Springtime zooplankton size structure over the continental shelf of the Bay of BiscaY

Linking lower and higher trophic levels requires special focus on the essential role played by mid-trophic levels, i.e., the zooplankton. One of the most relevant pieces of information regarding zooplankton in terms of flux of energy lies in its size structure. In this study, an extensive data set of size measurements is presented, covering parts of the western European continental shelf and slope, from the Galician coast to the Ushant front, during the springs from 2005 to 2012. Zooplankton size spectra were estimated using measurements carried out in situ with the Laser Optical Plankton Counter (LOPC) and with an image analysis of WP2 net samples (200 μm mesh size) performed following the ZooScan methodology. The LOPC counts and sizes particles within 100–2000 μm of spherical equivalent diameter (ESD), whereas the WP2/ZooScan allows for counting, sizing and identification of zooplankton from ~ 400 μm ESD. The difference between the LOPC (all particles) and the WP2/ZooScan (zooplankton only) was assumed to provide the size distribution of non-living particles, whose descriptors were related to a set of explanatory variables (including physical, biological and geographic descriptors). A statistical correction based on these explanatory variables was further applied to the LOPC size distribution in order to remove the non-living particles part, and therefore estimate the size distribution of zooplankton. This extensive data set provides relevant information about the zooplankton size distribution variability, productivity and trophic transfer efficiency in the pelagic ecosystem of the Bay of Biscay at a regional and interannual scale

Climatic and palaeoceanographic changes during the Pliensbachian (Early Jurassic) 2 inferred from clay mineralogy and stable isotope (C-O) geochemistry (NW Europe)

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.Available online 17 January 2017The Early Jurassic was broadly a greenhouse climate period that was punctuated by short warm and cold climatic events, positive and negative excursions of carbon isotopes, and episodes of enhanced organic matter burial. Clay minerals from Pliensbachian sediments recovered from two boreholes in the Paris Basin, are used here as proxies of detrital supplies, runoff conditions, and palaeoceanographic changes. The combined use of these minerals with ACCEPTED MANUSCRIPT ACCEPTED MANUSCRIPT stable isotope data (C-O) from bulk carbonates and organic matter allows palaeoclimatic reconstructions to be refined for the Pliensbachian. Kaolinite/illite ratio is discussed as a reliable proxy of the hydrological cycle and runoff from landmasses. Three periods of enhanced runoff are recognised within the Pliensbachian. The first one at the SinemurianPliensbachian transition shows a significant increase of kaolinite concomitant with the negative carbon isotope excursion at the so-called Sinemurian Pliensbachian Boundary Event (SPBE). The Early/Late Pliensbachian transition was also characterised by more humid conditions. This warm interval is associated with a major change in oceanic circulation during the Davoei Zone, likely triggered by sea-level rise; the newly created palaeogeography, notably the flooding of the London-Brabant Massif, allowed boreal detrital supplies, including kaolinite and chlorite, to be exported to the Paris Basin. The last event of enhanced runoff occurred during the late Pliensbachian (Subdonosus Subzone of the Margaritatus Zone), which occurred also during a warm period, favouring organic matter production and preservation. Our study highlights the major role of the London Brabant Massif in influencing oceanic circulation of the NW European area, as a topographic barrier (emerged lands) during periods of lowstand sea-level and its flooding during period of high sea-level. This massif was the unique source of smectite in the Paris Basin. Two episodes of smectite-rich sedimentation (‘smectite events’), coincide with regressive intervals, indicating emersion of the London Brabant Massif and thus suggesting that an amplitude of sea-level change high enough to be linked to glacio-eustasy. This mechanism is consistent with sedimentological and geochemical evidences of continental ice growth notably during the Latest Pliensbachian (Spinatum Zone), and possibly during the Early Pliensbachian (late Jamesoni/early Ibex Zones).The study was supported by the “Agence Nationale pour la Gestion des Déchets Radioactifs” (Andra––French National Radioactive Waste Management Agency)

