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Search Results: 1 - 10 of 39 matches for " Anastassia Pogoutse "
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NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction
Alex N Nguyen Ba, Anastassia Pogoutse, Nicholas Provart, Alan M Moses
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-202
Abstract: In this paper, we present an analysis of characterized NLSs in yeast, and find, despite the large number of nuclear import pathways, that NLSs seem to show similar patterns of amino acid residues. We test current prediction methods and observe a low true positive rate. We therefore suggest an approach using hidden Markov models (HMMs) to predict novel NLSs in proteins. We show that our method is able to consistently find 37% of the NLSs with a low false positive rate and that our method retains its true positive rate outside of the yeast data set used for the training parameters.Our implementation of this model, NLStradamus, is made available at: http://www.moseslab.csb.utoronto.ca/NLStradamus/ webciteEukaryotic cells are defined by the presence of their nucleus. The nuclear membrane enclosing the genetic material of the cell is selective in its import of material through its nuclear pores and this translocation is mediated by cellular mechanisms [1,2].Proteins entering the nucleus must do so through proteins forming the nuclear pores: the nuclear pore complex [3,4]. The pores allow the passive diffusion of small proteins, but bigger proteins entering the nucleus are usually bound by karyopherin complexes on their nuclear localization signal [5]. Although there are many nuclear import pathways in eukaryotic cells, most of these have not been characterized in detail. The best understood is the classical NLS pathway. The recognition of classical NLSs on nuclear proteins is done by the importin-α subunit which in turn is recognized by the importin-β subunit. This trimer (cargo, importin-α and importin-β) is then imported to the nucleus after series of enzymatic steps [1,6]. Other families of NLSs are independent of importin-α, and may bind directly to one of the members of the importin-β superfamily [1].Classical NLSs show characteristic patterns of basic residues loosely matching two consensus sequences, K(K/R)X(K/R) and KRX10–12KRXK, termed the 'monopartite' and 'bip
Democratization, Europeanization and Regionalization beyond the European Union: Search for Empirical Evidence
Obydenkova,Anastassia
European Integration Online Papers , 2006,
Abstract: This paper gives a viewpoint on a controversial issue of transnational regional cooperation (TRC) in Eurasia covering the analysis of cooperation between Europe and the regions of Russia. By promoting the favorable regime of transnational regional cooperation, both sides become more effective in managing such common problems as mutual security, political, economic and environmental challenges; illegal immigration; drug- and human-trafficking; etc. What is needed for the successful development of TRC in Eurasian context? What factors make a crucial impact on the development of regional cooperation, whether it is further "inclusion" or "exclusion" of the regions from cooperation with European neighbors? Is it the geopolitical location of the regions that makes regional cooperation more feasible or are there other factors that influence the success of this process? How might the regulatory and administrative tools of central government facilitate or complicate this process? To answer these questions, the study attempts to re-conceptualize the theories of integration, Europeanization, and regionalism. Then, it addresses the role of ethnicity, economical development, and geopolitical factors in the establishment and development of transnational regional cooperation. It also investigates the importance of "domestic-policy factors" (reforms in the federal governments) in the development of TRC.
Democratization, Europeanization and Regionalization beyond the European Union: Search for Empirical Evidence
Anastassia Obydenkova
European Integration Online Papers , 2006,
Abstract: This paper gives a viewpoint on a controversial issue of transnational regional cooperation (TRC) in Eurasia covering the analysis of cooperation between Europe and the regions of Russia. By promoting the favorable regime of transnational regional cooperation, both sides become more effective in managing such common problems as mutual security, political, economic and environmental challenges; illegal immigration; drug- and human-trafficking; etc. What is needed for the successful development of TRC in Eurasian context? What factors make a crucial impact on the development of regional cooperation, whether it is further "inclusion" or "exclusion" of the regions from cooperation with European neighbors? Is it the geopolitical location of the regions that makes regional cooperation more feasible or are there other factors that influence the success of this process? How might the regulatory and administrative tools of central government facilitate or complicate this process? To answer these questions, the study attempts to re-conceptualize the theories of integration, Europeanization, and regionalism. Then, it addresses the role of ethnicity, economical development, and geopolitical factors in the establishment and development of transnational regional cooperation. It also investigates the importance of "domestic-policy factors" (reforms in the federal governments) in the development of TRC.
