ALBERT

Beschreibung: The paper describes the architecture for a data repository and distribution system to be used in the case of a SETI detection event. This system is conceptually modelled after the Deep Space Network, although the hardware and infrastructure involved are different and substantially less expensive to operate. The system is designed to accommodate a large number of users from a variety of fields who wish to contribute to the analysis and comprehension effort that would follow the detection of an information-bearing signal.

Beschreibung: Under the potential to reconstruct the past climatic and atmospheric conditions from a deep ice core in the coastal Antarctic site (Styx Glacier), an 8.84 m long firn core (73°50.975′ S, 163°41.640′ E; 1623 m a.s.l.) was initially studied to propose a reliable age scale for the local estimation of snow accumulation rate. The seasonal variations of δ18O, methanesulfonic acid (MSA) and non-sea-salt sulfate (nssSO42–) were used for the firn core dating and revealed 25 annual peaks (from 1990 to 2014) with volcanic sulfate signal. The observed declining trend in annual accumulation rate with a mean value of 146 ± 60 kg m–2 a–1 is likely to be linked to the changes of sea-ice extent in the Ross Sea region. Moreover, the temporal variation of the annual mean δ18O, an annual flux of MSA and nssSO42– also likely to be under the influence of ice-covered and open water area. This study suggests a potential to recover past changes in an oceanic environment and will be useful for the interpretation of the long ice core drilled at the same site.

Beschreibung: Clouds play an important role in the Arctic surface radiative budget, impacting the seasonal evolution of Arctic sea-ice cover. We explore the large-scale impacts of springtime and early summer (March through July) cloud and radiative fluxes on sea ice by comparing these fluxes to seasonal ice volume losses over the central Arctic basin, calculated for available observational years 2004–2007 (ICESat) and 2011–2017 (CryoSat-2). We also supplement observation data with sea-ice volume computed from the Pan-Arctic Ice–Ocean Modeling and Assimilation System (PIOMAS) during summer months. We find that the volume of sea ice lost over the melt season is most closely related to observed downwelling longwave radiation in March and early summer (June and July) longwave cloud radiative forcing, which together explain a large fraction of interannual variability in seasonal sea-ice volume loss (R2 = 0.71, p = 0.007). We show that downwelling longwave fluxes likely impact the timing of melt onset near the sea-ice edge, and can limit the magnitude of ice thickening from March to April. Radiative fluxes in June and July are likely critical to seasonal volume loss because modeled data show the greatest ice volume reductions occur during these months.

Beschreibung: Fishermen are known to try to avoid fishing in stormy weather, as storms pose a physical threat to fishers, their vessels, and their gear. In this article, a dataset and methods are developed to investigate the degree to which fishers avoid storms, estimate storm aversion parameters, and explore how this response varies across vessel characteristics and across regions of the United States. The data consist of vessel-level trip-taking decisions from six federal fisheries across the United States combined with marine storm warning data from the National Weather Service. The estimates of storm aversion can be used to parameterize predictive models. Fishers’ aversion to storms decreases with increasing vessel size and increases with the severity of the storm warning. This information contributes to our understanding of the risk-to-revenue trade-off that fishers evaluate every time they consider going to sea, and of the propensity of fishers to take adaptive actions to avoid facing additional physical risk.

Beschreibung: Sardine Sardinops sagax is an ecologically and economically important Clupeid found off the entire South African coast that includes both coastal upwelling and western boundary current systems. Although the management of the sardine fisheries historically assumed a single, panmictic population, the existence of three, semi-discrete subpopulations has recently been hypothesized. We conducted otolith δ18O and microstructure analyses to investigate nursery habitat temperatures and early life growth rates, respectively, of sardine collected from three biogeographic regions around South Africa’s coast to test that hypothesis. Analyses indicated that for both summer- and winter-captured adults and summer-captured juveniles, fishes from the west coast grew significantly slower in water that was several degrees cooler than those from the south and east coasts. This suggests that mixing of sardines between regions, particularly the west and other coasts, is relatively limited and supports the hypothesis of semi-discrete subpopulations. However, the west-south differences disappeared in the results for winter-captured juveniles, suggesting that differences in early life conditions between regions may change seasonally, and/or that all or most winter-captured juveniles originated from the west coast. Further elucidating the interactions between South African sardine subpopulations and the mechanisms thereof is important for sustainable harvesting of this species.

Beschreibung: We present a high-resolution spatial study of ocean surface carbon dioxide partial pressure (pCO2), temperature and salinity coupled with a seismic survey performed in subpolar waters with a variable presence of glaciers along the coastal margins of Admiralty Bay and the Bransfield Strait, northern Antarctic Peninsula, during the late spring season. Three zones were identified in this bay. The shallow and relatively fresh SHALLOW GLACIER THAW zone in the inner portion of the bay had high freshwater inputs from active glacial meltwater channels, representing higher pCO2 levels (median ~438 μatm) than the shallow and relatively salty SHALLOW zone without glaciers along the margins and dominated by macroalgae communities at the bottom, which showed relatively low pCO2 levels (median ~371 μatm). The deep and relatively salty CENTRE zone was highly influenced by seawater intrusions from the Bransfield Strait, representing intermediate pCO2 levels (median ~397 μatm). The net sea-air CO2 fluxes in late spring obtained from the high-resolution surface survey in Admiralty Bay indicate a condition of near neutral air-sea CO2 flux, with a median (25–75% interquartile range) value of -0.07 mmol m-2 day-1 (ranging from -12.21 to +4.33 mmol m-2 day-1), contrasting with the slight source to the atmosphere estimated from measurements only in the CENTRE zone. This finding suggests that temperature-sensitive metabolic and physical-chemical processes may cause significant variability in the ocean surface distribution of CO2 over short shoreline distances in the northern Antarctic Peninsula.

Beschreibung: Although luminescence sensitivity of quartz grains of desert sands has been used in discriminating provenance, it still remains unclear about its spatiotemporal variations and climatic implications. In this paper, the luminescence sensitivity of quartz grains from the northern margin of the Chinese Loess Plateau (CLP) was studied using single-aliquot optically stimulated luminescence (OSL) and “pseudo” single-grain OSL measurements. Our results indicate that the OSL sensitivities have lower values in sand/loess beds and higher values in paleosols. We suggest that the variations in OSL sensitivity of quartz grains with depth on the CLP are mainly influenced by the origin of the quartz grains as they are related to the loess-sized material production processes and the migration of desert regions. More quartz grains of glacial origin with lower luminescence sensitivity, together with the reduced durations of irradiation and exposure cycles induced by shorter transport distance due to desert expansion, account for the lower luminescence sensitivity of glacial periods. Moreover, both the mountain processes and the retreat–advance of deserts are ultimately related to climatic changes, therefore, the orbital scale variations of luminescence sensitivity are controlled by glacial–interglacial oscillations on the CLP.

