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News Article | December 7, 2016
Site: www.eurekalert.org

In West African cities, male circumcision rates in 1950 were negatively correlated with HIV-2 prevalence from 1985, according to a study published December 7, 2016 in the open-access journal PLOS ONE by João Sousa from the University of Leuven, Belgium, and colleagues. The HIV-2 virus likely emerged in humans around 1930-40 and is less widespread than the predominant HIV-1, remaining mostly within West Africa. Whilst male circumcision is known to be associated with reduced HIV-1 prevalence, because the foreskin is highly vulnerable to infection, the association between male circumcision and HIV-2 prevalence had not previously been examined. The authors of the present study gathered the published results of large scale HIV-2 serosurveys, conducted from 1985 onwards, of the populations of 30 West African cities. They combined estimates of historical male circumcision frequency in 218 West African ethnic groups with demographic data to estimate male circumcision frequency for each West African city at various time points. The researchers then matched HIV-2 prevalence with the estimated male circumcision frequency in each city to identify any correlation. The authors found that cities with higher male circumcision rates in 1950 generally tended to have lower HIV-2 prevalence at the time of the first serosurveys in 1985-91. Generally, male circumcision was far less common than it is today, and varied more by country. Cities in two countries, Guinea-Bissau and Côte d'Ivoire, which are thought to have acted as epicenters during the emergence of HIV-2, had particularly low male circumcision rates, reinforcing the negative correlation. Whilst the data on male circumcision and HIV-2 prevalence were obtained in different years, making it difficult to link the two directly, the authors state that HIV-2 may only have been able to achieve high prevalence in West African cities where a substantial proportion of the population was uncircumcised. "Lack of circumcision may have been a driving factor in initial HIV-2 emergence," says Sousa. In your coverage please use this URL to provide access to the freely available paper: http://journals. Citation: Sousa JD, Temudo MP, Hewlett BS, Camacho RJ, Müller V, Vandamme A-M (2016) Male Circumcision and the Epidemic Emergence of HIV-2 in West Africa. PLoS ONE 11(12): e0166805. doi:10.1371/journal.pone.0166805 Funding: The research done by JDS and AMV in this study has been supported in part by grant G.0611.09N, funded by the Fonds voor Wetenschappelijk Onderzoek - Flanders (FWO, http://www. ), Belgium. MPT's fieldwork in Guinea-Bissau was conducted within the framework of the project "The prophetess and the rice farmer: innovations in religion, agriculture and gender in Guinea-Bissau", PTDC/AFR/111546/2009, funded by Fundação para a Ciência e Tecnologia, (FCT, http://www. ), Portugal. VM is a Fellow of the Parmenides Center for the Conceptual Foundations of Science, part of Parmenides Foundation, Germany. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist.


Kun A.,Parmenides Center for the Conceptual Foundations of Science | Kun A.,MTA ELTE MTMT Ecology Research Group | Szilagyi A.,Parmenides Center for the Conceptual Foundations of Science | Szilagyi A.,MTA ELTE Theoretical Biology and Evolutionary Ecology Research Group | And 6 more authors.
Annals of the New York Academy of Sciences | Year: 2015

The RNA world hypothesis of the origin of life, in which RNA emerged as both enzyme and information carrier, is receiving solid experimental support. The prebiotic synthesis of biomolecules, the catalytic aid offered by mineral surfaces, and the vast enzymatic repertoire of ribozymes are only pieces of the origin of life puzzle; the full picture can only emerge if the pieces fit together by either following from one another or coexisting with each other. Here, we review the theory of the origin, maintenance, and enhancement of the RNA world as an evolving population of dynamical systems. The dynamical view of the origin of life allows us to pinpoint the missing and the not fitting pieces: (1) How can the first self-replicating ribozyme emerge in the absence of template-directed information replication? (2) How can nucleotide replicators avoid competitive exclusion despite utilizing the very same resources (nucleobases)? (3) How can the information catastrophe be avoided? (4) How can enough genes integrate into a cohesive system in order to transition to a cellular stage? (5) How can the way information is stored and metabolic complexity coevolve to pave to road leading out of the RNA world to the present protein-DNA world? © 2015 New York Academy of Sciences.


