Integration of bioenergetics in an individual-based model to hindcast anchovy dynamics in the Bay of Biscay

The population of European anchovy of the Bay of Biscay collapsed at the beginning of the 21st century, causing the closure of its fishery between 2005 and 2010. In order to study both the human and environmental causes of the anchovy population dynamics, an approach coupling individual bioenergetics to an individual-based model was applied between 2000 and 2015. This modelling framework was forced with outputs from a physical-biogeochemical model. In addition to a base-case scenario with realistic forcing, alternative scenarios were run without interannual variability in either fishing mortality or environmental conditions. During the decrease in population biomass, a high fishing pressure coincided with a combination of environmental variables promoting the appearance of large individuals that could not survive severe winters because of their high energetic demands. The recovery of the population was favoured by a period of warm years with abundant food favouring the winter survival of age 1 individuals, in coincidence with the closure of the fishery. Our modelling approach also allows to test the consequences of a retrospective implementation of the current harvest control rule from 2000 which, according to our results, would have prevented the collapse of the population and avoided the fishery closure

t(4;12)(q11-q21;p13)

Review on t(4;12)(q11-q21;p13), with data on clinics, and the genes involved

Observation of mesospheric air inside the arctic stratospheric polar vortex in early 2003

During several balloon flights inside the Arctic polar vortex in early 2003, unusual trace gas distributions were observed, which indicate a strong influence of mesospheric air in the stratosphere. The tuneable diode laser (TDL) instrument SPIRALE (Spectroscopie InFrarouge par Absorption de Lasers Embarqués) measured unusually high CO values (up to 600 ppb) on 27 January at about 30 km altitude. The cryosampler BONBON sampled air masses with very high molecular Hydrogen, extremely low SF6 and enhanced CO values on 6 March at about 25 km altitude. Finally, the MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) Fourier Transform Infra-Red (FTIR) spectrometer showed NOy values which are significantly higher than NOy* (the NOy derived from a correlation between N2O and NOy under undisturbed conditions), on 21 and 22 March in a layer centred at 22 km altitude. Thus, the mesospheric air seems to have been present in a layer descending from about 30 km in late January to 25 km altitude in early March and about 22 km altitude on 20 March. We present corroborating evidence from a model study using the KASIMA (KArlsruhe Simulation model of the Middle Atmosphere) model that also shows a layer of mesospheric air, which descended into the stratosphere in November and early December 2002, before the minor warming which occurred in late December 2002 lead to a descent of upper stratospheric air, cutting of a layer in which mesospheric air is present. This layer then descended inside the vortex over the course of the winter. The same feature is found in trajectory calculations, based on a large number of trajectories started in the vicinity of the observations on 6 March. Based on the difference between the mean age derived from SF6 (which has an irreversible mesospheric loss) and from CO2 (whose mesospheric loss is much smaller and reversible) we estimate that the fraction of mesospheric air in the layer observed on 6 March, must have been somewhere between 35% and 100%

Dispersal Modeling of Fish Early Life Stages: Sensitivity with Application to Atlantic Cod in the Western Gulf of Maine

As an initial step in establishing mechanistic relationships between environmental variability and recruitment in Atlantic cod Gadhus morhua along the coast of the western Gulf of Maine, we assessed transport success of larvae from major spawning grounds to nursery areas with particle tracking using the unstructured grid model FVCOM (finite volume coastal ocean model). In coastal areas, dispersal of early planktonic life stages of fish and invertebrate species is highly dependent on the regional dynamics and its variability, which has to be captured by our models. With state-of-the-art forcing for the year 1995, we evaluate the sensitivity of particle dispersal to the timing and location of spawning, the spatial and temporal resolution of the model, and the vertical mixing scheme. A 3 d frequency for the release of particles is necessary to capture the effect of the circulation variability into an averaged dispersal pattern of the spawning season. The analysis of sensitivity to model setup showed that a higher resolution mesh, tidal forcing, and current variability do not change the general pattern of connectivity, but do tend to increase within-site retention. Our results indicate strong downstream connectivity among spawning grounds and higher chances for successful transport from spawning areas closer to the coast. The model run for January egg release indicates 1 to 19 % within-spawning ground retention of initial particles, which may be sufficient to sustain local populations. A systematic sensitivity analysis still needs to be conducted to determine the minimum mesh and forcing resolution that adequately resolves the complex dynamics of the western Gulf of Maine. Other sources of variability, i.e. large-scale upstream forcing and the biological environment, also need to be considered in future studies of the interannual variability in transport and survival of the early life stages of cod

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

Validation and data characteristics of methane and nitrous oxide profiles observed by MIPAS and processed with Version 4.61 algorithm