Beschreibung: Two satellite datasets are used to characterize winter landfast first-year sea-ice (FYI), deformed FYI (DFYI) and multiyear sea-ice (MYI) roughness in the Canadian Arctic Archipelago (CAA): (1) optical Multi-angle Imaging SpectroRadiometer (MISR) and (2) synthetic aperture radar Sentinel-1. The Normalized Difference Angular Index (NDAI) roughness proxy derived from MISR, and backscatter from Sentinel-1 are intercompared. NDAI and backscatter are also compared to surface roughness derived from an airborne LiDAR track covering a subset of FYI and MYI (no DFYI). Overall, NDAI and backscatter are significantly positively correlated when all ice type samples are considered. When individual ice types are evaluated, NDAI and backscatter are only significantly correlated for DFYI. Both NDAI and backscatter are correlated with LiDAR-derived roughness (r = 0.71 and r = 0.74, respectively). The relationship between NDAI and roughness is greater for MYI than FYI, whereas for backscatter and ice roughness, the relationship is greater for FYI than MYI. Linear regression models are created for the estimation of FYI and MYI roughness from NDAI, and FYI roughness from backscatter. Results suggest that using a combination of Sentinel-1 backscatter for FYI and MISR NDAI for MYI may be optimal for mapping winter sea-ice roughness in the CAA.

Beschreibung: Drumlins form at the ice/bed interface through subglacial processes that are not directly observable. The internal stratigraphy of drumlins provides insight into how they developed and associated subglacial processes, but traditional stratigraphic logging techniques are limited to natural exposures and excavations. Using ground-penetrating radar, we imaged the internal stratigraphy of seven drumlins from a recently exposed drumlin field in the forefield of Múlajökull, Iceland. Data were collected with 100 and 200 MHz antennas with maximum resolvable depths of 8 and 4 m, respectively. Longitudinal echograms contained coherent down-ice dipping reflectors over the lengths of the drumlins. Near the drumlin heads (i.e., stoss sides), down-glacier dipping beds lie at high angles to the surface, whereas on the lee sides, the down-glacier dipping beds lie at low angles, or conform, to drumlin surfaces. Transverse echograms exhibited unconformities along the flanks of drumlin heads and conformable bedding across the lee side widths of the drumlins. These observations were ground-truthed with stratigraphic logs from a subset of drumlins and good agreement was found. The stratigraphic patterns support previous conclusions that drumlins at Múlajökull formed on a deformable bed through both depositional and erosional processes which may alternate between its surge and quiescent phases.

Beschreibung: Ancient cities are excellent spatiotemporal indicators for the study of historical human activities and environmental change. The ancient city of Sanchahe is located at the southern margin of the Mu Us Desert, China. It is an ideal location for studying the complex relationships between historical desertification and human activities. Field observations of the ancient city walls, a well, and a spring, as well as 14C dating, grain size, spatial analysis of archaeological sites, and analyses of historical seismicity, indicated that neotectonics may have contributed to crustal uplift and accelerated fluvial incision of the Wuding River. This rapid incision caused a decline in groundwater levels, which is an important reason for the irreversible environmental degradation around Sanchahe city over the past 800 yr. This study provides new evidence for such environmental degradation and may contribute to a better understanding of historical desertification in the Mu Us Desert.

Beschreibung: CerealsDB (www.cerealsdb.uk.net) is an online repository of mainly hexaploid wheat (Triticum aestivum) single nucleotide polymorphisms (SNPs) and genotyping data. The CerealsDB website has been designed to enable wheat breeders and scientists to select the appropriate markers for research breeding tasks, such as marker-assisted selection. We report a large update of genotyping information for over 6000 wheat accessions and describe new webtools for exploring and visualizing the data. We also describe a new database of quantitative trait loci that links phenotypic traits to CerealsDB SNP markers and allelic scores for each of those markers. CerealsDB is an open-access website that hosts information on wheat SNPs considered useful for both plant breeders and research scientists. The latest CerealsDB database is available at https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php.

Beschreibung: Progress towards ecosystem-based fisheries management calls for useful tools to prioritize actions. To select suitable methods for local circumstances, evaluating approaches used in other jurisdictions can be a cost-effective first step. We tested Productivity Susceptibility Analysis (PSA) to assess the potential vulnerability of the marine fish community in the Skagerrak–Kattegat (Eastern North Sea) to possible interactions with all Swedish fisheries operating in the area. This analysis combines attributes for a species productivity with attributes related to the susceptibility to capture to quantify a single score for vulnerability: high, medium, or low risk. Results indicate that demersal trawl and gillnet fisheries were associated with the highest risk levels if interaction occurs, i.e. having the highest prevalence of species with potentially high vulnerability to the fisheries. Mixed results were seen when comparing the assessment results with available data. The main benefit of utilizing PSA in the area is the comprehensiveness of the assessment, including data-deficient fisheries and species. Drawbacks include potential overestimation of actual risks. Overall, together with available data, PSA in the studied area provides a comprehensive map of potential risks for further actions and may progress a science-based, precautionary management of the area.

Beschreibung: While fisheries provide food and employment for hundreds of millions of people, they also can have significant impact on biodiversity. We explore the potential of area-based fisheries management to simultaneously maintain biodiversity and high levels of sustainable food production. We used two illustrative examples of fisheries that have different gear types, areas, and species to evaluate the trade-off between biodiversity and harvest. We calculate the optimal effort by gear and area that maximizes a weighted objective function of biodiversity and harvest, ranging from 100% of the weight on harvest to 100% on biodiversity. We found for both case studies that the trade-off was highly convex, with win–win solutions allowing for high levels of both fishery harvest and conservation. This is achieved by reducing or eliminating fishing effort that negatively impacts high conservation value species while maintaining fishing effort with gears and in areas where there is low conservation impact. We suggest that, in most fisheries, such situations can be found and that effective area-based management can provide for high levels of biodiversity protection and food production.

Beschreibung: A Fast Ice Prediction System (FIPS) was constructed and is the first regional land-fast sea-ice forecasting system for the Antarctic. FIPS had two components: (1) near-real-time information on the ice-covered area from MODIS and SAR imagery that revealed, tidal cracks, ridged and rafted ice regions; (2) a high-resolution 1-D thermodynamic snow and ice model (HIGHTSI) that was extended to perform a 2-D simulation on snow and ice evolution using atmospheric forcing from ECMWF: either using ERA-Interim reanalysis (in hindcast mode) or HERS operational 10-day predictions (in forecast mode). A hindcast experiment for the 2015 season was in good agreement with field observations, with a mean bias of 0.14 ± 0.07 m and a correlation coefficient of 0.98 for modeled ice thickness. The errors are largely caused by a cold bias in the atmospheric forcing. The thick snow cover during the 2015 season led to modeled formation of extensive snow ice and superimposed ice. The first FIPS operational service was performed during the 2017/18 season. The system predicted a realistic ice thickness and onset of snow surface melt as well as the area of internal ice melt. The model results on the snow and ice properties were considered by the captain of R/V Xuelong when optimizing a low-risk route for on-ice transportation through fast ice to the coastal Zhongshan Station.

Beschreibung: The evolution of melt ponds on Arctic sea ice in summer is one of the main factors that affect sea-ice albedo and hence the polar climate system. Due to the different spectral properties of open water, melt pond and sea ice, the melt pond fraction (MPF) can be retrieved using a fully constrained least-squares algorithm, which shows a high accuracy with root mean square error ~0.06 based on the validation experiment using WorldView-2 image. In this study, the evolution of ponds on first-year and multiyear ice in the Canadian Arctic Archipelago was compared based on Sentinel-2 and Landsat 8 images. The relationships of pond coverage with air temperature and albedo were analysed. The results show that the pond coverage on first-year ice changed dramatically with seasonal maximum of 54%, whereas that on multiyear ice changed relatively flat with only 30% during the entire melting period. During the stage of pond formation, the ponds expanded rapidly when the temperature increased to over 0°C for three consecutive days. Sea-ice albedo shows a significantly negative correlation (R = −1) with the MPF in melt season and increases gradually with the refreezing of ponds and sea ice.

