| 1. |
- Tabiri, S, et al.
(author)
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- 2021
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swepub:Mat__t
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| 2. |
- Bravo, L, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
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| 5. |
- Belt, S. T., et al.
(author)
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An inter-laboratory investigation of the Arctic sea ice biomarker proxy IP25 in marine sediments : key outcomes and recommendations
- 2014
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In: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 10:1, s. 155-166
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Journal article (peer-reviewed)abstract
- We describe the results of an inter-laboratory investigation into the identification and quantification of the Arctic sea ice biomarker proxy IP25 in marine sediments. Seven laboratories took part in the study, which consisted of the analysis of IP25 in a series of sediment samples from different regions of the Arctic, sub-Arctic and Antarctic, additional sediment extracts and purified standards. The results obtained allowed 4 key outcomes to be determined. First, IP25 was identified by all laboratories in sediments from the Canadian Arctic with inter-laboratory variation in IP25 concentration being substantially larger than within individual laboratories. This greater variation between laboratories was attributed to the difficulty in accurately determining instrumental response factors for IP25, even though laboratories were supplied with appropriate standards. Second, the identification of IP25 by 3 laboratories in sediment from SW Iceland that was believed to represent a blank, was interpreted as representing a better limit of detection or quantification for such laboratories, contamination or mis-identification. These alternatives could not be distinguished conclusively with the data available, although it is noted that the precision of these data was significantly poorer compared with the other IP25 concentration measurements. Third, 3 laboratories reported the occurrence of IP25 in a sediment sample from the Antarctic Peninsula even though this biomarker is believed to be absent from the Southern Ocean. This anomaly is attributed to a combined chromatographic and mass spectrometric interference that results from the presence of a di-unsaturated highly branched isoprenoid (HBI) pseudo-homologue of IP25 that occurs in Antarctic sediments. Finally, data are presented that suggest that extraction of IP25 is consistent between Accelerated Solvent Extraction (ASE) and sonication methods and that IP25 concentrations based on 7-hexylnonadecane as an internal standard are comparable using these methods. Recoveries of some more unsaturated HBIs and the internal standard 9-octylheptadecene, however, were lower with the ASE procedure, possibly due to partial degradation of these more reactive chemicals as a result of higher temperatures employed with this method. For future measurements, we recommend the use of reference sediment material with known concentration(s) of IP25 for determining and routinely monitoring instrumental response factors. Given the significance placed on the presence (or otherwise) of IP25 in marine sediments, some further recommendations pertaining to quality control are made that should also enable the two main anomalies identified here to be addressed.
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| 6. |
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| 7. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 8. |
- Wong, L. E., et al.
(author)
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Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data
- 2008
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In: Journal of Biomolecular Nmr. - : Springer Science and Business Media LLC. - 0925-2738 .- 1573-5001. ; 42:2, s. 77-86
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Journal article (peer-reviewed)abstract
- The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa C-13,(15) N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation.
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