Description: Journal of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.5b01698

Description: During the last decade, the number of three-dimensional structures solved by X-ray crystallography has increased dramatically. By 2014, it had crossed the landmark of 100 000 biomolecular structures deposited in the Protein Data Bank. This tremendous increase in successfully crystallized proteins is primarily owing to improvements in cloning strategies, the automation of the crystallization process and new innovative approaches to monitor crystallization. However, these improvements are mainly restricted to soluble proteins, while the crystallization and structural analysis of membrane proteins or proteins that undergo major post-translational modifications remains challenging. In addition, the need for relatively large crystals for conventional X-ray crystallography usually prevents the analysis of dynamic processes within cells. Thus, the advent of high-brilliance synchrotron and X-ray free-electron laser (XFEL) sources and the establishment of serial crystallography (SFX) have opened new avenues in structural analysis using crystals that were formerly unusable. The successful structure elucidation of cathepsin B, accomplished by the use of microcrystals obtained by in vivo crystallization in baculovirus-infected Sf9 insect cells, clearly proved that crystals grown intracellularly are very well suited for X-ray analysis. Here, methods by which in vivo crystals can be obtained, isolated and used for structural analysis by novel highly brilliant XFEL and synchrotron-radiation sources are summarized and discussed.

Description: The upwelling area off North-West Africa is characterized by high export production, high nitrate and low oxygen concentration in bottom waters. The underlying sediment consists of sands that cover most of the continental shelf. Due to their permeability sands allow for fast advective pore water transport and can exhibit high rates of nitrogen (N) loss via denitrification as reported for anthropogenically eutrophied regions. However, N loss from sands underlying naturally eutrophied waters is not well studied, and in particular, N loss from the North-West African shelf is poorly constrained. During two research cruises in April/May 2010/2011, sediment was sampled along the North-West African shelf and volumetric denitrification rates were measured in sediment layers down to 8 cm depth using slurry incubations with 15N-labeled nitrate. Areal N loss was calculated by integrating volumetric rates down to the nitrate penetration depth derived from pore water profiles. Areal N loss was neither correlated with water depth nor with bottom water concentrations of nitrate and oxygen but was strongly dependent on sediment grain size and permeability. The derived empirical relation between benthic N loss and grains size suggests that pore water advection is an important regulating parameter for benthic denitrification in sands and further allowed extrapolating rates to an area of 53,000 km2 using detailed sediment maps. Denitrification from this region amounts to 995 kt yr−1 (average 3.6 mmol m−2 d−1) which is 4 times higher than previous estimates based on diffusive pore water transport. Sandy sediments cover 50–60% of the continental shelf and thus may contribute significantly to the global benthic N loss.

Description: Innovative robotic technologies are a key to study ocean processes in space and time. The work carried out during the ROBEX-Demonstration Mission on RV Polarstern will test the capability of new and innovative technologies, developed during the HGF Alliance ROBEX, in deep-sea environments. Investigations will include Arctic benthic and pelagic ecosystems strongly influenced by climate change, such as marine arctic sediments hosting gas hydrates and arctic deep-sea benthic communities. Different robotic platforms, including 3 types of crawler, glider, AUV, UAVs and senor systems (like Lab-on-a- Chip and multi-O2-profiler) are described and mission scenarios presented. The use of these new underwater technologies will improve our capabilities to improve our knowledge on the effects of climate change on the Arctic ecosystem and ocean observation.

Description: Large amounts of the greenhouse gas methane are released from the seabed but liberation of methane to the atmosphere is mitigated by aerobic methanotrophs in the water column. The size and activity of methanotrophic communities are thought to be mainly determined by nutrient and redox dynamics, but little is known about the effects of water mass transport. Here, we show that cold bottom waters at methane seeps west off Svalbard, which contained a large number of aerobic methanotrophs, were rapidly displaced by warmer waters with a considerably smaller methanotrophic community. This water mass exchange, caused by short-term variations of the West Spitsbergen Current strongly reduced methanotrophic activity. Currents are common at many methane seeps and could thus be a globally important control on methane oxidation in the water column.

Description: In this paper we provide an overview of new knowledge on oxygen depletion (hypoxia) and related phenomena in aquatic systems resulting from the EU-FP7 project HYPOX (“In situ monitoring of oxygen depletion in hypoxic ecosystems of coastal and open seas, and landlocked water bodies”, www.hypox.net). In view of the anticipated oxygen loss in aquatic systems due to eutrophication and climate change, HYPOX was set up to improve capacities to monitor hypoxia as well as to understand its causes and consequences. Temporal dynamics and spatial patterns of hypoxia were analyzed in field studies in various aquatic environments, including the Baltic Sea, the Black Sea, Scottish and Scandinavian fjords, Ionian Sea lagoons and embayments, and Swiss lakes. Examples of episodic and rapid (hours) occurrences of hypoxia, as well as seasonal changes in bottom-water oxygenation in stratified systems, are discussed. Geologically driven hypoxia caused by gas seepage is demonstrated. Using novel technologies, temporal and spatial patterns of watercolumn oxygenation, from basin-scale seasonal patterns to meter-scale sub-micromolar oxygen distributions, were resolved. Existing multidecadal monitoring data were used to demonstrate the imprint of climate change and eutrophication on long-term oxygen distributions. Organic and inorganic proxies were used to extend investigations on past oxygen conditions to centennial and even longer timescales that cannot be resolved by monitoring. The effects of hypoxia on faunal communities and biogeochemical processes were also addressed in the project. An investigation of benthic fauna is presented as an example of hypoxia-devastated benthic communities that slowly recover upon a reduction in eutrophication in a system where naturally occurring hypoxia overlaps with anthropogenic hypoxia. Biogeochemical investigations reveal that oxygen intrusions have a strong effect on the microbially mediated redox cycling of elements. Observations and modeling studies of the sediments demonstrate the effect of seasonally changing oxygen conditions on benthic mineralization pathways and fluxes. Data quality and access are crucial in hypoxia research. Technical issues are therefore also addressed, including the availability of suitable sensor technology to resolve the gradual changes in bottom-water oxygen in marine systems that can be expected as a result of climate change. Using cabled observatories as examples, we show how the benefit of continuous oxygen monitoring can be maximized by adopting proper quality control. Finally, we discuss strategies for state-of-the-art data archiving and dissemination in compliance with global standards, and how ocean observations can contribute to global earth observation attempts.

Description: AB: The methane seepage area off West Spitzbergen, which was first discovered in 2008, is reported to feature more than 250 gas bubbles release sites in water depth between 150 and 400 m. Because the depth zone overlaps with the boundary of gas hydrate stability and since this area has experienced a warming of the northward-flowing West Spitzbergen current by 1°C over the last 30 years, it has been speculated that the gas seepage is connected to recent gas hydrate dissociation. However, so far comprehensive biogeochemical studies, which could support this hypothesis, are lacking. In August 2011, we will conduct an expedition with the German RV Poseidon to explore the seafloor and water column in the vicinity of the gas seeps to search for physical, geochemical, biological, and geological characteristics that could provide information about the persistence of the gas seepage. In case the gas venting is caused by recent gas hydrate dissociation, we expect to find rather virgin sediments with respect to common cold-seep characteristics such as methanotrophic activity and the presence of chemosynthetic organisms and authigenic carbonates; whereas a full establishment of these features would support the idea of a long-lasting process. Anomalies in porewater characteristics provide further information about gas hydrate formation/dissociation dynamics. We will present preliminary results from the RV Poseidon expedition to provide fresh insights into this exciting research area. Data will includ