Beschreibung: We report apatite fission-track and 10Be terrestrial cosmogenic nuclide (TCN) dating of 14 moraine boulders originating from inland Terre Adélie, East Antarctica. These data show cooling of the Proterozoic Terre Adélie craton at 〈 ~120°C between 350 and 300 Ma, suggesting 〉 4 km temperate glacial erosion during the Late Palaeozoic Ice Age, followed by nearly null Mesozoic erosion and low glacial erosion (〈 2 km) in the Cenozoic. Based on glacial flux maps, the origin of the boulders may be located ~400 km upstream. Preliminary TCN (10Be) datings of moraine boulders cluster within the last 30 ka. Cosmogenic ages from the Lacroix Nunatak suggest a main deglaciation after the Younger Dryas at c. 10 ka, while those of Cap Prud'homme mostly cluster at 0.6 ka, in agreement with an exhumation of boulders during the Little Ice Age.

Beschreibung: Glacial environments exhibit temporally variable microseismicity. To investigate how microseismicity influences event detection, we implement two noise-adaptive digital power detectors to process seismic data from Taylor Glacier, Antarctica. We add scaled icequake waveforms to the original data stream, run detectors on the hybrid data stream to estimate reliable detection magnitudes and compare analytical magnitudes predicted from an ice crack source model. We find that detection capability is influenced by environmental microseismicity for seismic events with source size comparable to thermal penetration depths. When event counts and minimum detectable event sizes change in the same direction (i.e. increase in event counts and minimum detectable event size), we interpret measured seismicity changes as ‘true’ seismicity changes rather than as changes in detection. Generally, one detector (two degree of freedom (2dof)) outperforms the other: it identifies more events, a more prominent summertime diurnal signal and maintains a higher detection capability. We conclude that real physical processes are responsible for the summertime diurnal inter-detector difference. One detector (3dof) identifies this process as environmental microseismicity; the other detector (2dof) identifies it as elevated waveform activity. Our analysis provides an example for minimizing detection biases and estimating source sizes when interpreting temporal seismicity patterns to better infer glacial seismogenic processes.

Beschreibung: Repeatability of study setups and reproducibility of research results by underlying data are major requirements in science. Until now, abstract models for describing the structural logic of studies in environmental sciences are lacking and tools for data management are insufficient. Mandatory for repeatability and reproducibility is the use of sophisticated data management solutions going beyond data file sharing. Particularly, it implies maintenance of coherent data along workflows. Design data concern elements from elementary domains of operations being transformation, measurement and transaction. Operation design elements and method information are specified for each consecutive workflow segment from field to laboratory campaigns. The strict linkage of operation design element values, operation values and objects is essential. For enabling coherence of corresponding objects along consecutive workflow segments, the assignment of unique identifiers and the specification of their relations are mandatory. The abstract model presented here addresses these aspects, and the software DiversityDescriptions (DWB-DD) facilitates the management of thusly connected digital data objects and structures. DWB-DD allows for an individual specification of operation design elements and their linking to objects. Two workflow design use cases, one for DNA barcoding and another for cultivation of fungal isolates, are given. To publish those structured data, standard schema mapping and XML-provision of digital objects are essential. Schemas useful for this mapping include the Ecological Markup Language, the Schema for Meta-omics Data of Collection Objects and the Standard for Structured Descriptive Data. Data pipelines with DWB-DD include the mapping and conversion between schemas and functions for data publishing and archiving according to the Open Archival Information System standard. The setting allows for repeatability of study setups, reproducibility of study results and for supporting work groups to structure and maintain their data from the beginning of a study. The theory of ‘FAIR++’ digital objects is introduced.

Beschreibung: The accuracy of sea-ice motion products provided by the National Snow and Ice Data Center (NSIDC) and the Ocean and Sea Ice Satellite Application Facility (OSI-SAF) was validated with data collected by ice drifters that were deployed in the western Arctic Ocean in 2014 and 2016. Data from both NSIDC and OSI-SAF products exhibited statistically significant (p 〈 0.001) correlation with drifter data. The OSI-SAF product tended to overestimate ice speed, while underestimation was demonstrated for the NSIDC product, especially for the melt season and the marginal ice zone. Monthly Lagrangian trajectories of ice floes were reconstructed using the products. Larger spatial variability in the deviation between NSIDC and drifter trajectories was observed than that of OSI-SAF, and seasonal variability in the deviation for NSIDC was observed. Furthermore, trajectories reconstructed using the NSIDC product were sensitive to variations in sea-ice concentration. The feasibility of using remote-sensing products to characterize sea-ice deformation was assessed by evaluating the distance between two arbitrary positions as estimated by the products. Compared with the OSI-SAF product, relative errors are lower (

Beschreibung: Hydrogen cyanide (HCN) is considered a fundamental molecule in prebiotic chemistry experiments due to the fact that it could have an important role as raw material to form more complex molecules, as well as it could be an intermediate molecule in chemical reactions. However, the primitive scenarios in which this molecule might be available have been widely discussed. Hydrothermal systems have been considered as abiotic reactors and ideal niches for chemical evolution. Nevertheless, several experiments have shown that high temperatures and pressures could be adverse to the stability of organic molecules. Thus, it is necessary to carry out systematic experiments to study the synthesis, stability and fate of organic molecules in hydrothermal scenarios. In this work, we performed experiments focused on the stability and fate of HCN under a simple hydrothermal system scenario: the thermolysis of HCN at 100°C, at acidic and basic pH and in the presence of Mg-montmorillonite. Furthermore, we analysed the products from HCN thermolysis and highlighted the role of these chemical species as prebiotic molecules under a hydrothermal scenario.

Beschreibung: The cross-sectional profile of a glacial valley can be obtained with a variational principle in which the friction against the valley walls and the glacier bed is extremized, subject to a Lagrangian constraint. We show that the actual valley profile maximizes the friction, thus settling an old debate.

Beschreibung: The objective of this study was to identify attitudes towards the scientific search for extraterrestrial life among students from public and private universities in Peru. This research was inspired by similar studies, realized in Sweden, which used the same instrument adapting it to our reality. The process consisted of a survey of the Peruvian student population by targeting it in different regions of Peru. The sample consisted of 1237 students from different academic areas. The findings show that 92% of the students believe in the existence of life outside our planet, with differences between the subgroups surveyed.

Beschreibung: Astrobiology has been gaining increasing scientific prominence and public attention as the search for life beyond Earth continues to make significant headway on multiple fronts. In view of these recent developments, the fascinating and dynamic etymology of astrobiology is elucidated, and thus shown to encompass a plethora of vivid characters drawn from different continents, religions, ideologies and centuries.

Beschreibung: Quantifying the rate of wave attenuation in sea ice is key to understanding trends in the Antarctic marginal ice zone extent. However, a paucity of observations of waves in sea ice limits progress on this front. We deployed 14 waves-in-ice observation systems (WIIOS) on Antarctic sea ice during the Polynyas, Ice Production, and seasonal Evolution in the Ross Sea expedition (PIPERS) in 2017. The WIIOS provide in situ measurement of surface wave characteristics. Two experiments were conducted, one while the ship was inbound and one outbound. The sea ice throughout the experiments generally consisted of pancake and young ice

Beschreibung: Recent application of Fourier transform near infra-red spectroscopy (FT-NIRS) to predict age in fish otoliths has gained attention among fisheries managers as a potential alternative to costly production ageing of managed species. We assessed the age prediction capability of FT-NIRS scans in whole otoliths from red snapper, Lutjanus campechanus, collected from the US Gulf of Mexico and US Atlantic Ocean (South Atlantic). Otoliths were scanned with an FT-NIR spectrometer and resulting spectral signatures were regressed with traditionally estimated ages via partial least squares regression to produce calibration models, which were validated for predictive capability against test sets of otoliths. Calibration models successfully predicted age with R2 ranging 0.94–0.95, mean squared error ≤1.8 years, and bias 31 years were not well predicted, possibly due to light attenuation in the thickest otoliths. Our results suggest that FT-NIRS can improve efficiency in production ageing for fisheries management while maintaining data quality standards.

