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| 2. |
- Christensen, Thorbjørn Erik Køppen, et al.
(author)
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Flexible design in the stomatopod dactyl club
- 2023
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In: IUCrJ. - 2052-2525. ; 10:Pt 3, s. 288-296
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Journal article (peer-reviewed)abstract
- The stomatopod is a fascinating animal that uses its weaponized appendage dactyl clubs for breaking mollusc shells. Dactyl clubs are a well studied example of biomineralized hierarchical structures. Most research has focused on the regions close to the action, namely the impact region and surface composed of chitin and apatite crystallites. Further away from the site of impact, the club has lower mineralization and more amorphous phases; these areas have not been as actively studied as their highly mineralized counterparts. This work focuses on the side of the club, in what is known as the periodic and striated regions. A combination of laboratory micro-computed tomography, synchrotron X-ray diffraction mapping and synchrotron X-ray fluorescence mapping has shown that the mineral in this region undergoes the transition from an amorphous to a crystalline phase in some, but not all, clubs. This means that this side region can be mineralized by either an amorphous phase, calcite crystallites or a mixture of both. It was found that when larger calcite crystallites form, they are organized (textured) with respect to the chitin present in this biocomposite. This suggests that chitin may serve as a template for crystallization when the side of the club is fully mineralized. Further, calcite crystallites were found to form as early as 1 week after moulting of the club. This suggests that the side of the club is designed with a significant safety margin that allows for a variety of phases, i.e. the club can function independently of whether the side region has a crystalline or amorphous mineral phase.
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| 3. |
- Diesend, Jan, et al.
(author)
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Fractional 2 '-O-methylation in the ribosomal RNA of Dictyostelium discoideum supports ribosome heterogeneity in Amoebozoa
- 2022
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 12:1
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Journal article (peer-reviewed)abstract
- A hallmark of ribosomal RNA (rRNA) are 2 '-O-methyl groups that are introduced sequence specifically by box C/D small nucleolar RNAs (snoRNAs) in ribonucleoprotein particles. Most data on this chemical modification and its impact on RNA folding and stability are derived from organisms of the Opisthokonta supergroup. Using bioinformatics and RNA-seq data, we identify 30 novel box C/D snoRNAs in Dictyostelium discoideum, many of which are differentially expressed during the multicellular development of the amoeba. By applying RiboMeth-seq, we find 49 positions in the 17S and 26S rRNA 2 '-O-methylated. Several of these nucleotides are substoichiometrically modified, with one displaying dynamic modification levels during development. Using homology-based models for the D. discoideum rRNA secondary structures, we localize many modified nucleotides in the vicinity of the ribosomal A, P and E sites. For most modified positions, a guiding box C/D snoRNA could be identified, allowing to determine idiosyncratic features of the snoRNA/rRNA interactions in the amoeba. Our data from D. discoideum represents the first evidence for ribosome heterogeneity in the Amoebozoa supergroup, allowing to suggest that it is a common feature of all eukaryotes.
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| 4. |
- Grünewald, Tilman A., et al.
(author)
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Mapping the 3D orientation of nanocrystals and nanostructures in human bone: Indications of novel structural features
- 2020
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In: Science advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:24
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Journal article (peer-reviewed)abstract
- Bone is built from collagen fibrils and biomineral nanoparticles. In humans, they are organized in lamellar twisting patterns on the microscale. It has been a central tenet that the biomineral nanoparticles are co-aligned with the bone nanostructure. Here, we reconstruct the three-dimensional orientation in human lamellar bone of both the nanoscale features and the biomineral crystal lattice from small-angle x-ray scattering and wide-angle x-ray scattering, respectively. While most of the investigated regions show well-aligned nanostructure and crystal structure, consistent with current bone models, we report a localized difference in orientation distribution between the nanostructure and the biomineral crystals in specific bands. Our results show a robust and systematic, but localized, variation in the alignment of the two signals, which can be interpreted as either an additional mineral fraction in bone, a preferentially aligned extrafibrillar fraction, or the result of transverse stacking of mineral particles over several fibrils.
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| 5. |
- Jensen, Alexander Bernthz, et al.
(author)
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Very large-scale diffraction investigations enabled by a matrix-multiplication facilitated radial and azimuthal integration algorithm : MatFRAIA
- 2022
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In: Journal of Synchrotron Radiation. - 1600-5775. ; 29, s. 1420-1428
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Journal article (peer-reviewed)abstract
- As synchrotron facilities continue to generate increasingly brilliant X-rays and detector speeds increase, swift data reduction from the collected area detector images to more workable 1D diffractograms becomes of increasing importance. This work reports an integration algorithm that can integrate diffractograms in real time on modern laptops and can reach 10 kHz integration speeds on modern workstations using an efficient pixel-splitting and parallelization scheme. This algorithm is limited not by the computation of the integration itself but is rather bottlenecked by the speed of the data transfer to the processor, the data decompression and/or the saving of results. The algorithm and its implementation is described while the performance is investigated on 2D scanning X-ray diffraction/fluorescence data collected at the interface between an implant and forming bone.
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| 6. |
- Malmström, Lars, et al.
(author)
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Quantitative proteogenomics of human pathogens using DIA-MS.