La construction sociale de l’altérité en Grèce
Anastassia Tsoukala
Cahiers Balkaniques , 2011,
Abstract: L'état grec, à ses débuts, s'est appuyé sur une identité collective mythique qui a subi de graves traumatismes et doit aujourd'hui se reconstruire.La création de l’état grec moderne s’est appuyée sur une identité collective mythique, qui s’articulait autour d’une société prétendument homogène sur le plan démographique, d’une population éparpillée en dehors des frontières du pays qu’il convenait d’y intégrer en menant des guerres irrédentistes, et d’une continuité historique ininterrompue depuis l’Antiquité. L’arrivée massive des réfugiés grecs en 1922 a mis en rude épreuve cette identité nationale. Alors que l’état leur a immédiatement accordé des droits civiques, la majorité de la société leur a réservé un accueil hostile qui les a rapidement marginalisés. Un nouveau déchirement suivit, la guerre civile (1949), or, tout au long de sa durée et surtout une fois terminée, cette guerre fut niée, ou réduite à la seule figure du communiste manipulateur–manipulé qui permettait d’apporter des réponses réconfortantes à des questions douloureuses sur le plan politique, social et démographique du pays. Préserver cette image de la menace communiste a, donc, impliqué l’imposition du silence. Sa remise en question, récente, est-elle aussi en voie de construction. The Modern Greek state was created on the basis of a collective, mythical identity. This identity was predicated upon an allegedly homogeneous population scattered well beyond the borders of the country, with all its irredentist aspirations, and upon an imagined historical continuity that was uninterrupted since Antiquity. The massive arrival of Greek refugees in 1922 put this national identity severely to the test. Whereas the state immediately granted them civil rights, they were not welcomed by most of Greek society, which promptly marginalised them. A new rupture followed in the form of the Civil War (1949). In the course of this conflict, and more especially afterwards, the war was denied, or reduced to the lone figure of the communist—at once manipulator and manipulated—which made it possible to give comforting answers to the country's painful political, social and demographic questions. Preserving this image of the communist threat therefore necessitated silence—a silence only recently broken.
Local-Global principles for certain images of Galois representations
Anastassia Etropolski
Mathematics , 2015,
Abstract: Let $K$ be a number field and let $E/K$ be an elliptic curve whose mod $\ell$ Galois representation locally has image contained in a group $G$, up to conjugacy. We classify the possible images for the global Galois representation in the case where $G$ is a Cartan subgroup or the normalizer of a Cartan subgroup. When $K = \mathbf{Q}$, we deduce a counterexample to the local-global principle in the case where $G$ is the normalizer of a split Cartan and $\ell = 13$. In particular, there are at least three elliptic curves (up to twist) over $\mathbf{Q}$ whose mod $13$ image of Galois is locally contained in the normalizer of a split Cartan, but whose global image is not.
Er81 is a downstream target of Pax6 in cortical progenitors
Tran Tuoc, Anastassia Stoykova
BMC Developmental Biology , 2008, DOI: 10.1186/1471-213x-8-23
Abstract: We identified and analyzed the regulatory function of an evolutionarily conserved upstream DNA sequence in the putative mouse Er81 promoter. Three potential Pax6 binding sites were identified in this region. We found that the presence of one of these sites is necessary and sufficient for full activation of the Er81 promoter in Pax6-transfected HeLa cells, while other still unknown factors appear to contribute to Er81 promoter activity in cortical progenitors and neuronal cells. The results suggest that endogenous Pax6, which is expressed at the highest level in progenitors of the rostrolateral cortex, exerts region-specific control of Er81 activity, thus specifying a subpopulation of layer 5 projection neurons.We conclude that the genetic interplay between the transcription factors, Pax6 and Er81, is responsible, in part, for the regional specification of a distinct sublineage of layer 5 projection neurons.In the mammalian neocortex (pallium), neurons with striking morphological and functional diversity are organized radially in six layers, and tangentially into numerous functional domains. Only recently have the molecular and cellular mechanisms that guide the process of corticogenesis responsible for this organization begun to be resolved [1,2]. The main source of cortical projection neurons is the population of pluripotent radial glial progenitors (RG), which divide asymmetrically at the apical surface of the ventricular zone (VZ) and generate both neuronal and glial progeny [3]. After midgestation, RG generate neuronal progenitors, termed intermediate or basal progenitors (BPs), that divide symmetrically at the basal surface of the VZ and in the subventricular zone (SVZ). Thus, while the asymmetric division of RG progenitors gives rise to progeny with distinct cell fates, the symmetric division of BPs primarily modulates the number of cells in previously established neuronal cell lineages [4]. The projection neurons of the lower (6 and 5) and upper (4–2) layers
Structures of Li-Doped Alkali Clusters are Dictated by AO-Hybridization
Anastassia N. Alexandrova
Physics , 2012,
Abstract: Hybridization of atomic orbitals is a widely appreciated phenomenon whose impact on the structure and properties of, for example, organic molecules is well-established. Here, we demonstrate that hybridization also dramatically impacts the shapes of small alkali metal clusters. The seemingly similar and valence-iso-electronic LiNa4- and LiK4- clusters adopt very different global minimum structures: LiNa4- is a planar C2v (1A1) species distorted from the perfect pentagon due to the pseudo Jahn-Teller effect, and LiK4- is a planar square D4h (1A1g) species with Li being in the centre. This effect is rooted in the different degrees of the 2s-2p hybridization in Li in response to binding to Na versus K. Li inside the Na cluster exhibits a strong 2s-2p mixing, to achieve stronger covalent bonding. In contrast, Li inside of the K cluster does not show any hybridization, and the LiK4- cluster is reminiscent of an ionic salt. These differences are tied to the relative electronegativities of Li, Na, and K, and overlap of the valence atomic orbitals of Li with those of Na versus those of K. Atomic orbital hybridization is thus a pronounced effect in clusters, the understanding of which is important for the use of clusters in material science or catalysis, and designing clusters of desired shapes.