Beschreibung: This article investigates the diet of the snow crab (Chionoecetes opilio) and its feeding intensity in the Barents Sea. Data show that snow crab has a diverse diet that includes almost all types of benthic invertebrates living in the Barents Sea. There are differences between the diets of females and males and of juveniles and adults. Juveniles and females typically occupy shallow areas with communities of bivalve molluscs, while males typically live deeper on slopes and depressions where polychaetes and crustaceans are the most abundant groups. Stomach contents were analysed to determine the species composition and frequency of occurrence of various benthic taxa. Consumption of food was estimated and compared with data from the Russian seas of the Pacific region. The total annual consumption of macrozoobenthos by snow crab was calculated in accordance with its current distribution in the Barents Sea. Snow crab consumes at least 30 000 tonnes of benthos annually, which amounts to 0.1–0.2% of the total macrozoobenthic biomass in the investigated area. The population of snow crab causes the largest impact on the benthic communities in the northeastern part of the Barents Sea and near the south side of the Novaya Zemlya archipelago.

Beschreibung: Deglaciation of high mountain rockwalls alters slope stability as rockwalls become more sensitive to modifications in environmental factors (e.g. seasonal temperature variations). In the past decades, increasing efforts focused on studying deglaciated Alpine rockwalls. Yet, currently deglaciating rockfaces remain unstudied. Here, we quantify surface area variations of massive ice bodies lying on high mountain rockwalls (ice aprons) in the French sector of the Mont Blanc massif between the end of the Little Ice Age (LIA) and 2018. Surface area estimates are computed from terrestrial and aerial oblique photographs via photogrammetry. This technique allows using photographs taken without scientific intent, and to tap into diverse historical or recent photographic catalogs. We derive an ice apron surface area model from precipitation records and the positive degree-days. The studied ice aprons shrank from 1854 to the 1950s, before expanding until the end of the 1990s. The beginning of the 21st century shows a decrease in surface area, leading to the complete melt of one of the studied ice aprons in 2017. Observed variations correlate with modeled surface area, suggesting strong sensitivity of ice aprons to changes in climatic variables. By studying site-specific correlations, we explore the importance of local drivers over the balance of ice aprons.

Beschreibung: Until the late 19th century, extensive beds of flat oyster Ostrea edulis populated the Central North Sea, which have vanished after intensive fisheries. At present, various initiatives are being carried out to investigate the potential to restore this former key species in the area. This historical ecological study contributes by delineating the former oyster bed area and through an assessment of its limits against known gradients in the North Sea. Extensive data from historical maps, texts, and ship-based surveys were used to synthesize our knowledge on the former beds. It was revealed that the area with oyster beds covered ∼6.2% of the total North Sea bottom, with a delineation that could partly be explained by hydrodynamic and temperature gradients. The position and extent of the area are notably different from the area that is used in recent feasibility studies on the restoration of North Sea oyster beds. The offshore oysters lived on muddy sand in relatively cold conditions, and there are several indications that their reproductive rate was low. The apparent disappearance of cold water adapted flat oysters will challenge restoration projects. This study provides indispensable information for the future restoration of flat oyster beds in the North Sea.

Beschreibung: This study focused on the ability of the Antarctic bacterium Rhodococcus sp. strain AQ5-14 to survive exposure to and to degrade high concentrations of phenol at 0.5 g l-1. After initial evaluation of phenol-degrading performance, the effects of salinity, pH and temperature on the rate of phenol degradation were examined. The optimum conditions for phenol degradation were pH 7 and 0.4 g l-1 NaCl at a temperature of 25°C (83.90%). An analysis using response surface methodology (RSM) and the Plackett-Burman design identified salinity, pH and temperature as three statistically significant factors influencing phenol degradation. The maximum bacterial growth was observed (optical density at 600 nm = 0.455), with medium conditions of pH 6.5, 22.5°C and 0.47 g l-1 NaCl in the central composite design of the RSM experiments enhancing phenol degradation to 99.10%. A central composite design was then used to examine the interactions among these three variables and to determine their optimal levels. There was excellent agreement (R2 = 0.9785) between experimental and predicted values, with less strong but still good agreement (R2 = 0.8376) between the predicted model values and those obtained experimentally under optimized conditions. Rhodococcus sp. strain AQ5-14 has excellent potential for the bioremediation of phenol.

Beschreibung: The article addresses old ‘west-east discourses’ and how they continue to develop in the high north, and, not least, in the Norwegian petroleum debate. Adopting a discourse analytical perspective the author shows how environmental safety is used as an argument in favour of Norway producing oil in the Barents Sea at the earliest possible moment. This is only feasible if a connection is made in the public mind between Russia and the environment. These views, it is argued, stem from ideas about Russia that gained currency after the demise of the Soviet Union. While they perhaps have less to do with Russia's petroleum industry and environmental performance today, they nevertheless have a strong impact on how challenges in the high north and Arctic region are perceived. And, perhaps even more importantly, they define freedom of action and available options. In this paper all references to government departments refer to those of Norway.

Beschreibung: The effectiveness of international environmental cooperation is a theoretical and methodological challenge that has captured the interest of scholars and students of international relations in the recent years. This article is an evaluation of international environmental cooperation in northwest Russia by applying an approach developed in the Institutional Dimensions of Global Environmental Change (IDGEC) research programme of the International Human Dimension Programme (IHDP). The IDGEC approach emphasises the importance of complex diagnostics of institutional environmental arrangements in terms of performance. The approach relates to the effects of international environmental cooperation in terms of sustainability, efficiency, fairness, and robustness. The article focuses on Russian and Nordic experiences of international environmental cooperation, and the assessment of performance has been done by the participants themselves. According to the results of interviews and questionnaires, the cooperation is considered institutionally effective and robust in general. However, views about the environmental effects vary. Some problems exist that are related to sustainability and fairness, but the most critical issue is the lack of domestic environmental capacity in Russia.

Beschreibung: The thermal conductivity and diffusivity of natural snow computed from Fourier-type analyses of annual snow temperature variations are shown to be strongly temperature dependent. The computed temperature coefficients of-0.007 and -0.012 deg-1 respectively, agree well with older laboratory experiments carried out on polycrystalline ice.

Beschreibung: The movement at a marginal location on the Ward Hunt Ice Shelf, northern Ellesmere Island, was determined by repeated survey measurements with theodolite and geodimeter. The purpose and duration of the field work, and reduction of the observational data are described, and the resulting mean ice velocity of 0.53 m year-1 is discussed. Strain-rates of a 1 km by 1 km deformation figure are determined. The parameters n and B of Glen’s power flow law are determined by using the equations given by Nye and Weertman. The results are compared with experimental data. Computed ice stresses show that the “ridge-and-trough" structure on the ice shelf surface is not originated by internal ice forces. The elevations of all survey markers have been determined from vertical-angle measurements, and the peculiarities of atmospheric refraction in near-surface layers are discussed.

