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Yu H, Amador GJ, Cribellier A, Klaassen M, de Knegt HJ, Naguib M, Nijland R, Nowak L, Prins HHT, Snijders L, Tyson C, Muijres FT. Edge computing in wildlife behavior and ecology. Trends Ecol Evol 2024; 39:128-130. [PMID: 38142163 DOI: 10.1016/j.tree.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 12/25/2023]
Abstract
Modern sensor technologies increasingly enrich studies in wildlife behavior and ecology. However, constraints on weight, connectivity, energy and memory availability limit their implementation. With the advent of edge computing, there is increasing potential to mitigate these constraints, and drive major advancements in wildlife studies.
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Affiliation(s)
- Hui Yu
- Experimental Zoology Group, Wageningen University & Research, Wageningen, the Netherlands.
| | - Guillermo J Amador
- Experimental Zoology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Antoine Cribellier
- Experimental Zoology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Geelong, Australia
| | - Henrik J de Knegt
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Marc Naguib
- Behavioral Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Lukasz Nowak
- Experimental Zoology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Herbert H T Prins
- Department of Animal Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Lysanne Snijders
- Behavioral Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Chris Tyson
- Behavioral Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Florian T Muijres
- Experimental Zoology Group, Wageningen University & Research, Wageningen, the Netherlands
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Wolff HB, Davidson LA, Merks RMH. Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf. Bull Math Biol 2019; 81:3322-3341. [PMID: 30927191 PMCID: PMC6677868 DOI: 10.1007/s11538-019-00599-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 03/11/2019] [Indexed: 11/16/2022]
Abstract
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles and predict the collective cell behavior that follows from a set of interaction rules. In particular, vertex-based models are a popular tool for studying the mechanics of confluent, epithelial cell layers. They represent the junctions between three (or sometimes more) cells in confluent tissues as point particles, connected using structural elements that represent the cell boundaries. A disadvantage of these models is that cell-cell interfaces are represented as straight lines. This is a suitable simplification for epithelial tissues, where the interfaces are typically under tension, but this simplification may not be appropriate for mesenchymal tissues or tissues that are under compression, such that the cell-cell boundaries can buckle. In this paper, we introduce a variant of VMs in which this and two other limitations of VMs have been resolved. The new model can also be seen as on off-the-lattice generalization of the Cellular Potts Model. It is an extension of the open-source package VirtualLeaf, which was initially developed to simulate plant tissue morphogenesis where cells do not move relative to one another. The present extension of VirtualLeaf introduces a new rule for cell-cell shear or sliding, from which cell rearrangement (T1) and cell extrusion (T2) transitions emerge naturally, allowing the application of VirtualLeaf to problems of animal development. We show that the updated VirtualLeaf yields different results than the traditional vertex-based models for differential adhesion-driven cell sorting and for the neighborhood topology of soft cellular networks.
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Affiliation(s)
- Henri B Wolff
- Centrum Wiskunde and Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands
- Departments of Bioengineering, Developmental Biology, and Computational and Systems Biology, University of Pittsburgh, Bioscience Tower 3-5059 3501 Fifth Avenue, Pittsburgh, PA, USA
- Department of Epidemiology and Biostatistics, Decision Modeling Center VUmc, Amsterdam UMC location VUmc, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - Lance A Davidson
- Departments of Bioengineering, Developmental Biology, and Computational and Systems Biology, University of Pittsburgh, Bioscience Tower 3-5059 3501 Fifth Avenue, Pittsburgh, PA, USA.
| | - Roeland M H Merks
- Centrum Wiskunde and Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands.
- Mathematical Institute, University Leiden, P.O. Box 9512, 2300 RA, Leiden, The Netherlands.
