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  • 1
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    Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low‐cost device is presented that functions as a cover for 96‐well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi‐crystal screening campaigns.
    Description: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Keywords: 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 2
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    Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple‐edge anomalous diffraction (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type.
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz‐kesterite structure type in contrast to the literature. image
    Keywords: 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 3
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    The copper(II)‐binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The growth of diffraction‐quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high‐affinity copper(II)‐binding tripeptide GHK was fused to the N‐terminus of a GFP variant and an MBP‐FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square‐pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S‐atom positions could also be located in log‐likelihood‐gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR‐SAD phasing.
    Description: A novel three‐residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described. image
    Keywords: 548 ; phasing ; crystallization ; GHK ; SAD
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  • 4
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    Determining paracrystallinity in mixed‐tacticity polyhydroxybutyrates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: Recently, the authors reported on the development of crystallinity in mixed‐tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X‐ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.
    Description: A method to robustly determine paracrystalline contents from Rietveld‐refined powder X‐ray data is presented and discussed for the example of mixed‐tacticity polyhydroxybutyrates. image
    Keywords: 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 5
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    Concepts for nondestructive and depth‐resolved X‐ray residual stress analysis in the near‐surface region of nearly single crystalline materials with mosaic structure (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Two evaluation concepts for nondestructive depth‐resolved X‐ray residual stress analysis in the near‐surface region of materials with cubic symmetry and nearly single crystalline structure are introduced by simulated examples. Both concepts are based on the same data acquisition strategy, which consists in the determination of lattice‐spacing depth profiles along the ⟨hkl⟩ poles by stepwise sample rotation around the scattering vector. Segmentation of these profiles parallel to the sample surface provides the lattice strain state as a function of depth. The first evaluation concept extends the crystallite group method developed for materials with pronounced crystallographic texture by the feature of depth resolution and can be applied to samples with arbitrary orientation. The second evaluation concept, which adapts the linear regression approach of the sin2ψ method for the case of single crystalline materials, is restricted to samples with (001) orientation. The influence of the strain‐free lattice parameter a0 on residual stress analysis using both evaluation concepts is discussed on the basis of explicitly derived relations.
    Description: Two data evaluation concepts are proposed for nondestructive and depth‐resolved X‐ray residual stress analysis by means of energy‐dispersive diffraction on materials featuring cubic symmetry and a nearly single crystalline structure. image
    Keywords: 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 6
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    X‐ray dichroism in polyimide caused by non‐resonant scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Dichroism is one of the most important optical effects in both the visible and the X‐ray range. Besides absorption, scattering can also contribute to dichroism. This paper demonstrates that, based on the example of polyimide, materials can show tiny dichroism even far from electronic resonances due to scattering. Although the effect is small, it can lead to a measurable polarization change and might have influence on highly sensitive polarimetric experiments.
    Description: Aligned molecules, for example in polyimide foils, lead to small dichroism even far from resonances, which can be revealed by high‐precision X‐ray polarimetry. image
    Keywords: 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 7
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    Elastic stiffness coefficients of thiourea from thermal diffuse scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high‐energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X‐ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high‐energy photons extends the applicability of the TDS‐based approach to organic compounds which would suffer from radiation damage at lower photon energies.
    Description: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Keywords: 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 8
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    Fast fitting of reflectivity data of growing thin films using neural networks (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-03
    Description: X‐ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α‐sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.
    Description: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Keywords: 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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  • 9
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    Numerically stable form factor of any polygon and polyhedron (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small‐angle scattering by nanocrystals.
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities. image
    Keywords: 548 ; form factors ; polyhedra ; Fourier shape transform
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  • 10
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    Crystal structure of a calcium(II)–pyrroloquinoline quinone (PQQ) complex outside a protein environment (2021)
    5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-04-14
    Description: Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium‐ and lanthanide‐dependent alcohol dehydrogenases, and has been known for over 30 years. Crystal structures of Ca–MDH enzymes (MDH is methanol dehydrogenase) have been known for some time; however, crystal structures of PQQ with biorelevant metal ions have been lacking in the literature for decades. We report here the first crystal structure analysis of a Ca–PQQ complex outside the protein environment, namely, poly[[undecaaquabis(μ‐4,5‐dioxo‐4,5‐dihydro‐1H‐pyrrolo[2,3‐f]quinoline‐2,7,9‐tricarboxylato)tricalcium(II)] dihydrate], {[Ca3(C14H3N2O8)2(H2O)11]·2H2O}n. The complex crystallized as Ca3PQQ2·13H2O with Ca2+ in three different positions and PQQ3−, including an extensive hydrogen‐bond network. Similarities and differences to the recently reported structure with biorelevant europium (Eu2PQQ2) are discussed.
    Description: Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium‐ and lanthanide‐dependent alcohol dehydrogenases. The crystal structure of a Ca–PQQ complex (Ca3PQQ2·13H2O) is reported for the first time outside a protein environment. image
    Description: research
    Keywords: 548 ; pyrroloquinoline quinone ; calcium ; PQQ ; methanol dehydrogenase ; crystal structure ; FID-GEO-DE-7
    Language: English
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  • 11
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    ROBL‐II at ESRF: a synchrotron toolbox for actinide research (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: ROBL‐II provides four different experimental stations to investigate actinide and other alpha‐ and beta‐emitting radionuclides at the new EBS storage ring of ESRF within an energy range of 3 to 35 keV. The XAFS station consists of a highly automatized, high sample throughput installation in a glovebox, to measure EXAFS and conventional XANES of samples routinely at temperatures down to 10 K, and with a detection limit in the sub‐p.p.m. range. The XES station with its five bent‐crystal analyzer, Johann‐type setup with Rowland circles of 1.0 and 0.5 m radii provides high‐energy resolution fluorescence detection (HERFD) for XANES, XES, and RIXS measurements, covering both actinide L and M edges together with other elements accessible in the 3 to 20 keV energy range. The six‐circle heavy duty goniometer of XRD‐1 is equipped for both high‐resolution powder diffraction as well as surface‐sensitive CTR and RAXR techniques. Single crystal diffraction, powder diffraction with high temporal resolution, as well as X‐ray tomography experiments can be performed at a Pilatus 2M detector stage (XRD‐2). Elaborate radioprotection features enable a safe and easy exchange of samples between the four different stations to allow the combination of several methods for an unprecedented level of information on radioactive samples for both fundamental and applied actinide and environmental research.
    Description: ROBL‐II at ESRF provides four experimental stations to investigate actinides with X‐ray absorption and emission spectroscopy, and with surface, high‐resolution powder, and single‐crystal X‐ray diffractometry.
    Keywords: 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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  • 12
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    ATSAS 3.0: expanded functionality and new tools for small‐angle scattering data analysis (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
    Description: ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems. image
    Keywords: 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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  • 13
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    XGANDALF – extended gradient descent algorithm for lattice finding (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real‐time feedback during serial crystallography experiments. It is implemented in an open‐source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
    Description: A description and evaluation are given of XGANDALF, extended gradient descent algorithm for lattice finding, an algorithm developed for fast and accurate indexing of snapshot diffraction patterns. image
    Keywords: 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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  • 14
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    pinkIndexer – a universal indexer for pink‐beam X‐ray and electron diffraction snapshots (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink‐beam X‐ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit‐cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink‐beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi‐monochromatic X‐rays and with electrons the algorithm indexed more patterns than other programs tested.
    Description: pinkIndexer, an algorithm developed for indexing of snapshot diffraction patterns recorded with pink‐beam X‐rays, monochromatic X‐rays and electrons, is described and its use evaluated. image
    Keywords: 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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  • 15
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    Crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-17
    Description: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal‐binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine‐dependent inhibitor compounds.
    Description: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Keywords: 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 16
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    Staircase array of inclined refractive multi‐lenses for large field of view pixel super‐resolution scanning transmission hard X‐ray microscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: Owing to the development of X‐ray focusing optics during the past decades, synchrotron‐based X‐ray microscopy techniques allow the study of specimens with unprecedented spatial resolution, down to 10 nm, using soft and medium X‐ray photon energies, though at the expense of the field of view (FOV). One of the approaches to increase the FOV to square millimetres is raster‐scanning of the specimen using a single nanoprobe; however, this results in a long data acquisition time. This work employs an array of inclined biconcave parabolic refractive multi‐lenses (RMLs), fabricated by deep X‐ray lithography and electroplating to generate a large number of long X‐ray foci. Since the FOV is limited by the pattern height if a single RML is used by impinging X‐rays parallel to the substrate, many RMLs at regular intervals in the orthogonal direction were fabricated by tilted exposure. By inclining the substrate correspondingly to the tilted exposure, 378000 X‐ray line foci were generated with a length in the centimetre range and constant intervals in the sub‐micrometre range. The capability of this new X‐ray focusing device was first confirmed using ray‐tracing simulations and then using synchrotron radiation at BL20B2 of SPring‐8, Japan. Taking account of the fact that the refractive lens is effective for focusing high‐energy X‐rays, the experiment was performed with 35 keV X‐rays. Next, by scanning a specimen through the line foci, this device was used to perform large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy (PSR‐STHXM) with a 780 ± 40 nm spatial resolution within an FOV of 1.64 cm × 1.64 cm (limited by the detector area) and a total scanning time of 4 min. Biomedical implant abutments fabricated via selective laser melting using Ti–6Al–4V medical alloy were measured by PSR‐STHXM, suggesting its unique potential for studying extended and thick specimens. Although the super‐resolution function was realized in one dimension in this study, it can be expanded to two dimensions by aligning a pair of presented devices orthogonally.
    Description: A new X‐ray focusing device generates hundreds of thousands of line foci, periodically spaced in the sub‐micrometre range, with centimetre length. It enables to achieve large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy. image
    Keywords: 502.82 ; inclined refractive X‐ray multi‐lens array ; pixel super‐resolution ; scanning transmission hard X‐ray microscopy ; deep X‐ray lithography and electroplating
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  • 17
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    A new concept for temporal gating of synchrotron X‐ray pulses (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-02
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented. First experimental tests of the concept yield a diffraction efficiency of 0.18%; however, the calculations indicate a theoretical efficiency and contrast of 〉30% and 10−5, respectively. The full efficiency of the pulse picker has not been reached yet due to a long‐range thermal deformation of the sample after absorption of the excitation laser. This method can be implemented in a broad spectral range (100 eV to 20 keV) and is only minimally invasive to an existing setup.
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Keywords: 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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  • 18
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    The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP at BESSY II (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-06
    Description: The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP for optical pump/X‐ray probe experiments at the electron storage ring BESSY II is dedicated to investigating the structural response of thin film samples and heterostructures after their excitation with ultrashort laser pulses and/or electric field pulses. It enables experiments with access to symmetric and asymmetric Bragg reflections via a four‐circle diffractometer and it is possible to keep the sample in high vacuum and vary the sample temperature between ∼15 K and 350 K. The femtosecond laser system permanently installed at the beamline allows for optical excitation of the sample at 1028 nm. A non‐linear optical setup enables the sample excitation also at 514 nm and 343 nm. A time‐resolution of 17 ps is achieved with the `low‐α' operation mode of the storage ring and an electronic variation of the delay between optical pump and hard X‐ray probe pulse conveniently accesses picosecond to microsecond timescales. Direct time‐resolved detection of the diffracted hard X‐ray synchrotron pulses use a gated area pixel detector or a fast point detector in single photon counting mode. The range of experiments that are reliably conducted at the endstation and that detect structural dynamics of samples excited by laser pulses or electric fields are presented.
    Description: The KMC‐3 XPP endstation of the synchrotron BESSY II is dedicated to time‐resolved studies of structural dynamics of matter upon optical and/or electrical excitation using hard X‐ray diffraction with an accessible time range from 17 ps to several microseconds. image
    Keywords: 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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  • 19
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    Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n‐propoxide (sodium n‐propanolate, NaOnPr), sodium n‐butoxide (sodium n‐butanolate, NaOnBu) and sodium n‐pentoxide (sodium n‐amylate, NaOnAm) were determined from powder X‐ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space‐group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti‐PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n‐propoxide n‐propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert‐amylate tert‐amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2‐methyl‐2‐butyl). Their crystal structures were determined by single‐crystal X‐ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen‐bond networks diverge widely among the solvate structures. The hydrogen‐bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
    Description: The crystal structures of NaOEt, NaOPr, NaOBu and NaOAm (Am = amyl = pentyl) were determined from powder data. These compounds crystallize in an anti‐PbO structure in the space groups P21m and P4/nmm. Additionally, solvates with the composition NaOEt·2EtOH, NaOPr·2PrOH, NaOiPr·5iPrOH and NaOtAm·tAmOH were synthesized, and their structures were determined from single crystals. They form interesting chain structures of different compositions and topologies. image
    Keywords: 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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  • 20
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    Small‐angle X‐ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Small‐angle X‐ray scattering from GaN nanowires grown on Si(111) is measured in the grazing‐incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X‐ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root‐mean‐square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre‐long facet, already gives rise to a strong intensity reduction.
