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Sample records for cleave complex clustered

  1. Photoinduced release of Zn2+ with ZinCleav-1: a nitrobenzyl-based caged complex.

    PubMed

    Bandara, H M Dhammika; Kennedy, Daniel P; Akin, Elif; Incarvito, Christopher D; Burdette, Shawn C

    2009-09-07

    Caged complexes are metal ion chelators that release analytes when exposed to light of a specific wavelength. The synthesis and properties of ZinCleav-1, a cage for Zn(2+) that fragments upon photolysis, is reported. The general uncaging strategy involves integrating a nitrobenzyl group on the backbone of the ligand so that a carbon-heteroatom bond is cleaved by the photoreaction. The caged complex was obtained using a new synthetic strategy involving a Strecker synthesis to prepare a key aldehyde intermediate. ZinCleav-1 has a K(d) of 0.23 pM for Zn(2+) as measured by competitive titration with [Zn(PAR)(2)] (PAR = 4-(2-pyridyl-2-azo) resorcinol). The quantum yield for ZinCleav-1 is 2.4% and 0.55% for the apo and Zn(2+) complex, respectively. The ability of ZinCleav-1 to increase free [Zn(2+)] is calculated theoretically using the binding constants for the uncaged photoproducts, and demonstrated practically by using a fluorescent sensor to image the liberated Zn(2+). Free Zn(2+) may function as a neurotransmitter and have a role in the pathology of several neurological diseases. Studying these physiological functions remains challenging because Zn(2+) is silent to most common spectroscopic techniques. We expect ZinCleav-1 to be the first in a class of caged complexes that will facilitate biological investigations.

  2. In situ investigation of the mobility of small gold clusters on cleaved MgO surfaces

    NASA Technical Reports Server (NTRS)

    Metois, J. J.; Heinemann, K.; Poppa, H.

    1976-01-01

    The mobility of small clusters of gold (about 10 A in diameter) on electron-beam-cleaved MgO surfaces was studied by in situ transmission electron microscopy under controlled vacuum and temperature conditions. During the first 10 min following a deposition at room temperature, over 10 per cent of the crystallites moved over short distances (about 20 A) discontinuously, with a velocity greater than 150 A/sec. Eighty per cent of the mobility events were characterized by the avoidance of proximity of other crystallites, and this was tentatively explained as the result of repulsive elastic forces between the interacting crystallites.

  3. Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERα in complex with synthetic ligands

    SciTech Connect

    Cura, Vincent; Gangloff, Monique; Eiler, Sylvia; Moras, Dino; Ruff, Marc

    2008-01-01

    A new crystallization strategy: the presence of cleaved thioredoxin fusion is critical for crystallization of the estrogen nuclear receptor ligand binding domain in complex with synthetic ligands. This novel technique should be regarded as an interesting alternative for crystallization of difficult proteins. The ligand-binding domain (LBD) of human oestrogen receptor α was produced in Escherichia coli as a cleavable thioredoxin (Trx) fusion in order to improve solubility. Crystallization trials with either cleaved and purified LBD or with the purified fusion protein both failed to produce crystals. In another attempt, Trx was not removed from the LBD after endoproteolytic cleavage and its presence promoted nucleation and subsequent crystal growth, which allowed the structure determination of two different LBD–ligand–coactivator peptide complexes at 2.3 Å resolution. This technique is likely to be applicable to other low-solubility proteins.

  4. Micro-ultrasonic cleaving of cell clusters by laser-generated focused ultrasound and its mechanisms

    PubMed Central

    Baac, Hyoung Won; Lee, Taehwa; Guo, L. Jay

    2013-01-01

    Laser-generated focused ultrasound (LGFU) is a unique modality that can produce single-pulsed cavitation and strong local disturbances on a tight focal spot (<100 μm). We utilize LGFU as a non-contact, non-thermal, high-precision tool to fractionate and cleave cell clusters cultured on glass substrates. Fractionation processes are investigated in detail, which confirms distinct cell behaviors in the focal center and the periphery of LGFU spot. For better understanding of local disturbances under LGFU, we use a high-speed laser-flash shadowgraphy technique and then fully visualize instantaneous microscopic processes from the ultrasound wave focusing to the micro-bubble collapse. Based on these visual evidences, we discuss possible mechanisms responsible for the focal and peripheral disruptions, such as a liquid jet-induced wall shear stress and shock emissions due to bubble collapse. The ultrasonic micro-fractionation is readily available for in vitro cell patterning and harvesting. Moreover, it is significant as a preliminary step towards high-precision surgery applications in future. PMID:24010006

  5. Effective DNA binding and cleaving tendencies of malonic acid coupled transition metal complexes

    NASA Astrophysics Data System (ADS)

    Pravin, Narayanaperumal; Utthra, Ponnukalai Ponya; Kumaravel, Ganesan; Raman, Natarajan

    2016-11-01

    Eight transition metal complexes were designed to achieve maximum biological efficacy. They were characterized by elemental analysis and various other spectroscopic techniques. The monomeric complexes were found to espouse octahedral geometry and non-electrolytic nature. The DNA interaction propensity of the complexes with calf thymus DNA (CT-DNA), studied at physiological pH by spectrophotometric, spectrofluorometric, cyclic voltammetry, and viscometric techniques revealed intercalation as the possible binding mode. Fascinatingly, the complexes were found to exhibit greater binding strength than that of the free ligands. A strong hypochromism and a slight red shift were exhibited by complex 5 among the other complexes. The intrinsic binding constant values of all the complexes compared to cisplatin reveal that they are excellent metallonucleases than that of cisplatin. The complexes were also shown to reveal displacement of the ethidium bromide, a strong intercalator using fluorescence titrations. Gel electrophoresis was used to divulge the competence of the complexes in cleaving the supercoiled pBR322 plasmid DNA. From the results, it is concluded that the complexes, especially 5, are excellent chemical nucleases in the presence of H2O2. Furthermore, the in vitro antimicrobial screening of the complexes exposes that these complexes are excellent antimicrobial agents. Overall the effect of coligands is evident from the results of all the investigations.

  6. Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERα in complex with synthetic ligands

    PubMed Central

    Cura, Vincent; Gangloff, Monique; Eiler, Sylvia; Moras, Dino; Ruff, Marc

    2008-01-01

    The ligand-binding domain (LBD) of human oestrogen receptor α was produced in Escherichia coli as a cleavable thioredoxin (Trx) fusion in order to improve solubility. Crystallization trials with either cleaved and purified LBD or with the purified fusion protein both failed to produce crystals. In another attempt, Trx was not removed from the LBD after endoproteolytic cleavage and its presence promoted nucleation and subsequent crystal growth, which allowed the structure determination of two different LBD–ligand–coactivator peptide complexes at 2.3 Å resolution. This technique is likely to be applicable to other low-solubility proteins. PMID:18097104

  7. Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERalpha in complex with synthetic ligands.

    PubMed

    Cura, Vincent; Gangloff, Monique; Eiler, Sylvia; Moras, Dino; Ruff, Marc

    2008-01-01

    The ligand-binding domain (LBD) of human oestrogen receptor alpha was produced in Escherichia coli as a cleavable thioredoxin (Trx) fusion in order to improve solubility. Crystallization trials with either cleaved and purified LBD or with the purified fusion protein both failed to produce crystals. In another attempt, Trx was not removed from the LBD after endoproteolytic cleavage and its presence promoted nucleation and subsequent crystal growth, which allowed the structure determination of two different LBD-ligand-coactivator peptide complexes at 2.3 A resolution. This technique is likely to be applicable to other low-solubility proteins.

  8. DNA clustering and genome complexity.

    PubMed

    Dios, Francisco; Barturen, Guillermo; Lebrón, Ricardo; Rueda, Antonio; Hackenberg, Michael; Oliver, José L

    2014-12-01

    Early global measures of genome complexity (power spectra, the analysis of fluctuations in DNA walks or compositional segmentation) uncovered a high degree of complexity in eukaryotic genome sequences. The main evolutionary mechanisms leading to increases in genome complexity (i.e. gene duplication and transposon proliferation) can all potentially produce increases in DNA clustering. To quantify such clustering and provide a genome-wide description of the formed clusters, we developed GenomeCluster, an algorithm able to detect clusters of whatever genome element identified by chromosome coordinates. We obtained a detailed description of clusters for ten categories of human genome elements, including functional (genes, exons, introns), regulatory (CpG islands, TFBSs, enhancers), variant (SNPs) and repeat (Alus, LINE1) elements, as well as DNase hypersensitivity sites. For each category, we located their clusters in the human genome, then quantifying cluster length and composition, and estimated the clustering level as the proportion of clustered genome elements. In average, we found a 27% of elements in clusters, although a considerable variation occurs among different categories. Genes form the lowest number of clusters, but these are the longest ones, both in bp and the average number of components, while the shortest clusters are formed by SNPs. Functional and regulatory elements (genes, CpG islands, TFBSs, enhancers) show the highest clustering level, as compared to DNase sites, repeats (Alus, LINE1) or SNPs. Many of the genome elements we analyzed are known to be composed of clusters of low-level entities. In addition, we found here that the clusters generated by GenomeCluster can be in turn clustered into high-level super-clusters. The observation of 'clusters-within-clusters' parallels the 'domains within domains' phenomenon previously detected through global statistical methods in eukaryotic sequences, and reveals a complex human genome landscape dominated

  9. Formation of Cluster Complexes by Cluster-Cluster-Collisions

    NASA Astrophysics Data System (ADS)

    Ichihashi, Masahiko; Odaka, Hideho

    2015-03-01

    Multi-element clusters are interested in their chemical and physical properties, and it is expected that they are utilized as catalysts, for example. Their properties critically depend on the size, composition and atomic ordering, and it should be important to adjust the above parameters for their functionality. One of the ways to form a multi-element cluster is to employ a low-energy collision between clusters. Here, we show characteristic results obtained in the collision between a neutral Ar cluster and a size-selected Co cluster ion. Low-energy collision experiment was accomplished by using a newly developed merging-beam apparatus. Cobalt cluster ions were produced by laser ablation, and mass-selected. On the other hand, argon clusters were prepared by the supersonic expansion of Ar gas. Both cluster beams were merged together in an ion guide, and ionic cluster complexes were mass-analyzed. In the collision of Co2+ and ArN, Co2Arn+ (n = 1 - 30) were observed, and the total intensity of Co2Arn+ (n >= 1) is inversely proportional to the relative velocity between Co2+ and ArN. This suggests that the charge-induced dipole interaction between Co2+ and a neutral Ar cluster is dominant in the formation of the cluster complex, Co2+Arn.

  10. A tri-copper(II) complex displaying DNA-cleaving properties and antiproliferative activity against cancer cells.

    PubMed

    Suntharalingam, Kogularamanan; Hunt, Douglas J; Duarte, Alexandra A; White, Andrew J P; Mann, David J; Vilar, Ramon

    2012-11-19

    A new disubstituted terpyridine ligand and the corresponding tri-copper(II) complex have been prepared and characterised. The binding affinity and binding mode of this tri-copper complex (as well as the previously reported mono- and di-copper analogues) towards duplex DNA were determined by using UV/Vis spectroscopic titrations and fluorescent indicator displacement (FID) assays. These studies showed the three complexes to bind moderately (in the order of 10(4)  M(-1)) to duplex DNA (ct-DNA and a 26-mer sequence). Furthermore, the number of copper centres and the nature of the substituents were found to play a significant role in defining the binding mode (intercalative or groove binding). The nuclease potential of the three complexes was investigated by using circular plasmid DNA as a substrate and analysing the products by agarose-gel electrophoresis. The cleaving activity was found to be dependent on the number of copper centres present (cleaving potency was in the order: tri-copper>di-copper>mono-copper). Interestingly, the tri-copper complex was able to cleave DNA without the need of external co-reductants. As this complex displayed the most promising nuclease properties, cell-based studies were carried out to establish if there was a direct link between DNA cleavage and cellular toxicity. The tri-copper complex displayed high cytotoxicity against four cancer cell lines. Of particular interest was that it displayed high cytotoxicity against the cisplatin-resistant MOLT-4 leukaemia cell line. Cellular uptake studies showed that the tri-copper complex was able to enter the cell and more importantly localise in the nucleus. Immunoblotting analysis (used to monitor changes in protein levels related to the DNA damage response pathway) and DNA-flow cytometric studies suggested that this tri-copper(II) complex is able to induce cellular DNA damage. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Nucleotide cleaving agents and method

    DOEpatents

    Que, Jr., Lawrence; Hanson, Richard S.; Schnaith, Leah M. T.

    2000-01-01

    The present invention provides a unique series of nucleotide cleaving agents and a method for cleaving a nucleotide sequence, whether single-stranded or double-stranded DNA or RNA, using and a cationic metal complex having at least one polydentate ligand to cleave the nucleotide sequence phosphate backbone to yield a hydroxyl end and a phosphate end.

  12. Caught after the Act: a human A-type metallocarboxypeptidase in a product complex with a cleaved hexapeptide.

    PubMed

    Bayés, Alex; Fernández, Daniel; Solà, Maria; Marrero, Aniebrys; García-Piqué, Sonia; Avilés, Francesc X; Vendrell, Josep; Gomis-Rüth, F Xavier

    2007-06-12

    A/B-type metallocarboxypeptidases (MCPs) are among the most thoroughly studied proteolytic enzymes, and their catalytic mechanisms have been considered as prototypes even for several unrelated metalloprote(in)ase families. It has long been postulated that the nature of the side chains of at least five substrate residues, i.e., P4-P1', influence Km and kcat and that once the peptide or protein substrate is cleaved, both products remain in the first instance bound to the active-site cleft of the enzyme in a double-product complex. Structural details of binding of substrate to the nonprimed side of the cleft have largely relied on complexes with protein inhibitors and peptidomimetic small-molecule inhibitors that do not span the entire groove. In the former, the presence of N-terminal globular protein domains participating in large-scale interactions with the surface of the cognate catalytic domain outside the active-site cleft mostly conditions the way their C-terminal tails bind to the cleft. Accordingly, they may not be accurate models for a product complex. We hereby provide the structural details of a true cleaved double-product complex with a hexapeptide of an MCP engaged in prostate cancer, human carboxypeptidase A4, employing diffraction data to 1.6 A resolution (Rcryst and Rfree = 0.159 and 0.176, respectively). These studies provide detailed information about subsites S5-S1' and contribute to our knowledge of the cleavage mechanism, which is revisited in light of these new structural insights.

  13. Spectral characterization, cyclic voltammetry, morphology, biological activities and DNA cleaving studies of amino acid Schiff base metal(II) complexes.

    PubMed

    Neelakantan, M A; Rusalraj, F; Dharmaraja, J; Johnsonraja, S; Jeyakumar, T; Sankaranarayana Pillai, M

    2008-12-15

    Metal complexes are synthesized with Schiff bases derived from o-phthalaldehyde (opa) and amino acids viz., glycine (gly) l-alanine (ala), l-phenylalanine (pal). Metal ions coordinate in a tetradentate or hexadentate manner with these N(2)O(2) donor ligands, which are characterized by elemental analysis, molar conductance, magnetic moments, IR, electronic, (1)H NMR and EPR spectral studies. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). Based on EPR studies, spin-Hamiltonian and bonding parameters have been calculated. The g-values calculated for copper complexes at 300K and in frozen DMSO (77K) indicate the presence of the unpaired electron in the dx2-y2 orbital. The evaluated metal-ligand bonding parameters showed strong in-plane sigma- and pi-bonding. X-ray diffraction (XRD) and scanning electron micrography (SEM) analysis provide the crystalline nature and the morphology of the metal complexes. The cyclic voltammograms of the Cu(II)/Mn(II)/VO(II) complexes investigated in DMSO solution exhibit metal centered electroactivity in the potential range -1.5 to +1.5V. The electrochemical data obtained for Cu(II) complexes explains the change of structural arrangement of the ligand around Cu(II) ions. The biological activity of the complexes has been tested on eight bacteria and three fungi. Cu(II) and Ni(II) complexes show an increased activity in comparison to the controls. The metal complexes of opapal Schiff base were evaluated for their DNA cleaving activities with calf-thymus DNA (CT DNA) under aerobic conditions. Cu(II) and VO(II) complexes show more pronounced activity in presence of the oxidant.

  14. Spectral characterization, cyclic voltammetry, morphology, biological activities and DNA cleaving studies of amino acid Schiff base metal(II) complexes

    NASA Astrophysics Data System (ADS)

    Neelakantan, M. A.; Rusalraj, F.; Dharmaraja, J.; Johnsonraja, S.; Jeyakumar, T.; Sankaranarayana Pillai, M.

    2008-12-01

    Metal complexes are synthesized with Schiff bases derived from o-phthalaldehyde (opa) and amino acids viz., glycine (gly) L-alanine (ala), L-phenylalanine (pal). Metal ions coordinate in a tetradentate or hexadentate manner with these N 2O 2 donor ligands, which are characterized by elemental analysis, molar conductance, magnetic moments, IR, electronic, 1H NMR and EPR spectral studies. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). Based on EPR studies, spin-Hamiltonian and bonding parameters have been calculated. The g-values calculated for copper complexes at 300 K and in frozen DMSO (77 K) indicate the presence of the unpaired electron in the d orbital. The evaluated metal-ligand bonding parameters showed strong in-plane σ- and π-bonding. X-ray diffraction (XRD) and scanning electron micrography (SEM) analysis provide the crystalline nature and the morphology of the metal complexes. The cyclic voltammograms of the Cu(II)/Mn(II)/VO(II) complexes investigated in DMSO solution exhibit metal centered electroactivity in the potential range -1.5 to +1.5 V. The electrochemical data obtained for Cu(II) complexes explains the change of structural arrangement of the ligand around Cu(II) ions. The biological activity of the complexes has been tested on eight bacteria and three fungi. Cu(II) and Ni(II) complexes show an increased activity in comparison to the controls. The metal complexes of opapal Schiff base were evaluated for their DNA cleaving activities with calf-thymus DNA (CT DNA) under aerobic conditions. Cu(II) and VO(II) complexes show more pronounced activity in presence of the oxidant.

  15. Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis.

    PubMed

    Blower, Tim R; Williamson, Benjamin H; Kerns, Robert J; Berger, James M

    2016-02-16

    Mycobacterium tuberculosis (Mtb) infects one-third of the world's population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone-gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone-enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. These concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance.

  16. Crystal structure and stability of gyrase–fluoroquinolone cleaved complexes from Mycobacterium tuberculosis

    PubMed Central

    Williamson, Benjamin H.; Kerns, Robert J.; Berger, James M.

