Genome Size, Karyotype Polymorphism and Chromosomal Evolution in Trypanosoma cruzi

Background: The Trypanosoma cruzi genome was sequenced from a hybrid strain (CL Brener). However, high allelic variation and the repetitive nature of the genome have prevented the complete linear sequence of chromosomes being determined. Determining the full complement of chromosomes and establishing syntenic groups will be important in defining the structure of T. cruzi chromosomes. A large amount of information is now available for T. cruzi and Trypanosoma brucei, providing the opportunity to compare and describe the overall patterns of chromosomal evolution in these parasites. Methodology/Principal Findings: The genome sizes, repetitive DNA contents, and the numbers and sizes of chromosomes of nine strains of T. cruzi from four lineages (TcI, TcII, TcV and TcVI) were determined. The genome of the TcI group was statistically smaller than other lineages, with the exception of the TcI isolate Tc1161 (Jose-IMT). Satellite DNA content was correlated with genome size for all isolates, but this was not accompanied by simultaneous amplification of retrotransposons. Regardless of chromosomal polymorphism, large syntenic groups are conserved among T. cruzi lineages. Duplicated chromosome-sized regions were identified and could be retained as paralogous loci, increasing the dosage of several genes. By comparing T. cruzi and T. brucei chromosomes, homologous chromosomal regions in T. brucei were identified. Chromosomes Tb9 and Tb11 of T. brucei share regions of syntenic homology with three and six T. cruzi chromosomal bands, respectively. Conclusions: Despite genome size variation and karyotype polymorphism, T. cruzi lineages exhibit conservation of chromosome structure. Several syntenic groups are conserved among all isolates analyzed in this study. The syntenic regions are larger than expected if rearrangements occur randomly, suggesting that they are conserved owing to positive selection. Mapping of the syntenic regions on T. cruzi chromosomal bands provides evidence for the occurrence of fusion and split events involving T. brucei and T. cruzi chromosomes.

LOCAL WELL POSEDNESS, ASYMPTOTIC BEHAVIOR AND ASYMPTOTIC BOOTSTRAPPING FOR A CLASS OF SEMILINEAR EVOLUTION EQUATIONS OF THE SECOND ORDER IN TIME

A class of semilinear evolution equations of the second order in time of the form u(tt)+Au+mu Au(t)+Au(tt) = f(u) is considered, where -A is the Dirichlet Laplacian, 92 is a smooth bounded domain in R(N) and f is an element of C(1) (R, R). A local well posedness result is proved in the Banach spaces W(0)(1,p)(Omega)xW(0)(1,P)(Omega) when f satisfies appropriate critical growth conditions. In the Hilbert setting, if f satisfies all additional dissipativeness condition, the nonlinear Semigroup of global solutions is shown to possess a gradient-like attractor. Existence and regularity of the global attractor are also investigated following the unified semigroup approach, bootstrapping and the interpolation-extrapolation techniques.

Robust relations between CCN and the vertical evolution of cloud drop size distribution in deep convective clouds

In-situ measurements in convective clouds (up to the freezing level) over the Amazon basin show that smoke from deforestation fires prevents clouds from precipitating until they acquire a vertical development of at least 4 km, compared to only 1-2 km in clean clouds. The average cloud depth required for the onset of warm rain increased by similar to 350 m for each additional 100 cloud condensation nuclei per cm(3) at a super-saturation of 0.5% (CCN0.5%). In polluted clouds, the diameter of modal liquid water content grows much slower with cloud depth (at least by a factor of similar to 2), due to the large number of droplets that compete for available water and to the suppressed coalescence processes. Contrary to what other studies have suggested, we did not observe this effect to reach saturation at 3000 or more accumulation mode particles per cm(3). The CCN0.5% concentration was found to be a very good predictor for the cloud depth required for the onset of warm precipitation and other microphysical factors, leaving only a secondary role for the updraft velocities in determining the cloud drop size distributions. The effective radius of the cloud droplets (r(e)) was found to be a quite robust parameter for a given environment and cloud depth, showing only a small effect of partial droplet evaporation from the cloud's mixing with its drier environment. This supports one of the basic assumptions of satellite analysis of cloud microphysical processes: the ability to look at different cloud top heights in the same region and regard their r(e) as if they had been measured inside one well developed cloud. The dependence of r(e) on the adiabatic fraction decreased higher in the clouds, especially for cleaner conditions, and disappeared at r(e)>=similar to 10 mu m. We propose that droplet coalescence, which is at its peak when warm rain is formed in the cloud at r(e)=similar to 10 mu m, continues to be significant during the cloud's mixing with the entrained air, cancelling out the decrease in r(e) due to evaporation.

Charged Kaon Interferometric Probes of Space-Time Evolution in Au plus Au Collisions at s(NN)=200 GeV

Bose-Einstein correlations of charged kaons are used to probe Au+Au collisions at s(NN)=200 GeV and are compared to charged pion probes, which have a larger hadronic scattering cross section. Three-dimensional Gaussian source radii are extracted, along with a one-dimensional kaon emission source function. The centrality dependences of the three Gaussian radii are well described by a single linear function of N(part)(1/3) with a zero intercept. Imaging analysis shows a deviation from a Gaussian tail at r greater than or similar to 10 fm, although the bulk emission at lower radius is well described by a Gaussian. The presence of a non-Gaussian tail in the kaon source reaffirms that the particle emission region in a heavy-ion collision is extended, and that similar measurements with pions are not solely due to the decay of long-lived resonances.

Physical approximations for the nonlinear evolution of perturbations in inhomogeneous dark energy scenarios

The abundance and distribution of collapsed objects such as galaxy clusters will become an important tool to investigate the nature of dark energy and dark matter. Number counts of very massive objects are sensitive not only to the equation of state of dark energy, which parametrizes the smooth component of its pressure, but also to the sound speed of dark energy, which determines the amount of pressure in inhomogeneous and collapsed structures. Since the evolution of these structures must be followed well into the nonlinear regime, and a fully relativistic framework for this regime does not exist yet, we compare two approximate schemes: the widely used spherical collapse model and the pseudo-Newtonian approach. We show that both approximation schemes convey identical equations for the density contrast, when the pressure perturbation of dark energy is parametrized in terms of an effective sound speed. We also make a comparison of these approximate approaches to general relativity in the linearized regime, which lends some support to the approximations.

Evolution of perturbations of squashed Kaluza-Klein black holes: Escape from instability

The squashed Kaluza-Klien (KK) black holes differ from the Schwarzschild black holes with asymptotic flatness or the black strings even at energies for which the KK modes are not excited yet, so that squashed KK black holes open a window in higher dimensions. Another important feature is that the squashed KK black holes are apparently stable and, thereby, let us avoid the Gregory-Laflamme instability. In the present paper, the evolution of scalar and gravitational perturbations in time and frequency domains is considered for these squashed KK black holes. The scalar field perturbations are analyzed for general rotating squashed KK black holes. Gravitational perturbations for the so-called zero mode are shown to be decayed for nonrotating black holes, in concordance with the stability of the squashed KK black holes. The correlation of quasinormal frequencies with the size of extra dimension is discussed.

Decoherence-free evolution of time-dependent superposition states of two-level systems and thermal effects

In this paper we detail some results advanced in a recent letter [Prado et al., Phys. Rev. Lett. 102, 073008 (2009).] showing how to engineer reservoirs for two-level systems at absolute zero by means of a time-dependent master equation leading to a nonstationary superposition equilibrium state. We also present a general recipe showing how to build nonadiabatic coherent evolutions of a fermionic system interacting with a bosonic mode and investigate the influence of thermal reservoirs at finite temperature on the fidelity of the protected superposition state. Our analytical results are supported by numerical analysis of the full Hamiltonian model.

Musical genres: beating to the rhythms of different drums

Online music databases have increased significantly as a consequence of the rapid growth of the Internet and digital audio, requiring the development of faster and more efficient tools for music content analysis. Musical genres are widely used to organize music collections. In this paper, the problem of automatic single and multi-label music genre classification is addressed by exploring rhythm-based features obtained from a respective complex network representation. A Markov model is built in order to analyse the temporal sequence of rhythmic notation events. Feature analysis is performed by using two multi-variate statistical approaches: principal components analysis (unsupervised) and linear discriminant analysis (supervised). Similarly, two classifiers are applied in order to identify the category of rhythms: parametric Bayesian classifier under the Gaussian hypothesis (supervised) and agglomerative hierarchical clustering (unsupervised). Qualitative results obtained by using the kappa coefficient and the obtained clusters corroborated the effectiveness of the proposed method.

Nonadiabatic Coherent Evolution of Two-Level Systems under Spontaneous Decay

In this Letter we extend current perspectives in engineering reservoirs by producing a time-dependent master equation leading to a nonstationary superposition equilibrium state that can be nonadiabatically controlled by the system-reservoir parameters. Working with an ion trapped inside a nonideal cavity, we first engineer effective interactions, which allow us to achieve two classes of decoherence-free evolution of superpositions of the ground and excited ionic levels: those with a time-dependent azimuthal or polar angle. As an application, we generalize the purpose of an earlier study [Phys. Rev. Lett. 96, 150403 (2006)], showing how to observe the geometric phases acquired by the protected nonstationary states even under nonadiabatic evolution.

Geodynamic evolution of the SW Variscides: Orogenic collapse shown by new tectonometamorphic and isotopic data from western Ossa-Morena Zone, SW Iberia