    Description: The intensity of small‐angle X‐ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre‐long side facet notably changes the intensity curves. image
    Keywords: 548 ; nanowires ; Porod's law ; facet truncation rods ; small‐angle X‐ray scattering ; SAXS ; grazing‐incidence small‐angle X‐ray scattering ; GISAXS
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  • 21
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    The accuracy of protein models automatically built into cryo‐EM maps with ARP/wARP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Recent developments in cryogenic electron microscopy (cryo‐EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high‐resolution cryo‐EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo‐EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main‐chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo‐EM maps is comparable to that of X‐ray crystallographic models at similar local cryo‐EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
    Keywords: 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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  • 22
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    Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-05
    Description: Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single‐crystal X‐ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
    Description: A new orthocarbonate, Sr2CO4, was synthesized under extreme pressure and temperature conditions of 92 GPa and 2500 K, respectively. The crystal structure of the compound s fully characterized in situ by synchrotron single‐crystal X‐ray diffraction and DFT calculations were employed to provide insight into its equation of state, Raman and IR spectra, and bonding. image
    Keywords: 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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  • 23
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    Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
    Keywords: 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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  • 24
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-27
    Description: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite‐type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower‐symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non‐existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 25
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    Comparison and evaluation of pair distribution functions, using a similarity measure based on cross‐correlation functions (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-20
    Description: An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross‐correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross‐correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product‐moment correlation coefficient, using polymorph IV of barbituric acid as an example.
    Description: A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross‐correlation functions is introduced and evaluated. image
    Keywords: 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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  • 26
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    Novel experimental setup for megahertz X‐ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser (EuXFEL) (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The high‐precision X‐ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X‐ray Free‐Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump–probe X‐ray diffraction experiments in the DAC are described and their implementation demonstrated during the First User Community Assisted Commissioning experiment. X‐ray heating and diffraction of Bi under pressure, obtained using 20 fs X‐ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in the DAC.
    Description: The high‐precision X‐ray diffraction (XRD) setup for work with diamond anvil cells (DACs) in Interaction Chamber 2 of the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser is described. image
    Keywords: 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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  • 27
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    The anisotropy in the optical constants of quartz crystals for soft X‐rays (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from orientation‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near‐edge regions.
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from polarization‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge. image
    Keywords: 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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  • 28
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    Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-05
    Description: Mixed ionic electronic conducting ceramics Nd6−yWO12−δ (δ is the oxygen deficiency) provide excellent stability in harsh environments containing strongly reactive gases such as CO2, CO, H2, H2O or H2S. Due to this chemical stability, they are promising and cost‐efficient candidate materials for gas separation, catalytic membrane reactors and protonic ceramic fuel cell technologies. As in La6−yWO12−δ, the ionic/electronic transport mechanism in Nd6−yWO12−δ is expected to be largely controlled by the crystal structure, the conclusive determination of which is still lacking. This work presents a crystallographic study of Nd5.8WO12−δ and molybdenum‐substituted Nd5.7W0.75Mo0.25O12−δ prepared by the citrate complexation route. High‐resolution synchrotron and neutron powder diffraction data were used in combined Rietveld refinements to unravel the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ. Both investigated samples crystallize in a defect fluorite crystal structure with space group Fm3m and doubled unit‐cell parameter due to cation ordering. Mo replaces W at both Wyckoff sites 4a and 48h and is evenly distributed, in contrast with La6−yWO12−δ. X‐ray absorption spectroscopy as a function of partial pressure pO2 in the near‐edge regions excludes oxidation state changes of Nd (Nd3+) and W (W6+) in reducing conditions: the enhanced hydrogen permeation, i.e. ambipolar conduction, observed in Mo‐substituted Nd6−yWO12−δ is therefore explained by the higher Mo reducibility and the creation of additional – disordered – oxygen vacancies.
    Description: The crystal structures of non‐substituted and Mo‐substituted neodymium tungstates are described in detail through neutron diffraction and high‐resolution X‐ray diffraction. Combined X‐ray and neutron diffraction refinements and electron probe micro‐analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X‐ray absorption spectroscopy in the near‐edge regions confirmed no changes in the oxidation states of Nd and W.
    Keywords: 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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  • 29
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    High‐temperature treatments of niobium under high vacuum, dilute air‐ and nitrogen‐atmospheres as investigated by in situ X‐ray absorption spectroscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: Niobium metal foils were heat‐treated at 900°C under different conditions and in situ investigated with time‐resolved X‐ray absorption fine‐structure (EXAFS and XANES) measurements. The present study aims to mimic the conditions usually applied for heat treatments of Nb materials used for superconducting radiofrequency cavities, in order to better understand the evolving processes during vacuum annealing as well as for heat treatments in controlled dilute gases. Annealing in vacuum in a commercially available cell showed a substantial amount of oxidation, so that a designated new cell was designed and realized, allowing treatments under clean high‐vacuum conditions as well as under well controllable gas atmospheres. The experiments performed under vacuum demonstrated that the original structure of the Nb foils is preserved, while a detailed evaluation of the X‐ray absorption fine‐structure data acquired during treatments in dilute air atmospheres (10−5 mbar to 10−3 mbar) revealed a linear oxidation with the time of the treatment, and an oxidation rate proportional to the oxygen (air) pressure. The structure of the oxide appears to be very similar to that of polycrystalline NbO. The cell also permits controlled exposures to other reactive gases at elevated temperatures; here the Nb foils were exposed to dilute nitrogen atmospheres after a pre‐conditioning of the studied Nb material for one hour under high‐vacuum conditions, in order to imitate typical conditions used for nitrogen doping of cavity materials. Clear structural changes induced by the N2 exposure were found; however, no evidence for the formation of niobium nitride could be derived from the EXAFS and XANES experiments. The presented results establish the feasibility to study the structural changes of the Nb materials in situ during heat treatments in reactive gases with temporal resolution, which are important to better understand the underlaying mechanisms and the dynamics of phase formation during those heat treatments in more detail.
    Keywords: 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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  • 30
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    Pressure‐induced Pb–Pb bonding and phase transition in Pb2SnO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: High‐pressure single‐crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator‐to‐semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory‐based calculations show that at ambient conditions the channels in the structure host the stereochemically‐active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
    Description: The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT‐based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb2+ ions with increasing pressure. image
    Keywords: 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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    A discussion on `Domain formation and phase transitions in the wurtzite‐based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front‐runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Description: A scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points. image
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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    X‐SPEC: a 70 eV to 15 keV undulator beamline for X‐ray and electron spectroscopies (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: X‐SPEC is a high‐flux spectroscopy beamline at the KIT (Karlsruhe Institute of Technology) Synchrotron for electron and X‐ray spectroscopy featuring a wide photon energy range. The beamline is equipped with a permanent magnet undulator with two magnetic structures of different period lengths, a focusing variable‐line‐space plane‐grating monochromator, a double‐crystal monochromator and three Kirkpatrick–Baez mirror pairs. By selectively moving these elements in or out of the beam, X‐SPEC is capable of covering an energy range from 70 eV up to 15 keV. The flux of the beamline is maximized by optimizing the magnetic design of the undulator, minimizing the number of optical elements and optimizing their parameters. The beam can be focused into two experimental stations while maintaining the same spot position throughout the entire energy range. The first experimental station is optimized for measuring solid samples under ultra‐high‐vacuum conditions, while the second experimental station allows in situ and operando studies under ambient conditions. Measurement techniques include X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS).
    Description: X‐SPEC is a high‐flux undulator beamline for electron and X‐ray spectroscopy with an energy range from 70 eV to 15 keV. It offers X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS) for in vacuo, in situ and operando sample environments. image
    Keywords: 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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    Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF‐Global‐Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross‐correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF‐Global‐Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF‐Global‐Fit is in excellent agreement with the published crystal structure data.
    Keywords: 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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    Structural basis of chitin utilization by a GH20 β‐N‐acetylglucosaminidase from Vibrio campbellii strain ATCC BAA‐1116 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-01
    Description: Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β‐N‐acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA‐1116. Crystal structures of wild‐type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N‐terminal carbohydrate‐binding domain linked to a small α+β domain and a C‐terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
    Description: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Keywords: 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-09-29
    Description: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Description: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Description: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Description: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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    Volcanic-Island Lateral Collapses and Their Submarine Deposits (2021)
    Springer
    In:  In: Volcanic Debris Avalanches. , ed. by Roverato, M., Dufresne, A. and Procter, J. Springer, Cham, pp. 255-279, 25 pp. ISBN 978-3-030-57411-6
    Details
    Publication Date: 2021-01-19
    Description: Landslide deposits offshore many volcanic islands provide evidence of catastrophic lateral collapses. These deposits span a larger volume range than their continental equivalents, and can generate devastating tsunamis. All historical volcanic-island lateral collapses have occurred in arc settings, and have been characterised by rapid failure and efficient tsunami generation. The varied morphology of their deposits is influenced both by lithological properties and the nature of the substrate. Many deposits show evidence of extensive seafloor erosion and transformation into debris flows, and the propagation of frontally-confined sediment deformation beyond and beneath the primary deposit. Mobilised volumes can far exceed that of the initial failure, and accurate deposit interpretation requires internal geophysical imaging and sampling. Around intraplate ocean-island volcanoes, multi-unit turbidites suggest that lateral collapses may occur in discrete stages; although this would reduce their overall tsunamigenic potential, the volumes of individual stages of collapse remain very large. Numerical models of both landslide and tsunami processes in ocean-island settings are difficult to test, and the smaller collapses that typify island arcs are an important focus of research due to their higher global frequency, availability of direct failure and tsunami observations, and a need to better understand the signals of incipient collapse to develop approaches for tsunami hazard mitigation.
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  • 39
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    Learning Visual Free Space Detection for Deep-Diving Robots (2021)
    Springer
    In:  In: Pattern Recognition. ICPR International Workshops and Challenges. , ed. by Del Bimbo, A., Cucchiara, R., Sclaroff, S., Farinella, G. M., Mei, T., Bertini, M., Escalante, H. J. and Vezzani, R. Springer, Cham, pp. 398-413.
    Details
    Publication Date: 2021-08-02
    Description: Since the sunlight only penetrates a few hundred meters into the ocean, deep-diving robots have to bring their own light sources for imaging the deep sea, e.g., to inspect hydrothermal vent fields. Such co-moving light sources mounted not very far from a camera introduce uneven illumination and dynamic patterns on seafloor structures but also illuminate particles in the water column and create scattered light in the illuminated volume in front of the camera. In this scenario, a key challenge for forward-looking robots inspecting vertical structures in complex terrain is to identify free space (water) for navigation. At the same time, visual SLAM and 3D reconstruction algorithms should only map rigid structures, but not get distracted by apparent patterns in the water, which often resulted in very noisy maps or 3D models with many artefacts. Both challenges, free space detection, and clean mapping could benefit from pre-segmenting the images before maneuvering or 3D reconstruction. We derive a training scheme that exploits depth maps of a reconstructed 3D model of a black smoker field in 1400 m water depth, resulting in a carefully selected, ground-truthed data set of 1000 images. Using this set, we compare the advantages and drawbacks of a classical Markov Random Field-based segmentation solution (graph cut) and a deep learning-based scheme (U-Net) to finding free space in forward-looking cameras in the deep ocean.
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    Deep Sea Robotic Imaging Simulator (2021)
    Springer
    In:  In: Pattern Recognition. ICPR International Workshops and Challenges. , ed. by Del Bimbo, A., Cucchiara, R., Sclaroff, S., Farinella, G. M., Mei, T., Bertini, M., Escalante, H. J. and Vezzani, R. Springer, Cham, pp. 375-389.
    Details
    Publication Date: 2021-08-03
    Description: Nowadays underwater vision systems are being widely applied in ocean research. However, the largest portion of the ocean - the deep sea - still remains mostly unexplored. Only relatively few image sets have been taken from the deep sea due to the physical limitations caused by technical challenges and enormous costs. Deep sea images are very different from the images taken in shallow waters and this area did not get much attention from the community. The shortage of deep sea images and the corresponding ground truth data for evaluation and training is becoming a bottleneck for the development of underwater computer vision methods. Thus, this paper presents a physical model-based image simulation solution, which uses an in-air texture and depth information as inputs, to generate underwater image sequences taken by robots in deep ocean scenarios. Different from shallow water conditions, artificial illumination plays a vital role in deep sea image formation as it strongly affects the scene appearance. Our radiometric image formation model considers both attenuation and scattering effects with co-moving spotlights in the dark. By detailed analysis and evaluation of the underwater image formation model, we propose a 3D lookup table structure in combination with a novel rendering strategy to improve simulation performance. This enables us to integrate an interactive deep sea robotic vision simulation in the Unmanned Underwater Vehicles simulator. To inspire further deep sea vision research by the community, we release the source code of our deep sea image converter to the public (https://www.geomar.de/en/omv-research/robotic-imaging-simulator).
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    Optimization of Multi-LED Setups for Underwater Robotic Vision Systems (2021)
    Springer
    In:  In: Pattern Recognition. ICPR International Workshops and Challenges. , ed. by Del Bimbo, A., Cucchiara, R., Sclaroff, S., Farinella, G. M., Mei, T., Bertini, M., Escalante, H. J. and Vezzani, R. Springer, Cham, pp. 390-397, 8 pp.
    Details
    Publication Date: 2021-03-08
    Description: In deep water conditions, vision systems mounted on underwater robotic platforms require artificial light sources to illuminate the scene. The particular lighting configurations significantly influence the quality of the captured underwater images and can make their analysis much harder or easier. Nowadays, classical monolithic Xenon flashes are gradually being replaced by more flexible setups of multiple powerful LEDs. However, this raises the question of how to arrange these light sources, given different types of seawater and-depending-on different flying altitudes of the capture platforms. Hence, this paper presents a rendering based coarse-to-fine approach to optimize recent multi-light setups for underwater vehicles. It uses physical underwater light transport models and target ocean and mission parameters to simulate the underwater images as would be observed by a camera system with particular lighting setups. This paper proposes to systematically vary certain design parameters such as each LED’s orientation and analyses the rendered image properties (such as illuminated image area and light uniformity) to find optimal light configurations. We report first results on a real, ongoing AUV light design process for deep sea mission conditions.