    2016-01-01

    Mycobacterium tuberculosis (Mtb) infects one-third of the world’s population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone–gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone–enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. These concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance. PMID:26792525

  17. Plasma levels of C1- inhibitor complexes and cleaved C1- inhibitor in patients with hereditary angioneurotic edema.

    PubMed Central

    Cugno, M; Nuijens, J; Hack, E; Eerenberg, A; Frangi, D; Agostoni, A; Cicardi, M

    1990-01-01

    C1- inhibitor (C1(-)-Inh) catabolism in plasma of patients with hereditary angioneurotic edema (HANE) was assessed by measuring the complexes formed by C1(-)-Inh with its target proteases (C1-s, Factor XIIa, and kallikrein) and a modified (cleaved) inactive form of C1(-)-Inh (iC1(-)-Inh). This study was performed in plasma from 18 healthy subjects and 30 patients with HANE in remission: 20 with low antigen concentration (type I) and 10 (from 5 different kindreds) with dysfunctional protein (type II). Both type-I and type-II patients had increased C1(-)-C1(-)-Inh complexes (P less than 0.0001), which in type I inversely correlated with the levels of C1(-)-Inh (P less than 0.001). iC1(-)-Inh was normal in all type-I patients and in type-II patients from three families with increased C1(-)-Inh antigen, whereas iC1(-)-Inh was higher than 20 times the normal values in patients from the remaining two families with C1(-)-Inh antigen in the normal range. None of the subjects had an increase of either Factor XIIa-C1(-)-Inh or kallikrein-C1(-)-Inh complexes. This study shows that the hypercatabolism of C1(-)-Inh in HANE patients at least in part occurs via the formation of complexes with C1- and that genetically determined differences in catabolism of dysfunctional C1(-)-Inh proteins are present in type-II patients. Images PMID:2318974

  18. Atomic clusters with addressable complexity

    NASA Astrophysics Data System (ADS)

    Wales, David J.

    2017-02-01

    A general formulation for constructing addressable atomic clusters is introduced, based on one or more reference structures. By modifying the well depths in a given interatomic potential in favour of nearest-neighbour interactions that are defined in the reference(s), the potential energy landscape can be biased to make a particular permutational isomer the global minimum. The magnitude of the bias changes the resulting potential energy landscape systematically, providing a framework to produce clusters that should self-organise efficiently into the target structure. These features are illustrated for small systems, where all the relevant local minima and transition states can be identified, and for the low-energy regions of the landscape for larger clusters. For a 55-particle cluster, it is possible to design a target structure from a transition state of the original potential and to retain this structure in a doubly addressable landscape. Disconnectivity graphs based on local minima that have no direct connections to a lower minimum provide a helpful way to visualise the larger databases. These minima correspond to the termini of monotonic sequences, which always proceed downhill in terms of potential energy, and we identify them as a class of biminimum. Multiple copies of the target cluster are treated by adding a repulsive term between particles with the same address to maintain distinguishable targets upon aggregation. By tuning the magnitude of this term, it is possible to create assemblies of the target cluster corresponding to a variety of structures, including rings and chains.

  19. Competitive cluster growth in complex networks

    NASA Astrophysics Data System (ADS)

    Moreira, André A.; Paula, Demétrius R.; Costa Filho, Raimundo N.; Andrade, José S., Jr.

    2006-06-01

    In this work we propose an idealized model for competitive cluster growth in complex networks. Each cluster can be thought of as a fraction of a community that shares some common opinion. Our results show that the cluster size distribution depends on the particular choice for the topology of the network of contacts among the agents. As an application, we show that the cluster size distributions obtained when the growth process is performed on hierarchical networks, e.g., the Apollonian network, have a scaling form similar to what has been observed for the distribution of a number of votes in an electoral process. We suggest that this similarity may be due to the fact that social networks involved in the electoral process may also possess an underlining hierarchical structure.

  20. Synthesis, hydrolytic DNA-cleaving activities and cytotoxicities of EDTA analogue-tethered pyrrole-polyamide dimer-based Ce(IV) complexes.

    PubMed

    Yang, Jian-Wei; Lin, Yan-Ling; Dong, Cheng; Zhou, Chun-Qiong; Chen, Jin-Xiang; Wang, Bo; Zhou, Zhong-Zhen; Sun, Bin; Chen, Wen-Hua

    2014-11-24

    Two EDTA analogue-tethered C2-symmetrical dimeric monopyrrole-polyamide 5 and dipyrrole-polyamide 6, and their corresponding Ce(IV) complexes Ce-5 and Ce-6 were synthesized and fully characterized. Agarose gel electrophoresis studies on pBR322 DNA cleavage indicate that complexes Ce-5 and Ce-6 exhibited potent DNA-cleaving activities under physiological conditions. The maximal first-order rate constants (kmax's) were (0.42 ± 0.02) h(-1) for Ce-5 and (0.52 ± 0.02) h(-1) for Ce-6, respectively, suggesting that both complexes catalyzed the cleavage of supercoiled DNA by up to approximately 10(8)-fold. Complex Ce-6 exhibited ca 10-fold higher overall catalytic activity (kmax/KM) than Ce-5, which may be ascribed to its higher DNA-binding affinity. Inhibition experiments and a model study convincingly suggest that both complexes Ce-5 and Ce-6 functioned as hydrolytic DNA-cleavers. In addition, both complexes were found to display moderate inhibitory activity toward A549 and HepG-2 cells. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  1. An unlikely DNA cleaving agent: A photo-active trinuclear Cu(II) complex based on hexaazatriphenylene.

    PubMed

    Williams, Dominique E; Fischer, Christina M; Kassai, Miki; Gude, Lourdes; Fernández, María-José; Lorente, Antonio; Grant, Kathryn B

    2017-03-01

    This paper describes the synthesis of a trinuclear Cu(II) complex (4) containing a central 1,4,5,8,9,12-hexaazatriphenylene-hexacarboxylate (hat) core (3). Low, micromolar concentrations of the negatively charged parent ligand 3 and the neutral trinuclear complex 4 were found to photocleave negatively charged pUC19 plasmid DNA with high efficiency at neutral pH (350nm, 50min, 22°C). The interactions of complex 4 with double-helical DNA were studied in detail. Scavenger and colorimetric assays pointed to the formation of Cu(I), superoxide anion radicals, hydrogen peroxide, and hydroxyl radicals during photocleavage reactions. UV-visible absorption, circular dichroism, DNA thermal denaturation, and fluorescence data suggested that the Cu(II) complex contacts double-stranded DNA in an external fashion. The persistent association of ligand 3 and complex 4 with Na(I) and/or other cations in aqueous solution might facilitate electrostatic DNA interactions.

  2. High Fat Diet Enhances β-Site Cleavage of Amyloid Precursor Protein (APP) via Promoting β-Site APP Cleaving Enzyme 1/Adaptor Protein 2/Clathrin Complex Formation

    PubMed Central

    Maesako, Masato; Uemura, Maiko; Tashiro, Yoshitaka; Sasaki, Kazuki; Watanabe, Kiwamu; Noda, Yasuha; Ueda, Karin; Asada-Utsugi, Megumi; Kubota, Masakazu; Okawa, Katsuya; Ihara, Masafumi; Shimohama, Shun; Uemura, Kengo; Kinoshita, Ayae

    2015-01-01

    Obesity and type 2 diabetes are risk factors of Alzheimer’s disease (AD). We reported that a high fat diet (HFD) promotes amyloid precursor protein (APP) cleavage by β-site APP cleaving enzyme 1 (BACE1) without increasing BACE1 levels in APP transgenic mice. However, the detailed mechanism had remained unclear. Here we demonstrate that HFD promotes BACE1/Adaptor protein-2 (AP-2)/clathrin complex formation by increasing AP-2 levels in APP transgenic mice. In Swedish APP overexpressing Chinese hamster ovary (CHO) cells as well as in SH-SY5Y cells, overexpression of AP-2 promoted the formation of BACE1/AP-2/clathrin complex, increasing the level of the soluble form of APP β (sAPPβ). On the other hand, mutant D495R BACE1, which inhibits formation of this trimeric complex, was shown to decrease the level of sAPPβ. Overexpression of AP-2 promoted the internalization of BACE1 from the cell surface, thus reducing the cell surface BACE1 level. As such, we concluded that HFD may induce the formation of the BACE1/AP-2/clathrin complex, which is followed by its transport of BACE1 from the cell surface to the intracellular compartments. These events might be associated with the enhancement of β-site cleavage of APP in APP transgenic mice. Here we present evidence that HFD, by regulation of subcellular trafficking of BACE1, promotes APP cleavage. PMID:26414661

  3. Activation of blood coagulation factor VIIa with cleaved tissue factor extracellular domain and crystallization of the active complex.

    PubMed

    Kirchhofer, D; Guha, A; Nemerson, Y; Konigsberg, W H; Vilbois, F; Chène, C; Banner, D W; D'Arcy, A

    1995-08-01

    Exposure of blood to tissue factor leads to the formation of a high affinity tissue factor/factor VIIa complex which initiates blood coagulation. As a first step toward obtaining structural information of this enzyme system, a complex of active-site inhibited factor VIIa (F.VIIai) and soluble tissue factor (sTF) was prepared for crystallization. Crystals were obtained, but only after long incubation times. Analysis by SDS-PAGE and mass spectrometry indicated the presence of sTF fragments similar to those formed by proteolytic digestion with subtilisin (Konigsberg, W., Nemerson, Y., Fang, C., Lin, T.-C. Thromb. Haemost. 69:1171, 1993). To test the hypothesis that limited proteolysis of sTF facilitated the crystallization of the complex, sTF fragments were generated by subtilisin digestion and purified. Analysis by tandem mass spectrometry showed the presence of nonoverlapping N- and C-terminal sTF fragments encompassing more than 90% of the tissue factor extracellular domain. Enzymatic assays and binding studies demonstrated that an equimolar mixture of N- and C-terminal fragments bound to factor VIIa and fully restored cofactor activity. A complex of F.VIIai and sTF fragments was prepared for crystallization. Crystals were obtained using microseeding techniques. The best crystals had maximum dimensions of 0.12 x 0.12 x 0.6 mm and showed diffraction to a resolution of 3 A.

  4. Calpain Cleaves Most Components in the Multiple Aminoacyl-tRNA Synthetase Complex and Affects Their Functions.

    PubMed

    Lei, Hui-Yan; Zhou, Xiao-Long; Ruan, Zhi-Rong; Sun, Wei-Cheng; Eriani, Gilbert; Wang, En-Duo

    2015-10-23

    Nine aminoacyl-tRNA synthetases (aaRSs) and three scaffold proteins form a super multiple aminoacyl-tRNA synthetase complex (MSC) in the human cytoplasm. Domains that have been added progressively to MSC components during evolution are linked by unstructured flexible peptides, producing an elongated and multiarmed MSC structure that is easily attacked by proteases in vivo. A yeast two-hybrid screen for proteins interacting with LeuRS, a representative MSC member, identified calpain 2, a calcium-activated neutral cysteine protease. Calpain 2 and calpain 1 could partially hydrolyze most MSC components to generate specific fragments that resembled those reported previously. The cleavage sites of calpain in ArgRS, GlnRS, and p43 were precisely mapped. After cleavage, their N-terminal regions were removed. Sixty-three amino acid residues were removed from the N terminus of ArgRS to form ArgRSΔN63; GlnRS formed GlnRSΔN198, and p43 formed p43ΔN106. GlnRSΔN198 had a much weaker affinity for its substrates, tRNA(Gln) and glutamine. p43ΔN106 was the same as the previously reported p43-derived apoptosis-released factor. The formation of p43ΔN106 by calpain depended on Ca(2+) and could be specifically inhibited by calpeptin and by RNAi of the regulatory subunit of calpain in vivo. These results showed, for the first time, that calpain plays an essential role in dissociating the MSC and might regulate the canonical and non-canonical functions of certain components of the MSC.

  5. Evaluating the Immunogenicity of a Disulfide-Stabilized, Cleaved, Trimeric Form of the Envelope Glycoprotein Complex of Human Immunodeficiency Virus Type 1

    PubMed Central

    Beddows, Simon; Schülke, Norbert; Kirschner, Marc; Barnes, Kelly; Franti, Michael; Michael, Elizabeth; Ketas, Thomas; Sanders, Rogier W.; Maddon, Paul J.; Olson, William C.; Moore, John P.

    2005-01-01

    The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) complex comprises three gp120 exterior glycoproteins each noncovalently linked to a gp41 transmembrane glycoprotein. Monomeric gp120 proteins can elicit antibodies capable of neutralizing atypically sensitive test viruses in vitro, but these antibodies are ineffective against representative primary isolates and the gp120 vaccines failed to provide protection against HIV-1 transmission in vivo. Alternative approaches to raising neutralizing antibodies are therefore being pursued. Here we report on the antibody responses generated in rabbits against a soluble, cleaved, trimeric form of HIV-1JR-FL Env. In this construct, the gp120 and gp41 moieties are covalently linked by an intermolecular disulfide bond (SOS gp140), and an I559P substitution has been added to stabilize gp41-gp41 interactions (SOSIP gp140). We investigated the value of DNA priming and compared the use of membrane-bound and soluble priming antigens and of repeat boosting with soluble and particulate protein antigen. Compared to monomeric gp120, SOSIP gp140 trimers elicited approximately threefold lower titers of anti-gp120 antibodies. Priming with DNA encoding a membrane-bound form of the SOS gp140 protein, followed by several immunizations with soluble SOSIP gp140 trimers, resulted in antibodies capable of neutralizing sensitive strains at high titers. A subset of these sera also neutralized, at lower titers, HIV-1JR-FL and some other primary isolates in pseudovirus and/or whole-virus assays. Neutralization of these viruses was immunoglobulin mediated and was predominantly caused by antibodies to gp120 epitopes, but not the V3 region. PMID:15994775

  6. A graph clustering method for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Zhou, HongFang; Li, Jin; Li, JunHuai; Zhang, FaCun; Cui, YingAn

    2017-03-01

    Information mining from complex networks by identifying communities is an important problem in a number of research fields, including the social sciences, biology, physics and medicine. First, two concepts are introduced, Attracting Degree and Recommending Degree. Second, a graph clustering method, referred to as AR-Cluster, is presented for detecting community structures in complex networks. Third, a novel collaborative similarity measure is adopted to calculate node similarities. In the AR-Cluster method, vertices are grouped together based on calculated similarity under a K-Medoids framework. Extensive experimental results on two real datasets show the effectiveness of AR-Cluster.

  7. Motion of clusters on complex surfaces

    NASA Astrophysics Data System (ADS)

    Alkis, Sabri; Krause, Jeffrey; Cheng, Hai-Ping

    2007-03-01

    Polymer and organic molecule assemblies have been investigated intensely in the past decade, due to their vast range of applications in nano-molecular electronics and as bio-sensors. In particular, self-assembled monolyers (SAMs) of alkanethiol on the Au(111) surface are used widely in surface studies because they are simple structurally, stable thermodynamically and have well-defined order. In this project, inspired by recent experiments, we use classical molecular dynamics simulations to study motions of Agn clusters with various sizes on the alkanthiol SAMs. We report detailed results on dynamics, diffusion, and sintering processes of these nano-clusters.

  8. Pinning control of clustered complex networks with different size

    NASA Astrophysics Data System (ADS)

    Fu, Chenbo; Wang, Jinbao; Xiang, Yun; Wu, Zhefu; Yu, Li; Xuan, Qi

    2017-08-01

    In pinning control of complex networks, it is found that, with the same pinning effort, the network can be better controlled by pinning the large-degree nodes. But in the clustered complex networks, this preferential pinning (PP) strategy is losing its effectiveness. In this paper, we demonstrate that in the clustered complex networks, especially when the clusters have different size, the random pinning (RP) strategy performs much better than the PP strategy. Then, we propose a new pinning strategy based on cluster degree. It is revealed that the new cluster pinning strategy behaves better than RP strategy when there are only a smaller number of pinning nodes. The mechanism is studied by using eigenvalue and eigenvector analysis, and the simulations of coupled chaotic oscillators are given to verify the theoretical results. These findings could be beneficial for the design of control schemes in some practical systems.

  9. Globular cluster formation with multiple stellar populations from hierarchical star cluster complexes

    NASA Astrophysics Data System (ADS)

    Bekki, Kenji

    2017-01-01

    Most old globular clusters (GCs) in the Galaxy are observed to have internal chemical abundance spreads in light elements. We discuss a new GC formation scenario based on hierarchical star formation within fractal molecular clouds. In the new scenario, a cluster of bound and unbound star clusters (`star cluster complex', SCC) that have a power-law cluster mass function with a slope (β) of 2 is first formed from a massive gas clump developed in a dwarf galaxy. Such cluster complexes and β = 2 are observed and expected from hierarchical star formation. The most massive star cluster (`main cluster'), which is the progenitor of a GC, can accrete gas ejected from asymptotic giant branch (AGB) stars initially in the cluster and other low-mass clusters before the clusters are tidally stripped or destroyed to become field stars in the dwarf. The SCC is initially embedded in a giant gas hole created by numerous supernovae of the SCC so that cold gas outside the hole can be accreted onto the main cluster later. New stars formed from the accreted gas have chemical abundances that are different from those of the original SCC. Using hydrodynamical simulations of GC formation based on this scenario, we show that the main cluster with the initial mass as large as [2 - 5] × 105M⊙ can accrete more than 105M⊙ gas from AGB stars of the SCC. We suggest that merging of hierarchical star cluster complexes can play key roles in stellar halo formation around GCs and self-enrichment processes in the early phase of GC formation.

  10. Simple versus complex PTSD: a cluster analytic investigation.

    PubMed

    Taylor, Steven; Asmundson, Gordon J G; Carleton, R Nicholas

    2006-01-01

    A cluster analytic investigation was conducted on measures of PTSD associated features (e.g., personality pathology, dissociative tendencies) to investigate whether empirically-defined clusters correspond to Herman's [1992, Complex PTSD: a syndrome in survivors of prolonged and repeated trauma. Journal of Traumatic Stress, 5, 377-391; 1997, Trauma and recovery (Rev. ed.). New York: Basic Books] distinction between simple and complex PTSD. Results from a sample of 60 PTSD patients were broadly consistent with this distinction, although some inconsistencies were observed. Treatment outcome generally did not differ between the two clusters. Implications for classifying and treating PTSD are discussed.

  11. Symmetries, Cluster Synchronization, and Isolated Desynchronization in Complex Networks

    NASA Astrophysics Data System (ADS)

    Pecora, Louis

    2015-03-01

    Many networks are observed to produce patterns of synchronized clusters, but it has been difficult to predict these clusters in general or understand the conditions for their formation. We show the intimate connection between network symmetry and cluster synchronization. We apply computational group theory to reveal the clusters and determine their stability. In complex networks the symmetries can number in the millions, billions, and more. The connection between symmetry and cluster synchronization is experimentally explored using an electro-optic network. We observe and explain a surprising and common phenomenon (isolated desynchronization) in which some clusters lose synchrony while leaving others connected to them synchronized. We show the isolated desynchronization is intimately related to the decomposition of the group of symmetries into subgroups. The results could guide the design of new power grid systems or lead to new understanding of the dynamical behavior of networks ranging from neural to social.

