ALBERT

Description: The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable region of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Together, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.

Description: Sialic acid groups of protein N -glycans are important determinants of biological activity. Exposed at the end of the glycan chain, they are potential targets for glycan remodeling. Sialyltransferases (STs; EC 2.4.99) are the enzymes that catalyze the sialic acid transfer from a CMP-activated donor on to a carbohydrate acceptor in vivo. Recombinant expression of the full-length human β-galactoside α2,6 sialyltransferase I (ST6Gal-I) was hampered and therefore variants with truncated N-termini were investigated. We report on the distinct properties of two N-terminally truncated versions of ST6Gal-I, namely 89ST6Gal-I and 108ST6Gal-I, which were successfully expressed in human embryonic kidney cells. The different properties of these enzymes result most probably from the loss of interactions from helix α1 in the 108ST6Gal-I variant, which plays a role in acceptor substrate binding. The K m for N -acetyl- d -lactosamine was 10-fold increased for 108ST6Gal-I (84 mM) as compared to 89ST6Gal-I (8.3 mM). The two enzyme variants constitute a suitable tool box for the terminal modification of N -glycans. While the enzyme 89ST6Gal-I exhibited both ST (di-sialylation) and sialidase activity on a monoclonal antibody, the enzyme 108ST6Gal-I showed only ST activity with specificity for mono-sialylation.

Description: We evaluate the spatial and temporal evolution of Earth's long-wavelength surface dynamic topography since the Jurassic using a series of high-resolution global mantle convection models. These models are Earth-like in terms of convective vigour, thermal structure, surface heat-flux and the geographic distribution of heterogeneity. The models generate a degree-2-dominated spectrum of dynamic topography with negative amplitudes above subducted slabs (i.e. circum-Pacific regions and southern Eurasia) and positive amplitudes elsewhere (i.e. Africa, north-western Eurasia and the central Pacific). Model predictions are compared with published observations and subsidence patterns from well data, both globally and for the Australian and southern African regions. We find that our models reproduce the long-wavelength component of these observations, although observed smaller-scale variations are not reproduced. We subsequently define geodynamic rules for how different surface tectonic settings are affected by mantle processes: (i) locations in the vicinity of a subduction zone show large negative dynamic topography amplitudes; (ii) regions far away from convergent margins feature long-term positive dynamic topography; and (iii) rapid variations in dynamic support occur along the margins of overriding plates (e.g. the western US) and at points located on a plate that rapidly approaches a subduction zone (e.g. India and the Arabia Peninsula). Our models provide a predictive quantitative framework linking mantle convection with plate tectonics and sedimentary basin evolution, thus improving our understanding of how subduction and mantle convection affect the spatio-temporal evolution of basin architecture.

Description: Paleogeographic reconstructions are important to understand Earth's tectonic evolution, past eustatic and regional sea level change, hydrocarbon genesis, and to constrain and interpret the dynamic topography predicted by time-dependent global mantle convection models. Several global paleogeographic maps have been compiled and published but they are generally presented as static maps with varying temporal resolution and fixed spatial resolution. Existing global paleogeographic maps are also tied to a particular plate motion model, making it difficult to link them to alternative digital plate tectonic reconstructions. To address this limitation, we developed a workflow to reverse-engineer global paleogeographic maps to their present-day coordinates and enable them to be linked to any tectonic reconstruction. Published paleogeographic compilations are also tied to fixed input datasets. We used fossil data from the Paleobiology Database to identify inconsistencies between fossils paleo-environments and published paleogeographic maps, and to improve the location of inferred terrestrial-marine boundaries by resolving these inconsistencies. As a result, the overall consistency ratio between the paleogeography and fossil collections was improved from 76.9 % to 96.1 %. We estimated the surface areas of global paleogeographic features (shallow marine environments, landmasses, mountains and ice sheets), and reconstructed the global continental flooding history since the late Paleozoic based on the amended paleogeographies. Finally, we discuss the relationships between emerged land area and total continental crust area through time, continental growth models, and strontium isotope (87Sr/86Sr) signatures in ocean water. Our study highlights the flexibility of digital paleogeographic models linked to state-of-the-art plate tectonic reconstructions in order to better understand the interplay of continental growth and eustasy, with wider implications for understanding Earth's paleotopography, ocean circulation, and the role of mantle convection in shaping long-wavelength topography.

