A method for directed evolution and functional cloning of enzymes

A general scheme is described for the in vitro evolution of protein catalysts in a biologically amplifiable system. Substrate is covalently and site specifically attached by a flexible tether to the pIII coat protein of a filamentous phage that also displays the catalyst. Intramolecular conversion of substrate to product provides a basis for selecting active catalysts from a library of mutants, either by release from or attachment to a solid support. This methodology has been developed with the enzyme staphylococcal nuclease as a model. An analysis of factors influencing the selection efficiency is presented, and it is shown that phage displaying staphylococcal nuclease can be enriched 100-fold in a single step from a library-like ensemble of phage displaying noncatalytic proteins. Additionally, this approach should allow one to functionally clone natural enzymes, based on their ability to catalyze specific reactions (e.g., glycosyl transfer, sequence-specific proteolysis or phosphorylation, polymerization, etc.) rather than their sequence- or structural homology to known enzymes.

Frontiers of finance: Evolution and efficient markets

In this review article, we explore several recent advances in the quantitative modeling of financial markets. We begin with the Efficient Markets Hypothesis and describe how this controversial idea has stimulated a number of new directions of research, some focusing on more elaborate mathematical models that are capable of rationalizing the empirical facts, others taking a completely different tack in rejecting rationality altogether. One of the most promising directions is to view financial markets from a biological perspective and, specifically, within an evolutionary framework in which markets, instruments, institutions, and investors interact and evolve dynamically according to the “law” of economic selection. Under this view, financial agents compete and adapt, but they do not necessarily do so in an optimal fashion. Evolutionary and ecological models of financial markets is truly a new frontier whose exploration has just begun.

Regulatory evolution and the origin of the bilaterians

The adult body plan of bilaterians is achieved by imposing regional specifications on pluripotential cells. The establishment of spatial domains is governed in part by regulating expression of transcription factors. The key to understanding bilaterian evolution is contingent on our understanding of how the regulation of these transcription factors influenced bilaterian stem-group evolution.

Evolution and divergence of sodium channel genes in vertebrates

Invertebrate species possess one or two Na+ channel genes, yet there are 10 in mammals. When did this explosive growth come about during vertebrate evolution? All mammalian Na+ channel genes reside on four chromosomes. It has been suggested that this came about by multiple duplications of an ancestral chromosome with a single Na+ channel gene followed by tandem duplications of Na+ channel genes on some of these chromosomes. Because a large-scale expansion of the vertebrate genome likely occurred before the divergence of teleosts and tetrapods, we tested this hypothesis by cloning Na+ channel genes in a teleost fish. Using an approach designed to clone all of the Na+ channel genes in a genome, we found six Na+ channel genes. Phylogenetic comparisons show that each teleost gene is orthologous to a Na+ channel gene or gene cluster on a different mammalian chromosome, supporting the hypothesis that four Na+ channel genes were present in the ancestors of teleosts and tetrapods. Further duplications occurred independently in the teleost and tetrapod lineages, with a greater number of duplications in tetrapods. This pattern has implications for the evolution of function and specialization of Na+ channel genes in vertebrates. Sodium channel genes also are linked to homeobox (Hox) gene clusters in mammals. Using our phylogeny of Na+ channel genes to independently test between two models of Hox gene evolution, we support the hypothesis that Hox gene clusters evolved as (AB) (CD) rather than {D[A(BC)]}.

Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

Many bacteria live only within animal cells and infect hosts through cytoplasmic inheritance. These endosymbiotic lineages show distinctive population structure, with small population size and effectively no recombination. As a result, endosymbionts are expected to accumulate mildly deleterious mutations. If these constitute a substantial proportion of new mutations, endosymbionts will show (i) faster sequence evolution and (ii) a possible shift in base composition reflecting mutational bias. Analyses of 16S rDNA of five independently derived endosymbiont clades show, in every case, faster evolution in endosymbionts than in free-living relatives. For aphid endosymbionts (genus Buchnera), coding genes exhibit accelerated evolution and unusually low ratios of synonymous to nonsynonymous substitutions compared to ratios for the same genes for enterics. This concentration of the rate increase in nonsynonymous substitutions is expected under the hypothesis of increased fixation of deleterious mutations. Polypeptides for all Buchnera genes analyzed have accumulated amino acids with codon families rich in A+T, supporting the hypothesis that substitutions are deleterious in terms of polypeptide function. These observations are best explained as the result of Muller's ratchet within small asexual populations, combined with mutational bias. In light of this explanation, two observations reported earlier for Buchnera, the apparent loss of a repair gene and the overproduction of a chaperonin, may reflect compensatory evolution. An alternative hypothesis, involving selection on genomic base composition, is contradicted by the observation that the speedup is concentrated at nonsynonymous sites.

ndhF sequence evolution and the major clades in the sunflower family.

