RESUMEN
We study a united-atom model of the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethyl)sulfonylamide to determine to what extent there exist curves in the phase diagram along which the microscopic dynamics are invariant when expressed in dimensionless, or reduced, form. The initial identification of these curves, termed isodynes, is made by noting that contours of reduced shear viscosity and reduced self-diffusion coefficient coincide to a good approximation. Choosing specifically the contours of reduced viscosity as nominal isodynes, further simulations were carried out for state points on these, and other aspects of dynamics were investigated to study their degree of invariance. These include the mean-squared displacement, shear-stress autocorrelation function, and various rotational correlation functions. These were invariant to a good approximation, with the main exception being rotations of the anion about its long axis. The dynamical features that are invariant have in common that they are aspects that would be relevant for a coarse-grained description of the system; specifically, removing the most microscopic degrees of freedom in principle leads to a simplification of the potential energy landscape, which allows for the existence of isodynes.
RESUMEN
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, the most 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 indirect mechanisms. 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.