- Mathematical Institute and Institute of Biology, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
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Boas SEM, Carvalho J, van den Broek M, Weijers EM, Goumans MJ, Koolwijk P, Merks RMH. A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants. PLoS Comput Biol 2018; 14:e1006239. [PMID: 29979675 PMCID: PMC6072121 DOI: 10.1371/journal.pcbi.1006239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/02/2018] [Accepted: 05/28/2018] [Indexed: 11/19/2022] Open
Abstract
In experimental assays of angiogenesis in three-dimensional fibrin matrices, a temporary scaffold formed during wound healing, the type and composition of fibrin impacts the level of sprouting. More sprouts form on high molecular weight (HMW) than on low molecular weight (LMW) fibrin. It is unclear what mechanisms regulate the number and the positions of the vascular-like structures in cell cultures. To address this question, we propose a mechanistic simulation model of endothelial cell migration and fibrin proteolysis by the plasmin system. The model is a hybrid, cell-based and continuum, computational model based on the cellular Potts model and sets of partial-differential equations. Based on the model results, we propose that a positive feedback mechanism between uPAR, plasmin and transforming growth factor β1 (TGFβ1) selects cells in the monolayer for matrix invasion. Invading cells releases TGFβ1 from the extracellular matrix through plasmin-mediated fibrin degradation. The activated TGFβ1 further stimulates fibrin degradation and keeps proteolysis active as the sprout invades the fibrin matrix. The binding capacity for TGFβ1 of LMW is reduced relative to that of HMW. This leads to reduced activation of proteolysis and, consequently, reduced cell ingrowth in LMW fibrin compared to HMW fibrin. Thus our model predicts that endothelial cells in LMW fibrin matrices compared to HMW matrices show reduced sprouting due to a lower bio-availability of TGFβ1. Therapies for a range of medical conditions, including cancer, wound healing and diabetic retinopathy can benefit from a better control over the growth of blood vessels. The chemical properties of fibrin, the material that forms scabs in wounds and can also occur in large concentrations in tumors, can regulate the degree of blood vessel growth (angiogenesis). Angiogenesis can be mimicked in cell cultures. These allow us to modulate the chemical properties of fibrin and study the effect on angiogenesis. Fibrin occurs in high molecular weight (HMW) and in low molecular weight (LMW) forms. Interestingly, there is more ingrowth of angiogenic-like structures into HMW than in LMW fibrin, but the mechanisms are poorly understood. To get more insight into these, we constructed a computational model. Using the model, we propose and analyse a hypothetical mechanism for sprouting that could explain the differences in endothelial cell sprouting in LMW and HMW fibrin matrices. Our model suggests that cells digest fibrin, thus creating space for ingrowth. At the same time, digestion frees growth factors bound to fibrin, that activates further secretion of digestive enzymes by the cells. We propose that the resulting positive feedback loop spontaneously selects cells in the endothelial monolayer for ingrowth and helps the blood vessel sprout move deeper into the fibrin. This could be a complementary mechanism to lateral-inhibition by Delta-Notch for the selection of leader cells, also called ‘tip cells’. Our model predicts that endothelial cells in LMW fibrin compared to HMW fibrin show reduced sprouting due to a lower bio-availability of TGFβ1.
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Affiliation(s)
- Sonja E. M. Boas
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
- Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Joao Carvalho
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal
| | - Marloes van den Broek
- Amsterdam Cardiovascular Sciences, VU University medical Center, Dept. of Physiology, Amsterdam, The Netherlands
| | - Ester M. Weijers
- Amsterdam Cardiovascular Sciences, VU University medical Center, Dept. of Physiology, Amsterdam, The Netherlands
| | - Marie-José Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieter Koolwijk
- Amsterdam Cardiovascular Sciences, VU University medical Center, Dept. of Physiology, Amsterdam, The Netherlands
| | - Roeland M. H. Merks
- Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands
- Mathematical Institute, Leiden University, Leiden, The Netherlands
- * E-mail:
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Speth DR, Lagkouvardos I, Wang Y, Qian PY, Dutilh BE, Jetten MSM. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria. Microb Ecol 2017; 74:1-5. [PMID: 28074246 PMCID: PMC5486813 DOI: 10.1007/s00248-017-0929-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/01/2017] [Indexed: 05/21/2023]
Abstract
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.
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Affiliation(s)
- Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
- Division for Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technische Universität München, Freising, Germany
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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