ProViz: protein interaction visualization and exploration

SUMMARY: ProViz is a tool for the visualization of protein-protein interaction networks, developed by the IntAct European project. It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI. AVAILABILITY: ProViz is available under the GPL and may be freely downloaded. Source code and binaries are available at http://cbi.labri.fr/eng/proviz.htm CONTACT: david.sherman@labri.fr     

Connexins and their channels in cell growth and cell death

Direct communication between cells, mediated by gap junctions, is nowadays considered as an indispensable mechanism in the maintenance of cellular homeostasis. In fact, gap junctional intercellular communication is actively involved in virtually all aspects of the cellular life cycle, ranging from cell growth to cell death. For a long time, it was believed that this was merely a result of the capacity of gap junctions to control the direct intercellular exchange of essential cellular messengers. However, recent data show that the picture is more complicated than initially thought, as structural precursors of gap junctions, connexins and gap junction hemichannels, can affect the cellular homeostatic balance independently of gap junctional intercellular communication. In this paper, we summarize the current knowledge concerning the roles of connexins and their channels in the control of cellular homeostasis, with the emphasis on cell growth and cell death. We also briefly discuss the role of gap junctional intercellular communication in carcinogenesis and the potential use of connexins as tools for cancer therapy.     

Nitrogen Behaviour and Nitrous Oxide Emission in the Tidal Seine River Estuary (France) as Influenced by Human Activities in the Upstream Watershed

The Seine River estuary (France) is the receptacle of a drainage basin characterised by high population density, heavy industrial activity and intensive agriculture. Whereas nitrate concentrations are high due to diffuse sources in the upstream drainage basin, ammonium mainly originates from the effluents of the Achères wastewater treatment plant (WWTP) downstream from Paris and its suburbs (6.5 million equivalent-inhabitants). Ammonium is mostly nitrified in the tidal freshwater estuary and nitrification causes a strong summer oxygen deficit. Average longitudinal summer profiles of oxygen and nitrogen concentrations for two periods, between 1993–1997 and 1998–2003 in dry hydrological conditions (excluding the wet years 2000 and 2001) clearly reflect the changes due to the improved treatment of wastewater from Paris and its suburbs. On the basis of daily water flux data and twice monthly nitrogen measurements at the boundaries of the upstream freshwater estuarine section (108 km), we calculated nitrification and denitrification fluxes, whose annual averages were 43 and 71 × 10³ kg N d⁻¹ respectively from 1993 to 2003, with summer values (July–September) representing 73 and 57% of the annual fluxes, respectively. The degree of denitrification in the upper estuary appears to be closely related to the nitrification, itself more loosely related to the amount of reduced nitrogen (Kjeldahl) brought by the treated effluents from the Achères WWTP. We estimated the total N₂O emissions to about 40 kg N d⁻¹ (25–60 kg N d⁻¹) in the same sector.     

Overcoming Electrode‐Induced Losses in Organic Solar Cells by Tailoring a Quasi‐Ohmic Contact to Fullerenes via Solution‐Processed Alkali Hydroxide Layers

It is shown that the performance of inverted organic solar cells can be significantly improved by facilitating the formation of a quasi‐ohmic contact via solution‐processed alkali hydroxide (AOH) interlayers on top of n‐type metal oxide (aluminum zinc oxide, AZO, and zinc oxide, ZnO) layers. AOHs significantly reduce the work function of metal oxides, and are further proven to effectively passivate defect states in these metal oxides. The interfacial energetics of these electron collecting contacts with a prototypical electron acceptor (C₆₀) are investigated to reveal the presence of a large interface dipole and a new interface state between the Fermi energy and the C₆₀ highest occupied molecular orbital for AOH‐modified AZO contacts. These novel interfacial gap states are a result of ground‐state electron transfer from the metal hydroxide‐functionalized AZO contact to the adsorbed molecules, which are hypothesized to be electronically hybridized with the contact. These interface states tail all the way to the Fermi energy, providing for a highly n‐doped (metal‐like) interfacial molecular layer. Furthermore, the strong “light‐soaking” effect is no longer observed in devices with a AOH interface.     

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches

Many studies on phage biology are based on isolation methods that may inadvertently select for narrow-host-range phages. Consequently, broad-host-range phages, whose ecological significance is largely unexplored, are consistently overlooked. To enhance research on such polyvalent phages, we developed two sequential multihost isolation methods and tested both culture-dependent and culture-independent phage libraries for broad infectivity. Lytic phages isolated from activated sludge were capable of interspecies or even interorder infectivity without a significant reduction in the efficiency of plating (0.45 to 1.15). Two polyvalent phages (PX1 of the Podoviridae family and PEf1 of the Siphoviridae family) were characterized in terms of adsorption rate (3.54 × 10⁻¹⁰ to 8.53 × 10⁻¹⁰ ml/min), latent time (40 to 55 min), and burst size (45 to 99 PFU/cell), using different hosts. These phages were enriched with a nonpathogenic host (Pseudomonas putida F1 or Escherichia coli K-12) and subsequently used to infect model problematic bacteria. By using a multiplicity of infection of 10 in bacterial challenge tests, >60% lethality was observed for Pseudomonas aeruginosa relative to uninfected controls. The corresponding lethality for Pseudomonas syringae was ∼50%. Overall, this work suggests that polyvalent phages may be readily isolated from the environment by using different sequential hosts, and this approach should facilitate the study of their ecological significance as well as enable novel applications.     

