Intergenic and external transcribed spacers of ribosomal RNA genes in lizard-infecting Leishmania: molecular structure and phylogenetic relationship to mammal-infecting Leishmania in the subgenus Leishmania (Leishmania)

To establish the relationships of the lizard- and mammal-infecting Leishmania, we characterized the intergenic spacer region of ribosomal RNA genes from L. tarentolae and L. hoogstraali. The organization of these regions is similar to those of other eukaryotes. The intergenic spacer region was approximately 4 kb in L. tarentolae and 5.5 kb in L. hoogstraali. The size difference was due to a greater number of 63-bp repetitive elements in the latter species. This region also contained another element, repeated twice, that had an inverted octanucleotide with the potential to form a stem-loop structure that could be involved in transcription termination or processing events. The ribosomal RNA gene localization showed a distinct pattern with one chromosomal band (2.2 Mb) for L. tarentolae and two (1.5 and 1.3 Mb) for L. hoogstraali. The study also showed sequence differences in the external transcribed region that could be used to distinguish lizard Leishmania from the mammalian Leishmania. The intergenic spacer region structure features found among Leishmania species indicated that lizard and mammalian Leishmania are closely related and support the inclusion of lizard-infecting species into the subgenus Sauroleishmania proposed by Saf'janova in 1982.

Structural determinants for membrane association and dynamic organization of the hepatitis C virus NS3-4A complex.

Hepatitis C virus (HCV) NS3-4A is a membrane-associated multifunctional protein harboring serine protease and RNA helicase activities. It is an essential component of the HCV replication complex and a prime target for antiviral intervention. Here, we show that membrane association and structural organization of HCV NS3-4A are ensured in a cooperative manner by two membrane-binding determinants. We demonstrate that the N-terminal 21 amino acids of NS4A form a transmembrane alpha-helix that may be involved in intramembrane protein-protein interactions important for the assembly of a functional replication complex. In addition, we demonstrate that amphipathic helix alpha(0), formed by NS3 residues 12-23, serves as a second essential determinant for membrane association of NS3-4A, allowing proper positioning of the serine protease active site on the membrane. These results allowed us to propose a dynamic model for the membrane association, processing, and structural organization of NS3-4A on the membrane. This model has implications for the functional architecture of the HCV replication complex, proteolytic targeting of host factors, and drug design.

Dynamic properties of human brain structure: learning-related changes in cortical areas and associated fiber connections.

Recent findings in neuroscience suggest that adult brain structure changes in response to environmental alterations and skill learning. Whereas much is known about structural changes after intensive practice for several months, little is known about the effects of single practice sessions on macroscopic brain structure and about progressive (dynamic) morphological alterations relative to improved task proficiency during learning for several weeks. Using T1-weighted and diffusion tensor imaging in humans, we demonstrate significant gray matter volume increases in frontal and parietal brain areas following only two sessions of practice in a complex whole-body balancing task. Gray matter volume increase in the prefrontal cortex correlated positively with subject's performance improvements during a 6 week learning period. Furthermore, we found that microstructural changes of fractional anisotropy in corresponding white matter regions followed the same temporal dynamic in relation to task performance. The results make clear how marginal alterations in our ever changing environment affect adult brain structure and elucidate the interrelated reorganization in cortical areas and associated fiber connections in correlation with improvements in task performance.

Exploring the effect of aminoglycoside guanidinylation on ligands for Tau exon 10 splicing regulatory element RNA

We describe the effect of guanidinylation of the aminoglycoside moiety on acridine-neamine-containing ligands for the stem-loop structure located at the exon 10-5′-intron junction of Tau pre-mRNA, an important regulatory element of tau gene alternative splicing. On the basis of dynamic combinatorial chemistry experiments, ligands that combine guanidinoneamine and two different acridines were synthesized and their RNA-binding properties were compared with those of their amino precursors. Fluorescence titration experiments and UV-monitored melting curves revealed that guanidinylation has a positive effect both on the binding affinity and specificity of the ligands for the stemloop RNA, as well as on the stabilization of all RNA sequences evaluated, particularly some mutated sequences associated with the development of FTDP-17 tauopathy. However, this correlation between binding affinity and stabilization due to guanidinylation was only found in ligands containing a longer spacer between the acridine and guanidinoneamine moieties, since a shorter spacer produced the opposite effect (e.g. lower binding affinity and lower stabilization). Furthermore, spectroscopic studies suggest that ligand binding does not significantly change the overall RNA structure upon binding (circular dichroism) and that the acridine moiety might intercalate near the bulged region of the stem->loop structure (UV-Vis and NMR spectroscopy).

Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription.