An extensive sequence comparison of the chloroplast ndhF gene from all major clades of the largest flowering plant family (Asteraceae) shows that this gene provides approximately 3 times more phylogenetic information than rbcL. This is because it is substantially longer and evolves twice as fast. The 5' region (1380 bp) of ndhF is very different from the 3' region (855 bp) and is similar to rbcL in both the rate and the pattern of sequence change. The 3' region is more A+T-rich, has higher levels of nonsynonymous base substitution, and shows greater transversion bias at all codon positions. These differences probably reflect different functional constraints on the 5' and 3' regions of ndhF. The two patterns of base substitutions of ndhF are particularly advantageous for phylogenetic reconstruction because the conserved and variable segments can be used for older and recent groups, respectively. Phylogenetic analyses of 94 ndhF sequences provided much better resolution of relationships than previous molecular and morphological phylogenies of the Asteraceae. The ndhF tree identified five major clades: (i) the Calyceraceae is the sister family of Asteraceae; (ii) the Barnadesioideae is monophyletic and is the sister group to the rest of the family; (iii) the Cichorioideae and its two basal tribes Mutisieae and Cardueae are paraphyletic; (iv) four tribes of Cichorioideae (Lactuceae, Arctoteae, Liabeae, and Vernonieae) form a monophyletic group, and these are the sister clade of the Asteroideae; and (v) the Asteroideae is monophyletic and includes three major clades.

Cultural variation in Africa: role of mechanisms of transmission and adaptation.

Cultural inheritance can be considered as a mechanism of adaptation made possible by communication, which has reached its greatest development in humans and can allow long-term conservation or rapid change of culturally transmissible traits depending on circumstances and needs. Conservativeness/flexibility is largely modulated by mechanisms of sociocultural transmission. An analysis was carried out by testing the fit of three models to 47 cultural traits (classified in six groups) in 277 African societies. Model A (demic diffusion) is conservation over generations, as shown by correlations of cultural traits with language, used as a measure of historical connection. Model B (environmental adaptation) is measured by correlation to the natural environment. Model C (cultural diffusion) is the spread to neighbors by social contact in an epidemic-like fashion and was tested by measuring the tightness of geographic clustering of the traits. Most traits examined, in particular those affecting family structure and kinship, showed great conservation over generations, as shown by the fit of model A. They are most probably transmitted by family members. This is in agreement with the theoretical demonstration that cultural transmission in the family (vertical) is the most conservative one. Some traits show environmental effects, indicating the importance of adaptation to physical environment. Only a few of the 47 traits showed tight geographic clustering indicating that their spread to nearest neighbors follows model C, as is usually the case for transmission among unrelated people (called horizontal transmission).

Hayek and complexity: coordination, evolution and methodology in social adaptive systems

The affinity between the work of the Austrian economist Friedrich A. Hayek and the approach of Complexity Economics is widely recognized by the literature. In spite of this, there still is a lack of studies that seek to analyze in depth the relationship between Hayek and complexity. This dissertation is a contribution to the filling of this large gap in the literature. In the first part of the work, we analyze the various periods in the development of Hayek\'s vision of complexity, showing that this vision is strongly present in his works on knowledge, competition, methodology, evolution, and spontaneous order. In the second part, we explore how Hayek was influenced by two of the main precursors of modern complexity theory - cybernetics and general system theory - from the time he was working on his book on theoretical psychology, The Sensory Order (1952), until the end of his intellectual career.

Slaying the Hydra: Al Qaeda's Evolution and America's Plan of Attack

In response to 9/11, the U.S. launched airstrikes in Afghanistan against al Qaeda to diminish its ability to conduct future attacks. Next, the U.S. turned its attention to Iraq. A series of problems and missteps there subsequently created an opportunity for al Qaeda to evolve, aligning itself with active insurgencies and other terrorist groups around the world. This paper identifies the largely preemptive strategies employed by the U.S. and analyzes how those efforts positively and negatively impacted the War on Terror. While some significant gains were made, the results show that al Qaeda remains a threat to the international community and demands more effective U.S. and international counter-radicalization strategies, including diplomacy and aid, to curb its global appeal.

