Glacier response to the change in atmospheric circulation in the eastern Mediterranean during the Last Glacial Maximum

In this study, we document glacial deposits and reconstruct the glacial history in the Karagöl valley system in the eastern Uludağ in northwestern Turkey based on 42 cosmogenic 10Be exposure ages from boulders and bedrock. Our results suggest the Last Glacial Maximum (LGM) advance prior to 20.4 ± 1.2 ka and at least three re-advances until 18.6 ± 1.2 ka during the global LGM within Marine Isotope Stage-2. In addition, two older advances of unknown age are geomorphologically well constrained, but not dated due to the absence of suitable boulders. Glaciers advanced again two times during the Lateglacial. The older is exposure dated to not later than 15.9 ± 1.1 ka and the younger is attributed to the Younger Dryas (YD) based on field evidence. The timing of the glaciations in the Karagöl valley correlates well with documented archives in the Anatolian and Mediterranean mountains and the Alps. These glacier fluctuations may be explained by the change in the atmospheric circulation pattern during the different phases of North Atlantic Oscillation (NAO) winter indices.

What Limits Bacterial Production in the Suboxic Region of Permanently Ice-Covered Lake Bonney, Antarctica?

Bacterial production assays (thymidine incorporation rates) were used to evaluate the activity of heterotrophic bacteria at the chemocline region in both the East (ELB) and West (WLB) Lobes of permanently ice-covered Lake Bonney, in the Taylor Valley of Antarctica. The magnitude of activity varied dramatically within the depth interval of 1 to 2 m from moderate to very low levels below the chemocline, especially in the East Lobe, where chemical distributions indicate the absence of a normally functioning nitrogen cycle. Several parameters (e.g. addition of nutrients or chelators, dilution) were manipulated in incubation experiments in order to identify factors that would enhance activity in the suboxic deep waters of the East Lobe. Activity, in terms of thymidine incorporation, was consistently detected in the deep-water communities, implying that, although the water may be 'toxic', the cells remain viable. None of the treatments resulted in consistent enhancement of thymidine incorporation rates in samples from below the chemocline. Bacterial populations above the chemocline appear to be phosphorus-limited. The nature of the limitation, toxicity or inhibition that limits bacterial activity in the suboxic waters has not been identified.

Retrospective analysis of a nonforecasted rain-on-snow flood in the Alps – a matter of model limitations or unpredictable nature?

A rain-on-snow flood occurred in the Bernese Alps, Switzerland, on 10 October 2011, and caused significant damage. As the flood peak was unpredicted by the flood forecast system, questions were raised concerning the causes and the predictability of the event. Here, we aimed to reconstruct the anatomy of this rain-on-snow flood in the Lötschen Valley (160 km2) by analyzing meteorological data from the synoptic to the local scale and by reproducing the flood peak with the hydrological model WaSiM-ETH (Water Flow and Balance Simulation Model). This in order to gain process understanding and to evaluate the predictability. The atmospheric drivers of this rain-on-snow flood were (i) sustained snowfall followed by (ii) the passage of an atmospheric river bringing warm and moist air towards the Alps. As a result, intensive rainfall (average of 100 mm day-1) was accompanied by a temperature increase that shifted the 0° line from 1500 to 3200 m a.s.l. (meters above sea level) in 24 h with a maximum increase of 9 K in 9 h. The south-facing slope of the valley received significantly more precipitation than the north-facing slope, leading to flooding only in tributaries along the south-facing slope. We hypothesized that the reason for this very local rainfall distribution was a cavity circulation combined with a seeder-feeder-cloud system enhancing local rainfall and snowmelt along the south-facing slope. By applying and considerably recalibrating the standard hydrological model setup, we proved that both latent and sensible heat fluxes were needed to reconstruct the snow cover dynamic, and that locally high-precipitation sums (160 mm in 12 h) were required to produce the estimated flood peak. However, to reproduce the rapid runoff responses during the event, we conceptually represent likely lateral flow dynamics within the snow cover causing the model to react "oversensitively" to meltwater. Driving the optimized model with COSMO (Consortium for Small-scale Modeling)-2 forecast data, we still failed to simulate the flood because COSMO-2 forecast data underestimated both the local precipitation peak and the temperature increase. Thus we conclude that this rain-on-snow flood was, in general, predictable, but requires a special hydrological model setup and extensive and locally precise meteorological input data. Although, this data quality may not be achieved with forecast data, an additional model with a specific rain-on-snow configuration can provide useful information when rain-on-snow events are likely to occur.

