GODAE systems in operation

During the last 15 years, operational oceanography systems have been developed in several countries around the world. These developments have been fostered primarily by the Global Ocean Data Assimilation Experiment (GODAE), which coordinated these activities, encouraged partnerships, and facilitated constructive competition. This multinational coordination has been very beneficial for the development of operational oceanography. Today, several systems provide routine, real-time ocean analysis, forecast, and reanalysis products. These systems are based on (1) state-of-the-art Ocean General Circulation Model (OGCM) configurations, either global or regional (basin-scale), with resolutions that range from coarse to eddy-resolving, and (2) data assimilation techniques ranging from analysis correction to advanced three- or four-dimensional variational schemes. These systems assimilate altimeter sea level anomalies, sea surface temperature data, and in situ profiles of temperature and salinity, including Argo data. Some systems have implemented downscaling capacities, which consist of embedding higher-resolution local systems in global and basin-scale models (through open boundary exchange of data), especially in coastal regions, where small scale-phenomena are important, and also increasing the spatial resolution for these regional/coastal systems to be able to resolve smaller scales (so-called downscaling). Others have implemented coupling with the atmosphere and/or sea ice. This paper provides a short review of these operational GODAE systems.Published76-914.6. Oceanografia operativa per la valutazione dei rischi in aree marineN/A or not JCRope

GODAE systems in operation

During the last 15 years, operational oceanography systems have emerged in several countries around the world. This emergence has been largely fostered by the GODAE experiment, during which each nation engaged in this activity have organised partnership and constructive competition. This trans-national coordination was very beneficial for the development of operational oceanography, leading to economies of scales and more targeted actions. Today, several systems provide routine real-time ocean analysis and forecast and/or reanalysis products. They are all based on (i) state-of-the-art primitive equation baroclinic Ocean General Circulation Model (OGCM) configurations, either global or regional (basin-scale), with resolutions that range from coarse to eddy resolving and (ii) data assimilation techniques whose complexity ranges from simple analysis correction to advanced 4D variational schemes. They assimilate altimeter sea level anomalies, remotely sensed SST such as GHRSST products and in situ profiles of T and S, including ARGO. Some systems have implemented downscaling capacities in specific regions of interest including shelf/coastal seas. Some also have implemented coupling with the atmosphere and/or the prognostic sea ice in polar regions. They are the GODAE system in operation. They are reviewed in this paper. The GODAE system discussed here include: (1) BLUElink OceanMAPS, (2) C-NOOFS, , (3) ECCO, (4) FOAM, (5) HYCOM/NCODA, (6) MERCATOR, (7) MFS, (8) MOVE/MRI.COM, (9) NLOM/NCOM, (10) NMEFC, (11) RTOFS and (12) TOPAZ.SubmittedNice, France3.11. Oceanografia Operativaope

GODAE systems in operation

During the last 15 years, operational oceanography systems have been developed in several countries around the world. These developments have been fostered primarily by the Global Ocean Data Assimilation Experiment (GODAE), which coordinated these activities, encouraged partnerships, and facilitated constructive competition. This multinational coordination has been very beneficial for the development of operational oceanography. Today, several systems provide routine, real-time ocean analysis, forecast, and reanalysis products. These systems are based on (1) state-of-the-art Ocean General Circulation Model (OGCM) configurations, either global or regional (basin-scale), with resolutions that range from coarse to eddy-resolving, and (2) data assimilation techniques ranging from analysis correction to advanced three- or four-dimensional variational schemes. These systems assimilate altimeter sea level anomalies, sea surface temperature data, and in situ profiles of temperature and salinity, including Argo data. Some systems have implemented downscaling capacities, which consist of embedding higher-resolution local systems in global and basin-scale models (through open boundary exchange of data), especially in coastal regions, where small scale-phenomena are important, and also increasing the spatial resolution for these regional/coastal systems to be able to resolve smaller scales (so-called downscaling). Others have implemented coupling with the atmosphere and/or sea ice. This paper provides a short review of these operational GODAE systems

