Transcriptome profiling during a natural host-parasite interaction

BACKGROUND: Infection outcome in some coevolving host-pathogens is characterised by host-pathogen genetic interactions, where particular host genotypes are susceptible only to a subset of pathogen genotypes. To identify candidate genes responsible for the infection status of the host, we exposed a Daphnia magna host genotype to two bacterial strains of Pasteuria ramosa, one of which results in infection, while the other does not. At three time points (four, eight and 12 h) post pathogen exposure, we sequenced the complete transcriptome of the hosts using RNA-Seq (Illumina). RESULTS: We observed a rapid and transient response to pathogen treatment. Specifically, at the four-hour time point, eight genes were differentially expressed. At the eight-hour time point, a single gene was differentially expressed in the resistant combination only, and no genes were differentially expressed at the 12-h time point. CONCLUSIONS: We found that pathogen-associated transcriptional activity is greatest soon after exposure. Genome-wide resistant combinations were more likely to show upregulation of genes, while susceptible combinations were more likely to be downregulated, relative to controls. Our results also provide several novel candidate genes that may play a pivotal role in determining infection outcomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1838-0) contains supplementary material, which is available to authorized users

Theoretical Investigation of Small Alkali Cation-Molecule Clusters: A Model Potential Approach

We present here a model potential study of the microsolvation of alkali cations M+ (M = Na, K, Rb, Cs) in various solvents (water, methanol, dimethyl ether (DME)). The potential energy surfaces (PES) are explored with the Monte Carlo growth method (MCGM) to find the most significant equilibrium structures of M+-(solvent)n clusters (n = 2, 4). The structures as well as the binding energies are favorably compared to the best ab initio calculations found in the literature and to experimental results. This good agreement is only obtained if we take into account the anisotropy of the polarizability tensor for the solvent molecule. Under these conditions, the atomic parameters included in our model potential framework are found to be transferable from water to methanol and DME. An analysis of the different physical components of the interaction energy shows that the only important n-body term for the description of these systems is the polarization one

A Comparative Study of Maize and Miscanthus Regarding Cell-Wall Composition and Stem Anatomy for Conversion into Bioethanol and Polymer Composites

International audienceDue to an increasing demand for environmentally sustainable products, miscanthus and maize stover represent interesting lignocellulosic resources for conversion into biofuels and biomaterials. The overall purpose was to compare miscanthus and maize regarding cell-wall composition and stem anatomy for conversion into bioethanol and polymer composites using partial least squares regressions. For each of the two crops, six contrasted genotypes were cultivated in complete block design, and harvested. Internodes below the main cob for maize, and on the first aboveground internode for miscanthus, were analyzed for biochemistry and anatomy. Their digestibility was predicted using crop-specific near infrared calibrations, and the mechanical properties were evaluated in stem-based composites. On average, the internode cross-section of miscanthus anatomy was characterized by a thick rind (26.2 %) and few but dense pith-bundles (3.5 nb/mm²), while cell-wall constituted 95.2 % of the dry matter with high lignin (243.2 mg/g) and cellulose concentrations (439.7 mg/g). Maize internode-anatomy showed large cross-sections (397.5 mm²), pith with the presence of numerous bundles and non-lignified-pith fractions (22.3 % of the section). Its cellwall biochemistry displayed high concentrations of hemicelluloses, galactose, arabinose, xylose and ferulic acid. Cell-wall, lignin and cellulose concentrations were positively correlated with rind-fraction and pith-bundle-density, which explained strong mechanical properties as shown in miscanthus. Hemicelluloses, galactose, arabinose and ferulic acid concentrations were positively correlated with pith fraction and stem cross-section, revealing high digestibility as shown in maize. This underlines interesting traits for further comparative genetic studies, as maize represents a good model for digestibility and miscanthus for composites