Recent, independent and anthropogenic origins of Trypanosoma cruzi hybrids.

The single celled eukaryote Trypanosoma cruzi, a parasite transmitted by numerous species of triatomine bug in the Americas, causes Chagas disease in humans. T. cruzi generally reproduces asexually and appears to have a clonal population structure. However, two of the six major circulating genetic lineages, TcV and TcVI, are TcII-TcIII inter-lineage hybrids that are frequently isolated from humans in regions where chronic Chagas disease is particularly severe. Nevertheless, a prevalent view is that hybridisation events in T. cruzi were evolutionarily ancient and that active recombination is of little epidemiological importance. We analysed genotypes of hybrid and non-hybrid T. cruzi strains for markers representing three distinct evolutionary rates: nuclear GPI sequences (n = 88), mitochondrial COII-ND1 sequences (n = 107) and 28 polymorphic microsatellite loci (n = 35). Using Maximum Likelihood and Bayesian phylogenetic approaches we dated key evolutionary events in the T. cruzi clade including the emergence of hybrid lineages TcV and TcVI, which we estimated to have occurred within the last 60,000 years. We also found evidence for recent genetic exchange between TcIII and TcIV and between TcI and TcIV. These findings show that evolution of novel recombinants remains a potential epidemiological risk. The clearly distinguishable microsatellite genotypes of TcV and TcVI were highly heterozygous and displayed minimal intra-lineage diversity indicative of even earlier origins than sequence-based estimates. Natural hybrid genotypes resembled typical meiotic F1 progeny, however, evidence for mitochondrial introgression, absence of haploid forms and previous experimental crosses indicate that sexual reproduction in T. cruzi may involve alternatives to canonical meiosis. Overall, the data support two independent hybridisation events between TcII and TcIII and a recent, rapid spread of the hybrid progeny in domestic transmission cycles concomitant with, or as a result of, disruption of natural transmission cycles by human activities

Wild Trypanosoma cruzi I genetic diversity in Brazil suggests admixture and disturbance in parasite populations from the Atlantic Forest region

Background Trypanosoma cruzi (Kinetoplastida, Trypanosomatidae) infection is an ancient and widespread zoonosis distributed throughout the Americas. Ecologically, Brazil comprises several distinct biomes: Amazonia, Cerrado, Caatinga, Pantanal and the Atlantic Forest. Sylvatic T. cruzi transmission is known to occur throughout these biomes, with multiple hosts and vectors involved. Parasite species-level genetic diversity can be a useful marker for ecosystem health. Our aims were to: investigate sylvatic T. cruzi genetic diversity across different biomes, detect instances of genetic exchange, and explore the possible impact of ecological disturbance on parasite diversity at an intra-species level. Methods We characterised 107 isolates of T. cruzi I (TcI; discrete typing unit, DTU I) from different major Brazilian biomes with twenty-seven nuclear microsatellite loci. A representative subset of biologically cloned isolates was further characterised using ten mitochondrial gene loci. We compared these data generated from Brazilian TcI isolates from around America. Results Genetic diversity was remarkably high, including one divergent cluster that branched outside the known genetic diversity of TcI in the Americas. We detected evidence for mitochondrial introgression and genetic exchange between the eastern Amazon and Caatinga. Finally, we found strong signatures of admixture among isolates from the Atlantic Forest region by comparison to parasites from other study sites. Conclusions Atlantic Forest sylvatic TcI populations are highly fragmented and admixed by comparison to others around Brazil. We speculate on: the possible causes of Atlantic Forest admixture; the role of T. cruzi as a sentinel for ecosystem health, and the impact disrupted sylvatic transmission cycles might have on accurate source attribution in oral outbreaks

Multiple mitochondrial introgression events and heteroplasmy in trypanosoma cruzi revealed by Maxicircle MLST and next generation sequencing

Background Mitochondrial DNA is a valuable taxonomic marker due to its relatively fast rate of evolution. In Trypanosoma cruzi, the causative agent of Chagas disease, the mitochondrial genome has a unique structural organization consisting of 20–50 maxicircles (∼20 kb) and thousands of minicircles (0.5–10 kb). T. cruzi is an early diverging protist displaying remarkable genetic heterogeneity and is recognized as a complex of six discrete typing units (DTUs). The majority of infected humans are asymptomatic for life while 30–35% develop potentially fatal cardiac and/or digestive syndromes. However, the relationship between specific clinical outcomes and T. cruzi genotype remains elusive. The availability of whole genome sequences has driven advances in high resolution genotyping techniques and re-invigorated interest in exploring the diversity present within the various DTUs. Methodology/Principal Findings To describe intra-DTU diversity, we developed a highly resolutive maxicircle multilocus sequence typing (mtMLST) scheme based on ten gene fragments. A panel of 32 TcI isolates was genotyped using the mtMLST scheme, GPI, mini-exon and 25 microsatellite loci. Comparison of nuclear and mitochondrial data revealed clearly incongruent phylogenetic histories among different geographical populations as well as major DTUs. In parallel, we exploited read depth data, generated by Illumina sequencing of the maxicircle genome from the TcI reference strain Sylvio X10/1, to provide the first evidence of mitochondrial heteroplasmy (heterogeneous mitochondrial genomes in an individual cell) in T. cruzi. Conclusions/Significance mtMLST provides a powerful approach to genotyping at the sub-DTU level. This strategy will facilitate attempts to resolve phenotypic variation in T. cruzi and to address epidemiologically important hypotheses in conjunction with intensive spatio-temporal sampling. The observations of both general and specific incidences of nuclear-mitochondrial phylogenetic incongruence indicate that genetic recombination is geographically widespread and continues to influence the natural population structure of TcI, a conclusion which challenges the traditional paradigm of clonality in T. cruzi