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  • 42
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    Impact of marine heatwaves on seagrass ecosystems (2021)
    Springer
    In:  In: Ecosystem collapse and climate change. , ed. by Canadell, J. G. and Jackson, R. B. Ecological studies, 241 . Springer, Cham, pp. 345-364, 20 pp. ISBN 978-3-030-71330-0
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    Publication Date: 2021-07-29
    Description: Seagrass meadows deliver important ecosystem services such as nutrient cycling, enhanced biodiversity, and contribution to climate change mitigation and adaption through carbon sequestration and coastal protection. Seagrasses, however, are facing the impacts of ocean warming and marine heatwaves, which are altering their ecological structure and function. Shifts in species composition, mass mortality events, and loss of ecosystem complexity after sudden extreme climate events are increasingly common, weakening the ecosystem services they provide. In the west coast of Australia, Shark Bay holds between 0.7 and 2.4% of global seagrass extent (〉4300 km2), but in the austral summer of 2010/2011, the Ningaloo El Niño marine heatwave resulted in the collapse of ~1300 km2 of seagrass ecosystem extent. The loss of the seagrass canopy resulted in the erosion and the likely remineralization of ancient carbon stocks into 2–4 Tg CO2-eq over 6 years following seagrass loss, increasing emissions from land-use change in Australia by 4–8% per annum. Seagrass collapse at Shark Bay also impacted marine food webs, including dugongs, dolphins, cormorants, fish communities, and invertebrates. With increasing recurrence and intensity of marine heatwaves, seagrass resilience is being compromised, underlining the need to implement conservation strategies. Such strategies must precede irreversible climate change-driven tipping points in ecosystem functioning and collapse and result from synchronized efforts involving science, policy, and stakeholders. Management should aim to maintain or enhance the resilience of seagrasses, and using propagation material from heatwave-resistant meadows to restore impacted regions arises as a challenging but promising solution against climate change threats. Although scientific evidence points to severe impacts of extreme climate events on seagrass ecosystems, the occurrence of seagrass assemblages across the planet and the capacity of humans to modify the environment sheds some light on the capability of seagrasses to adapt to changing ecological niches.
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    Dr. Ilse Seibold, née Usbeck, 1925–2021: Considered by many as a consecutive memory of major geoscientists (2021)
    Springer
    In:  International Journal of Earth Sciences, 110 . pp. 1879-1881.
    Details
    Publication Date: 2021-09-23
    Description: Summary of Ilse Seibold's vita Ilse Seibold, née Usbeck, was born May 8, 1925 in Breslau, Silesia, and went to school in Halle/Saale during WW2. She started her studies of geology and paleontology at the University of Halle and at the Humboldt University in Berlin, and later at the University of Tübingen, where she received her doctorate as micropaleontologist in 1951 with Otto Schindewolf as her supervisor. She remained active as productive scientist over many decades. In 1952, she married Dr. Eugen Seibold, who in 1958 became professor at Kiel University, founded one of Europe's most important institutes for marine geology, and later became president of the German Science Foundation (DFG), and subsequently of the European Science Foundation (ESF). Being a scientist herself Ilse Seibold soon evolved to a deeply reflective insider of geological sciences. She followed her husband during his scientific career from his appointments in Tübingen, Bonn, Karlsruhe, Kiel, to Bonn and Strasbourg/Freiburg i.Br. She accompanied Eugen on his sabbatical leave at Scripps Institution of Oceanography in La Jolla, CA. She participated in countless international scientific meetings. Together with Eugen she published many papers that document her independence and autonomy as scientist. She gained deep insights into the origins of the geosciences and their historical evolution, up to the ideas of fine arts. We are happy that she documented in her publications a broad range of her scientific and distinguished-humane impressions.
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    Dynamic Coupling of Near-Field and Far-Field Models (2020)
    Springer
    In:  In: Deep Oil Spills: Facts, Fate, and Effects. , ed. by Murawski, S. A., Ainsworth, C. H., Gilbert, S., Hollander, D. J., Paris, C. B., Schlüter, M. and Wetzel, D. L. Springer, Cham, Switzerland, pp. 139-154. ISBN 978-3-030-11604-0
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    Publication Date: 2021-01-18
    Description: Deepwater spills pose a unique challenge for reliable predictions of oil transport and fate, since live oil spewing under very high hydrostatic pressure has characteristics remarkably distinct from oil spilling in shallow water. It is thus important to describe in detail the complex thermodynamic processes occurring in the near-field, meters above the wellhead, and the hydrodynamic processes in the far-field, up to kilometers away. However, these processes are typically modeled separately since they occur at different scales. Here we directly couple two oil prediction applications developed during the Deepwater Horizon blowout operating at different scales: the near-field Texas A&M Oilspill Calculator (TAMOC) and the far-field oil application of the Connectivity Modeling System (oil-CMS). To achieve this coupling, new oil-CMS modules were developed to read TAMOC output, which consists of the description of distinct oil droplet “types,” each of specific size and pseudo-component mixture that enters at a given mass flow rate, time, and position into the far field. These variables are transformed for use in the individual-based framework of CMS, where each droplet type fits into a droplet size distribution (DSD). Here we used 19 pseudo-components representing a large range of hydrocarbon compounds and their respective thermodynamic properties. Simulation results show that the dispersion pathway of the different droplet types varies significantly. Indeed, some droplet types remain suspended in the subsea over months, while others accumulate in the surface layers. In addition, the decay rate of oil pseudo-components significantly alters the dispersion, denoting the importance of more biodegradation and dissolution studies of chemically and naturally dispersed live oil at high pressure. This new modeling tool shows the potential for improved accuracy in predictions of oil partition in the water column and of advancing impact assessment and response during a deepwater spill.
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    Physical and Chemical Properties of Oil and Gas Under Reservoir and Deep-Sea Conditions (2020)
    Springer
    In:  In: Deep Oil Spills: Facts, Fate, and Effects. , ed. by Murawski, S. A., Ainsworth, C. H., Gilbert, S., Hollander, D. J., Paris, C. B., Schlüter, M. and Wetzel, D. L. Springer, Cham, Switzerland, pp. 25-42. ISBN 978-3-030-11604-0
    Details
    Publication Date: 2021-01-18
    Description: Petroleum is one of the most complex naturally occurring organic mixtures. The physical and chemical properties of petroleum in a reservoir depend on its molecular composition and the reservoir conditions (temperature, pressure). The composition of petroleum varies greatly, ranging from the simplest gas (methane), condensates, conventional crude oil to heavy oil and oil sands bitumen with complex molecules having molecular weights in excess of 1000 daltons (Da). The distribution of petroleum constituents in a reservoir largely depends on source facies (original organic material buried), age (evolution of organisms), depositional environment (dysoxic versus anoxic), maturity of the source rock (kerogen) at time of expulsion, primary/secondary migration, and in-reservoir alteration such as biodegradation, gas washing, water washing, segregation, and/or mixing from different oil charges. These geochemical aspects define the physical characteristics of a petroleum in the reservoir, including its density and viscosity. When the petroleum is released from the reservoir through an oil exploration accident like in the case of the Deepwater Horizon event, several processes are affecting the physical and chemical properties of the petroleum from the well head into the deep sea. A better understanding of these properties is crucial for the development of near-field oil spill models, oil droplet and gas bubble calculations, and partitioning behavior of oil components in the water. Section 3.1 introduces general aspects of the origin of petroleum, the impact of geochemical processes on the composition of a petroleum, and some molecular compositional and physicochemical background information of the Macondo well oil. Section 3.2 gives an overview over experimental determination of all relevant physicochemical properties of petroleum, especially of petroleum under reservoir conditions. Based on the phase equilibrium modeling using equations of state (EOS), a number of these properties can be predicted which is presented in Sect. 3.3 along with a comparison to experimental data obtained with methods described in Sect. 3.2.
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    Landslide susceptibility zoning in a catchment of Zagros Mountains using fuzzy logic and GIS (2020)
    Springer
    In:  Environmental Earth Sciences, 79 (Article number: 204).
    Details
    Publication Date: 2021-01-08
    Description: Landslide is one of the dangerous types of natural hazards. This phenomenon causes damages in many countries every year. A detailed landslide hazard assessment is necessary to reduce these damages. This research aims to map the landslide susceptibility zoning (LSZ) using the fuzzy logic method and GIS in the Sorkhab basin as a part of the Zagros fold and thrust belt (FTB), northwestern Iran. All slide types were recorded in fieldwork as landslide inventory. Based on the results, four types, i.e., debris slide, earth slide, and rock fall and complex of landslides, was identified in the region. Then, the effect of each landslide contributing factor including topographical elevation heights, slope classes, aspect classes, geological units, proximity to faults, land covers, rainfall classes, and proximity to streams was constructed in GIS and subsequently normalized using fuzzy membership functions. Finally, by combining all standardized layers using the fuzzy gamma operator, a final map of LSZ was produced. The results showed that a 0.9 fuzzy gamma operator has a high accuracy for the LSZ map in the study area. Besides, the accuracy of the LSZ map revealed a strong relationship (R2) between susceptibility classes, and landslide inventory was calculated using a scatter plot equal to 0.79. Hence, the method represented an appropriate accuracy in predicting the landslide susceptibility in the study area.
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    International Union of Geodesy and Geophysics (IUGG) in: The Geodesist’s Handbook 2020 (2020)
    Springer
    In:  Journal of Geodesy, 94 (11). pp. 81-196.
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    Publication Date: 2021-02-23
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    The pandemic push: can COVID-19 reinvent conferences to models rooted in sustainability, equitability and inclusion? (2020)
    Springer
    In:  Socio-Ecological Practice Research, 2 (3). pp. 253-256.
    Details
    Publication Date: 2021-01-08
    Description: The COVID-19 pandemic necessitates a change in conference formats for 2020. This shift offers a unique opportunity to address long-standing inequities in access and issues of sustainability associated with traditional conference formats, through testing online platforms. However, moving online is not a panacea for all of these concerns, particularly those arising from uneven distribution of access to the Internet and other technology. With conferences and events being forced to move online, this is a critical juncture to examine how online formats can be used to best effect and to reduce the inequities of in-person meetings. In this article, we highlight that a thoughtful and equitable move to online formats could vastly strengthen the global socio-ecological research community and foster cohesive and effective collaborations, with ecology and society being the ultimate beneficiaries.
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  • 49
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    Climate Change Impacts on Groundwater Resources in the Coastal Karstic Adriatic Area: A Case Study from the Dinaric Karst (2020)
    Springer
    In:  Natural Resources Research, 29 (3). pp. 1975-1988.
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    Publication Date: 2021-01-08
    Description: The Bokanjac–Poličnik system, as a complex set of mutually interrelated Dinaric karst catchments and sub-catchments, is a highly vulnerable and limited groundwater source for the wider Zadar area in northern Dalmatia, Croatia. Based on hydrogeological, hydrochemical, and hydrological research, including the prediction of groundwater discharge by the end of the twenty-first century, a complex study was performed with the following main aims: (1) groundwater protection in the present state, (2) assessment of future groundwater protection, and (3) prediction of drinking water availability and quality under the predicted climate change conditions. Long-term prediction of changes in groundwater quantity, as well as investigations of trends in groundwater quality, will allow us to protect this essential natural resource with respect to possible negative trends. The results showed that a significant decrease in the quantity of available groundwater is possible and that extraction will have to be well planned because any decrease in the groundwater pressure in this area will cause a further decrease in quality, especially regarding the possibility of seawater intrusions into the aquifer. The results of this study were incorporated in sanitary protection zones.
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  • 50
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    Habitat utilization and feeding ecology of small round goby in a shallow brackish lagoon (2020)
    Springer
    In:  Marine Biodiversity, 50 (5). Art.Nr. 88.
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    Publication Date: 2021-01-08
    Description: We examined small-scale distribution and feeding ecology of a non-native fish species, round goby (Neogobius melanostomus (Pallas, 1814)), in different habitats of a coastal lagoon situated in the south-western Baltic Sea. First observations of round goby in this lagoon were reported in 2011, 3 years before the current study was conducted, and information on this species’ basic ecology in different habitats is limited. We found that mainly juvenile round gobies are non-randomly distributed between habitats and that abundances potentially correlate positively with vegetation density and thus structural complexity of the environment. Abundances were highest in shallower, more densely vegetated habitats indicating that these areas might act as a refuge for small round gobies by possibly offering decreased predation risk and better feeding resources. Round goby diet composition was distinct for several length classes suggesting an ontogenetic diet shift concerning crustacean prey taxa between small (≤ 50 mm total length, feeding mainly on zooplankton) and medium individuals (51–100 mm, feeding mainly on benthic crustaceans) and another diet shift of increasing molluscivory with increasing body size across all length classes. Differences in round goby diet between habitats within the smallest length class might potentially be related to prey availability in the environment, which would point to an opportunistic feeding strategy. Here, we offer new insights into the basic ecology of round goby in littoral habitats, providing a better understanding of the ecological role of this invasive species in its non-native range, which might help to assess potential consequences for native fauna and ecosystems.
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    The Global Biogeochemical Silicon Cycle (2009)
    Springer
    In:  Silicon, 1 (4). pp. 207-213.
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    Publication Date: 2017-10-05
    Description: Silicon is one of the most important elements in the current age of the anthropocene. It has numerous industrial applications, and supports a high-tech multi-billion Euro industry. Silicon has a fascinating biological and geological cycle, interacting with other globally important biogeochemical cycles. In this review, we bring together both biological and geological aspects of the silicon cycle to provide a general, comprehensive review of the cycling of silicon in the environment. We hope this review will provide inspiration for researchers to study this fascinating element, as well as providing a background environmental context to those interested in silicon.