Urban expansion and its impact on urban agriculture – remote sensing based change analysis of Kizinga and Mzinga Valley – Dar Es Salaam, Tanzania

Urban agriculture is a phenomenon that can be observed world-wide, particularly in cities of devel-oping countries. It is contributing significantly to food security and food safety and has sustained livelihood of the urban and peri-urban low income dwellers in developing countries for many years. Population increase due to rural-urban migration and natural, coupled with formal as well as infor-mal urbanization are competing with urban farming for available space and scarce water resources. A multitemporal multisensoral urban change analysis over the period of 25 years (1982-2007) was performed in order to measure and visualize the urban expansion along the Kizinga and Mzinga valley in the South of Dar es Salaam. Airphotos and VHR satellite data were analyzed by using a combination of a composition of anisotropic textural measures and spectral information. The study revealed that unplanned built-up area is expanding continuously and vegetation covers and agricultural lands decline at a fast rate. The validation showed that the overall classification accuracy varied depending on the database. The extracted built-up areas were used for visual in-terpretation mapping purposes and served as information source for another research project. The maps visualize an urban congestion and expansion of nearly 18% of the total analyzed area that had taken place in the Kizinga valley between 1982 and 2007. The same development can be ob-served in the less developed and more remote Mzinga valley between 1981 and 2002. Both areas underwent fast changes where land prices still tend to go up and an influx of people both from rural and urban areas continuously increase density with the consequence of increasing multiple land use interests.

The deglaciation history of the Simplon region (southern Swiss Alps) constrained by 10Be exposure dating of ice-molded bedrock surfaces

The deglaciation history of the Swiss Alps after the Last Glacial Maximum involved the decay of several ice domes and the subsequent disintegration of valley glaciers at high altitude. Here we use bedrock exposure dating to reconstruct the temporal and spatial pattern of ice retreat at the Simplon Pass (altitude: ∼2000 m) located 40 km southwest of the ‘Rhône ice dome’. Eleven 10Be exposure ages from glacially polished quartz veins and ice-molded bedrock surfaces cluster tightly between 13.5 ± 0.6 ka and 15.4 ± 0.6 ka (internal errors) indicating that the Simplon Pass depression became ice-free at 14.1 ± 0.4 ka (external error of mean age). This age constraint is interpreted to record the melting of the high valley glaciers in the Simplon Pass region during the warm Bølling–Allerød interstadial shortly after the Oldest Dryas stadial. Two bedrock samples collected a few hundred meters above the pass depression yield older 10Be ages of 17.8 ± 0.6 ka and 18.0 ± 0.6 ka. These ages likely reflect the initial downwasting of the Rhône ice dome and the termination of the ice transfluence from the ice dome across the Simplon Pass toward the southern foreland. There, the retreat of the piedmont glacier in Val d’Ossola was roughly synchronous with the decay of the Rhône ice dome in the interior of the mountain belt, as shown by 10Be ages of 17.7 ± 0.9 ka and 16.1 ± 0.6 ka for a whaleback at ∼500 m elevation near Montecrestese in northern Italy. In combination with well-dated paleoclimate records derived from lake sediments, our new age data suggest that during the deglaciation of the European Alps the decay of ice domes was approximately synchronous with the retreat of piedmont glaciers in the foreland and was followed by the melting of high-altitude valley glaciers after the transition from the Oldest Dryas to the Bølling–Allerød, when mean annual temperatures rose rapidly by ∼3 °C.

The Role of Forest Soils in a Northern New England Effluent Management System

The Carrabassett Valley Sanitary District in Carrabassett Valley, Maine has utilized both a forest spray irrigation system and a Snowfluent™ system for the treatment of their wastewater effluent. This study was designed to evaluate potential changes in soil properties after approximately 20 years of treatment in the forested spray irrigation site and three years of treatment in the field Snowfluent™ site. In addition, grass yield and composition were evaluated on the field study sites. After treatment with effluent or Snowfluent™, soils showed an increase in soil exchangeable Ca, Mg, Na, and K, base saturation, and pH. While most constituents were higher in treated soils, available P was lower in treated soils compared to the controls. This difference was attributed to higher rates of P mineralization from soil organic matter due to an irrigation effect of the treatment, depleting available P pools despite the P addition with the treatment. Most of the differences due to treatment were greatest at the surface and diminished with depth. Depth patterns in soil properties mostly reflected the decreasing influence of organic matter and its decomposition products with depth as evidenced by significantly higher total C in the surface compared to lower horizons. There were decreasing concentrations of total N, and exchangeable or extractable Ca, Mg, Na, K, Mn, Zn, and P with depth. In addition, there was decreasing BS with depth, driven primarily by declining exchangeable Ca and Mg. Imgation with Snowfluent™ altered the chemical composition of the grass on the site. All element concentrations were significantly higher in the grass foliage except for Ca. The differences were attributed to the additional nutrients and moisture derived from the Snowfluent™. The use of forest spray imgation and Snowfluent™ as a wastewater treatment strategy appears to work well. The soil and vegetation were able to retain most of the applied nutrients, and do not appear to be moving toward saturation. Vegetation management may be a key tool for managing nutrient accumulation on the grass sites as the system ages.

