Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen

Modern agriculture favours the selection and spread of novel plant diseases. Furthermore, crop genetic resistance against pathogens is often rendered ineffective within a few years of its commercial deployment. Leptosphaeria maculans, the cause of phoma stem canker of oilseed rape, develops gene-for-gene interactions with its host plant, and has a high evolutionary potential to render ineffective novel sources of resistance in crops. Here, we established a four-year field experiment to monitor the evolution of populations confronted with the newly released Rlm7 resistance and to investigate the nature of the mutations responsible for virulence against Rlm7. A total of 2551 fungal isolates were collected from experimental crops of a Rlm7 cultivar or a cultivar without Rlm7. All isolates were phenotyped for virulence and a subset was genotyped with neutral genetic markers. Virulent isolates were investigated for molecular events at the AvrLm4-7 locus. Whilst virulent isolates were not found in neighbouring crops, their frequency had reached 36% in the experimental field after four years. An extreme diversity of independent molecular events leading to virulence was identified in populations, with large-scale Repeat Induced Point mutations or complete deletion of AvrLm4-7 being the most frequent. Our data suggest that increased mutability of fungal genes involved in the interactions with plants is directly related to their genomic environment and reproductive system. Thus, rapid allelic diversification of avirulence genes can be generated in L. maculans populations in a single field provided that large population sizes and sexual reproduction are favoured by agricultural practices.     

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here, we present a nucleotide resolution catalog of single-nucleotide, multi-nucleotide, and structural variants in 39 Drosophila melanogaster Genetic Reference Panel inbred lines. Using an integrative, local assembly-based approach for variant discovery, we identify more than 3.6 million distinct variants, among which were more than 800,000 unique insertions, deletions (indels), and complex variants (1 to 6,000 bp). While the SNP density is higher near other variants, we find that variants themselves are not mutagenic, nor are regions with high variant density particularly mutation-prone. Rather, our data suggest that the elevated SNP density around variants is mainly due to population-level processes. We also provide insights into the regulatory architecture of gene expression variation in adult flies by mapping cis-expression quantitative trait loci (cis-eQTLs) for more than 2,000 genes. Indels comprise around 10% of all cis-eQTLs and show larger effects than SNP cis-eQTLs. In addition, we identified two-fold more gene associations in males as compared to females and found that most cis-eQTLs are sex-specific, revealing a partial decoupling of the genomic architecture between the sexes as well as the importance of genetic factors in mediating sex-biased gene expression. Finally, we performed RNA-seq-based allelic expression imbalance analyses in the offspring of crosses between sequenced lines, which revealed that the majority of strong cis-eQTLs can be validated in heterozygous individuals.     

Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation

Smyd3 is a lysine methyltransferase implicated in chromatin and cancer regulation. Here we show that Smyd3 catalyzes histone H4 methylation at lysine 5 (H4K5me). This novel histone methylation mark is detected in diverse cell types and its formation is attenuated by depletion of Smyd3 protein. Further, Smyd3-driven cancer cell phenotypes require its enzymatic activity. Thus, Smyd3, via H4K5 methylation, provides a potential new link between chromatin dynamics and neoplastic disease.     

Effects of Acidification, Sodium Chloride, and Moisture Levels on Wheat Dough: II. Modeling of Bread Texture and Staling Kinetics

The effect of three experimental factors pH (addition of lactic acid and sodium hydroxide), water, and sodium chloride (NaCl) addition on wheat bread making performance (volume, baking loss, crumb firmness, crumb grain features) and the crumb staling during storage was studied. The staling behavior was modeled with the Avrami equation and with linear regressions. All bread quality parameters were reliably modeled using response surface methodology (up to R ² ?=?0.97). The crumb staling behavior was better described by a linear regression than by the rate constant k of the Avrami equation (R ² ?=?0.87 / R ² ?=?0.36). The highest volume can be achieved with the experimental values pH 5.39, 0.41?g NaCl 100?g^?1 flour and 68.7?g water 100?g^?1 flour. Correlation analysis revealed significant linear dependency of dough rheology (complex shear modulus) on the firmness of the bread crumb (r?=?0.73) and staling attributes (r????0.73). Dough microstructural properties showed significant but low correlation with bread making performance attributes.     

Effects of Acidification, Sodium Chloride, and Moisture Levels on Wheat Dough: I. Modeling of Rheological and Microstructural Properties

The rheological attributes of polymers as wheat dough are strongly related to its microstructure. To quantify dough protein microstructure confocal laser scanning microscopy combined with image analysis was used. The effect of three experimental factors pH (addition of lactic acid and sodium hydroxide), water addition, and sodium chloride (NaCl) addition on empirical and fundamental rheological properties as well as microstructural protein properties were studied and modeled by applying a response surface methodology. The obtained models revealed high correlations between the experimental factors and the complex shear modulus (R ²?=?0.97), dough resistance (R_max ^k; R ²?=?0.91) and stickiness (R ²?=?0.93). Furthermore it was possible to determine microstructural attributes as the area fraction (R ²?=?0.88) and Feret??s diameter (R ²?=?0.86) as a function of pH, water and NaCl addition. Especially measures of R^k _max revealed highly significant correlations with the protein microstructure as the branching index (r?=?0.79).     

Testing semiochemicals from aphid,plant and conspecific: attraction of Harmonia axyridis

Abstract Harmonia axyridis Pallas (Coleoptera: Coccinellidae) is an invasive specie affecting the dynamics and composition of several guilds. Nowadays, no biological control method is available to reduce the populations of this harmful coccinellid. Attractants and semiochemicals seem to be the best alternative but only few studies have tested the impact of semiochemicals on this Asian lady beetle. In this work, through wind‐tunnel experiments, semiochemicals from aphids (Z,E‐nepetalactone, [E]‐β‐farnesene, α‐pinene and β‐pinene), from coccinellids ([‐]‐β‐caryophyllene) and from the nettle Urtica dioica L. were evaluated as potential attractants. The nettle volatile compounds ([Z]‐3‐hexenol and [E]‐2‐hexenal) were extracted using a Clevenger Apparatus^® and identified by headspace gas chromatography–mass spectroscopy. In the wind‐tunnel experiments, the main components of the aphid alarm pheromone as well as a component of the aphid sexual pheromone strongly attracted both sexes of the Asian lady beetle while (‐)‐β‐caryophyllene only attracted few individuals and had no impact on the males. The nettle extract as well as the (Z)‐3‐hexenol oriented both males and females to the odor source. The (E)‐2‐hexenal was shown to have no effect on females even if this green leaf volatile attracted males. Because Z,E‐nepetalactone was identified as the most efficient attractant in the wind‐tunnel experiments, this volatile was also tested in a potato field where H. axyridis has been showed to respond to this semiochemical. This study highlighted that Z,E‐nepetalactone orientated the Asian lady beetle H. axyridis under natural conditions, indicating that this volatile compound could certainly help for an efficient biological control approach against this invasive specie.     

β-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel

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Highlights? The rigid N-terminal helix of VDAC stabilizes the cylindrical β-barrel ? Removal of the helix leads to elliptical, semicollapsed pore shapes ? Semicollapse can quantitatively explain conductance and selectivity of closed VDAC ? The N terminus acts as a switch controlling VDAC entry into the closed state     

Nucleosome positioning and nucleosome stacking: two faces of the same coin

Nucleosomes are regularly spaced along eukaryotic genomes. In the emerging model, known as "statistical positioning", this spacing is due to steric repulsion between nucleosomes and to the presence of nucleosome excluding barriers on the genome. However, new experimental evidence recently challenged the "statistical positioning" model (Z. Zhang et al., Science, 2011, 332(6032), 977-980). We propose here that the regular spacing can be better explained by adding attractive interactions between nucleosomes. In our model those attractions are due to the fact that nucleosomes are stacked in regular chromatin fibers. In a self-reinforcing mechanism, regular nucleosome spacing promotes in turn nucleosome stacking. We first show that this model can precisely account for the nucleosome spacing observed in Saccharomyces cerevisiae. We then use a simple toy model to show that attraction between nucleosomes can fasten the formation of the chromatin fiber.     

Genome-wide transcript profiling indicates induction of energy-generating pathways and an adaptive immune response in the liver of sows during lactation

The present study aimed to explore the lactation-induced changes in hepatic gene expression in sows (Sus scrofa) during lactation. Using a porcine whole-genome microarray a total of 632 differentially expressed genes in the liver of lactating compared to non-lactating sows could be identified. Enrichment analysis revealed that the differentially expressed genes were mainly involved in fatty acid metabolism, pyruvate metabolism, glutathione metabolism, glycine, serine and threonine metabolism, citrate cycle, glycerophospholipid metabolism, PPAR signaling, and focal adhesion. The most striking observation with respect to intermediary metabolism was that genes involved in fatty acid catabolism, the catabolism of gluconeogenic amino acids, the citrate cycle and the respiratory chain were up-regulated in the liver of sows during lactation. With respect to immune response, it could be demonstrated that genes encoding acute phase proteins and genes involved in tissue repair were up-regulated and genes encoding adhesion molecules were down-regulated in the liver of sows during lactation. The results indicate that energy-generating pathways and pathways involved in the delivery of gluconeogenic substrates are induced in sow liver during lactation. The alterations of expression of genes encoding proteins involved in immune response suggest that lactation in sows may cause an adaptive immune response that possibly counteracts hepatic inflammation.     

Anti-Chlamydial Th17 Responses Are Controlled by the Inducible Costimulator Partially through Phosphoinositide 3-Kinase Signaling

We previously showed that mice deficient in the Inducible Costimulator ligand (ICOSL-KO) develop more severe disease and lung pathology with delayed bacterial clearance upon respiratory infection of Chlamydia muridarum. Importantly, the exacerbation of disease in ICOSL-KO mice was seen despite heightened IFN-γ/Th1 responses, the major defense mechanisms against Chlamydia. To gain insight into the mechanism of ICOS function in this model, we presently analyzed anti-Chlamydia immune responses in mice lacking the entire ICOS (ICOS-KO) versus knock-in mice expressing a mutant ICOS (ICOS-Y181F) that has selectively lost the ability to activate phosphoinositide 3-kinase (PI3K). Like ICOSL-KO mice, ICOS-KO mice showed worse disease with elevated IFN-γ/Th1 responses compared to wild-type (WT) mice. ICOS-Y181F mice developed much milder disease compared to ICOS-KO mice, yet they were still not fully protected to the WT level. This partial protection in ICOS-Y181F mice could not be explained by the magnitude of IFN-γ/Th1 responses since these mice developed a similar level of IFN-γ response compared to WT mice. It was rather IL-17/Th17 responses that reflected disease severity: IL-17/Th17 response was partially impaired in ICOS-Y181F mice compared to WT, but was substantially stronger than that of ICOS-KO mice. Consistently, we found that both polarization and expansion of Th17 cells were partially impaired in ICOS-Y181F CD4 T cells, and was further reduced in ICOS-KO CD4 T cells in vitro. Our results indicate that once the IFN-γ/Th1 response is above a threshold level, the IL-17/Th17 response becomes a limiting factor in controlling Chlamydia lung infection, and that ICOS plays an important role in promoting Th17 responses in part through the activation of PI3K.