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    Spatial Variability of Trace Metals and Inorganic Nutrients in Surface Waters of Todos Santos Bay, México in the Summer of 2005 During a Red Tide Algal Bloom (2009)
    Springer
    In:  Archives of Environmental Contamination and Toxicology, 56 (4). pp. 707-716.
    Details
    Publication Date: 2018-03-09
    Description: Dissolved and particulate metals (Ag, Cd, Co, Cu, Ni, and Zn) and nutrients (PO4, NO3, and H4SiO4) were measured in Todos Santos Bay (TSB) in August 2005. Two sources producing local gradients were identified: one from a dredge discharge area (DDA) and another south of the port and a creek. The average concentrations of dissolved Cd and Zn (1.3 and 15.6 nM, respectively) were higher by one order of magnitude than the surrounding Pacific waters, even during upwelling, and it is attributed to the presence of a widespread and long-lasting red tide coupled with some degree of local pollution. A clear spatial gradient (10 to 6 pM), from coast to offshore, of dissolved Ag was evident, indicating the influence of anthropogenic inputs. The particulate fraction of all metals, except Cu, showed a factor of ~3 decrease in concentrations from the DDA to the interior of the bay. The metal distributions were related to the bay’s circulation by means of a numerical model that shows a basically surface-wind-driven offshore current with subsurface compensation currents toward the coast. Additionally, the model shows strong vertical currents over the DDA. Principal component analysis revealed three possible processes that could be influencing the metal concentrations within TSB: anthropogenic inputs (Cd, Ag, and Co), biological proceses (NO3, Zn, and Cu), and upwelling and mixing (PO4, H4SiO4, Cd, and Ni). The most striking finding of this study was the extremely high Cd concentrations, which have been only reported in highly contaminated areas. As there was a strong red tide, it is hypothesized that the dinoflagellates are assimilating the Cd, which is rapidly remineralized and being concentrated on the stratified surface layers.
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    Complement: coming full circle (2009)
    Springer
    In:  Archivum Immunologiae et Therapiae Experimentalis, 57 (6). pp. 393-407.
    Details
    Publication Date: 2017-10-11
    Description: The complement system has long been known to be a major element of innate immunity. Traditionally, it was regarded as the first line of defense against invading pathogens, leading to opsonization and phagocytosis or the direct lysis of microbes. However, from the second half of the twentieth century on, it became clear that complement is also intimately involved in the induction and “fine tuning” of adaptive B- and T-cell responses as well as lineage commitment. This growing recognition of the complement system’s multifunctional role in immunity is consistent with the recent paradigm that complement is also necessary for the successful contraction of an adaptive immune response. This review aims at giving a condensed overview of complement’s rise from a simple innate stop-and-go system to an essential and efficient participant in general immune homeostasis and acquired immunity.
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  • 54
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    Temporal Trends of Dissolved Trace Metals in Jamaica Bay, NY: Importance of Wastewater Input and Submarine Groundwater Discharge in an Urban Estuary (2009)
    Springer
    In:  Estuaries and Coasts, 32 (3). pp. 535-550.
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    Publication Date: 2018-03-09
    Description: Jamaica Bay, NY, is a highly urbanized estuary within the boroughs of New York City conspicuously lacking published information on dissolved trace metal concentrations. The current study examines the distribution and cycling of trace metals in that embayment with data gathered during cruises in November 2004, April 2005, and June 2006. Most of the metal distributions (Fe, Zn, Co, Ag, Cu, Pb, Ni) in the water column are explained by the input of substantial volumes of treated wastewater effluent. However, several lines of evidence suggest that submarine groundwater discharge (SGD) is also an important source of dissolved Fe, Zn, Co, Ni, and isotopically distinct stable Pb ratios (206Pb, 207Pb, 208Pb) in the Bay. Conversely, the recirculated seawater component of SGD is an apparent sink for dissolved Mo. This study provides the first measurements of dissolved trace metals in the Jamaica Bay water column and subterranean estuary and provides evidence for trace metal input due to SGD.
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    Gravity crustal models and heat flow measurements for the Eurasia Basin, Arctic Ocean (2009)
    Springer
    In:  Marine Geophysical Researches, 30 (4). pp. 277-292.
    Details
    Publication Date: 2018-06-12
    Description: The Gakkel Ridge in the Arctic Ocean with its adjacent Nansen and Amundsen Basins is a key region for the study of mantle melting and crustal generation at ultraslow spreading rates. We use free-air gravity anomalies in combination with seismic reflection and wide-angle data to compute 2-D crustal models for the Nansen and Amundsen Basins in the Arctic Ocean. Despite the permanent pack-ice cover two geophysical transects cross both entire basins. This means that the complete basin geometry of the world’s slowest spreading system can be analysed in detail for the first time. Applying standard densities for the sediments and oceanic crystalline crust, the gravity models reveal an unexpected heterogeneous mantle with densities of 3.30 × 103, 3.20 × 103 and 3.10 × 103 kg/m3 near the Gakkel Ridge. We interpret that the upper mantle heterogeneity mainly results from serpentinisation and thermal effects. The thickness of the oceanic crust is highly variable throughout both transects. Crustal thickness of less than 1 km dominates in the oldest parts of both basins, increasing to a maximum value of 6 km near the Gakkel Ridge. Along-axis heat flow is highly variable and heat flow amplitudes resemble those observed at fast or intermediate spreading ridges. Unexpectedly, high heat flow along the Amundsen transect exceeds predicted values from global cooling curves by more than 100%.
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    Earliest diagenesis in scleractinian coral skeletons: implications for palaeoclimate-sensitive geochemical archives (2009)
    Springer
    In:  Facies, 55 (2). pp. 161-201.
    Details
    Publication Date: 2017-06-07
    Description: Live-collected samples of four common reefbuilding coral genera (Acropora, Pocillopora, Goniastrea, Porites) from subtidal and intertidal settings of Heron Reef, Great Barrier Reef, show extensive early marine diagenesis where parts of the coralla less than 3 years old contain abundant macro- and microborings and aragonite, high-Mg calcite, low-Mg calcite, and brucite cements. Many types of cement are associated directly with microendoliths and endobionts that inhabit parts of the corallum recently abandoned by coral polyps. The occurrence of cements that generally do not precipitate in normal shallow seawater (e.g., brucite, low-Mg calcite) highlights the importance of microenvironments in coral diagenesis. Cements precipitated in microenvironments may not reXect ambient seawater chemistry. Hence, geochemical sampling of these cements will contaminate trace-element and stable-isotope inventories used for palaeoclimate and dating analysis. Thus, great care must be taken in vetting samples for both bulk and microanalysis of geochemistry. Visual inspection using scanning electron microscopy may be required for vetting in many cases.
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    Nutrient ratios and phytoplankton community structure in the large, shallow, eutrophic, subtropical Lakes Okeechobee (Florida, USA) and Taihu (China) (2009)
    Springer
    In:  Limnology, 10 (3). pp. 215-227.
    Details
    Publication Date: 2017-10-06
    Description: Analysis of ten- and four-year datasets for the large, shallow, subtropical, and eutrophic Lakes Okeechobee (USA) and Taihu (China), respectively, suggest that resource-ratio explanations for cyanobacteria dominance may not apply to these two lakes. Datasets were examined to identify relationships between nutrient ratios [total nitrogen (TN):total phosphorus (TP) and ammonium (NH4+):oxidized N (NOx)] and phytoplankton community structure (as proportions of cyanobacteria and diatoms to total phytoplankton biomass). Datasets were pooled by sampling month, averaged lake-wide, and analyzed with linear regression. In Okeechobee, the cyanobacteria proportion increased and the diatom proportion decreased with increasing TN:TP. In Taihu, cyanobacteria decreased with increasing TN:TP, but the opposite trend observed for diatoms was marginally significant. Okeechobee cyanobacteria increased and diatoms decreased with increasing NH4+:NOx, but no significant relationships between phytoplankton and NH4+:NOx were observed in Taihu. Both lakes had significant relationships between phytoplankton community structure and total nutrients, but these relationships were the opposite of those expected. Relationships between phytoplankton community structure and water quality parameters from the previous month resulted in improved relationships, suggesting a predictive capability. Statistical analysis of the entire datasets (not pooled) supported these and additional relationships with other parameters, including temperature and water clarity.
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    Distribution of cephalopod paralarvae in relation to the regional oceanography of the western Iberia (2009)
    Oxford Univ. Press
    In:  Journal of Plankton Research, 31 (1). pp. 73-91.
    Details
    Publication Date: 2019-01-22
    Description: The present study analyses the distribution of cephalopod paralarvae off the Portuguese coast. The effects of temporal and physical variables on Loligo vulgaris, Octopus vulgaris, sepiolid and ommastrephid abundances are analysed with generalized linear models. Their distribution patterns are discussed in relation to mesoscale features, including currents, thermal fronts and coastal upwelling cross-shelf transport, prevailing in the western Iberia upwelling system. Paralarvae of the neritic species occur during a considerably extended period of the year with two or three abundance peaks within the highly productive upwelling system of the western Portuguese coast and contrasting with the Gulf of Cadiz area. Temperature and upwelling were shown to be the most important variables in modulating seasonality and distribution of these paralarvae. The influence of the physical environment is particularly pronounced for the paralarvae of O. vulgaris, following distinct patterns according to the oceanography of the western Iberia and the Gulf of Cadiz systems. The paralarvae of oceanic species, which in many cases have their northern limit of distribution at these latitudes, were mainly found in the southern part of the sampling area. The distribution of these species indicates that the prevailing oceanographic features of the Gulf of Cadiz system, especially fronts, together with temperature act as boundaries to geographic dispersal, contributing to an area of high cephalopod biodiversity in the southern Portuguese waters.
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    Influence of structural setting on sulphur isotopes in Archean orogenic gold deposits, Eastern Goldfields Province, Yilgarn, Western Australia (2009)
    Springer
    In:  Mineralium Deposita, 44 (2). pp. 129-150.
    Details
    Publication Date: 2016-09-19
    Description: The published mean δ34S values of ore-related pyrites from orogenic gold deposits of the Eastern Goldfields Province, Yilgarn Craton lie between −4‰ and +4‰. As for orogenic gold deposits worldwide, most deposits have positive means and a restricted range of δ34S values, but some have negative means and wider ranges of δ34S values. Wall-rock carbonation and back-mixing of similar-source fluids with different fluid pathways can explain some of the more negative δ34S signatures. However, structural setting appears to be the most important factor controlling ore-fluid oxidation state and hence the distribution of δ34S values in gold-related pyrites. Shear-hosted deposits appear to have experienced fluid-dominated processes such as phase separation, whereas stockwork, vein-hosted or disseminated deposits formed under conditions of greater rock buffering. At Victory-Defiance, in particular, negative δ34S values are more common in gently dipping dilational structures, compared to more compressional steeply dipping structures. It appears most likely that fluid-pressure fluctuations during fault-valve cycles establish different fluid-flow regimes in structures with different orientations. Rapid fluid-pressure fluctuations in dilational structures during seismic activity can cause partitioning of reduced gas phases from the ore fluid during extreme phase separation and hence are an effective method of ore-fluid oxidation, leading to large, local fluctuations in oxidation state. It is thus not necessary to invoke mixing with oxidised magmatic fluids to explain δ34S signatures indicative of oxidation. In any case, available, robust geochronology in the Eastern Goldfields Province does not support the direct involvement of oxidised magmatic fluids from adjacent granitic intrusions in orogenic gold genesis. Thus, negative mean δ34S values and large variations in δ34S values of ore-related pyrites in world-class orogenic gold deposits are interpreted to result from multiple mechanisms of gold precipitation from a single, ubiquitous ore fluid in varying structural settings, rather than from the involvement of oxidised ore fluids from a different source. Such signatures are indicative, but not diagnostic, of anomalously large orogenic gold systems.
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    Inversion of Scholte wave dispersion and waveform modeling for shallow structure of the Ninetyeast Ridge (2009)
    Springer
    In:  Journal of Seismology, 13 . pp. 543-559.
    Details
    Publication Date: 2017-08-09
    Description: The construction of S-wave velocity models of marine sediments down to hundreds of meters below the seafloor is important in a number of disciplines. One of the most significant trends in marine geophysics is to use interface waves to estimate shallow shear velocities which play an important role in determining the shallow crustal structure. In marine settings, the waves trapped near the fluid-solid interface are called Scholte waves, and this is the subject of the study. In 1998, there were experiments on the Ninetyeast Ridge (Central Indian Ocean) to study the shallow seismic structure at the drilled site. The data were acquired by both ocean bottom seismometer and ocean bottom hydrophone. A new type of seafloor implosion sources has been used in this experiment, which successfully excited fast and high frequency (> 500 Hz) body waves and slow, intermediate frequency (〈 20 Hz) Scholte waves. The fundamental and first higher mode Scholte waves have both been excited by the implosion source. Here, the Scholte waves are investigated with a full waveform modeling and a group velocity inversion approach. Shear wave velocities for the uppermost layers of the region are inferred and results from the different methods are compared. We find that the full waveform modeling is important to understand the intrinsic attenuation of the Scholte waves between 1 and 20 Hz. The modeling shows that the S-wave velocity varies from 195 to 350 m/s in the first 16 m of the uppermost layer. Depths levels of high S-wave impedance contrasts compare well to the layer depth derived from a P-wave analysis as well as from drilling data. As expected, the P- to S-wave velocity ratio is very high in the uppermost 16 m of the seafloor and the Poisson ratio is nearly 0.5. Depth levels of high S-wave impedance contrasts are comparable to the layer depth derived from drilling data.
