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: Chemical ozone loss in the Arctic stratosphere was investigated for the twelve years between 1991 and 2003 employing the ozone-tracer correlation method. For this method, the change in the relation between ozone and a long-lived tracer is considered for all twelve years over the lifetime of the polar vortex to calculate chemical ozone loss. Both the accumulated local ozone loss in the lower stratosphere and the column ozone loss were derived consistently, mainly on the basis of HALOE satellite observations. HALOE measurements do not cover the polar region homogeneously over the course of the winter. Thus, to derive an early winter reference function for each of the twelve years, all available measurements were additionally used; for two winters climatological considerations were necessary. Moreover, a detailed quantification of uncertainties was performed. This study further demonstrates the interaction between meteorology and ozone loss. The connection between temperature conditions and chlorine activation, and in turn, the connection between chlorine activation and ozone loss, becomes obvious in the HALOE HCl measurements. Additionally, the degree of homogeneity of ozone loss within the vortex was shown to depend on the meteorological conditions. Results derived here are in general agreement with the results obtained by other methods for deducing polar ozone loss. Differences occur mainly owing to different time periods considered in deriving accumulated ozone loss. However, very strong ozone losses as deduced from SAOZ for January in winters 1993-1994 and 1995-1996 cannot be identified using available HALOE observations in the early winter. In general, strong accumulated ozone loss was found to occur in conjunction with a strong cold vortex containing a large volume of possible PSC existence (VPSC), whereas moderate ozone loss was found if the vortex was less strong and moderately warm. Hardly any ozone loss was calculated for very warm winters with small amounts of VPSC during the entire winter. This study supports the linear relationship between VPSC and the accumulated ozone loss reported by Rex et al. (2004) if VPSC was averaged over the entire winter period. Here, further meteorological factors controlling ozone loss were additionally identified if VPSC was averaged over the same time interval as that for which the accumulated ozone loss was deduced. A significant difference in ozone loss (of ≈36DU) was found due to the different duration of solar illumination of the polar vortex of at maximum 4 hours per day in the observed years. Further, the increased burden of aerosols in the atmosphere after the Pinatubo volcanic eruption in 1991 significantly increased the extent of chemical ozone loss.

Description: The MIPAS instrument onboard the ESA Envisat satellite operated from July 2002 until April 2012. The infrared limb emission measurements represent a unique dataset of day and night observations of polar stratospheric clouds (PSCs) up to both poles. Cloud detection sensitivity is comparable to spaceborne lidars, and it is possible to classify different cloud types from the spectral measurements in different atmospheric windows regions. Here we present a new PSC classification scheme based on the combination of a well-established two-colour ratio method and multiple 2D brightness temperature difference probability density functions. The method is a simple probabilistic classifier based on Bayes' theorem with a strong independence assumption. The method has been tested in conjunction with a database of radiative transfer model calculations of realistic PSC particle size distributions, geometries, and composition. The Bayesian classifier distinguishes between solid particles of ice and nitric acid trihydrate (NAT), as well as liquid droplets of super-cooled ternary solution (STS). The classification results are compared to coincident measurements from the space borne lidar CALIOP instrument over the temporal overlap of both satellite missions (June 2006 to March 2012). Both datasets show a good agreement for the specific PSC classes, although the viewing geometries, vertical and horizontal resolution are quite different. Discrepancies are observed for the MIPAS ice class. The Bayesian classifier for MIPAS identifies substantially more ice clouds in the southern hemisphere polar vortex than CALIOP. This disagreement is attributed in parts to the difference in the sensitivity on mixed-type clouds. Ice seems to dominate the spectral behaviour in the limb infrared spectra and may cause an overestimation in ice occurrence compared to the real fraction of ice within the PSC area in the polar vortex. The entire MIPAS measurement period was processed with the new classification approach. Examples like the detection of the Antarctic NAT belt during early winter, and its possible link to mountain wave events over the Antarctic Peninsula, which are observed by the AIRS instrument, are highlighting the importance of a climatology of in total 9 southern and 10 northern hemisphere winters. The new dataset is valuable both for detailed process studies, and for comparisons with and improvements of the PSC parameterisations used in chemistry transport and climate models.

Description: Current stratospheric chemical model simulations underestimate substantially the large ozone loss rates that are derived for the Arctic from ozone sondes for January of some years. Until now, no explanation for this discrepancy has been found. Here, we examine the influence of intrusions of mid-latitude air into the polar vortex on these ozone loss estimates. This study focuses on the winter 1991/92, because during this winter the discrepancy between simulated and experimentally derived ozone loss rates is reported to be the largest. Also during the considered period the vortex was disturbed by a strong warming event with large-scale intrusions of mid-latitude air into the polar vortex, which is quite unusual for this time of the year. The study is based on simulations performed with the Chemical Lagrangian Model of the Stratosphere (CLaMS). Two methods for determination the ozone loss are investigated, the so-called vortex average approach and the Match method. The simulations for January 1992 show that the intrusions induce a reduction of vortex average ozone mixing ratio corresponding to a systematic offset of the ozone loss rate of about 12 ppb per day. This should be corrected for in the vortex average method. The simulations further suggest, that these intrusions do not cause a significant bias for the Match method due to effective quality control measures in the Match technique.