| 1. |
- Allentoft, Morten E., et al.
(author)
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Population genomics of post-glacial western Eurasia
- 2024
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In: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
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Journal article (peer-reviewed)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. |
- Allentoft, Morten E., et al.
(author)
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100 ancient genomes show repeated population turnovers in Neolithic Denmark
- 2024
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In: Nature. - 0028-0836 .- 1476-4687. ; 625, s. 329-337
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Journal article (peer-reviewed)abstract
- Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1–4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5–7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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| 3. |
- Farnelid, Hanna, et al.
(author)
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Putative N-2-fixing heterotrophic bacteria associated with dinoflagellate-Cyanobacteria consortia in the low-nitrogen Indian Ocean
- 2010
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In: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 61:2, s. 105-117
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Journal article (peer-reviewed)abstract
- Heterotrophic dinoflagellates bearing unicellular cyanobacterial symbionts are common within the order Dinophysiales. However, the ecological role of these symbionts is unclear. Due to the occurrence of such consortia in oceanic waters characterized by low nitrogen concentrations, we hypothesized that the symbionts fix gaseous nitrogen (N-2). Individual heterotrophic dinoflagellates containing cyanobacterial symbionts were isolated from the open Indian Ocean and off Western Australia, and characterized using light microscopy, transmission electron microscopy (TEM), and nitrogenase (nifH) gene amplification, cloning, and sequencing. Cyanobacteria, heterotrophic bacteria and eukaryotic algae were recognized as symbionts of the heterotrophic dinoflagellates. nifH gene sequences were obtained from 23 of 37 (62%) specimens of dinoflagellates (Ornithocercus spp. and Amphisolenia spp.). Interestingly, only 2 specimens contained cyanobacterial nifH sequences, while 21 specimens contained nifH genes related to heterotrophic bacteria. Of the 137 nifH sequences obtained 68% were most similar to Alpha-, Beta-, and Gammaproteobacteria, 8% clustered with anaerobic bacteria, and 5% were related to second alternative nitrogenases (anfH). Twelve sequences from 5 host cells formed a discrete cluster which may represent a not yet classified nifH cluster. Eight dinoflagellates contained only 1 type of nifH sequence (>99% sequence identity) but overall the putative N-2-fixing symbionts did not appear host specific and mixed assemblages were often found in single host cells. This study provides the first insights into the nifH diversity of dinoflagellate symbionts and suggests a symbiotic co-existence of non-diazotrophic cyanobacteria and N-2-fixing heterotrophic bacteria in heterotrophic dinoflagellates.
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| 4. |
- Assar, Alireza, et al.
(author)
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Gettering in PolySi/SiOx Passivating Contacts Enables Si-Based Tandem Solar Cells with High Thermal and Contamination Resilience
- 2022
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In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 14:12, s. 14342-14358
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Journal article (peer-reviewed)abstract
- Multijunction solar cells in a tandem configuration could further lower the costs of electricity if crystalline Si (c-Si) is used as the bottom cell. However, for direct monolithic integration on c-Si, only a restricted number of top and bottom cell architectures are compatible, due to either epitaxy or high-temperature constraints, where the interface between subcells is subject to a trade-off between transmittance, electrical interconnection, and bottom cell degradation. Using polySi/SiOx passivating contacts for Si, this degradation can be largely circumvented by tuning the polySi/SiOx stacks to promote gettering of contaminants admitted into the Si bottom cell during the top cell synthesis. Applying this concept to the low-cost top cell chalcogenides Cu2ZnSnS4 (CZTS), CuGaSe2 (CGSe), and AgInGaSe2 (AIGSe), fabricated under harsh S or Se atmospheres above 550 degrees C, we show that increasing the heavily doped polySi layer thickness from 40 to up to 400 nm prevents a reduction in Si carrier lifetime by 1 order of magnitude, with final lifetimes above 500 mu s uniformly across areas up to 20 cm(2). In all cases, the increased resilience was correlated with a 99.9% reduction in contaminant concentration in the c-Si bulk, provided by the thick polySi layer, which acts as a buried gettering layer in the tandem structure without compromising the Si passivation quality. The Si resilience decreased as AIGSe > CGSe > CZTS, in accordance with the measured Cu contamination profiles and higher annealing temperatures. An efficiency of up to 7% was achieved for a CZTS/Si tandem, where the Si bottom cell is no longer the limiting factor.
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| 5. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 6. |
- Borgbo, Tanni, et al.
(author)
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Genotyping common FSHR polymorphisms based on competitive amplification of differentially melting amplicons (CADMA).