  12. Globular cluster formation with multiple stellar populations from hierarchical star cluster complexes

    NASA Astrophysics Data System (ADS)

    Bekki, Kenji

    2017-05-01

    Most old globular clusters (GCs) in the Galaxy are observed to have internal chemical abundance spreads in light elements. We discuss a new GC formation scenario based on hierarchical star formation within fractal molecular clouds. In the new scenario, a cluster of bound and unbound star clusters ('star cluster complex', SCC) that have a power-law cluster mass function with a slope (β) of 2 is first formed from a massive gas clump developed in a dwarf galaxy. Such cluster complexes and β = 2 are observed and expected from hierarchical star formation. The most massive star cluster ('main cluster'), which is the progenitor of a GC, can accrete gas ejected from asymptotic giant branch (AGB) stars initially in the cluster and other low-mass clusters before the clusters are tidally stripped or destroyed to become field stars in the dwarf. The SCC is initially embedded in a giant gas hole created by numerous supernovae of the SCC so that cold gas outside the hole can be accreted on to the main cluster later. New stars formed from the accreted gas have chemical abundances that are different from those of the original SCC. Using hydrodynamical simulations of GC formation based on this scenario, we show that the main cluster with the initial mass as large as [2-5] × 105 M⊙ can accrete more than 105 M⊙ gas from AGB stars of the SCC. We suggest that merging of hierarchical SSCs can play key roles in stellar halo formation around GCs and self-enrichment processes in the early phase of GC formation.

  13. Cellular uptake and cytotoxicity of octahedral rhenium cluster complexes.

    PubMed

    Choi, Soo-Jin; Brylev, Konstantin A; Xu, Jing-Zhe; Mironov, Yuri V; Fedorov, Vladimir E; Sohn, Youn Soo; Kim, Sung-Jin; Choy, Jin-Ho

    2008-11-01

    Cellular uptake behavior of a novel class of octahedral rhenium cluster compounds, hexahydroxo complexes K(4)[{Re(6)S(8)}(OH)(6)].8H(2)O (1) and K(4)[{Re(6)Se(8)}(OH)(6)].8H(2)O (2), was evaluated in human cervical adenocarcinoma HeLa cells. Confocal microscopy and flow cytometry studies demonstrated that rhenium cluster 1 was not internalized into cell, while rhenium cluster 2 was. Conjugation of a polymer to rhenium cluster 1, namely the derivative K(4)[{Re(6)S(8)}(OH)(5)L] (3) (L is amphiphilic diblock copolymer MPEG550-CH(2)CONH-GlyPheLeuGlyPheLeu-COO(-)), considerably enhanced cellular uptake in a concentration-dependent manner and was predominantly localized in the cytoplasm and nucleus upon incubation time. The uptake of rhenium cluster 2 was mediated by energy-dependent endocytosis, whereas rhenium cluster 3 was directly ingested into cells by cell-fusion-like mechanism. According to the cytotoxicity evaluation test, both rhenium clusters 2 and 3 did not exhibit acute cytotoxic effects up to 50 microM, at the practical concentration level of biological applications. It is, therefore, expected that the rhenium cluster complexes can be promising potential candidates as diagnostic agents for medical treatment.

  14. Cluster type EAS array of the NEVOD experimental complex

    NASA Astrophysics Data System (ADS)

    Amelchakov, M. B.; Ampilogov, N. V.; Astapov, I. I.; Barbashina, N. S.; Bogdanov, A. G.; Chiavassa, A.; Gromushkin, D. M.; Khokhlov, S. S.; Kokoulin, R. P.; Kompaniets, K. G.; Likiy, O. I.; Ovchinnikov, V. V.; Petrukhin, A. A.; Saavedra, O.; Shulzhenko, I. A.; Yashin, I. I.

    2017-06-01

    A new NEVOD-EAS array for detection of extensive air showers (EAS) in the energy range 1015-1017 eV is being created in MEPhI (Moscow, Russia) on the basis of the Experimental complex NEVOD. It will be operated in conjunction with the Cherenkov water detector NEVOD and coordinate detector DECOR, as well as with detectors URAN and TREK which are now being constructed. The array will allow determining of the size, axis position and arrival direction of EAS registered by aforementioned installations. The NEVOD-EAS registering system is organized in a cluster principle. Each cluster of the shower array is an independent system which includes 16 scintillation counters of EAS electron-photon component combined in 4 detector stations and registering electronics. Cluster electronics performs digitizing of analog signals, selection of events according to intra-cluster triggering conditions, time-stamping of events and monitoring of cluster operational parameters. Information on events and operational parameters is transferred to the central DAQ post of control and synchronization. In 2015-2016, the central part of the NEVOD-EAS array was created and launched into operation. It includes 4 clusters located at different altitudes at area of 104 m2 around the complex. The paper discribes the features of the distributed cluster type registering system of the NEVOD-EAS shower array, as well as the main characteristics of clusters and their elements.

  15. Contact factor proteases and the complexes formed with alpha 2-macroglobulin can interfere in protein C assays by cleaving amidolytic substrates.

    PubMed

    Mackie, I J; Gallimore, M; Machin, S J

    1992-10-01

    Plasma from women taking combined oral contraceptives and cold-activated plasma contain proteases which cleave chromogenic substrates in protein C assays in the absence of protein C activators such as Protac. This spontaneous activity makes a background substraction necessary and makes protein C (PC) assays less accurate. We investigated two commonly used substrates < Glu-Pro-Arg-pNA (S-2366) and 2AcOH.H-D-Lys(Cbo)-Pro-Arg-pNA (PC substrate) and found that cold-activated normal and protein C-deficient plasmas gave absorbance values up to 300 times higher than buffer blanks. FXIa cleaves these substrates but activity was not blocked by corn or lima bean trypsin inhibitors, soy bean trypsin inhibitor (SBTI), hirudin or epsilon-amino-n-caproic acid (EACA). Kaolin activation of normal, FXI, FIX, FVIII, FVII and protein C-deficient, but not of FXII or prekallikrein (PKK)-deficient plasmas led to cleavage of chromogenic substrate for protein C. The protein C substrates were cleaved by purified kallikrein and alpha- and beta-FXIIa. Immunoabsorption with alpha 2-macroglobulin (alpha 2M) antibodies removed 60% of the alpha 2M and 70% of the activity on PC Substrate. Gel filtration of normal plasma on Sephadex G-150 gave a single peak of protein C activity and antigen in the included volume. After cold activation of the fractions, a second protein C-like peak appeared in the void volume, but with no detectable protein C antigen. This peak coincided with alpha 2M (chromogenic and ELISA) and plasma kallikrein (S-2302), but FXII (measured with a substrate insensitive to kallikrein) eluted separately.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Nucleoside modification with boron clusters and their metal complexes.

    PubMed

    Wojtczak, Blazej A; Olejniczak, Agnieszka B; Lesnikowski, Zbigniew J

    2009-09-01

    General methods for the synthesis of nucleosides modified with borane clusters and metallacarborane complexes are presented. These include: (1) the click chemistry approach based on Huisgen 1,3-dipolar cycloaddition and (2) tethering of the metallacarborane group to the aglycone of a nucleoside via a dioxane ring opening in oxonium metallacarborane derivatives. The proposed methodologies broaden the availability of nucleoside-borane cluster conjugates and open up new areas for their applications.

  17. Multiscale ensemble clustering for finding modules in complex networks.

    PubMed

    Kim, Eun-Youn; Hwang, Dong-Uk; Ko, Tae-Wook

    2012-02-01

    The identification of modules in complex networks is important for the understanding of systems. Here, we propose an ensemble clustering method incorporating node groupings in various sizes and the sequential removal of weak ties between nodes which are rarely grouped together. This method successfully detects modules in various networks, such as hierarchical random networks and the American college football network, with known modular structures. Some of the results are compared with those obtained by modularity optimization and K-means clustering.

  18. Ionization reactions of ion complexes in mesoscopic water clusters

    NASA Astrophysics Data System (ADS)

    Consta, Styliani; Kapral, Raymond

    1999-12-01

    The free energy and dynamics of the dissociation reactions of the [Na+(Cl-)2] ion complex in mesoscopic water clusters are examined. The free energy surface shows the existence of stable single and double solvent-separated complex species formed from ionization of the stable double-contact ion complex. The reaction occurs on the cluster surface for mesoscale clusters composed of tens of water molecules. Passage between stable species is an activated process but barrier crossing has a large diffusive component so that dynamical corrections to transition state theory are large. The structure of the decay of the time-dependent rate constant reflects the diffusive character of the recrossing dynamics so that a plateau is not established on a 10 ps time scale in contrast to ionization dynamics in bulk fluids.

  19. Mathematical modelling of complex contagion on clustered networks

    NASA Astrophysics Data System (ADS)

    O'sullivan, David J.; O'Keeffe, Gary; Fennell, Peter; Gleeson, James

    2015-09-01

    The spreading of behavior, such as the adoption of a new innovation, is influenced bythe structure of social networks that interconnect the population. In the experiments of Centola (Science, 2010), adoption of new behavior was shown to spread further and faster across clustered-lattice networks than across corresponding random networks. This implies that the “complex contagion” effects of social reinforcement are important in such diffusion, in contrast to “simple” contagion models of disease-spread which predict that epidemics would grow more efficiently on random networks than on clustered networks. To accurately model complex contagion on clustered networks remains a challenge because the usual assumptions (e.g. of mean-field theory) regarding tree-like networks are invalidated by the presence of triangles in the network; the triangles are, however, crucial to the social reinforcement mechanism, which posits an increased probability of a person adopting behavior that has been adopted by two or more neighbors. In this paper we modify the analytical approach that was introduced by Hebert-Dufresne et al. (Phys. Rev. E, 2010), to study disease-spread on clustered networks. We show how the approximation method can be adapted to a complex contagion model, and confirm the accuracy of the method with numerical simulations. The analytical results of the model enable us to quantify the level of social reinforcement that is required to observe—as in Centola’s experiments—faster diffusion on clustered topologies than on random networks.

  20. Encounter Complexes for Clustering Network Flow (Briefing Charts)

    DTIC Science & Technology

    2015-01-01

    JAN 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Encounter Complexes For Clustering Network Flow 5a...2015. 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 37

  1. Clustering determines the dynamics of complex contagions in multiplex networks

    NASA Astrophysics Data System (ADS)

    Zhuang, Yong; Arenas, Alex; Yaǧan, Osman

    2017-01-01

    We present the mathematical analysis of generalized complex contagions in a class of clustered multiplex networks. The model is intended to understand spread of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is especially useful in problems related to spreading and percolation. The results present nontrivial dependencies between the clustering coefficient of the networks and its average degree. In particular, several phase transitions are shown to occur depending on these descriptors. Generally speaking, our findings reveal that increasing clustering decreases the probability of having global cascades and their size, however, this tendency changes with the average degree. There exists a certain average degree from which on clustering favors the probability and size of the contagion. By comparing the dynamics of complex contagions over multiplex networks and their monoplex projections, we demonstrate that ignoring link types and aggregating network layers may lead to inaccurate conclusions about contagion dynamics, particularly when the correlation of degrees between layers is high.

  2. The galaxy population of the complex cluster system Abell 3921

    NASA Astrophysics Data System (ADS)

    Pranger, Florian; Böhm, Asmus; Ferrari, Chiara; Diaferio, Antonaldo; Hunstead, Richard; Maurogordato, Sophie; Benoist, Christophe; Brinchmann, Jarle; Schindler, Sabine

    2013-09-01

    Context. We present a spectrophotometric analysis of the galaxy population in the area of the merging cluster Abell 3921 at z = 0.093. Aims: We investigate the impact of the complex cluster environment on galaxy properties such as morphology or star formation rate. Methods: We combine multi-object spectroscopy from the two-degree field (2dF) spectrograph with optical imaging taken with the ESO Wide Field Imager. We carried out a redshift analysis and determine cluster velocity dispersions using biweight statistics. Applying a Dressler-Shectman test we sought evidence of cluster substructure. Cluster and field galaxies were investigated with respect to [OII] and Hα equivalent width, star formation rate, and morphological descriptors, such as concentration index and Gini coefficient. We studied these cluster galaxy properties as a function of clustercentric distance and investigated the spatial distribution of various galaxy types. Results: Applying the Dressler-Shectman test, we find a third component (A3921-C) in addition to the two main subclusters (A3921-A and A3921-B) that are already known. The re-determined mass ratio between the main components A and B is ~2:1. Similar to previous studies of galaxy clusters, we find that a large fraction of the disk galaxies close to the cluster core show no detectable star formation. These are likely systems that are quenched due to ram pressure stripping. Interestingly, we also find quenched spirals at rather large distances of 3-4 Mpc from the cluster core. Conclusions: A3921-C might be a group of galaxies falling onto the main cluster components. We speculate that the unexpected population of quenched spirals at large clustercentric radii in A3921-A and A3921-B might be an effect of the ongoing cluster merger: shocks in the ICM might give rise to enhanced ram pressure stripping and at least in part be the cause for the quenching of star formation. These quenched spirals might be an intermediate stage in the morphological

  3. Structural and functional clusters of complex brain networks

    NASA Astrophysics Data System (ADS)

    Zemanová, Lucia; Zhou, Changsong; Kurths, Jürgen

    2006-12-01

    Recent research using the complex network approach has revealed a rich and complicated network topology in the cortical connectivity of mammalian brains. It is of importance to understand the implications of such complex network structures in the functional organization of the brain activities. Here we study this problem from the viewpoint of dynamical complex networks. We investigate synchronization dynamics on the corticocortical network of the cat by modeling each node (cortical area) of the network with a sub-network of interacting excitable neurons. We find that the network displays clustered synchronization behavior, and the dynamical clusters coincide with the topological community structures observed in the anatomical network. Our results provide insights into the relationship between the global organization and the functional specialization of the brain cortex.

  4. The bithorax complex of Drosophila an exceptional Hox cluster.

    PubMed

    Maeda, Robert K; Karch, François

    2009-01-01

    In his 1978 seminal paper, Ed Lewis described a series of mutations that affect the segmental identities of the segments forming the posterior two-thirds of the Drosophila body plan. In each class of mutations, particular segments developed like copies of a more-anterior segment. Genetic mapping of the different classes of mutations led to the discovery that their arrangement along the chromosome paralleled the body segments they affect along the anteroposterior axis of the fly. As all these mutations mapped to the same cytological location, he named this chromosomal locus after its founding mutation. Thus the first homeotic gene (Hox) cluster became known as the bithorax complex (BX-C). Even before the sequencing of the BX-C, the fact that these similar mutations grouped together in a cluster, lead Ed Lewis to propose that the homeotic genes arose through a gene duplication mechanism and that these clusters would be conserved through evolution. With the identification of the homeobox in the early 1980s, Lewis' first prediction was confirmed. The two cloned Drosophila homeotic genes, Antennapedia and Ultrabithorax, were indeed related genes. Using the homeobox as an entry point, homologous genes have since been cloned in many other species. Today, Hox clusters have been discovered in almost all metazoan phyla, confirming Lewis' second prediction. Remarkably, these homologous Hox genes are also arranged in clusters with their order within each cluster reflecting the anterior boundary of their domain of expression along the anterior-posterior axis of the animal. This correlation between the genomic organization and the activity along the anteroposterior body axis is known as the principle of "colinearity." The description of the BX-C inspired decades of developmental and evolutionary biology. And although this first Hox cluster led to the identification of many important features common to all Hox gene clusters, it now turns out that the fly Hox clusters are rather

  5. UV and VUV ionization of organic molecules, clusters, and complexes.

    PubMed

    Marksteiner, Markus; Haslinger, Philipp; Sclafani, Michele; Ulbricht, Hendrik; Arndt, Markus

    2009-09-17

    The generation of organic particle beams is studied in combination with photoionization using UV radiation at 266 nm and vacuum ultraviolet (VUV) light at 157 nm. Single-photon ionization with pulsed VUV light turns out to be sensitive enough to detect various large neutral biomolecular complexes ranging from metal-amino acid complexes to nucleotide clusters and aggregates of polypeptides. Different biomolecular clusters are shown to exhibit rather specific binding characteristics with regard to the various metals that are codesorbed in the source. We also find that the ion signal of gramicidin can be increased by a factor of 15 when the photon energy is increased from 4.66 to 7.9 eV.

  6. The globular cluster system of NGC 1316. IV. Nature of the star cluster complex SH2

    NASA Astrophysics Data System (ADS)

    Richtler, T.; Husemann, B.; Hilker, M.; Puzia, T. H.; Bresolin, F.; Gómez, M.

    2017-05-01

    Context. The light of the merger remnant NGC 1316 (Fornax A) is dominated by old and intermediate-age stars. The only sign of current star formation in this big galaxy is the Hii region SH2, an isolated star cluster complex with a ring-like morphology and an estimated age of 0.1 Gyr at a galactocentric distance of about 35 kpc. A nearby intermediate-age globular cluster, surrounded by weak line emission and a few more young star clusters, is kinematically associated. The origin of this complex is enigmatic. Aims: We want to investigate the nature of this star cluster complex. The nebular emission lines permit a metallicity determination which can discriminate between a dwarf galaxy or other possible precursors. Methods: We used the Integral Field Unit (IFU) of the VIMOS instrument at the Very Large Telescope of the European Southern Observatory in high dispersion mode to study the morphology, kinematics, and metallicity employing line maps, velocity maps, and line diagnostics of a few characteristic spectra. Results: The line ratios of different spectra vary, indicating highly structured Hii regions, but define a locus of uniform metallicity. The strong-line diagnostic diagrams and empirical calibrations point to a nearly solar or even super-solar oxygen abundance. The velocity dispersion of the gas is highest in the region offset from the bright clusters. Star formation may be active on a low level. There is evidence for a large-scale disk-like structure in the region of SH2, which would make the similar radial velocity of the nearby globular cluster easier to understand. Conclusions: The high metallicity does not fit to a dwarf galaxy as progenitor. We favour the scenario of a free-floating gaseous complex having its origin in the merger 2 Gyr ago. Over a long period the densities increased secularly until finally the threshold for star formation was reached. SH2 illustrates how massive star clusters can form outside starbursts and without a considerable field

  7. The globular cluster system of NGC 1316. III. Kinematic complexity

    NASA Astrophysics Data System (ADS)

    Richtler, T.; Hilker, M.; Kumar, B.; Bassino, L. P.; Gómez, M.; Dirsch, B.

