Enzyme-mediated spatial segregation on individual polymeric support beads: application to generation and screening of encoded combinatorial libraries.

Proteolysis of short N alpha-protected peptide substrates bound to polyoxyethylene-polystyrene beads releases selectively free amino sites in the enzyme-accessible "surface" area. The substantial majority of functional sites in the "interior" of the polymeric support are not reached by the enzyme and remain uncleaved (protected). Subsequent synthesis with two classes of orthogonal protecting groups-N alpha-tert-butyloxycarbonyl (Boc) and N alpha-9-fluorenylmethyloxy-carbonyl (Fmoc)-allows generation of two structures on the same bead. The surface structure is available for receptor interactions, whereas the corresponding interior structure is used for coding. Coding structures are usually readily sequenceable peptides. This "shaving" methodology was illustrated by the preparation of a peptide-encoded model peptide combinatorial library containing 1.0 x 10(5) members at approximately 6-fold degeneracy. From this single library, good ligands were selected for three different receptors: anti-beta-endorphin anti-body, streptavidin, and thrombin, and the binding structures were deduced correctly by sequencing the coding peptides present on the same beads.

Characterization of spatial–temporal patterns in dynamic speckle sequences using principal component analysis

Abstract. Speckle is being used as a characterization tool for the analysis of the dynamics of slow-varying phenomena occurring in biological and industrial samples at the surface or near-surface regions. The retrieved data take the form of a sequence of speckle images. These images contain information about the inner dynamics of the biological or physical process taking place in the sample. Principal component analysis (PCA) is able to split the original data set into a collection of classes. These classes are related to processes showing different dynamics. In addition, statistical descriptors of speckle images are used to retrieve information on the characteristics of the sample. These statistical descriptors can be calculated in almost real time and provide a fast monitoring of the sample. On the other hand, PCA requires a longer computation time, but the results contain more information related to spatial–temporal patterns associated to the process under analysis. This contribution merges both descriptions and uses PCA as a preprocessing tool to obtain a collection of filtered images, where statistical descriptors are evaluated on each of them. The method applies to slow-varying biological and industrial processes.

Short Communication Over-Winter Channel Bed Temperature Regimes Generated by Contrasting Snow Accumulation in a High Arctic River

We report experimental results of near-surface winter temperatures along and adjacent to the channel bed of a High Arctic river on Melville Island, Canada. Temperature loggers 5cm below the ground surface in areas where the terrain suggests varying snow accumulation patterns revealed that the maximum winter difference between air and near-surface temperatures ranged from 0 to +30°C during the winter of 2012–13, and that shallow near-surface freezing conditions were delayed for up to 21 days in some locations. Cooling to -10°C was delayed for up to 117 days. Modelled temperature at the top of permafrost indicates that permafrost at locations with thick snow can be up to 8°C warmer than those with thin snow. This thermal evidence for an ameliorated surface environment indicates the potential for substantial extended microbial and biogeochemical cycling during early winter. Rapid thaw of the bed during initiation of snowmelt in spring also indicates a high degree of hydrological connectivity. Therefore, snow-filled channels may contribute to biogeochemical and aquatic cycling in High Arctic rivers.

Catchment characteristics and soil and water chemistry of the San Francisco basin and subbasins, Ecuador

In this study, the Mean Transit Time and Mixing Model Analysis methods are combined to unravel the runoff generation process of the San Francisco River basin (73.5 km**2) situated on the Amazonian side of the Cordillera Real in the southernmost Andes of Ecuador. The montane basin is covered with cloud forest, sub-páramo, pasture and ferns. Nested sampling was applied for the collection of streamwater samples and discharge measurements in the main tributaries and outlet of the basin, and for the collection of soil and rock water samples. Weekly to biweekly water grab samples were taken at all stations in the period April 2007-November 2008. Hydrometric data, Mean Transit Time and Mixing Model Analysis allowed preliminary evaluation of the processes controlling the runoff in the San Francisco River basin. Results suggest that flow during dry conditions mainly consists of lateral flow through the C-horizon and cracks in the top weathered bedrock layer, and that all subcatchments have an important contribution of this deep water to runoff, no matter whether pristine or deforested. During normal to low precipitation intensities, when antecedent soil moisture conditions favour water infiltration, vertical flow paths to deeper soil horizons with subsequent lateral subsurface flow contribute most to streamflow. Under wet conditions in forested catchments, streamflow is controlled by near surface lateral flow through the organic horizon. Exceptionally, saturation excess overland flow occurs. By absence of the litter layer in pasture, streamflow under wet conditions originates from the A horizon, and overland flow.

