| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- Bergum Johanson, Lisbeth, et al.
(author)
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«La elva leve»: Alta-saken som rollespill i historieundervisninga
- 2019
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In: Nordidactica. - Karlstad : CSD Karlstad. - 2000-9879. ; :2019:2, s. 72-89
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Journal article (peer-reviewed)abstract
- The annual staging of a role play for school pupils called “La elva leve” (‘Let the River Live’) at Alta museum addresses the conflict over the building of a hydroelectric power plant in the Alta-Kautokeino watercourse between 1978-82. The confrontation has an important legacy, not least by bringing the issue of Sámi Indigenous rights into the national limelight. This article discusses how the role play might serve as a starting point for teaching pupils about the conflict’s consequences for Sámi rights, and interrogates the degree to which this kind of role play might benefit the pupils’ awareness of history. Drawing on observations and interviews, we found that the pupils were strongly engaged in the play and that they found it both interesting and educational. However, while they also gained more knowledge about the conflict itself, there was little evidence that they connected the conflict to the Sámi struggle for indigenous rights, or that their historical consciousness expanded significantly.
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| 5. |
- Felix, Janine F, et al.
(author)
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Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index.
- 2016
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In: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 25:2, s. 389-403
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Journal article (peer-reviewed)abstract
- A large number of genetic loci are associated with adult body mass index. However, the genetics of childhood body mass index are largely unknown. We performed a meta-analysis of genome-wide association studies of childhood body mass index, using sex- and age-adjusted standard deviation scores. We included 35 668 children from 20 studies in the discovery phase and 11 873 children from 13 studies in the replication phase. In total, 15 loci reached genome-wide significance (P-value < 5 × 10(-8)) in the joint discovery and replication analysis, of which 12 are previously identified loci in or close to ADCY3, GNPDA2, TMEM18, SEC16B, FAIM2, FTO, TFAP2B, TNNI3K, MC4R, GPR61, LMX1B and OLFM4 associated with adult body mass index or childhood obesity. We identified three novel loci: rs13253111 near ELP3, rs8092503 near RAB27B and rs13387838 near ADAM23. Per additional risk allele, body mass index increased 0.04 Standard Deviation Score (SDS) [Standard Error (SE) 0.007], 0.05 SDS (SE 0.008) and 0.14 SDS (SE 0.025), for rs13253111, rs8092503 and rs13387838, respectively. A genetic risk score combining all 15 SNPs showed that each additional average risk allele was associated with a 0.073 SDS (SE 0.011, P-value = 3.12 × 10(-10)) increase in childhood body mass index in a population of 1955 children. This risk score explained 2% of the variance in childhood body mass index. This study highlights the shared genetic background between childhood and adult body mass index and adds three novel loci. These loci likely represent age-related differences in strength of the associations with body mass index.
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| 6. |
- Fredriksson, Maria, et al.
(author)
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The cell wall composition of Norway spruce earlywood and latewood revisited
- 2017
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In: ; , s. 148-153
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Conference paper (other academic/artistic)abstract
- It is well known that the xylem of gymnosperm trees consists mainly of tracheids and that the dimensions of these cells change over the growth season in temperate regions. When looking at a micrograph of a cross section of a growth ring, it can be seen that early in the season tracheids have larger radial diameters and thin walls, while tracheids formed later in the growth season have smaller radial diameters and thicker walls. However, information on possible chemical differences between these two regions of the growth ring is less abundant. According to a few published studies, earlywood normally contains more lignin relative to cellulose compared to latewood. For studies based on traditional compositional analysis and with results given per gram dry matter, this result is hardly surprising, as it simply expresses that a larger part of earlywood cell wall material consists of lignin-rich middle lamella because cells have larger diameters and thinner walls. However, a few studies based on ultraviolet microscopy indicate that differences in biopolymer composition also are seen when individual cell wall layers are analysed. In this study, we used Raman microspectroscopy to assess the relative biopolymer composition of earlywood and latewood secondary cell walls from Norway spruce (Picea abies (L.) Karst.) and compared the biopolymer composition to infrared spectroscopy performed on isolated earlywood and latewood from the exact same growth rings.
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| 7. |
- Fredriksson, Maria, et al.
