The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene

Abstract Background Little is known about the diversity, phylogenetic relationships, and biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids. Methods Small Subunit rRNA (SSU rRNA) and glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) genes were employed for phylogenetic inferences. Trypanosomes from crocodilians were obtained by haemoculturing. Growth behaviour, morphology, and ultrastructural features complement the molecular description of two new species strongly supported by phylogenetic analyses. Results The inferred phylogenies disclosed a strongly supported crocodilian-restricted clade comprising three subclades. The subclade T. grayi comprised the African Trypanosoma grayi from Crocodylus niloticus and tsetse flies. The subclade T. ralphi comprised alligatorid trypanosomes represented by Trypanosoma ralphi n. sp. from Melanosuchus niger, Caiman crocodilus and Caiman yacare from Brazilian river basins. T. grayi and T. ralphi were sister subclades. The basal subclade T. terena comprised alligatorid trypanosomes represented by Trypanosoma terena n. sp. from Ca. yacare sharing hosts and basins with the distantly genetic related T. ralphi. This subclade also included the trypanosome from Ca. crocodilus from the Orinoco basin in Venezuela and, unexpectedly, a trypanosome from the African crocodilian Osteolaemus tetraspis. Conclusion The close relationship between South American and African trypanosomes is consistent with paleontological evidence of recent transoceanic dispersal of Crocodylus at the Miocene/Pliocene boundaries (4–5 mya), and host-switching of trypanosomes throughout the geological configuration of South American hydrographical basins shaping the evolutionary histories of the crocodilians and their trypanosomes.

The phylogeography of trypanosomes from South American alligatorids and African crocodilids is consistent with the geological history of South American river basins and the transoceanic dispersal of Crocodylus at the Miocene

Background: Little is known about the diversity, phylogenetic relationships, and biogeography of trypanosomes infecting non-mammalian hosts. In this study, we investigated the influence of host species and biogeography on shaping the genetic diversity, phylogenetic relationship, and distribution of trypanosomes from South American alligatorids and African crocodilids. Methods: Small Subunit rRNA (SSU rRNA) and glycosomal Glyceraldehyde Phosphate Dehydrogenase (gGAPDH) genes were employed for phylogenetic inferences. Trypanosomes from crocodilians were obtained by haemoculturing. Growth behaviour, morphology, and ultrastructural features complement the molecular description of two new species strongly supported by phylogenetic analyses. Results: The inferred phylogenies disclosed a strongly supported crocodilian-restricted clade comprising three subclades. The subclade T. grayi comprised the African Trypanosoma grayi from Crocodylus niloticus and tsetse flies. The subclade T. ralphi comprised alligatorid trypanosomes represented by Trypanosoma ralphi n. sp. From Melanosuchus niger, Caiman crocodilus and Caiman yacare from Brazilian river basins. T. grayi and T. ralphi were sister subclades. The basal subclade T. terena comprised alligatorid trypanosomes represented by Trypanosoma terena n. sp. from Ca. yacare sharing hosts and basins with the distantly genetic related T. ralphi. This subclade also included the trypanosome from Ca. crocodilus from the Orinoco basin in Venezuela and, unexpectedly, a trypanosome from the African crocodilian Osteolaemus tetraspis. Conclusion: The close relationship between South American and African trypanosomes is consistent with paleontological evidence of recent transoceanic dispersal of Crocodylus at the Miocene/Pliocene boundaries (4–5 mya), and host-switching of trypanosomes throughout the geological configuration of South American hydrographical basins shaping the evolutionary histories of the crocodilians and their trypanosomes.

All-optical passive quasi-regeneration in transoceanic 40 Gbit/s return-to-zero transmission systems with strong dispersion management

A method of all-optical passive quasi-regeneration in transoceanic 40 Gbit/s return-to-zero transmission systems with strong dispersion management was described. The use of in-line nonlinear optical loop mirrors (NOLM) by the method was demonstrated. The quasi-regeneration of signals performed by NOLMs was found to improve the systems's performance.

Stable propagation of solitons with increased energy through the combined action of dispersion management and periodic saturable absorption

It is shown, through numerical simulations, that by using a combination of dispersion management and periodic saturable absorption it is possible to transmit solitonlike pulses with greatly increased energy near to the zero net dispersion wavelength. This system is shown to support the stable propagation of solitons over transoceanic distances for a wide range of input powers.

Dispersion-managed solitons: a new paradigm for high data rate

The WDM properties of dispersion managed (DM) solitons and the reduction in Gordon-Haus jitter means that it is possible to contemplate multiple channels each at 10 Gbit/s for transoceanic distances without the need for elaborate soliton control. This paper will concentrate on fundamental principles of DM solitons, but will use these principles to indicate optimum maps for future high-speed soliton systems.

Numerical modelling of dispersion managed soliton transmission

This thesis presents the results of numerical modelling of the propagation of dispersion managed solitons. The theory of optical pulse propagation in single mode optical fibre is introduced specifically looking at the use of optical solitons for fibre communications. The numerical technique used to solve the nonlinear Schrödinger equation is also introduced. The recent developments in the use of dispersion managed solitons are reviewed before the numerical results are presented. The work in this thesis covers two main areas; (i) the use of a saturable absorber to control the propagation of dispersion managed solutions and (ii) the upgrade of the installed standard fibre network to higher data rates through the use of solitons and dispersion management. Saturable absorbe can be used to suppress the build up of noise and dispersive radiation in soliton transmission lines. The use of saturable absorbers in conjunction with dispersion management has been investigated both as a single pulse and for the transmission of a 10Gbit/s data pattern. It is found that this system supports a new regime of stable soliton pulses with significantly increased powers. The upgrade of the installed standard fibre network to higher data rates through the use of fibre amplifiers and dispersion management is of increasing interest. In this thesis the propagation of data at both 10Gbit/s and 40Gbit/s is studied. Propagation over transoceanic distances is shown to be possible for 10Gbit/s transmission and for more than 2000km at 40Gbit/s. The contribution of dispersion managed solitons in the future of optical communications is discussed in the thesis conclusions.

Dispersion-managed solitons: a new paradigm for high data rate

The WDM properties of dispersion managed (DM) solitons and the reduction in Gordon-Haus jitter means that it is possible to contemplate multiple channels each at 10 Gbit/s for transoceanic distances without the need for elaborate soliton control. This paper will concentrate on fundamental principles of DM solitons, but will use these principles to indicate optimum maps for future high-speed soliton systems.

Stable propagation of solitons with increased energy through the combined action of dispersion management and periodic saturable absorption

It is shown, through numerical simulations, that by using a combination of dispersion management and periodic saturable absorption it is possible to transmit solitonlike pulses with greatly increased energy near to the zero net dispersion wavelength. This system is shown to support the stable propagation of solitons over transoceanic distances for a wide range of input powers.

Simulations of pollutant dispersion at toll plazas using three-dimensional CFD models

Toll plazas are particularly susceptible to build-ups of vehicle-emitted pollutants because vehicles pass through in low gear. To look at this, three-dimensional computational fluid dynamics simulations of pollutant dispersion are used on the standard k e turbulence model. The effects of wind speed, wind direction and topography on pollutant dispersion were discussed. The Wuzhuang toll plaza on the Hefei-Nanjing expressway is considered, and the effects of the retaining walls along both sides of the plaza on pollutant dispersion is analysed. There are greater pollutant concentrations near the tollbooths as the angle between the direction of the wind and traffic increases implying that retaining walls impede dispersion. The slope of the walls has little influence on the variations in pollutant concentration.