Organic geochemistry on sediment profiles from the Arctic Ocean

During the ARCTIC '91-Expedition with RV 'Polarstern', several Multicorer and Kastenlot-cores were recovered along a profile crossing the eastern part of the Arctic Ocean. The investigated cores consist mainly of clayey-silty sediments, and some units with a higher sand content. In this thesis, detailed sedimentological and organic-geochemical investigations were performed. In part, the near surface sediments were AMS-14C dated making it possible to Interpret the results of the organic-geochemical investigations in terms of climatic changes (isotopic stage 2 to the Holocene). The more or less absence of foraminifers within the long cores prevented the development of an oxygen isotope stratigraphy. Only the results of core PS2174-5 from the Amundsen-Basin could be discussed in terms of the climatic change that could be dated back to oxygen isotope stage 7. Detailed organic-geochemical investigations in the central Arctic Ocean are rare. Therefore, several different organic-geochemical methods were used to obtain a wide range of data for the Interpretation of the organic matter. The high organic carbon content of the surface sediments is derived from a high input of terrigenous organic matter. The terrigenous organic material is most likely entrained within the sea-ice On the Siberian shelves and released during ice-drift over the Arctic Ocean. Other factors such as iceberg-transport and turbidites are also responsible for the high input of terrigenous organic matter. Due to the more or less closed sea-ice Cover, the Arctic Ocean is known as a low productivity system. A model shows, that only 2 % of the organic matter in central Arctic Ocean sediments is of a marine origin. The influence of the West-Spitsbergen current increases the marine organic matter content to 16 %. Short chain n-alkanes (C17 and C19) can be used as a marker of marine productivity in the Arctic Ocean. Higher contents of short chain n-alkanes exist in surface sediments of the Lomonosov-Ridge and the Makarov-Basin, indicating a higher marine productivity caused by a reduced sea-ice Cover. The Beaufort-Gyre and Transpolar-Drift drift Patterns could be responsible for the lower sea-ice distribution in this region. The sediments of Stage 2 and Stage 3 in this region are also dominated by a higher content of short chain-nalkanes indicating a comparable ice-drift Pattern during that time. The content and composition of organic carbon in the sediments of core PS2174-5 reflect glaciallinterglacial changes. Interglacial stages 7 and 5e show a low organic carbon content (C 0,5 %) and, as indicated by high hydrogen-indices, low CIN-ratios, higher content of n-alkanes (C17 and C19) and a higher opal content, a higher marine productivity. In the Holocene, a high content of foraminifers, coccoliths, ostracodes, and sponge spicules indicate higher surface-water productivity. Nevertheless, the low hydrogenindices reveal a high content of terrigenous organic matter. Therefore, the Holocene seems to be different from interglacials 7 and 5e. During the glacial periods (stages 6, upper 5, and 4), TOC-values are significantly higher (0.7 to 1.3 %). In addition, low hydrogen-indices, high CIN-ratios, low short chain n-alkanes and opal contents provide evidence for a higher input of terrigenous organic matter and reduced marine productivity. The high lignin content in core sections with high TOC-contents, substantiates the high input of terrigenous organic matter. Changes in the content and composition of the organic carbon is believed to vary with the fluctuations in sea-level and sea-ice coverage.