(author)
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The cell wall composition of Norway spruce earlywood and latewood revisited
- 2018
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In: International Wood Products Journal. - : Informa UK Limited. - 2042-6445 .- 2042-6453. ; 9:2, s. 80-85
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Journal article (peer-reviewed)abstract
- The xylem of gymnosperm trees consists mainly of tracheids, which generally have larger radial diameters and thinner walls in earlywood than in latewood. Information on possible chemical differences is limited, but according to a few studies, earlywood normally contains more lignin relative to cellulose than latewood. However, for methods giving results per gram dry matter, this result is expected since a larger part of the earlywood cell wall material consists of lignin-rich middle lamella. In this study, we used Raman microspectroscopy to assess relative biopolymer composition of earlywood and latewood secondary cell walls from mature sapwood of Norway spruce (Picea abies (L.) Karst.). In addition, infrared spectroscopy of isolated earlywood and latewood from the same growth rings as well as additional growth rings was performed. Both methods showed significantly higher relative lignin content in the earlywood which confirms results from earlier studies.
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| 8. |
- Huang, Weiwei, et al.
(author)
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Annual variations in Norway spruce xylem studied using infrared micro-spectroscopy
- 2019
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In: Forests. - : MDPI AG. - 1999-4907. ; 10:2
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Journal article (peer-reviewed)abstract
- In temperate environments, ring width, cell size and cell wall thickness within the xylem of trees are known to be affected by climate conditions. Less is known about the effect of climate conditions on the chemical characteristics of the xylem, which are important for the susceptibility of the tissue towards fungal infections as well as for the degradability of the material within the forest ecosystem. We explored the use of infrared microspectroscopy to investigate the possible effects of temperature and drought on the relative amount of cell wall biopolymers, i.e. the ratios between cellulose, hemicellulose and lignin in the earlywood xylem cell walls of Norway spruce (Picea abies (L.) Karst.) in temperate forests. Drought and warm temperatures were significantly correlated to the hemicellulose to lignin ratio of the earlywood formed the following year, perhaps due to a reduced amount of stored resources being available for xylem formation.
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| 9. |
- Krogh, Kristian B. R. M., et al.
(author)
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Characterization and kinetic analysis of a thermostable GH3 beta-glucosidase from Penicillium brasilianum
- 2010
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In: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 86:1, s. 143-154
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Journal article (peer-reviewed)abstract
- A GH3 beta-glucosidase (BGL) from Penicillium brasilianum was purified to homogeneity after cultivation on a cellulose and xylan rich medium. The BGL was identified in a genomic library, and it was successfully expressed in Aspergillus oryzae. The BGL had excellent stability at elevated temperatures with no loss in activity after 24 h of incubation at 60A degrees C at pH 4-6, and the BGL was shown to have significantly higher stability at these conditions in comparison to Novozym 188 and to other fungal GH3 BGLs reported in the literature. The BGL had significant lower affinity for cellobiose compared with the artificial substrate para-nitrophenyl-beta-d-glucopyranoside (pNP-Glc) and further, pronounced substrate inhibition using pNP-Glc. Kinetic studies demonstrated the high importance of using cellobiose as substrate and glucose as inhibitor to describe the inhibition kinetics of BGL taking place during cellulose hydrolysis. A novel assay was developed to characterize this glucose inhibition on cellobiose hydrolysis. The assay uses labelled glucose-C-13(6) as inhibitor and subsequent mass spectrometry analysis to quantify the hydrolysis rates.
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| 10. |
- Krogh, K.B.R.M., et al.
(author)
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Characterization and kinetic analysis of a thermostable GH3 β-glucosidase from Penicillum brasilianum
- 2010
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In: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 86:86, s. 143-154
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Journal article (peer-reviewed)abstract
- A GH3 β-glucosidase (BGL) from Penicillum brasilianum was purified to homogeneity after cultivation on a cellulose and xylan rich medium. The BGL was identified in a genomic library, and it was successfully expressed in Aspergillus oryzae. The BGL had excellent stability at elevated temperatures with no loss in activity after 24 h of incubation at 60°C at pH 4-6, and the BGL was shown to have significantly higher stability at these conditions in comparison to Novozym 188 and to other fungal GH3 BGLs reported in the literature. The BGL had significant lower afinity for cellobiose compared with the artificial substrate para-nitrophenyl-β-D-glucopyranoside (pNP-Glc)and further, pronounced substrate inhibition using p-NP-Glc. Kinetic studies demonstrated the high importance of using cellbiose as substrate and glucose as inhibitor to describe the inhibition kinetics of BGL taking place during cellulose hydrolysis. A novel assay was developed to characterize this glucose inhibition on cellobiose hydrolosis. The assay uses labelled glucose-13C6 as inhibitor and subsequent mass spectrometry analysis to quantify the hydrolysis rates
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