Gene duplication in an African cichlid adaptive radiation

Background Gene duplication is a source of evolutionary innovation and can contribute to the divergence of lineages; however, the relative importance of this process remains to be determined. The explosive divergence of the African cichlid adaptive radiations provides both a model for studying the general role of gene duplication in the divergence of lineages and also an exciting foray into the identification of genomic features that underlie the dramatic phenotypic and ecological diversification in this particular lineage. We present the first genome-wide study of gene duplication in African cichlid fishes, identifying gene duplicates in three species belonging to the Lake Malawi adaptive radiation (Metriaclima estherae, Protomelas similis, Rhamphochromis “chilingali”) and one closely related species from a non-radiated riverine lineage (Astatotilapia tweddlei). Results Using Astatotilapia burtoni as reference, microarray comparative genomic hybridization analysis of 5689 genes reveals 134 duplicated genes among the four cichlid species tested. Between 51 and 55 genes were identified as duplicated in each of the three species from the Lake Malawi radiation, representing a 38%–49% increase in number of duplicated genes relative to the non-radiated lineage (37 genes). Duplicated genes include several that are involved in immune response, ATP metabolism and detoxification. Conclusions These results contribute to our understanding of the abundance and type of gene duplicates present in cichlid fish lineages. The duplicated genes identified in this study provide candidates for the analysis of functional relevance with regard to phenotype and divergence. Comparative sequence analysis of gene duplicates can address the role of positive selection and adaptive evolution by gene duplication, while further study across the phylogenetic range of cichlid radiations (and more generally in other adaptive radiations) will determine whether the patterns of gene duplication seen in this study consistently accompany rapid radiation

Phase Transition between the Cholesteric and Twist Grain Boundary C Phases

The upper critical temperature Tc2 for the phase transition between the Cholesteric phase (N*) and the Twist Grain Boundary C phase with the layer inclination tilted to the pitch axis (TGBct) in thermotropic liquid crystals is determined by the mean field Chen-Lubensky approach. We show that the N*-TGBct phase transition is split in two with the appearance of either the TGBA or the TGB2q phase in a narrow temperature interval below Tc2. The latter phase is novel in being superposed from two degenerate TGBct phases with different (left and right) layers inclinations to the pitch axis.Comment: Phys. Rev. E, to be publ; 24 pages, RevTeX + 3 ps figure

Quantum Interference of Tunably Indistinguishable Photons from Remote Organic Molecules

We demonstrate two-photon interference using two remote single molecules as bright solid-state sources of indistinguishable photons. By varying the transition frequency and spectral width of one molecule, we tune and explore the effect of photon distinguishability. We discuss future improvements on the brightness of single-photon beams, their integration by large numbers on chips, and the extension of our experimental scheme to coupling and entanglement of distant molecules

Boundary Effects in Chiral Polymer Hexatics

Boundary effects in liquid-crystalline phases can be large due to long-ranged orientational correlations. We show that the chiral hexatic phase can be locked into an apparent three-dimensional N+6 phase via such effects. Simple numerical estimates suggest that the recently discovered "polymer hexatic" may actually be this locked phase.Comment: 4 pages, RevTex, 3 included eps figure

NEW RECORDS FOR \u3ci\u3eACERIA ANTHOCOPTES\u3c/i\u3e (ACARI: ERIOPHYIDAE) OCCURRING ON CANADA THISTLE IN COLORADO, NEBRASKA, AND WYOMING, U.S.A.

Canada thistle [Cirsium arvense (L.) Scop.] growing in eastern Colorado, Wyoming and western Nebraska were surveyed for the presence and distribution of Aceria anthocoptes (Nal.). Of the 34 sites surveyed in 2004, mites were abundant at 42%, present in lesser numbers at 52%, and not present at 6% of the sites. In 2005, two new sites were added and ten sites sampled in 2004 were revisited. Of these 12 sites, mites were abundant at 17%, present to a lesser extent at 58%, and not present at 25% of the sites. The results demonstrate that Canada thistle growing in this region commonly harbor A. anthocoptes. How long A. anthocoptes has been present in this region is unknown, however, anecdotal evidence demonstrating a dramatic decline in the population of Canada thistle at one Colorado site from 2000 to 2007 suggests that the mite may have been present since 2002

Iterated Moire Maps and Braiding of Chiral Polymer Crystals

In the hexagonal columnar phase of chiral polymers a bias towards cholesteric twist competes with braiding along an average direction. When the chirality is strong, screw dislocations proliferate, leading to either a tilt grain boundary phase or a new "moire state" with twisted bond order. Polymer trajectories in the plane perpendicular to their average direction are described by iterated moire maps of remarkable complexity.Comment: 10 pages (plain tex) 3 figures uufiled and appende

