Phenotypic effect of mutations in evolving populations of RNA molecules

Background. The secondary structure of folded RNA sequences is a good model to map phenotype onto genotype, as represented by the RNA sequence. Computational studies of the evolution of ensembles of RNA molecules towards target secondary structures yield valuable clues to the mechanisms behind adaptation of complex populations. The relationship between the space of sequences and structures, the organization of RNA ensembles at mutation-selection equilibrium, the time of adaptation as a function of the population parameters, the presence of collective effects in quasispecies, or the optimal mutation rates to promote adaptation all are issues that can be explored within this framework. Results. We investigate the effect of microscopic mutations on the phenotype of RNA molecules during their in silico evolution and adaptation. We calculate the distribution of the effects of mutations on fitness, the relative fractions of beneficial and deleterious mutations and the corresponding selection coefficients for populations evolving under different mutation rates. Three different situations are explored: the mutation-selection equilibrium (optimized population) in three different fitness landscapes, the dynamics during adaptation towards a goal structure (adapting population), and the behavior under periodic population bottlenecks (perturbed population). Conclusions. The ratio between the number of beneficial and deleterious mutations experienced by a population of RNA sequences increases with the value of the mutation rate µ at which evolution proceeds. In contrast, the selective value of mutations remains almost constant, independent of µ, indicating that adaptation occurs through an increase in the amount of beneficial mutations, with little variations in the average effect they have on fitness. Statistical analyses of the distribution of fitness effects reveal that small effects, either beneficial or deleterious, are well described by a Pareto distribution. These results are robust under changes in the fitness landscape, remarkably when, in addition to selecting a target secondary structure, specific subsequences or low-energy folds are required. A population perturbed by bottlenecks behaves similarly to an adapting population, struggling to return to the optimized state. Whether it can survive in the long run or whether it goes extinct depends critically on the length of the time interval between bottlenecks. © 2010 Stich et al; licensee BioMed Central Ltd.

Adaptation and gain pool summation:Alternative models and masking data

Foley [J. Opt. Soc. Am. A 11 (1994) 1710] has proposed an influential psychophysical model of masking in which mask components in a contrast gain pool are raised to an exponent before summation and divisive inhibition. We tested this summation rule in experiments in which contrast detection thresholds were measured for a vertical 1 c/deg (or 2 c/deg) sine-wave component in the presence of a 3 c/deg (or 6 c/deg) mask that had either a single component oriented at -45° or a pair of components oriented at ±45°. Contrary to the predictions of Foley's model 3, we found that for masks of moderate contrast and above, threshold elevation was predicted by linear summation of the mask components in the inhibitory stage of the contrast gain pool. We built this feature into two new models, referred to as the early adaptation model and the hybrid model. In the early adaptation model, contrast adaptation controls a threshold-like nonlinearity on the output of otherwise linear pathways that provide the excitatory and inhibitory inputs to a gain control stage. The hybrid model involves nonlinear and nonadaptable routes to excitatory and inhibitory stages as well as an adaptable linear route. With only six free parameters, both models provide excellent fits to the masking and adaptation data of Foley and Chen [Vision Res. 37 (1997) 2779] but unlike Foley and Chen's model, are able to do so with only one adaptation parameter. However, only the hybrid model is able to capture the features of Foley's (1994) pedestal plus orthogonal fixed mask data. We conclude that (1) linear summation of inhibitory components is a feature of contrast masking, and (2) that the main aftereffect of spatial adaptation on contrast increment thresholds can be assigned to a single site. © 2002 Elsevier Science Ltd. All rights reserved.

Selling, resistance and reconciliation:a critical discursive approach to subsidiary role evolution in MNEs

Studies of political dynamics between multinational enterprise (MNE) parents and subsidiaries during subsidiary role evolution have focused largely on control and resistance. This paper adopts a critical discursive approach to enable an exploration of subtle dynamics in the way that both headquarters and subsidiaries subjectively reconstruct their independent-interdependent relationships with each other during change. We draw from a real-time qualitative study of a revealing case of charter change in an important European subsidiary of an MNE attempting to build closer integration across European country operations. Our results illustrate the role of three discourses – selling, resistance and reconciliation – in the reconstruction of the subsidiary–parent relationship. From this analysis we develop a process framework that elucidates the important role of these three discourses in the reconstruction of subsidiary roles, showing how resistance is not simply subversive but an important part of integration. Our findings contribute to a better understanding of the micro-level political dynamics in subsidiary role evolution, and of how voice is exercised in MNEs. This study also provides a rare example of discourse-based analysis in an MNE context, advancing our knowledge of how discursive methods can help to advance international business research more generally.

Like grandfather, like grandson: Erasmus and Charles Darwin on evolution

Last year (2009) marked the bicentenary of Charles Darwin's birth and the sesquicentenary of The Origin of Species. This article examines the influence of Erasmus Darwin on Charles's evolutionary thought and shows how, in many ways, Erasmus anticipated his much better-known grandson. It discusses the similarity in the mindsets of the two Darwins, asks how far the younger Darwin was exposed to the elder's evolutionary thought, examines the similarities and differences in their theories of evolution, and ends by showing the surprising similarity between their theories of inheritance. Erasmus's influence on Charles is greater than customarily acknowledged, and now is an opportune time to bring the grandfather out from behind the glare of his stellar grandson.

Knowledge-based development in leading regions across the globe:an exploratory analysis of the co-evolution of resources, capabilities, and outputs

It is widely observed that the global geography of innovation is rapidly evolving. This paper presents evidence concerning the contemporary evolution of the globe's most productive regions. The paper uncovers the underlying structure and co-evolution of knowledge-based resources, capabilities and outputs across these regions. The analysis identifies two key trends by which the economic evolution and growth patterns of these regions are differentiated-namely, knowledge-based growth and labour market growth. The knowledge-based growth factor represents the underlying commonality found between the growth of economic output, earnings and a range of knowledge-based resources. The labour market growth factor represents the capability of regions to draw on their human capital. Overall, spectacular knowledge-based growth of leading Chinese regions is evident, highlighting a continued shift of knowledge-based resources to Asia. It is concluded that regional growth in knowledge production investment and the capacity to draw on regional human capital reserves are neither necessarily traded-off nor complementary to each other. © 2012 Urban Studies Journal Limited.

The evolution of logistics service providers and the role of Internet-based applications in facilitating global operations

The need for global logistics services has increased dramatically and become extremely complex and dynamic as a result of a number of changes in manufacturing and in industrial production. In response, the logistics industry is changing in a variety of ways, including mergers to form integrated transportation service providers, outsourcing and increased use of information technology. The aim of this chapter is to provide an overview of the evolution and the most important trends in the logistics services provider (LSP) industry. Specific emphasis will be given to the role of Internet-based applications. Within this context, the chapter will also present the role of logistics e-marketplaces. In particular, based on the secondary research of currently existing logistics on-line marketplaces, an analysis and classification of them is provided with the aim of identifying service gaps. The analysis reveals that logistics electronic marketplaces, despite the increased range of services currently offered, still face limitations with reference to integrated customs links or translation services, which both reduce the efficiency of global operations.