| 1. |
- Allentoft, Morten E., et al.
(författare)
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Population genomics of post-glacial western Eurasia
- 2024
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
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Tidskriftsartikel (refereegranskat)abstract
- Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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| 2. |
- Gustafsson, Anders, et al.
(författare)
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Cathodoluminescence investigations of dark-line defects in platelet-based InGaN nano-LED structures
- 2024
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Ingår i: Nanotechnology. - : IOP Publishing Ltd. - 0957-4484 .- 1361-6528. ; 35:25
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the optical properties of heterostructured InGaN platelets aiming at red emission, intended for use as nano-scaled light-emitting diodes. The focus is on the presence of non-radiative emission in the form of dark line defects. We have performed the study using hyperspectral cathodoluminescence imaging. The platelets were grown on a template consisting of InGaN pyramids, flattened by chemical mechanical polishing. These templates are defect free, whereas the dark line defects are introduced in the lower barrier and tend to propagate through all the subsequent layers, as revealed by the imaging of different layers in the structure. We conclude that the dark line defects are caused by stacking mismatch boundaries introduced by multiple seeding and step bunching at the edges of the as-polished, dome shaped templates. To avoid these defects, we suggest that the starting material must be flat rather than dome shaped.
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| 3. |
- Gustafsson, Anders, et al.
(författare)
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Cathodoluminescence investigations of dark-line defects in platelet-based InGaN nano-LED structures
- 2024
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Ingår i: Nanotechnology. - : IOP Publishing Ltd. - 0957-4484 .- 1361-6528. ; 35:25
-
Tidskriftsartikel (refereegranskat)abstract
- We have investigated the optical properties of heterostructured InGaN platelets aiming at red emission, intended for use as nano-scaled light-emitting diodes. The focus is on the presence of non-radiative emission in the form of dark line defects. We have performed the study using hyperspectral cathodoluminescence imaging. The platelets were grown on a template consisting of InGaN pyramids, flattened by chemical mechanical polishing. These templates are defect free, whereas the dark line defects are introduced in the lower barrier and tend to propagate through all the subsequent layers, as revealed by the imaging of different layers in the structure. We conclude that the dark line defects are caused by stacking mismatch boundaries introduced by multiple seeding and step bunching at the edges of the as-polished, dome shaped templates. To avoid these defects, we suggest that the starting material must be flat rather than dome shaped.
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| 4. |
- Lindh, Anders, et al.
(författare)
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A model for granite evolution based on non-equilibrium magma separation : evidence from the Gharib and Qattar fluorite-bearing granites, Eastern Desert, Egypt
- 2019
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Ingår i: International Journal of Earth Sciences. - : Springer Science and Business Media LLC. - 1437-3254 .- 1437-3262. ; 108:4, s. 1201-1232
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Tidskriftsartikel (refereegranskat)abstract
- We present 77 new granite whole-rock analyses from the Qattar and Gharib areas, Eastern Desert, Egypt. Both areas include a “normal” granite and either a hypersolvus (Gharib) or an almost plagioclase-free granite (Qattar) enriched in fluorite. According to earlier results, F influences element distribution in granitic melts forming complexes with specific elements as Nb, Ta, Ga, Hf, Th, Zn, Sn, whereas F excludes Ba and Sr. We use principal component analyses to split the granite into chemical groups allowing an unbiased study of the inter-group element distribution. This adds the heavy REEs and Y to the earlier lists of elements with an affinity for F. The light REEs show a decreasing affinity with decreasing atomic mass; fluorine separates Sm from Nd, whereas Zr follows La. Opposite to some, but in accordance with other earlier results, the ratio Nb/Ta is higher in the fluorite-enriched than in the other granite. Weak tetrad effects are present. Zircon in the hypersolvus granite is high in common lead. We suggest F to be instrumental for separating Pb 2+ from Pb 4+ . Two hypotheses may explain the occurrence of the two contrasting granites: they have either different sources, or they are co-magmatic, but the magma was split into two discrete types. We apply the second hypothesis as our working hypothesis. The liquidus has a gentler slope with pressure than the diapir requiring crystallisation to be most important in the lower part of the magma chamber. Our hypothesis suggests that globules of magma, enriched in volatile components, form during crystallisation due to slow diffusion rates in the crystallizing magma. Elements accompanying F are distributed into this magma batch, which has a lowered density and viscosity than the rest of the magma due to its increased contents of volatile components. A mushroom-formed diapir rises, forming the hypersolvus (or almost plagioclase-free) granite. Due to an edge effect, it is concentrated close to the wall of the magma chamber. The size and form of the outcropping granite depend on the intersection of the diapir with the erosion surface. Fluorine only makes it possible to follow the process. The model may be generalised to explain the diversification of non-F enriched granite, since the buoyancy of a magma batch several thousand m 3 in size has a much larger impact on the system than the small negative buoyancy of crystals or small crystal aggregates. A-type granite classified merely from its trace element content may form from separated F-enriched magma batches. This may be the reason for their high frequency in the Eastern Desert.