Development of strategies for effective communication of food risks and benefits across Europe: Design and conceptual framework of the FoodRisC project

The FoodRisC project is funded under the Seventh Framework Programme (CORDIS FP7) of the European Commission; Grant agreement no.: 245124. Copyright @ 2011 Barnett et al.BACKGROUND: European consumers are faced with a myriad of food related risk and benefit information and it is regularly left up to the consumer to interpret these, often conflicting, pieces of information as a coherent message. This conflict is especially apparent in times of food crises and can have major public health implications. Scientific results and risk assessments cannot always be easily communicated into simple guidelines and advice that non-scientists like the public or the media can easily understand especially when there is conflicting, uncertain or complex information about a particular food or aspects thereof. The need for improved strategies and tools for communication about food risks and benefits is therefore paramount. The FoodRisC project ("Food Risk Communication - Perceptions and communication of food risks/benefits across Europe: development of effective communication strategies") aims to address this issue. The FoodRisC project will examine consumer perceptions and investigate how people acquire and use information in food domains in order to develop targeted strategies for food communication across Europe.METHODS/DESIGN: This project consists of 6 research work packages which, using qualitative and quantitative methodologies, are focused on development of a framework for investigating food risk/benefit issues across Europe, exploration of the role of new and traditional media in food communication and testing of the framework in order to develop evidence based communication strategies and tools. The main outcome of the FoodRisC project will be a toolkit to enable coherent communication of food risk/benefit messages in Europe. The toolkit will integrate theoretical models and new measurement paradigms as well as building on social marketing approaches around consumer segmentation. Use of the toolkit and guides will assist policy makers, food authorities and other end users in developing common approaches to communicating coherent messages to consumers in Europe.DISCUSSION: The FoodRisC project offers a unique approach to the investigation of food risk/benefit communication. The effective spread of food risk/benefit information will assist initiatives aimed at reducing the burden of food-related illness and disease, reducing the economic impact of food crises and ensuring that confidence in safe and nutritious food is fostered and maintained in Europe.This article is available through the Brunel Open Access Publishing Fund

Defects in Chiral Columnar Phases: Tilt Grain Boundaries and Iterated Moire Maps

Biomolecules are often very long with a definite chirality. DNA, xanthan and poly-gamma-benzyl-glutamate (PBLG) can all form columnar crystalline phases. The chirality, however, competes with the tendency for crystalline order. For chiral polymers, there are two sorts of chirality: the first describes the usual cholesteric-like twist of the local director around a pitch axis, while the second favors the rotation of the local bond-orientational order and leads to a braiding of the polymers along an average direction. In the former case chirality can be manifested in a tilt grain boundary phase (TGB) analogous to the Renn-Lubensky phase of smectic-A liquid crystals. In the latter case we are led to a new "moire" state with twisted bond order. In the moire state polymers are simultaneously entangled, crystalline, and aligned, on average, in a common direction. In the moire state polymers are simultaneously entangled, crystalline, and aligned, on average, in a common direction. In this case the polymer trajectories in the plane perpendicular to their average direction are described by iterated moire maps of remarkable complexity, reminiscent of dynamical systems.Comment: plain TeX, (33 pages), 17 figures, some uufiled and included, the remaining available at ftp://ftp.sns.ias.edu/pub/kamien/ or by request to [email protected]

Tunneling Between a Pair of Parallel Hall Droplets

In this paper, we examine interwell tunneling between a pair of fractional quantum Hall liquids in a double quantum well system in a tilted magnetic field. Using a variational Monte Carlo method, we calculate moments of the intra-Landau level tunneling spectrum as a function of in-plane field component $B_{\parallel}$ and interwell spacing $d$. This is done for variety of incompressible states including a pair of $\nu=1/3$ layers ([330]), pair of $\nu=1/5$ layers ([550]), and Halperin's [331] state. The results suggest a technique to extract interwell correlations from the tunneling spectral data.Comment: 21 pages and 8 figures (included), RevTeX, preprint no. UCSDCU

A Phylogenetic Index for Cichlid Microsatellite Primers

Microsatellites abound in most organisms and have proven useful for a range of genetic and genomic studies. Once primers have been created, they can be applied to populations or taxa that have diverged from the source taxon. We use PCR amplification, in a 96-well format, to determine the presence and absence of 46 microsatellite loci in 13 cichlid species. At least one primer set amplified a product in each species tested, and some products were present in nearly all species. These results are compared to the known phylogenetic relationships among cichlids. While we do not address intraspecies variation, our results present a phylogenetic index for the success of microsatellite PCR primer product amplification, thus providing information regarding a collection of primers that are applicable to wide range of species. Through the use of such a uniform primer panel, the potential impact for cross species would be increased