Beschreibung: Values of δ18OSMOW measured on ice from 250 m depth at old “Byrd station”. Antarctica, averaged about A monotonie trend in values through the 16 cm long core piece suggested that part of an annual layer was represented. Snow accumulation in excess of 14.4 g cm-2 year-1 ca 1 700 years B.P. is indicated.

Beschreibung: Grain-boundary thickness in polycrystalline ice is a function of time (age), salinity, tempera-turf ·, and mode of sample preparation. It is directly proportional to the salinity of the ice and the number-average grain diameter (spheres) or edge-length (cubes). Practically the total salt content resides in the grain boundary for low salinity ice samples. The gram-boundary thickness S is also directly proportional to growth time of the grains raised to a power n(n = 0.25 to 0.3) and increases exponentially with absolute temperature for constant salinity and age. The energy of activation for growth increases with salinity. The results of the grain-boundary thickness calculations are useful for evaluating grain-boundary diffusion coefficients.

Beschreibung: The Regenerative Enclosed Life Support Module Simulator (REMS) was designed to simulate the conditions aboard the International Space Station (ISS). This unique terrestrial, encapsulated environment for humans and their associated organisms allowed investigations into the microbial communities within an enclosed habitat system, primarily with respect to diversity, phylogeny and the possible impact on human health. To assess time- and/or condition-dependent changes in microbial diversity within REMS, a total of 27 air samples were collected during three consecutive months. The microbial burden and diversity were elucidated using culture-dependent and culture-independent molecular methods. The results indicate that during controlled conditions the total microbial burden detected by culture-dependent techniques (below a detectable level to 102 cells m−3of air) and intracellular ATP assay was significantly low (102–103 cells m−3of air), but increased during the uncontrolled post-operation phase (∼104 cells m−3of air). Only Gram-positive and α-proteobacteria grew under tested culture conditions, with a predominant occurrence ofMethylobacterium radiotolerans, andSphingomonas yanoikuyae. Direct DNA extraction and 16S rDNA sequencing methodology revealed a broader diversity of microbes present in the REMS air (51 species). Unlike culture-dependent analysis, both Gram-positive and proteobacteria were equally represented, while members of a few proteobaterial groups dominated (Rhodopseudomonas,Sphingomonas,Acidovorax,Ralstonia,Acinetobacter,Pseudomonas, andPsychrobacter). Although the presence of several opportunistic pathogens warrants further investigation, the results demonstrated that routine maintenance such as controlling the humidity, crew’s daily cleaning, and air filtration were effective in reducing the microbial burden in the REMS.

Beschreibung: Results art, presented of spectral analyses of the surface and bedrock profiles along a flow line of the Wilkes ice cap and the surface along the Greenland E.G.I.G. profile. Although the bedrock appears irregular over all was velengths studied, the ice-cap surface is typically characterized by a smooth curve with small-scale surface undulations superimposed on it. The following relations of Budd (1969, 19701 are confirmed. The “damping factor" or ratio of the bedrock amplitude to the surface amplitude is a minimum for wavelengths λ about 3.3 times the ice thickness. The surface lags the bed in the direction of motion by λ/4. The magnitude of the minimum damping factor φm is typically least near the coast, and increases inland depending on the ice thickness Z, the velocity V, and the mean ice viscosity η (which is a function of stress and temperature) according to where p is the mean ice density and g is the gravitational acceleration. Thus the determination of the damping factors provides a valuable means of estimating the ice flow parameter η.

Beschreibung: Recent observations on Bjornbo Gletscher (lat. 71°., long. 25° W.), East Greenland, have revealed that it has several features characteristic of a surging glacier. One outstanding feature is the occurrence of drop-like ice masses in the lower part of the glacier which do not appear to belong to the main glacier. A detailed petrographic comparison between the morainic debris surrounding these drop-like ice masses and the rocks occurring in the upper part of the glacier has been made. The results indicate that these drop-like ice masses have been inserted into the main glacier. This drop-like form is explained as being due to ice transport from the side valleys, and this occurred over a short period of time during the movement (or surge) of the main glacier. Because of the highly variable rock types occurring in the respective accumulation zones, petrographic examinations of other moraines in the ablation zone have been used to trace them back to their respective firn fields.The main glacier and the tributary glaciers are today static. Bjørnbo Gletscher is therefore characterized by both static and moving phases, and its dynamics are the same as those of surging glaciers. The quiescent phase is estimated to have been about 100 years. The next surge will presumably occur around 1990,

Beschreibung: A new technique for precisely detecting chlorides in ice has been developed. It is based on a microchemical contact reaction which takes place when a thin surface layer of ice melts through a membrane filter previously soaked in a concentrated solution of silver nitrate and dried. The silver chloride thus formed is reduced to metallic silver under ultra-violet light. The results on natural hailstones and laboratory doped ice show that foreign molecules are mainly segregated along the grain boundaries rather than being captured in the ice lattice.The technique, which makes quantitative evaluations possible, appears promising in all experimental studies on natural ice (hailstones and sea ice) and on ice artificially grown in the laboratory (by accretion or by freezing of solutions).

Beschreibung: Surface deformations in the neighborhood of a crevasse field were measured over short (3 m) gage lengths in order to study flow conditions associated with crevasse formation. The results obtained were unusual in that they were inconsistent with large-scale results found by previous workers. It was concluded that the presence of small-scale surface effects, such as fractures, pot-holes and healed crevasses give rise to small-scale deformation fields with large spatial and temporal variations and that there is a lower limit of gage length below which deformation measurements pertinent to regional (low phenomena cannot be made. This lower limit is apparently an order of magnitude greater than the spacing of the features which give rise to localized effects.

Beschreibung: The hypothesis of the explosion of a number of planets and moons of our Solar System during its 4.6-billion-year history is in excellent accord with all known observational constraints, even without adjustable parameters orad hochelper hypotheses. Many of its boldest predictions have been fulfilled. In most instances, these predictions were judged highly unlikely by the current standard models. Moreover, in several cases, the entire exploded planet model was at risk of being falsified if the predictions failed. The successful predictions include: (1) satellites of asteroids; (2) satellites of comets; (3) salt water in meteorites; (4) ‘roll marks’ leading to boulders on asteroids; (5) the time and peak rate of the 1999 Leonid meteor storm; (6) explosion signatures for asteroids; (7) the strongly spiked energy parameter for new comets; (8) the distribution of black material on slowly rotating airless bodies; (9) splitting velocities of comets; (10) the asteroid-like nature ofDeep Impacttarget Comet Tempel 1; and (11) the presence of high-formation-temperature minerals in theStardustcomet dust sample return. In physics and astronomy, hypotheses are either falsified if their predictions fail, or proved to be of value if they succeed. By all existing evidence, the exploded planet hypothesis has proved far more useful than the half-dozen or so hypotheses it would replace. Among the many important corollaries are these. (a) Perhaps as many as six former planets of our Solar System have exploded over its 4.6-billion-year history. (b) In particular, Mars is not an original planet, but a former moon of an exploded planet. (c) As a major player in Solar System evolution, the exploded planet scenario must be considered as a likely propagation vehicle for the spread of biogenic organisms. We conclude with a brief mention of three possible planetary explosion mechanisms.

