Aryl Sulfonates in Inversions at Secondary Carbohydrate Hydroxyl Groups: A New and Improved Route Toward 3-Azido-3-deoxy-beta-D-galactopyranosides

A method of using benzenesulfonates and imidazylates as leaving groups at the secondary C3 galactopyranose carbon, instead of the commonly used less stable triflate leaving group, to facilitate scale-up and improve reproducibility is disclosed. The benzenesulfonates and imidazylates were proven to be significantly more stable than the corresponding triflates and the method was used to devise an improved route toward 3-azido-3-deoxy-beta-D-galactopyranosides

Atlantic Water Boundary Current Along the Southern Yermak Plateau, Arctic Ocean

The major ocean current that carries heat into the Arctic Ocean splits into three main branches of Atlantic Water (AW) and recirculations when it encounters the Yermak Plateau (YP) located north of Svalbard. While the branches that cross the plateau and recirculations have been extensively studied, there has been limited observation of the transport and variability of the Yermak branch. In this study, we present year-round observations from an array of three moorings that were deployed across the boundary current on the southern slope of the YP. The temporal-averaged sections show a surface-intensified AW core, which is strongest in winter but also persistent throughout the record within the upper 500 m. The volume transport of AW is highest in fall (1.4 ± 0.2 Sv; 1 Sv = 106 m3 s−1) and decreases to 0.8 ± 0.1 Sv in summer. Beneath a surface-intensified core, the velocity profile has a minimum at middepth, gradually increasing toward the bottom. This cold, bottom-intensified current is detectable in all seasons and reaches a maximum transport of 1.5 Sv in spring. The transport of AW is regulated by wind stress curl and coastal upwelling along the northwestern shelf of Svalbard. A positive wind stress curl increases the volume transport in the Yermak branch, thereby reducing the Svalbard branch transport. Eddy kinetic energy is surface-intensified and decreases to negligible values below 500 m. In the upper 500 m, the average baroclinic conversion in winter and summer is about 1 × 10−5 W m−3, which is 4–10 times the barotropic conversion rates.publishedVersio

Tools and data services registry: a community effort to document bioinformatics resources

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools

Dissipation measurements using temperature microstructure from an underwater glider

Microstructure measurements of temperature and current shear are made using an autonomous underwater glider. The glider is equipped with fast-response thermistors and airfoil shear probes, providing measurements of dissipation rate of temperature variance, χχ, and of turbulent kinetic energy, εε, respectively. Furthermore, by fitting the temperature gradient variance spectra to a theoretical model, an independent measurement of εε is obtained. Both Batchelor (εBεB) and Kraichnan (εKεK) theoretical forms are used. Shear probe measurements are reported elsewhere; here, the thermistor-derived εBεB and εKεK are compared to the shear probe results, demonstrating the possibility of dissipation measurements using gliders equipped with thermistors only. A total of 152 dive and climb profiles are used, collected during a one-week mission in the Faroe Bank Channel, sampling the turbulent dense overflow plume and the ambient water above. Measurement of εε with thermistors using a glider requires careful consideration of data quality. Data are screened for glider flight properties, measurement noise, and the quality of fits to the theoretical models. Resulting dissipation rates from the two independent methods compare well for dissipation rates below 2×10−7 W kg−1. For more energetic turbulence, thermistors underestimate dissipation rates significantly, caused primarily by increased uncertainty in the time response correction. Batchelor and Kraichnan spectral models give very similar results. Concurrent measurements of εε and χχ are used to compute the dissipation flux coefficient ΓΓ (or so-called apparent mixing efficiency). A wide range of values is found, with a mode value of Γ≈0.14Γ≈0.14, in agreement with previous studies. Gliders prove to be suitable platforms for ocean microstructure measurements, complementary to existing methods

Molecular basis for galectin-ligand interactions : Design, synthesis and analysis of ligands

Galectins are a class of β-galactoside-binding proteins that bind glycoconjugates and have been implicated in cancer, regulation of immunity and inflammation. Design and synthesis have achieved highly potent and selective galectin ligands that can inhibit interactions with glycoproteins and have consequent cellular effects. These ligands can be used as tools to further elucidate the roles of galectins in biological processes, and also, potentially, to diagnose and treat diseases. The present theis is about further development of such galectin ligands. A more robust synthetic route to 3-azido-3-deoxy-β-D-galactopyranosides, key intermediates in the synthesis of previous galectin ligands, has been developed. Bis-3-(4-aryl-1,2,3-triazol-1-yl)-thiodigalactosides are potent galectin-1 and galectin-3 ligands and by screening different aryl groups, the affinities and selectivities for galectin-1 and galectin-3 were improved. In case of galectin-1, the aryl group binds in a smaller binding pocket than in galectin-3, thus five-membered heterocycles were screened with the 2-thiazole having the highest galectin-1 affinity. In case of galectin-3, substituted phenyls were screened with the 3,4,5-trifluorophenyl having the highest galectin-3 affinity. Introducing these aryl groups onto thiodigalactosides resulted in ligands with single-digit nM affinity and 10-50 fold selectivity towards either of galectin-1 or galectin-3. Structural analysis of the galectin-3 ligands identified orthogonal multipolar fluorine-amide interactions and cation-π interactions as main contributors to the high affinity. Based on these findings, monosaccharide derivatives with high selectivity and low nM galectin-3 affinities were developed. Galectin-3 is a biomarker used to diagnose heart failure and through immobilization of a highly potent galectin-3 ligand in a microtiter plate, an assay has been developed that binds both intact and truncated galectin-3 C-terminal domain