    2014-09-01

    discernable out to 3' radius. The kinematic major axis of NGC 1316 is misaligned by about 10° with the photometric major axis, which might indicate a triaxial symmetry. A simple spherical model like that suggested by dynamical analyses of planetary nebulae also reproduces the velocity dispersions of the faint globular clusters. Conclusions: The central dark matter density of the present model resembles a giant elliptical galaxy. This contradicts population properties which indicate spiral galaxies as pre-merger components. Modified Newtonian dynamics (MOND) would provide a solution, but the kinematical complexity of NGC 1316 does not allow a really firm conclusion. However, NGC 1316 might anyway be a problem for a cold dark matter scenario, if the high dark matter density in the inner region is confirmed in future studies. Based on observations obtained with the VLT at ESO, Cerro Paranal, Chile under the programme 078.B-0856.Appendices are available in electronic form at http://www.aanda.org

  8. Knockout driven reactions in complex molecules and their clusters

    NASA Astrophysics Data System (ADS)

    Gatchell, Michael; Zettergren, Henning

    2016-08-01

    Energetic ions lose some of their kinetic energy when interacting with electrons or nuclei in matter. Here, we discuss combined experimental and theoretical studies on such impulse driven reactions in polycyclic aromatic hydrocarbons (PAHs), fullerenes, and pure or mixed clusters of these molecules. These studies show that the nature of excitation is important for how complex molecular systems respond to ion/atom impact. Rutherford-like nuclear scattering processes may lead to prompt atom knockout and formation of highly reactive fragments, while heating of the molecular electron clouds in general lead to formation of more stable and less reactive fragments. In this topical review, we focus on recent studies of knockout driven reactions, and present new calculations of the angular dependent threshold (displacement) energies for such processes in PAHs. The so-formed fragments may efficiently form covalent bonds with neighboring molecules in clusters. These unique molecular growth processes may be important in astrophysical environments such as low velocity shock waves.

  9. Glutathione-complexed [2Fe-2S] clusters function in Fe-S cluster storage and trafficking.

    PubMed

    Fidai, Insiya; Wachnowsky, Christine; Cowan, J A

    2016-10-01

    Glutathione-coordinated [2Fe-2S] complex is a non-protein-bound [2Fe-2S] cluster that is capable of reconstituting the human iron-sulfur cluster scaffold protein IscU. This complex demonstrates physiologically relevant solution chemistry and is a viable substrate for iron-sulfur cluster transport by Atm1p exporter protein. Herein, we report on some of the possible functional and physiological roles for this novel [2Fe-2S](GS4) complex in iron-sulfur cluster biosynthesis and quantitatively characterize its role in the broader network of Fe-S cluster transfer reactions. UV-vis and circular dichroism spectroscopy have been used in kinetic studies to determine second-order rate constants for [2Fe-2S] cluster transfer from [2Fe-2S](GS4) complex to acceptor proteins, such as human IscU, Schizosaccharomyces pombe Isa1, human and yeast glutaredoxins (human Grx2 and Saccharomyces cerevisiae Grx3), and human ferredoxins. Second-order rate constants for cluster extraction from these holo proteins were also determined by varying the concentration of glutathione, and a likely common mechanism for cluster uptake was determined by kinetic analysis. The results indicate that the [2Fe-2S](GS4) complex is stable under physiological conditions, and demonstrates reversible cluster exchange with a wide range of Fe-S cluster proteins, thereby supporting a possible physiological role for such centers.

  10. Thiol surface complexation on growing CdS clusters

    SciTech Connect

    Swayambunathan, V.; Hayes, D.; Schmidt, K.H.; Liao, Y.X.; Meisel, D. )

    1990-05-09

    The growth of small CdS colloidal particles has been initiated by pulse radiolytic release of sulfide from thiol (3-mercapto-1,2-propanediol, RSH) in the presence of Cd{sup 2+} ions. The kinetics and stoichiometry of the ensuring reactions were followed by conductivity, absorption spectroscopy, and light-scattering techniques. The final CdS product has been identified by electron diffraction. The formation of Cd-thiolate complexes at the surface of the particles is indicated by conductivity and by energy dispersive analysis of X-ray (EDAX) results. The rate of formation of CdS clusters is strongly pH dependent due to the pH effect on the stability of Dd{sup 2+}/HS{sup {minus}} complexes. At low pHs (4.0-5.3) the growth mechanism is proposed to be primarily a cluster-molecule process. At this pH range Cd{sup 2+} ions at the CdS particle surface complex with thiolate ions stronger than in the bulk of the solution. The size control of the particles by thiols is proposed to result from a competition of thiolate ions with HS{sup {minus}} ions for cadmium ions at the surface of the growing particles.

  11. Fuzzy nodes recognition based on spectral clustering in complex networks

    NASA Astrophysics Data System (ADS)

    Ma, Yang; Cheng, Guangquan; Liu, Zhong; Xie, Fuli

    2017-01-01

    In complex networks, information regarding the nodes is usually incomplete because of the effects of interference, noise, and other factors. This results in parts of the network being blurred and some information having an unknown source. In this paper, a spectral clustering algorithm is used to identify fuzzy nodes and solve network reconstruction problems. By changing the fuzzy degree of placeholders, we achieve various degrees of credibility and accuracy for the restored network. Our approach is verified by experiments using open source datasets and simulated data.

  12. Heptanuclear lanthanide [Ln7] clusters: from blue-emitting solution-stable complexes to hybrid clusters.

    PubMed

    Canaj, Angelos B; Tsikalas, George K; Philippidis, Aggelos; Spyros, Apostolos; Milios, Constantinos J

    2014-09-07

    The use of LH3 (2-(β-naphthalideneamino)-2-hydroxymethyl-1-propanol) and aibH (2-amino-isobutyric acid) in 4f chemistry has led to the isolation of eight new isostructural lanthanide complexes. More specifically, the reaction of the corresponding lanthanide nitrate salt with LH3 and aibH in MeOH, under solvothermal conditions in the presence of NEt3, led to the isolation and characterization of seven complexes with the general formulae [Ln(III)7(OH)2(L')9(aib)]·4MeOH (Ln = Gd, ·4MeOH; Tb, ·4MeOH; Dy, ·4MeOH; Ho, ·4MeOH; Er, ·4MeOH; Tm, ·4MeOH; Yb, ·4MeOH L' = the dianion of the Schiff base between naphthalene aldehyde and 2-amino-isobutyric acid). Furthermore, the isostructural Y(III) analogue, cluster [Y(III)7(OH)2(L')9(aib)]·4MeOH (·4MeOH), was synthesized in a similar manner to . The structure of all eight clusters describes a distorted [M(III)6] octahedron which encapsulates a seventh M(III) ion in an off-centre fashion. Dc magnetic susceptibility studies in the 5-300 K range for complexes reveal the presence of dominant antiferromagnetic exchange interactions within the metallic clusters as evidenced by the negative Weiss constant, θ, while ac magnetic susceptibility measurements show temperature and frequency dependent out-of-phase signals for the [Dy(III)7] analogue (·4MeOH), suggesting potential single molecule magnetism character. Furthermore, for complex , simulation of its dc magnetic susceptibility data yielded very weak antiferromagnetic interactions within the metallic centres. Solid-state emission studies for all clusters display ligand-based emission, while extended 1D and 2D NMR studies for ·4MeOH reveal that the species retain their structural integrity in solution. In addition, TGA measurements for , and revealed excellent thermal stability up to 340 °C for the clusters.

  13. Invariant Chain Complexes and Clusters as Platforms for MIF Signaling.

    PubMed

    Lindner, Robert

    2017-02-10

    Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking.

  14. Invariant Chain Complexes and Clusters as Platforms for MIF Signaling

    PubMed Central

    Lindner, Robert

    2017-01-01

    Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking. PMID:28208600

  15. An Efficient Catalytic DNA that Cleaves L-RNA

    PubMed Central

    Tram, Kha; Xia, Jiaji; Gysbers, Rachel; Li, Yingfu

    2015-01-01

    Many DNAzymes have been isolated from synthetic DNA pools to cleave natural RNA (D-RNA) substrates and some have been utilized for the design of aptazyme biosensors for bioanalytical applications. Even though these biosensors perform well in simple sample matrices, they do not function effectively in complex biological samples due to ubiquitous RNases that can efficiently cleave D-RNA substrates. To overcome this issue, we set out to develop DNAzymes that cleave L-RNA, the enantiomer of D-RNA, which is known to be completely resistant to RNases. Through in vitro selection we isolated three L-RNA-cleaving DNAzymes from a random-sequence DNA pool. The most active DNAzyme exhibits a catalytic rate constant ~3 min-1 and has a structure that contains a kissing loop, a structural motif that has never been observed with D-RNA-cleaving DNAzymes. Furthermore we have used this DNAzyme and a well-known ATP-binding DNA aptamer to construct an aptazyme sensor and demonstrated that this biosensor can achieve ATP detection in biological samples that contain RNases. The current work lays the foundation for exploring RNA-cleaving DNAzymes for engineering biosensors that are compatible with complex biological samples. PMID:25946137

  16. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis[OPEN

    PubMed Central

    Willmann, Matthew R.

    2016-01-01

    RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5′ end to the 3′ end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome. PMID:27758893

  17. Synthesis of supramolecular iron (III) complexes by cluster aggregation

    NASA Astrophysics Data System (ADS)

    Seddon, Elisa Joy

    2000-12-01

    Biologically, iron is a ubiquitous and versatile metal, found in the active sites of proteins responsible for both oxygen and electron transport. Multinuclear iron-oxo proteins are either dinuclear, or contain many iron atoms; the [Fe2O] unit occurs in hemerythrin (Hr), ribonucleotide reductase, purple acid phosphatase (POP) and methane monooxygenase (MMO), whereas ferritin (Ft) can store up to 4500 iron atoms. Iron storage and transport are essential for protecting biological organisms from free iron, since free Fe(II) ions, will react with dioxygen to form destructive organic radicals, and free Fe(III) ions form insoluble iron hydroxide aggregates under physiological conditions. The tendency of iron to form molecular aggregates in systems containing water or alcohol, together with the fact that each iron atom possesses a large number of unpaired electrons (5 for high-spin FeIII) often results in products possessing large spin ground states (S). The current record-holder for iron is a Fe19 complex, with at least 33 unpaired electrons in the ground state (S = 33/2). Hence, iron is also important in the rapidly developing field of molecular magnetic materials. For these two reasons, the preparation of iron clusters with new topologies and properties has become a major goal of many synthetic inorganic groups, including our own. In this thesis work, synthetic and spectroscopic methods of inorganic coordination chemistry were used to achieve two different goals: firstly, to synthesize dinuclear iron complexes with the use of tetradentate ligands in order to study the magnetic interactions between the two metal centers; and secondly, to identify reactions and characterize the products whereby pre-formed iron oxide clusters undergo aggregation reactions to produce higher nuclearity products. The tetradentate ligands investigated were a bis-(beta-diketone) ligand L and a bis-bpy ligand L'. The reactions involving L and Fe(III) reagents produced complexes with a triple

  18. Unsaturated platinum-rhenium cluster complexes. Synthesis, structures and reactivity.

    PubMed

    Adams, Richard D; Captain, Burjor; Smith, Mark D; Beddie, Chad; Hall, Michael B

    2007-05-09

    Two new compounds PtRe3(CO)12(PBut3)(micro-H)3, 9, and PtRe2(CO)9(PBut3)(micro-H)2, 10, were obtained from the reaction of Pt(PBut3)2 with Re3(CO)12(micro-H3), 8, at room temperature. Compound 9 contains a butterfly cluster of four metals formed by the insertion of the platinum atom from a Pt(PBut3) group into one of the hydride-bridged metal-metal bonds of 8. The three hydrido ligands are bridging ligands across each of three new Pt-Re bonds. Compound 10 contains a triangular PtRe2 cluster with two hydrido ligands; one bridges a Pt-Re bond, and the other bridges the Re-Re bond. The new compound Pt2Re2(CO)7(PBut3)2(micro-H)2, 11, was obtained from the reaction of 8 with Pt(PBut3)2 in hexane at reflux. Compound 11 was also obtained from 10 by reaction with an additional quantity of Pt(PBut3)2. Compound 11 contains a tetrahedral cluster of four metal atoms with two dynamically active hydrido ligands. A CO ligand on one of the two platinum atoms also exchanges between the two platinum atoms rapidly on the NMR time scale. Compound 11 is electronically unsaturated and was found to add hydrogen at room temperature to form the tetrahydrido cluster complex, Pt2Re2(CO)7(PBut3)2(micro-H)4, 12. Compound 12 has a structure similar to 11 but contains one triply bridging hydrido ligand, two edge bridging hydrido ligands, and one terminal hydrido ligand on one of the two platinum atoms. A kinetic isotope effect D/H of 1.5(1) was determined for the addition of H2 to 11. Hydrogen can be eliminated from 12 by heating to 97 degrees C or by the application of UV-vis irradiation at room temperature. Compound 12 adds CO at room temperature to yield the complex Pt2Re2(CO)8(PBut3)2(micro-H)4, 13, which contains a planar cluster of four metal atoms with a Pt-Pt bond and four edge bridging hydrido ligands. Compounds 11 and 12 react with Pt(PBut3)2 to yield the known five metal cluster complexes Pt3Re2(CO)6(PBut3)3(micro-H)2, 14, and Pt3Re2(CO)6(PBut3)3(micro-H)4, 15, respectively. Density

  19. Laser Spectroscopy of Small Mass Selected Metal Clusters and Complexes

    NASA Astrophysics Data System (ADS)

    Robbins, David Lee

    1995-01-01

    been reported and furthermore no other metal dimer-ligand complex had been reported prior to these studies. The metal dimer work is relevant to surface adsorption and catalysis and represents the simplest adsorption experiment to date, that is adsorption of a ligand on the smallest metal cluster surface. The Mg^+ -N_2 study along with other recently investigated ion-molecule complexes are the first such complexes to be investigated.

  20. Analysis of cluster explosive synchronization in complex networks.

    PubMed

    Ji, Peng; Peron, Thomas K D M; Rodrigues, Francisco A; Kurths, Jürgen

    2014-12-01

    Correlations between intrinsic dynamics and local topology have become a new trend in the study of synchronization in complex networks. In this paper, we investigate the influence of topology on the dynamics of networks made up of second-order Kuramoto oscillators. In particular, based on mean-field calculations, we provide a detailed investigation of cluster explosive synchronization (CES) [Phys. Rev. Lett. 110, 218701 (2013)] in scale-free networks as a function of several topological properties. Moreover, we investigate the robustness of discontinuous transitions by including an additional quenched disorder, and we show that the phase coherence decreases with increasing strength of the quenched disorder. These results complement the previous findings regarding CES and also fundamentally deepen the understanding of the interplay between topology and dynamics under the constraint of correlating natural frequencies and local structure.

  1. A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.

    PubMed

    Pfeiffenberger, Erik; Chaleil, Raphael A G; Moal, Iain H; Bates, Paul A

    2017-03-01

    Reliable identification of near-native poses of docked protein-protein complexes is still an unsolved problem. The intrinsic heterogeneity of protein-protein interactions is challenging for traditional biophysical or knowledge based potentials and the identification of many false positive binding sites is not unusual. Often, ranking protocols are based on initial clustering of docked poses followed by the application of an energy function to rank each cluster according to its lowest energy member. Here, we present an approach of cluster ranking based not only on one molecular descriptor (e.g., an energy function) but also employing a large number of descriptors that are integrated in a machine learning model, whereby, an extremely randomized tree classifier based on 109 molecular descriptors is trained. The protocol is based on first locally enriching clusters with additional poses, the clusters are then characterized using features describing the distribution of molecular descriptors within the cluster, which are combined into a pairwise cluster comparison model to discriminate near-native from incorrect clusters. The results show that our approach is able to identify clusters containing near-native protein-protein complexes. In addition, we present an analysis of the descriptors with respect to their power to discriminate near native from incorrect clusters and how data transformations and recursive feature elimination can improve the ranking performance. Proteins 2017; 85:528-543. © 2016 Wiley Periodicals, Inc.

  2. ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy

    PubMed Central

    Andronov, Leonid; Orlov, Igor; Lutz, Yves; Vonesch, Jean-Luc; Klaholz, Bruno P.

    2016-01-01

    Super-resolution microscopy (PALM, STORM etc.) provides a plethora of fluorescent signals in dense cellular environments which can be difficult to interpret. Here we describe ClusterViSu, a method for image reconstruction, visualization and quantification of labelled protein clusters, based on Voronoi tessellation of the individual fluorescence events. The general applicability of this clustering approach for the segmentation of super-resolution microscopy data, including for co-localization, is illustrated on a series of important biological objects such as chromatin complexes, RNA polymerase, nuclear pore complexes and microtubules. PMID:27068792

  3. Synthesis, characterization, and structure of reduced tungsten chalcogenide cluster complexes

    SciTech Connect

    Xiaobing, Xie

    1997-10-17

    Over the previous twenty years, ternary molybdenum chalcogenides of the general formula MxMo6Y8 (M = ternary metal cation; Y = chalcogenide), known as Chevrel phases, have been extensively studied. Many of these compounds have been found to have superconductivity, catalytic activity and ionic conductivity. The rich chemistry of the Chevrel phases raises considerable interest in finding the tungsten analogues of these phases. However, no such analogue has ever been synthesized, although the Chevrel phases are usually prepared directly from elements at high temperatures above 1000{degrees}C. The absence of the tungsten analogues may be caused by their thermodynamic instability at such high temperatures. Thus it might be necessary to avoid high-temperature synthetic procedures in order to establish the ternary and binary tungsten chalcogenides. A major focus of the McCarley research group has been on the preparation of M6Y8L6 (M = Mo, W; Y = S, Se, Te) cluster complexes as low temperature pathways to the Chevrel phases.

  4. Effect of mitochondrial complex I inhibition on Fe-S cluster protein activity

    SciTech Connect

    Mena, Natalia P.; Bulteau, Anne Laure; Salazar, Julio; Hirsch, Etienne C.; Nunez, Marco T.

