Neuronal K-Cl Cotransporter : Transcriptional Mechanisms of KCC2 Gene Regulation

K-Cl cotransporter 2 (KCC2) maintains a low intracellular Cl concentration required for fast hyperpolarizing responses of neurons to classical inhibitory neurotransmitters γ-aminobutyric acid (GABA) and glycine. Decreased Cl extrusion observed in genetically modified KCC2-deficient mice leads to depolarizing GABA responses, impaired brain inhibition, and as a consequence to epileptic seizures. Identification of mechanisms regulating activity of the SLC12A5 gene, which encodes the KCC2 cotransporter, in normal and pathological conditions is, thus, of extreme importance. Multiple reports have previously elucidated in details a spatio-temporal pattern of KCC2 expression. Among the characteristic features are an exclusive neuronal specificity, a dramatic upregulation during embryonic and early postnatal development, and a significant downregulation by neuronal trauma. Numerous studies confirmed these expressional features, however transcriptional mechanisms predetermining the SLC12A5 gene behaviour are still unknown. The aim of the presented thesis is to recognize such transcriptional mechanisms and, on their basis, to create a transcriptional model that would explain the established SLC12A5 gene behaviour. Up to recently, only one KCC2 transcript has been thought to exist. A particular novelty of the presented work is the identification of two SLC12A5 gene promoters (SLC12A5-1a and SLC12A5-1b) that produce at least two KCC2 isoforms (KCC2a and KCC2b) differing by their N-terminal parts. Even though a functional 86Rb+ assay reveals no significant difference between transport activities of the isoforms, consensus sites for several protein kinases, found in KCC2a but not in KCC2b, imply a distinct kinetic regulation. As a logical continuation, the current work presents a detailed analysis of the KCC2a and KCC2b expression patterns. This analysis shows an exclusively neuron-specific pattern and similar expression levels for both isoforms during embryonic and neonatal development in rodents. During subsequent postnatal development, the KCC2b expression dramatically increases, while KCC2a expression, depending on central nervous system (CNS) area, either remains at the same level or moderately decreases. In an attempt to explain both the neuronal specificity and the distinct expressional kinetics of the KCC2a and KCC2b isoforms during postnatal development, the corresponding SLC12A5-1a and SLC12A5-1b promoters have been subjected to a comprehensive bioinformatical analysis. Binding sites of several transcription factors (TFs), conserved in the mammalian SLC12A5 gene orthologs, have been identified that might shed light on the observed behaviour of the SLC12A5 gene. Possible roles of these TFs in the regulating of the SLC12A5 gene expression have been elucidated in subsequent experiments and are discussed in the current thesis.

Evaluating viewpoint entropy for ribbon representation of protein structure

While many measures of viewpoint goodness have been proposed in computer graphics, none have been evaluated for ribbon representations of protein secondary structure. To fill this gap, we conducted a user study on Amazon’s Mechanical Turk platform, collecting human viewpoint preferences from 65 participants for 4 representative su- perfamilies of protein domains. In particular, we evaluated viewpoint entropy, which was previously shown to be a good predictor for human viewpoint preference of other, mostly non-abstract objects. In a second study, we asked 7 molecular biology experts to find the best viewpoint of the same protein domains and compared their choices with viewpoint entropy. Our results show that viewpoint entropy overall is a significant predictor of human viewpoint preference for ribbon representations of protein secondary structure. However, the accuracy is highly dependent on the complexity of the structure: while most participants agree on good viewpoints for small, non-globular structures with few secondary structure elements, viewpoint preference varies considerably for complex structures. Finally, experts tend to choose viewpoints of both low and high viewpoint entropy to emphasize different aspects of the respective structure.

RF Sputtered Er2O3 Thin Films as High-k Gate Dielectrics for Germanium MOS Devices

We report the material and electrical properties of Erbium Oxide (Er2O3) thin films grown on n-Ge (100) by RF sputtering. The properties of the films are correlated with the processing conditions. The structural characterization reveals that the films annealed at 550 degrees C, has densified as compared to the as-grown ones. Fixed oxide charges and interface charges, both of the order of 10(13)/cm(2) is observed.

Soft gluon k(t)-resummation and the Froissart bound

We study soft gluon k(t)-resurnmation and the relevance of InfraRed (IR) gluons for the energy dependence of total hadronic cross-sections. In our model, consistency with the Froissart bound is directly related to the ansatz that the IR behaviour of the QCD coupling constant follows an inverse power law.

