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- Zhou Hagström, Nanna, 1993-, et al.
(författare)
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Megahertz-rate Ultrafast X-ray Scattering and Holographic Imaging at the European XFEL
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence, and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, we present the results from the first megahertz repetition rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL. We illustrate the experimental capabilities that the SCS instrument offers, resulting from the operation at MHz repetition rates and the availability of the novel DSSC 2D imaging detector. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative examples, providing an ideal test-bed for operation at megahertz rates. Nevertheless, our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.
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- Agosta, Lorenzo, et al.
(författare)
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Improved Sampling in Ab Initio-Based Free Energy Calculations of Amino Acids at Solid-Liquid Interfaces : A Tight-Binding Assessment on TiO2 Anatase (101)
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Atomistic simulations are powerful for probing molecules at bioinorganic interfaces and excellent complements to scarcely available experimental techniques. The free energy controls the adsorption behavior of molecules on nanosurfaces, and is therefore a quantity of particular importance. Advanced sampling techniques can efficiently explore the adsorption free energy landscape, but molecular simulations with classical (Newtownian) dynamics fail to capture charge transfer and polarization at the solid-liquid interface. First principle simulations do not suffer from this limitation but come with a heavy computational load. Here, we introduce an efficient protocol to explore the free energy of adsorption in the ab initio framework. This approach accurately models the complex phenomena at bio-inorganic surfaces on the nanoscale and properly samples the relevant thermodynamic properties. We present a case study of adsorption of the Lysine and Aspartate amino acids on the anatase (101) TiO2 surface with the tight binding method. The high values of the calculated adsorption free energies highlight the importance of a proper description of the electronic state for surface binding processes.
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- Dorafshan, Eshagh, et al.
(författare)
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Does Ash1 counteract Polycomb repression by methylating H3K36?
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Polycomb repression is critical to maintain cell type specific genome expression programs in a wide range of multicellular animals. Equally important but less studied is the Trithorax group system, which safeguards Polycomb target genes from the repression in cells where they have to remain active. Based on in vitro studies it was proposed that the Trithorax group system acts via methylation of histone H3 at Lysine 4 (H3K4) and Lysine 36 (H3K36) thereby inhibiting histone methyltransferase activity of the Polycomb complexes. This hypothesis is yet to be comprehensively tested in vivo. Here we used the power of the Drosophila model to investigate how the Trithorax group protein Ash1 and the H3K36 methylation counteract Polycomb repression. We show, for the first time, that Ash1 is the only Drosophila H3K36-specific methyltransferase required to prevent excessive Polycomb repression of homeotic genes. Unexpectedly, our experiments revealed no correlation between the extent of H3K36 methylation and the resistance to Polycomb repression. Furthermore, we find that complete substitution of the zygotic histone H3 with a variant in which Lysine 36 is replaced by Arginine does not cause excessive repression of Drosophila homeotic genes. Together with earlier studies, our results suggest that the model, where the Trithorax group proteins methylate histone H3 to inhibit the histone methyltransferase activity of the Polycomb complexes, may need to be reevaluated.
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- Guy, Lionel, et al.
(författare)
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Low-coverage pyrosequencing reveals recombination and run-off replication in Bartonella henselae strains
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Bartonella henselae is a natural intracellular colonizer of cats, and is transferred by blood-sucking insect vectors. It is also an opportunistic human pathogen. Two strains of B. henselae, thought to be representative of the diversity of the species, were selected for low-coverage 454 sequencing. The comparison of these two strains to the published Houston-1 reveals very high nucleotide identity and low substitution and recombination, with the remarkable exception of phages and host-interaction genes such as type IV and V secretion systems. Among the few variable genes of unknown function, BH14680, an alpha-Proteobacteria-specific gene, shows faster evolution in Bartonella compared to other alpha-Proteobacteria. Its 5’ end, which is likely coding for a domain exposed extracellularly, is under positive or very relaxed selection, and might be involved in host-interaction processes. Finally, we show that a simple genome coverage analysis reveal major genomic events such as duplications and unusual replication modes, such as the run-off replication. The latter, combined with a gene transfer agent, is thought to be a novel way to increase substitution and recombination frequencies. An extensive analysis of all bacterial pyrosequencing projects showed that it is probably Bartonella-specific.
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- Khalili, Bita, et al.
(författare)
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Associations between common genetic variants and income provide insights about the socioeconomic health gradient
- 2024
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We conducted a genome-wide association study (GWAS) on income among individuals of European descent and leveraged the results to investigate the socio-economic health gradient (N=668,288). We found 162 genomic loci associated with a common genetic factor underlying various income measures, all with small effect sizes. Our GWAS-derived polygenic index captures 1 - 4% of income variance, with only one-fourth attributed to direct genetic effects. A phenome-wide association study using this polygenic index showed reduced risks for a broad spectrum of diseases, including hypertension, obesity, type 2 diabetes, coronary atherosclerosis, depression, asthma, and back pain. The income factor showed a substantial genetic correlation (0.92, s.e. = .006) with educational attainment (EA). Accounting for EA's genetic overlap with income revealed that the remaining genetic signal for higher income related to better mental health but reduced physical health benefits and increased participation in risky behaviours such as drinking and smoking.
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