    2011-06-03

    Highlights: {yields} Mitochondrial complex I inhibition resulted in decreased activity of Fe-S containing enzymes mitochondrial aconitase and cytoplasmic aconitase and xanthine oxidase. {yields} Complex I inhibition resulted in the loss of Fe-S clusters in cytoplasmic aconitase and of glutamine phosphoribosyl pyrophosphate amidotransferase. {yields} Consistent with loss of cytoplasmic aconitase activity, an increase in iron regulatory protein 1 activity was found. {yields} Complex I inhibition resulted in an increase in the labile cytoplasmic iron pool. -- Abstract: Iron-sulfur (Fe-S) clusters are small inorganic cofactors formed by tetrahedral coordination of iron atoms with sulfur groups. Present in numerous proteins, these clusters are involved in key biological processes such as electron transfer, metabolic and regulatory processes, DNA synthesis and repair and protein structure stabilization. Fe-S clusters are synthesized mainly in the mitochondrion, where they are directly incorporated into mitochondrial Fe-S cluster-containing proteins or exported for cytoplasmic and nuclear cluster-protein assembly. In this study, we tested the hypothesis that inhibition of mitochondrial complex I by rotenone decreases Fe-S cluster synthesis and cluster content and activity of Fe-S cluster-containing enzymes. Inhibition of complex I resulted in decreased activity of three Fe-S cluster-containing enzymes: mitochondrial and cytosolic aconitases and xanthine oxidase. In addition, the Fe-S cluster content of glutamine phosphoribosyl pyrophosphate amidotransferase and mitochondrial aconitase was dramatically decreased. The reduction in cytosolic aconitase activity was associated with an increase in iron regulatory protein (IRP) mRNA binding activity and with an increase in the cytoplasmic labile iron pool. Since IRP activity post-transcriptionally regulates the expression of iron import proteins, Fe-S cluster inhibition may result in a false iron deficiency signal. Given that

  5. The complex star cluster system of NGC 1316 (Fornax A)

    NASA Astrophysics Data System (ADS)

    Sesto, Leandro A.; Faifer, Favio R.; Forte, Juan C.

    2016-10-01

    This paper presents Gemini-gri' high-quality photometry for cluster candidates in the field of NGC 1316 (Fornax A) as part of a study that also includes GMOS spectroscopy. A preliminary discussion of the photometric data indicates the presence of four stellar cluster populations with distinctive features in terms of age, chemical abundance and spatial distribution. Two of them seem to be the usually old (metal poor and metal rich) populations typically found in elliptical galaxies. In turn, an intermediate-age (5 Gyr) globular cluster population is the dominant component of the sample (as reported by previous papers). We also find a younger cluster population with a tentative age of ≈ 1 Gyr.

  6. Detection of protein complex from protein-protein interaction network using Markov clustering

    NASA Astrophysics Data System (ADS)

    Ochieng, P. J.; Kusuma, W. A.; Haryanto, T.

    2017-05-01

    Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks.

  7. Reconstructing Histories of Complex Gene Clusters on a Phylogeny

    NASA Astrophysics Data System (ADS)

    Vinař, Tomáš; Brejová, Broňa; Song, Giltae; Siepel, Adam

    Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. These clusters are one of the major sources of evolutionary innovation, and they are linked to multiple diseases, including HIV and a variety of cancers. Understanding their evolutionary histories is a key to the application of comparative genomics methods in these regions of the genome. We propose a probabilistic model of gene cluster evolution on a phylogeny, and an MCMC algorithm for reconstruction of duplication histories from genomic sequences in multiple species. Several projects are underway to obtain high quality BAC-based assemblies of duplicated clusters in multiple species, and we anticipate use of our methods in their analysis. Supplementary materials are located at http://compbio.fmph.uniba.sk/suppl/09recombcg/

  8. A Near-infrared Survey of the Rosette Complex: Clues of Early Cluster Evolution

    NASA Astrophysics Data System (ADS)

    Román-Zúñiga, Carlos G.; Lada, Elizabeth A.; Ferreira, Bruno

    2008-05-01

    The majority of stars in our galaxy are born in embedded clusters, which can be considered the fundamental units of star formation. We have recently surveyed the star forming content of the Rosette Complex using FLAMINGOS in order to investigate the properties of its embedded clusters. We discuss the results of our near-infrared imaging survey. In particular, we on the first evidence for the early evolution and expansion of the embedded clusters. In addition we present data suggesting a temporal sequence of cluster formation across the cloud and discuss the influence of the HII region on the star forming history of the Rosette.

  9. Network analysis of three-dimensional complex plasma clusters in a rotating electric field.

    PubMed

    Laut, I; Räth, C; Wörner, L; Nosenko, V; Zhdanov, S K; Schablinski, J; Block, D; Thomas, H M; Morfill, G E

    2014-02-01

    Network analysis was used to study the structure and time evolution of driven three-dimensional complex plasma clusters. The clusters were created by suspending micron-size particles in a glass box placed on top of the rf electrode in a capacitively coupled discharge. The particles were highly charged and manipulated by an external electric field that had a constant magnitude and uniformly rotated in the horizontal plane. Depending on the frequency of the applied electric field, the clusters rotated in the direction of the electric field or remained stationary. The positions of all particles were measured using stereoscopic digital in-line holography. The network analysis revealed the interplay between two competing symmetries in the cluster. The rotating cluster was shown to be more cylindrical than the nonrotating cluster. The emergence of vertical strings of particles was also confirmed.

  10. Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe–S Assembly Complex

    PubMed Central

    Fox, Nicholas G.; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Barondeau, David P.

    2015-01-01

    Iron–sulfur (Fe–S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe–S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe–S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe–S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe–S assembly complex. Here the kinetics of Fe–S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe–S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe–S assembly complex. PMID:26016518

  11. Protein Complex Detection via Weighted Ensemble Clustering Based on Bayesian Nonnegative Matrix Factorization

    PubMed Central

    Ou-Yang, Le; Dai, Dao-Qing; Zhang, Xiao-Fei

    2013-01-01

    Detecting protein complexes from protein-protein interaction (PPI) networks is a challenging task in computational biology. A vast number of computational methods have been proposed to undertake this task. However, each computational method is developed to capture one aspect of the network. The performance of different methods on the same network can differ substantially, even the same method may have different performance on networks with different topological characteristic. The clustering result of each computational method can be regarded as a feature that describes the PPI network from one aspect. It is therefore desirable to utilize these features to produce a more accurate and reliable clustering. In this paper, a novel Bayesian Nonnegative Matrix Factorization(NMF)-based weighted Ensemble Clustering algorithm (EC-BNMF) is proposed to detect protein complexes from PPI networks. We first apply different computational algorithms on a PPI network to generate some base clustering results. Then we integrate these base clustering results into an ensemble PPI network, in the form of weighted combination. Finally, we identify overlapping protein complexes from this network by employing Bayesian NMF model. When generating an ensemble PPI network, EC-BNMF can automatically optimize the values of weights such that the ensemble algorithm can deliver better results. Experimental results on four PPI networks of Saccharomyces cerevisiae well verify the effectiveness of EC-BNMF in detecting protein complexes. EC-BNMF provides an effective way to integrate different clustering results for more accurate and reliable complex detection. Furthermore, EC-BNMF has a high degree of flexibility in the choice of base clustering results. It can be coupled with existing clustering methods to identify protein complexes. PMID:23658709

  12. Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization.

    PubMed

    Ou-Yang, Le; Dai, Dao-Qing; Zhang, Xiao-Fei

    2013-01-01

    Detecting protein complexes from protein-protein interaction (PPI) networks is a challenging task in computational biology. A vast number of computational methods have been proposed to undertake this task. However, each computational method is developed to capture one aspect of the network. The performance of different methods on the same network can differ substantially, even the same method may have different performance on networks with different topological characteristic. The clustering result of each computational method can be regarded as a feature that describes the PPI network from one aspect. It is therefore desirable to utilize these features to produce a more accurate and reliable clustering. In this paper, a novel Bayesian Nonnegative Matrix Factorization (NMF)-based weighted Ensemble Clustering algorithm (EC-BNMF) is proposed to detect protein complexes from PPI networks. We first apply different computational algorithms on a PPI network to generate some base clustering results. Then we integrate these base clustering results into an ensemble PPI network, in the form of weighted combination. Finally, we identify overlapping protein complexes from this network by employing Bayesian NMF model. When generating an ensemble PPI network, EC-BNMF can automatically optimize the values of weights such that the ensemble algorithm can deliver better results. Experimental results on four PPI networks of Saccharomyces cerevisiae well verify the effectiveness of EC-BNMF in detecting protein complexes. EC-BNMF provides an effective way to integrate different clustering results for more accurate and reliable complex detection. Furthermore, EC-BNMF has a high degree of flexibility in the choice of base clustering results. It can be coupled with existing clustering methods to identify protein complexes.

  13. The multitude of iron-sulfur clusters in respiratory complex I.

    PubMed

    Gnandt, Emmanuel; Dörner, Katerina; Strampraad, Marc F J; de Vries, Simon; Friedrich, Thorsten

    2016-08-01

    Respiratory complex I couples the electron transfer from NADH to ubiquinone with the translocation of protons across the membrane. Complex I contains one non-covalently bound flavin mononucleotide and, depending on the species, up to ten iron-sulfur (Fe/S) clusters as cofactors. The reason for the presence of the multitude of Fe/S clusters in complex I remained enigmatic for a long time. The question was partly answered by investigations on the evolution of the complex revealing the stepwise construction of the electron transfer domain from several modules. Extension of the ancestral to the modern electron input domain was associated with the acquisition of several Fe/S-proteins. The X-ray structure of the complex showed that the NADH oxidation-site is connected with the quinone-reduction site by a chain of seven Fe/S-clusters. Fast enzyme kinetics revealed that this chain of Fe/S-clusters is used to regulate electron-tunneling rates within the complex. A possible function of the off-pathway cluster N1a is discussed. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

  14. Link-Prediction Enhanced Consensus Clustering for Complex Networks.

    PubMed

    Burgess, Matthew; Adar, Eytan; Cafarella, Michael

    2016-01-01

    Many real networks that are collected or inferred from data are incomplete due to missing edges. Missing edges can be inherent to the dataset (Facebook friend links will never be complete) or the result of sampling (one may only have access to a portion of the data). The consequence is that downstream analyses that "consume" the network will often yield less accurate results than if the edges were complete. Community detection algorithms, in particular, often suffer when critical intra-community edges are missing. We propose a novel consensus clustering algorithm to enhance community detection on incomplete networks. Our framework utilizes existing community detection algorithms that process networks imputed by our link prediction based sampling algorithm and merges their multiple partitions into a final consensus output. On average our method boosts performance of existing algorithms by 7% on artificial data and 17% on ego networks collected from Facebook.

  15. Biochemical analysis of hatchet self-cleaving ribozymes

    PubMed Central

    Li, Sanshu; Lünse, Christina E.; Harris, Kimberly A.; Breaker, Ronald R.

    2015-01-01

    Hatchet RNAs are members of a novel self-cleaving ribozyme class that was recently discovered by using a bioinformatics search strategy. The consensus sequence and secondary structure of this class includes 13 highly conserved and numerous other modestly conserved nucleotides interspersed among bulges linking four base-paired substructures. A representative hatchet ribozyme from a metagenomic source requires divalent ions such as Mg2+ to promote RNA strand scission with a maximum rate constant of ∼4 min−1. As with all other small self-cleaving ribozymes discovered to date, hatchet ribozymes employ a general mechanism for catalysis involving the nucleophilic attack of a ribose 2′-oxygen atom on an adjacent phosphorus center. Kinetic characteristics of the reaction demonstrate that members of this ribozyme class have an essential requirement for divalent metal ions and that they might have a complex active site that employs multiple catalytic strategies to accelerate RNA cleavage by internal phosphoester transfer. PMID:26385510

  16. Electronic, Magnetic, and Redox Properties and O2 Reactivity of Iron(II) and Nickel(II) o-Semiquinonate Complexes of a Tris(thioether) Ligand: Uncovering the Intradiol Cleaving Reactivity of an Iron(II) o-Semiquinonate Complex.

    PubMed

    Wang, Peng; Killian, Michelle M; Saber, Mohamed R; Qiu, Tian; Yap, Glenn P A; Popescu, Codrina V; Rosenthal, Joel; Dunbar, Kim R; Brunold, Thomas C; Riordan, Charles G

    2017-09-05

    The iron(II) semiquinonate character within the iron(III) catecholate species has been proposed by numerous studies to account for the O2 reactivity of intradiol catechol dioxygenases, but a well-characterized iron(II) semiquinonate species that exhibits intradiol cleaving reactivity has not yet been reported. In this study, a detailed electronic structure description of the first iron(II) o-semiquinonate complex, [PhTt(tBu)]Fe(phenSQ) [PhTt(tBu) = phenyltris(tert-butylthiomethyl)borate; phenSQ = 9,10-phenanthrenesemiquinonate; Wang et al. Chem. Commun. 2014, 50, 5871-5873], was generated through a combination of electronic and Mössbauer spectroscopies, SQUID magnetometry, and density functional theory (DFT) calculations. [PhTt(tBu)]Fe(phenSQ) reacts with O2 to generate an intradiol cleavage product, diphenic anhydride, in 16% yield. To assess the dependence of the intradiol reactivity on the identity of the metal ion, the nickel analogue, [PhTt(tBu)]Ni(phenSQ), and its derivative, [PhTt(tBu)]Ni(3,5-DBSQ) (3,5-DBSQ = 3,5-di-tert-butyl-1,2-semiquinonate), were prepared and characterized by X-ray crystallography, mass spectrometry, (1)H NMR and electronic spectroscopies, and SQUID magnetometry. DFT calculations, evaluated on the basis of the experimental data, support the electronic structure descriptions of [PhTt(tBu)]Ni(phenSQ) and [PhTt(tBu)]Ni(3,5-DBSQ) as high-spin nickel(II) complexes with antiferromagnetically coupled semiquinonate ligands. Unlike its iron counterpart, [PhTt(tBu)]Ni(phenSQ) decomposes slowly in an O2 atmosphere to generate 14% phenanthrenequinone with a negligible amount of diphenic anhydride. [PhTt(tBu)]Ni(3,5-DBSQ) does not react with O2. This dramatic effect of the metal-ion identity supports the hypothesis that a metal(III) alkylperoxo species serves as an intermediate in the intradiol cleaving reactions. The redox properties of all three complexes were probed using cyclic voltammetry and differential pulse voltammetry, which indicate an

  17. Dynamics of Abell 3266 - I. An optical view of a complex merging cluster

    NASA Astrophysics Data System (ADS)

    Dehghan, Siamak; Johnston-Hollitt, Melanie; Colless, Matthew; Miller, Rowan

    2017-07-01

    We present spectroscopy of 880 galaxies within a 2° field around the massive, merging cluster Abell 3266. This sample, which includes 704 new measurements, was combined with the existing redshifts measurements to generate a sample of over 1300 spectroscopic redshifts; the largest spectroscopic sample in the vicinity of A3266 to date. We define a cluster sub-sample of 790 redshifts that lie within a velocity range of 14 000 to 22 000 km s-1 and within 1° of the cluster centre. A detailed structural analysis finds A3266 to have a complex dynamical structure containing six groups and filaments to the north of the cluster as well as a cluster core that can be decomposed into two components split along a northeast-southwest axis, consistent with previous X-ray observations. The mean redshift of the cluster core is found to be 0.0594 ± 0.0005 and the core velocity dispersion is given as 1462^{+99}_{-99} km s-1. The overall velocity dispersion and redshift of the entire cluster and related structures are 1337^{+67}_{-67} km s-1 and 0.0596 ± 0.0002, respectively, though the high velocity dispersion does not represent virialized motions but rather is due to relative motions of the cluster components. We posit A3266 is seen following a merger along the northeast-southwest axis; however, the rich substructure in the rest of the cluster suggests that the dynamical history is more complex than just a simple merger with a range of continuous dynamical interactions taking place. It is thus likely that turbulence in A3266 is very high, even for a merging cluster.

  18. Experimental studies of complex crater formation under cluster implantation of solids

    NASA Astrophysics Data System (ADS)

    Prasalovich, S.; Popok, V.; Persson, P.; Campbell, E. E. B.

    2005-10-01

    The results of a systematic study of surface defect formation after energetic Arn+ (n = 12, 22, 32, 54) and Xen+ (n = 4, 16) cluster ion implantation into silicon and sapphire are presented. Implantation energies vary from 3 to 18 keV/ion. Two cases of comparative studies are carried out: the same cluster species are implanted into two different substrates, i.e. Arn+ cluster ions into silicon and sapphire and two different cluster species Arn+ and Xen+ are implanted into the same kind of substrate (silicon). Atomic force, scanning electron and transmission electron microscopies (AFM, SEM and TEM) are used to study the implanted samples. The analysis reveals the formation of two types of surface erosion defects: simple and complex (with centrally positioned hillock) craters. It is found that the ratio of simple to complex crater formation as well as the hillock dimensions depend strongly on the cluster species, size and impact energy as well as on the type of substrate material. Qualitative models describing the two comparative cases of cluster implantation, the case of different cluster species and the case of different substrate materials, are proposed.

  19. Membrane skeleton orchestrates the platelet glycoprotein (GP) Ib-IX complex clustering and signaling.

    PubMed

    Shang, Dan; Zhang, Zuping; Wang, Qian; Ran, Yali; Shaw, Tanner S; Van, John N; Peng, Yuandong

    2016-10-01

    Platelet glycoprotein Ib-IX complex is affixed to the membrane skeleton through interaction with actin binding protein 280 (ABP-280). We find that removal of the ABP-280 binding sites in GP Ibα cytoplasmic tail has little impact on the complex clustering induced by antibody crosslinking. However, large truncation of the GP Ibα cytoplasmic tail allows the formation of larger patches of the complex, suggesting that an ABP-280 independent force may exist. Besides, we observe that the signaling upon GP Ib-IX clustering is elicited in both membrane lipid domain dependent and independent manner, a choice that relies on how the membrane skeleton interacts with the complex. Our findings suggest a more complex mechanism for how the membrane skeleton regulates the GP Ib-IX function. © 2016 IUBMB Life, 68(10):823-829, 2016.

  20. Clustering of ventricular arrhythmic complexes in heart rhythm

    NASA Astrophysics Data System (ADS)

    Sokolova, Anastasia; Bogachev, Mikhail I.; Bunde, Armin

    2011-02-01

    We study the statistics of intervals τ between ventricular premature complexes (VPCs) in 24-h electrocardiogram records obtained from PhysioNet data source. We find that the long-term memory inherent in the heartbeat intervals leads to power laws in the probability density function P(τ) between VPCs for τ>6 s. As a consequence, the probability W(t,Δt) that at least one VPC will occur within the next time interval Δt, if the last VPC occurred t time units intervals ago, decays by a power law of t. Based on these results, we suggest a method to obtain a priori information about the occurrence of the next VPC, and how to predict it. We think that usage of this a priori information could be useful for the improvement of the algorithms in healthcare monitoring devices with alarm facilities.

  1. Directed clustering coefficient as a measure of systemic risk in complex banking networks

    NASA Astrophysics Data System (ADS)

    Tabak, Benjamin M.; Takami, Marcelo; Rocha, Jadson M. C.; Cajueiro, Daniel O.; Souza, Sergio R. S.

    2014-01-01

    Recent literature has focused on the study of systemic risk in complex networks. It is clear now, after the crisis of 2008, that the aggregate behavior of the interaction among agents is not straightforward and it is very difficult to predict. Contributing to this debate, this paper shows that the directed clustering coefficient may be used as a measure of systemic risk in complex networks. Furthermore, using data from the Brazilian interbank network, we show that the directed clustering coefficient is negatively correlated with domestic interest rates.