On the Structure of Contractible Edges in k-connected Partial k-trees

Contraction of an edge e merges its end points into a new single vertex, and each neighbor of one of the end points of e is a neighbor of the new vertex. An edge in a k-connected graph is contractible if its contraction does not result in a graph with lesser connectivity; otherwise the edge is called non-contractible. In this paper, we present results on the structure of contractible edges in k-trees and k-connected partial k-trees. Firstly, we show that an edge e in a k-tree is contractible if and only if e belongs to exactly one (k + 1) clique. We use this characterization to show that the graph formed by contractible edges is a 2-connected graph. We also show that there are at least |V(G)| + k - 2 contractible edges in a k-tree. Secondly, we show that if an edge e in a partial k-tree is contractible then e is contractible in any k-tree which contains the partial k-tree as an edge subgraph. We also construct a class of contraction critical 2k-connected partial 2k-trees.

Two-level k-means clustering algorithm for k-tau relationship establishment and linear-time classification

Partitional clustering algorithms, which partition the dataset into a pre-defined number of clusters, can be broadly classified into two types: algorithms which explicitly take the number of clusters as input and algorithms that take the expected size of a cluster as input. In this paper, we propose a variant of the k-means algorithm and prove that it is more efficient than standard k-means algorithms. An important contribution of this paper is the establishment of a relation between the number of clusters and the size of the clusters in a dataset through the analysis of our algorithm. We also demonstrate that the integration of this algorithm as a pre-processing step in classification algorithms reduces their running-time complexity.

Studies on diamond-like carbon and novel diamond-like carbon polymer hybrid coatings deposited with filtered pulsed arc discharge method

The main obstacle for the application of high quality diamond-like carbon (DLC) coatings has been the lack of adhesion to the substrate as the coating thickness is increased. The aim of this study was to improve the filtered pulsed arc discharge (FPAD) method. With this method it is possible to achieve high DLC coating thicknesses necessary for practical applications. The energy of the carbon ions was measured with an optoelectronic time-of-flight method. An in situ cathode polishing system used for stabilizing the process yield and the carbon ion energies is presented. Simultaneously the quality of the coatings can be controlled. To optimise the quality of the deposition process a simple, fast and inexpensive method using silicon wafers as test substrates was developed. This method was used for evaluating the suitability of a simplified arc-discharge set-up for the deposition of the adhesion layer of DLC coatings. A whole new group of materials discovered by our research group, the diamond-like carbon polymer hybrid (DLC-p-h) coatings, is also presented. The parent polymers used in these novel coatings were polydimethylsiloxane (PDMS) and polytetrafluoroethylene (PTFE). The energy of the plasma ions was found to increase when the anode-cathode distance and the arc voltage were increased. A constant deposition rate for continuous coating runs was obtained with an in situ cathode polishing system. The novel DLC-p-h coatings were found to be water and oil repellent and harder than any polymers. The lowest sliding angle ever measured from a solid surface, 0.15 ± 0.03°, was measured on a DLC-PDMS-h coating. In the FPAD system carbon ions can be accelerated to high energies (≈ 1 keV) necessary for the optimal adhesion (the substrate is broken in the adhesion and quality test) of ultra thick (up to 200 µm) DLC coatings by increasing the anode-cathode distance and using high voltages (up to 4 kV). An excellent adhesion can also be obtained with the simplified arc-discharge device. To maintain high process yield (5µm/h over a surface area of 150 cm2) and to stabilize the carbon ion energies and the high quality (sp3 fraction up to 85%) of the resulting coating, an in situ cathode polishing system must be used. DLC-PDMS-h coating is the superior candidate coating material for anti-soiling applications where also hardness is required.

Evaluation of polymeric nanomedicines targeted to PSMA: Effect of ligand on targeting efficiency

Targeted nanomedicines offer a strategy for greatly enhancing accumulation of a therapeutic within a specific tissue in animals. In this study, we report on the comparative targeting efficiency toward prostate-specific membrane antigen (PSMA) of a number of different ligands that are covalently attached by the same chemistry to a polymeric nanocarrier. The targeting ligands included a small molecule (glutamate urea), a peptide ligand, and a monoclonal antibody (J591). A hyperbranched polymer (HBP) was utilized as the nanocarrier and contained a fluorophore for tracking/analysis, whereas the pendant functional chain-ends provided a handle for ligand conjugation. Targeting efficiency of each ligand was assessed in vitro using flow cytometry and confocal microscopy to compare degree of binding and internalization of the HBPs by human prostate cancer (PCa) cell lines with different PSMA expression status (PC3-PIP (PSMA+) and PC3-FLU (PSMA−). The peptide ligand was further investigated in vivo, in which BALB/c nude mice bearing subcutaneous PC3-PIP and PC3-FLU PCa tumors were injected intravenously with the HBP-peptide conjugate and assessed by fluorescence imaging. Enhanced accumulation in the tumor tissue of PC3-PIP compared to PC3-FLU highlighted the applicability of this system as a future imaging and therapeutic delivery vehicle.

