• Quantitative analysis of azaspiracids in Azadinium spinosum cultures

      Jauffrais, Thierry; Herrenknecht, Christine; Séchet, Véronique; Sibat, Manoella; Tillmann, Urban; Krock, Bernd; Kilcoyne, Jane; Miles, Christopher O.; McCarron, Pearse; Amzil, Zouher; et al. (Springer, 2012)
      Azaspiracids (AZAs) are secondary metabolites of Azadinium spinosum that can accumulate in shellfish and cause food poisoning when consumed. We describe here an analytical procedure for the determination of AZAs in cultures of A. spinosum with a focus on the formation of AZA methyl esters as artefacts during extraction and sample pre-treatment. A. spinosum cells were collected from bioreactor cultures using centrifugation or filtration. Different extraction procedures were evaluated for formation of methyl ester artefacts, yield, and matrix effects. Filtration of cultures using glass-fibre filters led to increased formation of methyl esters, and centrifugation is recommended for recovery of cells. The extraction solvent (methanol (MeOH), acetone, and acetonitrile (MeCN)) did not significantly affect the yield of AZAs as long as the organic content was 80% or higher. However, the use of MeOH as extraction solvent led to increased formation of methyl esters. AZA1 recovery over two successive extractions was 100% at the 95% confidence level for acetone and MeOH. In standard-addition experiments, no significant matrix effects were observed in extracts of A. spinosum or Azadinium obesum up to a sample size of 4.5 × 109 μm3. Moreover, experiments carried out to clarify the formation and structure of methylated AZA analogues led to the description of two AZA methyl esters and to the correction of the chemical structures of AZAs29–32.
    • QUB Report: Review of Marine Spatial Planning Best Practice of Relevance to Ireland

      Flannery, Wesley (Marine Institute, 2014-11)
      This aim of this project is to contribute to the development of an appropriate Marine Spatial Planning (MSP) Framework for Ireland by reporting on MSP relevant to Ireland. This report details case study selection, evaluation and presentation of case study findings. The report also focuses on outlining how the lessons learned could be transferred to the Irish context.
    • Racial analyses of Dunmore East Herring stocks by means of the Otoliths

      Foster, M. (Fisheries Division, Department of Lands., 1963)
      Einarsson (1951) has shown that it is possible to separate in a mixed fishery the winter/spring spawned fish from summer/autumn spawned fish on the basis of the appearance of the nuclei of the otoliths. In general, the winter/spring spawned fish have small hyaline and opaque nuclei, whereas the summer/autumn spawned fish have large hyaline nuclei. Otoliths from herrings taken at Dunmore East in the period 1960 to 1964 were examined and classified using Einarsson's method.
    • Rainbow Trout Fry Syndrome

      Marine Institute (Marine Institute, 2011)
      This leaflet gives information on Rainbow Trout Fry Syndrome (RTFS). This disease is caused by a gram-negative, rod-like, filamentous bacterium, Flavobacterium psychrophilum. The disease is also known as bacterial cold water disease.
    • Rapid and highly variable warming of lake surface waters around the globe

      O'Reilly, C.M.; Sharma, S.; Gray, D.K.; Hampton, S.E.; Read, J.S.; Rowley, R.J.; Schneider, P.; Lenters, J.D.; McIntyre, P.B.; Kraemer, B.J.; et al. (American Geophysical Union, 2015)
      In this first worldwide synthesis of in situ and satellite-derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade 1) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors —from seasonally ice-covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade 1) to ice-free lakes experiencing increases in air temperature and solar radiation (0.53°C decade 1). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes.
    • The real map of Ireland, Ireland's marine territory: word association and pictures

      Marine Institute (Marine Institute, 2013)
      Ireland has a marine territory of up to 220 million acres (880,000km²) which is ten times the size of Irelands land area. The aim is to develop student’s perception that the map of “Ireland” also includes Ireland’s marine territory, thus introducing “The Real Map of Ireland”. Students will learn to identify key names and areas of Ireland’s marine territory that is under the sea through word and picture association.
    • Real-time PCR detection of Dinophysis species in Irish coastal waters

