First-principles investigation of spin polarized conductance in atomic carbon wire

We analyze spin-dependent energetics and conductance for one dimensional (1D) atomic carbon wires consisting of terminal magnetic (Co) and interior nonmagnetic (C) atoms sandwiched between gold electrodes, obtained employing first-principles gradient corrected density functional theory and Landauer's formalism for conductance. Wires containing an even number of interior carbon atoms are found to be acetylenic with sigma-pi bonding patterns, while cumulene structures are seen in wires containing odd number of interior carbon atoms, as a result of strong pi-conjugation. Ground states of carbon wires containing up to 13 C atoms are found to have anti-parallel spin configurations of the two terminal Co atoms, while the 14 C wire has a parallel Co spin configuration in the ground state. The stability of the anti-ferromagnetic state in the wires is ascribed to a super-exchange effect. For the cumulenic wires this effect is constant for all wire lengths. For the acetylenic wires, the super-exchange effect diminishes as the wire length increases, going to zero for the atomic wire containing 14 carbon atoms. Conductance calculations at the zero bias limit show spin-valve behavior, with the parallel Co spin configuration state giving higher conductance than the corresponding anti-parallel state, and a non-monotonic variation of conductance with the length of the wires for both spin configurations.Comment: revtex, 6 pages, 5 figure

Degree Landscapes in Scale-Free Networks

We generalize the degree-organizational view of real-world networks with broad degree-distributions in a landscape analogue with mountains (high-degree nodes) and valleys (low-degree nodes). For example, correlated degrees between adjacent nodes corresponds to smooth landscapes (social networks), hierarchical networks to one-mountain landscapes (the Internet), and degree-disassortative networks without hierarchical features to rough landscapes with several mountains. We also generate ridge landscapes to model networks organized under constraints imposed by the space the networks are embedded in, associated to spatial or, in molecular networks, to functional localization. To quantify the topology, we here measure the widths of the mountains and the separation between different mountains.Comment: 4 pages, 5 figure

Antigens in human glioblastomas and meningiomas: Search for tumour and onco-foetal antigens. Estimation of S-100 and GFA protein.

Extracts of glioblastomas and meningiomas were analysed by quantitative immunoelectrophoresis for the presence of foetal brain antigens and tumour-associated antigens, and levels of 2 normal brain-specific proteins were also determined. The following antibodies were used: monospecific anti-S-100 (glia specific); monospecific anti-GFA (glial fibrillary acidic protein), (astroglia specific); polyspecific anti-foetal brain (12-16th week of gestation); a polyspecific anti-glioblastoma antiserum, absorbed with insolubilized serum, haemolysate and normal brain extract; polyspecific anti-alpha-foetoprotein; and monospecific anti-ferritin. Using the antibodies raised against the tumours, several antigens not present in foetal or adult normal brain were found in the glioblastomas and the meningiomas. These antigens cross-reacted with antigens present in normal liver and were therefore not tumour-associated. S-100 was found in glioblastomas in approximately one tenth the amount in whole brain homogenate, whereas GFA was found 2-4 times enriched. The 2 proteins were absent in meningiomas. The possible use of the GFA protein as a marker for astroglial neoplasia is discussed. Five foetal antigens were found in foetal brain, but none in the tumours. alpha-Foetoprotein could only be demonstrated in foetal tissue extracts, including foetal brain, but not in tumours. Ferritin was detected in all tumour extracts, although the amounts determined were unrelated to histological tumour type

Updates in Rhea-a manually curated resource of biochemical reactions.

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models

Role of post-translational modifications at the β-subunit ectodomain in complex association with a promiscuous plant P4-ATPase.

P-type ATPases of subfamily IV (P4-ATPases) constitute a major group of phospholipid flippases that form heteromeric complexes with members of the Cdc50 (cell division control 50) protein family. Some P4-ATPases interact specifically with only one β-subunit isoform, whereas others are promiscuous and can interact with several isoforms. In the present study, we used a site-directed mutagenesis approach to assess the role of post-translational modifications at the plant ALIS5 β-subunit ectodomain in the functionality of the promiscuous plant P4-ATPase ALA2. We identified two N-glycosylated residues, Asn(181) and Asn(231) Whereas mutation of Asn(231) seems to have a small effect on P4-ATPase complex formation, mutation of evolutionarily conserved Asn(181) disrupts interaction between the two subunits. Of the four cysteine residues located in the ALIS5 ectodomain, mutation of Cys(86) and Cys(107) compromises complex association, but the mutant β-subunits still promote complex trafficking and activity to some extent. In contrast, disruption of a conserved disulfide bond between Cys(158) and Cys(172) has no effect on the P4-ATPase complex. Our results demonstrate that post-translational modifications in the β-subunit have different functional roles in different organisms, which may be related to the promiscuity of the P4-ATPase

A functional calcium-transporting ATPase encoded by chlorella viruses

Calcium-transporting ATPases (Ca2+ pumps) are major players in maintaining calcium homeostasis in the cell and have been detected in all cellular organisms. Here, we report the identification of two putative Ca2+ pumps, M535L and C785L, encoded by chlorella viruses MT325 and AR158, respectively, and the functional characterization of M535L. Phylogenetic and sequence analyses place the viral proteins in group IIB of P-type ATPases even though they lack a typical feature of this class, a calmodulin-binding domain. A Ca2+ pump gene is present in 45 of 47 viruses tested and is transcribed during virus infection. Complementation analysis of the triple yeast mutant K616 confirmed that M535L transports calcium ions and, unusually for group IIB pumps, also manganese ions. In vitro assays show basal ATPase activity. This activity is inhibited by vanadate, but, unlike that of other Ca2+ pumps, is not significantly stimulated by either calcium or manganese. The enzyme forms a 32P-phosphorylated intermediate, which is inhibited by vanadate and not stimulated by the transported substrate Ca2+, thus confirming the peculiar properties of this viral pump. To our knowledge this is the first report of a functional P-type Ca2+-transporting ATPase encoded by a virus