DAPPER: a data-mining resource for protein-protein interactions.

BACKGROUND: The identification of interaction networks between proteins and complexes holds the promise of offering novel insights into the molecular mechanisms that regulate many biological processes. With increasing volumes of such datasets, especially in model organisms such as Drosophila melanogaster, there exists a pressing need for specialised tools, which can seamlessly collect, integrate and analyse these data. Here we describe a database coupled with a mining tool for protein-protein interactions (DAPPER), developed as a rich resource for studying multi-protein complexes in Drosophila melanogaster. RESULTS: This proteomics database is compiled through mass spectrometric analyses of many protein complexes affinity purified from Drosophila tissues and cultured cells. The web access to DAPPER is provided via an accelerated version of BioMart software enabling data-mining through customised querying and output formats. The protein-protein interaction dataset is annotated with FlyBase identifiers, and further linked to the Ensembl database using BioMart's data-federation model, thereby enabling complex multi-dataset queries. DAPPER is open source, with all its contents and source code are freely available. CONCLUSIONS: DAPPER offers an easy-to-navigate and extensible platform for real-time integration of diverse resources containing new and existing protein-protein interaction datasets of Drosophila melanogaster.This work was supported financially by grants from the Cancer Research UK (CRUK), the Biotechnology and Biological Sciences Research Council and the Medical Research Council to DMG (C3/A11431, BB/I013938/1, G1001696), by a Cancer Research UK Career Development Fellowship to YK (C40697/A12874), and by Cancer Research UK grants to PPD (C12296/A8039 and C12296/A12541). ZL is on leave from the Biological Research Centre of the Hungarian Academy of Sciences (Institute of Biochemistry, Szeged, Hungary) and was supported by a Long-Term Fellowship of the Federation of European Biochemical Societies (FEBS)

Quantum oscillations in a centrosymmetric skyrmion-hosting magnet GdRu2Si2

We have performed magnetic torque and resistivity measurements on a centrosymmetric skyrmion-host GdRu2Si2, in which the dominant magnetic interaction leading to skyrmion formation is under debate. We observe both the de Haas-van Alphen and Shubnikov-de Haas oscillations in the forced ferromagnetic phase. The angular dependence of the quantum oscillation frequencies can be reproduced by the ab-initio calculation. The de Haas-van Alphen oscillation is also observed in the double-Q phase with a different frequency to that in the forced ferromagnetic phase, indicating a Fermi surface reconstruction due to the coupling between localized spins and conduction electrons. Based on these experimental findings, the magnetic interactions in this system are discussed.Comment: 11 pages, 8 figure

Urinary biomarker concentrations of captan, chlormequat, chlorpyrifos and cypermethrin in UK adults and children living near agricultural land

There is limited information on the exposure to pesticides experienced by UK residents living near agricultural land. This study aimed to investigate their pesticide exposure in relation to spray events. Farmers treating crops with captan, chlormequat, chlorpyrifos or cypermethrin provided spray event information. Adults and children residing ≤100 m from sprayed fields provided first-morning void urine samples during and outwith the spray season. Selected samples (1–2 days after a spray event and at other times (background samples)) were analysed and creatinine adjusted. Generalised Linear Mixed Models were used to investigate if urinary biomarkers of these pesticides were elevated after spray events. The final data set for statistical analysis contained 1518 urine samples from 140 participants, consisting of 523 spray event and 995 background samples which were analysed for pesticide urinary biomarkers. For captan and cypermethrin, the proportion of values below the limit of detection was greater than 80%, with no difference between spray event and background samples. For chlormequat and chlorpyrifos, the geometric mean urinary biomarker concentrations following spray events were 15.4 μg/g creatinine and 2.5 μg/g creatinine, respectively, compared with 16.5 μg/g creatinine and 3.0 μg/g creatinine for background samples within the spraying season. Outwith the spraying season, concentrations for chlorpyrifos were the same as those within spraying season backgrounds, but for chlormequat, lower concentrations were observed outwith the spraying season (12.3 μg/g creatinine). Overall, we observed no evidence indicative of additional urinary pesticide biomarker excretion as a result of spray events, suggesting that sources other than local spraying are responsible for the relatively low urinary pesticide biomarkers detected in the study population

Adaptability and phenotypic stability of resistance to two viral diseases and yields traits in Cassava

Cassava productivity is hampered by pests and diseases including cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). The main objective of this study was to identify stable superior genotypes that combine disease re-sistance and high yield. Sixteen cassava genotypes were planted in a randomized complete block design with three replications for six planting seasons (years) at five sites in Tanzania. The genotypes were assessed using the additive main effect and multiplicative interaction (AMMI) analysis, and highly significant

Local structure evolution in polycrystalline Zn1−x_{1-x}Mgx_xO (0≤x≤0.150\leq{x}\leq{0.15}) studied by Raman and by synchrotron x-ray pair distribution analysis