      Kavanagh, S.; Brennan, C.; O’Connor, L.; Moran, S.; Salas, R.; Lyons, J.; Silke, J.; Maher, M. (Springer Verlag, 2010)
      Diarrhetic shellfish toxin-producing Dinophysis species occur in Irish coastal waters throughout the year. Dinophysis acuta and Dinophysis acuminata are the most commonly occurring species and are responsible for the majority of closures of Irish mussel farms. This study describes the development of a qualitative real-time polymerase chain reaction (PCR) assay for identification of D. acuta and D. acuminata in Irish coastal waters. DNA sequence information for the D1-D2 region of the large ribosomal sub-unit (LSU) was obtained, following single-cell PCR of D. acuta and D. acuminata cells isolated from Irish coastal locations. PCR primers and hybridization probes, specific for the detection of D. acuta, were designed for real-time PCR on the LightCycler™. The LightCycler™ software melt curve analysis programme determined that D. acuta was identified by a melt-peak at 61°C, while D. acuminata cells produced a melt peak at 48°C. The limit of detection of the real-time PCR assay was determined to be one to ten plasmid copies of the LSU D1-D2 target region for both species and one to five D. acuminata cells. Lugol's preserved water samples were also tested with the assay. The real-time PCR assay identified Dinophysis species in 100% of samples found to contain Dinophysis species by light microscopy and had a greater than 90% correlation with light microscopy for identification of D. acuta and D. acuminata in the samples. The assay can identify and discriminate D. acuta and D. acuminata at low numbers in Irish waters and has the potential to add value to the Irish phytoplankton monitoring programme.
    • Recaptures of Adult Salmon tagged as smolts at Carrigadroghid

      Browne, J; Doyle, J (Department of Fisheries and Forestry (Trade and Information Section), 1979)
      A total of 2936 salmon were tagged at Carrigadroghid Co Cork in January 1973. From this tagging there were 34 recaptures, a return rate of 1.16%. In 1975 the number of salmon smolts tagged was 4860 and 18 were recovered, representing a return rate of 0.37%. Details of the recaptures resulting from these two tagging operations are given.
    • Recaptures of Irish Tagged Salmon off Greenland

      Browne, J (Department of Agriculture and Fisheries (Fisheries Division), 1977)
      Since tagging of smolts began in Ireland there have been sixteen distant water recaptures of adult salmon tagged as smolts or parr in Irish waters. Fifteen of these were recaptured from the Greenland fishery and one salmon was recovered from the Faroe Islands. The recaptures resulted from a number of salmon smolt and salmon parr tagging programmes. Some of these programmes were designed specifically to obtain information on the distant migrations of Irish salmon but other programmes were to study migrations and mortality in the home waters. Information on recaptures has been published elsewhere (Piggins 1970, Went 1973). This leaflet brings together all the available information on recaptures of tagged Irish salmon in distant waters up to December 1975 and gives background information on the tagging programmes.
    • Recent data suggest no further recovery in North Sea Large Fish Indicator

      Fung, Tak; Farnsworth, Keith D.; Reid, David G.; Rossberg, Axel G. (Oxford Journals, 2012)
      We detail the calculations of North Sea Large Fish Indicator values for 2009–2011, demonstrating an apparent stall in recovery. Therefore, recovery to the Marine Strategy Framework Directive's good environmental status of 0.3 by the 2020 deadline now looks less certain and may take longer than was expected using data from 2006 to 2008.
    • The recent population expansion of boarfish, Capros aper (Linnaeus, 1758): interactions of climate, growth and recruitment