Description: Carbon dioxide (CO2) liberated at arc volcanoes that intersect buried carbonate platforms plays a larger role in influencing atmospheric CO2 than those active margins lacking buried carbonate platforms. This study investigates the contribution of carbonate-intersecting arc activity on palaeo-atmospheric CO2 levels over the past 410 million years by integrating a plate motion model with an evolving carbonate platform development model. Our modelled subduction zone lengths and carbonate-intersecting arc lengths approximate arc activity with time, and can be used as input into fully-coupled models of CO2 flux between deep and shallow reservoirs. Continuous and cross-wavelet as well as wavelet coherence analyses were used to evaluate trends between carbonate-intersecting arc activity, non-carbonate-intersecting arc activity and total global subduction zone lengths and the proxy-CO2 record between 410 Ma and the present. Wavelet analysis revealed significant linked periodic behaviour between 75–50 Ma, where global carbonate-intersecting arc activity is relatively high and where peaks in palaeo-atmospheric CO2 is correlated with peaks in global carbonate-intersecting arc activity, characterised by a ~ 32 Myr periodicity and a 10 Myr lag of CO2 peaks after carbonate-intersecting arc length peaks. The linked behaviour may suggest that the relative abundance of carbonate-intersecting arcs played a role in affecting global climate during the Late Cretaceous to Early Paleogene greenhouse. At all other times, atmospheric CO2 emissions from carbonate-intersecting arcs were not correlated with the proxy-CO2 record. Our analysis did not support the idea that carbonate-intersecting arc activity is more important than non-carbonate intersecting arc activity in driving changes in palaeo-atmospheric CO2 levels. This suggests that tectonic controls are more elaborate than the subduction-related volcanic emissions component or that other feedback mechanisms between the geosphere, atmosphere and biosphere played larger roles in modulating climate in the Phanerozoic.

Description: Paleogeographic reconstructions are important to understand Earth's tectonic evolution, past eustatic and regional sea level change, paleoclimate and ocean circulation, deep Earth resources and to constrain and interpret the dynamic topography predicted by mantle convection models. Global paleogeographic maps have been compiled and published, but they are generally presented as static maps with varying map projections, different time intervals represented by the maps and different plate motion models that underlie the paleogeographic reconstructions. This makes it difficult to convert the maps into a digital form and link them to alternative digital plate tectonic reconstructions. To address this limitation, we develop a workflow to restore global paleogeographic maps to their present-day coordinates and enable them to be linked to a different tectonic reconstruction. We use marine fossil collections from the Paleobiology Database to identify inconsistencies between their indicative paleoenvironments and published paleogeographic maps, and revise the locations of inferred paleo-coastlines that represent the estimated maximum transgression surfaces by resolving these inconsistencies. As a result, the consistency ratio between the paleogeography and the paleoenvironments indicated by the marine fossil collections is increased from an average of 75 % to nearly full consistency (100 %). The paleogeography in the main regions of North America, South America, Europe and Africa is significantly revised, especially in the Late Carboniferous, Middle Permian, Triassic, Jurassic, Late Cretaceous and most of the Cenozoic. The global flooded continental areas since the Early Devonian calculated from the revised paleogeography in this study are generally consistent with results derived from other paleoenvironment and paleo-lithofacies data and with the strontium isotope record in marine carbonates. We also estimate the terrestrial areal change over time associated with transferring reconstruction, filling gaps and modifying the paleogeographic geometries based on the paleobiology test. This indicates that the variation of the underlying plate reconstruction is the main factor that contributes to the terrestrial areal change, and the effect of revising paleogeographic geometries based on paleobiology is secondary.