Composition of micronodules and host sediments from the Guatemala Basin

A complex of mineralogical techniques used in studies of near-surface layer hemipelagic sediments indicates that disordered todorokite and hexagonal birnessite dominate in manganese micronodules, whereas hexagonal birnessite is the main phase of micronodules from miopelagic sediments. Content of todorokite increases downward through the miopelagic sedimentary sequence; this can be reasonably explained by transformations of some other manganese minerals to todorokite. Occurrence of several manganese minerals in studied samples may reflect temporal and lateral variations in C_org content in sediments and respective local fluctuations in environmental conditions (pH, Eh, geochemical activity of Mn, etc.). Todorokite may have formed under the most anoxic conditions near the water-sediment interface.

Characteristics of samples obtained during the expedition to Bolshoy Lyakhovsky Island in July/August 2014

The German-Russian project CARBOPERM - Carbon in Permafrost, origin, quality, quantity, and degradation and microbial turnover - is devoted to studying soil organic matter history, degradation and turnover in coastal lowlands of Northern Siberia. The multidisciplinary project combines research from various German and Russian institutions and runs from 2013 to 2016. The project aims assessing the recent and the ancient trace gas budget over tundra soils in northern Siberia. Studied field sites are placed in the permafrost of the Lena Delta and on Bol'shoy Lyakhovsky, the southernmost island of the New Siberian Archipelago in the eastern Laptev Sea. Field campaigns to Bol'shoy Lyakhovsky in 2014 (chapter 2) were motivated by research on palaeoenvironmental and palaeoclimate reconstruction, sediment dating, near surface geophysics and microbiological research. In particular the field campaigns focussed on: - coring Quaternary strata with a ages back to ~200.000 years ago as found along the southern coast; they allow tracing microbial communities and organic tracers (i.e. lipids and biomarkers, sedimentary DNA) in the deposits across two climatic cycles (chapter 3), - instrumenting a borehole with a thermistor chain for measuring permafrost temperatures (chapter 3), - sampling Quaternary strata for dating permafrost formation periods based on the optical stimulated luminescence (OSL) technique (chapter 4), - sampling soil and geologic formations for carbon content in order to highlight potential release of CO2 and methane based on incubation experiments (chapter 5), - profiling near surface permafrost using ground-penetrating radar and geoelectrics for defining the spatial depositional context, where the cores are located (chapters 6 + 7).

Rock magnetic records and geochemical methods of sediment cores off NW Africa

Two gravity cores retrieved off NW Africa at the border of arid and subtropical environments (GeoB 13602-1 and GeoB 13601-4) were analyzed to extract records of Late Quaternary climate change and sediment export. We apply End Member (EM) unmixing to 350 acquisition curves of isothermal remanent magnetization (IRM). Our approach enables to discriminate rock magnetic signatures of aeolian and fluvial material, to determine biomineralization and reductive diagenesis. Based on the occurrence of pedogenically formed magnetic minerals in the fluvial and aeolian EMs, we can infer that goethite formed in favor to hematite in more humid climate zones. The diagenetic EM dominates in the lower parts of the cores and within a thin near-surface layer probably representing the modern Fe**2+/Fe**3+ redox boundary. Up to 60% of the IRM signal is allocated to a biogenic EM underlining the importance of bacterial magnetite even in siliciclastic sediments. Magnetosomes are found well preserved over most of the record, indicating suboxic conditions. Temporal variations of the aeolian and fluvial EMs appear to faithfully reproduce and support trends of dry and humid conditions on the continent. The proportion of aeolian to fluvial material was dramatically higher during Heinrich Stadials, especially during Heinrich Stadial 1. Dust export from the Arabian-Asian corridor appears to vary contemporaneous to increased dust fluxes on the continental margin of NW Africa emphasizing that melt-water discharge in the North Atlantic had an enormous impact on atmospheric dynamics.

