SDSS-FIRST-selected interacting galaxies: Optical long-slit spectroscopy study using MODS at the LBT

Context. In the hierarchical model of evolution of the Universe, galaxy mergers play an important role, especially at high redshifts. Interactions among galaxies appear to be associated with incidences of radio-loudness in quasars and it is of interest to study the galaxies that are in the process of interacting with each other, where there is at least one nucleus that is active in the radio regime. Aims. In order to understand the various processes taking place within colliding galaxies, it is important to study the radio and optical properties of these sources, as well as any possible correlations that might exist. Methods. To this end, we present optical long-slit spectroscopy data for ten pairs of interacting galaxies selected from SDSS-FIRST at redshifts of ~0.05, observed using the multi-object double spectrographs at the Large Binocular Telescope. Results. We used line fluxes extracted from the spectra of the nuclear regions of galaxies to plot optical diagnostic diagrams and estimate the masses of the central supermassive black holes, as well as their Eddington ratios. Additionally, we used previously published Effelsberg radio telescope data at 4.85 GHz and FIRST survey data at 1.4 GHz to estimate radio spectral slopes and the radio-loudness parameters for all of the radio-detected sources. We also used WISE data to plot a mid-infrared colour-colour diagram. Conclusions. We see that while the sample of galaxies covers all of the classes on the optical diagnostic diagrams, the sources that are radio-detected fall in the composite or transition region of the diagram. Additionally, we notice a trend of the highest radio-loudness parameter in a pair of interacting galaxies being associated with the galaxy that hosts the more massive central supermassive black hole. We do not see any obvious trends with respect to the radio spectral slope, radio-loudness parameter, and Eddington ratio. With respect to the mid-infrared data of the galaxies detected by WISE, we see that most of them have some type of contribution from star formation, however, two of them seem to have a significant contribution from an AGN as well

Charge Transfer from Regularized Symmetry-Adapted Perturbation Theory

16 pages, 16 figure

Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields

Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (<i>A</i>/<i>r</i>¹²) or Born–Mayer (<i>A</i> exp­(−<i>Br</i>)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater–ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born–Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born–Mayer functional form while still retaining many of the advantages of the Slater-ISA approach

Distributed Multipoles from a Robust Basis-Space Implementation of the Iterated Stockholder Atoms Procedure

The recently developed iterated stockholder atoms (ISA) approach of Lillestolen and Wheatley (<i>Chem. Commun.</i> <b>2008</b>, 5909) offers a powerful method for defining atoms in a molecule. However, the real-space algorithm is known to converge very slowly, if at all. Here, we present a robust, basis-space algorithm of the ISA method and demonstrate its applicability on a variety of systems. We show that this algorithm exhibits rapid convergence (taking around 10–80 iterations) with the number of iterations needed being unrelated to the system size or basis set used. Further, we show that the multipole moments calculated using this basis-space ISA method are as good as, or better than, those obtained from Stone’s distributed multipole analysis (<i>J. Chem. Theory Comput.</i> <b>2005</b>, <i>1</i>, 1128), exhibiting better convergence properties and resulting in better behaved penetration energies. This can have significant consequences in the development of intermolecular interaction models

Controlled In Meso Phase Crystallization – A Method for the Structural Investigation of Membrane Proteins

We investigated in meso crystallization of membrane proteins to develop a fast screening technology which combines features of the well established classical vapor diffusion experiment with the batch meso phase crystallization, but without premixing of protein and monoolein. It inherits the advantages of both methods, namely (i) the stabilization of membrane proteins in the meso phase, (ii) the control of hydration level and additive concentration by vapor diffusion. The new technology (iii) significantly simplifies in meso crystallization experiments and allows the use of standard liquid handling robots suitable for 96 well formats. CIMP crystallization furthermore allows (iv) direct monitoring of phase transformation and crystallization events. Bacteriorhodopsin (BR) crystals of high quality and diffraction up to 1.3 Å resolution have been obtained in this approach. CIMP and the developed consumables and protocols have been successfully applied to obtain crystals of sensory rhodopsin II (SRII) from Halobacterium salinarum for the first time

Crystallizing membrane proteins using lipidic mesophases

peer-reviewedThis paper was obtained through PEER (Publishing and the Ecology of European Research) http://www.peerproject.euA detailed protocol for crystallizing membrane proteins that makes use of lipidic mesophases is described. This has variously been referred to as the lipid cubic phase or in meso method. The method has been shown to be quite general in that it has been used to solve X-ray crystallographic structures of prokaryotic and eukaryotic proteins, proteins that are monomeric, homo- and hetero-multimeric, chromophore-containing and chromophore-free, and α-helical and β-barrel proteins. Its most recent successes are the human engineered β2-adrenergic and adenosine A2A G protein-coupled receptors. Protocols are provided for preparing and characterizing the lipidic mesophase, for reconstituting the protein into the monoolein-based mesophase, for functional assay of the protein in the mesophase, and for setting up crystallizations in manual mode. Methods for harvesting micro-crystals are also described. The time required to prepare the protein-loaded mesophase and to set up a crystallization plate manually is about one hour

