Dissecting the role of low-complexity regions in the evolution of vertebrate proteins

Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few aminoacids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Generation and nonlinear evolution of shore-oblique/transverse sand bars

The coupling between topography, waves and currents in the surf zone may selforganize to produce the formation of shore-transverse or shore-oblique sand bars on an otherwise alongshore uniform beach. In the absence of shore-parallel bars, this has been shown by previous studies of linear stability analysis, but is now extended to the finite-amplitude regime. To this end, a nonlinear model coupling wave transformation and breaking, a shallow-water equations solver, sediment transport and bed updating is developed. The sediment flux consists of a stirring factor multiplied by the depthaveraged current plus a downslope correction. It is found that the cross-shore profile of the ratio of stirring factor to water depth together with the wave incidence angle primarily determine the shape and the type of bars, either transverse or oblique to the shore. In the latter case, they can open an acute angle against the current (upcurrent oriented) or with the current (down-current oriented). At the initial stages of development, both the intensity of the instability which is responsible for the formation of the bars and the damping due to downslope transport grow at a similar rate with bar amplitude, the former being somewhat stronger. As bars keep on growing, their finite-amplitude shape either enhances downslope transport or weakens the instability mechanism so that an equilibrium between both opposing tendencies occurs, leading to a final saturated amplitude. The overall shape of the saturated bars in plan view is similar to that of the small-amplitude ones. However, the final spacings may be up to a factor of 2 larger and final celerities can also be about a factor of 2 smaller or larger. In the case of alongshore migrating bars, the asymmetry of the longshore sections, the lee being steeper than the stoss, is well reproduced. Complex dynamics with merging and splitting of individual bars sometimes occur. Finally, in the case of shore-normal incidence the rip currents in the troughs between the bars are jet-like while the onshore return flow is wider and weaker as is observed in nature.

Influence on present-day coastal dynamics and evolution of a relict subaqueous delta lobe: Sol de Riu lobe, Ebro Delta. Continental Shelf Research, 74: 94-104. doi:10.1016/j.csr.2013.11.021

We used high-resolution swath-bathymetry data to characterise the morphology of the abandoned subaqueous Sol de Riu delta lobe in the Ebro Delta, Western Mediterranean Sea. This study aims to assess the influence of an abandoned delta lobe on present-day coastal dynamics in a micro-tidal environment. Detailed mapping of the relict Sol de Riu lobe also showed a set of bedforms interpreted as footprints of human activities: seasonal V-shaped depressions on the middle shoreface due to boat anchoring and old trawling marks between 16 and 18 m water depth. Estimations of the mobility of bottom sediment showed that the shallowest shoreface (i.e. less than 7 m depth) is the most dynamic part of the relict lobe, while the middle shoreface experienced significant morphological changes since the lobe was abandoned. The deepest shoreface (i.e. water depth in excess of 15 m), which corresponds to the front of the lobe, is defined by a very small potential for morphological change. Simulations showed that while the relict lobe does not significantly affect the typical short period waves (Tp ≈4 s) in the study area, it does interfere with the most energetic wave conditions (Tp ≥ 7 s) acting as a shoal leading to the concentration of wave energy along the shoreline northwest of the lobe. The consequence of such modification of the high-energy wave propagation pattern by the relict lobe is an alteration of the wave-induced littoral sediment dynamics with respect to a situation without the lobe.

Microstructural evolution of primary crystallization in diffusion-controlled grain growth

A model has been developed for evaluating grain size distributions in primary crystallizations where the grain growth is diffusion controlled. The body of the model is grounded in a recently presented mean-field integration of the nucleation and growth kinetic equations, modified conveniently in order to take into account a radius-dependent growth rate, as occurs in diffusion-controlled growth. The classical diffusion theory is considered, and a modification of this is proposed to take into account interference of the diffusion profiles between neighbor grains. The potentiality of the mean-field model to give detailed information on the grain size distribution and transformed volume fraction for transformations driven by nucleation and either interface- or diffusion-controlled growth processes is demonstrated. The model is evaluated for the primary crystallization of an amorphous alloy, giving an excellent agreement with experimental data. Grain size distributions are computed, and their properties are discussed.

Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes

BACKGROUND: Understanding how alternative phenotypes arise from the same genome is a major challenge in modern biology. Eusociality in insects requires the evolution of two alternative phenotypes - workers, who sacrifice personal reproduction, and queens, who realize that reproduction. Extensive work on honeybees and ants has revealed the molecular basis of derived queen and worker phenotypes in highly eusocial lineages, but we lack equivalent deep-level analyses of wasps and of primitively eusocial species, the latter of which can reveal how phenotypic decoupling first occurs in the early stages of eusocial evolution. RESULTS: We sequenced 20 Gbp of transcriptomes derived from brains of different behavioral castes of the primitively eusocial tropical paper wasp Polistes canadensis. Surprisingly, 75% of the 2,442 genes differentially expressed between phenotypes were novel, having no significant homology with described sequences. Moreover, 90% of these novel genes were significantly upregulated in workers relative to queens. Differential expression of novel genes in the early stages of sociality may be important in facilitating the evolution of worker behavioral complexity in eusocial evolution. We also found surprisingly low correlation in the identity and direction of expression of differentially expressed genes across similar phenotypes in different social lineages, supporting the idea that social evolution in different lineages requires substantial de novo rewiring of molecular pathways. CONCLUSIONS: These genomic resources for aculeate wasps and first transcriptome-wide insights into the origin of castes bring us closer to a more general understanding of eusocial evolution and how phenotypic diversity arises from the same genome.

Factors that determine the evolution of high-growth businesses

The study herein discusses research aimed at elucidating the factors that contribute to a business' ability to maintain high growth. The database from the Iberian Balance Sheet Analysis System (SABI, from its initials in Spanish) was used to identify 250 industrial Catalonian businesses with high growth during 2004-2007. These companies participated in a survey on strategies and management practices; in 2013, they were re-analyzed to investigate the factors that contributed to continued growth for certain companies. Through diverse statistical techniques, business policies related to quality, innovation, internationalization and finance were shown to influence business growth and sustainability over time. High-growth businesses have been studied throughout the world, but this is the first study to investigate the evolution of businesses after a high-growth phase.

Input diffusion and the evolution of production networks

What determines which inputs are initially considered and eventually adopted in the productionof new or improved goods? Why are some inputs much more prominent than others? We modelthe evolution of input linkages as a process where new producers first search for potentially usefulinputs and then decide which ones to adopt. A new product initially draws a set of 'essentialsuppliers'. The search stage is then confined to the network neighborhood of the latter, i.e., to theinputs used by the essential suppliers. The adoption decision is driven by a tradeoff between thebenefits accruing from input variety and the costs of input adoption. This has important implicationsfor the number of forward linkages that a product (input variety) develops over time. Inputdiffusion is fostered by network centrality ? an input that is initially represented in many networkneighborhoods is subsequently more likely to be adopted. This mechanism also delivers a powerlaw distribution of forward linkages. Our predictions continue to hold when varieties are aggregatedinto sectors. We can thus test them, using detailed sectoral US input-output tables. We showthat initial network proximity of a sector in 1967 significantly increases the likelihood of adoptionthroughout the subsequent four decades. The same is true for rapid productivity growth in aninput-producing sector. Our empirical results highlight two conditions for new products to becomecentral nodes: initial network proximity to prospective adopters, and technological progress thatreduces their relative price. Semiconductors met both conditions.

Cenozoic evolution of eastern Iberia: structural data and dynamic model.

Iberia underwent intraplate deformation during the Mesozoic and Cenozoic. In eastem Ibena, compression took place during the Palaeogene and early Miocene, giving rise to the Iberian Chain, and extension started during the early Miocene in the coastal areas and the Valencia trough; during early Miocene compression continued in the western Iberian Chain whereas extension had started in the eastern Iberian Chain. From the kinematic data obtained from the major compressional and extensional structures formed dunng the Cenozoic, a simple dynamic model using Bott's (1959) formula is presented. The results show that both extension and compression may have been produced assuming a main horizontal stress-axis approximately N-S, in a similar direction that the convergence between Europe, Ibena and Afnca dunng the Cenozoic.

