Population genomics of the maize pathogen Ustilago maydis: demographic history and role of virulence clusters in adaptation

The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical, and genome-wide variation of genetic diversity in this fungal pathogen. We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 Myr. We show that both populations experienced a recent strong bottleneck starting around 10,000years ago, coinciding with the assumed time of maize domestication. Although the genome average genetic diversity is low compared with other fungal pathogens, we estimated that the rate of nonsynonymous adaptive substitutions is three times higher in genes located within virulence clusters compared with nonclustered genes, including nonclustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen

Uveitis manifestations in patients of the Swiss Inflammatory Bowel Disease Cohort Study.

The knowledge about risk factors for the onset of uveitis manifestations in patients with inflammatory bowel disease (IBD) is still limited. Here, we aimed to provide an overview of the clinical factors associated with the onset of uveitis in the Swiss IBD Cohort Study (SIBDCS). We included epidemiological and clinical data from 1840 patients with Crohn's disease (CD) and 1426 patients with ulcerative colitis (UC) followed up in the SIBDCS between 2006 and 2018. Associations between disease characteristics and uveitis were assessed in univariate and multivariate analyses. Overall, we identified 285 patients with uveitis. Uveitis was more frequent in patients with CD (11.1%; 205 of 1635) than UC (5.6%; 80 of 1346; odds ratio 2.11, p < 0.001). The occurrence of uveitis manifestations in patients with UC and CD was significantly associated with the onset of other extraintestinal manifestations, also in multivariate analyses. The onset of uveitis was associated with the hallmark features of severe disease in both CD and UC, including a higher clinical disease activity index and the use of immunomodulators or calcineurin inhibitors. In CD, uveitis was more frequent in females and showed a positive correlation with a positive family history of IBD. Our data demonstrate that uveitis in IBD occurs more often in CD as well as in women and is associated with a more severe disease course. This might guide physicians' awareness in at-risk patients to the presence of uveitis extraintestinal manifestations and help to improve patient care

Associations between fruit and vegetable intake and quality of life

Abstract Dysregulation of the immune response to microbiota is associated with inflammatory bowel disease (IBD), which can trigger intestinal fibrosis. MyD88 is a key component of microbiota signalling but its influence on intestinal fibrosis has not been clarified. Small bowel resections from donor-mice were transplanted subcutaneously into the neck of recipients C57BL/6 B6-MyD88tm1 Aki (MyD88−/−) and C57BL/6-Tg(UBC-green fluorescence protein (GFP))30Scha/J (GFP-Tg). Grafts were explanted up to 21 days after transplantation. Collagen layer thickness was determined using Sirius Red stained slides. In the mouse model of fibrosis collagen deposition and transforming growth factor-beta 1 (TGF-β1) expression was equal in MyD88+/+ and MyD88−/−, indicating that MyD88 was not essential for fibrogenesis. Matrix metalloproteinase (Mmp)9 expression was significantly decreased in grafts transplanted into MyD88−/− recipients compared to MyD88+/+ recipients (0.2 ± 0.1 vs. 153.0 ± 23.1, respectively, p < 0.05), similarly recruitment of neutrophils was significantly reduced (16.3 ± 4.5 vs. 25.4 ± 3.1, respectively, p < 0.05). Development of intestinal fibrosis appears to be independent of MyD88 signalling indicating a minor role of bacterial wall compounds in the process which is in contrast to published concepts and theories. Development of fibrosis appears to be uncoupled from acute inflammation

Individual and Multi Vortex Pinning in Systems with Periodic Pinning Arrays

We examine multi and individual vortex pinning in thin superconductors with periodic pinning arrays. For multi-vortex pinning we observe peaks in the critical current of equal magnitude at every matching field, while for individual vortex pinning we observe a sharp drop in the critical current after the first matching field in agreement with experiments. We examine the scaling of the critical current at commensurate and incommensurate fields for varied pinning strength and show that the depinning force at incommensurate fields decreases faster than at the commensurate fields.Comment: 4 figuure

Decay-assisted collinear resonance ionization spectroscopy: Application to neutron-deficient francium

This paper reports on the hyperfine-structure and radioactive-decay studies of the neutron-deficient francium isotopes $^{202-206}$Fr performed with the Collinear Resonance Ionization Spectroscopy (CRIS) experiment at the ISOLDE facility, CERN. The high resolution innate to collinear laser spectroscopy is combined with the high efficiency of ion detection to provide a highly-sensitive technique to probe the hyperfine structure of exotic isotopes. The technique of decay-assisted laser spectroscopy is presented, whereby the isomeric ion beam is deflected to a decay spectroscopy station for alpha-decay tagging of the hyperfine components. Here, we present the first hyperfine-structure measurements of the neutron-deficient francium isotopes $^{202-206}$Fr, in addition to the identification of the low-lying states of $^{202,204}$Fr performed at the CRIS experiment.Comment: Accepted for publication with Physical Review