GODAE systems in operation

During the last 15 years, operational oceanography systems have emerged in several countries around the world. This emergence has been largely fostered by the GODAE experiment, during which each nation engaged in this activity have organised partnership and constructive competition. This trans-national coordination was very beneficial for the development of operational oceanography, leading to economies of scales and more targeted actions. Today, several systems provide routine real-time ocean analysis and forecast and/or reanalysis products. They are all based on (i) state-of-the-art primitive equation baroclinic Ocean General Circulation Model (OGCM) configurations, either global or regional (basin-scale), with resolutions that range from coarse to eddy resolving and (ii) data assimilation techniques whose complexity ranges from simple analysis correction to advanced 4D variational schemes. They assimilate altimeter sea level anomalies, remotely sensed SST such as GHRSST products and in situ profiles of T and S, including ARGO. Some systems have implemented downscaling capacities in specific regions of interest including shelf/coastal seas. Some also have implemented coupling with the atmosphere and/or the prognostic sea ice in polar regions. They are the GODAE system in operation. They are reviewed in this paper. The GODAE system discussed here include: (1) BLUElink OceanMAPS, (2) C-NOOFS, , (3) ECCO, (4) FOAM, (5) HYCOM/NCODA, (6) MERCATOR, (7) MFS, (8) MOVE/MRI.COM, (9) NLOM/NCOM, (10) NMEFC, (11) RTOFS and (12) TOPAZ

B1 SOX Coordinate Cell Specification with Patterning and Morphogenesis in the Early Zebrafish Embryo

The B1 SOX transcription factors SOX1/2/3/19 have been implicated in various processes of early embryogenesis. However, their regulatory functions in stages from the blastula to early neurula remain largely unknown, primarily because loss-of-function studies have not been informative to date. In our present study, we systematically knocked down the B1 sox genes in zebrafish. Only the quadruple knockdown of the four B1 sox genes sox2/3/19a/19b resulted in very severe developmental abnormalities, confirming that the B1 sox genes are functionally redundant. We characterized the sox2/3/19a/19b quadruple knockdown embryos in detail by examining the changes in gene expression through in situ hybridization, RT–PCR, and microarray analyses. Importantly, these phenotypic analyses revealed that the B1 SOX proteins regulate the following distinct processes: (1) early dorsoventral patterning by controlling bmp2b/7; (2) gastrulation movements via the regulation of pcdh18a/18b and wnt11, a non-canonical Wnt ligand gene; (3) neural differentiation by regulating the Hes-class bHLH gene her3 and the proneural-class bHLH genes neurog1 (positively) and ascl1a (negatively), and regional transcription factor genes, e.g., hesx1, zic1, and rx3; and (4) neural patterning by regulating signaling pathway genes, cyp26a1 in RA signaling, oep in Nodal signaling, shh, and mdkb. Chromatin immunoprecipitation analysis of the her3, hesx1, neurog1, pcdh18a, and cyp26a1 genes further suggests a direct regulation of these genes by B1 SOX. We also found an interesting overlap between the early phenotypes of the B1 sox quadruple knockdown embryos and the maternal-zygotic spg embryos that are devoid of pou5f1 activity. These findings indicate that the B1 SOX proteins control a wide range of developmental regulators in the early embryo through partnering in part with Pou5f1 and possibly with other factors, and suggest that the B1 sox functions are central to coordinating cell fate specification with patterning and morphogenetic processes occurring in the early embryo

Use of satellite observations for operational oceanography: recent achievements and future prospects

The paper gives an overview of the development of satellite oceanography over the past five years focusing on the most relevant issues for operational oceanography. Satellites provide key essential variables to constrain ocean models and/or serve downstream applications. New and improved satellite data sets have been developed and have directly improved the quality of operational products. The status of the satellite constellation for the last five years was, however, not optimal. Review of future missions shows clear progress and new research and development missions with a potentially large impact for operational oceanography should be demonstrated. Improvement of data assimilation techniques and developing synergetic use of high resolution satellite observations are important future priorities

