ALBERT

Description: he use and development of post-genomic tools naturally depends on large-scale genome sequencing projects. The usefulness of post-genomic applications is dependent on the accuracy of genome annotations, for which the correct identification of intron-exon borders in complex genomes of eukaryotic organisms is often an error-prone task. Although automated algorithms for predicting intron-exon structures are available, supporting exon evidence is necessary to achieve comprehensive genome annotation. Besides cDNA and EST support, peptides identified via MS/MS can be used as extrinsic evidence in a proteogenomic approach. We describe an improved version of the Genomic Peptide Finder (GPF), which aligns de novo predicted amino acid sequences to the genomic DNA sequence of an organism while correcting for peptide sequencing errors and accounting for the possibility of splicing. We have coupled GPF and the gene finding program AUGUSTUS in a way that provides automatic structural annotations of the Chlamydomonas reinhardtii genome, using highly unbiased GPF evidence. A comparison of the AUGUSTUS gene set incorporating GPF evidence to the standard JGI FM4 (Filtered Models 4) gene set reveals 932 GPF peptides that are not contained in the Filtered Models 4 gene set. Furthermore, the GPF evidence improved the AUGUSTUS gene models by altering 65 gene models and adding three previously unidentified genes.

Description: The region offshore Eastern Java represents one of the few places where the early stage of oceanic plateau subduction is occurring. We study the little investigated Roo Rise oceanic plateau on the Indian plate, subducting beneath Eurasia. The presence of the abnormal bathymetric features entering the trench has a strong effect on the evolution of the subduction system, and causes additional challenges on the assessment of geohazard risks. We present integrated results of a refraction/wide-angle reflection tomography, gravity modelling, and multichannel reflection seismic imaging using data acquired in 2006 south of Java near 113°E. The composite structural model reveals the previously unresolved deep geometry of the oceanic plateau and the subduction zone. The oceanic plateau crust is on average 15 km thick and covers an area of about 100 000 km2. Within our profile the Roo Rise crustal thickness ranges between 18 and 12 km. The upper oceanic crust shows high degree of fracturing, suggesting heavy faulting. The forearc crust has an average thickness of 14 km, with a sharp increase to 33 km towards Java, as revealed by gravity modelling. The complex geometry of the backstop suggests two possible models for the structural formation within this segment of the margin: either accumulation of the Roo Rise crustal fragments above the backstop or alternatively uplift of the backstop caused by basal accumulation of crustal fragments. The subducting plateau is affecting the stress field within the accretionary complex and the backstop edge, which favours the initiation of large, potentially tsunamogenic earthquakes such as the 1994 Mw= 7.8 tsunamogenic event.

Description: All climate models predict a freshening of the North Atlantic at high latitude that may induce an abrupt change of the Atlantic Meridional Overturning Circulation (hereafter AMOC) if it resides in the bistable regime, where both a strong and a weak state coexist. The latter remains uncertain as there is no consensus among observations and ocean reanalyses, where the AMOC is bistable, versus most climate models that reproduce a mono-stable strong AMOC. A series of four hindcast simulations of the global ocean at 1/12° resolution, which is presently unique, are used to diagnose freshwater transport by the AMOC in the South Atlantic, an indicator of AMOC bistability. In all simulations, the AMOC resides in the bistable regime: it exports freshwater southward in the South Atlantic, implying a positive salt advection feedback that would act to amplify a decreasing trend in subarctic deep water formation as projected in climate scenarios.

Description: Monthly zonal mean climatologies of atmospheric measurements from satellite instruments can have biases due to the non-uniform sampling of the atmosphere by the instruments. We characterize potential sampling biases in stratospheric trace gas climatologies of the Stratospheric Processes and their Role in Climate (SPARC) Data Initiative using chemical fields from a chemistry climate model simulation and sampling patterns from 16 satellite-borne instruments. The exercise is performed for the long-lived stratospheric trace gases O3 and H2O. Monthly sample biases for O3 exceed 10% for many instruments in the high latitude stratosphere and in the upper troposphere/lower stratosphere, while annual mean sampling biases reach values of up to 20% in the same regions for some instruments. Sampling biases for H2O are generally smaller than for O3, although still notable in the upper troposphere/lower stratosphere and Southern Hemisphere high latitudes. The most important mechanism leading to monthly sampling bias is the non-uniform temporal sampling of many instruments, i.e., the fact that for many instruments, monthly means are produced from measurements which span less than the full month in question. Similarly, annual mean sampling biases are well explained by non-uniformity in the month-to-month sampling by different instruments. Non-uniform sampling in latitude and longitude are shown to also lead to non-negligible sampling biases, which are most relevant for climatologies which are otherwise free of sampling biases due to non-uniform temporal sampling.

Description: Large volumes of magma emplaced within sedimentary basins have been linked to multiple climate change events due to release of greenhouse gases such as CH4. Basin-scale estimates of thermogenic methane generation show that this process alone could generate enough greenhouse gases to trigger global incidents. However, the rates at which these gases are transported and released into the atmosphere are quantitatively unknown. We use a 2D, hybrid FEM/FVM model that solves for fully compressible fluid flow to quantify the thermogenic release and transport of methane and to evaluate flow patterns within these systems. Our results show that the methane generation potential in systems with fluid flow does not significantly differ from that estimated in diffusive systems. The values diverge when vigorous convection occurs with a maximum variation of about 50%. The fluid migration pattern around a cooling, impermeable sill alone generates hydrothermal plumes without the need for other processes such as boiling and/or explosive degassing. These fluid pathways are rooted at the edges of the outer sills consistent with seismic imaging. Methane venting at the surface occurs in three distinct stages and can last for hundreds of thousands of years. Our simulations suggest that although the quantity of methane potentially generated within the contact aureole can cause catastrophic climate change, the rate at which this methane is released into the atmosphere is too slow to trigger, by itself, some of the negative δ13C excursions observed in the fossil record over short time scales (〈 10,000 years).