Radionuclides measured on water bottle samples

Actinium is one of the rarest naturally occurring elements on earth. We measured its longest-lived isotope 227Ac (half-life 21.77 yr) for the first time in the water column of the Southeast Pacific, the Central Arctic, the Antarctic Circumpolar Current (ACC) and the Weddell Gyre (WG). Besides the profile in the Southeast Pacific, which confirms earlier findings about the role of diapycnal mixing for 227Ac distribution, we found three other different types of vertical profiles. These profiles point to a prominent role of advection for 227Ac distribution, especially in the Southern Ocean. Depending on the type of profile found, 227Ac is proposed as a tracer for different oceanographic questions. In the Southern Ocean, up to 4.93±0.32 dpm/m**3 227Ac is found close to the sea floor, which is the highest concentration ever observed in the ocean. Close to the sea surface in the WG, 0.46±0.05 dpm/m**3 227Acex (227Ac in excess of its progenitor 231Pa) is detected. We use 227Acex there to determine the upwelling velocity in the Eastern WG to be about 55 m/yr. In the ACC, Upper and Lower Circumpolar Deep Water (UCDW and LCDW) are found to differ clearly in their 227Acex activity. High 227Acex activities are therefore a promising tracer for recent inputs of LCDW to the sea surface, which may help to understand the role of deep upwelling for iron inputs into Antarctic surface waters. The expected release of 227Ac is compared with 228Ra to make sure that the large near-surface excess in the water column of the Southern Ocean is not due to lateral inputs by isopycnal mixing. Data from the Central Arctic and from a transect across the ACC confirm that 228Ra and 227Acex differ strongly in their sources. The first measurements of 227Ac on suspended matter (less than 1.7% of total 227Ac close to the sea floor) indicate that the particle reactivity of 227Ac is negligible in the open ocean, in agreement with earlier findings [Y. Nozaki, Nature 310 (1984) 486-488]. Despite the extremely low concentrations of 227Ac, new measurement techniques [W.S. Moore, R. Arnold, J. Geophys. Res. 101 (1996) 1321-1329] point to a comfortable and comparably simple determination of 227Ac in the future. Finally, 227Acex may become a widely used deep-sea specific tracer.

(Table 1) Summary statistics of taxa in samples of ODP Hole 181-1123B

Planktonic foraminifera are used to identify late Pliocene-Quaternary near surface water masses on the northeastern flank of Chatham Rise by comparison with faunas in core-tops east of New Zealand. In an overview study, distance measures, ordinations, and discriminant analysis are applied to 32 faunas from Site 1123B to identify similar faunas among 35 core-tops between 35 and 61°S east of New Zealand. Many Site 1123B faunas in the 2.72 myr interval sampled compare with those in core-tops on the northern side of Chatham Rise from a similar latitude, and are identified as transitional zone assemblages now associated with the subtropical gyre. This result is consistent with studies of late Quaternary planktonic foraminifera from this region and suggests that, typically, the Subtropical Front was locked to Chatham Rise through glacial and interglacial periods, at least back to the late Pliocene. However, a fauna at ca. 1.17 Ma compares with subpolar assemblages in core-tops between 44 and 48°S and identifies cooler surface water. Expectedly, closer sampling may reveal additional periods when southern water moved over the northeastern flank of Chatham Rise. Although the dominance of Globorotalia inflata, a species typical of the southern margin of subtropical gyres, is a principal feature of Site 1123B faunas, in a minority it is replaced as the most abundant species by dextral populations of Neogloboquadrina pachyderma, particularly about the time of the middle Pleistocene transition. Close analogues of these variant transitional assemblages are not present in core-tops about Chatham Rise but sediment trap and coretop data from other regions suggest that they identify high fertility in the mixed layer associated with upwelling or mixing of water masses. The proportion of sinistrally coiled Neogloboquadrina pachyderma rises to ca. 0.6 between ca. 2.45 and 2.57 Ma, soon after the intensification of Northern Hemisphere glaciation. Although the coiling data indicate subantarctic near surface water, the species remains rare. As the faunas retain their transitional zone character, only minor entrainment of subantarctic water may have occurred.