The ENVISAT validation programme for the atmospheric instruments MIPAS, SCIAMACHY and GOMOS is based on a number of balloon-borne, aircraft, satellite and ground-based correlative measurements. In particular the activities of validation scientists were coordinated by ESA within the ENVISAT Stratospheric Aircraft and Balloon Campaign or ESABC. As part of a series of similar papers on other species [this issue] and in parallel to the contribution of the individual validation teams, the present paper provides a synthesis of comparisons performed between MIPAS CH4 and N2O profiles produced by the current ESA operational software (Instrument Processing Facility version 4.61 or IPF v4.61, full resolution MIPAS data covering the period 9 July 2002 to 26 March 2004) and correlative measurements obtained from balloon and aircraft experiments as well as from satellite sensors or from ground-based instruments. In the middle stratosphere, no significant bias is observed between MIPAS and correlative measurements, and MIPAS is providing a very consistent and global picture of the distribution of CH4 and N2O in this region. In average, the MIPAS CH4 values show a small positive bias in the lower stratosphere of about 5%. A similar situation is observed for N2O with a positive bias of 4%. In the lower stratosphere/upper troposphere (UT/LS) the individual used MIPAS data version 4.61 still exhibits some unphysical oscillations in individual CH4 and N2O profiles caused by the processing algorithm (with almost no regularization). Taking these problems into account, the MIPAS CH4 and N2O profiles are behaving as expected from the internal error estimation of IPF v4.61 and the estimated errors of the correlative measurements

Simultaneous localization of MLL, AF4 and ENL genes in interphase nuclei by 3D-FISH: MLL translocation revisited

BACKGROUND: Haematological cancer is characterised by chromosomal translocation (e.g. MLL translocation in acute leukaemia) and two models have been proposed to explain the origins of recurrent reciprocal translocation. The first, established from pairs of translocated genes (such as BCR and ABL), considers the spatial proximity of loci in interphase nuclei (static "contact first" model). The second model is based on the dynamics of double strand break ends during repair processes (dynamic "breakage first" model). Since the MLL gene involved in 11q23 translocation has more than 40 partners, the study of the relative positions of the MLL gene with both the most frequent partner gene (AF4) and a less frequent partner gene (ENL), should elucidate the MLL translocation mechanism. METHODS: Using triple labeling 3D FISH experiments, we have determined the relative positions of MLL, AF4 and ENL genes, in two lymphoblastic and two myeloid human cell lines. RESULTS: In all cell lines, the ENL gene is significantly closer to the MLL gene than the AF4 gene (with P value < 0.0001). According to the static "contact first" model of the translocation mechanism, a minimal distance between loci would indicate a greater probability of the occurrence of t(11;19)(q23;p13.3) compared to t(4;11)(q21;q23). However this is in contradiction to the epidemiology of 11q23 translocation. CONCLUSION: The simultaneous multi-probe hybridization in 3D-FISH is a new approach in addressing the correlation between spatial proximity and occurrence of translocation. Our observations are not consistent with the static "contact first" model of translocation. The recently proposed dynamic "breakage first" model offers an attractive alternative explanation

Validation of MIPAS-ENVISAT NO2 operational data

The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument was launched aboard the environmental satellite ENVISAT into its sun-synchronous orbit on 1 March 2002. The short-lived species NO₂ is one of the key target products of MIPAS that are operationally retrieved from limb emission spectra measured in the stratosphere and mesosphere. Within the MIPAS validation activities, a large number of independent observations from balloons, satellites and ground-based stations have been compared to European Space Agency (ESA) version 4.61 operational NO₂ data comprising the time period from July 2002 until March 2004 where MIPAS measured with full spectral resolution. Comparisons between MIPAS and balloon-borne observations carried out in 2002 and 2003 in the Arctic, at mid-latitudes, and in the tropics show a very good agreement below 40 km altitude with a mean deviation of roughly 3%, virtually without any significant bias. The comparison to ACE satellite observations exhibits only a small negative bias of MIPAS which appears not to be significant. The independent satellite instruments HALOE, SAGE II, and POAM III confirm in common for the spring-summer time period a negative bias of MIPAS in the Arctic and a positive bias in the Antarctic middle and upper stratosphere exceeding frequently the combined systematic error limits. In contrast to the ESA operational processor, the IMK/IAA retrieval code allows accurate inference of NO₂ volume mixing ratios under consideration of all important non-LTE processes. Large differences between both retrieval results appear especially at higher altitudes, above about 50 to 55 km. These differences might be explained at least partly by non-LTE under polar winter conditions but not at mid-latitudes. Below this altitude region mean differences between both processors remain within 5% (during night) and up to 10% (during day) under undisturbed (September 2002) conditions and up to 40% under perturbed polar night conditions (February and March 2004). The intercomparison of ground-based NDACC observations shows no significant bias between the FTIR measurements in Kiruna (68&deg; N) and MIPAS in summer 2003 but larger deviations in autumn and winter. The mean deviation over the whole comparison period remains within 10%. A mean negative bias of 15% for MIPAS daytime and 8% for nighttime observations has been determined for UV-vis comparisons over Harestua (60&deg; N). Results of a pole-to-pole comparison of ground-based DOAS/UV-visible sunrise and MIPAS mid-morning column data has shown that the mean agreement in 2003 falls within the accuracy limit of the comparison method. Altogether, it can be indicated that MIPAS NO₂ profiles yield valuable information on the vertical distribution of NO₂ in the lower and middle stratosphere (below about 45 km) during day and night with an overall accuracy of about 10&ndash;20% and a precision of typically 5&ndash;15% such that the data are useful for scientific studies. In cases where extremely high NO₂ occurs in the mesosphere (polar winter) retrieval results in the lower and middle stratosphere are less accurate than under undisturbed atmospheric conditions

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