| 1. |
- Allentoft, Morten E., et al.
(författare)
-
100 ancient genomes show repeated population turnovers in Neolithic Denmark
- 2024
-
Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625, s. 329-337
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 2. |
- Allentoft, Morten E., et al.
(författare)
-
Population genomics of post-glacial western Eurasia
- 2024
-
Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 625:7994, s. 301-311
-
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.
|
|
| 3. |
- Aust, Birgit, et al.
(författare)
-
The Danish national return-to-work program - aims, content, and design of the process and effect evaluation
- 2012
-
Ingår i: Scandinavian Journal of Work, Environment and Health. - : Scandinavian Journal of Work, Environment and Health. - 0355-3140 .- 1795-990X. ; 38:2, s. 120-133
-
Tidskriftsartikel (refereegranskat)abstract
- The Danish national return-to-work (RTW) program aims to improve the management of municipal sickness benefit in Denmark. A study is currently ongoing to evaluate the RTW program. The purpose of this article is to describe the study protocol. The program includes 21 municipalities encompassing approximately 19 500 working-age adults on long-term sickness absence, regardless of reason for sickness absence or employment status. It consists of three core elements: (i) establishment of multidisciplinary RTW teams, (ii) introduction of standardized workability assessments and sickness absence management procedures, and (iii) a comprehensive training course for the RTW teams. The effect evaluation is based on a parallel group randomized trial and a stratified cluster-controlled trial and focuses on register-based primary outcomes-duration of sickness absence and RTW and questionnaire-based secondary outcomes such as health and workability. The process evaluation utilizes questionnaires, interviews, and municipal data. The effect evaluation tests whether participants in the intervention have a (i) shorter duration of full-time sickness absence, (ii) longer time until recurrent long-term sickness absence, (iii) faster full RTW, (iv) more positive development in health, workability, pain, and sleep; it also tests whether the program is (v) cost-effective. The process evaluation investigates: (i) whether the expected target population is reached; (ii) if the program is implemented as intended; (iii) how the beneficiaries, the RTW teams, and the external stakeholders experience the program; and (iv) whether contextual factors influenced the implementation. The program has the potential to contribute markedly to lowering human and economic costs and increasing labor force supply. First results will be available in 2013. The trial registrations are ISRCTN43004323, and ISRCTN51445682.
|
|
| 4. |
- Holm, Anne I. S., et al.
(författare)
-
Electronic coupling between cytosine bases in DNA single strands and i-motifs revealed from synchrotron radiation circular dichroism experiments
- 2010
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:14, s. 3426-3430
-
Tidskriftsartikel (refereegranskat)abstract
- In this work we have recorded synchrotron radiation circular dichroism (SRCD) spectra from 180 nm to 360 nm of cytosine strands [(dC)(n), n = 1, 2,..., 10] in aqueous solution at different pH values to reveal electronic coupling between bases in different ionisation states. The geometry of the strands is determined by the pH value and the strand length and the local organisation of the cytosines will determine the base-to-base interaction that impacts on the CD signal. At low pH where all bases are protonated, there is no signature of electronic coupling between the bases, and the SRCD spectrum is simply n times that of the n = 1 spectrum. At higher pH where all bases are neutral, the spectra for n > 1 differ from the monomer spectrum, which implies electronic coupling between bases. The correlation between the CD signal and n is linear, and the spatial extent of the excited state wavefunction is therefore over just two stacked bases both in the UV and VUV. At intermediate pH, the low-n spectra are different from the high-n spectra, and a transition is seen to occur at n = 6-8. We ascribe this behavior to the formation of i-motif structures between four (dC)(n) strands for high n.
|
|
| 5. |
- Holm, Anne Ivalu Sander, et al.
(författare)
-
Vacuum-ultraviolet circular dichroism spectroscopy of DNA : a valuable tool to elucidate topology and electronic coupling in DNA
- 2010
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:33, s. 9581-9596
-
Tidskriftsartikel (refereegranskat)abstract
- Circular dichroism (CD) is a powerful technique to obtain information on electronic transitions and has been used extensively for studies on DNA. Most experiments are done in the UV region but new information is often revealed from extending the wavelength region down into the vacuum ultraviolet (VUV) region. Such experiments are most easily carried out with synchrotron radiation (SR) light sources that provide large photon fluxes. Here we provide a summary of the SRCD data taken on different DNA strands with emphasis on results from our own laboratory within the last five years.(1-3) Signal intensities in the VUV are often significantly larger than those in the UV, and the electronic coupling between bases may increase with excitation energy. CD spectroscopy is particularly useful for investigating the extent of electronic coupling within a strand, i.e., the degree of delocalisation of the excited-state electronic wavefunction. The spatial extent of the wavefunction may be limited to just one base or it extends over two or more bases in a stack or between bases on different strands.(4,5) The actual character of the electronically excited state is linked to base composition and sequence as well as DNA folding motif (A-, B-, Z-DNA, triplexes, quadruplexes, etc.). The latter depends on experimental conditions such as solution acidity, temperature, ionic strength, and solvent.
|
|
| 6. |
- Meijer, S. L., et al.
(författare)
-
Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger
- 2009
-
Ingår i: Journal of Industrial Microbiology and Biotechnology. - : Oxford University Press (OUP). - 1367-5435 .- 1476-5535. ; 36:10, s. 1275-1280
-
Tidskriftsartikel (refereegranskat)abstract
- With the availability of the genome sequence of the filamentous fungus Aspergillus niger, the use of targeted genetic modifications has become feasible. This, together with the fact that A. niger is well established industrially, makes this fungus an attractive micro-organism for creating a cell factory platform for production of chemicals. Using molecular biology techniques, this study focused on metabolic engineering of A. niger to manipulate its organic acid production in the direction of succinic acid. The gene target for complete gene deletion was cytosolic ATP: citrate lyase (acl), which had previously been identified by using genome-scale stoichiometric metabolic model simulations. The acl gene was deleted using the bipartite gene-targeting method, and the mutant was characterized in batch cultivation. It was found that the succinic acid yield was increased threefold by deleting the acl gene. Additionally, the total amount of organic acids produced in the deletion strain was significantly increased. Genome-scale stoichiometric metabolic predictions can be used for identifying gene targets. Deletion of the acl led to increased succinic acid production by A. niger.
|
|
| 7. |
- Mortensen, Morten Fischer, et al.
