How sequence populations persist inside bacterial genomes

Compared to their eukaryotic counterparts, bacterial genomes are small and contain extremely tightly packed genes. Therefore, discovering a large number of short repetitive sequences in the genomes of Pseudomonads and Enterobacteria is unexpected. These sequences can independently replicate in the host genome and form populations that persist for millions of years. Here we model the interactions of intragenomic sequence populations with the bacterial host. In a simple model, sequence populations either expand until they drive the host to extinction or the sequence population gets purged from the genome. Including horizontal gene transfer does not change the qualitative outcome of the model and leads to the extinction of the sequence population. However, a sequence population can be stably maintained, if each sequence provides a benefit that decreases with increasing sequence population size. But concurrently, the replication of the sequence population needs to be costly to the host. Surprisingly, in regimes where horizontal gene transfer plays a role, the benefit conferred by the sequence population does not have to exceed the damage it causes. Together, our analyses provide a plausible scenario for the persistence of sequence populations in bacterial genomes. More importantly, we hypothesize a limited biologically relevant parameter range, which can be tested in future experiments

On the fitness of informative cues in complex environments

To be able to deal with uncertainty is of primary importance to all organisms. When cues provide information about the state of the environment, organisms can use them to respond flexibly. Thus information can provide fitness advantages. Without environmental cues, an organism can reduce the risks of environmental uncertainty by hedging its bets across different scenarios. Risk mitigation is then possible by adopting a life-history of bet-hedging, either randomly switching between phenotypes (diversifying bet-hedging) or adopting intermediate phenotypes (conservative bet-hedging). Hence, understanding patterns of bet-hedging is necessary in order to quantify the fitness benefit of environmental cues, since it provides a baseline fitness in the absence of informative cues. Quantifying fitness benefits in terms of mutual information reveals deep connections between Darwinian evolution and information theory. However, physiological constraints or complex ecological scenarios often lead to the number of environmental states to exceed that of potential phenotypes, or a single intermediate phenotype is adopted, as in the case of conservative bet-hedging. Incorporating these biological complexities, we generalise the relationship between information theory and Darwinian fitness. Sophisticated bet-hedging strategies combining diversifying and conservative bet-hedging - can then evolve. We show that, counterintuitively, environmental complexity can reduce, rather than increase, the number of phenotypes that an organism can adopt. In conclusion, we develop an information-theoretic extensible approach for investigating and quantifying fitness in ecological studies

Memory shapes microbial populations

Correct decision making is fundamental for all living organisms to thrive under environmental changes. The patterns of environmental variation and the quality of available information define the most favourable strategy among multiple options, from randomly adopting a phenotypic state to sensing and reacting to environmental cues. Cellular memory—the ability to track and condition the time to switch to a different phenotypic state—can help withstand environmental fluctuations. How does memory manifest itself in unicellular organisms? We describe the population-wide consequences of phenotypic memory in microbes through a combination of deterministic modelling and stochastic simulations. Moving beyond binary switching models, our work highlights the need to consider a broader range of switching behaviours when describing microbial adaptive strategies. We show that memory in individual cells generates patterns at the population level coherent with overshoots and non-exponential lag times distributions experimentally observed in phenotypically heterogeneous populations. We emphasise the implications of our work in understanding antibiotic tolerance and, in general, bacterial survival under fluctuating environments

Dynamics of a combined Medea-underdominant population transformation system

Background: Transgenic constructs intended to be stably established at high frequencies in wild populations have been demonstrated to “drive” from low frequencies in experimental insect populations. Linking such population transformation constructs to genes which render them unable to transmit pathogens could eventually be used to stop the spread of vector-borne diseases like malaria and dengue. Results: Generally, population transformation constructs with only a single transgenic drive mechanism have been envisioned. Using a theoretical modelling approach we describe the predicted properties of a construct combining autosomal Medea and underdominant population transformation systems. We show that when combined they can exhibit synergistic properties which in broad circumstances surpass those of the single systems. Conclusion: With combined systems, intentional population transformation and its reversal can be achieved readily. Combined constructs also enhance the capacity to geographically restrict transgenic constructs to targeted populations. It is anticipated that these properties are likely to be of particular value in attracting regulatory approval and public acceptance of this novel technology

Collective narratives catalyse cooperation

Humans invest in fantastic stories—mythologies. Recent evolutionary theories suggest that cultural selection may favour moralising stories that motivate prosocial behaviours. A key challenge is to explain the emergence of mythologies that lack explicit moral exemplars or directives. Here, we resolve this puzzle with an evolutionary model in which arbitrary mythologies transform a collection of egoistic individuals into a cooperative. We show how these otherwise puzzling amoral, nonsensical, and fictional narratives act as exquisitely functional coordination devices and facilitate the emergence of trust and cooperativeness in both large and small populations. Especially, in small populations, reflecting earlier hunter- gatherers communities, relative to our contemporary community sizes, the model is robust to the cognitive costs in adopting fictions

A common gene drive language eases regulatory process and eco-evolutionary extensions

Background Synthetic gene drive technologies aim to spread transgenic constructs into wild populations even when they impose organismal fitness disadvantages. The extraordinary diversity of plausible drive mechanisms and the range of selective parameters they may encounter makes it very difficult to convey their relative predicted properties, particularly where multiple approaches are combined. The sheer number of published manuscripts in this field, experimental and theoretical, the numerous techniques resulting in an explosion in the gene drive vocabulary hinder the regulators' point of view. We address this concern by defining a simplified parameter based language of synthetic drives. Results Employing the classical population dynamics approach, we show that different drive construct (replacement) mechanisms can be condensed and evaluated on an equal footing even where they incorporate multiple replacement drives approaches. Using a common language, it is then possible to compare various model properties, a task desired by regulators and policymakers. The generalization allows us to extend the study of the invasion dynamics of replacement drives analytically and, in a spatial setting, the resilience of the released drive constructs. The derived framework is available as a standalone tool. Conclusion Besides comparing available drive constructs, our tool is also useful for educational purpose. Users can also explore the evolutionary dynamics of future hypothetical combination drive scenarios. Thus, our results appraise the properties and robustness of drives and provide an intuitive and objective way for risk assessment, informing policies, and enhancing public engagement with proposed and future gene drive approaches

QMDS: A File System Metadata Management Service Supporting a Graph Data Model-Based Query Language

Proposes QMDS: a file system metadata management service that integrates all file system metadata and uses a graph model with attributes on nodes and edges

The role of freestream turbulence scale in subsonic flow separation

The clarification of the role of freestream turbulence scale in determining the location of boundary layer separation is discussed. Modifications to the test facility were completed. Wind tunnel flow characteristics, including turbulence parameters, were determined with two turbulence generating grids, as well as no grid. These results are summarized. Initial results on the role of scale on turbulent boundary layer separation on the upper surface of an airfoil model are also discussed