Stable isotope record of foraminifera from South Atlantic sediments with reconstruction of paleotemperatures and paleosalinities

Changes in surface water hydrography in the Southern Ocean (eastern Atlantic sector) could be reconstructed on the basis of isotope-geochemical and micropaleontological studies. A total of 75 high quality multicorer sediment surface samples from the southern South Atlantic Ocean and three Quaternary sediment cores, taken on a meridional transect across the Antarctic Circumpolar Current, have been investigated. The results of examining stable oxygen isotope compositions of 24 foraminiferal species and morphotypes were compared to the near-surface hydrography. The different foraminifera have been divided into four groups living at different depths in the upper water column. The 8180 differences between shallow-living (e.g. G. bulloides, N. pachyderma) and deeper-dwelling (e. g. G. inflata) species reflect the measured temperature gradient of the upper 250 m in the water column. Thus, the 6180 difference between shallow-living and deeper-living foraminifera can be used as an indicator for the vertical temperature gradient in the surface water of the Antarctic Circumpolar Current, which is independent of ice volume. All planktonic foraminifera in the surface sediment samples have been counted. 27 species and morphotypes have been selected, to form a reference data Set for statistical purposes. By using R- and Q-mode principal component analysis these planktonic foraminifera have been divided into four and five assemblages, respectively. The geographic distribution of these assemblages is mainly linked to the temperature of sea-surface waters. The five assemblages (factors) of the Q-mode principal component analysis account for 97.l % of the variance of original data. Following the transferfunction- technique a multiple regression between the Q-mode factors and the actual mean sea-surface environmental parameters resulted in a set of equations. The new transfer function can be used to estimate past sea-surface seasonal temperatures for paleoassemblages of planktonic foraminifera with a precision of approximately ±1.2°C. This transfer function F75-27-5 encompasses in particular the environmental conditions in the Atlantic sector of the Antarctic Circumpolar Current. During the last 140,000 years reconstructed sea-surface temperatures fluctuated in the present northern Subantarctic Zone (PS2076-1/3) at an amplitude of up to 7.5°C in summer and of up to 8.5°C in winter. In the present Polarfrontal Zone (PS1754-1) these fluctuations between glacials and interglacials show lower temperatures from 2.5 to 8.5°C in summer and from 1.0 to 5.0°C in winter, respectively. Compared to today, calculated oxygen isotope temperature gradients in the present Subantarctic Zone were lower during the last 140,000 years. This is an indicator for a good mixing of the upper water column. In the Polarfrontal Zone also lower oxygen isotope temperature gradients were found for the glacials 6, 4 and 2. But almost similar temperature gradients as today were found during the interglacial stages 5, 3 and the Holocene, which implicates a mixing of the upper water column compared to present. Paleosalinities were reconstructed by combining d18O-data and the evaluated transfer function paleotemperatures. Especially in the present Polarfrontal Zone (PS1754-1) and in the Antarctic Zone (PS1768-8), a short-term reduction of salinity up to 4 %o, could be detected. This significant reduction in sea-surface water salinity indicates the increased influx of melt-water at the beginning of deglaciation in the southern hemisphere at the end of the last glacial, approximately 16,500-13,000 years ago. The reconstruction of environmental Parameters indicates only small changes in the position of the frontal Systems in the eastern sector of the Antarctic Circumpolar Current during the last 140,000 years. The average position of the Subtropical Front and Subantarctic Front shifted approximately three latitudes between interglacials and glacials. The Antarctic Polar Front shifted approximately four latitudes. But substantial modifications of this scenario have been interpreted for the reconstruction of cold sea-surface temperatures at 41Â S during the oxygen isotope stages 16 and 14 to 12. During these times the Subtropical Front was probably shified up to seven latitudes northwards.

