Purification of a delayed hypersensitivity-inducing protein from Listeria monocytogenes

Abstract Cell-envelope fragments were prepared from Listeria monocytogenes L242, serotype 4b. Delayed hypersensitivity (DH)-inducing proteins were extracted with deoxycholate and separated into two fractions by filtration through a Sephacryl S-200 column equilibrated with deoxycholate buffer. The second peak eluting from the Sephacryl column was fractionated using ion exchange chromatography on a DEAE Sepharose CL-6B column in the presence of 6 M urea. A purified 20 400-Da protein which induced DH against L. monocytogenes was obtained by isocratic elution. Three other DH-inducing fractions containing several protein bands were eluted by a gradient of potassium thiocyanate (KSCN) in urea buffer. Our results indicate that denaturing conditions can be employed for the fractionation and purification of DH inducing proteins from L. monocytogenes . In addition, it is suggested that the procedure described might also be useful for the purification of other antigens involved in cellular immune reactions.     

Quantification of Fusarium graminearum in infected wheat by species specific real-time PCR applying a TaqMan Probe

A new real-time PCR based method was developed for the species-specific detection, identification and quantification of Fusarium graminearum in planta. It utilizes a TaqMan hybridisation probe targeting the beta-tubulin gene and a plasmid standard. The assay is highly specific giving no product with DNA of closely related species. It is very sensitive, detecting down to five gene copies per reaction, and is able to produce reliable quantitative data over a range of six orders of magnitude.     

Crop processing of <Emphasis Type="Italic">Olea europaea</Emphasis> L.: an experimental approach for the interpretation of archaeobotanical olive remains

Archaeobotanical research, ethnographic observations and laboratory experiments are put together to create model sequences of olive processing, which are developed, presented and explored as an aid for the interpretation of rich archaeobotanical assemblages of Olea. We conclude that the remains of different processing stages are reasonably distinctive in the archaeobotanical record and assist in the identification of different types of olive remains, such as fragmented olive stones, the inner kernels, and fruit flesh     

Habitat properties and plant traits interact as drivers of non‐native plant species’ seed production at the local scale

To answer the long‐standing question if we can predict plant invader success based on characteristics of the environment (invasibility) or the invasive species (invasiveness), or the combination of both, there is a need for detailed observational studies in which habitat properties, non‐native plant traits, and the resulting invader success are locally measured. In this study, we assess the interaction of gradients in the environmental and trait space on non‐native species fitness, expressed as seed production, for a set of 10 invasive and noninvasive non‐native species along a wide range of invaded sites in Flanders. In our multidimensional approach, most of the single environmental gradients (temperature, light availability, native plant species diversity, and soil fertility) and sets of non‐native plant traits (plant size, photosynthesis, and foliar chemical attributes) related positively with invader seed production. Yet correlation with seed production was much stronger when several environmental gradients were assessed in interaction, and even more so when we combined plant traits and habitat properties. The latter increased explanatory power of the models on average by 25% for invasive and by 7% for noninvasive species. Additionally, we report a 70‐fold higher seed production in invasive than in noninvasive species and fundamentally different correlations of seed production with plant traits and habitat properties in noninvasive versus invasive species. We conclude that locally measured traits and properties deserve much more attention than they currently get in invasion literature and thus encourage further studies combining this level of detail with the generality of a multiregion and multispecies approach across different stages of invasion.     

Query-driven module discovery in microarray data

MOTIVATION: Existing (bi)clustering methods for microarray data analysis often do not answer the specific questions of interest to a biologist. Such specific questions could be derived from other information sources, including expert prior knowledge. More specifically, given a set of seed genes which are believed to have a common function, we would like to recruit genes with similar expression profiles as the seed genes in a significant subset of experimental conditions. RESULTS: We introduce QDB, a novel Bayesian query-driven biclustering framework in which the prior distributions allow introducing knowledge from a set of seed genes (query) to guide the pattern search. In two well-known yeast compendia, we grow highly functionally enriched biclusters from small sets of seed genes using a resolution sweep approach. In addition, relevant conditions are identified and modularity of the biclusters is demonstrated, including the discovery of overlapping modules. Finally, our method deals with missing values naturally, performs well on artificial data from a recent biclustering benchmark study and has a number of conceptual advantages when compared to existing approaches for focused module search.