Stratigraphic update of the Cenozoic Sub-Numidian formations of the Tunisian Tell (North Africa): Tectonic/sedimentary evolution and correlations along the Maghrebian Chain

The Sub-Numidian Tertiary stratigraphic record of the Tunisian Tell has been updated by means of 11 stratigraphic successions belonging to the Maghrebian Flysch Basin (N-African Margin) reconstructed in the Tunisian Numidian Zone and the Triassic Dome Zone. The Sub-Numidian successions studied range from the Paleocene to the Priabonian, representing a major change in the sedimentation from the latest Cretaceous onwards. The Sub-Numidian succession and the Numidian Formation are separated by an Intermediate interval located between two erosive surfaces (local paraconformities). The stratigraphic analysis has revealed diachronous contacts between distal slope to basinal sedimentary formation, allowing the identification of an Early Eocene Chouabine marker bed. The integrated biostratigraphic analysis made by means of planktonic foraminifera and calcareous nannoplankton updates the ages of the formations studied, proving younger than previously thought. The new definition of the Sub-Numidian stratigraphy enables a better correlation with equivalent successions widely outcropping along the Maghrebian, Betic, and southern Apennine Chains. The study proposes a new evolutionary tectonic/sedimentary model for this Tunisian sector of the Maghrebian Chain during the Paleogene after the Triassic–Cretaceous extensional regime. This paleogeographic reorganization is considered a consequence of the beginning of the tectonic inversion (from extensional to compressional), leading to the end of the preorogenic sedimentation. Our results suggest a non-tabular stratigraphy (marked by lateral changes of lithofacies, variable thicknesses, and the presence of diachronous boundaries) providing significant elements for a re-evaluation of active petroleum systems on the quality, volume, distribution, timing of oil generation, and on the migration and accumulation of the oil.

The evolution and masses of the neutron star and donor star in the high mass X-ray binary OAO 1657−415

We report near-infrared radial velocity (RV) measurements of the recently identified donor star in the high mass X-ray binary (HMXB) system OAO 1657−415 obtained in the H band using ISAAC on the Very Large Telescope. Cross-correlation methods were employed to construct a RV curve with a semi-amplitude of 22.1 ± 3.5 km s−1. Combined with other measured parameters of this system it provides a dynamically determined neutron star (NS) mass of 1.42 ± 0.26 M⊙ and a mass of 14.3 ± 0.8 M⊙ for the Ofpe/WN9 highly evolved donor star. OAO 1657−415 is an eclipsing HMXB pulsar with the largest eccentricity and orbital period of any within its class. Of the 10 known eclipsing X-ray binary pulsars OAO 1657−415 becomes the ninth with a dynamically determined NS mass solution and only the second in an eccentric system. Furthermore, the donor star in OAO 1657−415 is much more highly evolved than the majority of the supergiant donors in other HMXBs, joining a small but growing list of HMXBs donors with extensive hydrogen depleted atmospheres. Considering the evolutionary development of OAO 1657−415, we have estimated the binding energy of the envelope of the mass donor and find that there is insufficient energy for the removal of the donor’s envelope via spiral-in, ruling out a common envelope evolutionary scenario. With its non-zero eccentricity and relatively large orbital period the identification of a definitive evolutionary pathway for OAO 1657−415 remains problematic, we conclude by proposing two scenarios which may account for OAO 1657−415 current orbital configuration.

Between continuation and adaptation: The Baltic states’ security policy and armed forces. OSW COMMENTARY 190/23.11.2015

The Baltic states have responded to the annexation of Crimea and the increased Russian military activity in the Nordic and Baltic region by taking measures to strengthen their own military potential. At the same time, they have intensified efforts to have the USA and NATO step up their military presence on their respective territories. Changes concerning the security policies and the armed forces of Lithuania, Latvia and Estonia have included increases in defence spending, the number of soldiers and members of volunteer Territorial Defence Forces, speeding up modernisation programmes, and – in the case of Lithuania – the reintroduction of conscription. In the coming years the Baltic states will focus on developing those of their military capabilities directly related to the defence of the country’s territory. However, Lithuania, Latvia and Estonia will not stop participating in the foreign missions of NATO, which is the guarantor of their security. The extent to which these plans can be implemented will depend primarily on the economic and demographic situations of Lithuania, Latvia and Estonia.

Chemical evolution and estimated flow velocity of water in the Trinity aquifer, south-central Texas /

Shipping list no.: 98-0242-P.

Emergent evolution and the development of societies /

London edition (K. Paul, Trench, Trubner) has title: Emergent evolution and the social.