Small Molecule LC-MS/MS Fragmentation Data Analysis and Application to Siderophore Identification

Rapid developments in tandem liquid chromatography-mass spectrometry (LC-MS/MS) have created wide interest in applications for the analysis of small molecule mixtures. MS/MS spectra can contain rich structural information, but because of the structural diversity of small molecules and different data acquisition methods, analysis algorithms and workflows frequently need to be tailored to individual research questions. This chapter shows how MATLAB can be used for LC-MS/MS-based structural characterization of small molecules. Starting with the import of raw data, ways for visualization and the creation of graphical user interfaces (GUIs) for individual applications are demonstrated. A selection of frequently used algorithms for pre-processing and data analysis is reviewed in context of their MATLAB implementation. The approaches are then tailored and applied to the analysis of iron-binding peptides (peptidic siderophores) by high-resolution LC-MS/MS. The method uses a database with siderophore structures to exploit prior knowledge about siderophore structural diversity for the interpretation of MS/MS spectra from known and new siderophores

Towards an assessment of Aeolus' Mie radiometric performance

The intensity of the return signal acquired by Aeolus depends on numerous factors such as the output laser energy, the state of the atmosphere along the line of sight, the characteristics of the target, the optical elements of the instrument and the alignment of laser beam and telescope. Already at an early stage of the mission, it was found that a significant part of the atmospheric backscatter signal was missing on the Rayleigh channel. Whereas the properties of the transmission and reception path of the Rayleigh channel can be simulated to a reasonable extent by the Aeolus End-To-End Simulator (E2S), it is much more difficult to align the simulation to the actual characteristics of the Mie channel, in particular to the transmission function of the Fizeau spectrometer. As a first attempt to assess the radiometric performance of Aeolus Mie channel, we are trying to derive a ratio between simulated and actual Aeolus signals. Therefore, we compare useful signals obtained with the E2S against measurements made with Aeolus in aerosol-laden atmospheric scenes. In this context, the backscatter and extinction measurements of portable ground-based Raman lidar systems from PollyNET as well as temperature and pressure information from external sources represent essential inputs for the simulation. Elevated, optically thick, vertically extended and preferably homogeneous aerosol layers are considered as the most suitable target. With the Raman lidars sensing a drifting aerosol layer from a fixed location and Aeolus as a mobile instrument sampling a quasi-fixed layer, optimisation is needed concerning the match of geolocation between the ground-based and space-borne measurements. Present ratios derived from scenes over Leipzig (Germany) and Al Dhaid (United Arabic Emirates) range from 0.6 to 0.9 (less measured signal than simulated). These factors show relative uncertainties of at least ±20% with expected error contributions based on the differences between Aeolus measurements, ground based measurements and simulation, i.e. location, heterogeneity of aerosol layers, E2S input parameters, assumptions in the handling of depolarised signals, potential cloud cover at altitudes higher than the measurement range, additional noise sources, etc. Reducing the number of contributors as well as their magnitude poses the biggest challenge for a reliable assessment of the Mie radiometric performance, which might only be achievable via statistical analyses on a larger number of cases

The Disunity of Consciousness

It is commonplace for both philosophers and cognitive scientists to express their allegiance to the "unity of consciousness". This is the claim that a subject’s phenomenal consciousness, at any one moment in time, is a single thing. This view has had a major influence on computational theories of consciousness. In particular, what we call single-track theories dominate the literature, theories which contend that our conscious experience is the result of a single consciousness-making process or mechanism in the brain. We argue that the orthodox view is quite wrong: phenomenal experience is not a unity, in the sense of being a single thing at each instant. It is a multiplicity, an aggregate of phenomenal elements, each of which is the product of a distinct consciousness-making mechanism in the brain. Consequently, cognitive science is in need of a multi-track theory of consciousness; a computational model that acknowledges both the manifold nature of experience, and its distributed neural basis

Tracer Survey in the Cape Verde Region Traceraufnahme in der Kapverdenregion Cruise No. 10, Leg 1 October 31 – December 06, 2008 Ponta Delgada (Portugal) – Mindelo (Cape Verde Islands)