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  • 61
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    Annual assessment of the predation of Mnemiopsis leidyi in a new invaded environment, the Kiel Fjord (Western Baltic Sea): a matter of concern? (2009)
    Oxford Univ. Press
    In:  Journal of Plankton Research, 31 (7). pp. 729-738.
    Details
    Publication Date: 2019-09-23
    Description: The sudden occurrence of the ctenophore Mnemiopsis leidyi has been reported recently from different regions of the Baltic Sea and it has been suggested that the species has invaded the whole basin. Here we provide the first set of quantitative data of seasonal diet composition and life history traits of M. leidyi and its predatory role in the pelagic ecosystem of the Western Baltic Sea. The size structure of the species appeared to be dominated by small size classes and only a few adults were as large as those reported in the native region of the species and in other invaded areas. We show that the species has a high preference for small-sized and slow swimming prey, mainly during the winter low temperature period. Barnacle nauplii appeared to be the main source of carbon for the over-wintering population of M. leidyi. A preference for copepods was only found during August when these prey contributed up to 20% of the gut composition. In summer, planula larvae of the jellyfish Aurelia aurita were the most abundant prey in the gut content (feeding rate of 621 ind. ctenophore−1day−1). We further found that at highest densities of the species, in summer, a significant predation on its larvae occurs, this being the major carbon source of adults. Overall, these results are discussed in the context of trade-offs M. leidyi faces in the new environment and adverse environmental conditions, which are likely forcing the species toward reduced sizes and also probably reducing its potential predatory impact in the Baltic Sea.
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    Identifying eastern Baltic cod nursery grounds using hydrodynamic modelling: knowledge for the design of Marine Protected areas (2009)
    Oxford Univ. Press
    In:  ICES Journal of Marine Science, 66 . pp. 101-108.
    Details
    Publication Date: 2019-09-23
    Description: Knowledge of the spatial and temporal distribution of juvenile cod is essential to closing the life cycle in population dynamic models, and it is a prerequisite for the design of Marine Protected Areas (MPAs) aiming at the protection of juveniles. In this study, we use a hydrodynamic model to examine the spatial distribution of eastern Baltic cod larvae and early juveniles. The transport patterns of the larvae spawned at the three major spawning grounds in the central Baltic Sea were investigated by drift model simulations for the period 1979–2004. We analysed potential habitats for their suitability for juvenile settlement, i.e. the change from pelagic to demersal life. The results revealed a clear dependence of the probability for successful settling on wind-induced drift of larval cod, which is controlled by the local atmospheric conditions over the Baltic Sea. Furthermore, we found evidence that the final destinations of juvenile cod drift routes are affected by decadal climate variability. Application of the methodology to MPA design is discussed, e.g. identifying the overlap of areas with a high probability of successful juvenile cod settlement and regions of high fishing effort in small-meshed fisheries targeting sprat and herring.
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    HLRS Project Report 2007/2008: "Simulating El Nino in an Eddy-Resolving Coupled Ocean-Ecosystem Model" (2009)
    Springer
    In:  In: High Performance Computing in Science and Engineering '08. Springer, Heidelberg, pp. 471-477613. ISBN 978-3-540-88301-2
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    Publication Date: 2019-09-23
    Type: Book chapter , PeerReviewed
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    NOD-Like Receptors-Pivotal Guardians of the Immunological Integrity of Barrier Organs (2009)
    Springer
    In:  In: Target Pattern Recognition in Innate Immunity. Advances in Experimental Medicine and Biology, 653 . Springer, Heidelberg, pp. 35-47. ISBN 978-1-4419-0900-8
    Details
    Publication Date: 2013-02-18
    Description: NOD-like receptors (NLRs) exert pivotal roles in innate immunity as sensors of exogenous or endogenous cellular danger signals. The NLR protein family has a characteristic domain architecture comprising a central nucleotide binding and oligomerization domain (NOD), an N-terminal effector binding domain and C-terminal leucine-rich repeats (LRRs). Mutations in NLR genes are genetically associated with a number of chronic inflammatory diseases of barrier organs. In this chapter, we focus on the influence of NLR regulation and function in the complex pathophysiology of mucosal homeostasis. The understanding of NLR biology may guide our future understanding of how the interaction between the human genome and the metagenome of transient and resident microbiota precipitates into chronic inflammatory disorders, such as Crohn's disease or atopy.
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  • 65
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    Climate impacts of recent multidecadal changes in Atlantic Ocean Sea Surface Temperature: A Multimodel comparison (2009)
    Springer
    In:  Climate Dynamics, 34 (7-8). pp. 1041-1058.
    Details
    Publication Date: 2016-09-13
    Description: During the twentieth century sea surface temperatures in the Atlantic Ocean exhibited prominent multidecadal variations. The source of such variations has yet to be rigorously established—but the question of their impact on climate can be investigated. Here we report on a set of multimodel experiments to examine the impact of patterns of warming in the North Atlantic, and cooling in the South Atlantic, derived from observations, that is characteristic of the positive phase of the Atlantic Multidecadal Oscillation (AMO). The experiments were carried out with six atmospheric General Circulation Models (including two versions of one model), and a major goal was to assess the extent to which key climate impacts are consistent between the different models. The major climate impacts are found over North and South America, with the strongest impacts over land found over the United States and northern parts of South America. These responses appear to be driven by a combination of an off-equatorial Gill response to diabatic heating over the Caribbean due to increased rainfall within the region and a Northward shift in the Inter Tropical Convergence Zone (ITCZ) due to the anomalous cross-equatorial SST gradient. The majority of the models show warmer US land temperatures and reduced Mean Sea Level Pressure during summer (JJA) in response to a warmer North Atlantic and a cooler South Atlantic, in line with observations. However the majority of models show no significant impact on US rainfall during summer. Over northern South America, all models show reduced rainfall in southern hemisphere winter (JJA), whilst in Summer (DJF) there is a generally an increase in rainfall. However, there is a large spread amongst the models in the magnitude of the rainfall anomalies over land. Away from the Americas, there are no consistent significant modelled responses. In particular there are no significant changes in the North Atlantic Oscillation (NAO) over the North Atlantic and Europe in Winter (DJF). Additionally, the observed Sahel drying signal in African rainfall is not seen in the modelled responses. Suggesting that, in contrast to some studies, the Atlantic Multidecadal Oscillation was not the primary driver of recent reductions in Sahel rainfall.
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    Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon (2009)
    Springer
    In:  Applied Microbiology and Biotechnology, 83 . pp. 175-188.
    Details
    Publication Date: 2019-09-23
    Description: The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats.
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    Semi Permeable Membrane Device Reveals indoor and outdoor contamination of Polychlorinated Biphenyls (PCBs) (2009)
    Springer
    In:  Toxicology and Environmental Health Sciences, 1 (2). pp. 92-96.
    Details
    Publication Date: 2016-05-24
    Description: Semi Permeable Membrane Device (SPMD) was deployed on an experimental basis for five days inside an Environmental Chemistry Laboratory and two sites outside the building in Kiel, Germany to understand the time-averaged contaminant profiles and concentrations of PCBs. Multi Dimensional High Resolution Gas Chromatography-Electron Capture Detection technique and high resolution clean up techniques were employed to SPMD derived triolein samples. Air concentrations were derived from well established mass transfer coefficients or rate constants for PCBs in SPMD. PCBs profiles in indoor and outdoor samples were distinctly different, exemplified by a particle free clean-up laboratory facility where particle associated higher chlorinated congeners were absent. SPMDs revealed the ‘occupational hazard’ to workers inside the building from chemical contamination derived from both building materials and chemicals used in the laboratory. Finger printing technique using principle component analysis (PCA) revealed that PCB contamination was derived from German commercial PCB mixtures. SPMD derived air concentrations in outdoor samples resembled levels recorded by similar devices in Europe. Ultimately, a simple sampling technique in combination with high resolution analytical techniques demonstrated the uptake of more than 60 PCB congeners within a short period of time.
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  • 68
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    Lipid dynamics and feeding of dominant Antarctic calanoid copepods in the eastern Weddell Sea in December (2009)
    Springer
    In:  Polar Biology, 32 (11). pp. 1597-1606.
    Details
    Publication Date: 2015-01-29
    Description: Lipid content, fatty acid composition, and feeding activity of the dominant Antarctic copepods, Calanoides acutus, Calanus propinquus, and Metridia gerlachei, were studied at a quasi-permanent station in the eastern Weddell Sea in December 2003. During 3 weeks of the spring phytoplankton development, total lipid levels of females and copepodite stages V (CVs) of C. acutus were almost doubled. Meanwhile, only a slight increase in total lipid content occurred in M. gerlachei, and no clear trend was observed in lipids of C. propinquus females. The pronounced increase of lipids in C. acutus was due to an accumulation of wax esters. The proportion of wax esters in the lipids of M. gerlachei was clearly lower, while triacylglycerols played a more important role. In C. propinquus, triacylglycerols were the only neutral lipid class. There were no pronounced changes in the feeding activity of M. gerlachei, whereas the feeding activity of C. acutus had rapidly increased with the development of the phytoplankton bloom in December, which explains its rapid lipid accumulation. The combination of gut content and fatty acid trophic marker analyses showed that C. acutus was feeding predominantly on diatoms. The typical diatom fatty acid marker, 16:1(n-7), slightly decreased and the tracer for flagellates, 18:4(n-3), increased in females and CVs of C. acutus. This shift indicates the time, when the significance of flagellates started to increase. The three copepod species exhibited different patterns of lipid accumulation in relation to their trophic niches and different duration of their active phases. The investigations filled a crucial data gap in the seasonal lipid dynamics of dominant calanoid copepods in the Weddell Sea in December and support earlier hypotheses on their energetic adaptations and life cycle strategies.
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    Detection of hemolytic bacteria from Palythoa caribaeorum (Cnidaria, Zoantharia) using a novel palytoxin-screening assay (2009)
    Springer
    In:  Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 96 (4). pp. 405-411.
    Details
    Publication Date: 2015-07-03
    Description: Palytoxin (PTX), one of the most potent and chemically complex marine toxins, is predominantly found in zoanthid corals and sporadically in dinoflagellates. Its biosynthesis and metabolic pathways are largely unknown. However, the widespread occurrence of the toxin in phylogenetically distinct marine organisms is consistent with its production by microorganisms and subsequent accumulation in the food chain. To investigate a possible microbial origin, bacteria from two zoanthid corals (Palythoa caribaeorum, Zoanthus pulchellus) and one sponge (Neofibularia nolitangere) were isolated. More than 250 bacteria were screened for hemolysis using a newly developed PTX-screening assay of which 7% showed PTX-like hemolytic activity. 16S rRNA gene sequencing revealed that these bacterial isolates belonged to strains of Bacillus cereus group (n = 11) as well as the genera Brevibacterium (n = 4) and Acinetobacter (n = 2). The results indicate the presence of Na+/K+-ATPase toxins and possibly PTX in hemolytic bacteria from P. caribaeorum.
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    Sediment partitioning and winnowing in a mixed eolian-marine system (Mauritanian shelf) (2009)
    Springer
    In:  Geo-Marine Letters, 29 (4). pp. 221-232.
    Details
    Publication Date: 2015-09-21
    Description: Continental shelf systems are highly dynamic sedimentary environments, where sediments from biogenic production as well as from terrigenous sources are redistributed in the shelf depositional system, and partly exported off the shelf to the slope and the deep sea. The Golfe d’Arguin (Mauritania, NW Africa) is dominated by such redistribution processes, involving clastic silt imported as dust from the Sahara desert and biogenic carbonates of marine origin. Indeed, surface-sediment grain size and mineralogy show a clear north–south partitioning of sediment type. Fine material is winnowed from the northern part of the gulf, and transported toward the southern part off the Banc d’Arguin, where coarse silt settles on the outer shelf and upper slope, at least down to 600 m water depth. Particles of the fine silt fraction, estimated in terms of eolian material collected aboard the research vessel, are thought to be exported further offshore as they correspond to grain sizes previously reported from adjacent deep-sea sediments. These findings suggest that the interpretation of dust records from the continental slope and rise off NW Africa must consider reworking and partitioning processes active on the Mauritanian shelf.
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    SUGAR (submarine gas hydrate reservoirs) (2009)
    Springer
    In:  Environmental Earth Sciences, 59 (2). pp. 485-487.
    Details
    Publication Date: 2018-09-12
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    Modelling seasonality in extreme precipitation (2009)
    Springer
    In:  The European Physical Journal Special Topics, 174 (1). pp. 99-111.
    Details
    Publication Date: 2020-03-20
    Description: We examine a statistical model for the description of the seasonal variation of extreme daily precipitation at 689 stations across the UK. The probability distribution for monthly maximum precipitation intensity is modelled with a generalised extreme-value distribution (GEV). Instead of modelling the distribution of precipitation maxima separately for every month, we propose an overall model with seasonally-varying location and scale parameters and a constant shape parameter. This model is tested against an augmented version with the shape parameter allowed to vary as well. Furthermore, we compare model adequacy for block length of one and two month and found no major improvements for the longer block-length. Based on this model, the 10 and 100-year return levels are calculated conditioned on the month of the year. The interpolation of return levels to a complete coverage of the UK allows for an identification of spatial patterns and their temporal evolution. These patterns suggest that different mechanisms for extreme precipitation are dominant in different regions of the UK.