Beschreibung: The degree and nature of association between trace metals (Cu, Pb, Zn, Ni, Ag, & Cd) and cyanobacterial mats, phytoplankton and sediments has been assessed in the Lake Vanda region of the Wright Valley, Victoria Land. Trace metal:Fe ratios and SEM imaging confirmed that apparent trace metal enrichment in cyanobacterial mats, relative to the sediment beneath, was due to incorporation of fine (sub-micron) sediment particles in the muciligenous matrix of the mat. In suspended particulate material (SPM) filtered from the oxic water of Lake Vanda and the Onyx River, the degree of trace metal binding to the SPM did not appear to correlate with phytoplankton content. Instead a positive correlation was observed between Fe and trace metal content. The SPM at the top of the lake water column, where only the finest sediment remains suspended, had the highest trace metal concentrations. It is concluded that the trace metal content of cyanobacterial mats and phytoplankton samples is primarily due to incorporation of fine sediment particles of high surface area which therefore enhance trace metal adsorption capacity. This reinforces the existing hypothesis that trace metal solubility in this environment is primarily controlled by abiotic processes.

Beschreibung: Field observations during a journey through the arid regions of the South American Andes in June-July 1969 are evaluated in conjunction with available air photographs and reports from adjacent regions of the High Andes. Results indicate an increase of the Pleistocene snow-line depression in the western Cordillera from about 700 m at lat. 12° S. to more than 1 500 m at lat. 30° S. The Pleistocene snow-line depression decreases from the Pacific to the Atlantic side of the Andes, but particularly strongly so on the poleward fringe of the arid region. From this geomorphic evidence it is suggested that the atmospheric circulation during the glacial period was characterized by an Equatorward displacement of the boundary between tropical easterlies and temperate-latitude westerlies.

Beschreibung: The analysis of steady-state flow over bedrock perturbations of Budd(1970[a]) is extended to evaluate the stress variations associated with the flow. In particular the four separate terms of the fundamental one-dimensional (longitudinal) stress equation (Budd,1968) are examined to show explicitly how the longitudinal stress gradient G, the base stress τ, the surface slope stress s, and the integrated second derivative of the shear stress T all vary over-a given wave.The result shows an error of a factor of 2 in some earlier studies relating longitudinal stress variations to the slope. This error resulted from the erroneous assumption that remains constant at its regional value. In fact the basal stress varies over the undulations in a similar way to the longitudinal stress gradient, and this is the same as the surface slope stress for long waves, but for short waves or less) requires the addition of the fourth term T, which then becomes dominant.

Beschreibung: Micrographs of the surface of evaporating polycrystalline ice containing impurities are presented. The micrographs show that impurities that enter the ice lattice substitutionally enhance the fine structure on the surface, but impurities rejected by the lattice suppress the fine structure. It is concluded that the observed fine structure is not an artifact of the machine but a real property of evaporating ice dependent upon the defects at the surface.

Beschreibung: The north-west margin of the main ice cap in south-western Ellesmere Island is fringed by ice-cored moraines. The formation of these moraines seems to be more complex than simple upwarping of the foliation bands at the margin of the ice cap. At one locality, where outer and inner zones can be distinguished on the basis of lithological composition, debris in the outer zone is composed of material from farther back under the ice cap than debris in the inner zone. In another locality, localized ridges cross each other independently of the trend of the main ridge.The time required to obtain the quantity of debris forming the moraine at the ice surface is estimated to be between 65 and 300 years.

Beschreibung: Polycrystalline ice, growing from the melt, can exert a pressure against an extended obstacle, even though it is free to grow in other directions. Pressures of over 0.2 bar (20kN m-2) have been measured with simple apparatus. This phenomenon may be important in explaining the frost-shattering of rocks.

Beschreibung: When rectangular single crystals of ice were subjected to uniaxial compression parallel to their Long axes and viewed between crossed polarizers, interference fringes were often observed. Some of these interference bands were associated with grain boundaries formed as a result of “kinking”. These can be explained in terms of the known anisotropic optical properties of ice and the change in the orientation of the optic axis across the boundary. This case has been analysed in detail with the aid of Jones’ calculus and good quantitative agreement exists between the theory and the experimental observations.Other interference bands were observed parallel to the trace of the basal plane on the surface of some deformed crystals. Alternative hypotheses for the explanation of this phenomenon have been considered and it seems probable that these bands are a result of slight random misorientations between adjacent slip lamellae. Applying Jones’ calculus to a simple model of such a deformed crystal indicates that the required misorientations are of the order of 1º If this explanation is correct, it implies that dislocations with non-basal Burgers vectors (probably c[0001]) make an active contribution to the deformation.

Beschreibung: Panspermia, the dissemination of life through space, would require resistance to the conditions found in space, including UV light. All known life forms depend on DNA to store information. In an effort to understand the liabilities of DNA to UV light and modes of DNA protection in terrestrial life forms, we established UV–VUV (125–340 nm) absorption spectra for dry DNA and its polymerized components and mononucleotides, as well as for a selection of potential UV screens ubiquitous in all organisms, including proteins, selected amino acids and amines (polyamines and tyramine). Montmorillonite clay was included as a potential abiotic UV screen. Among the potential screens tested, adenosine triphosphate (ATP) appeared to be particularly attractive, because its UV absorption spectrum was similar to that of DNA. We suggest that the use of ATP in UV protection could have pre-dated its current role in energy transfer. Spectroscopy also showed that UV absorption varied according to nucleotide content, suggesting that base pair usage could be a factor in adaptation to given UV environments and the availability of UV screens.

Beschreibung: About 5400 cal yr BP, a large landslide formed a 〉 400-m-tall dam in the upper Marsyandi River, central Nepal. The resulting lacustrine and deltaic deposits stretched 〉 7 km upstream, reaching a thickness of 120 m.14C dating of 7 wood fragments reveals that the aggradation and subsequent incision occurred remarkably quickly (∼ 500 yr). Reconstructed volumes of lacustrine (∼ 0.16 km3) and deltaic (∼ 0.09 km3) deposits indicate a bedload-to-suspended load ratio of 1:2, considerably higher than the ≤ 1:10 that is commonly assumed. At the downstream end of the landslide dam, the river incised a new channel through ≥ 70 m of Greater Himalayan gneiss, requiring a minimum bedrock incision rate of 13 mm/yr over last 5400 yr. The majority of incision presumably occurred over a fraction of this time, suggesting much higher rates. The high bedload ratio from such an energetic mountain river is a particularly significant addition to our knowledge of sediment flux in orogenic environments.

Beschreibung: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Fluorescence microscopy allows us to observe fluorescently labeled molecules in diverse biological processes and organelle structures within living cells. However, the diffraction limit restricts its spatial resolution to about half of its wavelength, limiting the capability of biological observation at the molecular level. Structured-illumination microscopy (SIM), a type of super-resolution microscopy, doubles the spatial resolution in all three dimensions by illuminating the sample with a patterned excitation light, followed by computer reconstruction. SIM uses a relatively low illumination power compared with other methods of super-resolution microscopy and is easily available for multicolor imaging. SIM has great potential for meeting the requirements of live-cell imaging. Recent developments in diverse types of SIM have achieved higher spatial (~50 nm lateral) and temporal (~100 Hz) resolutions. Here, we review recent advancements in SIM and discuss its application in noninvasive live-cell imaging.

Beschreibung: One of the most popular super-resolution microscopies that breaks the diffraction barrier is stimulated emission depletion (STED) microscopy. As the optical set-up of STED microscopy is based on a laser scanning microscopy (LSM) system, it potentially has several merits of LSM like confocal or two-photon excitation LSM. In this article, we first describe the principles of STED microscopy and then describe the features of our newly developed two-photon excitation STED microscopy. On the basis of our recent results and those of other researchers, we conclude by discussing future research and new technologies in this field.

