An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

Molluscs are the second most species-rich phylum in the animal kingdom, yet only 11 genomes of this group have been published so far. Here, we present the draft genome sequence of the pulmonate freshwater snail Radix auricularia. Six whole genome shotgun libraries with different layouts were sequenced. The resulting assembly comprises 4,823 scaffolds with a cumulative length of 910 Mb and an overall read coverage of 72×. The assembly contains 94.6% of a metazoan core gene collection, indicating an almost complete coverage of the coding fraction. The discrepancy of ∼690 Mb compared with the estimated genome size of R. auricularia (1.6 Gb) results from a high repeat content of 70% mainly comprising DNA transposons. The annotation of 17,338 protein coding genes was supported by the use of publicly available transcriptome data. This draft will serve as starting point for further genomic and population genetic research in this scientifically important phylum

TreeCol: a novel approach to estimating column densities in astrophysical simulations

We present TreeCol, a new and efficient tree-based scheme to calculate column densities in numerical simulations. Knowing the column density in any direction at any location in space is a prerequisite for modelling the propagation of radiation through the computational domain. TreeCol therefore forms the basis for a fast, approximate method for modelling the attenuation of radiation within large numerical simulations. It constructs a HEALPix sphere at any desired location and accumulates the column density by walking the tree and by adding up the contributions from all tree nodes whose line of sight contributes to the pixel under consideration. In particular when combined with widely-used tree-based gravity solvers the new scheme requires little additional computational cost. In a simulation with $N$ resolution elements, the computational cost of TreeCol scales as $N \log N$, instead of the $N^{5/3}$ scaling of most other radiative transfer schemes. TreeCol is naturally adaptable to arbitrary density distributions and is easy to implement and to parallelize. We discuss its accuracy and performance characteristics for the examples of a spherical protostellar core and for the turbulent interstellar medium. We find that the column density estimates provided by TreeCol are on average accurate to better than 10 percent. In another application, we compute the dust temperatures for solar neighborhood conditions and compare with the result of a full-fledged Monte Carlo radiation-transfer calculation. We find that both methods give very similar answers. We conclude that TreeCol provides a fast, easy to use, and sufficiently accurate method of calculating column densities that comes with little additional computational cost when combined with an existing tree-based gravity solver.Comment: 11 pages, 10 figures, submitted to MNRA

Trait compensation in marine gastropods: shell shape, avoidance behavior, and susceptibility to predation

Many organisms have evolved morphological and behavioral traits that reduce their susceptibility to predation. However, few studies have explicitly investigated the relationships between defensive traits and susceptibility. Here we demonstrate a negative correlation between morphological defenses and behavioral avoidance across several species of marine gastropod that is linked to vulnerability to crab predation. Snails that had relatively taller shell spires (high aspect ratio) showed greater responsiveness when exposed to predation cues than did species with disc-like shells (low aspect ratio). Our results suggest that the snail species most vulnerable to predation compensated by showing the highest levels of behavioral avoidance, and hence may be at a disadvantage in competition with less vulnerable species. This has important implications because the behavioral response of herbivorous gastropods to predation cues may play a central role in structuring rocky intertidal communities through trait-mediated indirect effects

A novel application of motion analysis for detecting stress responses in embryos at different stages of development.

Motion analysis is one of the tools available to biologists to extract biologically relevant information from image datasets and has been applied to a diverse range of organisms. The application of motion analysis during early development presents a challenge, as embryos often exhibit complex, subtle and diverse movement patterns. A method of motion analysis able to holistically quantify complex embryonic movements could be a powerful tool for fields such as toxicology and developmental biology to investigate whole organism stress responses. Here we assessed whether motion analysis could be used to distinguish the effects of stressors on three early developmental stages of each of three species: (i) the zebrafish Danio rerio (stages 19 h, 21.5 h and 33 h exposed to 1.5% ethanol and a salinity of 5); (ii) the African clawed toad Xenopus laevis (stages 24, 32 and 34 exposed to a salinity of 20); and iii) the pond snail Radix balthica (stages E3, E4, E6, E9 and E11 exposed to salinities of 5, 10 and 15). Image sequences were analysed using Sparse Optic Flow and the resultant frame-to-frame motion parameters were analysed using Discrete Fourier Transform to quantify the distribution of energy at different frequencies. This spectral frequency dataset was then used to construct a Bray-Curtis similarity matrix and differences in movement patterns between embryos in this matrix were tested for using ANOSIM

Combining motion analysis and microfluidics--a novel approach for detecting whole-animal responses to test substances.