A note on the Hadwiger number of circular arc graphs

The intention of this note is to motivate the researchers to study Hadwiger's conjecture for circular arc graphs. Let η(G) denote the largest clique minor of a graph G, and let χ(G) denote its chromatic number. Hadwiger's conjecture states that η(G)greater-or-equal, slantedχ(G) and is one of the most important and difficult open problems in graph theory. From the point of view of researchers who are sceptical of the validity of the conjecture, it is interesting to study the conjecture for graph classes where η(G) is guaranteed not to grow too fast with respect to χ(G), since such classes of graphs are indeed a reasonable place to look for possible counterexamples. We show that in any circular arc graph G, η(G)less-than-or-equals, slant2χ(G)−1, and there is a family with equality. So, it makes sense to study Hadwiger's conjecture for this family.

DMT of Multi-hop Cooperative Networks-Part I: K-Parallel-Path Networks

We consider single-source, single-sink multi-hop relay networks, with slow-fading Rayleigh fading links and single-antenna relay nodes operating under the half-duplex constraint. While two hop relay networks have been studied in great detail in terms of the diversity-multiplexing tradeoff (DMT), few results are available for more general networks. In this two-part paper, we identify two families of networks that are multi-hop generalizations of the two hop network: K-Parallel-Path (KPP) networks and Layered networks. In the first part, we initially consider KPP networks, which can be viewed as the union of K node-disjoint parallel paths, each of length > 1. The results are then generalized to KPP(I) networks, which permit interference between paths and to KPP(D) networks, which possess a direct link from source to sink. We characterize the optimal DMT of KPP(D) networks with K >= 4, and KPP(I) networks with K >= 3. Along the way, we derive lower bounds for the DMT of triangular channel matrices, which are useful in DMT computation of various protocols. As a special case, the DMT of two-hop relay network without direct link is obtained. Two key implications of the results in the two-part paper are that the half-duplex constraint does not necessarily entail rate loss by a factor of two, as previously believed and that, simple AF protocols are often sufficient to attain the best possible DMT.

Phase diagram of the system Ca-Ti-O at 1200 K

Phase relations in the system Ca-Ti-O have been established by equilibration of several samples at 1200 K for prolonged periods and identification of phases in quenched samples by optical and scanning electron microscopy, XRD and EDS. Samples representing 20 compositions in the ternary system were analyzed. There was negligible solid solubility of Ca in the phases along the binary Ti-O, and of Ti in CaO. Four ternary oxides were identified: CaTiO3, Ca4Ti3O10 and Ca3Ti2O7 containing tetravalent titanium, and CaTi2O4 containing trivalent titanium. Tie-lines link calcium titanite (CaTi2O4) with the three calcium titanates (CaTiO3, Ca4Ti3O10 and Ca3Ti2O7), CaO, oxygen excess TiO1+delta and stoichiometric TiO. Tie-lines connect CaTiO3 with TiO2-x, Magneli phases TinO2n-1 (28 >= n >= 4), Ti3O5, Ti2O3 and TiO1+delta. CaO was found to coexist with TiO, and Ti-O solid solutions alpha and beta. The phase diagram is useful for understanding the mechanisms and kinetics of direct calciothermic reduction of TiO2 to metal and electrochemical reduction of TiO2 using graphite anode and molten CaCl2 electrolyte.

Avian diversification patterns across the K-Pg boundary: Influence of calibrations, datasets, and model misspecification

Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.

Thermodynamic activities in the Pb(Zr1-XTiX)O-3 solid solution at 1373 K

Although Pb(Zr1-XTiX)O-3 solid solution is the cornerstone of the piezoelectric ceramics, there is no information in the literature on thermodynamic activities of the component phases in the solid solution. Using inter-crystalline ion exchange equilibria between Pb(Zr1-XTiX)O-3 solid solution with cubic perovskite structure and (Zr1-YTiY)O-2 solid solutions with monoclinic and tetragonal structures, activities of PbTiO3 and PbZrO3 in the perovskite solid solution have been derived at 1373 K using the modified Gibbs-Duhem integration technique of Jacob and Jeffes. Tie-lines from the cubic solid solution are skewed towards the ZrO2 corner. Activities in the zirconia-rich (Zr1-YTiY)02 solid solutions are taken from a recent emf study. The results for the perovskite solid solution at 1373 K can be represented by a sub-regular solution model: Delta G(E.M) (J mol(-1)) = X-PbTiO3 X-PbZrO3(5280X(PbTiO3) - 1980X(PbZrO3)) where Delta G(E.M) is the excess Gibbs energy of mixing of the cubic solid solution and Xi represents the mole fraction of component i. There is a significant positive deviation from ideality for PbTiO3-rich compositions and mild negative deviation near the PbZrO3 corner. The cubic solid solution is intrinsically stable against composition fluctuations at temperatures down to 840 K. The results contrast sharply with the recent calorimetric data on enthalpy of mixing which signal instability of the cubic perovskite solid solution. (C) 2007 Elsevier B.V. All rights reserved.