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Introduction: The oral trichomonad Trichomonas tenax is increasingly appreciated as a likely contributor to periodontitis, a chronic inflammatory disease induced by dysbiotic microbiota, in humans and domestic animals and is strongly associated with its worst prognosis. Our current understanding of the molecular basis of T. tenax interactions with host cells and the microbiota of the oral cavity are still rather limited. One laboratory strain of T. tenax (Hs- 4:NIH/ATCC 30207) can be grown axenically and two draft genome assemblies have been published for that strain, although the structural and functional annotation of these genomes is not available. Methods: GenSAS and Galaxy were used to annotate two publicly available draft genomes for T. tenax, with a focus on protein-coding genes. A custom pipeline was used to annotate the CAZymes for T. tenax and the human sexually transmitted parasite Trichomonas vaginalis, themost well-characterized trichomonad. A combination of bioinformatics analyses was used to screen for homologs of T. vaginalis virulence and colonization factors within the T. tenax annotated proteins. Results: Our annotation of the two T. tenax draft genome sequences and their comparison with T. vaginalis proteins provide evidence for several candidate virulence factors. These include candidate surface proteins, secreted proteins and enzymes mediating potential interactions with host cells and/or members of the oral microbiota. The CAZymes annotation identified a broad range of glycoside hydrolase (GH) families, with the majority of these being shared between the two Trichomonas species. Discussion: The presence of candidate T. tenax virulence genes supports the hypothesis that this species is associated with periodontitis through direct and indirectmechanisms. Notably, several GH proteins could represent potential new virulence factors for both Trichomonas species. These data support a model where T. tenax interactions with host cells and members of the oral microbiota could synergistically contribute to the damaging inflammation characteristic of periodontitis, supporting a causal link between T. tenax and periodontitis. [ABSTRACT FROM AUTHOR]

As bioinformatics datasets grow ever larger, and analyses become increasingly complex, there is a need for data handling infrastructures to keep pace with developing technology. One solution is to apply Grid and Cloud technologies to address the computational requirements of analysing high throughput datasets. We present an approach for writing new, or wrapping existing applications, and a reference implementation of a framework, Microbase2.0, for executing those applications using Grid and Cloud technologies. We used Microbase2.0 to develop an automated Cloud-based bioinformatics workflow executing simultaneously on two different Amazon EC2 data centres and the Newcastle University Condor Grid. Several CPU years’ worth of computational work was performed by this system in less than two months. The workflow produced a detailed dataset characterising the cellular localisation of 3,021,490 proteins from 867 taxa, including bacteria, archaea and unicellular eukaryotes. Microbase2.0 is freely available from http://www.microbase.org.uk/.

In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats.

Mitochondria use transport proteins of the eukaryotic mitochondrial carrier family (MCF) to mediate the exchange of diverse substrates, including ATP, with the host cell cytosol. According to classical endosymbiosis theory, [...]

Microsporidia are highly specialized obligate intracellular parasites of other eukaryotes (including humans (1)) that show extreme reduction at the molecular, cellular and biochemical level (2,3). Although microsporidia have long been [...]

Author(s): Brendan Loftus (corresponding author) [1]; Iain Anderson [1]; Rob Davies [2]; U. Cecilia M. Alsmark [3]; John Samuelson [4]; Paolo Amedeo [1]; Paola Roncaglia [1]; Matt Berriman [2]; Robert [...]

Author(s): Ivan Hrdy [1]; Robert P. Hirt [2]; Pavel Dolezal [1]; Lucie Bardonová [1]; Peter G. Foster [3]; Jan Tachezy (corresponding author) [1]; T. Martin Embley (corresponding author) [2] Hydrogenosomes [...]

Author(s): Bryony A. P. Williams [1]; Robert P. Hirt [1]; John M. Lucocq [2]; T. Martin Embley (corresponding author) [1] Microsporidia are obligate intracellular parasites of several eukaryotes. They have [...]

Dimeric lgA (dlgA) transcytosis is mediated by polymeric immunoglobin (poly-lg) receptor, which belongs to the immunoglobulin-gene family. The poly-lg receptor is characterized by five lg-like domains taking part in ligand binding, a transmembrane segment and a cytoplasmic tail bearing the majority of information needed for intracellular trafficking. The phosphorylated residue involved in poly-lg receptor trafficking is speculated to be serine-664. Any mutation in Ser-664 leads to a decrease in the phosphorylation and a decrease in the rate of receptor transcytosis.