DIRS1 -like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms

Background  

Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. Considering their mutational abilities, TEs can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. DIRS1 -like retrotransposons are a particular group of retrotransposons according to their mode of transposition that implies a tyrosine recombinase. To date, they have been described in a restricted number of species in comparison with the LTR retrotransposons. In this paper, we determine the distribution of DIRS1 -like elements among 25 decapod species, 10 of them living in hydrothermal vents that correspond to particularly unstable environments.     

RUN and FYVE domain–containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4

Autophagy is a key degradative pathway coordinated by external cues, including starvation, oxidative stress, or pathogen detection. Rare are the molecules known to contribute mechanistically to the regulation of autophagy and expressed specifically in particular environmental contexts or in distinct cell types. Here, we unravel the role of RUN and FYVE domain–containing protein 4 (RUFY4) as a positive molecular regulator of macroautophagy in primary dendritic cells (DCs). We show that exposure to interleukin-4 (IL-4) during DC differentiation enhances autophagy flux through mTORC1 regulation and RUFY4 induction, which in turn actively promote LC3 degradation, Syntaxin 17–positive autophagosome formation, and lysosome tethering. Enhanced autophagy boosts endogenous antigen presentation by MHC II and allows host control of Brucella abortus replication in IL-4–treated DCs and in RUFY4-expressing cells. RUFY4 is therefore the first molecule characterized to date that promotes autophagy and influences endosome dynamics in a subset of immune cells.     

Role of Interaction and Nucleoside Diphosphate Kinase B in Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator Function by cAMP-Dependent Protein Kinase A

Cystic fibrosis results from mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP-dependent protein kinase A (PKA) and ATP-regulated chloride channel. Here, we demonstrate that nucleoside diphosphate kinase B (NDPK-B, NM23-H2) forms a functional complex with CFTR. In airway epithelia forskolin/IBMX significantly increases NDPK-B co-localisation with CFTR whereas PKA inhibitors attenuate complex formation. Furthermore, an NDPK-B derived peptide (but not its NDPK-A equivalent) disrupts the NDPK-B/CFTR complex in vitro (19-mers comprising amino acids 36–54 from NDPK-B or NDPK-A). Overlay (Far-Western) and Surface Plasmon Resonance (SPR) analysis both demonstrate that NDPK-B binds CFTR within its first nucleotide binding domain (NBD1, CFTR amino acids 351–727). Analysis of chloride currents reflective of CFTR or outwardly rectifying chloride channels (ORCC, DIDS-sensitive) showed that the 19-mer NDPK-B peptide (but not its NDPK-A equivalent) reduced both chloride conductances. Additionally, the NDPK-B (but not NDPK-A) peptide also attenuated acetylcholine-induced intestinal short circuit currents. In silico analysis of the NBD1/NDPK-B complex reveals an extended interaction surface between the two proteins. This binding zone is also target of the 19-mer NDPK-B peptide, thus confirming its capability to disrupt NDPK-B/CFTR complex. We propose that NDPK-B forms part of the complex that controls chloride currents in epithelia.     

Identification of target antigens of antiendothelial cell antibodies in healthy individuals: A proteomic approach

In order to identify target antigens of anti-endothelial cell (anti-EC) antibodies (AECA) in healthy individuals, we have used a proteomic approach combining 2-DE and immunoblotting. Whole cell protein extracts obtained from human umbilical vein EC (HUVEC) cultures were used as a source of antigens. Serum IgG from 12 healthy blood donors were tested at a concentration of 200 microg/mL. Targeted spots were identified by MS. The HUVEC proteome was composed of 884 protein spots. Among these, 61 +/- 25.8 (mean +/- SD) spots were recognized by serum IgG from healthy individuals, with marked differences from one individual to another. Among these spots, 11 were recognized by serum IgG from all healthy individuals tested. These spots corresponded to six different proteins with several spots corresponding to different isoforms of the same protein. Target antigens were: cytoskeletal proteins (beta-actin, alpha-tubulin, and vimentin); glycolytic enzymes (glucose-3-phosphate-deshydrogenase and alpha-enolase); and prolyl-4-hydroxylase beta subunit, a member of the disulfide isomerase family. This study shows that the repertoire of IgG AECA is heterogeneous among healthy individuals. IgG from all of the healthy individuals tested recognized a restricted set of highly conserved ubiquitous proteins playing key roles in cell biology and maintenance of homeostasis.     

Strategies of attack and defense in plant–oomycete interactions, accentuated for Phytophthora parasitica Dastur (syn. P. Nicotianae Breda de Haan)

Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to their particular physiological characteristics, no efficient treatments against diseases caused by these microorganisms are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. Available data are scarce, and genomic approaches were mainly developed for the two species, Phytophthora infestans and Phytophthora sojae. However, these two species are exceptions from, rather than representative species for, the genus. P. infestans is a foliar pathogen, and P. sojae infects a narrow range of host plants, while the majority of Phytophthora species are quite unselective, root-infecting pathogens. To represent this majority, Phytophthora parasitica emerges as a model for the genus, and genomic resources for analyzing its interaction with plants are developing. The aim of this review is to assemble current knowledge on cytological and molecular processes that are underlying plant–pathogen interactions involving Phytophthora species and in particular P. parasitica, and to place them into the context of a hypothetical scheme of co-evolution between the pathogen and the host.