Porcupine Bank Nephrops Grounds (FU16) 2023 UWTV Survey Report and catch scenarios for 2024

This report provides the results of the eleventh underwater television on the ‘Porcupine Bank Nephrops grounds’ ICES assessment area; Functional Unit 16. The survey was multi disciplinary in nature collecting UWTV and other ecosystem data. In total 71 UWTV stations were successfully completed (100% of the planned stations) in a randomised 6 nautical mile isometric grid covering the full spatial extent of the stock. The mean burrow density observed in 2023, adjusted for edge effect, was 0.27 burrows/m². The final krigged abundance estimate was 2002 million burrows with a CV of 3% and an estimated stock area of 7,130 km2 . The 2023 abundance estimate was 47% higher than in 2022. Using the 2023 estimate of abundance and updated stock data imply that catches in 2024 should be between 3677 and 4560 tonnes, according to the EU MAP and ICES MSY approach (assuming that all catch is landed). Four species of sea-pen (Virgularia mirabilis, Funiculina quadrangularis, Pennatula phosphorea and the deepwater sea-pen Kophobelemnon stelliferum) were observed during the survey. Trawl marks were also observed on 20% of the stations surveyed.Marine Institut

Aran, Galway Bay and Slyne Head Nephrops Grounds (FU17) 2023 UWTV Survey Report and catch scenarios for 2024

This report provides the main results and findings of the 21st annual underwater television survey on the Aran, Galway Bay and Slyne head Nephrops grounds, ICES assessment area; Functional Unit 17. The survey was multi-disciplinary in nature collecting UWTV, CTD and other ecosystem data. In 2023 a total of 44 UWTV stations were successfully completed, 34 on the Aran Grounds, 5 on Galway Bay and 5 on Slyne Head patches. The mean burrow density observed in 2023, adjusted for edge effect, was medium at 0.29 burrows/m². The final krigged burrow abundance estimate for the Aran Grounds was 356 million burrows with a CV (Coefficient of Variance; relative standard error) of 3%. The final abundance estimate for Galway Bay was 15 million and for Slyne Head was 5 million, with CVs of 7% and 4% respectively. The total abundance estimates have fluctuated considerably over the time series. The 2023 combined abundance estimate (375 million burrows) is 13% higher than in 2021, and it is below MSY Btrigger (540 million burrows). Using the 2023 estimate of abundance and updated stock data imply that catches in 2024 should be no more than 454 tonnes, according to the EU MAP and ICES MSY approach and assuming that discard rates and fishery selection patterns do not change from the average of 2020–2022. Virgularia mirabilis was the only sea-pen species observed on the UWTV footage. Trawl marks were present at 5% of the Aran stations surveyed.Marine Institut

FU19 Nephrops Grounds 2023 UWTV Survey Report and catch scenarios for 2024

This report provides the main results of the fourteenth underwater television survey of the various Nephrops patches in Functional Unit 19. The survey was multi disciplinary in nature collecting UWTV and other ecosystem data. In 2023 a total 42 UWTV stations were successfully completed. The mean density estimates varied considerably across the different patches. The 2023 raised abundance estimate showed a 15% decrease from the 2022 estimate and at 220 million burrows is below the MSY Btrigger reference point (430 million). Using the 2023 estimate of abundance and updated stock data implies catch in 2024 that correspond to the F ranges in the EU multi annual plan for Western Waters are between 224 and 248 tonnes (assuming that discard rates and fishery selection patterns do not change from the average of 2020–2022). One species of sea pen was observed; Virgularia mirabilis which has been observed on previous surveys of FU19. Trawl marks were observed at 10% of the stations surveyed.Marine Institut

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common molecular genetic pathway with classic lobular carcinomas

Pleomorphic lobular carcinomas (PLC) of the breast display histological features associated with classic invasive lobular carcinoma (ILC), yet they also exhibit more conspicuous nuclear atypia and pleomorphism, and an aggressive clinical behaviour. From a breast cancer progression perspective, it is unclear whether PLC is a variant of ILC or is a high-grade invasive ductal carcinoma (IDC) that has lost E-cadherin. The molecular features of 26 PLC were studied using immunohistochemistry [oestrogen receptor (ER), progesterone receptor (PR), HER2, p53 and E-cadherin], 0.9 Mb resolution, microarraybased comparative genomic hybridization (aCGH), fluorescent (FISH) and chromogenic (CISH)in situ hybridization and loss of heterozygosity. Comparative analysis was performed with aCGH data from PLC with classic ILC (16 cases) and high grade IDC (35 cases). PLCs were frequently ER- and PR-positive, E-cadherin-negative and occasionally HER2- and p53-positive. Recurrent copy number changes identified by aCGH included gains on 1q, 8q, 11q, 12q, 16p and 17q and losses on 8p, 11q, 13q, 16q and Xq. Highly recurrent 1q+ (100% of cases), 16p+ (93%), 11q− (53%) and 16q− (93%) and evidence of the der(1;16)/der(16)t(1;16) rearrangement, as detected by FISH, suggested that PLC had a ‘lobular genotype’. Focal amplifications were evident at 8p12-p11, 8q24, 11q13.1-q14.1, 12q14, 17q12 and 20q13. Loss of BRCA2 was detected in 40% of PLC by LOH. Comparative analysis of aCGH data suggested the molecular features of PLC (ER/PR-positive, Ecadherin-negative, 1q+, 11q−, 16p+ and 16q−) were more closely related to those of ILC than IDC, implicating an overlapping developmental pathway for these lobular tumour types. Molecular alterations found in PLC that are more typical of high-grade IDC than ILC (p53 and HER2 positivity, 8q+, 17q24-q25+, 13q− and amplification of 8q24, 12q14, 17q12 and 20q13) are likely to drive the high-grade and more aggressive biology of PLC. Copyright 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd