•Topological Hall effect found in Pt/Co/W multilayers with different signs of anisotropy.•Negative topological Hall contribution due to nucleated isolated skyrmions.•Positive topological Hall ...contribution isolated non-annihilated skyrmions.•Skyrmion numbers of complex domain structures reproduced micromagmetically.
The chirality of non-coplanar magnetic configurations, in magnetic materials with interfacial Dzyaloshinskii–Moriya interaction, gives rise to a local magnetic field generating an extra contribution to the anomalous Hall effect. This contribution, termed topological Hall effect (THE), is studied in three Pt/Co/W multi-layered samples with different effective anisotropy. A particularity of this system, compared to similar systems which show THE, is the existence of magnetically inactive layers at the Co/W interfaces. This implies that the coupling between the layers in this series of samples is mainly magnetostatic. The samples with positive or almost zero effective anisotropy show the same characteristics. These are reproduced by micromagnetic simulations. The sample with negative effective anisotropy shows a qualitatively different behaviour that can be assigned to its radically different domain structure. The values of THE are in the range 0.1–0.25 μΩ cm.
•Vortices on a family thin spherical sector shaped shells are stabilized by curvature.•Curvature is varied at constant size to single-out its contribution to vortex stabilization.•Stabilization is ...mainly driven by the exchange energy term.
Finite element micromagnetics are used to simulate the vortex and onion states on permalloy spherical shells with different curvatures. To distinguish between the effects of size and curvature (covaried in the typical semi-spherical or crescent shaped caps) a family of spherical sectors where the volume is varied at constant curvature is considered. This family is parametrized by intersecting cone angle. Permalloy is chosen as a typical case of an easy-surface magnet in which the demagnetization field bounds the magnetization to follow the curvature of the surface. The thickness of the shell is set to 3 nm, i.e. comparable to the exchange length, so that the local magnetization does not vary along the thickness of the shell. It is found that as the curvature increases the vortex states become favorable down to smaller sizes. This is mainly due to the increased exchange energy cost of the onion states at larger curvatures. Furthermore, it is found that at larger curvatures, stronger in-plane fields are required to destabilize the vortex states and turn them into onion states.
•Vector magnetometry valuable tool for mixed anisotropy layered magnetic systems.•Loops of perpendicular to the field component have a strong angular dependence.•Peaks of the perpendicular to the ...field component reveal decoupling.•Method not sensitive to systems combining layers having both perpendicular anisotropy.
Multilayered films consisting of layer stacks with different anisotropies are studied by vector magnetometry i.e. simultaneous measurement of the components Mx, My along and perpendicular to the applied field respectively. The quantity Mx2+My2 is used as measure of the homogeneity of the reversal. For the Co(6Å)/Pt(15Å)4/(Pt(s))/Co(10Å)/Pt(15Å)4 with s=0–45Å series consisting of a perpendicular anisotropy bottom four-bilayer-stack coupled to a planar anisotropy top four-bilayer-stack a peak of the My component is clearly observed at the Mx coercivity. This is a sign of homogeneous reversal but it can be shown that similar effects can arise by decoupling of two layers with different (in-plane/perpendicular) anisotropies which is the case for s>15Å. In order to study the latter effect, a Co(6Å)/Pt(15Å)4/W(15Å)/Co(24Å) sample is used as a reference as it consists of a perpendicular anisotropy bottom four-bilayer-stack coupled to a vanishing anisotropy top Co layer through a W layer (which creates a magnetically inactive interface permitting only dipolar coupling). In contrast for Co(5Å)/Pt(10Å)6/Pt(s)/Ni(15Å)/Pt(5Å)6 series consisting of two different coercivity stacks which both have perpendicular anisotropy the decoupling does not manifest by appearance of peaks in the My component.
Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult ...to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.
Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic ...transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus
there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30
species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
The current investigation shows a possible new pathway for more efficient and cost-effective energy-harvesting photovoltaic devices. Our approach could permit all emerging technologies that are ...currently used for indoors and smart buildings to go a step forward and could be used for outdoor applications. The investigated architecture is a very promising geometry especially for Dye-Sensitized Solar Cells (DSSCs). It turns their main drawback, the lowering of their efficiency and lifetime when operating at high solar irradiation density, into an asset by increasing the total active area per horizontal unit area for light harvesting, while preserving the active elements from degradation and extending durable lifetime. The investigated architecture is based on a symmetric “U” type geometry, which is constructed by a highly reflective material on the inner surface. Solar irradiation is reflected internally at the bottom of the construction and splits towards two opposite sided solar cells; the two cells form a cavity where the solar light multiplies and is successively absorbed. Consequently, the vertically incoming irradiation is reduced when reaching the vertical internal sides on which the DSSCs are mounted. Thus, the solar cells operate at low light intensities, which provide significant lifetime extension and efficiency enhancement. Interestingly, the electrical energy per effective surface unit, which is produced by the two vertical DSSCs, is at least equal to that of a standalone, vertically irradiated cell. The advantage of the new architecture is that protects DSSCs from their degradation and deterioration, although the entire system operates under high illumination. This makes the cells more efficient outdoors, with a comparable performance to indoor conditions.
Bacteria of the Borrelia burgdorferi sensu lato (s.l.) complex can cause Lyme borreliosis. Different B. burgdorferi s.l. genospecies vary in their host and vector associations and human pathogenicity ...but the genetic basis for these adaptations is unresolved and requires completed and reliable genomes for comparative analyses. The de novo assembly of a complete Borrelia genome is challenging due to the high levels of complexity, represented by a high number of circular and linear plasmids that are dynamic, showing mosaic structure and sequence homology. Previous work demonstrated that even advanced approaches, such as a combination of short-read and long-read data, might lead to incomplete plasmid reconstruction. Here, using recently developed high-fidelity (HiFi) PacBio sequencing, we explored strategies to obtain gap-free, complete and high quality Borrelia genome assemblies. Optimizing genome assembly, quality control and refinement steps, we critically appraised existing techniques to create a workflow that lead to improved genome reconstruction.
Despite the latest available technologies, stand-alone sequencing and assembly methods are insufficient for the generation of complete and high quality Borrelia genome assemblies. We developed a workflow pipeline for the de novo genome assembly for Borrelia using several types of sequence data and incorporating multiple assemblers to recover the complete genome including both circular and linear plasmid sequences.
Our study demonstrates that, with HiFi data and an ensemble reconstruction pipeline with refinement steps, chromosomal and plasmid sequences can be fully resolved, even for complex genomes such as Borrelia. The presented pipeline may be of interest for the assembly of further complex microbial genomes.
Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others to cause human disease, genomic and virulence ...characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies and phenotypic assays to compare C. jejuni isolates from patients who developed PI-IBS with those who did not. We show that variation in bacterial stress response (Cj0145_phoX), adhesion protein (Cj0628_CapA), and core biosynthetic pathway genes (biotin: Cj0308_bioD; purine: Cj0514_purQ; isoprenoid: Cj0894c_ispH) were associated with PI-IBS development. In vitro assays demonstrated greater adhesion, invasion, IL-8 and TNFα secretion on colonocytes with PI-IBS compared to PI-no-IBS strains. A risk-score for PI-IBS development was generated using 22 genomic markers, four of which were from Cj1631c, a putative heme oxidase gene linked to virulence. Our finding that specific Campylobacter genotypes confer greater in vitro virulence and increased risk of PI-IBS has potential to improve understanding of the complex host-pathogen interactions underlying this condition.
Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This ...approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10-6 s/s/y) and Campylobacter jejuni (3.4 x 10-6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.
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