(Table 2) Presence of plant remains in sediment core GIK14973, northern Kattegat

For the first time detailed physical properties were measured in addition to sedimentological parameters of near surface sediments of Kattegat channel system. This study has been accomplished on two sediment cores of different waterdepth of each Alkor-deep and Littorina-deep. The sediments of Littorina-deep, which have been dated with 210Pb-method, turned out to be surprisingly recent, with sedimentation rates up to 3,2 cm/year. Differences in physical properties lead to the assumption of lower sedimentation rates in Alkor-deep, the velocities of bottom and deepwater currents could be the cause of these differences in sedimentation rates. In Alkor-deep, the morphology runs parallel to the main direction of the bottom current. Therefore higher current velocities can be reached, which favor the erosion of fine sediment particles. Littorina-deep is located rectangular to the main direction of bottom currents. This might lead to an 'overflow' situation instead of a 'flow through'.

(Table 1) Heavy mineral content in sediments of the southern Mediterranean Ridge, Nile Cone and Egyptian Shelf

Petrographic analysis of Quaternary terrigenous sand layers in eastern Mediterranean cores reveals distinct mineralogical differences between the Egyptian Shelf-Nile Cone region and the southern part of the Mediterranean Ridge. A compositionally and texturally immature suite in Ridge cores, mixed with a Nile-derived assemblage, identifies a fresh non-recycled mineral component derived from proximal igneous and metamorphic surface or near-surface exposures, probably in the south-central Ridge area rather than from distal African sources. The presence of such basement terrains would be consistent with a compressive thrust-belt origin for this part of the Mediterranean Ridge.

High-resolution dynamical downscaling products for the North Slope of Alaska and surrounding areas, links to model result files

Climatic changes are most pronounced in northern high latitude regions. Yet, there is a paucity of observational data, both spatially and temporally, such that regional-scale dynamics are not fully captured, limiting our ability to make reliable projections. In this study, a group of dynamical downscaling products were created for the period 1950 to 2100 to better understand climate change and its impacts on hydrology, permafrost, and ecosystems at a resolution suitable for northern Alaska. An ERA-interim reanalysis dataset and the Community Earth System Model (CESM) served as the forcing mechanisms in this dynamical downscaling framework, and the Weather Research & Forecast (WRF) model, embedded with an optimization for the Arctic (Polar WRF), served as the Regional Climate Model (RCM). This downscaled output consists of multiple climatic variables (precipitation, temperature, wind speed, dew point temperature, and surface air pressure) for a 10 km grid spacing at three-hour intervals. The modeling products were evaluated and calibrated using a bias-correction approach. The ERA-interim forced WRF (ERA-WRF) produced reasonable climatic variables as a result, yielding a more closely correlated temperature field than precipitation field when long-term monthly climatology was compared with its forcing and observational data. A linear scaling method then further corrected the bias, based on ERA-interim monthly climatology, and bias-corrected ERA-WRF fields were applied as a reference for calibration of both the historical and the projected CESM forced WRF (CESM-WRF) products. Biases, such as, a cold temperature bias during summer and a warm temperature bias during winter as well as a wet bias for annual precipitation that CESM holds over northern Alaska persisted in CESM-WRF runs. The linear scaling of CESM-WRF eventually produced high-resolution downscaling products for the Alaskan North Slope for hydrological and ecological research, together with the calibrated ERA-WRF run, and its capability extends far beyond that. Other climatic research has been proposed, including exploration of historical and projected climatic extreme events and their possible connections to low-frequency sea-atmospheric oscillations, as well as near-surface permafrost degradation and ice regime shifts of lakes. These dynamically downscaled, bias corrected climatic datasets provide improved spatial and temporal resolution data necessary for ongoing modeling efforts in northern Alaska focused on reconstructing and projecting hydrologic changes, ecosystem processes and responses, and permafrost thermal regimes. The dynamical downscaling methods presented in this study can also be used to create more suitable model input datasets for other sub-regions of the Arctic.

Mixing Regimes in the Amundsen Basin of the Arctic Ocean

Thesis (Ph.D.)--University of Washington, 2016-06