  2. Optimized catalytic DNA-cleaving ribozymes

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor)

    1996-01-01

    The present invention discloses nucleic acid enzymes capable of cleaving nucleic acid molecules, including single-stranded DNA, in a site-specific manner under physiologic conditions, as well as compositions including same. The present invention also discloses methods of making and using the disclosed enzymes and compositions.

  3. Cyclopentanone ring-cleaved pleuromutilin derivatives.

    PubMed

    Springer, Dane M; Bunker, Amy; Luh, Bing-Yu; Sorenson, Margaret E; Goodrich, Jason T; Bronson, Joanne J; DenBleyker, Kenneth; Dougherty, Thomas J; Fung-Tomc, Joan

    2007-01-01

    Ring-cleaved pleuromutilin derivatives comprised of a [5.3.1] bicyclic core structure have been synthesized and evaluated in vitro as antibacterial agents. Four of the compounds described were found to have MICs

  4. Cluster formation by allelomimesis in real-world complex adaptive systems

    NASA Astrophysics Data System (ADS)

    Juanico, Dranreb Earl; Monterola, Christopher; Saloma, Caesar

    2005-04-01

    Animal and human clusters are complex adaptive systems and many organize in cluster sizes s that obey the frequency distribution D(s)∝s-τ . The exponent τ describes the relative abundance of the cluster sizes in a given system. Data analyses reveal that real-world clusters exhibit a broad spectrum of τ values, 0.7 (tuna fish schools) ⩽τ⩽4.61 (T4 bacteriophage gene family sizes). Allelomimesis is proposed as an underlying mechanism for adaptation that explains the observed broad τ spectrum. Allelomimesis is the tendency of an individual to imitate the actions of others and two cluster systems have different τ values when their component agents display unequal degrees of allelomimetic tendencies. Cluster formation by allelomimesis is shown to be of three general types: namely, blind copying, information-use copying, and noncopying. Allelomimetic adaptation also reveals that the most stable cluster size is formed by three strongly allelomimetic individuals. Our finding is consistent with available field data taken from killer whales and marmots.

  5. Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters.

    PubMed

    Shippy, Teresa D; Ronshaugen, Matthew; Cande, Jessica; He, Jianping; Beeman, Richard W; Levine, Michael; Brown, Susan J; Denell, Robin E

    2008-04-01

    The remarkable conservation of Hox clusters is an accepted but little understood principle of biology. Some organizational constraints have been identified for vertebrate Hox clusters, but most of these are thought to be recent innovations that may not apply to other organisms. Ironically, many model organisms have disrupted Hox clusters and may not be well-suited for studies of structural constraints. In contrast, the red flour beetle, Tribolium castaneum, which has a long history in Hox gene research, is thought to have a more ancestral-type Hox cluster organization. Here, we demonstrate that the Tribolium homeotic complex (HOMC) is indeed intact, with the individual Hox genes in the expected colinear arrangement and transcribed from the same strand. There is no evidence that the cluster has been invaded by non-Hox protein-coding genes, although expressed sequence tag and genome tiling data suggest that noncoding transcripts are prevalent. Finally, our analysis of several mutations affecting the Tribolium HOMC suggests that intermingling of enhancer elements with neighboring transcription units may constrain the structure of at least one region of the Tribolium cluster. This work lays a foundation for future studies of the Tribolium HOMC that may provide insights into the reasons for Hox cluster conservation.

  6. Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters

    PubMed Central

    Ronshaugen, Matthew; Cande, Jessica; He, JianPing; Beeman, Richard W.; Levine, Michael; Brown, Susan J.; Denell, Robin E.

    2008-01-01

    The remarkable conservation of Hox clusters is an accepted but little understood principle of biology. Some organizational constraints have been identified for vertebrate Hox clusters, but most of these are thought to be recent innovations that may not apply to other organisms. Ironically, many model organisms have disrupted Hox clusters and may not be well-suited for studies of structural constraints. In contrast, the red flour beetle, Tribolium castaneum, which has a long history in Hox gene research, is thought to have a more ancestral-type Hox cluster organization. Here, we demonstrate that the Tribolium homeotic complex (HOMC) is indeed intact, with the individual Hox genes in the expected colinear arrangement and transcribed from the same strand. There is no evidence that the cluster has been invaded by non-Hox protein-coding genes, although expressed sequence tag and genome tiling data suggest that noncoding transcripts are prevalent. Finally, our analysis of several mutations affecting the Tribolium HOMC suggests that intermingling of enhancer elements with neighboring transcription units may constrain the structure of at least one region of the Tribolium cluster. This work lays a foundation for future studies of the Tribolium HOMC that may provide insights into the reasons for Hox cluster conservation. PMID:18392875

  7. Ant colony clustering with fitness perception and pheromone diffusion for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Ji, Junzhong; Song, Xiangjing; Liu, Chunnian; Zhang, Xiuzhen

    2013-08-01

    Community structure detection in complex networks has been intensively investigated in recent years. In this paper, we propose an adaptive approach based on ant colony clustering to discover communities in a complex network. The focus of the method is the clustering process of an ant colony in a virtual grid, where each ant represents a node in the complex network. During the ant colony search, the method uses a new fitness function to percept local environment and employs a pheromone diffusion model as a global information feedback mechanism to realize information exchange among ants. A significant advantage of our method is that the locations in the grid environment and the connections of the complex network structure are simultaneously taken into account in ants moving. Experimental results on computer-generated and real-world networks show the capability of our method to successfully detect community structures.

  8. Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes.

    PubMed

    Liu, Meng; Chang, Dingran; Li, Yingfu

    2017-09-19

    DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors. This Account begins with the description of an accidental discovery on the sequence adaptability of a small DNAzyme known as "8-17", when we performed 16 parallel selections to search for DNAzymes that targeted each and every possible dinucleotide junction of RNA for cleavage. DNAzyme 8-17 dominated all the selection pools targeting purine-containing junctions. In-depth sequence analysis revealed that 8-17 could manifest itself in many sequence options defined by the requirement of four absolutely conserved nucleotides. This study also exposed the fact that 8-17 had poor activity toward pyrimidine-pyrimidine junctions. With this information in hand, we proceeded to the discovery of diverse non-8-17 DNAzymes that exhibited robust catalytic activity under physiological conditions. These DNAzymes were found to universally interact with their substrates through two Watson-Crick binding arms and have a catalytic core of varying length and secondary-structure complexity. RNA-cleaving DNAzymes were also isolated to function at acidic conditions (pH 3-5), and these molecules exhibited intriguing pH profiles, with the highest activity precisely matching the pH used for their selection. Interestingly, these DNAzymes appear to use non-Watson-Crick interactions in defining their structures. More recently, we have embarked on the development of ligand-responsive RNA-cleaving fluorogenic DNAzymes that can recognize specific bacterial pathogens

  9. Label propagation algorithm based on edge clustering coefficient for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Zhang, Xian-Kun; Tian, Xue; Li, Ya-Nan; Song, Chen

    2014-08-01

    The label propagation algorithm (LPA) is a graph-based semi-supervised learning algorithm, which can predict the information of unlabeled nodes by a few of labeled nodes. It is a community detection method in the field of complex networks. This algorithm is easy to implement with low complexity and the effect is remarkable. It is widely applied in various fields. However, the randomness of the label propagation leads to the poor robustness of the algorithm, and the classification result is unstable. This paper proposes a LPA based on edge clustering coefficient. The node in the network selects a neighbor node whose edge clustering coefficient is the highest to update the label of node rather than a random neighbor node, so that we can effectively restrain the random spread of the label. The experimental results show that the LPA based on edge clustering coefficient has made improvement in the stability and accuracy of the algorithm.

  10. Investigating the function of [2Fe–2S] cluster N1a, the off-pathway cluster in complex I, by manipulating its reduction potential

    PubMed Central

    Birrell, James A.; Morina, Klaudia; Bridges, Hannah R.; Friedrich, Thorsten; Hirst, Judy

    2013-01-01

    NADH:quinone oxidoreductase (complex I) couples NADH oxidation and quinone reduction to proton translocation across an energy-transducing membrane. All complexes I contain a flavin to oxidize NADH, seven iron–sulfur clusters to transfer electrons from the flavin to quinone and an eighth cluster (N1a) on the opposite side of the flavin. The role of cluster N1a is unknown, but Escherichia coli complex I has an unusually high-potential cluster N1a and its reduced flavin produces H2O2, not superoxide, suggesting that cluster N1a may affect reactive oxygen species production. In the present study, we combine protein film voltammetry with mutagenesis in overproduced N1a-binding subunits to identify two residues that switch N1a between its high- (E. coli, valine and asparagine) and low- (Bos taurus and Yarrowia lipolytica, proline and methionine) potential forms. The mutations were incorporated into E. coli complex I: cluster N1a could no longer be reduced by NADH, but H2O2 and superoxide production were unaffected. The reverse mutations (that increase the potential by ~0.16 V) were incorporated into Y. lipolytica complex I, but N1a was still not reduced by NADH. We conclude that cluster N1a does not affect reactive oxygen species production by the complex I flavin; it is probably required for enzyme assembly or stability. PMID:23980528

  11. Investigating the function of [2Fe-2S] cluster N1a, the off-pathway cluster in complex I, by manipulating its reduction potential.

    PubMed

    Birrell, James A; Morina, Klaudia; Bridges, Hannah R; Friedrich, Thorsten; Hirst, Judy

    2013-11-15

    NADH:quinone oxidoreductase (complex I) couples NADH oxidation and quinone reduction to proton translocation across an energy-transducing membrane. All complexes I contain a flavin to oxidize NADH, seven iron-sulfur clusters to transfer electrons from the flavin to quinone and an eighth cluster (N1a) on the opposite side of the flavin. The role of cluster N1a is unknown, but Escherichia coli complex I has an unusually high-potential cluster N1a and its reduced flavin produces H2O2, not superoxide, suggesting that cluster N1a may affect reactive oxygen species production. In the present study, we combine protein film voltammetry with mutagenesis in overproduced N1a-binding subunits to identify two residues that switch N1a between its high- (E. coli, valine and asparagine) and low- (Bos taurus and Yarrowia lipolytica, proline and methionine) potential forms. The mutations were incorporated into E. coli complex I: cluster N1a could no longer be reduced by NADH, but H2O2 and superoxide production were unaffected. The reverse mutations (that increase the potential by ~0.16 V) were incorporated into Y. lipolytica complex I, but N1a was still not reduced by NADH. We conclude that cluster N1a does not affect reactive oxygen species production by the complex I flavin; it is probably required for enzyme assembly or stability.

  12. Prospects of molybdenum and rhenium octahedral cluster complexes as X-ray contrast agents.

    PubMed

    Krasilnikova, Anna A; Shestopalov, Michael A; Brylev, Konstantin A; Kirilova, Irina A; Khripko, Olga P; Zubareva, Kristina E; Khripko, Yuri I; Podorognaya, Valentina T; Shestopalova, Lidiya V; Fedorov, Vladimir E; Mironov, Yuri V

    2015-03-01

    Investigation of new X-ray contrast media for radiography is an important field of science since discovering of X-rays in 1895. Despite the wide diversity of available X-ray contrast media the toxicity, especially nephrotoxicity, is still a big problem to be solved. The octahedral metal-cluster complexes of the general formula [{M6Q8}L6] can be considered as quite promising candidates for the role of new radiocontrast media due to the high local concentration of heavy elements, high tuning ability of ligand environment and low toxicity. To exemplify this, the X-ray computed tomography experiments for the first time were carried out on some octahedral cluster complexes of molybdenum and rhenium. Based on the obtained data it was proposed to investigate the toxicological proprieties of cluster complex Na2H8[{Re6Se8}(P(CH2CH2CONH2)(CH2CH2COO)2)6]. Observed low cytotoxic and acute toxic effects along with rapid renal excretion of the cluster complex evidence its perspective as an X-ray contrast media for radiography. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Neptunium(vi) chain and neptunium(vi/v) mixed valence cluster complexes.

    PubMed

    Cornet, Stéphanie M; Häller, L Jonas L; Sarsfield, Mark J; Collison, David; Helliwell, Madeleine; May, Iain; Kaltsoyannis, Nikolas

    2009-02-28

    The synthesis of [Np(VI)O(2)Cl(2)(thf)](n) offers the potential for more detailed exploration of neptunyl(vi) chemistry, while the synthesis of the mixed valence cluster complex [{Np(VI)O(2)Cl(2)}{Np(V)O(2)Cl(thf)(3)}(2)] allows molecular neptunyl(v) 'cation-cation' interactions to be probed.

  14. Adult Speakers' Tongue-Palate Contact Patterns for Bilabial Stops within Complex Clusters

    ERIC Educational Resources Information Center

    Zharkova, Natalia; Schaeffler, Sonja; Gibbon, Fiona E.

    2009-01-01

    Previous studies using Electropalatography (EPG) have shown that individuals with speech disorders sometimes produce articulation errors that affect bilabial targets, but currently there is limited normative data available. In this study, EPG and acoustic data were recorded during complex word final sps clusters spoken by 20 normal adults. A total…

  15. The Redox-Bohr group associated with iron-sulfur cluster N2 of complex I.

    PubMed

    Zwicker, Klaus; Galkin, Alexander; Dröse, Stefan; Grgic, Ljuban; Kerscher, Stefan; Brandt, Ulrich

    2006-08-11

    Proton pumping respiratory complex I (NADH:ubiquinone oxidoreductase) is a major component of the oxidative phosphorylation system in mitochondria and many bacteria. In mammalian cells it provides 40% of the proton motive force needed to make ATP. Defects in this giant and most complicated membrane-bound enzyme cause numerous human disorders. Yet the mechanism of complex I is still elusive. A group exhibiting redox-linked protonation that is associated with iron-sulfur cluster N2 of complex I has been proposed to act as a central component of the proton pumping machinery. Here we show that a histidine in the 49-kDa subunit that resides near iron-sulfur cluster N2 confers this redox-Bohr effect. Mutating this residue to methionine in complex I from Yarrowia lipolytica resulted in a marked shift of the redox midpoint potential of iron-sulfur cluster N2 to the negative and abolished the redox-Bohr effect. However, the mutation did not significantly affect the catalytic activity of complex I and protons were pumped with an unchanged stoichiometry of 4 H(+)/2e(-). This finding has significant implications on the discussion about possible proton pumping mechanism for complex I.

  16. Characterization of the laser cleaving on glass sheets with a line-shape laser beam

    NASA Astrophysics Data System (ADS)

    Wang, Yu-Zan; Lin, Jehnming

    2007-07-01

    A CO 2 laser with a line-shape beam was used to cleave a soda-lime glass substrate at various beam-rotation angles to the cutting direction. The stress distribution on the glass substrate cleaved by the laser beam has been analyzed in this study. An uncoupled thermal-elastic analysis was achieved by the ABAQUS software based on the finite element method. The numerical results show that the stress field of the fracture is caused by a complex stress state and the cleavages are significantly affected by the heat diffusion and beam rotation angle. At the rotation angle of zero degree to the cleaving direction, the phenomena of the chip formation have been found due to a large temperature gradient at the cleaving depth of the glass substrate.

  17. The Geometric Cluster Algorithm: Rejection-Free Monte Carlo Simulation of Complex Fluids

    NASA Astrophysics Data System (ADS)

    Luijten, Erik

    2005-03-01

    The study of complex fluids is an area of intense research activity, in which exciting and counter-intuitive behavior continue to be uncovered. Ironically, one of the very factors responsible for such interesting properties, namely the presence of multiple relevant time and length scales, often greatly complicates accurate theoretical calculations and computer simulations that could explain the observations. We have recently developed a new Monte Carlo simulation methodootnotetextJ. Liu and E. Luijten, Phys. Rev. Lett.92, 035504 (2004); see also Physics Today, March 2004, pp. 25--27. that overcomes this problem for several classes of complex fluids. Our approach can accelerate simulations by orders of magnitude by introducing nonlocal, collective moves of the constituents. Strikingly, these cluster Monte Carlo moves are proposed in such a manner that the algorithm is rejection-free. The identification of the clusters is based upon geometric symmetries and can be considered as the off-latice generalization of the widely-used Swendsen--Wang and Wolff algorithms for lattice spin models. While phrased originally for complex fluids that are governed by the Boltzmann distribution, the geometric cluster algorithm can be used to efficiently sample configurations from an arbitrary underlying distribution function and may thus be applied in a variety of other areas. In addition, I will briefly discuss various extensions of the original algorithm, including methods to influence the size of the clusters that are generated and ways to introduce density fluctuations.

  18. Complex Network Clustering by a Multi-objective Evolutionary Algorithm Based on Decomposition and Membrane Structure

    NASA Astrophysics Data System (ADS)

    Ju, Ying; Zhang, Songming; Ding, Ningxiang; Zeng, Xiangxiang; Zhang, Xingyi

    2016-09-01

    The field of complex network clustering is gaining considerable attention in recent years. In this study, a multi-objective evolutionary algorithm based on membranes is proposed to solve the network clustering problem. Population are divided into different membrane structures on average. The evolutionary algorithm is carried out in the membrane structures. The population are eliminated by the vector of membranes. In the proposed method, two evaluation objectives termed as Kernel J-means and Ratio Cut are to be minimized. Extensive experimental studies comparison with state-of-the-art algorithms proves that the proposed algorithm is effective and promising.

  19. Zwitterion-dianion complexes and anion-anion clusters with negative dissociation energies.

    PubMed

    Kass, Steven R

    2005-09-28

    Clusters of oxalate and malonate dianions with glycine in its zwitterionic form were found by ab initio and density functional theory calculations. Proton transfer is impeded by an electrostatic barrier, but the resulting anion-anion pairs form complexes despite having negative dissociation energies. A variety of X-/Y- species with exothermic dissociation energies ranging from 10 to 141 kcal mol-1, but large enough barriers to be experimentally produced, are reported. These dianions may represent an unrecognized control element in nature and provide a unique opportunity to probe electrostatic effects and a wealth of novel clusters.

