Evolutionary pressures on the yeast transcriptome

Codon usage bias (CUB) is the well known phenomenon that the frequency of synonymous codons is unequal. This is presumably the result of adaptive pressures favouring some codons over others. The underlying reason for this pressure is unknown, although a large number of possible driver mechanisms have been proposed; one of them is the decoding time. The standard model to calculate decoding time is the Gromadski- Rodnina model. Yet, recently, there have been a number of studies arguing to the effect that this conventional speed-model is not relevant to understand the dynamics of translation. However, results remain inconclusive so far. This contribution takes a novel approach to address this issue based on comparing mRNA with random synonymous variants to estimate the evolutionary pressures that have acted on the transcriptome. It emerges that over 70%of ORFs have been subject to a strong selection pressure for translation speed and that there is also a strong selection pressure for the avoidance of traffic jams. Finally, it is also shown that both homogeneous and very heterogeneous transcripts are over-represented. These results corroborate the validity of the Gromadski-Rodnina model

A Category Theoretical Argument Against the Possibility of Artificial Life

One of Robert Rosen's main contributions to the scientific community is summarized in his book 'Life itself'. There Rosen presents a theoretical framework to define living systems; given this definition, he goes on to show that living systems are not realisable in computational universes. Despite being well known and often cited, Rosen's central proof has so far not been evaluated by the scientific community. In this article we review the essence of Rosen's ideas leading up to his rejection of the possibility of real artificial life in silico. We also evaluate his arguments and point out that some of Rosen's central notions are ill- defined. The conclusion of this article is that Rosen's central proof is wrong

The Localization Hypothesis and Machines

In a recent article in 'Artificial Life', Chu and Ho suggested that Rosen's central result about the simulability of living systems might be flawed. This argument was later declared ''null and void'' by Louie. In this article the validity of Louie's objections are examined

Walking, hopping and jumping: a model of transcription factor dynamics on DNA

We present a model of how transcription factors scan DNA to find their specific binding sites. Following the classical work of Winter et al. (1981), our model assumes two modes of transcription factor dynamics. Adjacent moves, where the proteins make a single step movement to one side, or short walks where the transcription factors slide along the DNA several binding sites at a time. The purpose of this article is twofold. Firstly, we discuss how such a system can be efficiently modeled computationally. Secondly, we analyse how the mean first binding times of transcription factors to their specific time depends on key parameters of the system

Evolving strategies for single-celled organisms in multi-nutrient environments

When micro-organisms are in environments with multiple nutrients, they often preferentially utilise one first. A second is only utilised once the first is exhausted. Such a two-phase growth pattern is known as diauxic growth. Experimentally, this manifests itself through two distinct exponential growth phases separated by a lag phase of arrested growth. The dura- tion of the lag phase can be quite substantial. From an evolu- tionary point of view the existence of a lag phase is somewhat puzzling because it implies a substantial loss of growth op- portunity. Mutants with shorter lag phases would be prone to outcompete those with longer phases. Yet in nature, diauxic growth with lag phases appears to be a robust phenomenon. We introduce a model of the evolution of diauxic growth that captures the basic interactions regulating it in bacteria. We observe its evolution without a lag phase. We conclude that the lag phase is an adaptation that is only beneficial when fit- ness is averaged over a large number of environments

Evolving Biological Systems: Evolutionary Pressure to Inefficiency

The evolution of quantitative details (i.e. “parameter values”) of biological systems is highly under-researched. We use evolutionary algorithms to co-evolve parameters for a generic but biologically plausible topological differential equation model of nutrient uptake. In our model, evolving cells compete for a finite pool of nutrient resources. From our investigations it emerges that the choice of values is very important for the properties of the biological system. Our analysis also shows that clonal populations that are not subject to competition from other species best grow at a very slow rate. However, if there is co-evolutionary pressure, that is, if a population of clones has to compete with other cells, then the fast growth is essential, so as not to leave resources to the competitor. We find that this strategy, while favoured evolutionarily, is inef- ficient from an energetic point of view, that is less growth is achieved per unit of input nutrient. We conclude, that competition can lead to an evolutionary pressure towards inefficiency

Dynamical Hierarchies

<Guest Editor's Introduction&gt

Temperature and strain rate influence on AA5086 Forming Limit Curves: experimental results and discussion on the validity of the M-K model

International audienceDue to the high-strength to weigh ratio, corrosion resistance, good workability and weldability characteristics, aluminium alloys are increasingly used in many sectors. Researches on formability of aluminium alloy sheets have always been a hot topic these last years while very few works taking into both temperature and strain rate effects on formability limits can be found in the literature. In this study, the formability of sheet metal AA5086 is investigated at different temperatures (20, 150 and 200°C) and strain rates (0.02, 0.2 and 2 s-1) through a Marciniak test setup. Experimental results show that the formability of AA5086 increases with temperature and decreases with forming speed. Based on the analytical M-K theory, a Finite Element (FE) M-K model is proposed to predict the Forming Limit Curves (FLCs). A modified Ludwick hardening law with temperature and strain rate functions is proposed to describe the thermo-elasto-viscoplastic behavior of the material. The influence of the initial imperfection (f0) sensitivity in the FE M-K model is discussed and a strategy to calibrate f0 is proposed. The agreement between experimental and numerical FLCs indicates that the FE M-K model can be an effective model for predicting sheet metal formability under different operating conditions if the initial imperfection value is calibrated for each forming condition

Effect of material thermo-viscoplastic modeling on the prediction of forming limit curves of aluminium alloy 5086

International audienceA solution to improve the formability of aluminium alloy sheets can consist in investigating warm forming processes. The optimization of forming process parameters needs a precise evaluation of material properties and sheet metal formability for actual operating environment. Based on the analytical M-K theory, a Finite Element (FE) M-K model was proposed to predict Forming Limit Curves (FLCs) at different temperatures and strain rates. The influences of initial imperfection value (f 0) and material thermos-viscoplastic model on the FLCs are discussed in this work. The flow stresses of AA5086 were characterized by uniaxial tensile tests at different temperatures (20, 150 and 200°C) and equivalent strain rates (0.0125, 0.125 and 1.25 s −1). Three types of hardening models (power law model, saturation model and mixed model) were proposed and adapted to correlate the experimental flow stresses. The three hardening models were implemented into the FE M-K model in order to predict FLCs for different forming conditions. The predicted limit strains are very sensitive to the thermo-viscoplastic modeling of AA5086 and to the calibration of the initial geometrical imperfection which controls the onset of necking

Influence of temperature and strain rate on the formability of aluminium alloys: Comparison between experimental and predictive results

International audienceThe use of sheet metal forming processes can be limited by the formability of materials, especially in the case of aluminium alloys. To improve the formability, warm forming processes can be considered. In this work, the effects of temperature and strain rate on the formability of a given aluminium alloy (AA5086) have been studied by means of both experimental and predictive approaches. Experimental tests have been carried out with a Marciniak stamping experimental device. Forming limit curves (FLCs) have been established on a temperature range going from ambient temperature to 200°C and on a strain rate range going from quasi-static up to 2s-1. In order to predict the experimental temperature and strain rate sensitivities, a predictive model based on the finite element simulation of the classical Marciniak and Kuczynski (M-K) geometrical model is proposed. The limit strains obtained with this model are very sensitive to the thermo-viscoplastic behaviour modeling and to the calibration of the initial geometrical imperfection controlling the onset of necking