SNP discovery in European lobster (Homarus gammarus) using RAD sequencing

This is the final version. Available from Springer via the DOI in this recordThe European lobster (Homarus gammarus) is a decapod crustacean with a high market value and therefore their fisheries are of major importance to the economies they support. However, over-exploitation has led to profound stock declines in some regions such as Scandinavia and the Mediterranean. To manage this resource sustainably, knowledge of population structure and connectivity is crucial to inform management about dispersal, recruitment, stock identification and food traceability. We used restriction-site associated DNA sequencing to develop novel SNP markers from 55 individuals encompassing much of the species range; SNPs were quality filtered, ranked using F-statistics and the top 96 SNPs adequate for primer design were retained. SNP markers were developed with the aim of maximising the power to detect genetic differentiation between: (i) Atlantic and Mediterranean lobsters and (ii) Atlantic lobsters. This panel of SNPs provides a useful resource for future studies of population genetic structure and assignment in H. gammarus.Natural EnglandNatural Environment Research Council (NERC

Crossing the pond: genetic assignment detects lobster hybridisation

This is the final version. Available from the publisher via the DOI in this record.American lobsters (Homarus americanus) imported live into Europe as a seafood commodity have occasionally been released or escaped into the wild, within the range of an allopatric congener, the European lobster (H. gammarus). In addition to disease and competition, introduced lobsters threaten native populations through hybridisation, but morphological discriminants used for species identification are unable to discern hybrids, so molecular methods are required. We tested an array of 79 single nucleotide polymorphisms (SNPs) for their utility to distinguish 1,308 H. gammarus from 38 H. americanus and 30 hybrid offspring from an American female captured in Sweden. These loci provide powerful species assignment in Homarus, enabling the robust identification of hybrid and American individuals among a survey of European stock. Moreover, a subset panel of the 12 most powerful SNPs is sufficient to separate the two pure species, even when tissues have been cooked, and can detect the introduced component of hybrids. We conclude that these SNP loci can unambiguously identify hybrid lobsters that may be undetectable via basic morphology, and offer a valuable tool to investigate the prevalence of cryptic hybridisation in the wild. Such investigations are required to properly evaluate the potential for introgression of alien genes into European lobster populations.European Regional Development Fund (ERDF

The age of anxiety? It depends where you look: changes in STAI trait anxiety, 1970–2010

Purpose Population-level surveys suggest that anxiety has been increasing in several nations, including the USA and UK. We sought to verify the apparent anxiety increases by looking for systematic changes in mean anxiety questionnaire scores from research publications. Methods We analyzed all available mean State–Trait Anxiety Inventory scores published between 1970 and 2010. We collected 1703 samples, representing more than 205,000 participants from 57 nations. Results Results showed a significant anxiety increase worldwide, but the pattern was less clear in many individual nations. Our analyses suggest that any increase in anxiety in the USA and Canada may be limited to students, anxiety has decreased in the UK, and has remained stable in Australia. Conclusions Although anxiety may have increased worldwide, it might not be increasing as dramatically as previously thought, except in specific populations, such as North American students. Our results seem to contradict survey results from the USA and UK in particular. We do not claim that our results are more reliable than those of large population surveys. However, we do suggest that mental health surveys and other governmental sources of disorder prevalence data may be partially biased by changing attitudes toward mental health: if respondents are more aware and less ashamed of their anxiety, they are more likely to report it to survey takers. Analyses such as ours provide a useful means of double-checking apparent trends in large population surveys

The masses and density profiles of halos in a LCDM galaxy formation simulation

We investigate the internal structure and density profiles of halos of mass $10^{10}-10^{14}~M_\odot$ in the Evolution and Assembly of Galaxies and their Environment (EAGLE) simulations. These follow the formation of galaxies in a $\Lambda$CDM Universe and include a treatment of the baryon physics thought to be relevant. The EAGLE simulations reproduce the observed present-day galaxy stellar mass function, as well as many other properties of the galaxy population as a function of time. We find significant differences between the masses of halos in the EAGLE simulations and in simulations that follow only the dark matter component. Nevertheless, halos are well described by the Navarro-Frenk-White (NFW) density profile at radii larger than ~5% of the virial radius but, closer to the centre, the presence of stars can produce cuspier profiles. Central enhancements in the total mass profile are most important in halos of mass $10^{12}-10^{13}M_\odot$, where the stellar fraction peaks. Over the radial range where they are well resolved, the resulting galaxy rotation curves are in very good agreement with observational data for galaxies with stellar mass $M_*<5\times10^{10}M_\odot$. We present an empirical fitting function that describes the total mass profiles and show that its parameters are strongly correlated with halo mass

Historical translocations and stocking alter the genetic structure of a Mediterranean lobster fishery

This is the final version. Available on open access from Wiley via the DOI in this recordStocking is often used to supplement wild populations that are overexploited or have collapsed, yet it is unclear how this affects the genetic diversity of marine invertebrate populations. During the 1970s, a lobster stock enhancement program was carried out around the island of Corsica in the Mediterranean using individuals translocated from the Atlantic coast of France. This included the release of thousands of hatchery-reared postlarval lobsters and several adult individuals, but no monitoring plan was established to assess whether these animals survived and recruited to the population. In this study, we sampled European lobster (Homarus gammarus) individuals caught around Corsica and tested whether they showed Atlantic ancestry. Due to a natural marked phylogeographic break between Atlantic and Mediterranean lobsters, we hypothesized that lobsters with dominant (>0.50) Atlantic ancestry were descended from historical stocking releases. Twenty Corsican lobsters were genotyped at 79 single nucleotide polymorphisms, and assignment analysis showed that the majority (13) had dominant Atlantic ancestry. This suggests that the hatchery stocking program carried out in Corsica during the 1970s, using individuals translocated from the Atlantic coast of France, has likely augmented local recruitment but at a cost of altering the genetic structure of the Corsican lobster population.EU Agri‐tech CornwallBiotechnology and Biological Sciences Research Council (BBSRC)Natural Environment Research Council (NERC