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  • 73
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    Dietary effects on multi-element composition of European eel (Anguilla anguilla) otoliths (2009)
    Springer
    In:  Marine Biology, 156 (5). pp. 927-933.
    Details
    Publication Date: 2018-06-07
    Description: Otolith microchemistry is widely used as a tool to track individual migration pathways of diadromous fish under the assumption that the elemental composition of fish otoliths is directly influenced by the physicochemical properties of the surrounding water. Nevertheless, several endogenous factors are reported to affect element incorporation into fish otoliths and might lead to misinterpretations of migration studies. This study experimentally examined the influence of eight different diets on the microchemical composition of European eel (Anguilla anguilla) otoliths using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Seven natural prey types and one artificial diet were fed during 8 weeks in freshwater circuits. Results show for the first time that food has no significant influence on the incorporation of Na, Sr, Ba, Mg, Mn, Cu and Y into European eel otoliths. This indicates that the incorporation of elements usually chosen for migration studies is not affected by diet and that individual feeding behaviour of A. anguilla will not lead to any misinterpretation of migration pathways.
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    Improving SST reconstructions from coral Sr/Ca records: multiple corals from Tahiti (French Polynesia) (2009)
    Springer
    In:  International Journal of Earth Sciences, 98 . pp. 31-40.
    Details
    Publication Date: 2017-05-23
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  • 75
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    Photosynthetic picoplankton dynamics in Lake Tahoe: temporal and spatial niche partitioning among prokaryotic and eukaryotic cells (2009)
    Oxford Univ. Press
    In:  Journal of Plankton Research, 31 (11). pp. 1307-1320.
    Details
    Publication Date: 2020-07-20
    Description: Dynamics of prokaryotic and eukaryotic picophytoplankton were investigated over a 2-year time period using flow cytometry and combined with an in situ experiment in Lake Tahoe, USA to better characterize to which extent environmental factors control these communities. Pronounced seasonal patterns and clear temporal and spatial partitioning were observed between picocyanobacteria and picoeukaryotes. Picocyanobacteria dominated in the nutrient deficient upper water column during the stratified season, while picoeukaryotes reached maximum abundance during isothermal conditions and maintained high numbers in deep-water layers during the stratified season. Picocyanobacteria were more sensitive to high solar and UV radiation compared with picoeukaryotes, which were not affected by high solar radiation and nutrient enrichment stimulated their growth. The opposing response of these two populations is consistent with their vertical distribution: picocyanobacteria dominate below the 30% isolume and above the nitrocline depth, whereas picoeukaryotes increase in the vicinity of the nitrocline and thus increased nutrient concentration. This spatial separation of picophytoplankton groups along environmental gradients in Lake Tahoe is consistent with other deep-oligotrophic lakes and the marine environment, suggesting that these marine and freshwater organisms have similar ecophysiological requirements. These results highlight that the smallest photosynthetic communities show taxon-specific responses to mixing and resource availability, which affect the structure and dynamics of picophytoplankton.
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  • 76
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    Abiotic conditions in cephalopod (Sepia officinalis) eggs: embryonic development at low pH and high pCO2 (2009)
    Springer
    In:  Marine Biology, 156 . pp. 515-519.
    Details
    Publication Date: 2019-09-23
    Description: Low pO(2) values have been measured in the perivitelline fluids (PVF) of marine animal eggs on several occasions, especially towards the end of development, when embryonic oxygen consumption is at its peak and the egg case acts as a massive barrier to diffusion. Several authors have therefore suggested that oxygen availability is the key factor leading to hatching. However, there have been no measurements of PVF pCO(2) so far. This is surprising, as elevated pCO(2) could also constitute a major abiotic stressor for the developing embryo. As a first attempt to fill this gap in knowledge, we measured pO(2), pCO(2) and pH in the PVF of late cephalopod (Sepia officinalis) eggs. We found linear relationships between embryo wet mass and pO(2), pCO(2) and pH. pO(2) declined from 〉 12 kPa to less than 5 kPa, while pCO(2) increased from 0.13 to 0.41 kPa. In the absence of active accumulation of bicarbonate in the PVF, pH decreased from 7.7 to 7.2. Our study supports the idea that oxygen becomes limiting in cephalopod eggs towards the end of development; however, pCO(2) and pH shift to levels that have caused significant physiological disturbances in other marine ectothermic animals. Future research needs to address the physiological adaptations that enable the embryo to cope with the adverse abiotic conditions in their egg environment.
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  • 77
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    The Agulhas System as a Prime Example for the Use of Nesting Capabilities in Ocean Modelling (2009)
    Springer
    In:  In: High Performance Computing on Vector Systems 2009. , ed. by Resch, M., Roller, S., Benkert, K., Galle, M., Bez, W. and Kobayashi, H. Springer, Berlin, pp. 191-198. ISBN 978-3642039126
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    Publication Date: 2012-07-05
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  • 78
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    Sympagohydra tuuli (Cnidaria, Hydrozoa): first report from sea ice of the central Arctic Ocean and insights into histology, reproduction and locomotion (2009)
    Springer
    In:  Marine Biology, 156 . pp. 541-554.
    Details
    Publication Date: 2019-07-31
    Description: Various cnidarians have adapted their life style to interstitial habitats of marine sediments. Recently, for the first time a hydroid was reported from the interstitial brine channel system of Arctic fast ice. Due to its derived features, the new genus and species Sympagohydra tuuli was introduced. Here we describe findings of S. tuuli in sea ice at several sites within the central Arctic Ocean. In our view the results of this study do not allow assignment of Sympagohydra to any known family and we, therefore, suggest the introduction of a new family Sympagohydridae which is placed within the hydrozoan subclass Hydroidolina, order Anthomedusae, suborder Capitata. A first detailed histological analysis of S. tuuli is presented. In vivo analysis of locomotion and reproduction revealed a remarkable convergent evolution in S. tuuli and distant meiobenthic relatives. Shared traits are a flagellated epidermis enabling the animals to glide within small interstices by means of flagellar beating as well as an internalised embryogenesis. In S. tuuli gametogenesis occurs in the absence of gonophores inbetween gastro- and epidermis clearly separated from the epidermis. Budding was observed as the vegetative mode of reproduction. Documentation of feeding behaviour identified copepod nauplii and rotifers as prey items and demonstrates a high trophical position of the hydroids within the sympagic food web. Occurrence of reproducing individuals and pronounced tolerances towards changing temperatures and salinities indicate S. tuuli as a truly sympagic species.
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  • 79
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    The Origin of Hydrous, high-δ18O voluminous volcanism: Diverse Oxygen Isotope Values and High Magmatic Water Contents within the Volcanic Record of Klyuchevskoy Volcano, Kamchatka, Russia (2009)
    Springer
    In:  Contributions to Mineralogy and Petrology, 157 . pp. 209-230.
    Details
    Publication Date: 2016-09-21
    Description: Klyuchevskoy volcano, in Kamchatka’s subduction zone, is one of the most active arc volcanoes in the world and contains some of the highest δ18O values for olivines and basalts. We present an oxygen isotope and melt inclusion study of olivine phenocrysts in conjunction with major and trace element analyses of 14C- and tephrochronologically-dated tephra layers and lavas spanning the eruptive history of Klyuchevskoy. Whole-rock and groundmass analyses of tephra layers and lava samples demonstrate that both high-Mg (7–12.5 wt% MgO) and high-Al (17–19 wt% Al2O3, 3–6.5 wt% MgO) basalt and basaltic andesite erupted coevally from the central vent and flank cones. Individual and bulk olivine δ18O range from normal MORB values of 5.1‰ to values as high as 7.6‰. Likewise, tephra and lava matrix glass have high-δ18O values of 5.8–8.1‰. High-Al basalts dominate volumetrically in Klyuchevskoy’s volcanic record and are mostly high in δ18O. High-δ18O olivines and more normal-δ18O olivines occur in both high-Mg and high-Al samples. Most olivines in either high-Al or high-Mg basalts are not in oxygen isotopic equilibrium with their host glasses, and Δ18Oolivine–glass values are out of equilibrium by up to 1.5‰. Olivines are also out of Fe–Mg equilibrium with the host glasses, but to a lesser extent. Water concentrations in olivine-hosted melt inclusions from five tephra samples range from 0.4 to 7.1 wt%. Melt inclusion CO2 concentrations vary from below detection (〈50 ppm) to 1,900 ppm. These values indicate depths of crystallization up to ~17 km (5 kbar). The variable H2O and CO2 concentrations likely reflect crystallization of olivine and entrapment of inclusions in ascending and degassing magma. Oxygen isotope and Fe–Mg disequilibria together with melt inclusion data indicate that olivine was mixed and recycled between high-Al and high-Mg basaltic melts and cumulates, and Fe–Mg and δ18O re-equilibration processes were incomplete. Major and trace elements in the variably high-δ18O olivines suggest a peridotite source for the parental magmas. Voluminous, highest in the world with respect to δ18O, and hydrous basic volcanism in Klyuchevskoy and other Central Kamchatka depression volcanoes is explained by a model in which the ascending primitive melts that resulted from the hydrous melt fluxing of mantle wedge peridotite, interacted with the shallow high-δ18O lithospheric mantle that had been extensively hydrated during earlier times when it was part of the Kamchatka forearc. Following accretion of the Eastern Peninsula terrains several million years ago, a trench jump eastward caused the old forearc mantle to be beneath the presently active arc. Variable interaction of ascending flux-melting-derived melts with this older, high-δ18O lithospheric mantle has produced mafic parental magmas with a spectrum of δ18O values. Differentiation of the higher δ18O parental magmas has created the volumetrically dominant high-Al basalt series. Both basalt types incessantly rise and mix between themselves and with variable in δ18O cumulates within dynamic Klyuchevskoy magma plumbing system, causing biannual eruptions and heterogeneous magma products.
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  • 80
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    The cyanobacterial alkaloid nostocarboline: an inhibitor of acetylcholinesterase and trypsin (2009)
    Springer
    In:  Journal of Applied Phycology, 21 . pp. 103-110.
    Details
    Publication Date: 2018-01-19
    Description: Preselected cyanobacterial strains (available from culture collections and our own isolates), belonging primarily to the heterocystous cluster, were screened for inhibitors against butyrylcholinesterase. About one-half of the extracts exhibited inhibitory activity. Nostocarboline, the responsible metabolite in Nostoc 78–12A, was studied in more detail as an acetylcholinesterase (AChE) inhibitor. The compound showed potent activity against this enzyme (IC50 = 5.3 µM), and the Michaelis-Menten kinetics indicated a non-competitive component in the inhibitory mechanism. In addition, nostocarboline turned out to be a potent inhibitor of trypsin (IC50 = 2.8 µM), and thus is the first described cyanobacterial serine protease inhibitor of an alkaloid structure. The function of nostocarboline in aquatic ecosystems and its potential as a lead compound for the development of useful therapeutic AChE inhibitors is discussed.
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  • 81
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    Taxonomic diversity and identification problems of oncaeid microcopepods in the Mediterranean Sea (2009)
    Springer
    In:  Marine Biodiversity, 39 . pp. 131-145.
    Details
    Publication Date: 2017-10-05
    Description: The species diversity of the pelagic microcopepod family Oncaeidae collected with nets of 0.1-mm mesh size was studied at 6 stations along a west-to-east transect in the Mediterranean Sea down to a maximum depth of 1,000 m. A total of 27 species and two form variants have been identified, including three new records for the Mediterranean. In addition, about 20, as yet undescribed, new morphospecies were found (mainly from the genera Epicalymma and Triconia) which need to be examined further. The total number of identified oncaeid species was similar in the Western and Eastern Basins, but for some cooccurring sibling species, the estimated numerical dominance changed. The deep-sea fauna of Oncaeidae, studied at selected depth layers between 400 m and the near-bottom layer at 〉4,200 m depth in the eastern Mediterranean (Levantine Sea), showed rather constant species numbers down to ∼3,000 m depth. In the near-bottom layers, the diversity of oncaeids declined and species of Epicalymma strongly increased in numerical importance. The taxonomic status of all oncaeid species recorded earlier in the Mediterranean Sea is evaluated: 19 out of the 46 known valid oncaeid species are insufficiently described, and most of the taxonomically unresolved species (13 species) have originally been described from this area (type locality). The deficiencies in the species identification of oncaeids cast into doubt the allegedly cosmopolitan distribution of some species, in particular those of Mediterranean origin. The existing identification problems even of well-described oncaeid species are exemplified for the Oncaea mediacomplex, including O. media Giesbrecht, O. scottodicarloi Heron & Bradford-Grieve, and O. waldemari Bersano & Boxshall, which are often erroneously identified as a single species (O. media). The inadequacy in the species identification of Oncaeidae, in particular those from the Atlantic and Mediterranean, is mainly due to the lack of reliable identification keys for Oncaeidae in warm-temperate and/or tropical seas. Future efforts should be directed to the construction of identification keys that can be updated according to the latest taxonomic findings, which can be used by the non-expert as well as by the specialist. The adequate consideration of the numerous, as yet undescribed, microcopepod species in the world oceans, in particular the Oncaeidae, is a challenge for the study of the structure and function of plankton communities as well as for global biodiversity estimates.
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  • 82
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    Copepod growth and diatoms: insensitivity of Acartia tonsa to the composition of semi-natural plankton mixtures manipulated by silicon:nitrogen ratios in mesocosms (2009)
    Springer
    In:  Oecologia, 159 . pp. 207-215.