  20. Complex Network Clustering by a Multi-objective Evolutionary Algorithm Based on Decomposition and Membrane Structure

    PubMed Central

    Ju, Ying; Zhang, Songming; Ding, Ningxiang; Zeng, Xiangxiang; Zhang, Xingyi

    2016-01-01

    The field of complex network clustering is gaining considerable attention in recent years. In this study, a multi-objective evolutionary algorithm based on membranes is proposed to solve the network clustering problem. Population are divided into different membrane structures on average. The evolutionary algorithm is carried out in the membrane structures. The population are eliminated by the vector of membranes. In the proposed method, two evaluation objectives termed as Kernel J-means and Ratio Cut are to be minimized. Extensive experimental studies comparison with state-of-the-art algorithms proves that the proposed algorithm is effective and promising. PMID:27670156

  1. Characterization and prediction of IVF cycles generating "slow-cleaving" embryos.

    PubMed

    Tarin, J J; Romero, J L; Bonilla-Musoles, F

    1994-10-01

    To characterize and predict cycles generating open quote slow-cleaving closed quote embryos in in vitro fertilization, 86 cycles were retrospectively divided into two groups (open quote slow, closed quote n=41, and open quote fast, closed quote n=45) according to whether the number of blastomeres per embryo on day 3 was < or = or > than the mean of the distribution, respectively. Cycles generating open quote slow-cleaving closed quote embryos were treated with luteinizing hormone-releasing hormone agonist before ovarian stimulation for a shorter period (12.1 +/- 0.5 versus 15.6 +/- 1.1 days; P < or = 0.01) and had higher immaturity grade of oocyte-corona-cumulus complexes which resulted in embryos (1.6 +/- 0.1 vs 1.3 +/- 0.1; P < or = 0.05) when compared to cycles producing "fast-cleaving" embryos. Both variables entered in a logistic regression model applied in order to predict the probability of a cycle generating "slow-cleaving" embryos (goodness-of-fit chi-square = 180.0, degrees of freedom (df) = 80, P = 0.4786). This model predicted correctly 86.7% (13 of 15) of cycles generating "slow-cleaving" embryos and 83.3% (10 of 12) of cycles producing "fast-cleaving" embryos when the estimated probability of a cycle producing "slow-cleaving embryos" was > or = 0.7 or < or = 0.3, respectively. Shorter treatment with hormone-releasing hormone agonist before ovarian stimulation and higher immaturity grade of oocyte- corona-cumulus complexes which result in embryos are predictive characteristics of in vitro fertilization cycles generating "slow-cleaving" embryos.

  2. Ionic Complexes of Metal Oxide Clusters for Versatile Self-Assemblies.

    PubMed

    Li, Bao; Li, Wen; Li, Haolong; Wu, Lixin

    2017-06-20

    The combination of rational design of building components and suitable utilization of driving force affords spontaneous molecular assemblies with well-defined nanostructure and morphology over multiple length scales. The serious challenges in constructing assemblies with structural advantages for the realization of functions programmed into the building components usually lie ahead since the process that occurs does not always follow the expected roadmap in the absence of external intervention. Thus, prefabricated intermediates that help in governing the target self-assemblies are developed into a type of unique building blocks. Metal oxide cluster polyanions are considered as a type of molecular nanoclusters with size scale and structural morphology similar to those of many known inorganic particles and clusters but possess distinctive characteristics. Following the understanding of these clusters in self-assembly and the rationalization of their most efficient design strategy and approach, the obtained fundamental principles can also be applied in common nanoparticle- and cluster-based systems. On the other hand, the deliberate synergy offered by organic countercations that support the self-assembly of these clusters greatly expands the opportunity for the functionalization of complex building units via control of multiple interactions. The ionic combination of the inorganic clusters with hydrophilicity and the cationic organic component with hydrophobicity leads to discrete properties of the complexes. Significantly, the core-shell structure with rigid-flexible features and amphiphilicity will pave the way for hierarchical self-assemblies of the obtained complexes, while the intrinsic characteristics of the metal oxide clusters can be modulated through external physicochemical stimuli. Within this context, over the past decade we have extensively explored the ionic combination of inorganic polyanionic clusters with cationic organic amphiphiles and devoted our

  3. Opening of Carborane Cages by Metal Cluster Complexes: The Reaction of a Thiolate-Substituted Carborane with Triosmium Carbonyl Cluster Complexes.

    PubMed

    Adams, Richard D; Kiprotich, Joseph; Peryshkov, Dmitry V; Wong, Yuen Onn

    2016-08-15

    The reaction of Os3(CO)10(NCMe)2 with closo-o-(1-SCH3)C2B10H11 has yielded the complex Os3(CO)9[μ3-η(3)-C2B10H9(SCH3)](μ-H)2, 1, by the loss of the two NCMe ligands and one CO ligand from the Os3 cluster and the coordination of the sulfur atom and the activation of two B-H bonds with transfer of the hydrogen atoms to the cluster. Reaction of 1 with a second equivalent of Os3(CO)10(NCMe)2 yielded the complex Os3(CO)9(μ-H)[(μ3-η(3)-1,4,5-μ3-η(3)-6,10,11-C2B10H8S(CH3)]Os3(CO)9(μ-H)2, 2, that contains two triosmium triangles attached to the same carborane cage. The carborane cage was opened by cleavage of two B-C bonds and one B-B bond. The B-H group that was pulled out of the cage became a triply bridging group on one of the Os3 triangles but remains bonded to the cage by two B-B bonds. When heated to 150 °C, 2 was transformed into the complex Os3(CO)9(μ-H)[(μ3-η(3)-μ3-η(3)-C2B10H7S(CH3)]Os3(CO)9(μ-H), 3, by the loss of two hydrogen atoms and a rearrangement that led to further opening of the carborane cage. Reaction of 1 with a second equivalent of closo-o-(1-SCH3)C2B10H11 has yielded the complex Os3(CO)6)(μ3-η(3)-C2B10H9-R-SCH3) (μ3-η(3)-C2B10H10-S-SCH3)(μ-H)3, 4a, containing two carborane cages coordinated to one Os3 cluster. Compound 4a was isomerized to the compound Os3(CO)6(μ3-η(3)-C2B10H9-R-SCH3)(μ3-η(3)-C2B10H10-R-SCH3)(μ-H)3, 4b, by an inversion of stereochemistry at one of the sulfur atoms by heating to 174 °C.

  4. Adaptive fuzzy leader clustering of complex data sets in pattern recognition

    NASA Technical Reports Server (NTRS)

    Newton, Scott C.; Pemmaraju, Surya; Mitra, Sunanda

    1992-01-01

    A modular, unsupervised neural network architecture for clustering and classification of complex data sets is presented. The adaptive fuzzy leader clustering (AFLC) architecture is a hybrid neural-fuzzy system that learns on-line in a stable and efficient manner. The initial classification is performed in two stages: a simple competitive stage and a distance metric comparison stage. The cluster prototypes are then incrementally updated by relocating the centroid positions from fuzzy C-means system equations for the centroids and the membership values. The AFLC algorithm is applied to the Anderson Iris data and laser-luminescent fingerprint image data. It is concluded that the AFLC algorithm successfully classifies features extracted from real data, discrete or continuous.

  5. Complex nanoscale cage clusters built from uranyl polyhedra and phosphate tetrahedra

    SciTech Connect

    Unruh, Daniel K.; Ling, Jie; Qiu, Jie; Pressprich, Laura; Baranay, Melissa; Ward, Matthew; Burns, Peter C.

    2011-06-20

    Five cage clusters that self-assemble in alkaline aqueous solution have been isolated and characterized. Each is built from uranyl hexagonal bipyramids with two or three equatorial edges occupied by peroxide, and three also contain phosphate tetrahedra. These clusters contain 30 uranyl polyhedra; 30 uranyl polyhedra and six pyrophosphate groups; 30 uranyl polyhedra, 12 pyrophosphate groups, and one phosphate tetrahedron; 42 uranyl polyhedra; and 40 uranyl polyhedra and three pyrophosphate groups. These clusters present complex topologies as well as a range of compositions, sizes, and charges. Two adopt fullerene topologies, and the others contain combinations of topological squares, pentagons, and hexagons. An analysis of possible topologies further indicates that higher-symmetry topologies are favored.

  6. Adaptive fuzzy leader clustering of complex data sets in pattern recognition

    NASA Technical Reports Server (NTRS)

    Newton, Scott C.; Pemmaraju, Surya; Mitra, Sunanda

    1992-01-01

    A modular, unsupervised neural network architecture for clustering and classification of complex data sets is presented. The adaptive fuzzy leader clustering (AFLC) architecture is a hybrid neural-fuzzy system that learns on-line in a stable and efficient manner. The initial classification is performed in two stages: a simple competitive stage and a distance metric comparison stage. The cluster prototypes are then incrementally updated by relocating the centroid positions from fuzzy C-means system equations for the centroids and the membership values. The AFLC algorithm is applied to the Anderson Iris data and laser-luminescent fingerprint image data. It is concluded that the AFLC algorithm successfully classifies features extracted from real data, discrete or continuous.

  7. H ∞ Cluster Synchronization for a Class of Neutral Complex Dynamical Networks with Markovian Switching

    PubMed Central

    2014-01-01

    H ∞ cluster synchronization problem for a class of neutral complex dynamical networks (NCDNs) with Markovian switching is investigated in this paper. Both the retarded and neutral delays are considered to be interval mode dependent and time varying. The concept of H ∞ cluster synchronization is proposed to quantify the attenuation level of synchronization error dynamics against the exogenous disturbance of the NCDNs. Based on a novel Lyapunov functional, by employing some integral inequalities and the nature of convex combination, mode delay-range-dependent H ∞ cluster synchronization criteria are derived in the form of linear matrix inequalities which depend not only on the disturbance attenuation but also on the initial values of the NCDNs. Finally, numerical examples are given to demonstrate the feasibility and effectiveness of the proposed theoretical results. PMID:24892088

  8. Studying the Effect of a Composition of the Cluster Core in High-Radiopacity Cluster Complexes of Rhenium on Their Acute Toxicity In Vivo.

    PubMed

    Pozmogova, T N; Krasil'nikova, A A; Ivanov, A A; Shestopalov, M A; Gyrylova, S N; Shestopalova, L V; Shestopaloiv, A M; Shkurupy, V A

    2016-05-01

    An in vivo study was performed to evaluate the dependence of acute toxicity of high-radiopacity and luminescent octahedral cluster complexes of rhenium after intravenous injection on a composition of the cluster core. Changes in mouse body weight, water and food consumption, degree of intoxication, and morphological changes in the visceral organs were studied after intravenous injection of the following cluster complexes with various internal ligands (S, Se, or Te): Na4[{Re 6 Te 8 }(CN)6], Na4[{Re 6 Se 8 }(CN)6], and Na4[{Re 6 S 8 }(CN)6]. The Na4[{Re 6 S 8 } (CN)6] cluster complex was shown to be the safest for animals.

  9. Biodistribution of rhenium cluster complex K₄[Re6S8(CN)6] in the body of laboratory rats.

    PubMed

    Brylev, K A; Shestopalov, M A; Khripko, O P; Trunova, V A; Zvereva, V V; Wang, C C; Mironov, Yu V; Fedorov, V E

    2013-10-01

    We studied the biodistribution of luminescent octahedral rhenium cluster complex K4[Re6S8(CN)6], a promising agent for photodynamic therapy. It was shown that rhenium complex [Re6S8(CN)6](4-)is mainly accumulated in the liver, the central organ of metabolism, and can be excreted by the kidneys. The cluster complex was also accumulated in the spleen in significant amount, which makes it a promising agent for creation of preparations for diagnostics and treatment of lymphoproliferative disorders. The mean lethal dose of the cluster complex was 0.38 g/kg.

  10. Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex.

    PubMed

    Wu, Jianlan; Tang, Zhoufei; Gong, Zhihao; Cao, Jianshu; Mukamel, Shaul

    2015-04-02

    The energy absorbed in a light-harvesting protein complex is often transferred collectively through aggregated chromophore clusters. For population evolution of chromophores, the time-integrated effective rate matrix allows us to construct quantum kinetic clusters quantitatively and determine the reduced cluster-cluster transfer rates systematically, thus defining a minimal model of energy-transfer kinetics. For Fenna-Matthews-Olson (FMO) and light-havrvesting complex II (LCHII) monomers, quantum Markovian kinetics of clusters can accurately reproduce the overall energy-transfer process in the long-time scale. The dominant energy-transfer pathways are identified in the picture of aggregated clusters. The chromophores distributed extensively in various clusters can assist a fast and long-range energy transfer.

  11. Cluster N1 of complex I from Yarrowia lipolytica studied by pulsed EPR spectroscopy.

    PubMed

    Maly, T; Grgic, L; Zwicker, K; Zickermann, V; Brandt, U; Prisner, T

    2006-04-01

    After reduction with nicotinamide adenine dinucleotide (NADH), NADH:ubiquinone oxidoreductase (complex I) of the strictly aerobic yeast Yarrowia lipolytica shows clear signals from five different paramagnetic iron-sulfur (FeS) clusters (N1-N5) which can be detected using electron paramagnetic resonance (EPR) spectroscopy. The ligand environment and the assignment of several FeS clusters to specific binding motifs found in several subunits of the complex are still under debate. In order to characterize the hyperfine interaction of the surrounding nuclei with FeS cluster N1, one- and two-dimensional electron spin echo envelope modulation experiments were performed at a temperature of 30 K. At this temperature only cluster N1 contributes to the overall signal in a pulsed EPR experiment. The hyperfine and quadrupole tensors of a nitrogen nucleus and the isotropic and dipolar hyperfine couplings of two sets of protons could be determined by numerical simulation of the one- and two-dimensional spectra. The values obtained are in perfect agreement with a ferredoxin-like binding structure by four cysteine amino acid residues and allow the assignment of the nitrogen couplings to a backbone nitrogen nucleus and the proton couplings to the beta-protons of the bound cysteine residues.

  12. Complete characterization of the stability of cluster synchronization in complex dynamical networks.

    PubMed

    Sorrentino, Francesco; Pecora, Louis M; Hagerstrom, Aaron M; Murphy, Thomas E; Roy, Rajarshi

    2016-04-01

    Synchronization is an important and prevalent phenomenon in natural and engineered systems. In many dynamical networks, the coupling is balanced or adjusted to admit global synchronization, a condition called Laplacian coupling. Many networks exhibit incomplete synchronization, where two or more clusters of synchronization persist, and computational group theory has recently proved to be valuable in discovering these cluster states based on the topology of the network. In the important case of Laplacian coupling, additional synchronization patterns can exist that would not be predicted from the group theory analysis alone. Understanding how and when clusters form, merge, and persist is essential for understanding collective dynamics, synchronization, and failure mechanisms of complex networks such as electric power grids, distributed control networks, and autonomous swarming vehicles. We describe a method to find and analyze all of the possible cluster synchronization patterns in a Laplacian-coupled network, by applying methods of computational group theory to dynamically equivalent networks. We present a general technique to evaluate the stability of each of the dynamically valid cluster synchronization patterns. Our results are validated in an optoelectronic experiment on a five-node network that confirms the synchronization patterns predicted by the theory.

  13. Complete characterization of the stability of cluster synchronization in complex dynamical networks

    PubMed Central

    Sorrentino, Francesco; Pecora, Louis M.; Hagerstrom, Aaron M.; Murphy, Thomas E.; Roy, Rajarshi

    2016-01-01

    Synchronization is an important and prevalent phenomenon in natural and engineered systems. In many dynamical networks, the coupling is balanced or adjusted to admit global synchronization, a condition called Laplacian coupling. Many networks exhibit incomplete synchronization, where two or more clusters of synchronization persist, and computational group theory has recently proved to be valuable in discovering these cluster states based on the topology of the network. In the important case of Laplacian coupling, additional synchronization patterns can exist that would not be predicted from the group theory analysis alone. Understanding how and when clusters form, merge, and persist is essential for understanding collective dynamics, synchronization, and failure mechanisms of complex networks such as electric power grids, distributed control networks, and autonomous swarming vehicles. We describe a method to find and analyze all of the possible cluster synchronization patterns in a Laplacian-coupled network, by applying methods of computational group theory to dynamically equivalent networks. We present a general technique to evaluate the stability of each of the dynamically valid cluster synchronization patterns. Our results are validated in an optoelectronic experiment on a five-node network that confirms the synchronization patterns predicted by the theory. PMID:27152349

  14. Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets

    PubMed Central

    2010-01-01

    Background Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information. Most phylogenetic analysis methods utilize multiple alignment of sequences and are based on an evolutionary model. However, multiple alignment is not an automated procedure and requires human intervention to maintain alignment integrity and to produce phylogenies consistent with the functional splits in underlying sequences. To address this problem, we propose to use the alignment-free Relative Complexity Measure (RCM) combined with reduced amino acid alphabets to cluster protein families into functional subtypes purely on sequence criteria. Comparison with an alignment-based approach was also carried out to test the quality of the clustering. Results We demonstrate the robustness of RCM with reduced alphabets in clustering of protein sequences into families in a simulated dataset and seven well-characterized protein datasets. On protein datasets, crotonases, mandelate racemases, nucleotidyl cyclases and glycoside hydrolase family 2 were clustered into subfamilies with 100% accuracy whereas acyl transferase domains, haloacid dehalogenases, and vicinal oxygen chelates could be assigned to subfamilies with 97.2%, 96.9% and 92.2% accuracies, respectively. Conclusions The overall combination of methods in this paper is useful for clustering protein families into subtypes based on solely protein sequence information. The method is also flexible and computationally fast because it does not require multiple alignment of sequences. PMID:20718947

  15. Hexaazide octahedral molybdenum cluster complexes: Synthesis, properties and the evidence of hydrolysis

    NASA Astrophysics Data System (ADS)

    Vorotnikov, Yuri A.; Efremova, Olga A.; Novozhilov, Igor N.; Yanshole, Vadim V.; Kuratieva, Natalia V.; Brylev, Konstantin A.; Kitamura, Noboru; Mironov, Yuri V.; Shestopalov, Michael A.

    2017-04-01

    This article reports the synthesis, crystal structure of new molybdenum hexaazide cluster complex (nBu4N)2[{Mo6I8}(N3)6] (3) and comparison of its photophysical and electrochemical properties to those of earlier reported analogues (nBu4N)2[{Mo6X8}(N3)6] (X = Cl, Br). Additionally, the dimerisation of 3 as a result of hydrolysis was revealed by mass spectrometry and single crystal X-Ray diffraction. Indeed, the structurally characterised compound (nBu4N)4[({Mo6I8}(N3)5)2O] represents the first example of oxo-bridged dimer of octahedral molybdenum clusters complexes.

  16. Bimetallic octahedral ruthenium-nickel carbido cluster complexes. Synthesis and structural characterization.

    PubMed

    Saha, Sumit; Zhu, Lei; Captain, Burjor

    2013-03-04

    The reaction of Ru5(CO)15(μ5-C) with Ni(COD)2 in acetonitrile at 80 °C affords the bimetallic octahedral ruthenium-nickel cluster complex Ru5Ni(NCMe)(CO)15(μ6-C), 3. The acetonitrile ligand in 3 can be replaced by CO and NH3 to yield Ru5Ni(CO)16(μ6-C), 4, and Ru5Ni(NH3)(CO)15(μ6-C), 5, respectively. Photolysis of compound 3 in benzene and toluene solvent yielded the η(6)-coordinated benzene and toluene Ru5Ni carbido cluster complexes Ru5Ni(CO)13(η(6)-C6H6)(μ6-C), 6, and Ru5Ni(CO)13(η(6)-C7H8)(μ6-C), 7, respectively. All five new compounds were structurally characterized by single-crystal X-ray diffraction analyses.