Description: High-resolution 3-D seismic data acquired in the Sea of Marmara on the Western High, along the northwestern branch of the North Anatolian Fault (also known as the Main Marmara Fault), shed new light on the evolution of the deformation over the last 500–600 ka. Sedimentary sequences in ponded basins are correlated with glacioeustatic cycles and transitions between marine and low sea/lake environments in the Sea of Marmara. In the 3 × 11 km2 of the 3-D seismic survey, deformation over the last 405–490 ka is localized along the main fault branch and north of it, where N130°–N140° trending normal faults and N40°–N50° folding accommodated strike-slip deformation associated with active argillokinesis. There is some evidence that deformation was more distributed further back in the past, at least over the depth range (〈600 m below seafloor) of our survey. A N110° basin and buried ridge system were eventually cut by the presently active fault. The southern part of the basin was then uplifted, while the northern part was folded but continued to subside along the fault. A mass transport deposits complex dated between 405–490 ka shows a lateral displacement of 7.7 ± 0.3 km, corresponding to an estimated slip rate of 15.1–19.7 mm/a. We conclude that this strand of the Main Marmara Fault on the Western High has taken up most of the strike slip motion between the Anatolian and Eurasian plates over the last 405 ka at least.

Description: Storfjorden, which hosts a latent heat polynya, is a well known region of dense water formation. This Brine-enriched Shelf Water (BSW) displays substantial year to year variability in its properties, which is partly linked to interannual variations in ice production. Here we have developed a model based on high-resolution AMSR-E satellite sea-ice concentration data, available between 2002 and 2011, and atmospheric forcing to estimate the ice production in the polynya and associated salt release. The average modeled ice production for the epoch 2002–2011 is 47 km3 per year, corresponding to a salt release of 1200 × 109 kg. The two most anomalous winters were 2004–2005 (salt deficit of −367 × 109 kg) and 2007–2008 (salt excess of 398 × 109 kg). Available observations of BSW properties are relatively scarce during this period and are here augmented with data collected in March 2007 from an ice-tethered mooring to the northwest of the fjord. BSW was found up to the surface, with maximum salinity and density of 35.27 and 28.4 kg m−3, respectively, at 55 m. In addition, supercooled water was found down to 10 m under relatively mild atmospheric conditions. It is shown to have formed a week before, during an intense frazil ice formation episode, exceeding 2 km3 of frazil ice according to the model. Although observations remain too few to robustly assess the relation between ice production and BSW properties, there is suggestion of a direct impact for most anomalous years. The exceptional ice production in 2007–2008 is most likely the cause of the very saline BSW in 2008 and strong plume of dense water toward Fram Strait reported by other authors. Anomalous ice production appears predominantly driven by the duration of the freezing season and anomalous opening of the polynya.

Description: A critical question regarding the organic carbon cycle in the Arctic Ocean is whether the decline in ice extent and thickness and the associated increase in solar irradiance in the upper ocean will result in increased primary production and particulate organic carbon (POC) export. To assess spatial and temporal variability in POC export, under-ice export fluxes were measured with short-term sediment traps in the northern Laptev Sea in July-August-September 1995, north of the Fram Strait in July 1997, and in the Central Arctic in August–September 2012. Sediment traps were deployed at 2–5 m and 20–25 m under ice for periods ranging from 8.5 to 71 h. In addition to POC fluxes, total particulate matter, chlorophyll a, biogenic particulate silica, phytoplankton, and zooplankton fecal pellet fluxes were measured to evaluate the amount and composition of the material exported in the upper Arctic Ocean. Whereas elevated export fluxes observed on and near the Laptev Sea shelf were likely the combined result of high primary production, resuspension, and release of particulate matter from melting ice, low export fluxes above the central basins despite increased light availability during the record minimum ice extent of 2012 suggest that POC export was limited by nutrient supply during summer. These results suggest that the ongoing decline in ice cover affects export fluxes differently on Arctic shelves and over the deep Arctic Ocean and that POC export is likely to remain low above the central basins unless additional nutrients are supplied to surface waters.

Description: The atmospheric deposition of both macronutrients and micronutrients plays an important role in driving primary productivity, particularly in the low-latitude ocean. We report aerosol major ion measurements for five ship-based sampling campaigns in the western Pacific from similar to 25 degrees N to 20 degrees S and compare the results with those from Atlantic meridional transects (similar to 50 degrees N to 50 degrees S) with aerosols collected and analyzed in the same laboratory, allowing full incomparability. We discuss sources of the main nutrient species (nitrogen (N), phosphorus (P), and iron (Fe)) in the aerosols and their stoichiometry. Striking north-south gradients are evident over both basins with the Northern Hemisphere more impacted by terrestrial dust sources and anthropogenic emissions and the North Atlantic apparently more impacted than the North Pacific. We estimate the atmospheric supply rates of these nutrients and the potential impact of the atmospheric deposition on the tropical western Pacific. Our results suggest that the atmospheric deposition is P deficient relative to the needs of the resident phytoplankton. These findings suggest that atmospheric supply of N, Fe, and P increases primary productivity utilizing some of the residual excess phosphorus (P*) in the surface waters to compensate for aerosol P deficiency. Regional primary productivity is further enhanced via the stimulation of nitrogen fixation fuelled by the residual atmospheric iron and P*. Our stoichiometric calculations reveal that a P* of 0.1 mu mol L-1 can offset the P deficiency in atmospheric supply for many months. This study suggests that atmospheric deposition may sustain similar to 10% of primary production in both the western tropical Pacific.