    Details
    Publication Date: 2017-01-31
    Description: The feeding selectivity and the growth and reproductive success of the copepod Acartia tonsa have been studied in mesocosms fertilized at different Si:N ratios (0-1.75:1) and, therefore, at different compositions of the phytoplankton communities. Phytoplankton composition showed a strong response to nutrient ratios, with diatoms comprising > 90% at Si:N ratios > 1:1 of total biomass as opposed to 〈 20% at the lowest ratio. A. tonsa strongly preferred feeding on motile prey (flagellates and ciliates) to feeding on diatoms. Nevertheless, diatoms comprised a substantial part of the diet at the highest Si:N ratios. A. tonsa egg production and the final (after 4 weeks) abundance of adults and copepodites showed no response to Si:N ratios while nauplii production slightly increased with Si:N ratios. It is concluded that the frequently reported deleterious effect of diatoms on copepod reproduction is rather unusual when copepods are confronted with a naturally diverse phytoplankton assemblage instead of clonal cultures in the laboratory.
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  • 83
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    Post-Megaslide Slope Stability north of Svalbard, Arctic Ocean (2009)
    Springer
    In:  In: Submarine Mass Movements and Their Consequences. , ed. by Mosher, D. Advances in Natural and Technological Hazards Research, 28 . Springer, Berlin, pp. 279-287. ISBN 978-90-481-3070-2
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    Publication Date: 2012-02-23
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  • 84
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    Seasonal variability of copepod abundance in the Balearic region (Western Mediterranean) as an indicator of basin scale hydrological changes (2009)
    Springer
    In:  Hydrobiologia, 617 (1). pp. 3-16.
    Details
    Publication Date: 2018-07-02
    Description: Spatial and temporal changes of the copepod community have been investigated and related to the environmental variability of the Balearic Sea (Western Mediterranean). The period studied spans from 1994 to 1999 during which we analyzed the abundance and structure copepod variability over a cross-shore transect. Results showed a close link between hydrological changes and the variations of copepod abundance. The synchronous variability of copepods and hydrography indicated the rapid response of this zooplankton group to the inflow of cold and warm water masses coming through the study area. Cluster analysis revealed four main copepod assemblages that distinguished the coastal from the oceanic species and those species with different water masses preference. The copepod assemblage composed of Calanus helgolandicus, Clausocalanus arcuicornis, C. pergens, C. paululus, Calocalanus tenuis and Pleuromamma gracilis was associated with cool salty waters, whereas the assemblage formed by Temora stylifera, C. pavo, C. styliremis, Centropages bradyi and Acartia danae was related to warmer less saline Mediterranean waters. Moreover, it is suggested that changes in sea water temperature and salinity are linked to large-scale changes likely occurring at a basin scale, which is reflected in the Western Mediterranean mesoscale hydrographic changes. Therefore, it is stressed that changes in the Balearic copepod community can be used as potential tracers of the western Mediterranean water masses
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  • 85
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    U-Pb dating, Hf isotope characteristics and trace-REE-patterns of zircons from Medet porphyry copper deposit, Bulgaria: Implications for timing, duration and sources of ore-bearing magmatism (2009)
    Springer
    In:  Mineralogy and Petrology, 96 . pp. 19-41.
    Details
    Publication Date: 2019-09-23
    Description: Precise U–Pb geochronology, Hf isotope compositions and trace element distributions in zircons are combined in the present study to define the timing and sources of the magmatism forming the Medet porphyry copper deposit, Bulgaria. ID-TIMS U–Pb-zircon dating demonstrates that ore-bearing magmatism extended for less than 1.12 Ma. As inferred from the field relationships, it started with the intrusion of a quartz-monzodiorite at 90.59 ± 0.29 Ma followed by granodiorite porphyries at 90.47 ± 0.30 and 90.27 ± 0.60 Ma and by crosscutting aplite dykes at 90.12 ± 0.36 Ma. These units were overprinted by potassic alteration and host economic copper-(Mo–Au) mineralization. The main magmatic–hydrothermal activity ceased after that, and a later quartz-granodiorite porphyry dyke, dated at 89.26 ± 0.32 Ma, only contains an uneconomic quartz–pyrite mineralization. Assimilation of Lower Paleozoic rocks with a mantle to mantle–crust signature is characteristic of the fertile magma in the Medet deposit, as defined by positive ɛ-Hf values of the inherited zircons. The positive Ce-anomalies and the higher Eu/Eu* ratios of the zircons in the mineralized Cretaceous rocks of Medet deposit argue for crystallization from a generally more oxidized magma compared to the later quartz-granodiorite porphyry dyke. A change in paleostress conditions occurred during the intrusion of the Medet pluton and its dykes. The initial stage reveals E–W extension associated with N–S compression, whereas the younger granodiorite dyke was emplaced during subsequent N–S extension. The large-scale switch of the extensional stress regime during the mineralization was favourable for ore deposition by channelling the fluids and increasing the effective permeability.
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  • 86
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    Seasonal changes and population dynamics of the ctenophore Mnemiopsis leidyi after its first year of invasion in the Kiel Fjord, Western Baltic Sea (2009)
    Springer
    In:  Biological Invasions, 11 . pp. 873-882.
    Details
    Publication Date: 2019-09-23
    Description: We analyzed the seasonal variations of the ctenophore Mnemiopsis leidyi weekly collected since its first record in the western Baltic Sea in October 2006. The distribution pattern together with the seasonal dynamics and population outbreaks in late summer 2007 indicate recent successfully establishment of M. leidyi in this area. Seasonal changes showed two periods of high reproductive activity characterized by a population structure dominated by small size classes, followed by an increase of larger ones. These results further revealed that the bulk of the population remains in deep layers during the periods of low population density, whereas it appeared situated in upper layers during the proliferation of the species. We further emphasized the strength of the population outbreaks, which can reach abundances 〉10-fold higher in time periods shorter than a week. The predatory impact this species may have in pelagic ecosystems warns on the importance of its recent range of expansion.
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  • 87
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    Geochemical evolution of intraplate volcanism at Banks Peninsula, New Zealand : interaction between asthenospheric and lithospheric melts (2009)
    Oxford Univ. Press
    In:  Journal of Petrology, 50 (6). pp. 989-1023.
    Details
    Publication Date: 2019-08-08
    Description: Intraplate volcanism was widespread and occurred continuously throughout the Cenozoic on the New Zealand micro-continent, Zealandia, forming two volcanic endmembers: (1) monogenetic volcanic fields; (2) composite shield volcanoes. The most prominent volcanic landforms on the South Island of New Zealand are the two composite shield volcanoes (Lyttelton and Akaroa) forming the Banks Peninsula. We present new Ar-40/Ar-39 age and geochemical (major and trace element and Sr-Nd-Pb-Hf-O isotope) data for these Miocene endmembers of intraplate volcanism. Although volcanism persisted for similar to 7 Myr on Banks Peninsula, both shield volcanoes primarily formed over an similar to 1 Myr interval with small volumes of late-stage volcanism continuing for similar to 1 center dot 5 Myr after formation of the shields. Compared with normal Pacific mid-ocean ridge basalts (P-MORB), the low-silica (picritic to basanitic to alkali basaltic) Akaroa mafic volcanic rocks (9 center dot 4-6 center dot 8 Ma) have higher incompatible trace element concentrations and Sr and Pb isotope ratios but lower delta O-18 (4 center dot 6-4 center dot 9) and Nd and Hf isotope ratios than ocean island basalts (OIB) or high time-integrated U/Pb HIMU-type signatures, consistent with the presence of a hydrothermally altered recycled oceanic crustal component in their source. Elevated CaO, MnO and Cr contents in the HIMU-type low-silica lavas, however, point to a peridotitic rather than a pyroxenitic or eclogitic source. To explain the decoupling between major elements on the one hand and incompatible elements and isotopic compositions on the other, we propose that the upwelling asthenospheric source consists of carbonated eclogite in a peridotite matrix. Melts from carbonated eclogite generated at the base of the melt column metasomatized the surrounding peridotite before it crossed its solidus. Higher in the melt column the metasomatized peridotite melted to form the Akaroa low-silica melts. The older (12 center dot 3-10 center dot 4 Ma), high-silica (tholeiitic to alkali basaltic) Lyttelton mafic volcanic rocks have low CaO, MnO and Cr abundances suggesting that they were at least partially derived from a source with residual pyroxenite. They also have lower incompatible element abundances, higher fluid-mobile to fluid-immobile trace element ratios, higher delta O-18, and more radiogenic Sr but less radiogenic Pb-Nd-Hf isotopic compositions than the Akaroa volcanic rocks and display enriched (EMII-type) trace element and isotopic compositions. Mixing of asthenospheric (Akaroa-type) melts with lithospheric melts from pyroxenite formed during Mesozoic subduction along the Gondwana margin and crustal melts can explain the composition of the Lyttelton volcano basalts. Two successive lithospheric detachment/delamination events in the form of Rayleigh-Taylor instabilities could have triggered the upwelling and related decompression melting leading to the formation of the Lyttelton (first, smaller detachment event) and Akaroa (second, more extensive detachment event) volcanoes.
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  • 88
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    Epibiosis: Ecology, Effects and Defenses (2009)
    Springer
    In:  In: Marine Hard Bottom Communities: patterns, dynamics, diversity, and change. , ed. by Wahl, M. Springer Series: Ecological Studies, 206 . Springer, Heidelberg, pp. 61-72. ISBN 978-3-540-92703-7
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    Publication Date: 2012-07-05
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  • 89
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    Vertical distribution and dietary preferences of deep-sea copepods (Euchaetidae and Aetideidae; Calanoida) in the vicinity of the Antarctic Polar Front (2009)
    Springer
    In:  Polar Biology, 32 . pp. 679-689.
    Details
    Publication Date: 2019-08-29
    Description: Four Paraeuchaeta species and three aetideids were frequently encountered along 51°30′S in the Atlantic sector of the Southern Ocean. Paraeuchaeta antarctica was most abundant close to the Antarctic Polar Front. Within the genera Paraeuchaeta and Gaetanus, congeners usually partitioned the water column. Euchaetidae had high lipid (≤37% dry mass, DM in adult females) and wax ester contents (≤22% DM). Fatty acid composition of Paraeuchaeta spp. was dominated by monounsaturated moieties, especially 16:1(n-7) and 18:1(n-9), while fatty alcohols were mainly saturated. Surprisingly, only the bathypelagic P. barbata contained moderate amounts of 20:1(n-9) and 22:1(n-11) fatty acids (≤14%) and high levels of the respective fatty alcohols (≤50%), generally considered trophic biomarkers for calanid copepods as prey. Thus, herbivorous calanid copepods seem to be a readily available prey source at bathypelagic depths, indicating that their seasonal vertical migration provides a “trophic shortcut” from primary production at the surface to the interior of the ocean. Aetideidae also contained substantial levels of total lipid (14–36% DM), but wax esters contributed only up to 12% DM in copepodite stages C5 of Gaetanus spp., whereas other stages of Gaetanus and Aetideopsis minor only contained ≤6% DM of wax esters. The fatty acid compositions of Aetideidae were more balanced with 16:0, 18:1(n-9), 20:5(n-3), and 22:6(n-3) as important components, indicating a generally omnivorous feeding behaviour.
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  • 90
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    Diversity of Antibiotic-Active Bacteria Associated with the Brown Alga Laminaria saccharina from the Baltic Sea (2009)
    Springer
    In:  Marine Biotechnology, 11 . pp. 287-300.
    Details
    Publication Date: 2019-09-23
    Description: Bacteria associated with the marine macroalga Laminaria saccharina, collected from the Kiel Fjord (Baltic Sea, Germany), were isolated and tested for antimicrobial activity. From a total of 210 isolates, 103 strains inhibited the growth of at least one microorganism from the test panel including Gram-negative and Gram-positive bacteria as well as a yeast. Most common profiles were the inhibition of Bacillus subtilis only (30%), B. subtilis and Staphylococcus lentus (25%), and B. subtilis, S. lentus, and Candida albicans (11%). In summary, the antibiotic-active isolates covered 15 different activity patterns suggesting various modes of action. On the basis of 16S rRNA gene sequence similarities >99%, 45 phylotypes were defined, which were classified into 21 genera belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Phylogenetic analysis of 16S rRNA gene sequences revealed that four isolates possibly represent novel species or even genera. In conclusion, L. saccharina represents a promising source for the isolation of new bacterial taxa and antimicrobially active bacteria.
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  • 91
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    Taxonomy of Oncaeidae (Copepoda, Poecilostomatoida) from the Red Sea. - IX. Epicalymma bulbosa sp. nov., first record of the genus from the Red Sea (2009)
    Oxford Univ. Press
    In:  Journal of Plankton Research, 31 . pp. 1027-1043.
    Details
    Publication Date: 2018-06-05
    Description: The oncaeid genus Epicalymma comprises small copepod species usually living at meso- and bathypelagic depth layers in oceanic areas. The genus had previously been assumed to be absent from the Red Sea, due to the unusually high deep-sea temperatures and salinities in this area. In the present account a new species, Epicalymma bulbosa, is described from the Red Sea, which appears to be the only representative of the genus in the region. The new species is the smallest Epicalymma species so far recorded, with a total body length of ∼0.32 and ∼0.29 mm in the female and male, respectively. Apart from its small size, it differs from all known Epicalymma species by an extremely long exopodal seta on P5 in both sexes, and by a free exopod segment of P5 and a very long and basally swollen spinule on the syncoxa of the maxilliped in the female. In contrast to other Epicalymma species, which are distributed between 500 and 〉2500 m depth, the new species occurred much shallower (100–750 m) in the Red Sea, which may be interpretated as an avoidance mechanism of the unfavourable environmental conditions in the deep Red Sea. The taxonomic status of the new species within the genus Epicalymma is discussed and the few available ecological data on Epicalymma species in the world ocean are summarized.
