Highly syntenic and yet divergent: a tale of two Theilerias

The published genomic sequences of the two major host-transforming Theileria species of cattle represent a rich resource of information that has allowed novel bioinformatic and experimental studies into these important apicomplexan parasites. Since their publication in 2005, the genomes of T. annulata and T. parva have been utilised for a diverse range of applications, ranging from candidate antigen discovery to the identification of genetic markers for population analysis. This has led to advancements in the quest for a sub-unit vaccine, while providing a greater understanding of variation among parasite populations in the field. The unique ability of these Theileria species to induce host cell transformation is the subject of considerable scientific interest and the availability of full genomic sequences has provided new insights into this area of research. This article reviews the data underlying published comparative analyses, focussing on the general features of gene expression, the major Tpr/Tar multi-copy gene family and a re-examination of the predicted macroschizont secretome. Codon usage between the Theileria species is reviewed in detail, as this underpins ongoing comparative studies investigating selection at the intra- and inter-species level. The TashAT/TpshAT family of genes, conserved between T. annulata and T. parva, encodes products targeted to the host nucleus and has been implicated in contributing to the transformed bovine phenotype. Species-specific expansion and diversification at this critical locus is discussed with reference to the availability, in the near future, of genomic datasets which are based on non-transforming Theileria species

Fractal Characterizations of MAX Statistical Distribution in Genetic Association Studies

Two non-integer parameters are defined for MAX statistics, which are maxima of $d$ simpler test statistics. The first parameter, $d_{MAX}$, is the fractional number of tests, representing the equivalent numbers of independent tests in MAX. If the $d$ tests are dependent, $d_{MAX} < d$. The second parameter is the fractional degrees of freedom $k$ of the chi-square distribution $\chi^2_k$ that fits the MAX null distribution. These two parameters, $d_{MAX}$ and $k$, can be independently defined, and $k$ can be non-integer even if $d_{MAX}$ is an integer. We illustrate these two parameters using the example of MAX2 and MAX3 statistics in genetic case-control studies. We speculate that $k$ is related to the amount of ambiguity of the model inferred by the test. In the case-control genetic association, tests with low $k$ (e.g. $k=1$) are able to provide definitive information about the disease model, as versus tests with high $k$ (e.g. $k=2$) that are completely uncertain about the disease model. Similar to Heisenberg's uncertain principle, the ability to infer disease model and the ability to detect significant association may not be simultaneously optimized, and $k$ seems to measure the level of their balance

Determination of Effective Permittivity and Permeability of Metamaterials from Reflection and Transmission Coefficients

We analyze the reflection and transmission coefficients calculated from transfer matrix simulations on finite lenghts of electromagnetic metamaterials, to determine the effective permittivity and permeability. We perform this analysis on structures composed of periodic arrangements of wires, split ring resonators (SRRs) and both wires and SRRs. We find the recovered frequency-dependent permittivity and permeability are entirely consistent with analytic expressions predicted by effective medium arguments. Of particular relevance are that a wire medium exhibits a frequency region in which the real part of permittivity is negative, and SRRs produce a frequency region in which the real part of permeability is negative. In the combination structure, at frequencies where both the recovered real part of permittivity and permeability are simultaneously negative, the real part of the index-of-refraction is found also to be unambigously negative.Comment: *.pdf file, 5 figure

Soliton form factors from lattice simulations

The form factor provides a convenient way to describe properties of topological solitons in the full quantum theory, when semiclassical concepts are not applicable. It is demonstrated that the form factor can be calculated numerically using lattice Monte Carlo simulations. The approach is very general and can be applied to essentially any type of soliton. The technique is illustrated by calculating the kink form factor near the critical point in 1+1-dimensional scalar field theory. As expected from universality arguments, the result agrees with the exactly calculable scaling form factor of the two-dimensional Ising model.Comment: 5 pages, 3 figures; v2: discussion extended, references added, version accepted for publication in PR

Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes.

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z.&nbsp;scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst&nbsp;=&nbsp;0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst&nbsp;=&nbsp;0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci

Future policy implications of tidal energy array interactions

Tidal stream energy technology has progressed to a point where commercial exploitation of this sustainable resource is practical, but tidal physics dictates interactions between tidal farms that raise political, legal and managerial challenges that are yet to be met. Fully optimising the design of a turbine array requires its developer to know about other farms that will be built nearby in the future. Consequently future developments, even those in adjacent channels, have the potential to impact on project efficiency. Here we review the relevant physics, consider the implications for marine policy, and discuss potential solutions. Possible management paths range from minimal regulation to prioritise a free market, to strongly interventionist approaches that prioritise efficient resource use. An attractive exemplar of the latter is unitization, an approach to resource allocation widely used in the oil and gas industry. We argue that an interventionist approach is necessary if the greatest possible energy yield is to be produced for a given level of environmental impact