Data submission and curation for caArray, a standard based microarray data repository system

caArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG&#x2122;), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge. caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG&#x2122;. &#xd;&#xa;&#xd;&#xa;Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the MAGE-TAB, a spreadsheet-based format for annotating and communicating microarray data in a MIAME-compliant fashion (&#x22;http://www.mged.org/mage-tab&#x22;:http://www.mged.org/mage-tab). MAGE-TAB is built on community standards &#x2013; MAGE, MIAME, and Ontology. The components and work flow of MAGE-TAB files are organized in such a way which is already familiar to bench scientists and thus minimize the time and frustration of reorganizing their data before submission. The MAGE-TAB files are also structured to be machine readable so that they can be easily parsed into database. Users can control public access to experiment- and sample-level data and can create collaboration groups to support data exchange among a defined set of partners. &#xd;&#xa;&#xd;&#xa;All data submitted to caArray at NCI will go through strict curation by a group of scientists against these standards to make sure that the data are correctly annotated using proper controlled vocabulary terms and all required information are provided. Two of mostly used ontology sources are MGED ontology (&#x22;http://mged.sourceforge.net/ontologies/MGEDontology.php&#x22;:http://mged.sourceforge.net/ontologies/MGEDontology.php) and NCI thesaurus (&#x22;http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do&#x22;:http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). The purpose of data curation is to ensure easy comparison of results from different labs and unambiguous report of results. &#xd;&#xa;&#xd;&#xa;Data will also undergo automatic validation process before parsed into database, in which minimum information requirement and data consistency with the array designs are checked. Files with error found during validation are flagged with error message. Curators will re-examine those files and make necessary corrections before re-load the files. The iteration repeats until files are validated successfully. Data are then imported into the system and ready for access through the portal or through API. Interested parties are encouraged to review the installation package, documentation, and source code available from &#x22;http://caarray.nci.nih.gov&#x22;:http://caarray.nci.nih.gov

Monoolein Lipid Phases as Incorporation and Enrichment Materials for Membrane Protein Crystallization

The crystallization of membrane proteins in amphiphile-rich materials such as lipidic cubic phases is an established methodology in many structural biology laboratories. The standard procedure employed with this methodology requires the generation of a highly viscous lipidic material by mixing lipid, for instance monoolein, with a solution of the detergent solubilized membrane protein. This preparation is often carried out with specialized mixing tools that allow handling of the highly viscous materials while minimizing dead volume to save precious membrane protein sample. The processes that occur during the initial mixing of the lipid with the membrane protein are not well understood. Here we show that the formation of the lipidic phases and the incorporation of the membrane protein into such materials can be separated experimentally. Specifically, we have investigated the effect of different initial monoolein-based lipid phase states on the crystallization behavior of the colored photosynthetic reaction center from Rhodobacter sphaeroides. We find that the detergent solubilized photosynthetic reaction center spontaneously inserts into and concentrates in the lipid matrix without any mixing, and that the initial lipid material phase state is irrelevant for productive crystallization. A substantial in-situ enrichment of the membrane protein to concentration levels that are otherwise unobtainable occurs in a thin layer on the surface of the lipidic material. These results have important practical applications and hence we suggest a simplified protocol for membrane protein crystallization within amphiphile rich materials, eliminating any specialized mixing tools to prepare crystallization experiments within lipidic cubic phases. Furthermore, by virtue of sampling a membrane protein concentration gradient within a single crystallization experiment, this crystallization technique is more robust and increases the efficiency of identifying productive crystallization parameters. Finally, we provide a model that explains the incorporation of the membrane protein from solution into the lipid phase via a portal lamellar phase

Dissecting mitosis by RNAi in Drosophila tissue culture cells

Here we describe a detailed methodology to study the function of genes whose products function during mitosis by dsRNA-mediated interference (RNAi) in cultured cells of Drosophila melanogaster. This procedure is particularly useful for the analysis of genes for which genetic mutations are not available or for the dissection of complicated phenotypes derived from the analysis of such mutants. With the advent of whole genome sequencing it is expected that RNAi-based screenings will be one method of choice for the identification and study of novel genes involved in particular cellular processes. In this paper we focused particularly on the procedures for the proper phenotypic analysis of cells after RNAi-mediated depletion of proteins required for mitosis, the process by which the genetic information is segregated equally between daughter cells. We use RNAi of the microtubule-associated protein MAST/Orbit as an example for the usefulness of the technique

[(18)F] fluoromisonidazole and [(18)F] fluorodeoxyglucose positron emission tomography in response evaluation after chemo-/radiotherapy of non-small-cell lung cancer: a feasibility study

BACKGROUND: Experimental and clinical evidence suggest that hypoxia in solid tumours reduces their sensitivity to conventional treatment modalities modulating response to ionizing radiation or chemotherapeutic agents. The aim of the present study was to show the feasibility of determining radiotherapeutically relevant hypoxia and early tumour response by ([(18)F] Fluoromisonidazole (FMISO) and [(18)F]-2-fluoro-2'-deoxyglucose (FDG) PET. METHODS: Eight patients with non-small-cell lung cancer underwent PET scans. Tumour tissue oxygenation was measured with FMISO PET, whereas tumour glucose metabolism was measured with FDG PET. All PET studies were carried out with an ECAT EXACT 922/47(® )scanner with an axial field of view of 16.2 cm. FMISO PET consisted of one static scan of the relevant region, performed 180 min after intravenous administration of the tracer. The acquisition and reconstruction parameters were as follows: 30 min emission scanning and 4 min transmission scanning with 68-Ge/68-Ga rod sources. The patients were treated with chemotherapy, consisting of 2 cycles of gemcitabine (1200 mg/m(2)) and vinorelbine (30 mg/m(2)) followed by concurrent radio- (2.0 Gy/d; total dose 66.0 Gy) and chemotherapy with gemcitabine (300–500 mg/m(2)) every two weeks. FMISO PET and FDG PET were performed in all patients 3 days before and 14 days after finishing chemotherapy. RESULTS: FMISO PET allowed for the qualitative and quantitative definition of hypoxic sub-areas which may correspond to a localization of local recurrences. In addition, changes in FMISO and FDG PET measure the early response to therapy, and in this way, may predict freedom from disease, as well as overall survival. CONCLUSION: These preliminary results warrant validation in larger trials. If confirmed, several novel treatment strategies may be considered, including the early use of PET to evaluate the effectiveness of the selected therapy