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  • 92
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    Is the Indian Ocean SST variability a homogeneous diffusion process? (2009)
    Springer
    In:  Climate Dynamics, 33 (4). pp. 535-547.
    Details
    Publication Date: 2016-09-13
    Description: Whereas the predominance of El Nio Southern Oscillation (ENSO) mode in the tropical Pacific sea surface temperature (SST) variability is well established, no such consensus seems to have been reached by climate scientists regarding the Indian Ocean. While a number of researchers think that the Indian Ocean SST variability is dominated by an active dipolar-type mode of variability, similar to ENSO, others suggest that the variability is mostly passive and behaves like an autocorrelated noise. For example, it is suggested recently that the Indian Ocean SST variability is consistent with the null hypothesis of a homogeneous diffusion process. However, the existence of the basin-wide warming trend represents a deviation from a homogeneous diffusion process, which needs to be considered. An efficient way of detrending, based on differencing, is introduced and applied to the Hadley Centre ice and SST. The filtered SST anomalies over the basin (23.5N-29.5S, 30.5E-119.5E) are then analysed and found to be inconsistent with the null hypothesis on intraseasonal and interannual timescales. The same differencing method is then applied to the smaller tropical Indian Ocean domain. This smaller domain is also inconsistent with the null hypothesis on intraseasonal and interannual timescales. In particular, it is found that the leading mode of variability yields the Indian Ocean dipole, and departs significantly from the null hypothesis only in the autumn season.
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  • 93
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    The magmatic plumbing system beneath El Hierro (Canary Islands): constraints from phenocrysts and naturally quenched basaltic glasses (2009)
    Springer
    In:  Contributions to Mineralogy and Petrology, 157 (5). pp. 593-607.
    Details
    Publication Date: 2018-01-19
    Description: A thermobarometric and petrologic study of basanites erupted from young volcanic cones along the submarine portions of the three El Hierro rift zones (NE-Rift, NW-Rift and S-Ridge) has been performed to reconstruct magma plumbing and storage beneath the island. Mineral-melt thermobarometry applied to naturally quenched glass and clinopyroxene rims yields pressures ranging from 350 to 1070 MPa with about 80% of the calculated pressures being in the range of 600–800 MPa. This corresponds to a depth range of 19–26 km, implying that the main level of final crystal fractionation is within the uppermost mantle. No systematic dependence between sample locality and fractionation pressures could be observed. Olivine and clinopyroxene crystals in the rocks are complexly zoned and have, on an inter-sample as well as on an intra-sample scale, highly variable core and rim compositions. This can best be explained by mixing of multiply saturated (olivine, magnetite, clinopyroxene, ilmenite), moderately evolved magmas with more mafic magmas being either only saturated with olivine + spinel or with olivine + spinel + clinopyroxene. The inter-sample differences indicate derivation from small, isolated magma chambers which have undergone distinct fractionation and mixing histories. This is in contrast to oceanic intraplate volcanoes situated on plumes with high melt supply rates, e.g. Kilauea Volcano (Hawaii), where magma is mainly transported through a central conduit system and stored in a shallow magma chamber prior to injection into the rift zones. The plumbing system beneath El Hierro rather resembles the magma storage systems beneath, e.g. Madeira or La Palma, indicating that small, intermittent magma chambers might be a common feature of oceanic islands fed by plumes with relatively low fluxes, which results in only limited and periodic magma supply.
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  • 94
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    New physical characterization of the Fontana Lapilli basaltic Plinian eruption, Nicaragua (2009)
    Springer
    In:  Bulletin of Volcanology, 71 (3). pp. 337-355.
    Details
    Publication Date: 2019-09-23
    Description: The Fontana Lapilli deposit was erupted in the late Pleistocene from a vent, or multiple vents, located near Masaya volcano (Nicaragua) and is the product of one of the largest basaltic Plinian eruptions studied so far. This eruption evolved from an initial sequence of fluctuating fountain-like events and moderately explosive pulses to a sustained Plinian episode depositing fall beds of highly vesicular basaltic-andesite scoria (SiO2 〉 53 wt%). Samples show unimodal grain size distribution and a moderate sorting that are uniform in time. The juvenile component predominates (〉 96 wt%) and consists of vesicular clasts with both sub-angular and fluidal, elongated shapes. We obtain a maximum plume height of 32 km and an associated mass eruption rate of 1.4 × 108 kg s−1 for the Plinian phase. Estimates of erupted volume are strongly sensitive to the technique used for the calculation and to the distribution of field data. Our best estimate for the erupted volume of the majority of the climactic Plinian phase is between 2.9 and 3.8 km3 and was obtained by applying a power-law fitting technique with different integration limits. The estimated eruption duration varies between 4 and 6 h. Marine-core data confirm that the tephra thinning is better fitted by a power-law than by an exponential trend.
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  • 95
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    Insights into Li and Li isotope cycling and sub-arc metasomatism from veined mantle xenoliths, Kamchatka (2009)
    Springer
    In:  Contributions to Mineralogy and Petrology, 158 (2). pp. 197-222.
    Details
    Publication Date: 2016-09-21
    Description: Harzburgitic xenoliths cut by pyroxenite veins from Avachinsky volcano, Kamchatka, are derived from the sub-arc mantle and record element transfer from the slab to the arc. Olivine and orthopyroxene in the harzburgites have Li isotopic compositions (δ7Li = +2.8 to +5.6) comparable to estimates of the upper mantle (δ7Li ~ +4 ± 2). The pyroxenite veins, which represent modal metasomatism and may therefore provide information about the metasomatic agent, have mantle-normalized trace element characteristics that suggest overprinting of their mantle source by an aqueous, slab-derived fluid. These include relative enrichments of Pb over Ce, U over Th and Sr over Nd. Li is enriched relative to the HREE, and ortho- and clinopyroxene from the veins are in Li elemental and isotopic equilibrium with each other and the surrounding harzburgite. Vein samples (δ7Li = +3.0 to +5.0) do not record a significant slab-derived δ7Li signature. These observations can be reconciled if slab Li diffusively re-equilibrates in the mantle wedge. Modeling demonstrates that Li equilibration of small (1–2 cm width) veins or melt conduits is achieved at mantle wedge temperatures within 101–105 years. We conclude that strongly fractionated Li isotopic signatures cannot be sustained for long periods in the sub-arc mantle, at least at shallow (〈70 km) depths.
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  • 96
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    Mediterranean marine copepods: basin-scale trends of the calanoid Centropages typicus (2009)
    Springer
    In:  Hydrobiologia, 617 . pp. 41-53.
    Details
    Publication Date: 2018-07-02
    Description: The Mediterranean Sea is located in a crossroad of mid-latitude and subtropical climatic modes that enhance contrasting environmental conditions over both latitudinal and longitudinal ranges. Here, we show that the large-scale environmental forcing is reflected in the basin scale trends of the adult population of the calanoid copepod Centropages typicus. The species is distributed over the whole Mediterranean basin, and maximal abundances were found in the north-western basin associated to oceanic fronts, and in the Adriatic Sea associated to shallow and semi enclosed waters. The peak of main abundances of C. typicus correlates with the latitudinal temperature gradient and the highest seasonal abundances occurred in spring within the 14-18A degrees C temperature window. Such thermal cline may define the latitudinal geographic region where C. typicus seasonally dominates the > 200 mu m-sized spring copepod community in the Mediterranean Sea. The approach used here is generally applicable to investigate the large-scale spatial patterns of other planktonic organisms and to identify favourable environmental windows for population development.
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  • 97
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    Geochemical variations in the Cocos Plate subducting beneath Central America : implications for the composition of arc volcanism and the extent of the Galápagos Hotspot influence on the Cocos oceanic crust (2009)
    Springer
    In:  International Journal of Earth Sciences, 98 (4). pp. 901-913.
    Details
    Publication Date: 2019-09-23
    Description: New geochemical data from the Cocos Plate constrain the composition of the input into the Central American subduction zone and demonstrate the extent of influence of the Galapagos Hotspot on the Cocos Plate. Samples include sediments and basalts from Ocean Drilling Program (ODP) Site 1256 outboard of Nicaragua, gabbroic sills from ODP Sites 1039 and 1040, tholeiitic glasses from the Fisher Ridge off northwest Costa Rica, and basalts from the Galapagos Hotspot Track outboard of Central Costa Rica. Site 1256 basalts range from normal to enriched MORB in incompatible elements and have Pb and Nd isotopic compositions within the East Pacific Rise MORB field. The sediments have similar Pb-206/Pb-204 and only slightly more radiogenic Pb-207/Pb-204 and Pb-208/Pb-204 isotope ratios than the basalts. Altered samples from the subducting Galapagos Hotspot Track have similar Nd and Pb isotopic compositions to fresh Galapagos samples but have significantly higher Sr isotopic composition, indicating that the subduction input will have a distinct geochemical signature from Galapagos-type mantle material that may be present in the wedge beneath Costa Rica. Gabbroic sills from Sites 1039 and 1040 in East Pacific Rise (EPR) crust show evidence for influence of the Galapagos Hotspot similar to 100 km beyond the morphological hotspot track
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  • 98
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    Recruitment in a changing environment: the 2000s North Sea herring recruitment failure (2009)
    Oxford Univ. Press
    In:  ICES Journal of Marine Science, 66 (2). pp. 272-277.
    Details
    Publication Date: 2019-09-24
    Description: Environmentally induced change appears to be impacting the recruitment of North Sea herring (Clupea harengus). Despite simultaneously having a large adult population, historically low exploitation, and Marine Stewardship Council accreditation (implying sustainability), there have been an unprecedented 6 sequential years of poor juvenile production (recruitment). Analysis suggests that the poor recruitment arises during the larval overwintering phase, with recent survival rates greatly reduced. Contemporary warming of the North Sea has caused significant changes in the plankton community, and a recently identified regime shift around 2000 shows close temporal agreement with the reduced larval survival. It is, therefore, possible that we are observing the first consequences of this planktonic change for higher trophic levels. There is no indication of a recovery in recruitment in the short term. Fishing mortality is currently outside the agreed management plan, and forecasts show a high risk of the stock moving outside safe biological limits soon, potentially precipitating another collapse of the stock. However, bringing the realized fishing mortality back in line with the management plan would likely alleviate the problem. This illustrates again that recruitment is influenced by more than just spawning-stock biomass, and that changes in other factors can be of equal, or even greater, importance. In such dynamically changing environments, recent management success does not necessarily guarantee future sustainability.
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  • 99
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    Exploitation of secondary metabolites by animals: A response to homeostatic challenges (2009)
    Oxford Univ. Press
    In:  Integrative and Comparative Biology, 49 (3). pp. 314-328.
    Details
    Publication Date: 2020-07-28
    Description: We propose that the exploitation of the bioactive properties of secondary metabolites (SMs) by animals can provide a “treatment” against various challenges that perturb homeostasis in animals. The unified theoretical framework for the exploitation of SMs by animals is based on a synthesis of research from a wide range of fields and although it is focused on providing generalized predictions for herbivores that exploit SMs of plants, predictions can be applied to understand the exploitation of SMs by many animals. In this review, we argue that the probability of SM exploitation is determined by the relative difference between the cost of a homeostatic challenge and the toxicity of the SM and we provide various predictions that can be made when considering behavior under a homeostatic perspective. The notion that animals experience and respond to costly challenges by exploiting therapeutic SMs provides a relatively novel perspective to explain foraging behavior in herbivores, specifically, and behavior of animals in general. We provide evidence that animals can exploit the biological activity of SMs to mitigate the costs of infection by parasites, enhance reproduction, moderate thermoregulation, avoid predation, and increase alertness. We stress that a better understanding of animal behavior requires that ecologists look beyond their biases that SMs elicit punishment and consider a broader view of avoidance or selection of SMs relative to the homeostatic state. Finally, we explain how understanding exploitation of SMs by animals could be applied to advance practices of animal management and lead to discovery of new drugs.
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  • 100
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    Metazooplankton distribution across the Southern Indian Ocean with emphasis on the role of Larvaceans (2009)
    Oxford Univ. Press
    In:  Journal of Plankton Research, 31 (5). pp. 525-540.
    Details
    Publication Date: 2020-07-20
    Description: The abundance and depth distribution of metazoans 〉20 μm were investigated at seven stations across the Southern Indian Ocean (SIO), October–November 2006. Copepod nauplii, copepodites and larvaceans dominated the metazooplankton community. Copepodites were most abundant within Agulhas Current and Southern Ocean waters, decreasing toward subtropical/tropical areas, whereas larvaceans showed the inverse pattern. The fraction 〈200 μm contained the majority of the zooplankton enumerated, including 81, 23 and 93% of the larvacean, copepodite and nauplii abundances, respectively. The relative abundance of larvaceans compared with copepodites increased from 7 to 44% from South Africa towards Australia. Peak copepodite biomass was observed off South Africa, while larvacean biomass was 〈1% of the copepodite biomass there, increasing to 6% in tropical waters. Both copepodite and nauplii biomass were positively correlated to total Chl a (P 〈 0.0001), larvacean biomass was only significantly related to temperature (P = 0.0213). Despite their low biomass, larvacean production was estimated to exceed the copepod production up to five times. It appears that the abundance and role of larvaceans in the SIO has been severely underestimated in previous studies; thus future investigations into the fate of organic matter will remain incomplete if this group is not adequately considered.
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