Depinning of a vortex chain in a disordered flow channel

We study depinning of vortex chains in channels formed by static, disordered vortex arrays. Depinning is governed either by the barrier for defect nucleation or for defect motion, depending on whether the chain periodicity is commensurate or incommensurate with the surrounding arrays. We analyze the reduction of the gap between these barriers as function of disorder. At large disorder, commensurability becomes irrelevant and the pinning force is reduced to a small fraction of the ideal shear strength of ordered channels. Implications for experiments on channel devices are discussed.Comment: 5 pages, 4 figures. Accepted for publication in Europhysics Letter

Metastability in Josephson transmission lines

Thermal activation and macroscopic quantum tunneling in current-biased discrete Josephson transmission lines are studied theoretically. The degrees of freedom under consideration are the phases across the junctions which are coupled to each other via the inductances of the system. The resistively shunted junctions that we investigate constitute a system of N interacting degrees of freedom with an overdamped dynamics. We calculate the decay rate within exponential accuracy as a function of temperature and current. Slightly below the critical current, the decay from the metastable state occurs via a unique ("rigid") saddlepoint solution of the Euclidean action describing the simultaneous decay of the phases in all the junctions. When the current is reduced, a crossover to a regime takes place, where the decay occurs via an "elastic" saddlepoint solution and the phases across the junctions leave the metastable state one after another. This leads to an increased decay rate compared with the rigid case both in the thermal and the quantum regime. The rigid-to-elastic crossover can be sharp or smooth analogous to first- or second- order phase transitions, respectively. The various regimes are summarized in a current-temperature decay diagram.Comment: 11 pages, RevTeX, 3 PS-figures, revised versio

Functional Dissection of the Proton Pumping Modules of Mitochondrial Complex I

A catalytically active subcomplex of respiratory chain complex I lacks 14 of its 42 subunits yet retains half of its proton-pumping capacity, indicating that its membrane arm has two pump modules

Crossovers in the thermal decay of metastable states in discrete systems

The thermal decay of linear chains from a metastable state is investigated. A crossover from rigid to elastic decay occurs when the number of particles, the single particle energy barrier or the coupling strength between the particles is varied. In the rigid regime, the single particle energy barrier is small compared to the coupling strength and the decay occurs via a uniform saddlepoint solution, with all degrees of freedom decaying instantly. Increasing the barrier one enters the elastic regime, where the decay is due to bent saddlepoint configurations using the elasticity of the chain to lower their activation energy. Close to the rigid-to-elastic crossover, nucleation occurs at the boundaries of the system. However, in large systems, a second crossover from boundary to bulk nucleation can be found within the elastic regime, when the single particle energy barrier is further increased. We compute the decay rate in the rigid and in the elastic regimes within the Gaussian approximation. Around the rigid-to-elastic crossover, the calculations are performed beyond the steepest descent approximation. In this region, the prefactor exhibits a scaling property. The theoretical results are discussed in the context of discrete Josephson transmission lines and pancake vortex stacks that are pinned by columnar defects.Comment: 13 pages, RevTeX, 7 PS-figure

Global gene disruption in human cells to assign genes to phenotypes

Insertional mutagenesis in a haploid background can disrupt gene function[superscript 1]. We extend our earlier work by using a retroviral gene-trap vector to generate insertions in >98% of the genes expressed in a human cancer cell line that is haploid for all but one of its chromosomes. We apply phenotypic interrogation via tag sequencing (PhITSeq) to examine millions of mutant alleles through selection and parallel sequencing. Analysis of pools of cells, rather than individual clones[superscript 1] enables rapid assessment of the spectrum of genes involved in the phenotypes under study. This facilitates comparative screens as illustrated here for the family of cytolethal distending toxins (CDTs). CDTs are virulence factors secreted by a variety of pathogenic Gram-negative bacteria responsible for tissue damage at distinct anatomical sites[superscript 2]. We identify 743 mutations distributed over 12 human genes important for intoxication by four different CDTs. Although related CDTs may share host factors, they also exploit unique host factors to yield a profile characteristic for each CDT

Transport of Anthocyanins and other Flavonoids by the Arabidopsis ATP-Binding Cassette Transporter AtABCC2

