Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

BACKGROUND: Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in Pyrococcus using the mammalian two-hybrid system to determine the function of the hypothetical proteins. RESULTS: We examined 960 soluble proteins from Pyrococcus and selected 107 interactions based on luciferase reporter activity, which was then evaluated using a computational approach to assess the reliability of the interactions. We also analyzed the expression of the assay samples by western blot, and a few interactions by in vitro pull-down assays. We identified 11 hetero-interactions that we considered to be located at the same operon, as observed in Helicobacter pylori. We annotated and classified proteins in the selected interactions according to their orthologous proteins. Many enzyme proteins showed self-interactions, similar to those seen in other organisms. CONCLUSION: We found 13 unannotated proteins that interacted with annotated proteins; this information is useful for predicting the functions of the hypothetical Pyrococcus proteins from the annotations of their interacting partners. Among the heterogeneous interactions, proteins were more likely to interact with proteins within the same ortholog class than with proteins of different classes. The analysis described here can provide global insights into the biological features of the protein-protein interactions in P. horikoshii

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Effect of transient expression of fluorescent protein probes in synovial and myoblast cell lines

Here, we investigate the appropriate fluorescent proteins for use in the culture of synovial MH7A and myoblast C2C12 cells. Fluorescent signal intensities of 3 different fluorescent proteins were examined in these cell lines. The fluorescent intensity of transiently expressed AcGFP, DsRed, and mStrawberry were examined in these cell lines, and the influence of the amount of plasmid used on transfection efficiency and cell viability were investigated

Comparison of Arsenate and Molybdate Speciation in Hydrogenetic Ferromanganese Nodules

Marine ferromanganese oxides contain a large amount of trace elements, such as arsenic (As) and molybdenum (Mo). However, the host phases of tetrahedral AsO43- and MoO42- oxyanions therein have not been clearly identified thus far. In this work, we explored the mineralogical components of hydrogenetic (HG) ferromanganese nodules and compared the distribution behaviors of As and Mo. The X-ray diffraction (XRD) and X-ray absorption spectroscopy (XAS) analyses showed that the predominant manganese and iron phases were vernadite (delta-MnO2) and ferrihydrite, respectively. According to the sequential extraction examination, both As and Mo were associated with the iron (oxyhydr)oxide phases. However, the XAS analyses indicated that As was retained by the ferrihydrite phase via double corner-shared complexation, while Mo was preferentially adsorbed on delta-MnO2 via edge-shared complexation. The immobilization of As and Mo by HG ferromanganese samples was attributed to specific chemical binding (Delta G(chem)) rather than Coulombic interaction (Delta G(coul)) as proposed in previous studies. The comparison of Mo XAS spectra before and after extraction revealed the unreliability of the sequential extraction approach to determine the host phase of trace elements as a result of the potential readsorption risk. The different distribution trends of As and Mo were due to their disparate intrinsic properties (e.g., averaged dissociation constants of conjugate acids) and the diverse properties (i.e., surface site densify, adsorption equilibrium constant, and crystalline structure) of ferrihydrite and delta-MnO2. These research findings would be significant for evaluating the geochemical behaviors and environmental fate of trace elements in marine systems