Mortality and injuries of haddock (Melanogrammus aeglefinus) that are caught by pelagic longline

By-catches of haddock (Melanogrammus aeglefinus) below legal size (44 cm total length) in the seasonal pelagic longline fisheries for haddock off the coast of Finnmark, northern Norway, are often high. The small fish are torn off the hook at the vessel side by means of a crucifier or a gaff and returned to the sea. It is generally thought that most of the discarded haddock die. An investigation to quantify this mortality was done in the season for this fishery in 1997. The undersized haddock that were torn off the longline hook were recaptured by gently catching them in a dip net as they reached the sea surface. Survival of haddock torn off by means of crucifier alone was compared to haddock torn of the hook by means of a gaff. The fish were transferred in tanks onboard a vessel to holding pens made of small meshed knotless netting floating at the surface. They were visually monitored for 7-11 days. The control group consisted of haddock fished with clean hooks without barbs and gently released by hand. At the end of the observation period the live and dead fish were examined for external damage. The experiment showed a total mortality of 39% for fish that had been torn off by means of a crucifier, and 53% mortality of fish released by means of a gaff. The mortality of the control group was 9%. The injuries of the fish were also analysed

Mortality and injuries of haddock (Melanogrammus aeglefinus) that are caught by pelagic longline

By-catches of haddock (Melanogrammus aeglefinus) below legal size (44 cm total length) in the seasonal pelagic longline fisheries for haddock off the coast of Finnmark, northern Norway, are often high. The small fish are torn off the hook at the vessel side by means of a crucifier or a gaff and returned to the sea. It is generally thought that most of the discarded haddock die. An investigation to quantify this mortality was done in the season for this fishery in 1997. The undersized haddock that were torn off the longline hook were recaptured by gently catching them in a dip net as they reached the sea surface. Survival of haddock torn off by means of crucifier alone was compared to haddock torn of the hook by means of a gaff. The fish were transferred in tanks onboard a vessel to holding pens made of small meshed knotless netting floating at the surface. They were visually monitored for 7-11 days. The control group consisted of haddock fished with clean hooks without barbs and gently released by hand. At the end of the observation period the live and dead fish were examined for external damage. The experiment showed a total mortality of 39% for fish that had been torn off by means of a crucifier, and 53% mortality of fish released by means of a gaff. The mortality of the control group was 9%. The injuries of the fish were also analysed

Mortality and injuries of haddock, cod and saithe escaping through codend meshes and sorting grids

Mortalities and injuries of the gadoids haddock (Melanogrammus aeglefinus L.), cod (Gadus morhua L.) and saithe (Pollachius virens L.) were studied after codend and grid escapement in two full scale trials in 2000 and 2001 in the Barents Sea. The escaped fish were sampled using small meshed cages. Trawl caught controls were sampled by removing the cod end and attaching the cage directly to the cod end extension. In the 2001 trial, control fish were sampled in fish traps in addition. Acoustic closing and releasing devices were used to time the sampling. Survival rates of cod and saithe escaping through codend and sorting grid were 100%. Mortality of haddock were 26.2 to 50.4% (codend escapees), 1.6 to 20% (grid escapees), 4.1 to 26.5% (trawl caught controls) and 0% (trap caught controls). The haddock mortality and injuries decreased with increasing fish length in all groups, with a mortality peek of the mesh escapees with girth approximately the mesh size circumference. Cod and saithe had significantly less skin and fin injuries than haddock, and in general, frequency of skin injuries increased towards the tail. Grid escaped gadoids had significantly less skin and fin damages than the mesh and control groups

Mortality of North Sea herring that is crowded and subsequently slipped from a purse seine

Catch regulation by slipping whole or parts of the catch has traditionally been used in NE-Atlantic purse seine fisheries for pelagic species if the catches are considered too big or the quality or size of the fish is considered unsatisfactory. This is particularly the case when the prize differs between sizes or quality groups of fish (high grading) as is often found with herring. No information is, however, available on the survival rate of herring that is slipped from the purse seine or how significant this mortality is in relation to total fishing mortality. The aim of this study is to quantify mortality of herring crowded to different degrees in the purse seine and subsequently slipped. Large-scale open-sea survival experiments were carried out in the North Sea in 2008 and in 2009. Herring caught by purse seine were allowed to swim from the seine to large circular net pens in an early phase of hauling. Commercial crowding conditions were simulated by lifting the bottom of the net pen. The mortality rate four to five days after crowding ranged from 1.8% in the least crowded to 50.7% and 52.0% in the hardest crowded groups. Control group mortality was low, between 0.9% and 2.0%. These results provide important information on what crowding densities can be tolerated in the purse seine fisheries for herring and suggest a need to revise the legislation on slipping in these fisheries. Keywords: unaccounted mortality, slipping, purse seine, herring, crowdin