Tidal forcing, energetics, and mixing near the Yermak Plateau

The Yermak Plateau (YP), located northwest of Svalbard in Fram Strait, is the final passage for the inflow of warm Atlantic Water into the Arctic Ocean. The region is characterized by the largest barotropic tidal velocities in the Arctic Ocean. Internal response to the tidal flow over this topographic feature locally contributes to mixing that removes heat from the Atlantic Water. Here, we investigate the tidal forcing, barotropic-to-baroclinic energy conversion rates, and dissipation rates in the region using observations of oceanic currents, hydrography, and microstructure collected on the southern flanks of the plateau in summer 2007, together with results from a global high-resolution ocean circulation and tide model simulation. The energetics (depth-integrated conversion rates, baroclinic energy fluxes and dissipation rates) show large spatial variability over the plateau and are dominated by the luni-solar diurnal (K1) and the principal lunar semidiurnal (M2) constituents. The volume-integrated conversion rate over the region enclosing the topographic feature is approximately 1 GW and accounts for about 50% of the M2 and approximately all of the K1 conversion in a larger domain covering the entire Fram Strait extended to the North Pole. Despite the substantial energy conversion, internal tides are trapped along the topography, implying large local dissipation rates. An approximate local conversion–dissipation balance is found over shallows and also in the deep part of the sloping flanks. The baroclinic energy radiated away from the upper slope is dissipated over the deeper isobaths. From the microstructure observations, we inferred lower and upper bounds on the total dissipation rate of about 0.5 and 1.1 GW, respectively, where about 0.4–0.6 GW can be attributed to the contribution of hot spots of energetic turbulence. The domain-integrated dissipation from the model is close to the upper bound of the observed dissipation, and implies that almost the entire dissipation in the region can be attributed to the dissipation of baroclinic tidal energy

Microstructure Measurements from an Underwater Glider in the Turbulent Faroe Bank Channel Overflow

Measurements of ocean microstructure are made in the turbulent Faroe Bank Channel overflow using a turbulence instrument attached to an underwater glider. Dissipation rate of turbulent kinetic energy « is measured using airfoil shear probes.Acomparison is made between 152 profiles from dive and climb cycles of the glider during a 1-week mission in June 2012 and 90 profiles collected from the ship using a vertical microstructure profiler (VMP). Approximately one-half of the profiles are collocated. For 96% of the dataset, measurements are of high quality with no systematic differences between dives and climbs. The noise level is less than 5 x 10-¹¹ W kg-¹, comparable to the best microstructure profilers. The shear probe data are contaminated and unreliable at the turning depth of the glider and for U/ut < 20, where U is the flow past the sensor, ut =(ε/N)¹/² is an estimate of the turbulent velocity scale, and N is the buoyancy frequency. Averaged profiles of ε from the VMP and the glider agree to better than a factor of 2 in the turbulent bottom layer of the overflow plume, and beneath the stratified and sheared plume–ambient interface. The glider average values are approximately a factor of 3 and 9 times larger than the VMP values in the layers defined by the isotherms 3°–6° and 6°–9°C, respectively, corresponding to the upper part of the interface and above. The discrepancy is attributed to a different sampling scheme and the intermittency of turbulence. The glider offers a noise-free platform suitable for ocean microstructure measurements

Microstructure measurements using a glider in the Faroe Bank Channel Overflow

The application of turbulence instrumentation on underwater gliders is addressed, and two methods for glider-inferred dissipation rates of turbulent kinetic energy are evaluated against a ship-based vertical microstructure profiler. The well-established ship-based measurements are used as a reference for the analysis. A Slocum glider was deployed for one week in the Faroe Bank Channel, equipped with a MicroRider with turbulence sensors for velocity shear and temperature microstructure. Dissipation rates of turbulent kinetic energy are calculated from velocity shear by integrating the wavenumber spectrum after fitting it to the Nasmyth universal spectrum. Survey-averaged profiles from the glider's shear-derived dissipation rates have similar shape as that measured by the vertical microstructure profiler, but overestimate dissipation rates by up to a factor of 3 in the vicinity the turbulent interface, attributed to the glider's slanted path and inability to penetrate sufficiently undisturbed through the swift plume interface. Microstucture temperature profiles are used to calculate dissipation rates, which is done by fitting temperature gradient spectra to the universal Batchelor form using the maximum likelihood estimate. This method allows for automatic rejection criteria, which are applied to remove bad fits. Results compare reasonably well with the vertical microstructure profiler measurements, but are underestimated close to the bottom, which is a caveat of the Batchelor fit, consistent with a previous study. Overall, measurement of dissipation rates from gliders is a powerful addition to traditional shipborne turbulence profilers, as they make it possible to survey large areas by deploying several gliders. Measurements are reasonably accurate, and require much less dedicated ship time