Description: We investigate the extent to which commonly considered quantities, based on total column ozone observations and simulations, are applicable as measures of ozone loss in the polar vortices. Such quantities have been used frequently in ozone assessments by the World Meteorological Organization (WMO) and to assess the performance of chemistry-climate models. The most commonly considered quantity is monthly mean column ozone poleward of a latitude of 63° in spring. For the Arctic, these monthly means were found to be insensitive to the exact choice of the latitude threshold, unlike the Antarctic where greater sensitivity was found. Choosing a threshold based on the location of the transport barrier at the vortex boundary instead of geometric latitude led to a roughly similar year-to-year variability of the monthly means, but in particular years deviations of several tens of Dobson units occurred. Moreover, the minimum of daily total ozone minima poleward of a particular latitude, another popular measure, is debatable, insofar as it relies on one single measurement or model grid point. For Arctic conditions, this minimum value occurred often in air outside polar vortex, both in the observations and in a chemistry-climate model. As a result, we recommend that the minimum of daily minima no longer be used when comparing polar ozone loss in observations and models. As a possible alternative, we suggest considering the minimum of daily average total ozone poleward of a particular equivalent latitude (or in the vortex) in spring. This definition both obviates relying on one single data point and reduces the impact of year-to-year variability in the Arctic vortex breakup on ozone loss measures. However, compact relations of such simple measures with meteorological quantities that describe the potential for polar heterogeneous chlorine activation and thus ozone loss were not found. Therefore, we argue that where possible, more sophisticated measures of chemical polar ozone loss that include additional information to disentangle the impact of transport and chemistry on ozone, should be employed.

Description: The Satellite Application Facility on Climate Monitoring (CM-SAF) aims at the provision of satellite-derived geophysical parameter data sets suitable for climate monitoring. CM-SAF provides climatologies for Essential Climate Variables (ECV), as required by the Global Climate Observing System implementation plan in support of the UNFCCC. Several cloud parameters, surface albedo, radiation fluxes at the top of the atmosphere and at the surface as well as atmospheric temperature and humidity products form a sound basis for climate monitoring of the atmosphere. The products are categorized in monitoring data sets obtained in near real time and data sets based on carefully intercalibrated radiances. The CM-SAF products are derived from several instruments on-board operational satellites in geostationary and polar orbit, i.e., the Meteosat and NOAA satellites, respectively. The existing data sets will be continued using data from the instruments on-board the new EUMETSAT Meteorological Operational satellite (MetOP). The products have mostly been validated against several ground-based data sets both in situ and remotely sensed. The accomplished accuracy for products derived in near real time is sufficient to monitor variability on diurnal and seasonal scales. Products based on intercalibrated radiance data can also be used for climate variability analysis up to inter-annual scale. A central goal of the recently started Continuous Development and Operations Phase of the CM-SAF (2007–2012) is to further improve all CM-SAF data sets to a quality level that allows for studies of inter-annual variability.

Description: Satellite observations show that the enormous solar proton events (SPEs) in October–November 2003 had significant effects on the composition of the stratosphere and mesosphere in the polar regions. After the October–November 2003 SPEs and in early 2004 significant enhancements of NOx(=NO+NO2) in the upper stratosphere and lower mesosphere in the Northern Hemisphere were observed by several satellite instruments. Here we present global full chemistry calculations performed with the CLaMS model to study the impact of mesospheric NOx intrusions on Arctic polar ozone loss processes in the stratosphere. Several model simulations are preformed with different upper boundary conditions for NOx at 2000 K potential temperature (≈50 km altitude). In our study we focus on the impact of the non-local production of NOx which means the downward transport of enhanced NOx from the mesosphere in the stratosphere. The local production of NOx in the stratosphere is neglected. Our findings show that intrusions of mesospheric air into the stratosphere, transporting high burdens of NOx, affect the composition of the Arctic polar region down to about 400 K (≈17–18 km). We compare our simulated NOx and O3 mixing ratios with satellite observations by ACE-FTS and MIPAS processed at IMK/IAA and derive an upper limit for the ozone loss caused by enhanced mesospheric NOx. Our findings show that in the Arctic polar vortex (Equivalent Lat.〉70° N) the accumulated column ozone loss between 350–2000 K potential temperature (≈14–50 km altitude) caused by the SPEs in October–November 2003 in the stratosphere is up to 3.3 DU with an upper limit of 5.5 DU until end of November. Further we found that about 10 DU but lower than 18 DU accumulated ozone loss additionally occurs until end of March 2004 caused by the transport of mesospheric NOx-rich air in early 2004. In the lower stratosphere (350–700 K≈14–27 km altitude) the SPEs of October–November 2003 have negligible small impact on ozone loss processes until end of November and the mesospheric NOx intrusions in early 2004 yield ozone loss about 3.5 DU, but clearly lower than 6.5 DU until end of March. Overall, the non-local production of NOx is an additional variability to the existing variations of the ozone loss observed in the Arctic.