- 2015
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In: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 129, s. 98-107
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Journal article (peer-reviewed)abstract
- The increasing number of bacterial genomes in combination with reproducible quantitative proteome measurements provides new opportunities to explore how genetic differences modulate proteome composition and virulence. It is challenging to combine genome and proteome data as the underlying genome influences the proteome. We present a strategy to facilitate the integration of genome data from several genetically similar bacterial strains with data-independent analysis mass spectrometry (DIA-MS) for rapid interrogation of the combined data sets. The strategy relies on the construction of a composite genome combining all genetic data in a compact format, which can accommodate the fusion with quantitative peptide and protein information determined via DIA-MS. We demonstrate the method by combining data sets from whole genome sequencing, shotgun MS and DIA-MS from 34 clinical isolates of Streptococcus pyogenes. The data structure allows for fast exploration of the data showing that undetected proteins are on average more amenable to amino acid substitution than expressed proteins. We identified several significantly differentially expressed proteins between invasive and non-invasive strains. The work underlines how integration of whole genome sequencing with accurately quantified proteomes can further advance the interpretation of the relationship between genomes, proteomes and virulence.
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| 7. |
- Nygren, Mats, et al.
(author)
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The effect of Mg doping on the thermoelectric performance of Zn4Sb3 : International Conference on Thermoelectrics
- 2008
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In: Institute of Electrical and Electronics Engineers. - 1094-2734. ; , s. 382-385
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Journal article (peer-reviewed)abstract
- The effect of Mg doping of Zn4Sb3 on thermal and thermoelec. properties has been studied on 4 samples with a doping degree ranging from 0.1 to 2 at.% Mg, and compared to a pure, undoped sample. Lab. X-ray powder diffraction shows that all samples are pure single phase materials as further evidenced with higher confidence by Rietveld refinement of high resoln. synchrotron powder diffraction of the as synthesized 1 at.% and 2 at.% Mg doped samples. Zn4Sb3 undergoes a transition from the room temp. disordered phase to an ordered ' phase, going over an intermediate phase; differential scanning calorimetry show only small effects of doping on the phase transition temp. Phys. properties have been evaluated from 2-400 K for all samples. Some phys. property parameters are affected by doping, but no immediate improvement of ZT was achieved by the doping procedure. The reason for this is discussed in relation to differences in sample compaction.
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| 8. |
- Pedersen, Birgitte L., et al.
(author)
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Substitution in MxZn4-xSb3 : Effect on Thermal Stability, Crystal Structure, Phase Transitions, and Thermoelectric Performance
- 2010
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In: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 22:7, s. 2375-2383
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Journal article (peer-reviewed)abstract
- The effects of Cd substitution in MxZn4−xSb3 on the high-temperature thermal stability, low-temperature phase transitions and thermoelectric properties have been studied on three samples with a substitution degree of 0.1, 1, and 2 at % Cd (x = 0.004, 0.04, 0.08). The high-temperature thermal stability in atmospheric air of a 1% substituted sample is compared with an unsubstituted Zn4Sb3 sample. Multitemperature synchrotron powder diffraction data reveals that while only ∼42 wt % of the original Zn4Sb3 phase remains in the unsubstituted sample after three heating cycles to 625 K, 78 wt % is preserved in the Cd-substituted sample. Thus, Cd-substitution provides a significant improvement of the thermal stability of Zn4Sb3. Multitemperature synchrotron powder diffraction data measured between 90 and 300 K reveal that Cd substitution has a suppressing effect on the α′−α−β phase transitions. With increasing substitution, there is also a significant change in the individual Zn site occupancies. Differential scanning calorimetry shows an apparent correlation between Cd content and phase transition temperature. Thermoelectric properties have been measured from 2 to 400 K for all samples, and although some physical properties are significantly affected by doping, no immediate improvement of ZT was achieved.
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| 9. |
- Pedersen, Birgitte L., et al.
(author)
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The effect of Mg doping on the thermoelectric performance of Zn4Sb3
- 2009
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In: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 105:1, s. 13517-
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Journal article (peer-reviewed)abstract
- Cation doping studies of high performance thermoelectric (ZnSb3)-Sb-4 have so far focused on elements with larger electronegativity than Zn. Mg has a lower electronegativity than Zn, and, in the present paper, the effect of Mg doping of Zn4Sb3 on phase transition temperatures and thermal and thermoelectric properties have been studied on five samples with a doping degree ranging from 0.1 to 2 at. % Mg. The results are compared with data obtained for a pure, undoped sample. Laboratory x-ray powder diffraction shows that all samples are single phase materials as further evidenced with higher confidence by Rietveld refinement of high resolution synchrotron powder diffraction of as synthesized 1 and 2 at. % Mg doped samples. Multitemperature synchrotron powder diffraction and differential scanning calorimetry reveal a significant effect of Mg-doping on the low temperature phase transitions in one sample (0.5 at. % Mg), whereas the other samples showed only small or no effect. Physical properties have been evaluated from 2-400 K for all samples. Some physical property parameters are affected by doping but no immediate improvement of ZT was achieved. The reason for this is discussed in relation to differences in sample compaction.
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