Plan for VLBI observations of close approaches of Jupiter to compact extragalactic radio sources in 2014-2016
Anastassia Girdiuk,Oleg Titov
Physics , 2013,
Abstract: Very Long Baseline Interferometry is capable of measuring the gravitational delay caused by the Sun and planet gravitational fields. The post-Newtonian parameter $\gamma$ is now estimated with accuracy of $\sigma_{\gamma}=2\cdot 10^{-4}$ using a global set of VLBI data from 1979 to present (Lambert, Gontier, 2009), and $\sigma_{\gamma}=2\cdot10^{-5}$ by the Cassini spacecraft (Bertotti et. al, 2003). Unfortunately, VLBI observations in S- and X-bands very close to the Solar limb (less than 2-3 degrees) are not possible due to the strong turbulence in the Solar corona. Instead, the close approach of big planets to the line of sight of the reference quasars could be also used for testing of the general relativity theory with VLBI. Jupiter is the most appropriate among the big planets due to its large mass and relatively fast apparent motion across the celestial sphere. Six close approaches of Jupiter with quasars in 2014-2016 were found using the DE405/LE405 ephemerides, including one occultation in 2016. We have formed tables of visibility for all six events for VLBI radio telescopes participating in regular IVS programs. Expected magnitudes of the relativistic effects to be measured during these events are discussed in this paper.
How Metal Substitution Affects the Enzymatic Activity of Catechol-O-Methyltransferase
Manuel Sparta, Anastassia N. Alexandrova
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047172
Abstract: Catechol-O-methyltransferase (COMT) degrades catecholamines, such as dopamine and epinephrine, by methylating them in the presence of a divalent metal cation (usually Mg(II)), and S-adenosyl-L-methionine. The enzymatic activity of COMT is known to be vitally dependent on the nature of the bound metal: replacement of Mg(II) with Ca(II) leads to a complete deactivation of COMT; Fe(II) is slightly less than potent Mg(II), and Fe(III) is again an inhibitor. Considering the fairly modest role that the metal plays in the catalyzed reaction, this dependence is puzzling, and to date remains an enigma. Using a quantum mechanical / molecular mechanical dynamics method for extensive sampling of protein structure, and first principle quantum mechanical calculations for the subsequent mechanistic study, we explicate the effect of metal substitution on the rate determining step in the catalytic cycle of COMT, the methyl transfer. In full accord with experimental data, Mg(II) bound to COMT is the most potent of the studied cations and it is closely followed by Fe(II), whereas Fe(III) is unable to promote catalysis. In the case of Ca(II), a repacking of the protein binding site is observed, leading to a significant increase in the activation barrier and higher energy of reaction. Importantly, the origin of the effect of metal substitution is different for different metals: for Fe(III) it is the electronic effect, whereas in the case of Ca(II) it is instead the effect of suboptimal protein structure.
Structure, stability, and mobility of small Pd clusters on the stoichiometric and defective TiO$_2$ (110) surfaces
Jin Zhang,Anastassia N. Alexandrova
Physics , 2011, DOI: 10.1063/1.3657833
Abstract: We report on the structure and adsorption properties of Pd$_n$ ($n=1-4$) clusters supported on the rutile TiO$_2$ (110) surfaces with the possible presence of a surface oxygen vacancy or a subsurface Ti-interstitial atom. As predicted by the density functional theory, small Pd clusters prefer to bind to the stoichiometric titania surface or at sites near subsurface Ti-interstitial atoms. The adsorption of Pd clusters changes the electronic structure of the underlying surface. For the surface with an oxygen vacancy, the charge localization and ferromagnetic spin states are found to be largely attenuated owing to the adsorption of Pd clusters. The potential energy surfaces of the Pd monomer on different types of surfaces are also reported. The process of sintering is then simulated via the Metropolis Monte Carlo method. The presence of oxygen vacancy likely leads to the dissociation of Pd clusters. On the stoichiometric surface or surface with Ti-interstitial atom, the Pd monomers tend to sinter into larger clusters, whereas the Pd dimer, trimer and tetramer appear to be relatively stable below 600 K. This result agrees with the standard sintering model of transition metal clusters and experimental observations.
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