Regional Specialization in Communal Agriculture: The Shakers, 1850- 1880

When the Shakers established communal farms in the Ohio Valley, they encountered a new agricultural environment that was substantially different from the familiar soils, climates, and markets of New England and the Hudson Valley. The ways in which their response to these new conditions differed by region has not been well documented. We examine patterns of specialization among the Shakers using the manuscript schedules of the federal Agricultural Censuses from 1850 through 1880. For each Shaker unit, we also recorded a random sample of five farms in the same township (or all available farms if there were fewer than five). The sample of neighboring farms included 75 in 1850, 70 in the next two census years, and 66 in 1880. A Herfindahl-type index suggested that, although the level of specialization was less among the Shakers than their neighbors, trends in specialization by the Shakers and their neighbors were remarkably similar when considered by region. Both Eastern and Western Shakers were more heavily committed to dairy and produce than were their neighbors, while Western Shakers produced more grains than did Eastern Shakers, a pattern imitated in nearby family farms. Livestock and related production was far more important to the Eastern Shakers than to the Western Shakers, again similar to patterns in the census returns from other farms. We conclude that, despite the obvious scale and organizational differences, Shaker production decisions were based on the same comparative advantages that determined production decisions of family farms.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Geo-referenced photo-mosaics of the Menez Gwen Hydrothermal Vent (Mid-Atlantic Ridge)

The Menez Gwen hydrothermal vents, located on the flanks of a small young volcanic structure in the axial valley of the Menez Gwen seamount, are the shallowest known vent systems on the Mid-Atlantic Ridge that host chemosynthetic communities. Although visited several times by research cruises, very few images have been published of the active sites, and their spatial dimensions and morphologies remain difficult to comprehend. We visited the vents on the eastern flank of the small Menez Gwen volcano during cruises with RV Poseidon (POS402, 2010) and RV Meteor (M82/3, 2010), and used new bathymetry and imagery data to provide first detailed information on the extents, surface morphologies, spatial patterns of the hydrothermal discharge and the distribution of dominant megafauna of five active sites. The investigated sites were mostly covered by soft sediments and abundant white precipitates, and bordered by basaltic pillows. The hydrothermally-influenced areas of the sites ranged from 59 to 200 m**2. Geo-referenced photomosaics and video data revealed that the symbiotic mussel Bathymodiolus azoricus was the dominant species and present at all sites. Using literature data on average body sizes and biomasses of Menez Gwen B. azoricus, we estimated that the B. azoricus populations inhabiting the eastern flank sites of the small volcano range between 28,640 and 50,120 individuals with a total biomass of 50 to 380 kg wet weight. Based on modeled rates of chemical consumption by the symbionts, the annual methane and sulfide consumption by B. azoricus could reach 1760 mol CH4 yr**-1 and 11,060 mol H2S yr**-1. We propose that the chemical consumption by B. azoricus over at the Menez Gwen sites is low compared to the natural release of methane and sulfide via venting fluids.

Geochemistry of the oceanic crust from ocean drilling samples

This book presents new data on chemical and mineral compositions and on density of altered and fresh igneous rocks from key DSDP and ODP holes drilled on the following main tectonomagmatic structures of the ocean floor: 1. Mid-ocean ridges and abyssal plains and basins (DSDP Legs 37, 61, 63, 64, 65, 69, 70, 83, and 91 and ODP Legs 106, 111, 123, 129, 137, 139, 140, 148, and 169); 2. Seamounts and guyots (DSDP Legs 19, 55, and 62 and ODP Legs 143 and 144); 3. Intraplate rises (DSDP Legs 26, 33, 51, 52, 53, 72, and 74 and ODP Legs 104, 115, 120, 121, and 183); and 4. Marginal seas (DSDP Legs 19, 59, and 60 and ODP Legs 124, 125, 126, 127, 128, and 135). Study results of altered gabbro from the Southwest Indian Ridge (ODP Leg 118) and serpentinized ultramafic rocks from the Galicia margin (ODP Leg 103) are also presented. Samples were collected by the authors from the DSDP/ODP repositories, as well as during some Glomar Challenger and JOIDES Resolution legs. The book also includes descriptions of thin sections, geochemical diagrams, data on secondary mineral assemblages, and recalculated results of chemical analyses with corrections for rock density. Atomic content of each element can be quantified in grams per standard volume (g/1000 cm**3). The suite of results can be used to estimate mass balance, but parts of the data need additional work, which depends on locating fresh analogs of altered rocks studied here. Results of quantitative estimation of element mobility in recovered sections of the upper oceanic crust as a whole are shown for certain cases: Hole 504B (Costa Rica Rift) and Holes 856H, 857C, and 857D (Middle Valley, Juan de Fuca Ridge).