The transcription factors TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound preinitiation complex, whereas Brf1 and Brf2 are involved, as part of activities also containing TBP and Bdp1 and referred to here as Brf1-TFIIIB and Brf2-TFIIIB, in the recruitment of Pol III. Brf1-TFIIIB recruits Pol III to type 1 and 2 promoters and Brf2-TFIIIB to type 3 promoters such as the human U6 promoter. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1. Here we have tested truncated Brf2, as well as Brf2/TFIIB chimeric proteins for U6 transcription and for assembly of U6 preinitiation complexes. Our results characterize functions of various human Brf2 domains and reveal that the C-terminal domain is required for efficient association of the protein with U6 promoter-bound TBP and SNAP(c), a type 3 promoter-specific transcription factor, and for efficient recruitment of Bdp1. This in turn suggests that the C-terminal extensions in Brf1 and Brf2 are crucial to specific recruitment of Pol III over Pol II.

Age and size structure of gap-dynamic, old-growth boreal forest stands in Newfoundland

[Abstract]

Modal testing and numerical modeling of the dynamic properties of layered sheet-steel structure

Recently, due to the increasing total construction and transportation cost and difficulties associated with handling massive structural components or assemblies, there has been increasing financial pressure to reduce structural weight. Furthermore, advances in material technology coupled with continuing advances in design tools and techniques have encouraged engineers to vary and combine materials, offering new opportunities to reduce the weight of mechanical structures. These new lower mass systems, however, are more susceptible to inherent imbalances, a weakness that can result in higher shock and harmonic resonances which leads to poor structural dynamic performances. The objective of this thesis is the modeling of layered sheet steel elements, to accurately predict dynamic performance. During the development of the layered sheet steel model, the numerical modeling approach, the Finite Element Analysis and the Experimental Modal Analysis are applied in building a modal model of the layered sheet steel elements. Furthermore, in view of getting a better understanding of the dynamic behavior of layered sheet steel, several binding methods have been studied to understand and demonstrate how a binding method affects the dynamic behavior of layered sheet steel elements when compared to single homogeneous steel plate. Based on the developed layered sheet steel model, the dynamic behavior of a lightweight wheel structure to be used as the structure for the stator of an outer rotor Direct-Drive Permanent Magnet Synchronous Generator designed for high-power wind turbines is studied.

The study of RNA tertiary interactions in tRNA structure and function

Le rôle des deux paires de bases universelles inverse Hoogsteen U : A ( RHUAs ) présentent chez les ARNt standards , une dans la boucle T et l'autre dans le noyau de la forme en L , a été étudiée. Pour chacun des RHUAs , un criblage génétique spécialisé in vivo chez les bactéries , le système suppresseur ambre ( pour l'étude de la RHUA dans la boucle T ) et le système d'ARNt de la sélénocystéine ( tRNASec ) ( pour l'étude de la RHUA dans le noyau ) , ont été utilisé pour générer des variants fonctionnels à partir de multiples librairies combinatoires . Ces variants ont ensuite été séquencé et soumis à une analyse systématique qui comprend la modélisation informatique et un type d'analyse phylogénétique. Les résultats du système suppresseur ambre ont montré un ensemble de variants fonctionnels qui ne nécessitent pas le motif RHUA dans la boucle T et qui ont remplacé la méthode standard de l'interaction entre les boucles D et T avec une double hélice interboucle , ILDH . D'autres études ont abouti à la détermination d'un modèle In silico de l'alternative à la norme standard de la boucle T, sous le nom de type III . Les résultats du système tRNASec ont révélé que pour cette ARNt exceptionnel, l'absence de RHUA ( dans le noyau ) assure une flexibilité accrue qui est spécifiquement nécessaire pour la fonction de tRNASec . Ainsi, les ARNt standards , à la différence de tRNASec , avec la présence universelle de RHUA dans le noyau , a été naturellement sélectionnée pour être rigide . Pris ensemble, la RHUA joue un rôle essentiel dans la stabilisation des interactions tertiaires.

How the double spherules of infectious bronchitis virus impact our understanding of RNA virus replicative organelles

Powered by advances in electron tomography, recent studies have extended our understanding of how viruses construct "replication factories" inside infected cells. Their function, however, remains an area of speculation with important implications for human health. It is clear from these studies that whatever their purpose, organelle structure is dynamic (M. Ulasli, M. H. Verheije, C. A. de Haan, and F. Reggiori, Cell. Microbiol. 12:844-861, 2010) and intricate (K. Knoops, M. Kikkert, S. H. Worm, J. C. Zevenhoven-Dobbe, Y. van der Meer, et al., PLOS Biol. 6:e226, 2008). But by concentrating on medically important viruses, these studies have failed to take advantage of the genetic variation inherent in a family of viruses that is as diverse as the archaea, bacteria, and eukaryotes combined (C. Lauber, J. J. Goeman, M. del Carmen Parquet, P. T. Nga, E. J. Snijder, et al., PLOS Pathog. 9:e1003500, 2013). In this climate, Maier et al. (H. J. Maier, P. C. Hawes, E. M. Cottam, J. Mantell, P. Verkade, et al., mBio 4:e00801-13, 2013) explored the replicative structures formed by an avian coronavirus that appears to have diverged at an early point in coronavirus evolution and shed light on controversial aspects of viral biology.