Laser spectroscopy of francium isotopes at the borders of the region of reflection asymmetry

The magnetic dipole moments and changes in mean-square charge radii of the neutron-rich $^{218m,219,229,231}\text{Fr}$ isotopes were measured with the newly-installed Collinear Resonance Ionization Spectroscopy (CRIS) beam line at ISOLDE, CERN, probing the $7s~^{2}S_{1/2}$ to $8p~^{2}P_{3/2}$ atomic transition. The $\delta\langle r^{2}\rangle^{A,221}$ values for $^{218m,219}\text{Fr}$ and $^{229,231}\text{Fr}$ follow the observed increasing slope of the charge radii beyond $N~=~126$. The charge radii odd-even staggering in this neutron-rich region is discussed, showing that $^{220}\text{Fr}$ has a weakly inverted odd-even staggering while $^{228}\text{Fr}$ has normal staggering. This suggests that both isotopes reside at the borders of a region of inverted staggering, which has been associated with reflection-asymmetric shapes. The $g(^{219}\text{Fr}) = +0.69(1)$ value supports a $\pi 1h_{9/2}$ shell model configuration for the ground state. The $g(^{229,231}\text{Fr})$ values support the tentative $I^{\pi}(^{229,231}\text{Fr}) = (1/2^{+})$ spin, and point to a $\pi s_{1/2}^{-1}$ intruder ground state configuration.Comment: Accepted for publication with Physical Review

Torque magnetometry on single-crystal high temperature superconductors near the critical temperature: a scaling approach

Angular-dependent magnetic torque measurements performed near the critical temperature on single crystals of HgBa_{2}CuO_{4+y}, La_{2-x}Sr{x}CuO_{4}, and YBa_{2}Cu_{3}O_{6.93} are scaled, following the 3D XY model, in order to determine the scaling function dG^{\pm}(z)/dz which describes the universal critical properties near T_{c}. A systematic shift of the scaling function with increasing effective mass anisotropy \gamma = (m_{ab}*/m_{c}*)^{1/2} is observed, which may be understood in terms of a 3D-2D crossover. Further evidence for a 3D-2D crossover is found from temperature-dependent torque measurements carried out in different magnetic fields at different field orientations \delta, which show a quasi 2D "crossing region'' (M*,T*). The occurrence of this "crossing phenomenon'' is explained in a phenomenological way from the weak z dependence of the scaling function around a value z = z*. The "crossing'' temperature T* is found to be angular-dependent. Torque measurements above T_{c} reveal that fluctuations are strongly enhanced in the underdoped regime where the anisotropy is large, whereas they are less important in the overdoped regime.Comment: 9 pages, 10 figures, submitted to PR

The importance of loose tobacco when considering capping pack size

Caps on tobacco pack sizes should include loose tobacco,as pack size varies more for loose tobacco than factory-made cigarettes. This may simplify purchase decisions for consumers and inventory management for retailers. Standardizing pack dimensions as well as the quantity of product within packs would further limit the potential of tobacco companies to use the packaging as a promotional tool

High-resolution distribution modeling of a threatened short-range endemic plant informed by edaphic factors

Short-range endemic plants often have edaphic specializations that, with their restricted distributions, expose them to increased risk of anthropogenic extinction. Here, we present a modeling approach to understand habitat suitability for Ricinocarpos brevis R.J.F.Hend. & Mollemans (Euphorbiaceae), a threatened shrub confined to three isolated populations in the semi-arid south-west of Western Australia. The model is a maximum entropy species distribution projection constructed on the basis of physical soil characteristics and geomorphology data at approximately 25 m2 (1 arc-second) resolution. The model predicts the species to occur on shallow, low bulk density soils that are located high in the landscape. The model shows high affinity (72.1% average likelihood of occurrence) for the known populations of R. brevis, as well as identifying likely locations that are not currently known to support the species. There was a strong relationship between the likelihood of R. brevis occurrence and soil moisture content that the model estimated at a depth of 20 cm. We advocate that our approach should be standardized using publicly available data to generate testable hypotheses for the distribution and conservation management of short-range endemic plant species for all of continental Australia