Planktonic foraminifera in the Maastrichtian of Hor-Hahar

The lengthy warm, stable climate of the Cretaceous terminated in the Campanian with a cooling trend, interrupted in the early and latest Maastrichtian by two events of global warming, at ~70-68 Ma and at 65.78-65.57 Ma. These climatic oscillations had a profound effect on pelagic ecosystems, especially on planktic foraminiferal populations. Here we compare biotic responses in the tropical-subtropical (Tethyan) open ocean and mesotrophic (Zin Valley, Israel) and oligotrophic (Tunisia) slopes, which correlate directly with global warming and cooling. The two warming events coincide with blooms of Guembelitria, an extreme opportunist genus best known as the main survivor of the Cretaceous-Paleogene (K-Pg) catastrophe. In the Maastrichtian, Guembelitria bloomed in the uppermost surface water above shelf and slope environments but failed to reach the open ocean as it did at K-Pg. The coldest interval of the late Maastrichtian (~68-65.78 Ma) is marked by an acme of the otherwise rare species Gansserina gansseri, a deep-dwelling keeled globotruncanid. The G. gansseri acme event can be traced from the deep ocean even onto the Tethyan slope, marking copious production and circulation of cold intermediate water. This acme is abruptly terminated by extinction of the species, a dramatic reversal attributed to a short-term global warming episode. This extinction corresponds precisely with the second bloom of Guembelitria that began ~300 kyr prior to the K-Pg event. The antithetical relationship between blooming of Guembelitria and the G. gansseri acme reflects planktic foraminiferal sensitivity to warm-cool-warm-cool climatic oscillations marking the end of the Cretaceous.

Trace metals in sediments of the Var Canyon turbidite system at the DYFAMED station in the Ligurian Sea

The magnitude and the chronology of anthropogenic impregnation by Hg and other trace metals of environmental concern (V, Cr, Ni, Cu, Zn, Ag, Cd and Pb, including its stable isotopes) in the sediments are determined at the DYFAMED station, a site in the Ligurian Sea (Northwestern Mediterranean) chosen for its supposed open-sea characteristics. The DYFAMED site (VD) is located on the right levee of the Var Canyon turbidite system, at the end of the Middle Valley. In order to trace the influence of the gravity current coming from the canyon on trace metal distribution in the sediment, we studied an additional sediment core (VA) from a terrace of the Var Canyon, and material collected in sediment traps at the both sites at 20 m above sea bottom. The patterns of Hg and other trace element distribution profiles are interpreted using stable Pb isotope ratios as proxies for its sources, taking into account the sedimentary context (turbidites, redox conditions, and sedimentation rates). Major element distributions, coupled with the stratigraphic examination of the sediment cores point out the high heterogeneity of the deposits at VA, and major turbiditic events at both sites. At the DYFAMED site, we observed direct anthropogenic influence in the upper sediment layer (<2 cm), while on the Var Canyon site (VA), the anthropization concerns the whole sedimentary column sampled (19 cm). Turbiditic events superimpose their specific signature on trace metal distributions. According to the 210Pbxs-derived sedimentation rate at the DYFAMED site (0.4 mm yr-1), the Hg-enriched layer of the top core corresponds to the sediment accumulation of the last 50 years, which is the period of the highest increase in Hg deposition on a global scale. With the hypothesis of the absence of significant post-depositional redistribution of Hg, the Hg/C-org ratio changes between the surface and below are used to estimate the anthropogenic contribution to the Hg flux accumulated in the sediment. The Hg enrichment, from pre-industrial to the present time is calculated to be around 60%, consistent with estimations of global Hg models. However, based on the chemical composition of the trapped material collected in sediment traps, we calculated that epibenthic mobilization of Hg would reach 73%. Conversely, the Cd/C-org ratio decreases in the upper 5 cm, which may reflect the recent decrease of atmospheric Cd inputs or losses due to diagenetic processes.

Tab. 2: Gravity measurements of the Inntal underground at Thaur

A cross-section of the Inn-valley has been surveyed by refraction- and refiection-seismic and gravimetrie methods. The thickness of the Inn-va.!ley sediments is 340- 390 m. At the northern edge of the valley an intermediate layer between sediments and basement has been detected, which is up to 300 ITl thick. This zone seems to mark the boundary of the northern calcareous alps.