ICES. 2020. Working Group on Acoustic and Egg Surveys for Sardine and Anchovy in ICES areas 7, 8 and 9

he Working Group on Acoustic and Egg Surveys (WGACEGG) coordinates pelagic surveys for a number of stocks and provides monitoring for the two major sardine and anchovy stocks in ICES areas 6, 7, 8, and 9. The group evaluated small pelagic fish biomass indices derived from acoustic and Daily Egg Production Method (DEPM) surveys in ICES areas 6, 7, 8 and 9. These indices have been provided to the ICES Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA), the Working Group on Widely Distributed Stocks (WGWIDE) and the Herring Assessment Working Group for the Area South of 62ºN (HAWG) stock assessment group, to serve as fishery-independent input for analytical assessment purposes. DEPM and acoustic indices were derived based on data collected using independent methods. Acoustic- and DEPM-derived biomass indices from quasi-synoptic surveys conducted in the Bay of Biscay in spring were compared, to assess the presence of potential bias and to improve the precision of fish stock biomass estimates. The DEPM-based anchovy biomass index was 22% higher than the acoustic index in 2019. Unusual concentrations of anchovy in Eastern Cantabrian Sea, an area not covered by the acoustic survey, and the presence near the sea surface of actively spawning individuals possibly under-sampled by acoustics in central Bay of Bay had been postulated as potential causes of this discrepancy. No significant difference was found between sardine biomass indices derived from DEPM and acoustics in 2019. The group has updated its database of standard gridded maps covering the European Atlantic area. This initiative continues to inform on the spatial dynamics of various parameters collected during the surveys coordinated under the auspices of the group (fish acoustic densities, anchovy and sardine egg abundance, surface temperature and salinity). Results of an analysis of the time series of gridded maps (anchovy and sardine acoustic density, surface salinity and temperature) showed quantitative changes in the spatial and temporal distribution of anchovy and sardine over the last 15 years, and further define their habitats in European Atlantic waters in spring. The timing and spatial coverage of DEPM and acoustic surveys that will be conducted by group members in 2020 were planned to optimise the monitoring of anchovy and sardine populations and their pelagic environment in the European Atlantic area. The synoptic nature of the survey components has been assessed for each target species. A manual describing the protocols used during the DEPM surveys coordinated by the WGACEGG group was reviewed, and writing of a manual of WGACEGG acoustic surveys continued. Both manuals will be available in 2020. The final results of the 2017 sardine DEPM assessment were endorsed by the group

Validation of MIPAS HNO3 operational data

Nitric acid (HNO3) is one of the key products that are operationally retrieved by the European Space Agency (ESA) from the emission spectra measured by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) onboard ENVISAT. The product version 4.61/4.62 for the observation period between July 2002 and March 2004 is validated by comparisons with a number of independent observations from ground-based stations, aircraft/balloon campaigns, and satellites. Individual HNO3 profiles of the ESA MIPAS level-2 product show good agreement with those of MIPAS-B and MIPAS-STR (the balloon and aircraft version of MIPAS, respectively), and the balloon-borne infrared spectrometers MkIV and SPIRALE, mostly matching the reference data within the combined instrument error bars. In most cases differences between the correlative measurement pairs are less than 1 ppbv (5-10%) throughout the entire altitude range up to about 38 km (similar to 6 hPa), and below 0.5 ppbv (15-20% or more) above 30 km (similar to 17 hPa). However, differences up to 4 ppbv compared to MkIV have been found at high latitudes in December 2002 in the presence of polar stratospheric clouds. The degree of consistency is further largely affected by the temporal and spatial coincidence, and differences of 2 ppbv may be observed between 22 and 26 km (similar to 50 and 30 hPa) at high latitudes near the vortex boundary, due to large horizontal inhomogeneity of HNO3. Similar features are also observed in the mean differences of the MIPAS ESA HNO3 VMRs with respect to the ground-based FTIR measurements at five stations, aircraft-based SAFIRE-A and ASUR, and the balloon campaign IBEX. The mean relative differences between the MIPAS and FTIR HNO3 partial columns are within +/- 2%, comparable to the MIPAS systematic error of similar to 2%. For the vertical profiles, the biases between the MIPAS and FTIR data are generally below 10% in the altitudes of 10 to 30 km. The MIPAS and SAFIRE HNO3 data generally match within their total error bars for the mid and high latitude flights, despite the larger atmospheric inhomogeneities that characterize the measurement scenario at higher latitudes. The MIPAS and ASUR comparison reveals generally good agreements better than 10-13% at 20-34 km. The MIPAS and IBEX measurements agree reasonably well (mean relative differences within +/- 15%) between 17 and 32 km. Statistical comparisons of the MIPAS profiles correlated with those of Odin/SMR, ILAS-II, and ACE-FTS generally show good consistency. The mean differences averaged over individual latitude bands or all bands are within the combined instrument errors, and generally within 1, 0.5, and 0.3 ppbv between 10 and 40 km (similar to 260 and 4.5 hPa) for Odin/SMR, ILAS-II, and ACE-FTS, respectively. The standard deviations of the differences are between 1 to 2 ppbv. The standard deviations for the satellite comparisons and for almost all other comparisons are generally larger than the estimated measurement uncertainty. This is associated with the temporal and spatial coincidence error and the horizontal smoothing error which are not taken into account in our error budget. Both errors become large when the spatial variability of the target molecule is high.Peer reviewe

