Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

K.L. was funded by a junior research fellowship from the National Environmental Research Council, UK (NE/I020288/1, NBAF659).Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here, we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced postdivergence gene flow that ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of species divergence which is compatible with theoretical models that posit a role of inversions in speciation with gene flow.Publisher PDFPeer reviewe

An Introduction to Data Analysis in Asteroseismology

A practical guide is presented to some of the main data analysis concepts and techniques employed contemporarily in the asteroseismic study of stars exhibiting solar-like oscillations. The subjects of digital signal processing and spectral analysis are introduced first. These concern the acquisition of continuous physical signals to be subsequently digitally analyzed. A number of specific concepts and techniques relevant to asteroseismology are then presented as we follow the typical workflow of the data analysis process, namely, the extraction of global asteroseismic parameters and individual mode parameters (also known as peak-bagging) from the oscillation spectrum.Comment: Lecture presented at the IVth Azores International Advanced School in Space Sciences on "Asteroseismology and Exoplanets: Listening to the Stars and Searching for New Worlds" (arXiv:1709.00645), which took place in Horta, Azores Islands, Portugal in July 201

Conductance quantization and the 0.7x2e2/h conductance anomaly in one-dimensional hole systems

We have studied ballistic transport in a 1D channel formed using surface gate techniques on a back-gated, high-mobility, bilayer 2D hole system. At millikelvin temperatures, robust conductance quantization is observed in the quantum wire formed in the top layer of the bilayer system, without the gate instabilities that have hampered previous studies of 1D hole systems. Using source drain bias spectroscopy, we have measured the 1D subband spacings, which are 5-10 times smaller than in comparable GaAs electron systems, but 2-3 times larger than in previous studies of 1D holes. We also report the first observation of the anomalous conductance plateau at G = 0.7 x 2e2/h in a 1D hole system.Comment: 10 pages, 3 figure

Considerations in relation to off-site emergency procedures and response for nuclear accidents

The operation of nuclear facilities has, fortunately, not led to many accidents with off-site consequences. However, it is well-recognised that should a large release of radioactivity occur, the effects in the surrounding area and population will be significant. These effects can be mitigated by developing emergency preparedness and response plans prior to the operation of the nuclear facility that can be exercised regularly and implemented if an accident occurs. This review paper details the various stages of a nuclear accident and the corresponding aspects of an emergency preparedness plan that are relevant to these stages, both from a UK and international perspective. The paper also details how certain aspects of emergency preparedness have been affected by the accident at Fukushima Dai-ichi and as a point of comparison how emergency management plans were implemented following the accidents at Three Mile Island 2 and Chernobyl. In addition, the UK’s economic costing model for nuclear accidents COCO-2, and the UK’s Level-3 Probabilistic Safety Assessment code “PACE” are introduced. Finally, the factors that affect the economic impact of a nuclear accident, especially from a UK standpoint, are described

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space, where N is the number of organisms, $h$ is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database

A developmental analysis of communication between mothers and infants with Down's syndrome

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68850/2/10.1177_027112148300300110.pd

Extended Computation Tree Logic

We introduce a generic extension of the popular branching-time logic CTL which refines the temporal until and release operators with formal languages. For instance, a language may determine the moments along a path that an until property may be fulfilled. We consider several classes of languages leading to logics with different expressive power and complexity, whose importance is motivated by their use in model checking, synthesis, abstract interpretation, etc. We show that even with context-free languages on the until operator the logic still allows for polynomial time model-checking despite the significant increase in expressive power. This makes the logic a promising candidate for applications in verification. In addition, we analyse the complexity of satisfiability and compare the expressive power of these logics to CTL* and extensions of PDL

Application of phage display to high throughput antibody generation and characterization.

We have created a high quality phage display library containing over 1010 human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are