Unravelling the genetic basis for the rapid diversification of male genitalia between Drosophila species

In the last 240,000 years, males of the Drosophila simulans species clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These appendages are used for grasping the female during mating and so their divergence is most likely driven by sexual selection. Mapping studies indicate a highly polygenic and generally additive genetic basis for these morphological differences. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid phenotypic diversification. Here, we used new D. simulans/D. mauritiana introgression lines on chromosome 3L to generate higher resolution maps of posterior lobe and clasper differences between these species. We then carried out RNA-seq on the developing genitalia of both species to identify the expressed genes and those that are differentially expressed between the two species. This allowed us to test the function of expressed positional candidates during genital development in D. melanogaster. We identified several new genes involved in the development and possibly the evolution of these genital structures, including the transcription factors Hairy and Grunge. Furthermore, we discovered that during clasper development Hairy negatively regulates tartan (trn), a gene known to contribute to divergence in clasper morphology. Taken together, our results provide new insights into the regulation of genital development and how this has evolved between species

Intrinsic dielectric response in ferroelectric nano-capacitors

Measurements on 'free-standing' single-crystal barium titanate capacitors with thickness down to 75 nm show a dielectric response typical of large single crystals, rather than conventional thin films. There is a notable absence of any broadening or temperature shift of the dielectric peak or loss tangent. Peak dielectric constants of similar to25 000 are observed, and Curie-Weiss analysis demonstrates first order transformation behaviour. This is in dramatic contrast to results on conventionally deposited thin film capacitor heterostructures, which show large dielectric peak broadening and temperature shifts (e.g. Parker et al 2002 Appl. Phys. Lett. 81 340), as well as an apparent change in the nature-of the paraelectric-ferroelectric transition from first to second order. Our data are compatible with a recent model by Bratkovsky and Levanyuk (2004 Preprint cond-mat/0402100), which attributes dielectric peak broadening to gradient terms that will exist in any thin film capacitor heterostructure. The observed recovery of first order transformation behaviour is consistent with the absence of significant substrate clamping in our experiment, as modelled by Pertsev et al (1998,Phys. Rev. Lett. 80 1988), and illustrates that the second order behaviour seen in conventionally deposited thin films cannot be attributed to the effects of reduced dimensionality in the system, nor to the influence of an intrinsic universal interfacial capacitance associated with the electrode-ferroelectric interface.</p

Nanoscale ferroelectrics machined from single crystals

This paper summarises some of the most recent work that has been done on nanoscale ferroelectrics as a result of a joint collaborative research effort involving groups in Queen's University Belfast, the University of Cambridge and the University of St. Andrews. Attempts have been made to observe fundamental effects of reduced size, and increasing morphological complexity, on ferroelectric behaviour by studying the functional response and domain characteristics in nanoscale single crystal material, whose size and morphology have been defined by Focused Ion Beam (FIB) patterning. This approach to nanoshape fabrication has allowed the following broad statements to be made:\ud \ud (i) in single crystal BaTiO3 sheets, permittivity and phase transition behaviour is not altered from that of bulk material down to a thickness of ∼ 75 nm;\ud \ud (ii) in single crystal BaTiO3 sheets and nanowires changes in observed domain morphologies are consistent with large scale continuum modelin

Exploring the fundamental effects of miniaturisation on ferroelectrics by focused ion beam processing of single crystal material

The focused ion beam microscope has been used to make thin lamellae and nanoscale washers from single crystals of BaTiO3. The thin lamellae were used as the dielectric layers in ‘thin film’ capacitor heterostructures, and investigated for their functional behaviour. This gave insight into the dielectric properties of thin film ferroelectrics without the usual influences of substrate clamping, grain boundaries, through film microstructural and defect chemistry variation, and inherent asymmetry associated with the electrode-dielectric boundary conditions. In essence the investigation allowed the inherent dielectric response of thin film ferroelectrics to be examined. It was found that, unlike any conventionally grown thin film capacitor heterostructures made to date, the single crystal lamellae demonstrated bulk-like functional behaviour down to a thickness of∼75nm. The fabrication of nanoscalewashers, or doughnuts, has allowed an investigation into the kinds of domain configurations that occur in highly constrained and surface-dominated 3 Dimensional architectures using Scanning Transmission Electron Microscopy. Initial work shows the existence of ‘herringbone’ domain structures which look to be shape or field compensating