Flavonoids have important developmental, physiological, and ecological roles in plants and are primarily stored in the large central vacuole. Here we show that both an ATP-binding cassette (ABC) transporter(s) and an H+-antiporter(s) are involved in the uptake of cyanidin 3-O-glucoside (C3G) by Arabidopsis vacuolar membrane-enriched vesicles. We also demonstrate that vesicles isolated from yeast expressing the ABC protein AtABCC2 are capable of MgATP-dependent uptake of C3G and other anthocyanins. The uptake of C3G by AtABCC2 depended on the co-transport of glutathione (GSH). C3G was not altered during transport and a GSH conjugate was not formed. Vesicles from yeast expressing AtABCC2 also transported flavone and flavonol glucosides. We performed ligand docking studies to a homology model of AtABCC2 and probed the putative binding sites of C3G and GSH through site-directed mutagenesis and functional studies. These studies identified residues important for substrate recognition and transport activity in AtABCC2, and suggest that C3G and GSH bind closely, mutually enhancing each other’s binding. In conclusion, we suggest that AtABCC2 along with possibly other ABCC proteins are involved in the vacuolar transport of anthocyanins and other flavonoids in the vegetative tissue of Arabidopsis

Reduction of Hydrophilic Ubiquinones by the Flavin in Mitochondrial NADH:Ubiquinone Oxidoreductase (Complex I) and Production of Reactive Oxygen Species†

ABSTRACT: NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a complicated, energy-transducing, membrane-bound enzyme that contains 45 different subunits, a non-covalently bound flavin mononucleotide, and eight iron-sulfur clusters. The mechanisms of NADH oxidation and intramolecular electron transfer by complex I are gradually being defined, but the mechanism linking ubiquinone reduction to proton translocation remains unknown. Studies of ubiquinone reduction by isolated complex I are problematic because the extremely hydrophobic natural substrate, ubiquinone-10, must be substituted with a relatively hydrophilic analogue (such as ubiquinone-1). Hydrophilic ubiquinones are reduced by an additional, non-energy-transducing pathway (which is insensitive to inhibitors such as rotenone and piericidin A). Here, we show that inhibitor-insensitive ubiquinone reduction occurs by a ping-pong type mechanism, catalyzed by the flavin mononucleotide cofactor in the active site for NADH oxidation. Moreover, semiquinones produced at the flavin site initiate redox cycling reactions with molecular oxygen, producing superoxide radicals and hydrogen peroxide. The ubiquinone reactant is regenerated, so the NADH:Q reaction becomes superstoichiometric. Idebenone, an artificial ubiquinone showing promise in the treatment of Friedreich’s Ataxia, reacts at the flavin site. The factors which determine the balance of reactivity between the two sites of ubiquinone reduction (the energy-transducing site and the flavi

Extracellular and Luminal pH Regulation by Vacuolar H⁺-ATPase Isoform Expression and Targeting to the Plasma Membrane and Endosomes

Plasma membrane vacuolar H+ -ATPase (pm-V-ATPase) activity of tumor cells is a major factor in control of cytoplasmic and extracellular pH and metastatic potential, but the isoforms involved and the factors governing plasma membrane recruitment remain uncertain. Here, we examined expression, distribution and activity of V- ATPase isoforms in invasive prostate adenocarcinoma (PC-3) cells. Isoforms 1 and 3 were the most highly expressed forms of membrane subunit a, with a1 and a3 the dominant plasma membrane isoforms. Correlation between pm-V-ATPase activity and invasiveness was limited, but RNAi knockdown of either a isoform did slow cell proliferation and inhibit invasion in vitro. Isoform a1 was recruited to the cell surface from the early endosome/recycling complex pathway, its knockdown arresting transferrin receptor (TfR) recycling. Isoform a3 was associated with the late endosomal/lysosomal compartment. Both a isoforms associated with accessory protein Ac45, knockdown of which stalled transit of a1 and Tf-TfR, decreased proton efflux and reduced cell growth and invasiveness, this latter effect at least partly due to decreased delivery of the membrane-bound matrix metalloproteinase MMP-14 to the plasma membrane. These data indicate that in prostatic carcinoma cells, a1 and a3 isoform populations predominate in different compartments where they maintain different luminal pH. Ac45 plays a central role in navigating the V-ATPase to the plasma membrane, and hence is an important factor in expression of the invasive phenotype