Design and Synthesis of a Quintessential Self-Transmissible IncX1 Plasmid, pX1.0

DNA exchange in bacteria via conjugative plasmids is believed to be among the most important contributing factors to the rapid evolution- and diversification rates observed in bacterial species. The IncX1 plasmids are particularly interesting in relation to enteric bacteria, and typically carry genetic loads like antibiotic resistance genes and virulence factors. So far, however, a “pure” version of these molecular parasites, without genetic loads, has yet to be isolated from the environment. Here we report the construction of pX1.0, a fully synthesized IncX1 plasmid capable of horizontal transfer between different enteric bacteria. The designed pX1.0 sequence was derived from the consensus gene content of five IncX1 plasmids and three other, more divergent, members of the same phylogenetic group. The pX1.0 plasmid was shown to replicate stably in E. coli with a plasmid DNA per total DNA ratio corresponding to approximately 3–9 plasmids per chromosome depending on the growth phase of the host. Through conjugation, pX1.0 was able to self-transfer horizontally into an isogenic strain of E. coli as well as into two additional species belonging to the family Enterobacteriaceae. Our results demonstrate the immediate applicability of recent advances made within the field of synthetic biology for designing and constructing DNA systems, previously existing only in silica

Exportin 4 Interacts with Sox9 through the HMG Box and Inhibits the DNA Binding of Sox9

Sox9 is a transcription factor that is required for tissue development in mammals. In general, such transcription factors require co-regulators for precise temporal and spatial control of the activation and inactivation of the numerous genes necessary for precise development during embryogenesis. Here we identify a new Sox9 co-regulator: Using affinity chromatography with immobilized Sox9 protein, we identified exportin 4 (Exp4) as an interacting protein of Sox9 in human cultured cells. Interaction between endogenous Exp4 and Sox9 proteins was confirmed in the human osteosarcoma U2OS cells by immunoprecipitation experiments using anti-Sox9 antibody. siRNA depletion of Exp4 enhanced transcription of Sox9 target genes in U2OS cells, but did not affect nuclear localization of Sox9. These results suggest that Exp4 regulates Sox9 activity in the nucleus. Furthermore we found that the HMG box of Sox9 was responsible for binding to Exp4, and the HMG box was required for suppression of Sox9-mediated transcription. This contrasts with the known Sox9 co-regulators which bind to its transcriptional activation domain. Chromatin immunoprecipitation analyses revealed that Exp4 prevents Sox9 binding to the enhancers of its target genes. These results demonstrate that Exp4 acts as a Sox9 co-regulator that directly regulates binding of Sox9 to its target genes

SOX2 is frequently downregulated in gastric cancers and inhibits cell growth through cell-cycle arrest and apoptosis

SOX transcription factors are essential for embryonic development and play critical roles in cell fate determination, differentiation and proliferation. We previously reported that the SOX2 protein is expressed in normal gastric mucosae but downregulated in some human gastric carcinomas. To clarify the roles of SOX2 in gastric carcinogenesis, we carried out functional characterisation of SOX2 in gastric epithelial cell lines. Exogenous expression of SOX2 suppressed cell proliferation in gastric epithelial cell lines. Flow cytometry analysis revealed that SOX2-overexpressing cells exhibited cell-cycle arrest and apoptosis. We found that SOX2-mediated cell-cycle arrest was associated with decreased levels of cyclin D1 and phosphorylated Rb, and an increased p27Kip1 level. These cells exhibited further characteristics of apoptosis, such as DNA laddering and caspase-3 activation. SOX2 hypermethylation signals were observed in some cultured and primary gastric cancers with no or weak SOX2 expression. Among the 52 patients with advanced gastric cancers, those with cancers showing SOX2 methylation had a significantly shorter survival time than those without this methylation (P=0.0062). Hence, SOX2 plays important roles in growth inhibition through cell-cycle arrest and apoptosis in gastric epithelial cells, and the loss of SOX2 expression may be related to gastric carcinogenesis and poor prognosis