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| 5. |
- Persson, Axel, et al.
(författare)
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Correlating cathodoluminescence and scanning transmission electron microscopy for InGaN platelet nano-LEDs
- 2023
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 123:2
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Tidskriftsartikel (refereegranskat)abstract
- Structural defects are detrimental to the efficiency and quality of optoelectronic semiconductor devices. In this work, we study InGaN platelets with a quantum well structure intended for nano-LEDs emitting red light and how their optical properties, measured with cathodoluminescence, relate to the corresponding atomic structure. Through a method of spectroscopy-thinning-imaging, we demonstrate in plan-view how stacking mismatch boundaries intersect the quantum well in a pattern correlated with the observed diminished cathodoluminescence intensity. The results highlight the importance of avoiding stacking mismatch in small LED structures due to the relatively large region of non-radiative recombination caused by the mismatch boundaries.
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| 6. |
- Andersson, Erika, et al.
(författare)
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A contrast variation SANS and SAXS study of soil derived dissolved organic matter, and its interactions with hematite nanoparticles
- 2023
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Ingår i: JCIS Open. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Soil derived dissolved organic matter (DOM) is an important component of the carbon cycle and influences numerous biogeochemical processes, including the formation of mineral-organic associations. DOM ranges in size from small organic molecules to macromolecules and colloidal aggregates. In this study we have used small angle neutron (SANS) and X-ray (SAXS) scattering to characterize the colloidal DOM fraction from the organic layer of a boreal forest soil, and its interactions with hematite (α-Fe2O3) mineral nanoparticles. Comparison between SAXS and contrast variation SANS patterns revealed that the scattering form factor of the colloidal DOM aggregates was essentially independent of the scattering contrast, implying that the colloidal aggregates have an essentially homogeneous chemical composition, down to the nanometre length scale. Variation of the D2O/H2O ratio of the solvent yielded a SANS intensity minimum at ca. 40 vol % D2O, which was consistent with colloids composed of mainly polysaccharides. At pH 5.5 the pure hematite nanoparticles were colloidally stable in water and characterized by a ζ-potential of +25 mV and a hydrodynamic radius of ca. 70 nm. In the presence of DOM, the hematite nanoparticles lost the colloidal stability and aggregated into larger clusters, displaying a negative ζ-potential of ca. −25 mV. The charge reversal suggested that negatively charged polyanions of DOM adsorbed onto the hematite particles, possibly leading to bridging flocculation. Our results suggested that mainly low molecular weight components induced hematite aggregation because no or very limited interactions between DOM colloids and hematite were detected.
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| 7. |
- Andersson, Erika, et al.