Calibration of structure in a distributed forecasting model for a semiarid flash flood: dynamic surface storage and channel roughness

Flash floods pose a significant danger for life and property. Unfortunately, in arid and semiarid environment the runoff generation shows a complex non-linear behavior with a strong spatial and temporal non-uniformity. As a result, the predictions made by physically-based simulations in semiarid areas are subject to great uncertainty, and a failure in the predictive behavior of existing models is common. Thus better descriptions of physical processes at the watershed scale need to be incorporated into the hydrological model structures. For example, terrain relief has been systematically considered static in flood modelling at the watershed scale. Here, we show that the integrated effect of small distributed relief variations originated through concurrent hydrological processes within a storm event was significant on the watershed scale hydrograph. We model these observations by introducing dynamic formulations of two relief-related parameters at diverse scales: maximum depression storage, and roughness coefficient in channels. In the final (a posteriori) model structure these parameters are allowed to be both time-constant or time-varying. The case under study is a convective storm in a semiarid Mediterranean watershed with ephemeral channels and high agricultural pressures (the Rambla del Albujón watershed; 556 km 2 ), which showed a complex multi-peak response. First, to obtain quasi-sensible simulations in the (a priori) model with time-constant relief-related parameters, a spatially distributed parameterization was strictly required. Second, a generalized likelihood uncertainty estimation (GLUE) inference applied to the improved model structure, and conditioned to observed nested hydrographs, showed that accounting for dynamic relief-related parameters led to improved simulations. The discussion is finally broadened by considering the use of the calibrated model both to analyze the sensitivity of the watershed to storm motion and to attempt the flood forecasting of a stratiform event with highly different behavior.

Dynamic auroral structure in the vicinity of the polar cusp - multipoint observations during southward and northward IMF

The low- and high-latitude boundary layers of the earth's magnetosphere [low-latitude boundary layer (LLBL) and mantle] play important roles in transferring momentum and energy from the solar wind to the magnetosphere-ionosphere system. Particle precipitation, field-aligned current, auroral emission, ionospheric ion drift and ground magnetic perturbations are among the low-altitude parameters that show signatures of various plasma processes in the LLBL and the magnetopause current layer. Magnetic merging events, Kelvin-Helmholtz waves, and pressure pulses excited by the variable solar wind/magnetosheath plasma are examples of boundary phenomena that may be coupled to the ionosphere via field-aligned currents. Optical auroral observation, by photometry and all-sky TV cameras, is a unique technique for investigating the spatial and temporal structure of the electron precipitation associated with such phenomena. However, the distinction between the different boundary layer plasma populations cannot in general be unambiguously determined by optics alone. Additional information, such as satellite observations of particle boundaries and field-aligned currents, is needed in order to identify the plasma source(s) and the magnetosphere-ionosphere coupling mode(s). Two categories of auroral activity/structure in the vicinity of the polar cusp are discussed in this paper, based on combined ground and satellite data. In one case, the quasi-periodic sequence of auroral events at the polar cap boundary involves accelerated electrons (< 1 keV) moving poleward (< 1 km s-1) and azimuthally along the persistent cusp/cleft arc poleward boundary with velocities (< 4 km s-1), comparable to the local ionospheric ion drift during periods of southward IMF. A critical question is whether or not the optical events signify a corresponding plasma flow across the open/closed field line boundary in such cases. Near-simultaneous observations of magnetopause flux transfer events (FTEs) and such optical/ion drift events are reported. The reverse pattern of motion of discrete auroral forms is observed during positive interplanetary magnetic field (IMF) B(Z), i.e. equatorward motion into the cusp/cleft background arc from the poleward edge. Combined satellite and ground-based information for the latter cases indicate a source mechanism, poleward of the cusp at the high-latitude magnetopause or plasma mantle, giving rise to strong momentum transfer and electron precipitation structures within a approximately 200 km-wide latitudinal zone at the cusp/cleft poleward boundary. The striking similarities of auroral electrodynamics in the cleft/mantle region during northward and southward IMF indicate that a qualitatively similar solar wind-magnetosphere coupling mode is operating. It is suggested that, in both cases, the discrete auroral forms represent temporal/spatial structure of larger-scale convection over the polar magnetosphere.

Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A structure-dynamic approach to cortical organization: Number of paths and accessibility

A structure-dynamic approach to cortical systems is reported which is based on the number of paths and the accessibility of each node. The latter measurement is obtained by performing self-avoiding random walks in the respective networks, so as to simulate dynamics, and then calculating the entropies of the transition probabilities for walks starting from each node. Cortical networks of three species, namely cat, macaque and humans, are studied considering structural and dynamical aspects. It is verified that the human cortical network presents the highest accessibility and number of paths (in terms of z-scores). The correlation between the number of paths and accessibility is also investigated as a mean to quantify the level of independence between paths connecting pairs of nodes in cortical networks. By comparing the cortical networks of cat, macaque and humans, it is verified that the human cortical network tends to present the largest number of independent paths of length larger than four. These results suggest that the human cortical network is potentially the most resilient to brain injures. (C) 2009 Elsevier B.V. All rights reserved.