Beschreibung: The electrically automated ultrathin sectioning apparatus, which has been developed in recent years, can produce consecutive ultrathin sections with a diamond knife and a gallium ion beam. These newly developed apparatuses, however, have several shortcomings, such as the limited block cutting area, thermal damage to the sample by the focused ion beam and a sample electronic charge. To overcome these faults and for easier scanning electron microscopy three-dimensional fine structural reconstruction, we have developed a new cutting method using a deep ultraviolet laser, which we have named the ‘LANTome (Light Ablation Nanotome)’. Using this method, we confirmed the widening of sectioning areas, shortening of the sectioning time, automatic smoothing of rough surfaces, no sample electronic charge and minimal heat effects on the sample tissue, such as thermal denaturation.

Beschreibung: Recent advances in nanoscopy, which breaks the diffraction barrier and can visualize structures smaller than the diffraction limit in cells, have encouraged biologists to investigate cellular processes at molecular resolution. Since nanoscopy depends not only on special optics but also on ‘smart’ photophysical properties of photocontrollable fluorescent probes, including photoactivatability, photoswitchability and repeated blinking, it is important for biologists to understand the advantages and disadvantages of fluorescent probes and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available fluorescent probes based on both proteins and synthetic compounds applicable to nanoscopy and provide a guideline for selecting optimal probes for specific applications.

Beschreibung: As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy – or rather nanoscopy – to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem.

Beschreibung: Publication date: Available online 8 August 2015 Source: Quaternary Research Author(s): Socorro Lozano-García, Beatriz Ortega, Priyadarsi D. Roy, Laura Beramendi-Orosco, Margarita Caballero We inferred millennial-scale climate variations and paleohydrological conditions in the northern sector of the American tropics for 30.3–5.5 cal ka BP using geochemical characteristics of sediments from Lake Chalco in central Mexico. The sediment sequence is chronologically constrained with three tephra and nine radiocarbon dates. Temporal variations in titanium, total inorganic carbon, total organic carbon/titanium ratio, carbon/nitrogen ratio, and silica/titanium ratio indicate changes in runoff, salinity, productivity, and sources. Higher concentrations of Ti indicate more runoff during latest Marine Isotope Stage (MIS) 3 (30.3–28.6 cal ka BP). Runoff was lower during the last glacial maximum (LGM; 23–19 cal ka BP) than during the Heinrich 2 event (26–24 cal ka BP). The interval of reduced runoff continued up to 17.5 cal ka BP but increased during the Bølling/Allerød. Trends of decreasing runoff and increasing salinity are observed throughout MIS 1. Lake Chalco received less runoff during the LGM compared to deglaciation, opposite the trend of other North American tropical records. Different amounts of rainfall at different sites are possibly due to shifts in the position of the Intertropical Convergence Zone, changes in the size of the Altlantic warm pool, and varying sea-surface temperatures of the Atlantic and Pacific oceans.

Beschreibung: Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally . This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.

Beschreibung: Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola . BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae . The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea .

Beschreibung: Gene expression evolution occurs through changes in cis - or trans -regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus ) and within species (comparing two closely related S. cerevisiae strains).

Beschreibung: Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (~7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (~10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes.

Beschreibung: Publication date: Available online 31 July 2015 Source: Quaternary Research Author(s): Linda M. Reinink-Smith In northeastern Kuwait, ancient beach ridges and associated berms are separated from the present shoreline by a 4–6 km-wide sabkha. A diverse mollusk fauna in the beach ridges attests to a former open marine environment. A total of 21 AMS dates were obtained in this study. Thirteen mollusk samples from beach ridges yielded AMS dates ranging from ~ 6990 cal yr BP in the southeast to ~ 3370 cal yr BP in the northwest, suggesting a southeast to northwest age progression during the Holocene transgression. In contrast, four samples from berms throughout the study area yielded AMS dates of 5195–3350 cal yr BP showing no age progression; these berms consist largely of Conomurex persicus gastropods that aggregated by storms during a highstand at ~ 5000–3500 cal yr BP. The berms are presently at ~ + 6 m above sea level, 2–3 m above the beach ridges. Human settlements were common on the ridge crests before and after the highstand. Regression to present-day sea level commenced after the highstand, which is when the sabkha began forming. A landward, marine-built terrace, which yielded AMS dates > 43,500 14 C yr BP, probably formed during Marine Oxygen Isotope Stage 5e and hence is not genetically related to the beach ridges.

Beschreibung: Viruses rely completely on the hosts’ machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.

Beschreibung: Huntington's disease (HD) is a hereditary neurodegenerative disorder characterized by brain atrophy particularly in striatum leading to personality changes, chorea and dementia. Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase in the crossroad of many signaling pathways that is highly pleiotropic as it phosphorylates more than hundred substrates including structural, metabolic, and signaling proteins. Increased GSK-3 activity is believed to contribute to the pathogenesis of neurodegenerative diseases like Alzheimer's disease and GSK-3 inhibitors have been postulated as therapeutic agents for neurodegeneration. Regarding HD, GSK-3 inhibitors have shown beneficial effects in cell and invertebrate animal models but no evident efficacy in mouse models. Intriguingly, those studies were performed without interrogating GSK-3 level and activity in HD brain. Here we aim to explore the level and also the enzymatic activity of GSK-3 in the striatum and other less affected brain regions of HD patients and of the R6/1 mouse model to then elucidate the possible contribution of its alteration to HD pathogenesis by genetic manipulation in mice. We report a dramatic decrease in GSK-3 levels and activity in striatum and cortex of HD patients with similar results in the mouse model. Correction of the GSK-3 deficit in HD mice, by combining with transgenic mice with conditional GSK-3 expression, resulted in amelioration of their brain atrophy and behavioral motor and learning deficits. Thus, our results demonstrate that decreased brain GSK-3 contributes to HD neurological phenotype and open new therapeutic opportunities based on increasing GSK-3 activity or attenuating the harmful consequences of its decrease.

Beschreibung: Spinocerebellar ataxia type 6 (SCA6) is dominantly inherited neurodegenerative disease, caused by an expansion of CAG repeat encoding a polyglutamine (PolyQ) tract in the Ca v 2.1 voltage-gated calcium channel. Its key pathological features include selective degeneration of the cerebellar Purkinje cells (PCs), a common target for PolyQ-induced toxicity in various SCAs. Mutant Ca v 2.1 confers toxicity primarily through a toxic gain-of-function mechanism; however, its molecular basis remains elusive. Here, we studied the cerebellar gene expression patterns of young Sca6 -MPI 118Q/118Q knockin (KI) mice, which expressed mutant Ca v 2.1 from an endogenous locus and recapitulated many phenotypic features of human SCA6. Transcriptional signatures in the MPI 118Q/118Q mice were distinct from those in the Sca1 154Q/2Q mice, a faithful SCA1 KI mouse model. Temporal expression profiles of the candidate genes revealed that the up-regulation of genes associated with microglial activation was initiated before PC degeneration and was augmented as the disease progressed. Histological analysis of the MPI 118Q/118Q cerebellum showed the predominance of M1-like pro-inflammatory microglia and it was concomitant with elevated expression levels of tumor necrosis factor, interleukin-6, Toll-like receptor (TLR) 2 and 7. Genetic ablation of MyD88, a major adaptor protein conveying TLR signaling, altered expression patterns of M1/M2 microglial phenotypic markers in the MPI 118Q/118Q cerebellum. More importantly, it ameliorated PC loss and partially rescued motor impairments in the early disease phase. These results suggest that early neuroinflammatory response may play an important role in the pathogenesis of SCA6 and its modulation could pave the way for slowing the disease progression during the early stage of the disease.