      Coad, J.O.; Hüssy, K.; Farrell, E.D.; Clarke, M.W. (John Wiley & Sons, Inc, 2014)
      The objectives of this study were to evaluate whether temperature changes in the Northeast Atlantic influence the growth and recruitment dynamics of boarfish, Capros aper. Two geographically separate areas were examined, ‘north’ at the northern distribution range west of Ireland and ‘south’ on the main fishing grounds south of Ireland. No significant differences in length-at-age were observed between the two areas. Interannual otolith growth patterns were similar between the two areas with distinct years of faster and slower growth. In the ‘north’, no significant relationship between adult growth and temperature was observed, while growth in the ‘south’ was positively related to temperature up to approximately 16°C growth rates were suppressed in the years with temperatures above that. Recruitment showed a positive correlation with adult growth the previous year for the Spanish recruitment index only, suggesting spatial connectivity between the Celtic Sea and the Bay of Biscay. The age distributions were similar in both areas and despite the boarfish's longevity of >30 years, are dominated by the age classes corresponding to the years with high recruitment, suggesting that increased recruitment is responsible for the observed stock expansion.
    • Reconnaissance Survey of the Irish Continental Shelf/Shelf Edge - Atlantic Irish Regional Survey (AIRS) 1996: A GLORIA Survey of the Irish Continental Margin

      Unnithan, V; Shannon, P M; McGrane, K; Jacob, A W B; Readman, P W; Keary, R (Marine Institute, 2000)
      The Atlantic Irish Regional Survey (AIRS96) sidescan sonar survey was carried out in August 1996. Covering an area of 200,000 sq.km it represented the largest reconnaissance seabed survey of the Irish Continental Shelf region. It covered both margins, together with much of the basin floor, of the Irish sector of the Rockall Trough and extended into the northern part of the Porcupine Seabight. The objectives of this project were two fold: 1. Strategic: •to undertake, for the first time a preliminary reconnaissance survey of the Irish Continental Shelf/Shelf Edge, •to establish a strategic database on Shelf/Slope Edge conditions, •to provide training and experience to Irish researchers in state of the art marine surveying equipment (GLORIA) and data processing. 2. Scientific: •to document slope stability and mass wasting features on the margins of the Rockall Trough, •to map, where possible, occurrences of deep water carbonate mounds, •to investigate the sediment erosional, transport and depositional mechanisms that have shaped the present morphology of the region. The survey revealed a range of sedimentary features across the steep (i.e. >6º slope) margins and the basin floor in the Rockall Trough. Four classes of sedimentary feature are recognised: (1) mass failure, (2) canyon systems, (3) sediment fans, and (4) sediment drifts. The western margin is characterised by large-scale downslope mass movement features. The western and central parts of the basin floor in the Rockall Trough contain the Feni Sediment Ridge, a large Miocene-Recent contourite sediment accumulation draped by large sediment waves trending sub-parallel to the dominant modern current pattern. A large-scale downslope mass failure feature is recognised across 14,000 sq.km of the northeastern margin of the Rockall Trough. Smaller slides and slumps occur along the eastern margin in association with more prevalent canyon, channel and fan systems. A cluster of carbonate mounds was imaged in the northern part of the Porcupine Seabight. These represent part of one of the most extensive suites of deep-water carbonate mounds in the Atlantic Margin and are currently the subject of a number of new EU-funded research projects. Strong northward-directed bottom currents along the eastern margin are suggested to erode, circulate and re-deposit sediment on the basin floor and on the western margin of the Rockall Trough. The main terrigenous sedimentary input was from the Irish Mainland Shelf. A broad interplay of alongslope and downslope sediment transport processes shaped the morphology of the Rockall Trough, while tectonically-driven basin subsidence, Quaternary glaciations and glacio-eustatic sea-level fluctuations also influenced the overall sedimentation pattern in the Rockall Trough.
    • REDRISK: reduction of the virus risk in shellfish harvesting areas