The local structures of Zn$_{1-x}$Mg$_x$O alloys have been studied by Raman spectroscopy and by synchrotron x-ray pair distribution function (PDF) analysis. Within the solid solution range ($0\leq{x}\leq{0.15}$) of Zn$_{1-x}$Mg$_x$O, the wurtzite framework is maintained with Mg homogeneously distributed throughout the wurtzite lattice. The $E_2^\mathrm{high}$ Raman line of Zn$_{1-x}$Mg$_x$O displays systematic changes in response to the evolution of the crystal lattice upon the Mg-substitution. The red-shift and broadening of the $E_2^\mathrm{high}$ mode are explained by the expansion of hexagonal $ab$-dimensions, and compositional disorder of Zn/Mg, respectively. Synchrotron x-ray PDF analyses of Zn$_{1-x}$Mg$_x$O reveal that the Mg atoms have a slightly reduced wurtzite parameter $u$ and more regular tetrahedral bond distances than the Zn atoms. For both Zn and Mg, the internal tetrahedral geometries are independent of the alloy composition.Comment: 10 pages, 12 figures RevTe

1,3-Diphenyl-4,5-dihydro-1H-pyrazol-5-one

In the title pyrazolone derivative, C15H12N2O, the five-membered ring is approximately planar (r.m.s. deviation = 0.018 Å), and the N- and C-bound benzene rings are inclined to this plane [dihedral angles = 21.45 (10) and 6.96 (10)°, respectively] and form a dihedral angle of 20.42 (10)° with each other. Supra­molecular layers are formed in the crystal structure via C—H⋯O and C—H⋯N inter­actions, and these are assembled into double layers by C—H⋯π and π–π inter­actions between the pyrazole and C-bound benzene rings [ring centroid–centroid distance = 3.6476 (12) Å]. The double layers stack along the a axis being connected by π–π inter­actions between the N- and C-bound benzene rings [ring centroid–centroid distance = 3.7718 (12) Å]

Modulation of the virus-receptor interaction by mutations in the V5 loop of feline immunodeficiency virus (FIV) following in vivo escape from neutralising antibody

<b>BACKGROUND:</b> In the acute phase of infection with feline immunodeficiency virus (FIV), the virus targets activated CD4+ T cells by utilising CD134 (OX40) as a primary attachment receptor and CXCR4 as a co-receptor. The nature of the virus-receptor interaction varies between isolates; strains such as GL8 and CPGammer recognise a "complex" determinant on CD134 formed by cysteine-rich domains (CRDs) 1 and 2 of the molecule while strains such as PPR and B2542 require a more "simple" determinant comprising CRD1 only for infection. These differences in receptor recognition manifest as variations in sensitivity to receptor antagonists. In this study, we ask whether the nature of the virus-receptor interaction evolves in vivo.<p></p> <b>RESULTS:</b> Following infection with a homogeneous viral population derived from a pathogenic molecular clone, a quasispecies emerged comprising variants with distinct sensitivities to neutralising antibody and displaying evidence of conversion from a "complex" to a "simple" interaction with CD134. Escape from neutralising antibody was mediated primarily by length and sequence polymorphisms in the V5 region of Env, and these alterations in V5 modulated the virus-receptor interaction as indicated by altered sensitivities to antagonism by both anti-CD134 antibody and soluble CD134.<p></p> <b>CONCLUSIONS:</b> The FIV-receptor interaction evolves under the selective pressure of the host humoral immune response, and the V5 loop contributes to the virus-receptor interaction. Our data are consistent with a model whereby viruses with distinct biological properties are present in early versus late infection and with a shift from a "complex" to a "simple" interaction with CD134 with time post-infection.<p></p&gt

BiP Binding to the ER-Stress Sensor Ire1 Tunes the Homeostatic Behavior of the Unfolded Protein Response

Computational modeling and experimentation in the unfolded protein response reveals a role for the ER-resident chaperone protein BiP in fine-tuning the system's response dynamics

PARP16 is a tail-anchored endoplasmic reticulum protein required for the PERK- and IRE1α-mediated unfolded protein response

Poly(ADP-ribose) polymerases (PARPs; also known as ADP-ribosyl transferase D proteins) modify acceptor proteins with ADP-ribose modifications of varying length (reviewed in refs 1, 2, 3). PARPs regulate key stress response pathways, including DNA damage repair and the cytoplasmic stress response. Here, we show that PARPs also regulate the unfolded protein response (UPR) of the endoplasmic reticulum (ER). Human PARP16 (also known as ARTD15) is a tail-anchored ER transmembrane protein required for activation of the functionally related ER stress sensors PERK and IRE1α during the UPR. The third identified ER stress sensor, ATF6, is not regulated by PARP16. As is the case for other PARPs that function during stress, the enzymatic activity of PARP16 is upregulated during ER stress when it ADP-ribosylates itself, PERK and IRE1α. ADP-ribosylation by PARP16 is sufficient for activating PERK and IRE1α in the absence of ER stress, and is required for PERK and IRE1α activation during the UPR. Modification of PERK and IRE1α by PARP16 increases their kinase activities and the endonuclease activity of IRE1α. Interestingly, the carboxy-terminal luminal tail of PARP16 is required for PARP16 function during ER stress, suggesting that it transduces stress signals to the cytoplasmic PARP catalytic domain.National Cancer Institute (U.S.) (Cancer Center Support Core Grant P30-CA14051)National Institutes of Health (U.S.) (Grant 5R01 GM087465-02)Kathy and Curt Marble Cancer Research FundJeptha H. and Emily V. Wade FundVirginia and D.K. Ludwig Fund for Cancer Researc