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

Elucidating the Structure and Photophysics of Layered Perovskites through Cation Fluorination

Optoelectronic devices based on layered perovskites containing fluorinated cations display a well-documented improved stability and enhanced performance over non-fluorinated cations. The effect of fluorination on the crystal structure and photophysics, however, has received limited attention up until now. Here, 3-fluorophenethylammonium lead iodide ((3-FPEA)(2)PbI4) single crystals are investigated and their properties to the non-fluorinated ((PEA)(2)PbI4) variant are compared. The bulkier 3-FPEA cation increases the distortion of the inorganic layers, resulting in a blue-shifted absorbance and photoluminescence. Temperature-dependent photoluminescence spectroscopy reveals an intricate exciton substructure in both cases. The fluorinated variant shows hot-exciton resonances separated by 12 to 15 meV, values that are much smaller than the 40 to 46 meV found for (PEA)(2)PbI4. In addition, high-resolution spectra show that the emission at lower energies consists of a substructure, previously thought to be a single line. With the analysis on the resolved photoluminescence, a vibronic progression is excluded as the origin of the emission at lower energies. Instead, part of the excitonic substructure is proposed to originate from bound excitons. This work furthers the understanding of the photophysics of layered perovskites that has been heavily debated lately

Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules

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Evolutionary Ecology of Prokaryotic Immune Mechanisms.

Published onlineJournal ArticleReviewBacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.S.V.H. received funding from the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 660039. We also acknowledge the NERC, the BBSRC, the Royal Society, the Leverhulme Trust, the Wellcome Trust, and the AXA research fund for funding

Fungal model systems and the elucidation of pathogenicity determinants

Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.Peer reviewedPublisher PD

Photochromism in Ruddlesden-Popper copper-based perovskites:A light-induced change of coordination number at the surface

Ruddlesden-Popper organic-inorganic hybrid copper-based perovskites have been studied for decades owing to a variety of interesting properties, such as thermochromism and piezochromism, and the mechanisms behind these phenomena have been explained. Another possible property of these materials that has seldomly been investigated is photochromism. In this work, the photochromic properties of bis(phenethylammonium) tetrachlorocuprate (also known as phenethylammonium copper chloride) are reported for the first time. This material has attracted scientific interest owing to the fact that it shows both ferroelectric and ferromagnetic behavior. This work highlights the difference in stability between two Ruddlesden-Popper copper-based perovskites - with phenethylammonium (PEA) or methylammonium (MA) as the cations - during external stimuli. Various techniques, such as Raman and X-ray photoelectron spectroscopy, and grazing-incidence wide-angle X-ray scattering, combined with optical studies, were used to investigate the underlying photochemical processes at a molecular level. It is found that for the PEA compound, ultraviolet illumination causes a color change from yellow to brown. This is the result of two independent events, namely a Cu2+ reduction reaction and a transition from an octahedral copper-chloride structure to square-planar CuCl42-. After illumination, the material (brown color) is unstable in air, which is evident from a color change back to yellow. Interestingly, the similar compound bis(methylammonium) tetrachlorocuprate does not display photochromic behavior, which is attributed to the different nature of the two organic cations

Circulating Micro-RNAs as Potential Blood-Based Markers for Early Stage Breast Cancer Detection

INTRODUCTION: MicroRNAs (miRNAs, miRs) are a class of small, non-coding RNA molecules with relevance as regulators of gene expression thereby affecting crucial processes in cancer development. MiRNAs offer great potential as biomarkers for cancer detection due to their remarkable stability in blood and their characteristic expression in many different diseases. We investigated whether microarray-based miRNA profiling on whole blood could discriminate between early stage breast cancer patients and healthy controls. METHODS: We performed microarray-based miRNA profiling on whole blood of 48 early stage breast cancer patients at diagnosis along with 57 healthy individuals as controls. This was followed by a real-time semi-quantitative Polymerase Chain Reaction (RT-qPCR) validation in a separate cohort of 24 early stage breast cancer patients from a breast cancer screening unit and 24 age matched controls using two differentially expressed miRNAs (miR-202, miR-718). RESULTS: Using the significance level of p<0.05, we found that 59 miRNAs were differentially expressed in whole blood of early stage breast cancer patients compared to healthy controls. 13 significantly up-regulated miRNAs and 46 significantly down-regulated miRNAs in our microarray panel of 1100 miRNAs and miRNA star sequences could be detected. A set of 240 miRNAs that was evaluated by radial basis function kernel support vector machines and 10-fold cross validation yielded a specificity of 78.8%, and a sensitivity of 92.5%, as well as an accuracy of 85.6%. Two miRNAs were validated by RT-qPCR in an independent cohort. The relative fold changes of the RT-qPCR validation were in line with the microarray data for both miRNAs, and statistically significant differences in miRNA-expression were found for miR-202. CONCLUSIONS: MiRNA profiling in whole blood has potential as a novel method for early stage breast cancer detection, but there are still challenges that need to be addressed to establish these new biomarkers in clinical use

Molecular Doping Directed by a Neutral Radical

[Image: see text] Molecular doping makes possible tunable electronic properties of organic semiconductors, yet a lack of control of the doping process narrows its scope for advancing organic electronics. Here, we demonstrate that the molecular doping process can be improved by introducing a neutral radical molecule, namely nitroxyl radical (2,2,6,6-teramethylpiperidin-i-yl) oxyl (TEMPO). Fullerene derivatives are used as the host and 1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]imidazoles (DMBI-H) as the n-type dopant. TEMPO can abstract a hydrogen atom from DMBI-H and transform the latter into a much stronger reducing agent DMBI(•), which efficiently dopes the fullerene derivative to yield an electrical conductivity of 4.4 S cm(–1). However, without TEMPO, the fullerene derivative is only weakly doped likely by a hydride transfer following by an inefficient electron transfer. This work unambiguously identifies the doping pathway in fullerene derivative/DMBI-H systems in the presence of TEMPO as the transfer of a hydrogen atom accompanied by electron transfer. In the absence of TEMPO, the doping process inevitably leads to the formation of less symmetrical hydrogenated fullerene derivative anions or radicals, which adversely affect the molecular packing. By adding TEMPO we can exclude the formation of such species and, thus, improve charge transport. In addition, a lower temperature is sufficient to meet an efficient doping process in the presence of TEMPO. Thereby, we provide an extra control of the doping process, enabling enhanced thermoelectric performance at a low processing temperature