vascular networks as they branch from large to small vessels. These theories also predict seemingly unrelated phenomena, such as size limits on mammals. However, vascular networks are difficult to measure because there are billions of vessels that range in size from meters to micrometers. To test the foundations of biological scaling theories, we developed software that quickly measures thousands of in vivo vessels based on MRI. Data for vessel radii match predicted patterns but lengths do not. Our work suggests the need for new theoretical principles and should facilitate comparisons across organisms, spatial scales, and healthy and diseased tissue.
Collapse
Affiliation(s)
- Mitchell G Newberry
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Daniel B Ennis
- Department of Radiological Sciences, Biomedical Physics, and Bioengineering, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Van M Savage
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
| |
Collapse
|
48
|
Broly P, Devigne C, Deneubourg JL. Body shape in terrestrial isopods: A morphological mechanism to resist desiccation? J Morphol 2015; 276:1283-9. [PMID: 26289755 DOI: 10.1002/jmor.20418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/18/2015] [Accepted: 06/30/2015] [Indexed: 11/06/2022]
Abstract
Woodlice are fully terrestrial crustaceans and are known to be sensitive to water loss. Their half-ellipsoidal shapes represent simple models in which to investigate theoretical assumptions about organism morphology and rates of exchange with the environment. We examine the influence of surface area and mass on the desiccation rates in three eco-morphologically different species of woodlice: Oniscus asellus, Porcellio scaber, and Armadillidium vulgare. Our analysis indicates that the rate of water loss of an individual depends on both the initial weight and the body surface area. Interspecific and intraspecific analyses show that the mass-specific water loss rate of a species decreases along with the ratio of surface area to volume. In particular, we show that body shape explains the difference in mass-specific water loss rates between A. vulgare and P. scaber. This observation also explains several known ecological patterns, for example, the distribution and survivorship of individuals. However, in addition to body size and shape, water loss in terrestrial isopods depends also on the coefficient of permeability (i.e., a measure of water loss rate per surface unit), which is high in O. asellus and lower (and at similar levels) in P. scaber and A. vulgare. We discuss morphological, physiological, and behavioral aspects of water loss avoidance in terrestrial isopods.
Collapse
Affiliation(s)
- Pierre Broly
- Unité d'Ecologie Sociale, Université Libre De Bruxelles, Campus De La Plaine CP231, Boulevard Du Triomphe, Bruxelles, 1050, Belgium
| | - Cédric Devigne
- Laboratoire Ecologie & Biodiversité, Faculté De Gestion, Economie & Sciences, UCLILLE, 58 rue du Port, 59016 Lille cedex, France.,University Lille Nord de France - UDSL, Forensic Taphonomy Unit, F-59000 Lille, France
| | - Jean-Louis Deneubourg
- Unité d'Ecologie Sociale, Université Libre De Bruxelles, Campus De La Plaine CP231, Boulevard Du Triomphe, Bruxelles, 1050, Belgium
| |
Collapse
|
49
|
Packard GC. Quantifying the curvilinear metabolic scaling in mammals. ACTA ACUST UNITED AC 2015; 323:540-6. [DOI: 10.1002/jez.1946] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 05/05/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Gary C. Packard
- Department of Biology; Colorado State University; Fort Collins Colorado
| |
Collapse
|
50
|
|