Relative selectivity in trawls, longline and gillnets on Greenland halibut

Gear selection and sampling gears. Proceedings of the seventh IMR-PINRO Symposium. Murmansk, 23-24 June 1997.Selectivity parameters for Greenland halibut (Reinhardtius hippoglossoides, Walbaum) are compared to catches reported fiom trawl, gillnets and longline in the Norwegian scientific fisheries for Greenland halibut. A trouser trawl selectivity experiment reported here gives an L50 at 43 cm in 135 mm codend. A selectivity analysis of the gillnets using loglinear models is done, and show maximum retention probability for lengths at 40.6 - 63.8 cm for the five mesh-sizes used. The effect of the fishiig strategy is analysed in respect to the selectivity of the gear used and the diskibution of length and age in the catches. To avoid possible bias from strong dominating yearclasses and selection in these comparisons, length-at-age data are used. The sex-ratio in gillnet catches is shown to be a linear fiinction of meshsize. Our data show no trend in length distribution with depth. We show that calculated growth of female Greenland halibut is affected by the selectivity of the gears. It is shown that growth parameters calculated fiom gillnet catches may be biased due to the selection properties in the gillnets. These analyses will provide a better understanding of possible sarnpling bias when sampling a stock with only one gear

A Ten-microRNA Expression Signature Predicts Survival in Glioblastoma

Glioblastoma (GBM) is the most common and aggressive primary brain tumor with very poor patient median survival. To identify a microRNA (miRNA) expression signature that can predict GBM patient survival, we analyzed the miRNA expression data of GBM patients (n = 222) derived from The Cancer Genome Atlas (TCGA) dataset. We divided the patients randomly into training and testing sets with equal number in each group. We identified 10 significant miRNAs using Cox regression analysis on the training set and formulated a risk score based on the expression signature of these miRNAs that segregated the patients into high and low risk groups with significantly different survival times (hazard ratio [HR] = 2.4; 95% CI = 1.4–3.8; p<0.0001). Of these 10 miRNAs, 7 were found to be risky miRNAs and 3 were found to be protective. This signature was independently validated in the testing set (HR = 1.7; 95% CI = 1.1–2.8; p = 0.002). GBM patients with high risk scores had overall poor survival compared to the patients with low risk scores. Overall survival among the entire patient set was 35.0% at 2 years, 21.5% at 3 years, 18.5% at 4 years and 11.8% at 5 years in the low risk group, versus 11.0%, 5.5%, 0.0 and 0.0% respectively in the high risk group (HR = 2.0; 95% CI = 1.4–2.8; p<0.0001). Cox multivariate analysis with patient age as a covariate on the entire patient set identified risk score based on the 10 miRNA expression signature to be an independent predictor of patient survival (HR = 1.120; 95% CI = 1.04–1.20; p = 0.003). Thus we have identified a miRNA expression signature that can predict GBM patient survival. These findings may have implications in the understanding of gliomagenesis, development of targeted therapy and selection of high risk cancer patients for adjuvant therapy

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Mortality of mackerel (Scomber scombrus L.) after pursing and slipping from a purse seine

A new method was used to study the effect of crowding and subsequent slipping from a purse seine on the mortality of Atlantic mackerel (Scomber scombrus L.). Mackerel were allowed to swim from a purse seine through a transfer channel into two identical large floating net-pens. One pen was used as a control and was left floating in the sea without further treatment. The other was used to simulate crowding and slipping. The volume of the pen was gradually decreased by hoisting the bottom of the pen using a crane until the fish started to show panic reactions, and this volume was maintained for 15 min (2006) or 10 min (2007). The volume was then allowed to return to normal and the net-pens were left to drift freely in the open sea for 3–6 days. Five repeat experiments were performed, all of which showed that crowding has a major effect on survival rates. In all five experiments, mortality was higher among the crowded fish (80–100% mortality) than the controls (0.1–46% mortality), and the difference was significant (p = 0.01). The experiments demonstrate that excessive crowding before slipping mackerel from purse seines should be avoided, if possible, in order to avoid massive fish kills