Konnyu B.,Eötvös Loránd University | Szilagyi A.,MTA ELTE Theoretical Biology and Evolutionary Ecology Research Group | Szilagyi A.,Parmenides Center for the Conceptual Foundations of Science | Czaran T.,MTA ELTE Theoretical Biology and Evolutionary Ecology Research Group
Biology Direct | Year: 2015

Background: The RNA World hypothesis offers a plausible bridge from no-life to life on prebiotic Earth, by assuming that RNA, the only known molecule type capable of playing genetic and catalytic roles at the same time, could have been the first evolvable entity on the evolutionary path to the first living cell. We have developed the Metabolically Coupled Replicator System (MCRS), a spatially explicit simulation modelling approach to prebiotic RNA-World evolution on mineral surfaces, in which we incorporate the most important experimental facts and theoretical considerations to comply with recent knowledge on RNA and prebiotic evolution. In this paper the MCRS model framework has been extended in order to investigate the dynamical and evolutionary consequences of adding an important physico-chemical detail, namely explicit replicator structure - nucleotide sequence and 2D folding calculated from thermodynamical criteria - and their possible mutational changes, to the assumptions of a previously less detailed toy model. Results: For each mutable nucleotide sequence the corresponding 2D folded structure with minimum free energy is calculated, which in turn is used to determine the fitness components (degradation rate, replicability and metabolic enzyme activity) of the replicator. We show that the community of such replicators providing the monomer supply for their own replication by evolving metabolic enzyme activities features an improved propensity for stable coexistence and structural adaptation. These evolutionary advantages are due to the emergent uniformity of metabolic replicator fitnesses imposed on the community by local group selection and attained through replicator trait convergence, i.e., the tendency of replicator lengths, ribozyme activities and population sizes to become similar between the coevolving replicator species that are otherwise both structurally and functionally different. Conclusions: In the most general terms it is the surprisingly high extra viability of the metabolic replicator system that the present model adds to the MCRS concept of the origin of life. Surface-bound, metabolically coupled RNA replicators tend to evolve different, enzymatically active sites within thermodynamically stable secondary structures, and the system as a whole evolves towards the robust coexistence of a complete set of such ribozymes driving the metabolism producing monomers for their own replication. Reviewers: This article was reviewed by Gáspár Jékely, Anthony Poole and Armen Mulkidjanian © 2015 Könnyu et al.; licensee BioMed Central.


PubMed | Parmenides Center for the Conceptual Foundations of Science, CNRS Institute of Science and Supramolecular Engineering, University of Strasbourg and CNRS Chemistry, Biology and Innovation Laboratory
Type: Journal Article | Journal: Science (New York, N.Y.) | Year: 2016

The appearance of molecular replicators (molecules that can be copied) was probably a critical step in the origin of life. However, parasitic replicators would take over and would have prevented life from taking off unless the replicators were compartmentalized in reproducing protocells. Paradoxically, control of protocell reproduction would seem to require evolved replicators. We show here that a simpler population structure, based on cycles of transient compartmentalization (TC) and mixing of RNA replicators, is sufficient to prevent takeover by parasitic mutants. TC tends to select for ensembles of replicators that replicate at a similar rate, including a diversity of parasites that could serve as a source of opportunistic functionality. Thus, TC in natural, abiological compartments could have allowed life to take hold.


Szilagyi A.,Eötvös Loránd University | Szilagyi A.,Hungarian Academy of Sciences | Szilagyi A.,Parmenides Center for the Conceptual Foundations of Science | Zachar I.,Parmenides Center for the Conceptual Foundations of Science | And 3 more authors.
PLoS Computational Biology | Year: 2013

Models of competitive template replication, although basic for replicator dynamics and primordial evolution, have not yet taken different sequences explicitly into account, neither have they analyzed the effect of resource partitioning (feeding on different resources) on coexistence. Here we show by analytical and numerical calculations that Gause's principle of competitive exclusion holds for template replicators if resources (nucleotides) affect growth linearly and coexistence is at fixed point attractors. Cases of complementary or homologous pairing between building blocks with parallel or antiparallel strands show no deviation from the rule that the nucleotide compositions of stably coexisting species must be different and there cannot be more coexisting replicator species than nucleotide types. Besides this overlooked mechanism of template coexistence we show also that interesting sequence effects prevail as parts of sequences that are copied earlier affect coexistence more strongly due to the higher concentration of the corresponding replication intermediates. Template and copy always count as one species due their constraint of strict stoichiometric coupling. Stability of fixed-point coexistence tends to decrease with the length of sequences, although this effect is unlikely to be detrimental for sequences below 100 nucleotides. In sum, resource partitioning (niche differentiation) is the default form of competitive coexistence for replicating templates feeding on a cocktail of different nucleotides, as it may have been the case in the RNA world. Our analysis of different pairing and strand orientation schemes is relevant for artificial and potentially astrobiological genetics. © 2013 Szilágyi et al.


Kun A.,International Institute For Applied Systems Analysis | Kun A.,Parmenides Center for the Conceptual Foundations of Science | Kun A.,Eötvös Loránd University | Kun A.,Hungarian Academy of Sciences | Dieckmann U.,International Institute For Applied Systems Analysis
Nature Communications | Year: 2013

Although social structure is known to promote cooperation, by locally exposing selfish agents to their own deeds, studies to date assumed that all agents have access to the same level of resources. This is clearly unrealistic. Here we find that cooperation can be maintained when some agents have access to more resources than others. Cooperation can then emerge even in populations in which the temptation to defect is so strong that players would act fully selfishly if their resources were distributed uniformly. Resource heterogeneity can thus be crucial for the emergence and maintenance of cooperation. We also show that resource heterogeneity can hinder cooperation once the temptation to defect is significantly lowered. In all cases, the level of cooperation can be maximized by managing resource heterogeneity. © 2013 Macmillan Publishers Limited. All rights reserved.


Szathmary E.,Parmenides Center for the Conceptual Foundations of Science | Szathmary E.,Eötvös Loránd University
Journal of Theoretical Biology | Year: 2015

With his chemoton theory theoretical biologist and chemical engineer Tibor Gánti was one of the most outstanding intellects behind systems chemistry and the at the foundations of theoretical biology. A brief review of his oeuvre is presented. This essay introduces a special issue dedicated to his memory. © 2015 Published by Elsevier Ltd.


Ferdinandy B.,Eötvös Loránd University | Mones E.,Eötvös Loránd University | Vicsek T.,Eötvös Loránd University | Muller V.,Eötvös Loránd University | Muller V.,Parmenides Center for the Conceptual Foundations of Science
PLoS Computational Biology | Year: 2015

Outside Africa, the global phylogeography of HIV is characterized by compartmentalized local epidemics that are typically dominated by a single subtype, which indicates strong founder effects. We hypothesized that the competition of viral strains at the epidemic level may involve an advantage of the resident strain that was the first to colonize a population. Such an effect would slow down the invasion of new strains, and thus also the diversification of the epidemic. We developed a stochastic modelling framework to simulate HIV epidemics over dynamic contact networks. We simulated epidemics in which the second strain was introduced into a population where the first strain had established a steady-state epidemic, and assessed whether, and on what time scale, the second strain was able to spread in the population. Simulations were parameterized based on empirical data; we tested scenarios with varying levels of overall prevalence. The spread of the second strain occurred on a much slower time scale compared with the initial expansion of the first strain. With strains of equal transmission efficiency, the second strain was unable to invade on a time scale relevant for the history of the HIV pandemic. To become dominant over a time scale of decades, the second strain needed considerable (>25%) advantage in transmission efficiency over the resident strain. The inhibition effect was weaker if the second strain was introduced while the first strain was still in its growth phase. We also tested how possible mechanisms of interference (inhibition of superinfection, depletion of highly connected hubs in the network, one-time acute peak of infectiousness) contribute to the inhibition effect. Our simulations confirmed a strong first comer advantage in the competition dynamics of HIV at the population level, which may explain the global phylogeography of the virus and may influence the future evolution of the pandemic. © 2015 Ferdinandy et al.


PubMed | Parmenides Center for the Conceptual Foundations of Science
Type: Journal Article | Journal: Life (Basel, Switzerland) | Year: 2015

The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.


PubMed | Parmenides Center for the Conceptual Foundations of Science
Type: | Journal: Annals of the New York Academy of Sciences | Year: 2015

The RNA world hypothesis of the origin of life, in which RNA emerged as both enzyme and information carrier, is receiving solid experimental support. The prebiotic synthesis of biomolecules, the catalytic aid offered by mineral surfaces, and the vast enzymatic repertoire of ribozymes are only pieces of the origin of life puzzle; the full picture can only emerge if the pieces fit together by either following from one another or coexisting with each other. Here, we review the theory of the origin, maintenance, and enhancement of the RNA world as an evolving population of dynamical systems. The dynamical view of the origin of life allows us to pinpoint the missing and the not fitting pieces: (1) How can the first self-replicating ribozyme emerge in the absence of template-directed information replication? (2) How can nucleotide replicators avoid competitive exclusion despite utilizing the very same resources (nucleobases)? (3) How can the information catastrophe be avoided? (4) How can enough genes integrate into a cohesive system in order to transition to a cellular stage? (5) How can the way information is stored and metabolic complexity coevolve to pave to road leading out of the RNA world to the present protein-DNA world?

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