Investigating the effects of reduced size on the properties of ferroelectrics

A series of experiments has been undertaken to understand more about the fundamental origin of the thickness-induced permittivity collapse often observed in conventional thin film ferroelectric heterostructures. The various experiments are discussed, highlighting the eventual need to examine permittivity collapse in thin film single crystal material. It has been seen that dielectric collapse is not a direct consequence of reduced size, and neither is it a consequence of unavoidable physics associated with the ferroelectric-electrode boundary. Research on three-dimensional shape-constrained ferroelectrics, emphasizing self-assembled structures based on nanoporous alumina templates and on FIB-milled single crystals, is also presented, and appears to represent an exciting area for ongoing researc

Iterative Solvers for Discretized Stationary Euler Equations

Abstract In this paper we treat subjects which are relevant in the context of iterative methods in implicit time integration for compressible flow simulations. We present a novel renumbering technique, some strategies for choosing the time step in the implicit time integration, and a novel implementation of a matrix-free evaluation for matrix-vector products. For the linearized compressible Euler equations, we present various comparative studies within the QUADFLOW package concerning preconditioning techniques, ordering methods, time stepping strategies, and different implementations of the matrix-vector product. The main goal is to improve efficiency and robustness of the iterative method used in the flow solver.

Tensor image registration library: Deformable registration of stand‐alone histology images to whole‐brain post‐mortem MRI data

Background: Accurate registration between microscopy and MRI data is necessary for validating imaging biomarkers against neuropathology, and to disentangle complex signal dependencies in microstructural MRI. Existing registration methods often rely on serial histological sampling or significant manual input, providing limited scope to work with a large number of stand-alone histology sections. Here we present a customisable pipeline to assist the registration of stand-alone histology sections to whole-brain MRI data. Methods: Our pipeline registers stained histology sections to whole-brain post-mortem MRI in 4 stages, with the help of two photographic intermediaries: a block face image (to undistort histology sections) and coronal brain slab photographs (to insert them into MRI space). Each registration stage is implemented as a configurable stand-alone Python script using our novel platform, Tensor Image Registration Library (TIRL), which provides flexibility for wider adaptation. We report our experience of registering 87 PLP-stained histology sections from 14 subjects and perform various experiments to assess the accuracy and robustness of each stage of the pipeline. Results: All 87 histology sections were successfully registered to MRI. Histology-to-block registration (Stage 1) achieved 0.2–0.4 mm accuracy, better than commonly used existing methods. Block-to-slice matching (Stage 2) showed great robustness in automatically identifying and inserting small tissue blocks into whole brain slices with 0.2 mm accuracy. Simulations demonstrated sub-voxel level accuracy (0.13 mm) of the slice-to-volume registration (Stage 3) algorithm, which was observed in over 200 actual brain slice registrations, compensating 3D slice deformations up to 6.5 mm. Stage 4 combined the previous stages and generated refined pixelwise aligned multi-modal histology-MRI stacks. Conclusions: Our open-source pipeline provides robust automation tools for registering stand-alone histology sections to MRI data with sub-voxel level precision, and the underlying framework makes it readily adaptable to a diverse range of microscopy-MRI studies

The Digital Brain Bank, an open access platform for post-mortem datasets

Post-mortem MRI provides the opportunity to acquire high-resolution datasets to investigate neuroanatomy, and validate the origins of image contrast through microscopy comparisons. We introduce the Digital Brain Bank (open.win.ox.ac.uk/DigitalBrainBank), a data release platform providing open access to curated, multimodal post-mortem neuroimaging datasets. Datasets span three themes-Digital Neuroanatomist: datasets for detailed neuroanatomical investigations; Digital Brain Zoo: datasets for comparative neuroanatomy; Digital Pathologist: datasets for neuropathology investigations. The first Digital Brain Bank release includes twenty one distinctive whole-brain diffusion MRI datasets for structural connectivity investigations, alongside microscopy and complementary MRI modalities. This includes one of the highest-resolution whole-brain human diffusion MRI datasets ever acquired, whole-brain diffusion MRI in fourteen non-human primate species, and one of the largest post-mortem whole-brain cohort imaging studies in neurodegeneration. The Digital Brain Bank is the culmination of our lab’s investment into post-mortem MRI methodology and MRI-microscopy analysis techniques. This manuscript provides a detailed overview of our work with post-mortem imaging to date, including the development of diffusion MRI methods to image large post-mortem samples, including whole, human brains. Taken together, the Digital Brain Bank provides cross-scale, cross-species datasets facilitating the incorporation of post-mortem data into neuroimaging studies