The Evolution of the European Regulatory Framework for Electronic Communications

The paper reviews the historical transformation of the European regulatory framework for electronic communications from the era dominated by state-owned enterprises to the presence of regulated competition. In the course of these developments, the vision of the roles of the public and private sectors in electronic communications changed in expected and unexpected ways. While the period is characterized by a shift toward less direct state intervention, the intensity of regulation has increased in many areas. Most recently, in the wake of the financial crisis, new forms of state intervention can be observed, including public investment in communications infrastructure and public-private partnerships. As a result of the reforms, Europe has been able to achieve major successes but it also suffered unanticipated setbacks compared to other regions. The European Union emerged as the global leader in mobile communications during the 1990s and was able to roll-out first-generation broadband access networks more rapidly than many of its peers. Recently, however, Europe as a whole has not performed as well in deploying next-generation networks and advanced mobile communications services. The paper offers a political-economic explanation for these developments and assesses their effects on the performance of the European electronic communications sector and the economy. From this analysis, the European model emerges as a unique institutional arrangement with peculiar advantages and disadvantages. Once these are recognized, sensible next steps to build the strengths while avoiding the weaknesses of the model can be seen more clearly.

Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.

The seasonal evolution of high vertical–mode internal waves in a deep reservoir

The causal mechanism and seasonal evolution of the internal wave field in a deep, warm, monomictic reservoirare examined through the analysis of field observations and numerical techniques. The study period extends fromthe onset of thermal stratification in the spring until midsummer in 2005. During this time, wind forcing wasperiodic, with a period of 24 h (typical of land–sea breezes), and the thermal structure in the lake wascharacterized by the presence of a shallow surface layer overlying a thick metalimnion, typical of small to mediumsized reservoirs with deep outtakes. Basin-scale internal seiches of high vertical mode (ranging from mode V3 toV5) were observed in the metalimnion. The structure of the dominant modes of oscillation changed asstratification evolved on seasonal timescales, but in all cases, their periods were close to that of the local windforcing (i.e., 24 h), suggesting a resonant response. Nonresonant oscillatory modes of type V1 and V2 becamedominant after large frontal events, which disrupted the diurnal periodicity of the wind forcing

Factors influencing the evolution of e-commerce : an empirical analysis in a developed market economy

Peer-reviewed

Emergence and development of a financial cluster: the evolution of Andorra’s banking deposits in the long-term, 1931-2007

This paper explores the origins of Andorra’s financial cluster. It shows that the free movement of currency, the protection of infant industry, and geographical concentration lie at the foundation of the cluster’s competitive advantage. Drawing on a new set of data, the paper also provides for the first time an estimate of the total deposits held by Andorra’s banks between 1931 and 2007. Based on this new information, the paper reaches the conclusion that the development of the cluster went through four distinct phases in which large companies, acting as leaders, played an important role in enhancing the cluster’s business capabilities.

An analysis of the evolution of hydrometeorological extremes in newspapers: the case of Catalonia, 1982-2006

This contribution analyzes the evolution of perception of certain natural hazards over the past 25 years in a Mediterranean region. Articles from newspapers have been used as indicator. To this end a specific Spanish journal has been considered and an ACCESS database has been created with the summarized information from each news item. The database includes data such as the location of each specific article in the newspaper, its length, the number of pictures and figures, the headlines and a summary of the published information, including all the instrumental data. The study focused on hydrometeorological extremes, mainly floods and droughts, in the northeast of the Iberian Peninsula. The number of headlines per event, trends and other data have been analyzed and compared with "measured" information, in order to identify any bias that could lead to an erroneous perception of the phenomenon. The SPI index (a drought index based on standardized accumulated precipitation) has been calculated for the entire region, and has been used for the drought analysis, while a geodatabase implemented on a GIS built for all the floods recorded in Catalonia since 1900 (INUNGAMA) has been used to analyze flood evolution. Results from a questionnaire about the impact of natural hazards in two specific places have been also used to discuss the various perceptions between rural and urban settings. Results show a better correlation between the news about drought or water scarcity and SPI than between news on floods in Catalonia and the INUNGAMA database. A positive trend has been found for non-catastrophic floods, which is explained by decrease of the perception thresholds, the increase of population density in the most flood-prone areas and changes in land use.

The evolution of post-zygotic isolation barriers by immune-triggered hybrid incompatibilities in Arabidopsis thaliana

A long-standing question in evolutionary biology is what defines a species. The biological species concept considers a species as a population of individuals that interbreeds freely and produces viable offspring. Therefore, reproductive isolation is the essence of species. Hybrid necrosis is one form of post-zygotic reproductive isolation. In this chapter, we summarize what is known to date about this phenomenon and highlight progress made in the understanding of these immune-triggered hybrid incompatibilities through our research in the plant model Arabidopsis thaliana.