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Register a new userError catastrophe in the replication is resolved by innate proofreading during the polymerization process
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An important issue for the origins of life is how to ensure the accurate maintenance of information in replicating polymers in the face of inevitable errors. We investigate how this maintenance depends on reaction kinetics by incorporating elementary steps of polymerization into the population dynamics of polymers. We find that template-directed polymerization entails an inherent error-correction mechanism akin to kinetic proofreading, making a longer polymer more tolerant to an error catastrophe. Since this mechanism requires no enzyme, it is likely to operate under wide prebiotic conditions.
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Immunity is hypothesized to share limited resources with other physiological functions and may mediate life history trade-offs, for example between reproduction and survival. However, vertebrate immune defense is a complex system that consists of three components. To date, no study has assessed all of these components for the same animal model and within a given situation. Previous studies have determined that the acquired immunity of common eiders (Somateria mollissima) is suppressed during incubation. The present paper aims to assess the innate immune response in fasting eiders in relation to their initial body condition. Innate immunity was assessed by measuring plasma nitric oxide (NO) levels, prior to and after injection of lipopolysaccharides (LPS), a method which is easily applicable to many wild animals. Body condition index and corticosterone levels were subsequently determined as indicators of body condition and stress level prior to LPS injection. The innate immune response in eiders did not vary significantly throughout the incubation period. The innate immune response of eiders did not vary significantly in relation to their initial body condition but decreased significantly when corticosterone levels increased. However, NO levels after LPS injection were significantly and positively related to initial body condition, while there was a significant negative relationship with plasma corticosterone levels. Our study suggests that female eiders preserve an effective innate immune response during incubation and this response might be partially determined by the initial body condition.
All living cells need to coordinate DNA replication with growth and division to generate cell cycles that are stable in time. The bacterium Escherichia coli initiates replication at a volume per origin that on average is independent of the growth rate. It also adds an on average constant volume per origin between successive initiation events, independent of the initiation size. Yet, a molecular model that can explain these observations has been lacking. Here, we develop a mathematical model of DNA replication initiation in E. coli that is consistent with a wealth of experimental data. We first show that the previously proposed initiator titration model, which is based on the accumulation of the initiator protein DnaA on chromosomal titration sites, is not consistent with the experimental data. We then present a model that is based on an ultra-sensitive switch between an inactive form of DnaA and an active form that induces replication initiation. Our model shows that at low growth rates the switch is predominantly controlled by activation of DnaA via lipids and deactivation via the chromosomal site datA, while at high growth rates DARS2 and RIDA become essential. Crucially, in our mean-field model DNA replication is initiated at a constant volume per origin, qualifying our model as a sizer. Yet, we show that in a stochastic version of the same model the inevitable fluctuations in the components that control the DnaA activation switch naturally give rise to the experimentally observed adder correlations.
A broad range of membrane proteins display anomalous diffusion on the cell surface. Different methods provide evidence for obstructed subdiffusion and diffusion on a fractal space, but the underlying structure inducing anomalous diffusion has never been visualized due to experimental challenges. We addressed this problem by imaging the cortical actin at high resolution while simultaneously tracking individual membrane proteins in live mammalian cells. Our data confirm that actin introduces barriers leading to compartmentalization of the plasma membrane and that membrane proteins are transiently confined within actin fences. Furthermore, superresolution imaging shows that the cortical actin is organized into a self-similar meshwork. These results present a hierarchical nanoscale picture of the plasma membrane.
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which usually happens when the polymerase tries to incorporate a mismatched nucleotide triphosphate. Previous models have made simplifying assumptions such as neglecting the trailing polymerase behind the backtracking polymerase or assuming that the trailing polymerase is stationary. We derive exact analytic solutions of a stochastic model that includes locally interacting RNAPs by explicitly showing how a trailing RNAP influences the probability that an error is corrected or incorporated by the leading backtracking RNAP. We also provide two related methods for computing the mean times to error correction or incorporation given an initial local RNAP configuration.
Motivated by unexplained observations of low sulphur abundances in planetary nebulae (PNe) and the PG1159 class of post asymptotic giant branch (AGB) stars, we investigate the possibility that sulphur may be destroyed by nucleosynthetic processes in low-to-intermediate mass stars during stellar evolution. We use a 3 Msun, Z=0.01 evolutionary sequence to examine the consequences of high and low reaction rate estimates of neutron captures onto sulphur and neighbouring elements. In addition, we have tested high and low rates for the neutron producing reactions C13(alpha,n)O16 and Ne22(alpha,n)Mg25. We vary the mass width of a partially mixed zone (PMZ), which is responsible for the formation of a C13 pocket and is the site of the C13(alpha,n)O16 neutron source. We test PMZ masses from zero up to an extreme upper limit of the entire He-intershell mass at 10^-2 Msun. We find that the alternative reaction rates and variations to the partially mixed zone have almost no effect on surface sulphur abundances and do not reproduce the anomaly. To understand the effect of initial mass on our conclusions, 1.8 Msun and 6 Msun evolutionary sequences are also tested with similar results for sulphur abundances. We are able to set a constraint on the size of the PMZ, as PMZ sizes that are greater than half of the He-intershell mass (in the 3 Msun model) are excluded by comparison with neon abundances in planetary nebulae. We compare the 1.8 Msun models intershell abundances with observations of PG1159-035, whose surface abundances are thought to reflect the intershell composition of a progenitor AGB star. We find general agreement between the patterns of F, Ne, Si, P, and Fe abundances and a very large discrepancy for sulphur where our model predicts abundances that are 30-40 times higher than is observed in the star.
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