Preliminary results from the ECOCADIZ 2020-07 Spanish acoustic survey (01 – 14 August 2020)

The present working document summarises a part of the main results obtained from the Spanish (pelagic ecosystem-) acoustic survey conducted by IEO between 01st and 14th August 2020 in the Portuguese and Spanish shelf waters (20-200 m isobaths) off the Gulf of Cadiz (GoC) onboard the R/V Miguel Oliver. The 21 foreseen acoustic transects were sampled. A total of 26 valid fishing hauls were carried out for echo-trace ground-truthing purposes. Four additional night trawls were conducted to collect anchovy hydrated females (DEPM). This working document only provides abundance and biomass estimates for anchovy, sardine and chub mackerel, which are presented without age structure. The distribution of all the mid-sized and small pelagic fish species susceptible of being acoustically assessed is also shown from the mapping of their back-scattering energies. GoC anchovy acoustic estimates in summer 2020 were of 5153 million fish and 44 877 tones, with the bulk of the population occurring in the Spanish waters. The current biomass estimate becomes in the second historical maximum within the time-series. The estimates of sardine abundance and biomass in summer 2020 were 1923 million fish and 50 721 t, estimates close to the historical average, but lower than the values estimated last year and the most recent maxima reached in 2018. A total of 32 854 t and 448 million fish were estimated for Chub mackerel, estimates similar to the most recent ones and very close to the time-series average

Core module biomarker identification with network exploration for breast cancer metastasis

<p>Abstract</p> <p>Background</p> <p>In a complex disease, the expression of many genes can be significantly altered, leading to the appearance of a differentially expressed "disease module". Some of these genes directly correspond to the disease phenotype, (i.e. "driver" genes), while others represent closely-related first-degree neighbours in gene interaction space. The remaining genes consist of further removed "passenger" genes, which are often not directly related to the original cause of the disease. For prognostic and diagnostic purposes, it is crucial to be able to separate the group of "driver" genes and their first-degree neighbours, (i.e. "core module") from the general "disease module".</p> <p>Results</p> <p>We have developed COMBINER: COre Module Biomarker Identification with Network ExploRation. COMBINER is a novel pathway-based approach for selecting highly reproducible discriminative biomarkers. We applied COMBINER to three benchmark breast cancer datasets for identifying prognostic biomarkers. COMBINER-derived biomarkers exhibited 10-fold higher reproducibility than other methods, with up to 30-fold greater enrichment for known cancer-related genes, and 4-fold enrichment for known breast cancer susceptible genes. More than 50% and 40% of the resulting biomarkers were cancer and breast cancer specific, respectively. The identified modules were overlaid onto a map of intracellular pathways that comprehensively highlighted the hallmarks of cancer. Furthermore, we constructed a global regulatory network intertwining several functional clusters and uncovered 13 confident "driver" genes of breast cancer metastasis.</p> <p>Conclusions</p> <p>COMBINER can efficiently and robustly identify disease core module genes and construct their associated regulatory network. In the same way, it is potentially applicable in the characterization of any disease that can be probed with microarrays.</p

ALL-1/MLL1, a homologue of Drosophila TRITHORAX, modifies chromatin and is directly involved in infant acute leukaemia

Rearrangements of the ALL-1/MLL1 gene underlie the majority of infant acute leukaemias, as well as of therapy-related leukaemias developing in cancer patients treated with inhibitors of topoisomerase II, such as VP16 and doxorubicin. The rearrangements fuse ALL-1 to any of \u3e50 partner genes or to itself. Here, we describe the unique features of ALL-1-associated leukaemias, and recent progress in understanding molecular mechanisms involved in the activity of the ALL-1 protein and of its Drosophila homologue TRITHORAX