Repair rather than segregation of damage is the optimal unicellular aging strategy

BACKGROUND: How aging, being unfavourable for the individual, can evolve is one of the fundamental problems of biology. Evidence for aging in unicellular organisms is far from conclusive. Some studies found aging even in symmetrically dividing unicellular species; others did not find aging in the same, or in different, unicellular species, or only under stress. Mathematical models suggested that segregation of non-genetic damage, as an aging strategy, would increase fitness. However, these models failed to consider repair as an alternative strategy or did not properly account for the benefits of repair. We used a new and improved individual-based model to examine rigorously the effect of a range of aging strategies on fitness in various environments. RESULTS: Repair of damage emerges as the best strategy despite its fitness costs, since it immediately increases growth rate. There is an optimal investment in repair that outperforms damage segregation in well-mixed, lasting and benign environments over a wide range of parameter values. Damage segregation becomes beneficial, and only in combination with repair, when three factors are combined: (i) the rate of damage accumulation is high, (ii) damage is toxic and (iii) efficiency of repair is low. In contrast to previous models, our model predicts that unicellular organisms should have active mechanisms to repair damage rather than age by segregating damage. Indeed, as predicted, all organisms have evolved active mechanisms of repair whilst aging in unicellular organisms is absent or minimal under benign conditions, apart from microorganisms with a different ecology, inhabiting short-lived environments strongly favouring early reproduction rather than longevity. CONCLUSIONS: Aging confers no fitness advantage for unicellular organisms in lasting environments under benign conditions, since repair of non-genetic damage is better than damage segregation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-014-0052-x) contains supplementary material, which is available to authorized users

Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0

Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the “biofilms promote altruism” study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice

Improving Predictions for Helium Emission Lines

We have combined the detailed He I recombination model of Smits with the collisional transitions of Sawey & Berrington in order to produce new accurate helium emissivities that include the effects of collisional excitation from both the 2 (3)S and 2 (1) S levels. We present a grid of emissivities for a range of temperature and densities along with analytical fits and error estimates. Fits accurate to within 1% are given for the emissivities of the brightest lines over a restricted range for estimates of primordial helium abundance. We characterize the analysis uncertainties associated with uncertainties in temperature, density, fitting functions, and input atomic data. We estimate that atomic data uncertainties alone may limit abundance estimates to an accuracy of 1.5%; systematic errors may be greater than this. This analysis uncertainty must be incorporated when attempting to make high accuracy estimates of the helium abundance. For example, in recent determinations of the primordial helium abundance, uncertainties in the input atomic data have been neglected.Comment: ApJ, accepte

Association of proximal elements of social disadvantage with children's language development at 2 years: An analysis of data from the Children in Focus (CiF) sample from the ALSPAC birth cohort

This is the peer reviewed version of the following article: Law, J., Clegg, J., Rush, R., Roulstone, S. & Peters, T. J. (2018) Association of proximal elements of social disadvantage with children's language development at 2 years: An analysis of data from the Children in Focus (CiF) sample from the ALSPAC birth cohort. International Journal of Language & Communication Disorders, which has been published in final form at https://doi.org/10.1111/1460-6984.12442. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.Background: An association between social disadvantage and early language development is commonly reported in the literature, but less attention has been paid to the way that different aspects of social disadvantage affect both expressive and receptive language in the first 2 years of life. Aims: To examine the contributions of gender, parental report of early language skills and proximal social variables (the amount of stimulation in the home, the resources available to the child and the attitudes/emotional status of the primary carer and the support available to him/her) controlling for distal social variables (family income and maternal education) to children's expressive and receptive language development at 2 years in a community ascertained population cohort. Methods & Procedures: Data from 1314 children in the Children in Focus (CiF) sample from the Avon Longitudinal Study of Parents and Children (ALSPAC) were analyzed. Multivariable regression models identified the contribution of proximal (what parents do with their children) measures of social disadvantage adjusting for more distal (e.g., family income and material wealth) measures as well as early language development at 15 months to the development of verbal comprehension, expressive vocabulary and expressive grammar (word combinations) at 2 years of age. Outcome & Results: In the final multivariable models gender, earlier language and proximal social factors, co‐varying for distal factors predicted 36% of the variance for expressive vocabulary, 22% for receptive language and 27% for word combinations at 2 years. Language development at 15 months remained a significant predictor of outcomes at 24 months. Environmental factors were associated with both expressive scales but the picture was rather more mixed for receptive language suggesting that there may be different mechanisms underlying the different processes. Conclusions & Implications: This study supports the argument that social advantage makes a strong contribution to children's language development in the early years. The results suggest that what parents/carers do with their children is critical even when structural aspects of social disadvantage such as family income and housing have been taken into consideration although this relationship varies for different aspects of language. This has the potential to inform the targeting of public health interventions focusing on early language and pre‐literacy skills on the one hand and home learning environments on the other and, potentially, the two in combination.54pubpub

Dynamics of a colloid-stabilized cream

We use x-ray photon correlation spectroscopy to investigate the dynamics of a high volume fraction emulsion creaming under gravity. The dodecane-in-water emulsion has interfaces stabilized solely by colloidal particles (silica). The samples were observed soon after mixing: as the emulsion becomes compact we discern two regimes of ageing with a cross-over between them. The young emulsion has faster dynamics associated with creaming in a crowded environment accompanied by local rearrangements. The dynamics slow down for the older emulsion although our studies show that motion is associated with large intermittent events. The relaxation rate, as seen from the intensity autocorrelation function, depends linearly on the wave vector at all times; however, the exponent associated with the line shape changes from 1.5 for young samples to less than 1 as the emulsion ages. The combination of ballisticlike dynamics, an exponent that drops below 1 and large intermittent fluctuations has not been reported before.Comment: 8 pages, 5 figure