(författare)
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Generation and properties of organic colloids extracted by water from the organic horizon of a boreal forest soil
- 2023
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Ingår i: Geoderma. - : Elsevier BV. - 0016-7061. ; 432
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Tidskriftsartikel (refereegranskat)abstract
- Organic colloids are an important part of dissolved organic matter (DOM) yet many of their properties remain elusive. The main aims of this study were to assess how the colloidal properties of DOM extracted with water from an organic boreal soil horizon varied with the extraction protocol, and thereby provide insight into the nature of the DOM colloids and develop a mechanistic understanding of how the colloids were generated from the parent soil aggregates. This was accomplished by systematic variations of extraction temperature (4 °C–100 °C), time, mechanical agitation, and pH, together with a combination of chemical analyses, and light and X-ray scattering. Our results agreed with the previous identification of two main colloidal DOM species, one fractal cluster and a second, smaller colloidal DOM species described as chains or coils. Fractal clusters completely dominated the colloidal DOM in extracts from our soil at room temperature and below. Colloidal coils only existed in DOM extracted above room temperature, and their amount increased significantly between 50 °C–100 °C. Moreover, the temperature variation indicated that the fractal clusters partly dissolved into colloidal coils at elevated temperatures. Mechanical agitation at 4 °C significantly increased the amount of DOM extracted, increasing the concentrations of both fractal clusters and low-molecular weight organic compounds. While the clusters were extracted from agitated and non-agitated soil suspensions, the low molecular weight organics were mainly released by agitation. Based on the experimental observations, we propose a conceptual model where parent soil aggregates contain the fractal clusters in mobile and occluded forms, and that the occluded clusters co-exist with occluded low molecular weight organics. These occluded forms may be released by mechanical forces, increasing pH and temperature. At higher temperatures, the soil aggregates and the fractal clusters start to break up, and subsequently individual colloidal coils, presumably carbohydrates, disperse in the water phase. The model explains the origin and properties of the fractal clusters that completely dominate the colloidal DOM extracted from our soil at room temperature and below.
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| 8. |
- Anderung, Cecilia, et al.
(författare)
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Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle
- 2005
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Ingår i: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 102:24, s. 8431-8435
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Tidskriftsartikel (refereegranskat)abstract
- The geographic situation of the Iberian Peninsula makes it a natural link between Europe and North Africa. However, it is a matter of debate to what extent African influences via the Straits Gibraltar have affected Iberia's prehistoric development. Because early African pastoralist communities were dedicated to cattle breeding, a possible means to detect prehistoric African–Iberian contacts might be to analyze the origin of cattle breeds on the Iberian Peninsula. Some contemporary Iberian cattle breeds show a mtDNA haplotype, T1, that is characteristic to African breeds, generally explained as being the result of the Muslim expansion of the 8th century A.D., and of modern imports. To test a possible earlier African influence, we analyzed mtDNA of Bronze Age cattle from the Portalón cave at the Atapuerca site in northern Spain. Although the majority of samples showed the haplotype T3 that dominates among European breeds of today, the T1 haplotype was found in one specimen radiocarbon dated 1800 calibrated years B.C. Accepting T1 as being of African origin, this result indicates prehistoric African–Iberian contacts and lends support to archaeological finds linking early African and Iberian cultures. We also found a wild ox haplotype in the Iberian Bronze Age sample, reflecting local hybridization or backcrossing or that aurochs were hunted by these farming cultures.
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| 9. |
- De Beeck, Michiel Op, et al.
(författare)
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Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy
- 2024
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Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 90:2
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Tidskriftsartikel (refereegranskat)abstract
- In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffractionlimit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffractionlimit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose filmsby cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films,O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identificationof a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.
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| 10. |
- Ellström, Magnus, et al.
(författare)
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The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus.
- 2015
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941. ; 91:4
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Tidskriftsartikel (refereegranskat)abstract
- The amounts of carbon allocated to the fungal partner in ectomycorrhizal associations can vary substantially depending on the plant growth and the soil nutrient conditions, and the fungus may frequently be confronted with limitations in carbon. We used chemical analysis and transcriptome profiling to examine the physiological response of the ectomycorrhizal fungus Paxillus involutus to carbon starvation during axenic cultivation. Carbon starvation induced a decrease in the biomass. Concomitantly, ammonium, cell-wall material (chitin) and proteolytic enzymes were released into the medium, which suggest autolysis. Compared with the transcriptome of actively growing hyphae, about 45% of the transcripts analyzed were differentially regulated during C-starvation. Induced during starvation were transcripts encoding extracellular enzymes such as peptidases, chitinases, and laccases. In parallel, transcripts of N-transporters were upregulated, which suggest that some of the released nitrogen compounds were re-assimilated by the mycelium. The observed changes suggest that the carbon-starvation response in P. involutus is associated with complex cellular changes that involves autolysis, recycling of intracellular compounds by autophagy and reabsorption of the extracellular released material. The study provides molecular markers that can be used to examine the role of autolysis for the turnover and survival of the ectomycorrhizal mycelium in soils.
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