Capturing Degeneracy in the Immune System

Tieri, Paolo; Castellani, Gastone; Remondini, Daniel; Valensin, Silvana; Loroni, Jonathan; Salvioli, Stefano; Franceschi, Claudio

doi:10.1007/978-0-387-39241-7_7

Cited by 5 publications

(3 citation statements)

References 340 publications

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“…In the immune system, for instance, degeneracy of antigen receptors enables any single epitope to activate many different lymphocyte clones, and simultaneously any single lymphocyte clone is able to recognize many different epitopes [ 23 ]. Tieri et al [ 24 ], borrowing a term from Csete and Doyle [ 25 ], refer to the overlap between degeneracy and pluripotentiality as a bowtie. Many inputs funnel into a thin knot of interlocking networks and subsequently many corresponding outputs fan out.…”

Section: Biological Degeneracymentioning

confidence: 99%

Epigenomics and the concept of degeneracy in biological systems

Maleszka

Mason²,

Barron³

2013

Briefings in Functional Genomics

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Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability.

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Section: Biological Degeneracymentioning

confidence: 99%

Epigenomics and the concept of degeneracy in biological systems

Maleszka

Mason²,

Barron³

2013

Briefings in Functional Genomics

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“…In some cases, degeneracy facilitates adaptation through the provision of functional redundancy, whereas in other cases, it provides functional diversity and enables adaptive phenotypic change, as seen with CGV in natural populations (Beverly et al, 2011; Mellen, 2010; Nelson et al, 2011; Ozaki and Leonard, 2002). The adaptive immune response of T cells provides a practical example of degeneracy-driven adaptation that is useful for integrating, yet also distinguishing between, degeneracy and CGV (Tieri et al, 2007, 2010). Naïve T cells typically display similar (inactive) phenotypes under “normal” conditions (devoid of antigens), but can also reveal large phenotypic differences when presented with novel (antigen) environments that, in turn, drive rapid clonal expansion.…”

Section: Degeneracy Resolves the Apparent Contradiction Between Thmentioning

confidence: 99%

Degeneracy allows for both apparent homogeneity and diversification in populations

Whitacre

Atamas

2012

Biosystems

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Trait diversity – the substrate for natural selection – is necessary for adaptation through selection, particularly in populations faced with environmental changes that diminish population fitness. In habitats that remain unchanged for many generations, stabilizing selection maximizes exploitation of resources by reducing trait diversity to a narrow optimal range. One might expect that such ostensibly homogeneous populations would have a reduced potential for heritable adaptive responses when faced with fitness-reducing environmental changes. However, field studies have documented populations that, even after long periods of evolutionary stasis, can still rapidly evolve in response to changed environmental conditions. We argue that degeneracy, the ability of diverse population elements to function similarly, can satisfy both the current need to maximize fitness and the future need for diversity. Degenerate ensembles appear functionally redundant in certain environmental contexts and functionally diverse in others. We propose that genetic variation not contributing to the observed range of phenotypes in a current population, also known as cryptic genetic variation (CGV), is a specific case of degeneracy. We argue that CGV, which gradually accumulates in static populations in stable environments, reveals hidden trait differences when environments change. By allowing CGV accumulation, static populations prepare themselves for future rapid adaptations to environmental novelty. A greater appreciation of degeneracy’s role in resolving the inherent tension between current stabilizing selection and future directional selection has implications in conservation biology and may be applied in social and technological systems to maximize current performance while strengthening the potential for future changes.

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“…recognize) many different ligands and each antigen is recognized by many receptors [ 38 , 39 ]; a feature that has only recently been integrated into artificial immune system models, e.g. [ 40 - 42 ]. In gene regulation, each transcription factor can influence the expression of several different genes with distinct phenotypic effects.…”

Section: Robustness Through Diversity and Degeneracymentioning

confidence: 99%

Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems

Whitacre

Bender

2010

Theor Biol Med Model

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A generic mechanism - networked buffering - is proposed for the generation of robust traits in complex systems. It requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system. In models of genome:proteome mappings for which localized decision-making and modularity of genetic functions are assumed, we verify that such distributed compensatory effects cause enhanced robustness of system traits. The conditions needed for networked buffering to occur are neither demanding nor rare, supporting the conjecture that degeneracy may fundamentally underpin distributed robustness within several biotic and abiotic systems. For instance, networked buffering offers new insights into systems engineering and planning activities that occur under high uncertainty. It may also help explain recent developments in understanding the origins of resilience within complex ecosystems.

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Capturing Degeneracy in the Immune System

Cited by 5 publications

References 340 publications

Epigenomics and the concept of degeneracy in biological systems

Epigenomics and the concept of degeneracy in biological systems

Degeneracy allows for both apparent homogeneity and diversification in populations

Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems

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