Dynamic Structure Discovery and Repair for 3D Cell Assemblages

Ferreira, Giordano B. S.; Smiley, M.; Scheutz, Matthias; Levin, Michael

doi:10.7551/978-0-262-33936-0-ch059

Cited by 7 publications

(11 citation statements)

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“…The agent-based models (Ferreira et al, 2016;Ferreira et al, 2017a;Ferreira et al, 2017b) need to store too much information (paths of packets) in stem cells as well as too much communication between cells in discovering states. The information our model carries for regeneration is high-level and generic -minimum information on shape and entropy and neighbourhood rules.…”

Section: Discussionmentioning

confidence: 99%

“…An agent-based model is proposed in (Ferreira et al, 2016) to discover a 3D structure of stem cells and self-repair when a part is cut. The mechanism discovers the whole structure and repairs it from damage or cell death.…”

Section: Regeneration As a Biological Computing Processmentioning

confidence: 99%

“…Some researchers have introduced algorithmic models of regeneration that have focused on signal communication between stem cells and differentiated cells in a tissue De, Chakravarthy, & Levin, 2017;Ferreira, Smiley, Scheutz, & Levin, 2016;Tosenberger et al, 2015). These models have proposed rules for regenerating a given morphology and the existence of a coordinate system that guides the patterning of the organism.…”

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confidence: 99%

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A comprehensive conceptual and computational dynamics framework for Autonomous Regeneration Systems

Minh-Thai

Samarasinghe

Levin

2019

Preprint

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This paper presents a new conceptual and computational dynamics framework for damage detection and regeneration in multicellular structures similar to living animals. The model uniquely achieves complete and accurate regeneration from any damage anywhere in the system. We demonstrated the efficacy of the proposed framework on an artificial organism consisting of three tissue structures corresponding to the head, body and tail of a worm. Each structure consists of a stem cell surrounded by a tissue of differentiated cells. We represent a tissue as an Auto-Associative Neural Network (AANN) with local interactions and stem cells as a self-repair network with long-range interactions. We also propose another new concept, Information Field which is a mathematical abstraction over traditional components of tissues, to keep minimum pattern information of the tissue structures to be accessed by stem cells in extreme cases of damage. Through entropy, a measure of communication between a stem cell and differentiated cells, stem cells monitor the tissue pattern integrity, violation of which triggers damage detection and tissue repair. Stem cell network monitors its state and invokes stem cell repair in the case of stem cell damage. The model accomplishes regeneration at two levels: In the first level, damaged tissues with intact stem cells regenerate themselves. Here, stem cell identifies entropy change and finds the damage and regenerates the tissue in collaboration with the AANN. In the second level, involving missing whole tissues and stem cells, the remaining stem cell(s) access the information field to restore the stem cell network and regenerate missing tissues. In the case of partial tissue damage with missing stem cells, the two levels collaborate to accurately restore the stem cell network and tissues. This comprehensive hypothetical framework offers a new way to conceptualise regeneration for better understanding the regeneration processes in living systems. It could also be useful in biology for regenerative medicine and in engineering for building self-repairing biobots.

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Section: Discussionmentioning

confidence: 99%

Section: Regeneration As a Biological Computing Processmentioning

confidence: 99%

mentioning

confidence: 99%

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A comprehensive conceptual and computational dynamics framework for Autonomous Regeneration Systems

Minh-Thai

Samarasinghe

Levin

2019

Preprint

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“…Friston et al . [ 55 ] analyzed models in which “cells” both communicate their current states to their neighbors and update their states based on the signals received from their neighbors, finding that they are able to self-organize into a “body” with a specific target morphology [see also 56 , 57 , 58 ]. Modifying the interpretation of the signals received, in this model, leads to dysmorphologies [ 55 , 59 ].…”

Section: Building a Body Is Building An Environmentmentioning

confidence: 99%

Why isn’t sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution

Fields

Levin

2020

Communicative & Integrative Biology

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Animals that can reproduce vegetatively by fission or budding and also sexually via specialized gametes are found in all five primary animal lineages (Bilateria, Cnidaria, Ctenophora, Placozoa, Porifera). Many bilaterian lineages, including roundworms, insects, and most chordates, have lost the capability of vegetative reproduction and are obligately gametic. We suggest a developmental explanation for this evolutionary phenomenon: obligate gametic reproduction is the result of germline stem cells winning a winner-take-all competition with non-germline stem cells for control of reproduction and hence lineage survival. We develop this suggestion by extending Hamilton's rule, which factors the relatedness between parties into the cost/benefit analysis that underpins cooperative behaviors, to include similarity of cellular state. We show how coercive or deceptive cell-cell signaling can be used to make costly cooperative behaviors appear less costly to the cooperating party. We then show how competition between stem-cell lineages can render an ancestral combination of vegetative reproduction with facultative sex unstable, with one or the other process driven to extinction. The increased susceptibility to cancer observed in obligately-sexual lineages is, we suggest, a side-effect of deceptive signaling that is exacerbated by the loss of whole-body regenerative abilities. We suggest a variety of experimental approaches for testing our predictions.

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“…• propagation of light is less limited by distance than a signaling molecule, As additional models about regeneration of artificial multicellular organisms have been proposed, we can cite the regeneration of dead cells in previous studies: the twodimensional and three-dimensional shapes of Fleischer [26] , the star fish of Cussat-Blanc et al [27], and the bat of Djezzar et al [28]. In [29], an efficient cell-to-cell communication mechanism that allows the maintenance of Planarian worm-like shapes was introduced. The efficiency of the model has been verified in the light of random cell death.…”

Section: Quorum Sensingmentioning

confidence: 99%

A Computational Multiagent Model of Bioluminescent Bacteria for the Emergence of Self-Sustainable and Self-Maintaining Artificial Wireless Networks

Djezzar

Pérez

Djedi

et al. 2019

IJCAI

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Biology is a rich source of inspiration in designing digital artifacts capable of autonomous, cooperative and distributed behaviors. Particularly, conceptual links can be established between (1) communication networks and (2) colonies of bacteria that communicate using chemical molecules. The goal of this paper is to propose a computational multiagent model of an interspecies bacterial communication system, termed quorum sensing, and analyze its self-sustainability and its self-maintaining ability to cooperatively form artificial wireless networks. Specifically, we propose a bottom-up agent-based approach combined with Ordinary Differential Equations, which abstract the intracellular dynamics, such as a proposed metabolism model that serves as a basis underlying self-sustainable networks. Results show that artificial bacterial cells have regeneration abilities in the light of random cell death and selected area for cell death, and a metabolism allowing them to exploit their own produced energy to cooperate at the population level to exhibit near-optimal self-organizing light-producing behaviors. The resulting artificial networks display several beneficial properties and could be used for the emergence of resistant wireless network topologies without the use of overhead messages. Povzetek: Analizirano je komuniciranje med bakterijami, na osnovi katerih so razvite agentne metode za bolj odporna brezžična omrežja.

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Dynamic Structure Discovery and Repair for 3D Cell Assemblages

Cited by 7 publications

References 0 publications

A comprehensive conceptual and computational dynamics framework for Autonomous Regeneration Systems

A comprehensive conceptual and computational dynamics framework for Autonomous Regeneration Systems

Why isn’t sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution

A Computational Multiagent Model of Bioluminescent Bacteria for the Emergence of Self-Sustainable and Self-Maintaining Artificial Wireless Networks

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