Beschreibung: Publication date: Available online 8 August 2015 Source: Quaternary Research Author(s): Matthew E. Kirby, Edward J. Knell, William T. Anderson, Matthew S. lachniet, Jennifer Palermo, Holly Eeg, Ricardo Lucero, Rosa Murrieta, Andrea Arevalo, Emily Silveira, Christine A. Hiner Silver Lake is the modern terminal playa of the Mojave River in southern California (USA). As a result, it is well located to record both influences from the winter precipitation dominated San Bernardino Mountains – the source of the Mojave River – and from the late summer to early fall North American monsoon at Silver Lake. Here, we present various physical, chemical and biological data from a new radiocarbon-dated, 8.2 m sediment core taken from Silver Lake that spans modern through 14.8 cal ka BP. Texturally, the core varies between sandy clay, clayey sand, and sand-silt-clay, often with abrupt sedimentological transitions. These grain-size changes are used to divide the core into six lake status intervals over the past 14.8 cal ka BP. Notable intervals include a dry Younger Dryas chronozone, a wet early Holocene terminating 7.8 – 7.4 cal ka BP, a distinct mid-Holocene arid interval, and a late Holocene return to ephemeral lake conditions. A comparison to potential climatic forcings implicates a combination of changing summer – winter insolation and tropical and N Pacific sea-surface temperature dynamics as the primary drivers of Holocene climate in the central Mojave Desert.

Beschreibung: Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso , to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca . Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N -linked glycan library and PDB homologous/non-homologous N -glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign . Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Motivation: Impedance-based technologies are advancing methods for measuring proliferation of adherent cell cultures non-invasively and in real time. The analysis of the resulting data has so far been hampered by inappropriate computational methods and the lack of systematic data to evaluate the characteristics of the assay. Results: We used a commercially available system for impedance-based growth measurement (xCELLigence) and compared the reported cell index with data from microscopy. We found that the measured signal correlates linearly with the cell number throughout the time of an experiment with sufficient accuracy in subconfluent cell cultures. The resulting growth curves for various colon cancer cells could be well described with the empirical Richards growth model, which allows for extracting quantitative parameters (such as characteristic cycle times). We found that frequently used readouts like the cell index at a specific time or the area under the growth curve cannot be used to faithfully characterize growth inhibition. We propose to calculate the average growth rate of selected time intervals to accurately estimate time-dependent IC50 values of drugs from growth curves. Contact: nils.bluethgen@charite.de Supplementary information: Supplementary data are available at Bioinformatics online.

Beschreibung: Research Articles Graça Ermida Polar Record , FirstView Article(s) , 6 pages Abstract

Beschreibung: Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture ( Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.

Beschreibung: Cellular Ca 2+ homeostasis is tightly regulated and is pivotal to life. Inositol 1,4,5-trisphosphate receptors (IP 3 Rs) and ryanodine receptors (RyRs) are the major ion channels that regulate Ca 2+ release from intracellular stores. Although these channels have been extensively investigated in multicellular organisms, an appreciation of their evolution and the biology of orthologs in unicellular organisms is largely lacking. Extensive phylogenetic analyses reveal that the IP 3 R gene superfamily is ancient and diverged into two subfamilies, IP 3 R-A and IP 3 R-B/RyR, at the dawn of Opisthokonta. IP 3 R-B/RyR further diversified into IP 3 R-B and RyR at the stem of Filozoa. Subsequent evolution and speciation of Holozoa is associated with duplication of IP 3 R-A and RyR genes, and loss of IP 3 R-B in the vertebrate lineages. To gain insight into the properties of IP 3 R important for the challenges of multicellularity, the IP 3 R-A and IP 3 R-B family orthologs were cloned from Capsaspora owczarzaki, a close unicellular relative to Metazoa (designated as CO.IP 3 R-A and CO.IP 3 R-B). Both proteins were targeted to the endoplasmic reticulum. However, CO.IP 3 R-A, but strikingly not CO.IP 3 R-B, bound IP 3 , exhibited robust Ca 2+ release activity and associated with mammalian IP 3 Rs. These data indicate strongly that CO.IP 3 R-A as an exemplar of ancestral IP 3 R-A orthologs forms bona fide IP 3 -gated channels. Notably, however, CO.IP 3 R-A appears not to be regulated by Ca 2+ , ATP or Protein kinase A-phosphorylation. Collectively, our findings explore the origin, conservation, and diversification of IP 3 R gene families and provide insight into the functionality of ancestral IP 3 Rs and the added specialization of these proteins in Metazoa.

Beschreibung: Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity.

Beschreibung: The environment has profound effects on the expression of many traits and reaction norms describe the expression dynamics of a trait across a broad range of environmental conditions. Here, we analyze gene expression in Drosophila melanogaster across four different developmental temperatures (13–29 °C). Gene expression is highly plastic with 83.3% of the genes being differentially expressed. We distinguished three components of plasticity: 1) Dynamics of gene expression intensity (sum of change), 2) direction of change, and 3) curvature of the reaction norm (linear vs. quadratic). Studying their regulatory architecture we found that all three plasticity components were most strongly affected by the number of different transcription factors (TFs) binding to the target gene. More TFs were found in genes with less expression changes across temperatures. Although the effect of microRNAs was weaker, we consistently noted a trend in the opposite direction. The most plastic genes were regulated by fewer TFs and more microRNAs than less plastic genes. Different patterns of plasticity were also reflected by their functional characterization based on gene ontology. Our results suggest that reaction norms provide an important key to understand the functional requirements of natural populations exposed to variable environmental conditions.

Beschreibung: Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops , which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.

Beschreibung: Recent developments in the analysis of amino acid covariation are leading to breakthroughs in protein structure prediction, protein design, and prediction of the interactome. It is assumed that observed patterns of covariation are caused by molecular coevolution, where substitutions at one site affect the evolutionary forces acting at neighboring sites. Our theoretical and empirical results cast doubt on this assumption. We demonstrate that the strongest coevolutionary signal is a decrease in evolutionary rate and that unfeasibly long times are required to produce coordinated substitutions. We find that covarying substitutions are mostly found on different branches of the phylogenetic tree, indicating that they are independent events that may or may not be attributable to coevolution. These observations undermine the hypothesis that molecular coevolution is the primary cause of the covariation signal. In contrast, we find that the pairs of residues with the strongest covariation signal tend to have low evolutionary rates, and that it is this low rate that gives rise to the covariation signal. Slowly evolving residue pairs are disproportionately located in the protein’s core, which explains covariation methods’ ability to detect pairs of residues that are close in three dimensions. These observations lead us to propose the "coevolution paradox": The strength of coevolution required to cause coordinated changes means the evolutionary rate is so low that such changes are highly unlikely to occur. As modern covariation methods may lead to breakthroughs in structural genomics, it is critical to recognize their biases and limitations.

Beschreibung: We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC) 3 (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions are 1) utilizing 64-bit variables, thereby enabling ta(MC) 3 to process larger data sets than MrBayes; and 2) to use Kahan summation to improve accuracy, convergence rates, and consequently runtime. Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware. GPU MrBayes V3.1 is available from http://sourceforge.net/projects/mrbayes-gpu/ .