Square Patterns and Quasi-patterns in Weakly Damped Faraday Waves

Pattern formation in parametric surface waves is studied in the limit of weak viscous dissipation. A set of quasi-potential equations (QPEs) is introduced that admits a closed representation in terms of surface variables alone. A multiscale expansion of the QPEs reveals the importance of triad resonant interactions, and the saturating effect of the driving force leading to a gradient amplitude equation. Minimization of the associated Lyapunov function yields standing wave patterns of square symmetry for capillary waves, and hexagonal patterns and a sequence of quasi-patterns for mixed capillary-gravity waves. Numerical integration of the QPEs reveals a quasi-pattern of eight-fold symmetry in the range of parameters predicted by the multiscale expansion.Comment: RevTeX, 11 pages, 8 figure

Effects of Steady Flow on Magnetoacoustic-Gravity Surface Waves: I. The Weak Field Case

Magnetoacoustic gravity (MAG) waves have been studied for some time. In this article, we investigate the effect that a shear flow at a tangential discontinuity embedded in a gravitationally stratified and magnetised plasma has on MAG surface waves. The dispersion relation found is algebraically analogous to the relation of the non-flow cases obtained by Miles and Roberts (Solar Phys.141, 205, 1992), except for the introduction of a Doppler-shifted frequency for the eigenvalue. This feature, however, introduces rather interesting physics, including the asymmetric presence of forward- and backward-propagating surface waves. We find that increasing the equilibrium flow speed leads to a shift in the permitted regions of propagation for surface waves. For most wave number combinations this leads to the fast mode being completely removed, as well as more limited phase speed regimes for slow-mode propagation. We also find that upon increasing the flow, the phase speeds of the backward propagating waves are increased. Eventually, at high enough flow speeds, the wave’s direction of propagation is reversed and is in the positive direction. However, the phase speed of the forward-propagating wave remains mainly the same. For strong enough flows we find that the Kelvin–Helmholtz instability can also occur when the forward- and backward-propagating modes couple

Water wave propagation and scattering over topographical bottoms

Here I present a general formulation of water wave propagation and scattering over topographical bottoms. A simple equation is found and is compared with existing theories. As an application, the theory is extended to the case of water waves in a column with many cylindrical steps

Parenting the Premature Infant: Potential Iatrogenesis from the Neonatal Intensive Care Experience

(1) Developmental outcomes of premature infants are associated with the quality of the home environment and the level of parenting skills the family possesses. Successful development of the parenting role may be negatively influenced by the Neonatal Intensive Care Unit (NICU) environment and nursing practices. Identification of interventions that promote the development of parenting skills in the NICU can potentially improve developmental outcomes for premature infants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73814/1/j.1524-475X.1996.00046.x.pd

Influences on academics' approaches to development: voices from below

The purpose of this qualitative case study research was to explore faculty-based academics’ views on what influences their behaviours and attitudes towards their development. Informed by critical realist ontology, the data collection was carried out through narrative interviews with academics in two contrasting English Universities. Findings, or areas for reflection, have emerged about the constraints and enablements academics perceive in respect of their professional development. In particular, themes such as the significance of professional status; misaligned initiatives and priorities; the influence of supportive networks; and emergent personal, individual concerns have surfaced. The conclusion is drawn that the significance of agency raises the importance of responding to the ‘voices from below’

Resonantly damped surface and body MHD waves in a solar coronal slab with oblique propagation

The theory of magnetohydrodynamic (MHD) waves in solar coronal slabs in a zero-$\beta$ configuration and for parallel propagation of waves does not allow the existence of surface waves. When oblique propagation of perturbations is considered both surface and body waves are able to propagate. When the perpendicular wave number is larger than a certain value, the body kink mode becomes a surface wave. In addition, a sausage surface mode is found below the internal cut-off frequency. When non-uniformity in the equilibrium is included, surface and body modes are damped due to resonant absorption. In this paper, first, a normal-mode analysis is performed and the period, the damping rate, and the spatial structure of eigenfunctions are obtained. Then, the time-dependent problem is solved, and the conditions under which one or the other type of mode is excited are investigated.Comment: 19 pages, 9 figures, accepted for publication in Solar Physic

Structure optimization effects on the electronic properties of Bi2_2Sr2_2CaCu2_2O8_8

We present detailed first-principles calculations for the normal state electronic properties of the high T$_C$ superconductor Bi$_2$Sr$_2$CaCu$_2$O$_8$, by means of the linearized augmented plane wave (LAPW) method within the framework of density functional theory (DFT). As a first step, the body centered tetragonal (BCT) cell has been adopted, and optimized regarding its volume, $c/a$ ratio and internal atomic positions by total energy and force minimizations. The full optimization of the BCT cell leads to small but visible changes in the topology of the Fermi surface, rounding the shape of CuO$_2$ barrels, and causing both the BiO bands, responsible for the pockets near the \textit{\=M} 2D symmetry point, to dip below the Fermi level. We have then studied the influence of the distortions in the BiO plane observed in nature by means of a $\sqrt{2}\times\sqrt{2}$ orthorhombic cell (AD-ORTH) with $Bbmb$ space group. Contrary to what has been observed for the Bi-2201 compound, we find that for Bi-2212 the distortion does not sensibly shift the BiO bands which retain their metallic character. As a severe test for the considered structures we present Raman-active phonon frequencies ($q = 0$) and eigenvectors calculated within the frozen-phonon approximation. Focussing on the totally symmetric A$_{g}$ modes, we observe that for a reliable attribution of the peaks observed in Raman experiments, both $c$- and a-axis vibrations must be taken into account, the latter being activated by the in-plane orthorhombic distortion.Comment: 22 pages, 4 figure