The research cruise MSM10/1 was extremely successful. All programs were able to collect high quality data and the anticipated goals of the expedition were fully met. We have been able to carry out the first comprehensive survey of a tracer release in the Guinea Upwelling region (GUTRE) roughly seven month after the tracer was released at 8°N 23°W in April 2008. We have estimated that a total of 40% of the tracer was found during this cruise. While the horizontal spreading and mixing was larger than anticipated, the vertical extent of the tracer found was small. The low vertical tracer spreading rate estimates are supported by the micro structure profile data. The extensive survey of the upper 1000m of the oxygen minimum zone (OMZ) allowed comparing our sections with several previous surveys. We found that the lowest oxygen values in the core of the OMZ have dropped at record low values below 40 μmol/kg. The preliminary findings from the trace metal work focused on Fe ligand measurements shows a slight higher excess ligand concentration in the surface (50m) for three stations. The two other stations show a slight decrease at this depth. A large number of biochemical samples were taken and were analyzed in Kiel for DNA and RNA diversity. The tracer release experiment provided an ideal environment for repeated biochemical sampling in the same water mass

Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters

Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate the role of water for their spread in more detail, we characterized ESBL/Carbapenemase-producing bacteria from surface water and sediment samples using phenotypic and genotypic approaches. ESBL/Carbapenemase-producing isolates were obtained from water/sediment samples. Species and antibiotic resistance were determined. A subset of these isolates (n = 33) was whole-genome-sequenced and analyzed for the presence of antibiotic resistance genes and virulence determinants. Their relatedness to isolates associated with human infections was investigated using multilocus sequence type and cgMLST-based analysis. Eighty-nine percent of the isolates comprised of clinically relevant species. Fifty-eight percent exhibited a multidrug-resistance phenotype. Two isolates harbored the mobile colistin resistance gene mcr-1. One carbapenemase-producing isolate identified as Enterobacter kobei harbored bla(VIM-)(1). Two Escherichia coli isolates had sequence types (ST) associated with human infections (ST131 and ST1485) and a Klebsiella pneumoniae isolate was classified as hypervirulent. A multidrug-resistant (MDR) Pseudomonas aeruginosa isolate encoding known virulence genes associated with severe lung infections in cystic fibrosis patients was also detected. The presence of MDR and clinically relevant isolates in recreational and surface water underlines the role of aquatic environments as both reservoirs and hot spots for MDR bacteria. Future assessment of water quality should include the examination of the multidrug resistance of clinically relevant bacterial species and thus provide an important link regarding the spread of MDR bacteria in a One Health context.Peer reviewe

Dissolved cadmium in the Southern Ocean: Distribution, speciation, and relation to phosphate

We report isotope dilution analyses of dissolved cadmium (Cd) and electrochemical Cd speciation measurements in the Atlantic sector of the Southern Ocean. Bioavailable inorganic Cd is > 100 times higher in near-surface waters south of the Polar Front compared to the Subantarctic Zone because of upwelling and reduced complexation by organic Cd ligands. To trace local changes in the relation between Cd and P, we examine the deviations from a linear deep-water Cd vs. P relation (Cd*), and find that changes in Cd* coincide with the position of frontal systems and covary with primary productivity and total dissolved Mn and Fe concentrations. These covariations agree with potential local changes in phytoplankton Cd uptake rates, resulting from differences in the availability of Cd, Zn, Mn, and Fe. A band of negative Cd* values is associated with formation of Subantarctic Mode Water (SAMW) and Antarctic Intermediate Water (AAIW). In contrast to SAMW, which may export low Cd : P ratios from the Southern Ocean, the Cd : P ratios in AAIW increase by mixing with underlying Upper Circumpolar Deep Water before being exported from the Southern Ocean. Deep waters show constant Cd : P ratios, and both elements behave conservatively with end-member mixing between deep waters of the Weddell Gyre, the Antarctic Circumpolar Current, and inflowing North Atlantic Deep Water. Overall, our results support the hypothesis that the kink in the global Cd vs. P relation is largely caused by high Cd : P uptake ratios in the trace-nutrient–limited Southern Ocean

A 610-MHz survey of the ELAIS-N1 field with the Giant Metrewave Radio Telescope - Observations, data analysis and source catalogue

Observations of the ELAIS-N1 field taken at 610 MHz with the Giant Metrewave Radio Telescope are presented. Nineteen pointings were observed, covering a total area of 9 square degrees with a resolution of 6" x 5", PA +45 deg. Four of the pointings were deep observations with an rms of 40 microJy before primary beam correction, with the remaining fifteen pointings having an rms of 70 microJy. The techniques used for data reduction and production of a mosaicked image of the region are described, and the final mosaic is presented, along with a catalogue of 2500 sources detected above 6 sigma. This work complements the large amount of optical and infrared data already available on the region. We calculate 610-MHz source counts down to 270 microJy, and find further evidence for the turnover in differential number counts below 1 mJy, previously seen at both 610 MHz and 1.4 GHz.Comment: 12 pages, 18 figures, two tables. Table 1 can be found in full via http://www.mrao.cam.ac.uk/surveys/ . Accepted for publication in MNRA