      Guilfoyle, F.; Keaveney, S.; Flannery, J.; Doré, B. (Marine Institute, 2006)
      Filter feeding bivalve shellfish can accumulate human pathogenic bacteria and viruses if grown in sewage-contaminated waters. Current consumer protection legislation relies on classification of harvesting areas based on their sanitary quality, using E coli as an indicator of sewage contamination. Advances in viral monitoring have shown that E coli can underestimate the extent of the contamination. The most common cause of gastroenteritis associated with shellfish is norovirus, commonly known as winter vomiting virus. The REDRISK project was undertaken to investigate the main environmental factors that cause viral contamination in shellfish. The REDRISK project is part of a EU research pillar with parallel research being undertaken in the UK, France and Spain. A recently developed technique to quantify norovirus in shellfish, real-time PCR, has been used in the REDRISK project. Clew Bay, in Co. Mayo was chosen as the study area in Ireland. The bay is generally considered to have good water quality but with certain areas subject to intermittent sewage contamination. The cooperation of local producers and organisations such as the Clew Bay Marine Forum and the Native Oyster Co-op greatly helped the project. The project was divided into a two-phased approach. Phase one involved the identification of contamination sources impacting the bay through a sanitary survey and selection of appropriate sites for further study. Results of the first phase of this study were presented previously at this forum (Keaveney, et al 2006) and the characteristics of the sites selected for study and locations within the bay are shown in table 1 and figure 1 respectively. The second phase of the project focused on monitoring environmental conditions and microbiological levels in shellfish to identify environmental conditions leading to viral contamination. This paper reports the finding of this monitoring.
    • Report of the Study Group on Nephrops Surveys (SGNEPS)

      Doyle, J.; Lordan, C. (International Council for the Exploration of the Sea (ICES), 2013)
      The Study Group on Nephrops Surveys (SGNEPS) met in Ancona, Italy from 6–8 March 2012. The group consisted of 12 scientists from Ireland, Scotland, England, Northern Ireland, Spain, Denmark, Portugal and Italy under the chairmanship of Colm Lordan, Ireland. SGNEPS has an important role as the international coordina-tion group for Nephrops UWTV surveys in the North Atlantic and Mediterranean. Heretofore SGNEPS has focused on planning, protocols, quality control, design and survey development issues. At the 2012 meeting group compiled a table summarizing the station densities and precision levels of most annual Nephrops UWTV surveys. Large variations in survey station densities occur across the grounds currently sur-veyed. Station density, accuracy and precision trade-offs were investigated and dis-cussed in detail for the two main survey design types (random stratifies and grids). The main outcome of these deliberation was that a minimum precision level of <20% CV (also known as Relative Standard Error) should be attained for these types of surveys. There may be operational reasons why individual surveys should aim for higher precision than that (e.g. to ensure good coverage and accurate burrow surfac-es). In some areas station densities could be reduce to allow for improved coverage to previously unsurveyed Nephrops grounds. Progress towards integrated stock assess-ments for Nephrops which make use of all sources of fisheries dependent and inde-pendent information was reported to the group. There was consensus that the current ICES framework for assessing and providing catch options based on the UWTV sur-veys remains the most appropriate methodology for the moment. There has been significant progress since WKNEPH (ICES, 2007) in addressing many of the per-ceived uncertainties in the methodology. The remaining assumptions on burrow occupancy, burrow size, growth, discard survival can only be addressed through dedicated research projects of which there have been few. Several video enhancement and technological developments were presented to the group and these look very promising in terms of improving certainty of burrow identification and facilitating validation counts. The group also discussed the various Nephrops trawl surveys and biological sampling requirements under the DCF and concluded that the role of the group should be expanded to cover these in future.
    • Report on analysis of shellfish samples for the presence of Yessotoxins (YTX)

