Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris

Sidhu VK, Vorhölter F-J, Niehaus K, Watt SA. Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris. BMC Microbiology. 2008;8(1):87.Background: Outer membrane vesicles (OMVs) are released from the outer membrane of many Gram-negative bacteria. These extracellular compartments are known to transport compounds involved in cell-cell signalling as well as virulence associated proteins, e. g. the cytolysine from enterotoxic E. coli. Results: We have demonstrated that Xanthomonas campestris pv. campestris (Xcc) releases OMVs into the culture supernatant during growth. A proteome study identified 31 different proteins that associate with the OMV fraction of which half are virulence-associated. A comparison with the most abundant outer membrane ( OM) proteins revealed that some proteins are enriched in the OMV fraction. This may be connected to differences in the LPS composition between the OMVs and the OM. Furthermore, a comparison of the OMV proteomes from two different culture media indicated that the culture conditions have an impact on the protein composition. Interestingly, the proteins that are common to both culture conditions are mainly involved in virulence. Conclusion: Outer membrane vesicles released from the OM of Xcc contain membrane- and virulence-associated proteins. Future experiments will prove whether these structures can serve as "vehicles" for the transport of virulence factors into the host membrane

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Blom J, Albaum S, Doppmeier D, et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics. 2009;10(1): 154.Background:The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results: To support these studies EDGAR – ''Efficient Database framework for comparative Genome Analyses using BLAST score Ratios'' – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de webcite, where the precomputed data sets can be browsed

Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

<p>Abstract</p> <p>Background</p> <p>Bacterial spot of tomato and pepper is caused by four <it>Xanthomonas </it>species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, <it>Xanthomonas euvesicatoria </it>(<it>Xcv</it>) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10.</p> <p>Results</p> <p>We sequenced the genomes of <it>X. vesicatoria </it>(<it>Xv</it>) strain 1111 (ATCC 35937), <it>X. perforans </it>(<it>Xp</it>) strain 91-118 and <it>X. gardneri </it>(<it>Xg</it>) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced <it>Xcv </it>strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from <it>Xg </it>strain 101 and <it>Xv </it>strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in <it>Xcv</it>. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity.</p> <p>Conclusions</p> <p>Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.</p

Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium pv. campestris-2

He brackets with numeration indicate the sections taken from the gel for tryptic digestion. (B) Protein profiles of OMVs isolated from cultures grown in M9 medium and the outer membrane (OM) fraction prepared from the same culture.<p><b>Copyright information:</b></p><p>Taken from "Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium pv. campestris"</p><p>http://www.biomedcentral.com/1471-2180/8/87</p><p>BMC Microbiology 2008;8():87-87.</p><p>Published online 2 Jun 2008</p><p>PMCID:PMC2438364.</p><p></p

Teachers' perspectives on students' metacognitive strategies during mathematical modelling processed - A case study

The usage of metacognitive strategies can help students to avoid or to overcome cognitive barriers during modelling processes. For imparting relevant metacognitive strategies and supporting students during the modelling process, it is necessary that teachers act on a meta-meta level and monitor their students’ usage of metacognitive strategies. Therefore, the teachers’ perception of students’ metacognitive activities during modelling processes is of great importance. However, until now, there does not exist such a study. The study described in this chapter examines this topic in a qualitatively oriented intervention study. The results focus on one teacher, who showed a broadening of her perception of the students’ usage of metacognition in mathematical modelling processes

Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium pv. campestris-0

Ernatant of pv campestris strain B100 at a 30 k fold magnification (OMVs highlighted by arrows). (B) Immunogold electron microscopy of 1% (w/v) uranyl acetate stained cell at 14 k fold magnification after incubation with an anti-B100 antibody which was detected by a 10 nm gold particle bound to a goat anti-rabbit antibody (gold-labelled OMV highlighted by arrows). (C) Immunogold electron micrograph of 1% (w/v) uranyl acetate stained OMVs at 27 k fold magnification after incubation with an anti-B100 antibody detected with a 10 nm gold particle bound to an goat anti-rabbit antibody.<p><b>Copyright information:</b></p><p>Taken from "Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium pv. campestris"</p><p>http://www.biomedcentral.com/1471-2180/8/87</p><p>BMC Microbiology 2008;8():87-87.</p><p>Published online 2 Jun 2008</p><p>PMCID:PMC2438364.</p><p></p

Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium pv. campestris-3

Lar location or function. The pie charts indicate the number of proteins in each group isolated from OMVs collected from M9 medium (A) from XVM2 medium (B) and the outer membrane proteins isolated from cells grown in M9 medium (C). The percentage values within the pie chart give the amount of proteins grouped as virulence-associated, which comprise the groups of virulence factors and type III secretion proteins.<p><b>Copyright information:</b></p><p>Taken from "Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium pv. campestris"</p><p>http://www.biomedcentral.com/1471-2180/8/87</p><p>BMC Microbiology 2008;8():87-87.</p><p>Published online 2 Jun 2008</p><p>PMCID:PMC2438364.</p><p></p

Joy of mathematical modelling: a forgotten perspective?

We argue the relevance of including an affective perspective in the mathematical modelling education research and emphasise its importance for the teaching and learning of mathematical modelling at all levels, especially at the university. Our argument is supported by a recent survey of mathematics lecturers’ views on mathematical modelling, several follow-up interviews, and a review of literature on mathematical modelling that relates to enjoyment, pleasure, and appreciation. Findings from the survey and the follow-up interviews indicate that there is a group of practitioners who hold strong views on the importance of enjoyment in doing and teaching mathematical modelling