Towards a marine biorefinery through the hydrothermal liquefaction of macroalgae native to the United Kingdom

Hydrothermal liquefaction (HTL) is a promising biomass conversion method that can be incorporated into a biorefinery paradigm for simultaneous production of fuels, aqueous fertilisers and potential remediation of municipal or mariculture effluents. HTL of aquatic crops, such as marine macro- or microalgae, has significant potential for the UK owing to its extensive coastline. As such, macroalgae present a particularly promising feedstock for future UK biofuel production. This study aimed to bridge the gaps between previous accounts of macroalgal HTL by carrying out a more comprehensive screen of a number of species from all three major macroalgae classes, and examining the correlations between biomass biochemical composition and HTL reactivity. HTL was used to process thirteen South West UK macroalgae species from all three major classes (Chlorophyceae, Heterokontophyceae and Rhodophyceae) to produce bio-crude oil, a bio-char, gas and aqueous phase products. Chlorophyceae of the genus Ulva generated the highest bio-crude yields (up to 29.9% for U. lactuca). Aqueous phase phosphate concentrations of up to 236 mg L−1 were observed, obtained from the Rhodophyta, S. chordalis. Across the 13 samples, a correlation between increasing biomass lipids and increasing bio-crude yield was observed, as well as an increase in biomass nitrogen generally contributing to bio-crude nitrogen content. A broader range of macroalgae species has been examined than in any study previously and, by processing using identical conditions across all feedstocks, has enabled a more cohesive assessment of the effects of biochemical composition

Bioluminescent human breast cancer cell lines that permit rapid and sensitive in vivo detection of mammary tumors and multiple metastases in immune deficient mice

INTRODUCTION: Our goal was to generate xenograft mouse models of human breast cancer based on luciferase-expressing MDA-MB-231 tumor cells that would provide rapid mammary tumor growth; produce metastasis to clinically relevant tissues such as lymph nodes, lung, and bone; and permit sensitive in vivo detection of both primary and secondary tumor sites by bioluminescent imaging. METHOD: Two clonal cell sublines of human MDA-MB-231 cells that stably expressed firefly luciferase were isolated following transfection of the parental cells with luciferase cDNA. Each subline was passaged once or twice in vivo to enhance primary tumor growth and to increase metastasis. The resulting luciferase-expressing D3H1 and D3H2LN cells were analyzed for long-term bioluminescent stability, primary tumor growth, and distal metastasis to lymph nodes, lungs, bone and soft tissues by bioluminescent imaging. Cells were injected into the mammary fat pad of nude and nude-beige mice or were delivered systemically via intracardiac injection. Metastasis was also evaluated by ex vivo imaging and histologic analysis postmortem. RESULTS: The D3H1 and D3H2LN cell lines exhibited long-term stable luciferase expression for up to 4–6 months of accumulative tumor growth time in vivo. Bioluminescent imaging quantified primary mammary fat pad tumor development and detected early spontaneous lymph node metastasis in vivo. Increased frequency of spontaneous lymph node metastasis was observed with D3H2LN tumors as compared with D3H1 tumors. With postmortem ex vivo imaging, we detected additional lung micrometastasis in mice with D3H2LN mammary tumors. Subsequent histologic evaluation of tissue sections from lymph nodes and lung lobes confirmed spontaneous tumor metastasis at these sites. Following intracardiac injection of the MDA-MB-231-luc tumor cells, early metastasis to skeletal tissues, lymph nodes, brain and various visceral organs was detected. Weekly in vivo imaging data permitted longitudinal analysis of metastasis at multiple sites simultaneously. Ex vivo imaging data from sampled tissues verified both skeletal and multiple soft tissue tumor metastasis. CONCLUSION: This study characterized two new bioluminescent MDA-MB-231-luc human breast carcinoma cell lines with enhanced tumor growth and widespread metastasis in mice. Their application to current xenograft models of breast cancer offers rapid and highly sensitive detection options for preclinical assessment of anticancer therapies in vivo

Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa

Background:The ST313 sequence type ofSalmonellaTyphimurium causes invasive non-typhoidal salmonellosis and wasthought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified.Methods:We analysed the whole genome sequences ofS. Typhimurium isolates from UK patients that weregenerated following the introduction of routine whole-genome sequencing (WGS) ofSalmonella entericabyPublic Health England in 2014.Results:We found that 2.7% (84/3147) ofS. Typhimurium from patients in England and Wales were ST313 and wereassociated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguishedUK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The majority of genome degradationof African ST313 lineage 2 was conserved in the UK-ST313, but the African lineages carried a characteristic prophageand antibiotic resistance gene repertoire. These findings suggest that a strong selection pressure exists for certainhorizontally acquired genetic elements in the African setting. One UK-isolated lineage 2 strain that probably originatedin Kenya carried a chromosomally locatedblaCTX-M-15, demonstrating the continual evolution of this sequence type inAfrica in response to widespread antibiotic usage.Conclusions:The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in thisimportant sequence type. This study highlights thepower of routine WGS by public health agencies to makeepidemiologically significant deductions that would be missed by conventional microbiological methods. Wespeculate that the niche specialisation of sub-Saharan African ST313 lineages is driven in part by the acquisitionof accessory genome elements