96 Study of the stacking of DNA homoassociates by the extended cluster approach

Metropolis Monte Carlo method based on the extended cluster approach (Danilov, Dailidonis, van Mourik, & Fruchtl, 2011a, 2011b; Dailidonis, Danilov, Früchtl, & van Mourik, 2011) is used to investigate adenine–adenine (AA), guanine–guanine (GG), thymine–thymine (TT), and cytosine–cytosine (CC) homoassociates in a cluster consisting of 400 water molecules. The starting structures taken were AA N(7) amino symmetric, TT N(3) – O(4) symmetric, GG N(1) – O(6) symmetric, and CC N(3) amino symmetric base pairs. A water spherical cluster with the density of water at room temperature and a radius sphere equal 13.9 Å was used, which corresponds to the most difficult conditions for the formation of stacks (see Abraham, 1982). In spite of such initial conditions, it is shown that during the simulation, each base pair is transformed into a more favorable stacked configuration. The results obtained allow to observe the whole process of convergence for the first time (for more information, visit the Website http://biophys.in.ua/).     

Stereoselective Covalent Binding of Anti-benzo(a)pyrene Diol Epoxide to DNA Conformation of Enantiomer Adducts

Abstract

The conformation of adducts derived from the reactions and covalent binding of the (+) and (-) enantiomers of 7β, 8α-dihydroxy-9α, 10α-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (anti-BaPDE) with double-stranded calf thymus DNA in vitro were investigated utilizing the electric linear dichroism technique. The linear dichroism and absorption spectra of the covalent DNA complexes are interpreted in terms of a superposition of two types of binding sites. One of these conformations (site I) is a complex in which the plane of the pyrene residue is close to parallel (within 30°) to the planes of the DNA bases (quasi-intercalation), while the other (site II) is an external binding site; this latter type of adduct is attributed to the covalent binding of anti-BaPDE to the exocyclic amino group of deoxyguanine (N2-dG), while site I adducts are attributed to the 06-deoxyguanine and N6-deoxyadenine adducts identified in the product analysis of P. Brookes and M.R. Osborne (Carcinogenesis (1982) 3, 1223–1226). Site II adducts are dominant (~90% in the covalent complexes derived from the (+) enantiomer), but account for only 50±5% of the adducts in the case of the (—)-enantiomer. The orientation of site II complexes is different by 20±10° in the adducts derived from the binding of the (+) and the (—) enantiomers to DNA, the long axis of the pyrene chromophore being oriented more parallel to the axis of the DNA helix in the case of the (+) enantiomer. These findings support the proposals by Brookes and Osborne that the difference in spatial orientation of the N2-dG adducts of (-)-anti-BaPDE together with their lower abundance may account for the lower biological activity of the (—) enantiomer. The external site II adducts, rather than site I adducts, appear to be correlated with the biological activity of these comoounds.     

Enabling stem cell therapies for tissue repair: Current and future challenges

Stem cells embody the tremendous potential of the human body to develop, grow, and repair throughout life. Understanding the biologic mechanisms that underlie stem cell-mediated tissue regeneration is key to harnessing this potential. Recent advances in molecular biology, genetic engineering, and material science have broadened our understanding of stem cells and helped bring them closer to widespread clinical application. Specifically, innovative approaches to optimize how stem cells are identified, isolated, grown, and utilized will help translate these advances into effective clinical therapies. Although there is growing interest in stem cells worldwide, this enthusiasm must be tempered by the fact that these treatments remain for the most part clinically unproven. Future challenges include refining the therapeutic manipulation of stem cells, validating these technologies in randomized clinical trials, and regulating the global expansion of regenerative stem cell therapies.     

Immature and Mature Dengue Serotype 1 Virus Structures Provide Insight into the Maturation Process

Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation.     

Sub-state nationalism in Spain: primers and triggers of identity politics in Catalonia and the Basque Country

This article builds on recent attempts to explain divergent uses of sub-state nationalism to push for policies of assimilation or multiculturalism and drive popular support for independence. It analyses the dynamics of discourses and policies in Spain before, during and after peak times of identity politics to provide a more nuanced understanding of the conditions leading to the activation of identity-driven policies. Substantive ethnographic evidence is presented to explain recent alterations to national discourses of identity, surprising reversals of immigration policies, and the modulation of Catalan and Basque independence movements. The main finding is that both identity discourses and resulting policies depend on the affinity for identity politics at the sub-state level, and this affinity is in large part primed by the popular perception of how secure sub-state national identity is against the ‘official’ state narrative.     

