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

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

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)

Predicting selective drug targets in cancer through metabolic networks

The authors develop a genome-scale model of cancer metabolism and use it to predict genes that are essential for cancer cell growth. An array of target combinations are then identified that could potentially provide novel selective treatments for specific cancers

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

Integrating biogeochemistry and ecology into ocean data assimilation systems

Monitoring and predicting the biogeochemical state of the ocean and marine ecosystems is an important application of operational oceanography that needs to be expanded. The accurate depiction of the ocean's physical environment enabled by Global Ocean Data Assimilation Experiment (GODAE) systems, in both real-time and reanalysis modes, is already valuable for various for various applications, such as the fishing industry and fisheries management. However, most of these applications require accurate estimates of both physical and biogeochemical ocean conditions over a wide range of spatial and temporal scales. In this paper, we discuss recent developments that enable coupling new biogeochemical models and assimilation components with the existing GODAE systems, and we examine the potential of such systems in several areas of interest: phytoplankton biomass monitoring in the open ocean, ocean carbon cycle monitoring and assessment, marine ecosystem management at seasonal and longer time scales, and downscaling in coastal areas. A number of key requirements and research priorities are then identified for the future, GODAE systems will need to improve their representation of physical variables that are not yet considered essential, such as upper-ocean vertical fluxes that are critically important to biological activity. Further, the observing systems will need to be expanded in terms of in situ platforms (with intensified deployments of sensors for O-2 and chlorophyll, and inclusion of new sensors for nutrients, zooplankton, micronekton biomass, and others), satellite missions (e.g., hyperspectral instruments for ocean color, lidar systems for mixed-layer depths, and wide-swath altimeters for coastal sea level), and improved methods to assimilate these new measurements

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° 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° 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 10–20% and a precision of typically 5–15% 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

MethyCancer: the database of human DNA methylation and cancer

Cancer is ranked as one of the top killers in all human diseases and continues to have a devastating effect on the population around the globe. Current research efforts are aiming to accelerate our understanding of the molecular basis of cancer and develop effective means for cancer diagnostics, treatment and prognosis. An altered pattern of epigenetic modifications, most importantly DNA methylation events, plays a critical role in tumorigenesis through regulating oncogene activation, tumor suppressor gene silencing and chromosomal instability. To study interplay of DNA methylation, gene expression and cancer, we developed a publicly accessible database for human DNA Methylation and Cancer (MethyCancer, http://methycancer.genomics.org.cn). MethyCancer hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Furthermore, a powerful search tool is developed to provide user-friendly access to all the data and data connections. A graphical MethyView shows DNA methylation in context of genomics and genetics data facilitating the research in cancer to understand genetic and epigenetic mechanisms that make dramatic changes in gene expression of tumor cells

dbCRID: a database of chromosomal rearrangements in human diseases

Chromosomal rearrangement (CR) events result from abnormal breaking and rejoining of the DNA molecules, or from crossing-over between repetitive DNA sequences, and they are involved in many tumor and non-tumor diseases. Investigations of disease-associated CR events can not only lead to important discoveries about DNA breakage and repair mechanisms, but also offer important clues about the pathologic causes and the diagnostic/therapeutic targets of these diseases. We have developed a database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org), a comprehensive database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and—when possible—detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event. With 2643 records of disease-associated CR events curated from 1172 original studies, dbCRID is a comprehensive and dynamic resource useful for studying DNA breakage and repair mechanisms, and for analyzing the genetic basis of human tumor and non-tumor diseases

Million-year-scale alternation of warm–humid and semi-arid periods as a mid-latitude climate mode in the Early Jurassic (late Sinemurian, Laurasian Seaway)

Clay mineral and stable isotope (C, O) data are reported from the upper Sinemurian (Lower Jurassic) of the Cardigan Bay Basin (Llanbedr–Mochras Farm borehole, northwestern Wales) and the Paris Basin (Montcornet borehole, northern France) to highlight the prevailing environmental and climatic conditions. In both basins, located at similar palaeolatitudes of 30–35∘ N, the clay mineral assemblages comprise chlorite, illite, illite–smectite mixed layers (R1 I-S), smectite, and kaolinite in various proportions. Because the influence of burial diagenesis and authigenesis is negligible in both boreholes, the clay minerals are interpreted to be derived from the erosion of the Caledonian and Variscan massifs, including their basement and pedogenic cover. In the Cardigan Bay Basin, the variations in the proportions of smectite and kaolinite are inversely related to each other through the entire upper Sinemurian. As in the succeeding Pliensbachian, the upper Sinemurian stratigraphic distribution reveals an alternation of kaolinite-rich intervals reflecting strong hydrolysing conditions and smectite-rich intervals indicating a semi-arid climate. Kaolinite is particularly abundant in the upper part of the obtusum zone and in the oxynotum zone, suggesting more intense hydrolysing conditions likely coeval with warm conditions responsible for an acceleration of the hydrological cycle. In the north of the Paris Basin, the succession is less continuous compared to the Cardigan Bay Basin site, as the oxynotum zone and the upper raricostatum zone are either absent or highly condensed. The clay assemblages are dominantly composed of illite and kaolinite without significant stratigraphic trends, but a smectite-rich interval identified in the obtusum zone is interpreted as a consequence of the emersion of the London–Brabant Massif following a lowering of sea level. Following a slight negative carbon isotope excursion at the obtusum–oxynotum zone transition, a long-term decrease in δ13Corg from the late oxynotum–early raricostatum zones is recorded in the two sites and may precede or partly include the negative carbon isotope excursion of the Sinemurian–Pliensbachian Boundary Event, which is recognised in most basins worldwide and interpreted to signify a late pulse of the Central Atlantic Magmatic Province volcanism