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- Abdelmagid, N., et al.
(författare)
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Von Willebrand Factor Gene Variants Associate with Herpes simplex Encephalitis
- 2016
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Herpes simplex encephalitis (HSE) is a rare complication of Herpes simplex virus type-1 infection. It results in severe parenchymal damage in the brain. Although viral latency in neurons is very common in the population, it remains unclear why certain individuals develop HSE. Here we explore potential host genetic variants predisposing to HSE. In order to investigate this we used a rat HSE model comparing the HSE susceptible SHR (Spontaneously Hypertensive Rats) with the asymptomatic infection of BN (Brown Norway). Notably, both strains have HSV-1 spread to the CNS at four days after infection. A genome wide linkage analysis of 29 infected HXB/BXH RILs (recombinant inbred lines-generated from the prior two strains), displayed variable susceptibility to HSE enabling the definition of a significant QTL (quantitative trait locus) named Hse6 towards the end of chromosome 4 (160.89-174Mb) containing the Vwf (von Willebrand factor) gene. This was the only gene in the QTL with both cis-regulation in the brain and included several non-synonymous SNPs (single nucleotide polymorphism). Intriguingly, in human chromosome 12 several SNPs within the intronic region between exon 43 and 44 of the VWF gene were associated with human HSE pathogenesis. In particular, rs917859 is nominally associated with an odds ratio of 1.5 (95% CI 1.11-2.02; p-value = 0.008) after genotyping in 115 HSE cases and 428 controls. Although there are possibly several genetic and environmental factors involved in development of HSE, our study identifies variants of the VWF gene as candidates for susceptibility in experimental and human HSE.
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- Drinnenberg, IA, et al.
(författare)
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EvoChromo: towards a synthesis of chromatin biology and evolution
- 2019
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Ingår i: Development (Cambridge, England). - : The Company of Biologists. - 1477-9129 .- 0950-1991. ; 146:19
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Tidskriftsartikel (refereegranskat)abstract
- Over the past few years, interest in chromatin and its evolution has grown. To further advance these interests, we organized a workshop with the support of The Company of Biologists to debate the current state of knowledge regarding the origin and evolution of chromatin. This workshop led to prospective views on the development of a new field of research that we term ‘EvoChromo’. In this short Spotlight article, we define the breadth and expected impact of this new area of scientific inquiry on our understanding of both chromatin and evolution.
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- Ghylin, Trevor W, et al.
(författare)
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Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage
- 2014
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 8:12, s. 2503-2516
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Tidskriftsartikel (refereegranskat)abstract
- Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di- and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.
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- Hackman, T., et al.
(författare)
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From convective stellar dynamo simulations to Zeeman-Doppler images
- 2024
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 682
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Tidskriftsartikel (refereegranskat)abstract
- Context. Zeeman-Doppler imaging (ZDI) is used to reconstruct the surface magnetic field of late-type stars from high-resolution spectropolarimetric observations. The results are usually described in terms of characteristics of the field topology, such as poloidality versus toroidality and axisymmetry versus non-axisymmetry, in addition to the field strength. Aims. In this study, we want to test how well these characteristics are preserved when applying the ZDI method to simulated data. We are particularly interested in how accurately the field topology is preserved and to what extent stellar parameters, such as projected rotation velocity and rotation axis inclination, influence the reconstruction. Methods. For these tests, we used published magnetic field vector data from direct numerical magnetohydrodynamic simulations taken near the surface of the simulation domain. These simulations have variable rotation rates and therefore represent different levels of activity of an otherwise Sun-like setup with a convective envelope of solar thickness. Our ZDI reconstruction is based on spherical harmonics expansion. By comparing the original values to those of the reconstructed images, we study the ability to reconstruct the surface magnetic field in terms of various characteristics of the field. Results. In general, the ZDI method works as expected. The main large-scale features are reasonably well recovered, but the strength of the recovered magnetic field is just a fraction of the original input. The quality of the reconstruction shows clear correlations with the data quality. Furthermore, there are some spurious dependencies between stellar parameters and the characteristics of the field. Conclusions. Our study uncovers some limits of ZDI. Firstly, the recovered field strength will generally be lower than the ‘real’ value, as smaller structures with opposite polarities will be blurred in the inversion. This is also seen in the relative distribution of magnetic energy in terms of the angular degree `. Secondly, the axisymmetry is overestimated. The poloidality versus toroidality is better recovered. The reconstruction works better for a stronger field and faster rotation velocity. Still, the ZDI method works surprisingly well even for a weaker field and slow rotation provided the data have a high signal-to-noise ratio and good rotation phase coverage.
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