Electrical hypothesis of toxicity of the Cry toxins for mosquito larvae

Many electrical properties of insect larval guts have been studied, but their importance for toxicity of the Cry-type toxins has never been reported in the literature. In the present work, we observed potential-dependent permeabilization of plasma membrane by several polycationic peptides derived from the Cry11Bb protoxin. The peptide BTM-P1d, all D-type amino acid analogue of the earlier reported peptide BTM-P1, demonstrated high membrane-permeabilizing activity in experiments with isolated rat liver mitochondria, RBC (red blood cells) and mitochondria in homogenates of Aedes aegypti larval guts. Two larger peptides, BTM-P2 and BTM-P3, as well as the Cry11Bb protoxin treated with the protease extract of mosquito larval guts showed similar effects. Only protease-resistant BTM-P1d, in comparison with other peptides, displayed A. aegypti larval toxicity. Taking into account the potential-dependent mechanism of membrane permeabilization by studied fragments of the Cry11Bb protoxin and the literature data related to the distribution of membrane and transepithelial potentials in the A. aegypti larval midgut, we suggest an electrical hypothesis of toxicity of the Cry toxins for mosquito larvae. According to this hypothesis, the electrical field distribution is one of the factors determining the midgut region most susceptible for insertion of activated toxins into the plasma membrane to form pores. In addition, potential-dependent penetration of short active toxin fragments into the epithelial cells could induce permeabilization of mitochondria and subsequent apoptosis or necrosis.     

Two new Andean species of Neocorynura (Hymenoptera: Halictidae: Augochlorini) with notes on their biology

We describe and illustrate the male, female, and pupa of two new species of Neocorynura from the Colombian Andes, and provide information on their nesting behavior, host plants and social organization. Nests of Neocorynura iguaquensis sp. nov. Smith‐Pardo & Gonzalez and N. muiscae sp. nov. Smith‐Pardo & Gonzalez were found in flat or vertical banks, and contained one to three adult females. The percentage of multi‐female nests varied considerably from 8.3% to 40% of the total of dissected nests at different times in 2000 and 2003. The ovarian development, wing and mandibular wear of females in the nests with two or more females indicated that they were the offspring that remained in the nest before dispersal or a mother and a newly emerged daughter. Pollen taken from the nest cells and scopae of museum specimens showed that both species rely heavily on pollen of asteraceans and may be active year‐round. Details on the nest architecture and comments on the phylogenetic placement of both species are also provided. Direct observations on the multi‐female nests are required to determine whether or not such nests contain temporary assemblages or truly semisocial colonies.

Resumen

Describimos e ilustramos el macho, hembra y pupa de dos especies nuevas de Neocorynura de los Andes colombianos, y proporcionamos información sobre su biología de nidificación, plantas hospederas y organización social. Los nidos de Neocorynura iguaquensis sp. nov. Smith‐Pardo & Gonzalez y N. muiscae sp. nov. Smith‐Pardo & Gonzalez fueron encontrados en el suelo, en áreas planas o barrancos verticales, y tenían de una a tres hembras adultas. El porcentaje de nidos con más de una hembra varió considerablemente desde 8.3% al 40% del total de nidos disectados a diferentes meses en el año 2000 y 2003. El desarrollo ovárico, desgaste de las alas y mandíbulas de las hembras en los nidos con dos o más hembras indicaron que ellas fueron las crías que permanecieron en el nido antes de dispersarse o una madre con la hija recién nacida. El polen tomado de las celdas de cría y escopas de especimenes de museo mostró que ambas especies dependen principalmente de asteraceas y que podrían estar activas todo el año. También oferecemos detalles de la arquitectura del nidos y comentarios sobre la posición filogenética de ambas especies. Observaciones directas de los nido con más de una hembra son necesarias para determinar si tales nidos son agrupaciones temporales o verdaderas colonias semisociales.     

Structural Changes in Dengue Virus When Exposed to a Temperature of 37°C

Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This was confirmed by our cryo-electron microscopy images of dengue virus incubated at 37°C, where viruses change their surface from smooth to rough. Here we present the cryo-electron microscopy structures of dengue virus at 37°C. Image analysis showed four classes of particles. The three-dimensional (3D) map of one of these classes, representing half of the imaged virus population, shows that the E protein shell has expanded and there is a hole at the 3-fold vertices. Fitting E protein structures into the map suggests that all of the interdimeric and some intradimeric E protein interactions are weakened. The accessibility of some previously found cryptic epitopes on this class of particles is discussed.     

Crystal structure of head-to-head dimers of cholic and deoxycholic acid derivatives with different symmetric bridges

The crystal structure of three head-to-head dimers (having two cholic acid or deoxycholic acid units) linked at carbon atoms C3 by aromatic or alkyl bridges is studied. An internal coordinates system is necessary for describing the relative orientation in the space of the two bile acid residues. Five angles (three torsion and two common ones) are necessary for defining the relative position of both steroid residues in space. Carbon atoms C3 (which always carries a α-hydroxy group in natural bile acids), and C10 and C13 (which always carry β-methyl groups) of each steroid residue are suitable for this purpose. Furthermore, the distance between each C3 carbon atoms of both steroid residues will allow one to locate the steroids in space. The three dimers selected provide a large range of values for these angles. The packing, hydrogen bond network, and location of guest in the three crystals are discussed.