      Marine Institute (Marine Institute, 2001)
      In order to determine the cause of the positive mouse bioassay results obtained in mussel samples from several shellfish production areas (including Bantry Bay, Kenmare Bay, Cromane and Lough Foyle), samples were sent in December 2000 and January 2001 for analysis. Positive mouse bioassay results were obtained, using the Yasumoto (1978) assay, in the EU Reference Laboratory and using the Yasumoto (l 984) assay in the Italian Reference Laboratory. ASP toxins, Azaspiracid, Okadaic acid and DTXs were not detected. Yessotoxin, homoYessotoxins and analogues of Yessotoxins were not detected in the samples sent to the EU Reference Laboratory or the Italian Reference Laboratory. Prof. Yasumoto detected the presence of Yessotoxin and 45-hydroxyYessotoxin at the Japan Food Research Laboratory. 45-hydroxyYessotoxin is a shellfish metabolite of Yessotoxin, which occurs with time as the YTX is oxidised by the shellfish. The shellfish samples in which Yessotoxin and 45-hydroxy Yessotoxin were detected were taken from Bantry Bay, Roaring Water Bay (Summer 2000) and Mulroy Bay. If the initial detection of Yessotoxin and 45-hydroxyYessotoxin is confirmed in other samples, the Irish biotoxin management regime and the production cycles for shellfish (in particular mussels) will have to be adapted to encompass YTX.
    • Report on Inshore Surveys Around the Irish Coast

      Crowley, M A (Department of Agriculture and Fisheries (Fisheries Division), 1973)
      The purpose of this leaflet is to discuss the quantity and quality of some species of commercially valuable shellfish found in certain estuaries around the Irish coast. In recent years the shellfish industry has attracted considerable interest in Ireland, partly because of the demand in England and on the Continent of Europe for Irish shellfish and shellfish products and partly because of the interest which the general public has in fish farming.
    • Report on Sea Lice Epidemiology and Management in Ireland with Particular Reference to Potential Interactions with Wild Salmon (Salmo salar) and Freshwater Pearl Mussel (Margaritifera margaritifera) Populations

      Jackson, D.; O’Donohoe, P.; McDermott, T.; Kane, F.; Kelly, S.; Drumm, A. (Marine Institute, 2013)
      In 2009 two Non-Governmental organizations (NGOs) submitted a legal complaint (Anon. 2009 a) against Ireland to the EU Commission (EU Pilot Case 764/09/ENV1). The substance of the complaint was that Ireland was failing to comply with the Habitats Directive and the Environmental Impact Assessment Directive in three named fisheries; the Delphi (Bundorragha River), the Newport Fishery (Newport River) and the Ballynahinch Fishery (Ballynahinch River). The complainants also cited a failure to protect both the salmon (Salmo salar) and the freshwater pearl mussel (Margaritifera margaritifera). In responding to the complaint a detailed scientific investigation was undertaken. Long term research and specifically commissioned studies were accessed and their data drawn on to ensure a comprehensive and accurate response based on the best available scientific data and information. This report sets out this information, together with the associated studies and data which formed the basis of the scientific response to the complaint. The complaint was closed in favour of the State on the 11th of October 2012.
    • Report on the coded wire tag returns for 2001

      O'Maoileidigh, N.; McDermott, T.; Cullen, A. (Marine Institute, 2002)
      This report gives recapture details of microtagged salmon recovered during 2001 commercial fishing season in summary format. The report includes 2 sea winter recoveries, that is those fish which were released and migrated in 1999. The 1st sea winter results for these releases can be found in the 2000 report.
    • Report on the coded wire tag returns for 2002

      O'Maoileidigh, N.; McDermott, T.; Cullen, A. (Marine Institute, 2003)
      This report gives recapture details of microtagged salmon recovered during 2002 commercial fishing season in summary format. The report includes 2 sea winter recoveries, that is those fish which were released and migrated in 2000. The 1st sea winter results for these releases can be found in the 2001 report.
    • Report on the coded wire tag returns for 2003

      O'Maoileidigh, N.; McDermott, T.; Cullen, A. (Marine Institute, 2004)
      This report gives recapture details of microtagged salmon recovered during 2003 commercial fishing season in summary format. The report includes 2 sea winter recoveries, that is those fish which were released and migrated in 2001. The 1st sea winter results for these releases can be found in the 2002 report.