Blazars in the Fermi Era: The OVRO 40-m Telescope Monitoring Program

The Large Area Telescope (LAT) aboard the Fermi Gamma-ray Space Telescope provides an unprecedented opportunity to study gamma-ray blazars. To capitalize on this opportunity, beginning in late 2007, about a year before the start of LAT science operations, we began a large-scale, fast-cadence 15 GHz radio monitoring program with the 40-m telescope at the Owens Valley Radio Observatory (OVRO). This program began with the 1158 northern (declination>-20 deg) sources from the Candidate Gamma-ray Blazar Survey (CGRaBS) and now encompasses over 1500 sources, each observed twice per week with a ~4 mJy (minimum) and 3% (typical) uncertainty. Here, we describe this monitoring program and our methods, and present radio light curves from the first two years (2008 and 2009). As a first application, we combine these data with a novel measure of light curve variability amplitude, the intrinsic modulation index, through a likelihood analysis to examine the variability properties of subpopulations of our sample. We demonstrate that, with high significance (7-sigma), gamma-ray-loud blazars detected by the LAT during its first 11 months of operation vary with about a factor of two greater amplitude than do the gamma-ray-quiet blazars in our sample. We also find a significant (3-sigma) difference between variability amplitude in BL Lacertae objects and flat-spectrum radio quasars (FSRQs), with the former exhibiting larger variability amplitudes. Finally, low-redshift (z<1) FSRQs are found to vary more strongly than high-redshift FSRQs, with 3-sigma significance. These findings represent an important step toward understanding why some blazars emit gamma-rays while others, with apparently similar properties, remain silent.Comment: 23 pages, 24 figures. Submitted to ApJ

EU DEMO Remote Maintenance System development during the Pre-Concept Design Phase

During the EU DEMO Pre-Concept Design Phase, the remote maintenance team developed maintenance strategies and systems to meet the evolving plant maintenance requirements. These were constrained by the proposed tokamak architecture and the challenging environments but considered a range of port layouts and handling system designs. The design-driving requirements were to have short maintenance durations and to demonstrate power plant relevant technologies. Work concentrated on the in-vessel maintenance systems, where the design constraints are the most challenging and the potential impact on the plant design is highest. A robust blanket handling system design was not identified during the Pre-Concept Design Phase. Novel enabling technologies were identified and, where these were critical to the maintenance strategy and not being pursued elsewhere, proof-of-principle designs were developed and tested. Technology development focused on pipe joining systems such as laser bore cutting and welding, pipe alignment, and on the control systems for handling massive blankets. Maintenance studies were also conducted on the ex-vessel plant to identify the additional transport volumes required to support the plant layout. The strategic implications of using vessel casks, and of using containment cells with cell casks, was explored. This was motivated by the costs associated with the storage of casks, one of several ex-vessel systems that can drive the overall plant layout. This paper introduces the remote maintenance system designs, describes the main developments and achievements, and presents conclusions, lessons learned and recommendations for future work

LAYERS: a decision-support tool to illustrate and assess the supply and value chain for the energy transition

Climate change mitigation strategies are developed at international, national, and local authority levels. Technological solutions such as renewable energies (RE) and electric vehicles (EV) have geographically widespread knock-on effects on raw materials. In this paper, a decision-support and data-visualization tool named “LAYERS” is presented, which applies a material flow analysis to illustrate the complex connections along supply chains for carbon technologies. A case study focuses on cobalt for lithium-ion batteries (LIB) required for EVs. It relates real business data from mining and manufacturing to actual EV registrations in the UK to visualize the intended and unintended consequences of the demand for cobalt. LAYERS integrates a geographic information systems (GIS) architecture, database scheme, and whole series of stored procedures and functions. By means of a 3D visualization based on GIS, LAYERS conveys a clear understanding of the location of raw materials (from reserves, to mining, refining, manufacturing, and use) across the globe. This highlights to decision makers the often hidden but far-reaching geo-political implications of the growing demands for a range of raw materials that are needed to meet long-term carbon-reduction targets