- 2014
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In: Journal of Assisted Reproduction and Genetics. - : Springer Science and Business Media LLC. - 1058-0468 .- 1573-7330. ; 31:11, s. 1427-1436
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Journal article (peer-reviewed)abstract
- To provide an improved platform for simple, reliable, and cost-effective genotyping. Modern fertility treatments are becoming increasingly individualized in an attempt to optimise the follicular response and reproductive outcome, following controlled ovarian stimulation. As the field of pharmacogenetics evolve, genetic biomarkers such as polymorphisms of the follicle stimulating hormone receptor (FSHR) may be included as a predictive tool for individualized fertility treatment. However, the currently available genotyping methods are expensive, time-consuming or have a limited analytical sensitivity. Here, we present a novel version of "competitive amplification of differentially melting amplicons" (CADMA), providing an improved platform for simple, reliable, and cost-effective genotyping. Two CADMA based assays were designed for the two common polymorphisms of the FSHR gene: rs6165 (c.919A > G, p. Thr307Ala, FSHR 307) and rs6166 (c.2039A > G, p. Asn680Ser, FSHR 680). To evaluate the reliability of the new CADMA-based assays, the genotyping results were compared with two conventional PCR based genotyping methods; allele-specific PCR (AS-PCR) and Sanger sequencing. The genotype frequencies for both polymorphisms were 35 % (TT), 42 % (CT), and 23 % (CC), respectively. A 100 % accordance was observed between the CADMA-based genotyping results and sequencing results, whereas 5 discrepancies were observed between the AS-PCR results and the CADMA-based genotyping results. Comparing the CADMA-based assays to (AS-PCR) and Sanger sequencing, the CADMA based assays showed an improved analytical sensitivity and a wider applicability. The new assays provide a reliable, fast and user-friendly genotyping method facilitating a wider implication in clinical practise.
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| 7. |
- Brønnum-Hansen, Henrik, et al.
(author)
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Changes in life expectancy and lifespan variability by income quartiles in four Nordic countries : a study based on nationwide register data
- 2021
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In: BMJ Open. - : BMJ. - 2044-6055. ; 11:6
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Journal article (peer-reviewed)abstract
- Objectives Levels, trends or changes in socioeconomic mortality differentials are typically described in terms of means, for example, life expectancies, but studies have suggested that there also are systematic social disparities in the dispersion around those means, in other words there are inequalities in lifespan variation. This study investigates changes in income inequalities in mean and distributional measures of mortality in Denmark, Finland, Norway, and Sweden over two decades.Design Nationwide register-based study.Setting The Danish, Finnish, Norwegian and Swedish populations aged 30 years or over in 1997 and 2017.Main outcome measures Income-specific changes in life expectancy, lifespan variation and the contribution of 'early' and 'late' deaths to increasing life expectancy.Results Increases in life expectancy has taken place in all four countries, but there are systematic differences across income groups. In general, the largest gains in life expectancy were observed in Denmark, and the smallest increase among low-income women in Sweden and Norway. Overall, life expectancy increased and lifespan variation decreased with increasing income level. These differences grew larger over time. In all countries, a marked postponement of early deaths led to a compression of mortality in the top three income quartiles for both genders. This did not occur for the lowest income quartile.Conclusion Increasing life expectancy is typically accompanied by postponement of early deaths and reduction of lifespan inequality in the higher-income groups. However, Nordic welfare societies are challenged by the fact that postponing premature deaths among people in the lowest-income groups is not taking place.
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| 8. |
- Elstad, Jon Ivar, et al.
(author)
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Income security in Nordic welfare states for men and women who died when aged 55–69 years old
- 2019
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In: Journal of International and Comparative Social Policy. - : Cambridge University Press (CUP). - 2169-9763 .- 2169-978X. ; 35:2, s. 157-176
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Journal article (peer-reviewed)abstract
- Income security when health impairment or other social risks occur is a major objective of welfare states. This comparative study uses register data from four Nordic welfare states for examining equivalized disposable income during the last 12 years alive among men and women who died when aged 55–69 years old. The analysed outcome indicates the aggregate result of a varied set of income maintenance mechanisms. Median income increased in the Finnish, Norwegian and Swedish samples, but decreased somewhat in Denmark, probably due to relatively frequent transitions to retirement and larger income drops after retirement than in the other Nordic countries. Analyses of comparison samples weighted by propensity scores indicated a better income development among those who lived beyond the observation period than among those who died. The higher educated had a more favourable income development during the years prior to death than those with low education.
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| 9. |
- Farnelid, Hanna, et al.
(author)
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Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria
- 2011
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:4, s. e19223-
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Journal article (peer-reviewed)abstract
- Cyanobacteria are thought to be the main N-2-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations worldwide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N-2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.
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| 10. |
- Folkersen, Lasse, et al.
(author)
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Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals.
- 2020
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In: Nature metabolism. - : Springer Science and Business Media LLC. - 2522-5812. ; 2:10, s. 1135-1148
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Journal article (peer-reviewed)abstract
- Circulating proteins are vital in human health and disease and are frequently used as biomarkers for clinical decision-making or as targets for pharmacological intervention. Here, we map and replicate protein quantitative trait loci (pQTL) for 90 cardiovascular proteins in over 30,000 individuals, resulting in 451 pQTLs for 85 proteins. For each protein, we further perform pathway mapping to obtain trans-pQTL gene and regulatory designations. We substantiate these regulatory findings with orthogonal evidence for trans-pQTLs using mouse knockdown experiments (ABCA1 and TRIB1) and clinical trial results (chemokine receptors CCR2 and CCR5), with consistent regulation. Finally, we evaluate known drug targets, and suggest new target candidates or repositioning opportunities using Mendelian randomization. This identifies 11 proteins with causal evidence of involvement in human disease that have not previously been targeted, including EGF, IL-16, PAPPA, SPON1, F3, ADM, CASP-8, CHI3L1, CXCL16, GDF15 and MMP-12. Taken together, these findings demonstrate the utility of large-scale mapping of the genetics of the proteome and provide a resource for future precision studies of circulating proteins in human health.
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