The pre-Mesozoic geodynamic evolution of SW Iberia has been investigated on the basis of detailed structural analysis, isotope dating, and petrologic study of high-pressure (HP) rocks, revealing the superposition of several tectonometamorphic events: (1) An HP event older than circa 358 Ma is recorded in basic rocks preserved inside marbles, which suggests subduction of a continental margin. The deformation associated with this stage is recorded by a refractory graphite fabric and noncoaxial mesoscopic structures found within the host metasediments. The sense of shear is top to south, revealing thrusting synthetic with subduction (underthrusting) to the north. (2) Recrystallization before circa 358 Ma is due to a regional-scale thermal episode and magmatism. (3) Noncoaxial deformation with top to north sense of shear in northward dipping large-scale shear zones is associated with pervasive hydration and metamorphic retrogression under mostly greenschist facies. This indicates exhumation by normal faulting in a detachment zone confined to the top to north and north dipping shear zones during postorogenic collapse soon after 358 Ma ago (inversion of earlier top to south thrusts). (4) Static recrystallization at circa 318 Ma is due to regional-scale granitic intrusions. Citation: Rosas, F. M., F. O. Marques, M. Ballevre, and C. Tassinari (2008), Geodynamic evolution of the SW Variscides: Orogenic collapse shown by new tectonometamorphic and isotopic data from western Ossa-Morena Zone, SW Iberia, Tectonics, 27, TC6008, doi:10.1029/2008TC002333.

TAXONOMIC POSITION OF GUIRATINGIA MENDESI (MEGADESMIDAE) AND THE EVOLUTION OF PERMIAN ENDEMIC BIVALVE FAUNA OF THE PARANA BASIN, BRAZIL

The unusual bivalve Guiratingia mendesi is redescribed from the original material. Detailed analysis of hinge and muscle scars allows more refined designation of its taxonomic position and affinities to other Permian bivalves from the Parana Basin. Guiratingia mendesi is characterized by very small, anteriorly expanded shells, with a great number of muscle striae within the area delimited by the pallial line. A flattened area is noted alongside the commissure of shell. The presence of a triangular blunt tooth in the right valve allows its designation to Megadesmidae. The absence of accessory muscle scars ""a"" and ""b"" and pedal elevator indicate that the genus belongs to the Plesiocyprinellinae, a group of bivalves considered endemic to the Passa Dois Group. Guiratingia mendesi is found, however, in limestones of the Palermo Formation (Middle Artinskian), nearly 100 in below the base of the Irati Formation (Late Artinskian). Until now, it was believed that within the Permian succession of Parana Basin, pre-Irati bivalves were all gondwanic or cosmopolitan. Guiratingia mendesi was an endemic, active burrower that resembles Runnegariella fragilis from the Permian Teresina Formation. This indicates that during Palermo times restricted paleogeographic conditions have existed within the huge Parana epeiric sea, favoring endemicity, probably in marine bayments close to its margins. The presence of an anteriorly expanded shell in G mendesi is a condition also seen in other Mesozoic and Cenozoic anomalodesmatans, demonstrating the recurrence of shell forms in distinct lineages of this interesting group of bivalves.

A Complete Skull of an Early Cretaceous Sauropod and the Evolution of Advanced Titanosaurians

Advanced titanosaurian sauropods, such as nemegtosaurids and saltasaurids, were diverse and one of the most important groups of herbivores in the terrestrial biotas of the Late Cretaceous. However, little is known about their rise and diversification prior to the Late Cretaceous. Furthermore, the evolution of their highly-modified skull anatomy has been largely hindered by the scarcity of well-preserved cranial remains. A new sauropod dinosaur from the Early Cretaceous of Brazil represents the earliest advanced titanosaurian known to date, demonstrating that the initial diversification of advanced titanosaurians was well under way at least 30 million years before their known radiation in the latest Cretaceous. The new taxon also preserves the most complete skull among titanosaurians, further revealing that their low and elongated diplodocid-like skull morphology appeared much earlier than previously thought.

EVOLUTION AND LIFETIME OF TRANSIENT CLUMPS IN THE TURBULENT INTERSTELLAR MEDIUM

We study the evolution of dense clumps and provide an argument that the existence of the clumps is not limited by their crossing times. We claim that the lifetimes of the clumps are determined by turbulent motions on a larger scale, and we predict the correlation of clump lifetime with column density. We use numerical simulations to successfully test this relation. In addition, we study the morphological asymmetry and the magnetization of the clumps as functions of their masses.

Deep weathering and landscape evolution in a tropical plateau

The thick weathering profiles of humid tropical areas are an important, yet generally neglected, source of information on landscape evolution. Six complete profiles of the weathering mantle were sampled by drilling on the three stepped levels of the Campos do Jordao Plateau, on the NW flank of the Continental Rift of Southeastern Brazil. Mineralogical and micromorphological analyses of drill core samples, complemented by geochemical interpretations and by previous data on the upper saprolite, indicate continuity of a general lateritic trend during the entire process of mantle formation. Lateritization phases of different intensity were defined and considered to reflect adjustment to changes in environmental conditions created by the gradual uplift of the plateau to its present position. Older and more superficial materials related to intense lateritic weathering are characterized by allitization with direct formation of gibbsite from silicates, probably related to tropical climates existing immediately before the formation of the continental rift, during the Paleogene, and also before any significant increase in altitude. Monosialitization phase with general kaolinitization and restricted indirect formation of gibbsite from silicates could be associated to less aggressive climates that followed the Neogene (Miocene?) accentuation of uplift rates along the continental rift. The changes produced by uplift in the tropical climate eventually favored the development of a podzolization trend in soils above 1800m. (C) 2011 Elsevier BM. All rights reserved.