Small, early life stages, such as zebrafish embryos are increasingly used to assess the biological effects of chemical compounds in vivo. However, behavioural screens of such organisms are challenging in terms of both data collection (culture techniques, drug delivery and imaging) and data evaluation (very large data sets), restricting the use of high throughput systems compared to in vitro assays. Here, we combine the use of a microfluidic flow-through culture system, or BioWell plate, with a novel motion analysis technique, (sparse optic flow - SOF) followed by spectral analysis (discrete Fourier transformation - DFT), as a first step towards automating data extraction and analysis for such screenings. Replicate zebrafish embryos housed in a BioWell plate within a custom-built imaging system were subject to a chemical exposure (1.5% ethanol). Embryo movement was videoed before (30 min), during (60 min) and after (60 min) exposure and SOF was then used to extract data on movement (angles of rotation and angular changes to the centre of mass of embryos). DFT was subsequently used to quantify the movement patterns exhibited during these periods and Multidimensional Scaling and ANOSIM were used to test for differences. Motion analysis revealed that zebrafish had significantly altered movements during both the second half of the alcohol exposure period and also the second half of the recovery period compared to their pre-treatment movements. Manual quantification of tail flicking revealed the same differences between exposure-periods as detected using the automated approach. However, the automated approach also incorporates other movements visible in the organism such as blood flow and heart beat, and has greater power to discern environmentally-driven changes in the behaviour and physiology of organisms. We suggest that combining these technologies could provide a highly efficient, high throughput assay, for assessing whole embryo responses to various drugs and chemicals

A phenomics approach reveals interspecific differences in integrated developmental responses to chronic elevated temperatures

ABSTRACT Phenomics, high-dimensional organismal phenotyping, is advanced as a solution to quantifying complex developmental responses to elevated temperatures. ‘Energy proxy traits’ (EPTs) measure the phenotype as a spectrum of energy values across different temporal frequencies from pixel value fluctuations of video. Although they have proven effective in measuring the biology of complex and dynamic developing organisms, their utility in assessing environmental sensitivity of different species is untested. Using EPTs, we assess the relative thermal sensitivities of embryos of three species of freshwater snail with marked differences in their developmental event timings. Embryos of Lymnaea stagnalis, Radix balthica and Physella acuta were videoed hourly for the duration of their embryonic development at two temperatures: 20°C and 25°C. The video was used to calculate EPTs for the duration of their embryonic development, and during discrete physiological windows in development. Changes in energy spectra during development identified marked differences in thermal sensitivities between species, and suggest a relatively heightened sensitivity of gross rates of embryonic physiology and behaviour in embryos of R. balthica, developmental-window-specific thermal responses that reflect ontogenetic differences in observable physiologies, and temperature-induced changes in physiological event timing. EPTs enabled comparison of high-dimensional spectral phenotypes, providing a unique capability for assessing sensitivity continuously in developing individuals. Such integrative and scalable phenotyping is a prerequisite for improved understanding of the sensitivity of early life stages of different species.</jats:p

Comparative phenomics: a new approach to study heterochrony

Understanding the links between development and evolution is one of the major challenges of biology. ‘Heterochronies’, evolutionary alterations in the timings of development are posited as a key mechanism of evolutionary change, but their quantification requires gross simplification of organismal development. Consequently, how changes in event timings influence development more broadly is poorly understood. Here, we measure organismal development as spectra of energy in pixel values of video, creating high-dimensional landscapes integrating development of all visible form and function. This approach we termed ‘Energy proxy traits’ (EPTs) is applied alongside previously identified heterochronies in three freshwater pulmonate molluscs (Lymnaea stagnalis, Radix balthica and Physella acuta). EPTs were calculated from time-lapse video of embryonic development to construct a continuous functional time series. High-dimensional transitions in phenotype aligned with major sequence heterochronies between species. Furthermore, differences in event timings between conspecifics were associated with changes in high-dimensional phenotypic space. We reveal EPTs as a powerful approach to considering the evolutionary importance of alterations to developmental event timings. Reimagining the phenotype as energy spectra enabled continuous quantification of developmental changes in high-dimensional phenotypic space, rather than measurement of timings of discrete events. This approach has the possibility to transform how we study heterochrony and development more generally

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Consumer knowledge of and engagement with traditional takeaway and dark kitchen food outlets

Background Dark kitchens – delivery-only food outlets operating through digital technology platforms – are a contemporary addition to the food environment. Some concerns have been raised the ability for local authorities to identify and regulate these businesses, with growing concern around the nutritional quality of foods, food safety practices and the impact on the local food environment. The present work explores consumer understanding of and engagement with dark kitchen establishments. Methods Healthy adults living in the United Kingdom completed an online survey comprising of questions measuring participant demographics, engagement with takeaways and dark kitchens, purchasing behaviours and decision making, and knowledge and understanding around dark kitchens. Questions were primarily closed-ended and quantitative. Data were analysed using descriptive statistics. Results In total, 2,023 participants (46.3 ± 16.7 years) completed the survey. Forty percent purchased a takeaway at least weekly, often through aggregator applications (e.g., Just Eat, Deliveroo). Food was mainly purchased as a treat (79.3%), for enjoyment of the food or taste (60.8%) and for convenience (58.2%). When ordering, consumers considered the taste (88.1%), quality (83.5%), value for money (77.8%), and familiarity with (68.1%) and reputation of the business (60.0%). Only 24.7% of participants had heard of dark kitchens and 9.1% had knowingly purchased from one. After reading a working definition, 54.9% of consumers said they would purchase from a dark kitchen but most would want to know explicitly that they were ordering from these businesses. A major concern was trust in the food safety and hygiene standards. Conclusion Consumers are unfamiliar with dark kitchens and are not aware of or confident in identifying these businesses. This confusion and concerns around food safety means dark kitchens are often viewed negatively. Consumers would prefer more transparency in where their foods are being prepared to allow for more informed decision-making.</p