Evolving quorum sensing in digital organisms

Beckmann, Benjamin E.; McKinley, Philip K.

doi:10.1145/1569901.1569916

Cited by 12 publications

(17 citation statements)

References 30 publications

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“…The instruction set includes send-msg, msg-handler, and end-handler, whose functionality was discussed earlier. Various types of rotate instructions were tested [5], but the most effective were the single-step rotations, rotate-right and rotate-left, which enable an organism to rotate one cell to its right or left, respectively. Four different nop instructions were included (nop-A, nop-B, nop-C, and nop-X).…”

Section: Methodsmentioning

confidence: 99%

“…The amount of energy conserved by a deme determined its fitness, as defined in Equation 3. In this section, we review the results of those experiments, including analysis of an evolved genome; additional details can be found in [5]. Of the 20 runs, 15 exhibited energy conservation, so the discussion focuses on those populations.…”

Section: Evolution Of Quorum Sensingmentioning

confidence: 99%

“…Digital organisms are a type of self-replicating computer program, subject to mutations and natural selection, that exist in a computational environment. In an earlier study [5], we demonstrated the evolution of QS behavior in Avida populations. Specifically, we showed that populations are capable of evolving a strategy to collectively suppress self-replication when the population density reaches an evolved threshold.…”

Section: Introductionmentioning

confidence: 99%

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Evolution of Resistance to Quorum Quenching in Digital Organisms

et al. 2012

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Quorum sensing (QS) is a collective behavior whereby actions of individuals depend on the density of the surrounding population. Bacteria use QS to trigger secretion of digestive enzymes, formation and destruction of biofilms, and, in the case of pathogenic organisms, expression of virulence factors that cause disease. Investigations of mechanisms that prevent or disrupt QS, referred to as quorum quenching, are of interest because they provide a new alternative to antibiotics for treating bacterial infections. Traditional antibiotics either kill bacteria or inhibit their growth, producing selective pressures that promote resistant strains. In contrast, quorum quenching and other so-called anti-infective strategies focus on altering behavior. In this article we evolve QS in populations of digital organisms, a type of self-replicating computer program, and investigate the effects of quorum quenching on these populations. Specifically, we injected the populations with mutant organisms that were impaired in selected ways to disrupt the QS process. The experimental results indicate that the rate at which these mutants are introduced into a population influences both the evolvability of QS and the persistence of an existing QS behavior. Surprisingly, we also observed resistance to quorum quenching. Effectively, populations evolved resistance by reaching quorum at lower cell densities than did the parent strain. Moreover, the level of resistance was highest when the rate of mutant introduction increased over time. These results show that digital organisms can serve as a model to study the evolution and disruption of QS, potentially informing wet-lab studies aimed at identifying targets for anti-infective development.

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Section: Methodsmentioning

confidence: 99%

Section: Evolution Of Quorum Sensingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution of Resistance to Quorum Quenching in Digital Organisms

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“…In a prior study [12], we demonstrated that digital orProceedings of the Third IEEE International Conference on Self-Adaptive and Self-Organizing Systems, San Francisco, California, September 2009. (poster summary)…”

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confidence: 96%

“…In this study, we extend runs from [12] from 2, 500 deme generations to 5, 000 and observed 16 runs that evolved QS behavior. We then tested the robustness of the most abundant (dominant) genomes to the introduction of impaired mutants.…”

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Effects of Communication Impairments on Quorum Sensing

Beckmann

McKinley

Knoester

2009

2009 Third IEEE International Conference on Self-Adaptive and Self-Organizing Systems

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Motivations. Observations of behaviors in natural organisms provide useful insight into the complexity of selforganizing systems and the building blocks that underpin them. A behavior that is important to both biological and computational systems is quorum sensing (QS) [1], where sufficient group density triggers a collective group action. Quorum-sensing bacteria, for example, continually secrete and detect molecules called autoinducers (AIs) [2]. Under low-density conditions, AI molecules diffuse through the environment and go undetected. As the number of bacterial cells increases, so does the level of AI, eventually reaching a threshold that triggers a change in gene expression. Studies have shown that bacteria use quorum sensing in a wide variety of functions. In pathogenic bacteria, for instance, quorum sensing enables organisms to coordinate attacks and express virulence factors in sufficient quantities to overwhelm the host's immune response [3].

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Suicidal selection: Programmed cell death can evolve in unicellular organisms due solely to kin selection

Vostinar

Goldsby

Ofria

2019

Ecology and Evolution

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Unicellular organisms can engage in a process by which a cell purposefully destroys itself, termed programmed cell death (PCD). While it is clear that the death of specific cells within a multicellular organism could increase inclusive fitness (e.g., during development), the origin of PCD in unicellular organisms is less obvious. Kin selection has been shown to help maintain instances of PCD in existing populations of unicellular organisms; however, competing hypotheses exist about whether additional factors are necessary to explain its origin. Those factors could include an environmental shift that causes latent PCD to be expressed, PCD hitchhiking on a large beneficial mutation, and PCD being simply a common pathology. Here, we present results using an artificial life model to demonstrate that kin selection can, in fact, be sufficient to give rise to PCD in unicellular organisms. Furthermore, when benefits to kin are direct—that is, resources provided to nearby kin—PCD is more beneficial than when benefits are indirect—that is, nonkin are injured, thus increasing the relative amount of resources for kin. Finally, when considering how strict organisms are in determining kin or nonkin (in terms of mutations), direct benefits are viable in a narrower range than indirect benefits. Open Research Badges This article has been awarded Open Data and Open Materials Badges. All materials and data are publicly accessible via the Open Science Framework at https://github.com/anyaevostinar/SuicidalAltruismDissertation/tree/master/LongTerm.

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Evolving quorum sensing in digital organisms

Cited by 12 publications

References 30 publications

Evolution of Resistance to Quorum Quenching in Digital Organisms

Evolution of Resistance to Quorum Quenching in Digital Organisms

Effects of Communication Impairments on Quorum Sensing

Suicidal selection: Programmed cell death can evolve in unicellular organisms due solely to kin selection

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