Publications by authors named "Anton S Zadorin"

6 Publications

  • Page 1 of 1

Sex as information processing: Optimality and evolution.

Phys Rev E 2021 Jun;103(6-1):062413

Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, 75005 Paris, France.

The long-term growth rate of populations in varying environments quantifies the evolutionary value of processing the information that biological individuals inherit from their ancestors and acquire from their environment. Previous models were limited to asexual reproduction with inherited information coming from a single parent with no recombination. We present a general extension to sexual reproduction and an analytical solution for a particular but important case, the infinitesimal model of quantitative genetics which assumes traits to be normally distributed. We study with this model the conditions under which sexual reproduction is advantageous and can evolve in the context of autocorrelated or directionally varying environments, mutational biases, spatial heterogeneities, and phenotypic plasticity. Our results generalize and unify previous analyses. We also examine the proposal made by Geodakyan that the presence of two phenotypically distinct sexes permits an optimal adaptation to varying environments. We verify that conditions exists where sexual dimorphism is adaptive but find that its evolutionary value does not generally compensate for the twofold cost of males.
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http://dx.doi.org/10.1103/PhysRevE.103.062413DOI Listing
June 2021

Quantifying the Performance of Micro-Compartmentalized Directed Evolution Protocols.

Life (Basel) 2020 Feb 13;10(2). Epub 2020 Feb 13.

Laboratoire Gulliver, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France.

High-throughput, in vitro approaches for the evolution of enzymes rely on a random micro-encapsulation to link phenotypes to genotypes, followed by screening or selection steps. In order to optimise these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants of a library. Here, we introduce a new metric, the Selection Quality Index (SQI), which can be computed from a simple mock experiment, performed with a known initial fraction of active variants. In contrast to previous approaches, our index integrates the effect of random co-encapsulation, and comes with a straightforward experimental interpretation. We further show how this new metric can be used to extract general protocol efficiency trends or reveal hidden selection mechanisms such as a counterintuitive form of beneficial poisoning in the compartmentalized self-replication protocol.
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http://dx.doi.org/10.3390/life10020017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175308PMC
February 2020

Selection strategies for randomly partitioned genetic replicators.

Phys Rev E 2019 Jun;99(6-1):062416

Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France.

The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator expresses phenotypic compounds necessary to carry out its genetic replication. For example, viruses infect cells, where they express their own proteins and replicate. In this process, the host cell boundary limits the diffusion of the viral protein products, thereby ensuring that phenotypic compounds, such as proteins, promote the replication of the genes that encoded them. This role of maintaining spatial colocalization, also called genotype-phenotype linkage, is a critical function of compartments in natural selection. In most cases, however, individual replicating elements do not distribute systematically among the hosts, but are randomly partitioned. Depending on the replicator-to-host ratio, more than one variant may thus occupy some compartments, blurring the genotype-phenotype linkage and affecting the effectiveness of natural selection. We derive selection equations for a variety of such random multiple occupancy situations, in particular considering the effect of replicator population polymorphism and internal replication dynamics. We conclude that the deleterious effect of random multiple occupancy on selection is relatively benign, and may even completely vanish is some specific cases. In addition, given that higher mean occupancy allows larger populations to be channeled through the selection process, and thus provide a better exploration of phenotypic diversity, we show that it may represent a valid strategy in both natural and technological cases.
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http://dx.doi.org/10.1103/PhysRevE.99.062416DOI Listing
June 2019

Synthesis and materialization of a reaction-diffusion French flag pattern.

Nat Chem 2017 10 1;9(10):990-996. Epub 2017 May 1.

Laboratoire Jean Perrin, Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France.

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Second, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental programme.
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http://dx.doi.org/10.1038/nchem.2770DOI Listing
October 2017

Synthesis of programmable reaction-diffusion fronts using DNA catalyzers.

Phys Rev Lett 2015 Feb 9;114(6):068301. Epub 2015 Feb 9.

Laboratoire de photonique et de nanostructures, CNRS, route de Nozay, 91460 Marcoussis, France.

We introduce a DNA-based reaction-diffusion (RD) system in which reaction and diffusion terms can be precisely and independently controlled. The effective diffusion coefficient of an individual reaction component, as we demonstrate on a traveling wave, can be reduced up to 2.7-fold using a self-assembled hydrodynamic drag. The intrinsic programmability of this RD system allows us to engineer, for the first time, orthogonal autocatalysts that counterpropagate with minimal interaction. Our results are in excellent quantitative agreement with predictions of the Fisher-Kolmogorov-Petrovskii-Piscunov model. These advances open the way for the rational engineering of pattern formation in pure chemical RD systems.
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http://dx.doi.org/10.1103/PhysRevLett.114.068301DOI Listing
February 2015

Sirt1 suppresses RNA synthesis after UV irradiation in combined xeroderma pigmentosum group D/Cockayne syndrome (XP-D/CS) cells.

Proc Natl Acad Sci U S A 2013 Jan 24;110(3):E212-20. Epub 2012 Dec 24.

Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale, Université de Strasbourg, 67404 Illkirch, France.

Specific mutations in the XPD subunit of transcription factor IIH result in combined xeroderma pigmentosum (XP)/Cockayne syndrome (CS), a severe DNA repair disorder characterized at the cellular level by a transcriptional arrest following UV irradiation. This transcriptional arrest has always been thought to be the result of faulty transcription-coupled repair. In the present study, we showed that, following UV irradiation, XP-D/CS cells displayed a gross transcriptional dysregulation compared with "pure" XP-D cells or WT cells. Furthermore, global RNA-sequencing analysis showed that XP-D/CS cells repressed the majority of genes after UV, whereas pure XP-D cells did not. By using housekeeping genes as a model, we demonstrated that XP-D/CS cells were unable to reassemble these gene promoters and thus to restart transcription after UV irradiation. Furthermore, we found that the repression of these promoters in XP-D/CS cells was not a simple consequence of deficient repair but rather an active heterochromatinization process mediated by the histone deacetylase Sirt1. Indeed, RNA-sequencing analysis showed that inhibition of and/or silencing of Sirt1 changed the chromatin environment at these promoters and restored the transcription of a large portion of the repressed genes in XP-D/CS cells after UV irradiation. Our work demonstrates that a significant part of the transcriptional arrest displayed by XP-D/CS cells arises as a result of an active repression process and not simply as a result of a DNA repair deficiency. This dysregulation of Sirt1 function that results in transcriptional repression may be the cause of various severe clinical features in patients with XP-D/CS that cannot be explained by a DNA repair defect.
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http://dx.doi.org/10.1073/pnas.1213076110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549127PMC
January 2013
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