(författare)
-
Turfs and Timbers- Resource use in the construction of the Viking Age Ring Fortress Borgring, Southeast Denmark
- 2021
-
Ingår i: Danish Journal of Archaeology. - : Det Kgl. Bibliotek/Royal Danish Library. - 2166-2290 .- 2166-2282. ; 10, s. 1-18
-
Tidskriftsartikel (refereegranskat)abstract
- Viking Age ring fortresses were some of the largest construction projects in Danish prehistory. In this article we reconstruct the amount of turf and timber used in the construction of the Borgring ring fortress and estimate the resource area needed to supply the building materials. Using REVEALS pollen data modelling, we quantify the regional oak land cover and estimate the resource area. The results show that even though Borgring was built in an open cultural landscape, sufficient supply of oak for the construction would have been accessible within a few kilometres from the fortress.
|
|
| 8. |
- Nielsen, Lisbeth Munksgaard, et al.
(författare)
-
Effect of introducing thymine spacers into an adenine strand : Electronic decoupling?
- 2011
-
Ingår i: Journal of Photochemistry and Photobiology A. - : Elsevier BV. - 1010-6030 .- 1873-2666. ; 220:1, s. 1-3
-
Tidskriftsartikel (refereegranskat)abstract
- Electronic coupling between DNA bases governs the deexcitation pathways after light absorption as well as the ability of the DNA strand to conduct charge. UV excitation of single strands of adenine bases involves two adjacent bases while the spatial extent of the excited state wavefunction following VUV excitation is over eight bases. In this work, we have recorded synchrotron radiation circular dichroism spectra for a series of DNA strands on the form A(n)T(m)A(n), n = 1-5 and m = 1-3, in aqueous solution to study the effect of introducing thymine spacers on the electronic coupling between the adenines. We find that a single thymine spacer is enough to eliminate the strong coupling between the adenine bases for all excitation wavelengths between 175 nm and 330 nm.
|
|
| 9. |
- Albers, Eva, 1966, et al.
(författare)
-
Comparison of industrial xylose fermentation with yeast performed at different process scale
- 2012
-
Ingår i: 13th International Congress on Yeasts, ICY 2012, August 26-30, Madison, USA.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Second generation of bioethanol production with yeast from lignocellulosic material may contribute to a sustainable production of energy. However, the commercialization of cellulose-to-ethanol remains challenging due to various limitations in process technology and microbial physiology. Despite that the technical progress lately has come far, lignocellulose bioethanol production is still not well established in full production scale. Production scale demands large financial investments and to minimize the risk knowledge about cellular performance of the yeast as response to conditions of large scale is needed. Large scale may impose specific conditions that normally are not present in smaller scale. Such conditions are then needed to be identified and mimicked in smaller scale to obtain crucial scaling-up data. In this project, we wanted to establish scalable cultivation processes and compare the performance at different scales. Experiments were performed at three process scales: lab (1.5 l), process development unit (15 l) and demonstration (10 m3) scales, with an industrial recombinant xylose fermenting Saccharomyces cerevisiae strain and corn cob, bagasse, and spruce lignocellulosic material. It was found that separate fermentation and SSF experiments could be reproducible at all scales. An ethanol level could be obtained above 4 % which is the threshold for feasible down-stream processing. Demonstration scale experiments on xylose-rich liquid of pre-treated corn cobs resulted in a 90% conversion of xylose to ethanol and on the slurry in SSF cultivation an ethanol yield of 0.44 g/g xylose was obtained.
|
|
| 10. |
- Ayres Pereira, Marina, et al.
(författare)
-
Placental Sequestration of Plasmodium falciparum Malaria Parasites Is Mediated by the Interaction Between VAR2CSA and Chondroitin Sulfate A on Syndecan-1
- 2016
-
Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 12:8
-
Tidskriftsartikel (refereegranskat)abstract
- During placental malaria, Plasmodium falciparum infected erythrocytes sequester in the placenta, causing health problems for both the mother and fetus. The specific adherence is mediated by the VAR2CSA protein, which binds to placental chondroitin sulfate (CS) on chondroitin sulfate proteoglycans (CSPGs) in the placental syncytium. However, the identity of the CSPG core protein and the cellular impact of the interaction have remain elusive. In this study we identified the specific CSPG core protein to which the CS is attached, and characterized its exact placental location. VAR2CSA pull-down experiments using placental extracts from whole placenta or syncytiotrophoblast microvillous cell membranes showed three distinct CSPGs available for VAR2CSA adherence. Further examination of these three CSPGs by immunofluorescence and proximity ligation assays showed that syndecan-1 is the main receptor for VAR2CSA mediated placental adherence. We further show that the commonly used placental choriocarcinoma cell line, BeWo, express a different set of proteoglycans than those present on placental syncytiotrophoblast and may not be the most biologically relevant model to study placental malaria. Syncytial fusion of the BeWo cells, triggered by forskolin treatment, caused an increased expression of placental CS-modified syndecan-1. In line with this, we show that rVAR2 binding to placental CS impairs syndecan-1-related Src signaling in forskolin treated BeWo cells, but not in untreated cells.
|
|
