Evolutionary analysis of novel serine proteases in the venom gland transcriptome of Bitis gabonica rhinoceros

Background: Serine proteases are major components of viper venom and target various stages of the blood coagulation system in victims and prey. A better understanding of the diversity of serine proteases and other enzymes present in snake venom will help to understand how the complexity of snake venom has evolved and will aid the development of novel therapeutics for treating snake bites. Methodology and Principal Findings: Four serine protease-encoding genes from the venom gland transcriptome of Bitis gabonica rhinoceros were amplified and sequenced. Mass spectrometry suggests the four enzymes corresponding to these genes are present in the venom of B. g. rhinoceros. Two of the enzymes, rhinocerases 2 and 3 have substitutions to two of the serine protease catalytic triad residues and are thus unlikely to be catalytically active, though they may have evolved other toxic functions. The other two enzymes, rhinocerases 4 and 5, have classical serine protease catalytic triad residues and thus are likely to be catalytically active, however they have glycine rather than the more typical aspartic acid at the base of the primary specificity pocket (position 189). Based on a detailed analysis of these sequences we suggest that alternative splicing together with individual amino acid mutations may have been involved in their evolution. Changes within amino acid segments which were previously proposed to undergo accelerated change in venom serine proteases have also been observed. Conclusions and Significance: Our study provides further insight into the diversity of serine protease isoforms present within snake venom and discusses their possible functions and how they may have evolved. These multiple serine protease isoforms with different substrate specificities may enhance the envenomation effects and help the snake to adapt to new habitats and diets. Our findings have potential for helping the future development of improved therapeutics for snake bites.

Ensemble prediction of transitions of the North Atlantic eddy-driven jet

The consistency of ensemble forecasts from three global medium-range prediction systems with the observed transition behaviour of a three-cluster model of the North Atlantic eddy-driven jet is examined. The three clusters consist of a mid jet cluster taken to represent an undisturbed jet and south and north jet clusters representing southward and northward shifts of the jet. The ensemble forecasts span a period of three extended winters (October–February) from October 2007–February 2010. The mean probabilities of transitions between the clusters calculated from the ensemble forecasts are compared with those calculated from a 23-extended-winter climatology taken from the European Centre for Medium-Range Weather Forecasts 40-Year Re-analysis (ERA40) dataset. No evidence of a drift with increasing lead time of the ensemble forecast transition probabilities towards values inconsistent with the 23-extended-winter climatology is found. The ensemble forecasts of transition probabilities are found to have positive Brier Skill at 15 day lead times. It is found that for the three-extended-winter forecast set, probabilistic forecasts initialized in the north jet cluster are generally less skilful than those initialized in the other clusters. This is consistent with the shorter persistence time-scale of the north jet cluster observed in the ERA40 23-extended-winter climatology. Copyright © 2011 Royal Meteorological Society

Evolutionary genomics of the Fox genes: origin of gene families and the ancestry of gene clusters

Over the past decade genomic approaches have begun to revolutionise the study of animal diversity. In particular, genome sequencing programmes have spread beyond the traditional model species to encompass an increasing diversity of animals from many different phyla, as well as unicellular eukaryotes that are closely related to the animals. Whole genome sequences allow researchers to establish, with reasonable confidence, the full complement of any particular family of genes in a genome. Comparison of gene complements from appropriate genomes can reveal the evolutionary history of gene families, indicating when both gene diversification and gene loss have occurred. More than that, however, assembled genomes allow the genomic environment in which individual genes are found to be analysed and compared between species. This can reveal how gene diversification occurred. Here, we focus on the Fox genes, drawing from multiple animal genomes to develop an evolutionary framework explaining the timing and mechanism of origin of the diversity of animal Fox genes. Ancient linkages between genes are a prominent feature of the Fox genes, depicting a history of gene clusters, some of which may be relevant to understanding Fox gene function.

Identifying barriers and opportunities for transitions towards more sustainable agriculture through system analysis: the case of Vereda La Hoya, Colombia

The paper presents the results of studies which investigated farmers’ reasoning and behaviour with regards to the mis‐use of personal protective equipment and pesticide among smallholders in Colombia. First, the research approach is described. In particular, the structured mental models approach and the integrative agent‐centred framework are presented. These approaches permit to understand the farmers’ reasoning and behaviour in a system perspective. Second, the results are summarized. The methods adopted allowed not only for identifying the factors, but also the social dynamics influencing farmers. Finally, suggestions for interventions are provided, which are not limited to a technical fix, but address the underlying social causes of the problem.

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

Background: Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results: Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion: Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

Photo-induced phase transitions in azobenzene-doped liquid crystals

The effect of irradiation (UV-visible light) on a nematic liquid crystal doped with a photoactive azobenzene derivative was investigated. The selective irradiation results in either an E implies Z or Z implies E isomerization of the azobenzene unit. The effect of the isomerization is to cause a reversible depression of the liquid crystal to isotropic (LC implies l) phase transition temperature of the doped mixture, which can be monitored optically as an isothermal phase transition. This depression also results in a biphasic liquid crystal+isotropic region which is discussed. The authors investigate the cause and magnitude of the phase depression as a function of the amount of doped 4-butyl-4'-methoxyazobenzene (photoactive unit) in 4-cyano-4'-n-pentylbiphenyl (liquid crystal unit), and as a function of the percentage conversion of E implies Z (caused by isomerization) in the azobenzene. The photostationary state of the doped mixtures achieved by Z implies E isomerization is considered and its effect upon the transition temperature of the mixture and response time of the system is discussed. They discuss the implications of the photostationary state with regards to the reversibility of the photo-induced phase transition and hence potential applications.

Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots

Starch is the most widespread and abundant storage carbohydrate in crops and its production is critical to both crop yield and quality. As regards the starch content in the seeds of crop plants, there are distinct difference between grasses (Poaceae) and dicots. However, few studies have described the evolutionary pattern of genes in the starch biosynthetic pathway in these two groups of plants. In this study, therefore, an attempt was made to compare the evolutionary rate, gene duplication and selective pattern of the key genes involved in this pathway between the two groups, using five grasses and five dicots as materials. The results showed (i) distinct differences in patterns of gene duplication and loss between grasses and dicots; duplication in grasses mainly occurred prior to the divergence of grasses, whereas duplication mostly occurred in individual species within the dicots; there is less gene loss in grasses than in dicots; (ii) a considerably higher evolutionary rate in grasses than in dicots in most gene families analyzed; (iii) evidence of a different selective pattern between grasses and dicots; positive selection may have occurred asymmetrically in grasses in some gene families, e.g. AGPase small subunit. Therefore, we deduced that gene duplication contributes to, and a higher evolutionary rate is associated with, the higher starch content in grasses. In addition, two novel aspects of the evolution of the starch biosynthetic pathway were observed.

Evolutionary developmental biology: impact on systematic theory and practice, and the contribution of systematics

Evolutionary developmental genetics brings together systematists, morphologists and developmental geneticists; it will therefore impact on each of these component disciplines. The goals and methods of phylogenetic analysis are reviewed here, and the contribution of evolutionary developmental genetics to morphological systematics, in terms of character conceptualisation and primary homology assessment, is discussed. Evolutionary developmental genetics, like its component disciplines phylogenetic systematics and comparative morphology, is concerned with homology concepts. Phylogenetic concepts of homology and their limitations are considered here, and the need for independent homology statements at different levels of biological organisation is evaluated. The role of systematics in evolutionary developmental genetics is outlined. Phylogenetic systematics and comparative morphology will suggest effective sampling strategies to developmental geneticists. Phylogenetic systematics provides hypotheses of character evolution (including parallel evolution and convergence), stimulating investigations into the evolutionary gains and losses of morphologies. Comparative morphology identifies those structures that are not easily amenable to typological categorisation, and that may be of particular interest in terms of developmental genetics. The concepts of latent homology and genetic recall may also prove useful in the evolutionary interpretation of developmental genetic data.

The music instinct: the evolutionary basis of musicality

Why does music pervade our lives and those of all known human beings living today and in the recent past? Why do we feel compelled to engage in musical activity, or at least simply enjoy listening to music even if we choose not to actively participate? I argue that this is because musicality—communication using variations in pitch, rhythm, dynamics and timbre, by a combination of the voice, body (as in dance), and material culture—was essential to the lives of our pre-linguistic hominin ancestors. As a consequence we have inherited a desire to engage with music, even if this has no adaptive benefit for us today as a species whose communication system is dominated by spoken language. In this article I provide a summary of the arguments to support this view.

Sustainable urban development to 2050: complex transitions in the built environment of cities

The majority of the world’s population now live in cities. This poses great challenges, but also great opportunities in terms of tackling climate change, resource depletion and environmental degradation. Policy agendas have increasingly focused on how to develop and maintain ‘integrated sustainable urban development’, and a number of theoretical conceptualisations of urban transition have been formulated to help our thinking and understanding in both developed and developing countries. Drawing on examples around the world the paper aims to examine the key ‘critical success factors’ that need to be in place for cities to traverse a pathway to a more sustainable future in urban development terms by 2050. The paper explores how important the issues of ‘scale’ is in the context of complexity and fragmentation in the city’s built environment, identifies the lessons that can be learned for future sustainable urban development, and the further research which is needed to address future urban transitions to 2050.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Whole-genome sequencing offers new insights into the evolution of bacterial pathogens and the etiology of bacterial disease. Staph- ylococcus aureus is a major cause of bacteria-associated mortality and invasive disease and is carried asymptomatically by 27% of adults. Eighty percent of bacteremias match the carried strain. How- ever, the role of evolutionary change in the pathogen during the progression from carriage to disease is incompletely understood. Here we use high-throughput genome sequencing to discover the genetic changes that accompany the transition from nasal carriage to fatal bloodstream infection in an individual colonized with meth- icillin-sensitive S. aureus. We found a single, cohesive population exhibiting a repertoire of 30 single-nucleotide polymorphisms and four insertion/deletion variants. Mutations accumulated at a steady rate over a 13-mo period, except for a cluster of mutations preceding the transition to disease. Although bloodstream bacteria differed by just eight mutations from the original nasally carried bacteria, half of those mutations caused truncation of proteins, including a prema- ture stop codon in an AraC-family transcriptional regulator that has been implicated in pathogenicity. Comparison with evolution in two asymptomatic carriers supported the conclusion that clusters of pro- tein-truncating mutations are highly unusual. Our results demon- strate that bacterial diversity in vivo is limited but nonetheless detectable by whole-genome sequencing, enabling the study of evolutionary dynamics within the host. Regulatory or structural changes that occur during carriage may be functionally important for pathogenesis; therefore identifying those changes is a crucial step in understanding the biological causes of invasive bacterial disease.