ALBERT

Description: Background The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck (Anas platyrhynchos), an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu. Results We provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey. Conclusion Our results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots"). Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies.

Description: Background Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds. Results We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs. Conclusion This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents.

Description: Offshore south central Chile (35° S–42° S), the morphology of the lowermost continental slope and trench floor witnesses a voluminous submarine mass-wasting event. The blocky slide body deposited in the Chile Trench at 73°46´ W 35°35´ S was targeted for study during RRS JAMES COOK Cruise JC23 and termed Reloca Slide. Its size of about 24 km3, its steep and high headscarp, the spatial distribution of slide deposits and the cohesive nature of major slide blocks make it interesting to address the issue of tsunami generation. We have obtained seismic reflection data that partly reveal the internal structure of the slide body. Gravity core samples were retrieved that will allow the slide to be dated and linked to the history of sedimentation and slope stability along this particular segment of the Chilean convergent margin. At present we assume a Holocene age for the sliding event.

Description: A one-dimensional model of Fe speciation and biogeochemistry, coupled with the General Ocean Turbulence Model (GOTM) and a NPZD-type ecosystem model, is applied for the Tropical Eastern North Atlantic Time-Series Observatory (TENATSO) site. Among diverse processes affecting Fe speciation, this study is focusing on investigating the role of dust particles in removing dissolved iron (DFe) by a more complex description of particle aggregation and sinking, and explaining the abundance of organic Fe-binding ligands by modelling their origin and fate. The vertical distribution of different particle classes in the model shows high sensitivity to changing aggregation rates. Using the aggregation rates from the sensitivity study in this work, modelled particle fluxes are close to observations, with dust particles dominating near the surface and aggregates deeper in the water column. POC export at 1000 m is a little higher than regional sediment trap measurements, suggesting further improvement of modelling particle aggregation, sinking or remineralisation. Modelled strong ligands have a high abundance near the surface and decline rapidly below the deep chlorophyll maximum, showing qualitative similarity to observations. Without production of strong ligands, phytoplankton concentration falls to 0 within the first 2 years in the model integration, caused by strong Fe-limitation. A nudging of total weak ligands towards a constant value is required for reproducing the observed nutrient-like profiles, assuming a decay time of 7 years for weak ligands. This indicates that weak ligands have a longer decay time and therefore cannot be modelled adequately in a one-dimensional model. The modelled DFe profile is strongly influenced by particle concentration and vertical distribution, because the most important removal of DFe in deeper waters is colloid formation and aggregation. Redissolution of particulate iron is required to reproduce an observed DFe profile at TENATSO site. Assuming colloidal iron is mainly composed of inorganic colloids, the modelled colloidal to soluble iron ratio is lower that observations, indicating the importance of organic colloids.

Description: During phytoplankton growth a fraction of dissolved inorganic carbon (DIC) assimilated by phytoplankton is exuded in the form of dissolved organic carbon (DOC), which can be transformed into extracellular particulate organic carbon (POC). A major fraction of extracellular POC is associated with carbon of transparent exopolymer particles (TEP; carbon content = TEPC) that form from dissolved polysaccharides (PCHO). The exudation of PCHO is linked to an excessive uptake of DIC that is not directly quantifiable from utilisation of dissolved inorganic nitrogen (DIN), called carbon overconsumption. Given these conditions, the concept of assuming a constant stoichiometric carbon-to-nitrogen (C:N) ratio for estimating new production of POC from DIN uptake becomes inappropriate. Here, a model of carbon overconsumption is analysed, combining phytoplankton growth with TEPC formation. The model describes two modes of carbon overconsumption. The first mode is associated with DOC exudation during phytoplankton biomass accumulation. The second mode is decoupled from algal growth, but leads to a continuous rise in POC while particulate organic nitrogen (PON) remains constant. While including PCHO coagulation, the model goes beyond a purely physiological explanation of building up carbon rich particulate organic matter (POM). The model is validated against observations from a mesocosm study. Maximum likelihood estimates of model parameters, such as nitrogen- and carbon loss rates of phytoplankton, are determined. The optimisation yields results with higher rates for carbon exudation than for the loss of organic nitrogen. It also suggests that the PCHO fraction of exuded DOC was 63±20% during the mesocosm experiment. Optimal estimates are obtained for coagulation kernels for PCHO transformation into TEPC. Model state estimates are consistent with observations, where 30% of the POC increase was attributed to TEPC formation. The proposed model is of low complexity and is applicable for large-scale biogeochemical simulations.

Description: A one-dimensional model of the biogeochemistry and speciation of iron is coupled with the General Ocean Turbulence Model (GOTM) and a NPZD-type ecosystem model. The model is able to simulate the temporal patterns and vertical profiles of dissolved iron (dFe) in the upper ocean at the Bermuda Atlantic Time-series Study site reasonably well. Subsurface model profiles strongly depend on the parameter values chosen for the loss processes for iron, colloidal aggregation and scavenging onto particles. Estimates for these parameters based on observations in particle-rich waters result in depletion of dFe. A high stability constant of iron-binding organic ligands is required to reproduce the observed degree of organic complexation below the mixed layer. The scavenging residence time for iron in the model is shortest in spring and summer, because of the larger abundance of particles, and increases with depth towards values on the order of a hundred years. A solubility of atmospherically deposited iron higher than 2% lead to dFe concentrations incompatible with observations. Despite neglecting ultraviolet radiation, the model produces diurnal variations and mean vertical profiles of H2O2 and iron species that are in good agreement with observations.