  17. A Transition Metal Complex (Venus Flytrap Cluster) for Radioimmunodetection and Radioimmunotherapy

    NASA Astrophysics Data System (ADS)

    Paxton, Raymond J.; Beatty, Barbara G.; Hawthorne, M. Frederick; Varadarajan, Aravamuthan; Williams, Lawrence E.; Curtis, Frederick L.; Knobler, Carolyn B.; Beatty, J. David; Shiveley, John E.

    1991-04-01

    A novel transition metal complex, Venus flytrap cluster (VFC), is described for the preparation of radiolabeled antibodies. VFC contained 57Co, which was held tightly between the faces of two covalently bridged carborane ligands by cluster bonding of the metal with appropriate ligand orbitals. Anti-carcinoembryonic antigen monoclonal antibody T84.66 was conjugated to 57Co-VFC with full retention of immunological activity. Biodistribution studies in nude mice bearing carcinoembryonic antigen-producing tumors showed excellent tumor localization of 57Co-VFC-T84.66. The accumulation of radionuclide in normal liver was low and independent of dose, which may reflect the stability of the radionuclide complex. These results presage the use of VFC systems for binding transition metals that are clinically useful for radio-immunodiagnosis and radioimmunotherapy.

  18. Molecular orbital calculations of octahedral molybdenum cluster complexes with the DV-X{alpha} method

    SciTech Connect

    Imoto, Hideo; Saito, Taro; Adachi, Hirohiko

    1995-04-26

    Discrete variational-{Chi}{alpha} molecular orbital methods were applied to octahedral cluster complexes, [Mo{sub 6}X{sub 8}-(PH{sub 3}){sub 6}](X = S and Se). This structure is of interest due to its role in superconductivity of Chevrel plates. Level energies are discussed and factors contributing to their separations are categorized. Agreement with empirical XPS data is excellent.

  19. Detecting overlapping protein complexes by rough-fuzzy clustering in protein-protein interaction networks.

    PubMed

    Wu, Hao; Gao, Lin; Dong, Jihua; Yang, Xiaofei

    2014-01-01

    In this paper, we present a novel rough-fuzzy clustering (RFC) method to detect overlapping protein complexes in protein-protein interaction (PPI) networks. RFC focuses on fuzzy relation model rather than graph model by integrating fuzzy sets and rough sets, employs the upper and lower approximations of rough sets to deal with overlapping complexes, and calculates the number of complexes automatically. Fuzzy relation between proteins is established and then transformed into fuzzy equivalence relation. Non-overlapping complexes correspond to equivalence classes satisfying certain equivalence relation. To obtain overlapping complexes, we calculate the similarity between one protein and each complex, and then determine whether the protein belongs to one or multiple complexes by computing the ratio of each similarity to maximum similarity. To validate RFC quantitatively, we test it in Gavin, Collins, Krogan and BioGRID datasets. Experiment results show that there is a good correspondence to reference complexes in MIPS and SGD databases. Then we compare RFC with several previous methods, including ClusterONE, CMC, MCL, GCE, OSLOM and CFinder. Results show the precision, sensitivity and separation are 32.4%, 42.9% and 81.9% higher than mean of the five methods in four weighted networks, and are 0.5%, 11.2% and 66.1% higher than mean of the six methods in five unweighted networks. Our method RFC works well for protein complexes detection and provides a new insight of network division, and it can also be applied to identify overlapping community structure in social networks and LFR benchmark networks.

  20. Detecting Overlapping Protein Complexes by Rough-Fuzzy Clustering in Protein-Protein Interaction Networks

    PubMed Central

    Wu, Hao; Gao, Lin; Dong, Jihua; Yang, Xiaofei

    2014-01-01

    In this paper, we present a novel rough-fuzzy clustering (RFC) method to detect overlapping protein complexes in protein-protein interaction (PPI) networks. RFC focuses on fuzzy relation model rather than graph model by integrating fuzzy sets and rough sets, employs the upper and lower approximations of rough sets to deal with overlapping complexes, and calculates the number of complexes automatically. Fuzzy relation between proteins is established and then transformed into fuzzy equivalence relation. Non-overlapping complexes correspond to equivalence classes satisfying certain equivalence relation. To obtain overlapping complexes, we calculate the similarity between one protein and each complex, and then determine whether the protein belongs to one or multiple complexes by computing the ratio of each similarity to maximum similarity. To validate RFC quantitatively, we test it in Gavin, Collins, Krogan and BioGRID datasets. Experiment results show that there is a good correspondence to reference complexes in MIPS and SGD databases. Then we compare RFC with several previous methods, including ClusterONE, CMC, MCL, GCE, OSLOM and CFinder. Results show the precision, sensitivity and separation are 32.4%, 42.9% and 81.9% higher than mean of the five methods in four weighted networks, and are 0.5%, 11.2% and 66.1% higher than mean of the six methods in five unweighted networks. Our method RFC works well for protein complexes detection and provides a new insight of network division, and it can also be applied to identify overlapping community structure in social networks and LFR benchmark networks. PMID:24642838

  1. Ligation of erythrocyte CR1 induces its clustering in complex with scaffolding protein FAP-1

    PubMed Central

    Glodek, Aleksandra M.; Weaver, Gregory; Klickstein, Lloyd B.; Nicholson-Weller, Anne

    2008-01-01

    The primary identified function of complement receptor 1 (CR1/CD35) on primate erythrocytes is to bind complement-tagged inflammatory particles including microbes and immune complexes. When erythrocytes circulate through liver and spleen, sinusoidal phagocytes remove CR1-adherent particles and erythrocytes return to the circulation. This process of immune adherence clearance is important for host defense and prevention of autoimmunity. CR1 was previously described as clustered in the human erythrocyte membrane, which was thought to be necessary for binding complement-opsonized particles. In contrast, we demonstrate that on erythrocytes CR1 is not clustered, but dispersed, and able to bind complement-tagged particles. When fresh erythrocytes are solubilized by nonionic detergent, CR1 partitions to the cytoskeleton fraction. Using a PDZ-peptide array, CR1's cytoplasmic tail, which contains 2 PDZ-motifs, binds PDZ domains 2, 3, and 5 of Fas-associated phosphatase 1 (FAP-1), a scaffolding protein. We show that FAP-1, not previously recognized as an erythroid protein, is expressed on circulating erythrocytes. CR1 and FAP-1 coimmunoprecipitate, which confirms their molecular association. Disperse CR1 on erythrocytes may be advantageous for capturing immune-complexes, while ligation-induced CR1 clustering may prevent ingestion of the erythrocyte during the immune-complex transfer to the macrophages by keeping the opsonic stimulus localized thus preventing phagocyosis. PMID:18684861

  2. Voltage clustering in redox-active ligand complexes: mitigating electronic communication through choice of metal ion

    DOE PAGES

    Zarkesh, Ryan A.; Ichimura, Andrew S.; Monson, Todd C.; ...

    2016-02-01

    We used the redox-active bis(imino)acenapthene (BIAN) ligand to synthesize homoleptic aluminum, chromium, and gallium complexes of the general formula (BIAN)3M. The resulting compounds were characterized using X-ray crystallography, NMR, EPR, magnetic susceptibility and cyclic voltammetry measurements and modeled using both DFT and ab initio wavefunction calculations to compare the orbital contributions of main group elements and transition metals in ligand-based redox events. Ultimately, complexes of this type have the potential to improve the energy density and electrolyte stability of grid-scale energy storage technologies, such as redox flow batteries, through thermodynamically-clustered redox events.

  3. Voltage clustering in redox-active ligand complexes: mitigating electronic communication through choice of metal ion

    SciTech Connect

    Zarkesh, Ryan A.; Ichimura, Andrew S.; Monson, Todd C.; Tomson, Neil C.; Anstey, Mitchell R.

    2016-02-01

    We used the redox-active bis(imino)acenapthene (BIAN) ligand to synthesize homoleptic aluminum, chromium, and gallium complexes of the general formula (BIAN)3M. The resulting compounds were characterized using X-ray crystallography, NMR, EPR, magnetic susceptibility and cyclic voltammetry measurements and modeled using both DFT and ab initio wavefunction calculations to compare the orbital contributions of main group elements and transition metals in ligand-based redox events. Ultimately, complexes of this type have the potential to improve the energy density and electrolyte stability of grid-scale energy storage technologies, such as redox flow batteries, through thermodynamically-clustered redox events.

  4. The Fas-FADD Death Domain Complex Structure Unravels Signalling by Receptor Clustering

    SciTech Connect

    Scott, F.; Stec, B; Pop, C; Dobaczewska, M; Lee, J; Monosov, E; Robinson, H; Salvesen, G; Schwarzenbacher, R; Riedl, S

    2009-01-01

    The death inducing signalling complex (DISC) formed by Fas receptor, FADD (Fas-associated death domain protein) and caspase 8 is a pivotal trigger of apoptosis1, 2, 3. The Fas-FADD DISC represents a receptor platform, which once assembled initiates the induction of programmed cell death. A highly oligomeric network of homotypic protein interactions comprised of the death domains of Fas and FADD is at the centre of DISC formation4, 5. Thus, characterizing the mechanistic basis for the Fas-FADD interaction is crucial for understanding DISC signalling but has remained unclear largely because of a lack of structural data. We have successfully formed and isolated the human Fas-FADD death domain complex and report the 2.7 A crystal structure. The complex shows a tetrameric arrangement of four FADD death domains bound to four Fas death domains. We show that an opening of the Fas death domain exposes the FADD binding site and simultaneously generates a Fas-Fas bridge. The result is a regulatory Fas-FADD complex bridge governed by weak protein-protein interactions revealing a model where the complex itself functions as a mechanistic switch. This switch prevents accidental DISC assembly, yet allows for highly processive DISC formation and clustering upon a sufficient stimulus. In addition to depicting a previously unknown mode of death domain interactions, these results further uncover a mechanism for receptor signalling solely by oligomerization and clustering events.

  5. The structural and bonding evolution in cysteine-gold cluster complexes.

    PubMed

    Zhao, Yaxue; Zhou, Feng; Zhou, Huchen; Su, Haibin

    2013-02-07

    The bonding characteristics in cysteine-gold cluster complexes represented by thiolate (Au(n)·Cys(S) (n = 1, 3, 5, 7)) and thiol (Au(n)·Cys(SH) (n = 2, 4, 6, 8)) is investigated by density functional theory with 6-31G(d,p) and Lanl2DZ hybrid basis sets. The complexes exhibit very different bonding characteristic between these two forms. In the Au(n)·Cys(S) complexes, the charge transfers from gold clusters to sulfur atoms. The number of S-Au bonds in the Au(n)·Cys(S) complexes evolves from one to two when n is greater than three. For n equals three, i.e. Au(3)·Cys(S), its ground state only has one S-Au bond. While the only S-Au bond in Au(1)·Cys(S) is mainly covalent, the nature of the S-Au bond in other thiolates is featured with the combination of covalent and donor-acceptor interactions. In particular, one stable isomer of Au(3)·Cys(S) with two S-Au bonds, which is 2 kcal mol(-1) higher in energy than the corresponding ground state, consists of one covalent and one donor-acceptor S-Au bond explicitly. Moreover, the localized three center two electron bonds are formed within the Au clusters, which facilitates the formation of the two S-Au bonds in Au(5)·Cys(S) and Au(7)·Cys(S) complexes. In the Au(n)·Cys(SH) complexes, the donor-acceptor interaction prevails in the Au-SH bond by transferring lone pair electrons from the sulfur atom to the adjacent gold atom. Interestingly, the orbital with much more 6s-component in Au(4)·Cys(SH) enhances the donor-acceptor bonding character, thus yields the strongest bonding among all the Au(n)·Cys(SH) complexes studied in this paper. In general, the bonding strength between gold clusters and cysteine is positively correlated with the S-Au overlap-weighted bond order, but negatively correlated with the S-Au bond length. Lastly, the covalent and donor-acceptor S-Au bond strength is computed to be 48 and 18 kcal mol(-1), respectively.

  6. [Classification and Contribution Analysis of Aromatic Clusters in Protein-Ligand Complexes].

    PubMed

    Yamasaki, Hiroyuki; Koseki, Jun; Nishibata, Yoshihiko; Hirono, Shuichi

    2016-01-01

      Intermolecular interactions are key features in the stabilization or destabilization of complexes. In particular, interactions involving aromatic rings have been extensively studied both theoretically and experimentally. Studies have shown that aromatic-aromatic interactions can be categorized by ring-ring orientation into a variety of different types, such as stacking interactions and T-shaped interactions. Because these different orientations affect stabilization, analyses of such interactions, for example ab initio molecular orbital calculations, are applied to pairs of aromatic rings, both in model systems and real systems. An important series of aromatic-aromatic interactions include those between pairs of aromatic residues in proteins. These residues have been studied computationally using both a theoretical chemistry approach and a knowledge-based analys. Protein 3D structural information is essential for knowledge-based studies of aromatic-aromatic interactions in protein-ligand complexes. Some databases filter entries from the Protein Data Bank (PDB) using criteria that make them suitable for computational approaches involving specific research targets. Lanzarotti et al. have shown that aromatic clusters in which three or more aromatic residues are in close proximity to each other are found in many protein structures, expanding pairwise aromatic-aromatic interactions. Moreover, these clusters are thought to be important in terms of protein function, structural stability and ligand recognition. Here, we show that aromatic clusters, as well as individual proteins, are found in a variety of protein-ligand complexes. As such, we anticipate that these clusters might have a significant role in ligand binding and could help in efficient ligand design.

  7. Laser cleaving on glass sheets with multiple laser beams

    NASA Astrophysics Data System (ADS)

    Kuo, Yen-Liang; Lin, Jehnming

    2008-05-01

    A multiple laser system consisting of CO 2 line-shaped and Nd-YAG pulsed lasers was applied to cleave a soda-lime glass substrate in this study. Due to an increase of absorption coefficient of the wavelength of 1.06 μm for Nd-YAG laser on the soda-lime glass at high temperatures, the glass sheets were preheated by the CO 2 line-shaped laser and followed with the pulsed Nd-YAG laser to generate a mixture fracture mode on the substrate. The stress distribution on the glass substrate cleaved by the multiple laser beams has been analyzed. An uncoupled thermal-elastic analysis based on the finite-element method (FEM) was made. The numerical results show that the stress field of the fracture region is caused by a complex stress state and the cleavages are significantly affected by the pulsed laser. A clean cut of the soda-lime glass substrate could be obtained due to a large shear stress state on the cutting direction with the pulsed laser radiated on the glass substrate.

  8. Oligomeric rare-earth metal cluster complexes with endohedral transition metal atoms

    SciTech Connect

    Steinberg, Simon; Zimmermann, Sina; Brühmann, Matthias; Meyer, Eva; Rustige, Christian; Wolberg, Marike; Daub, Kathrin; Bell, Thomas; Meyer, Gerd

    2014-11-15

    Comproportionation reactions of rare-earth metal trihalides (RX{sub 3}) with the respective rare-earth metals (R) and transition metals (T) led to the formation of 22 oligomeric R cluster halides encapsulating T, in 19 cases for the first time. The structures of these compounds were determined by single-crystal X-ray diffraction and are composed of trimers ((T{sub 3}R{sub 11})X{sub 15}-type, P6{sub 3}/m), tetramers ((T{sub 4}R{sub 16})X{sub 28}(R{sub 4}) (P-43m), (T{sub 4}R{sub 16})X{sub 20} (P4{sub 2}/nnm), (T{sub 4}R{sub 16})X{sub 24}(RX{sub 3}){sub 4} (I4{sub 1}/a) and (T{sub 4}R{sub 16})X{sub 23} (C2/m) types of structure) and pentamers ((Ru{sub 5}La{sub 14}){sub 2}Br{sub 39}, Cc) of (TR{sub r}){sub n} (n=2–5) clusters. These oligomers are further enveloped by inner (X{sup i}) as well as outer (X{sup a}) halido ligands, which possess diverse functionalities and interconnect like oligomers through i–i, i–a and/or a–i bridges. The general features of the crystal structures for these new compounds are discussed and compared to literature entries as well as different structure types with oligomeric T centered R clusters. Dimers and tetramers originating from the aggregation of (TR{sub 6}) octahedra via common edges are more frequent than trimers and pentamers, in which the (TR{sub r}) clusters share common faces. - Graphical abstract: Rare earth-metal cluster complexes with endohedral transition metal atoms (TR{sub 6}) may connect via common edges or faces to form dimers, trimers, tetramers and pentamers of which the tetramers are the most prolific. Packing effects and electron counts play an important role. - Highlights: • Rare-earth metal cluster complexes encapsulate transition metal atoms. • Oligomers are built via connection of octahedral clusters via common edges or faces. • Dimers through pentamers with closed structures are known. • Tetramers including a tetrahedron of endohedral atoms are the most prolific.

  9. Cluster-dependent colistin hetero-resistance in Enterobacter cloacae complex.

    PubMed

    Guérin, François; Isnard, Christophe; Sinel, Clara; Morand, Philippe; Dhalluin, Anne; Cattoir, Vincent; Giard, Jean-Christophe

    2016-11-01

    Aims of this study were to: (i) evaluate whether the cluster membership could have an impact on hetero-resistance phenotype to colistin in the Enterobacter cloacae complex (ECC); and (ii) determine the genetic mechanism of colistin hetero-resistance in ECC. A collection of 124 clinical isolates belonging to 13 clusters were used to analyse the hetero-resistance phenotype (MICs were determined using the broth microdilution method, Etest and population analysis profiling). Different mutants (ΔphoP, ΔphoQ, ΔphoPQ, ΔpmrA, ΔpmrB, ΔpmrAB, ΔarnE, ΔarnF and ΔarnBCADTEF) were constructed and tested for their colistin hetero-resistance phenotype. Based on broth microdilution and Etest results, it was shown that the hetero-resistance to colistin depended on the cluster: strains from clusters I, II, IV, VII, IX, X, XI and XII were usually hetero-resistant, whereas those from clusters III, V, VI, VIII and XIII were categorized as susceptible. However, for some cluster V and VIII strains, a small proportion (<10(-7)) of cells appeared resistant when tested by population analysis profiling. From a mechanistic point of view, analysis of mutants revealed that the mechanism of hetero-resistance was mainly due to the expression of the arn operon and the phoP/phoQ two-component regulatory system. Because the colistin hetero-resistance appeared cluster-dependent in the ECC, it should be advocated to determine the cluster of the strain associated with the infection in parallel with the MIC of colistin. The resistance mechanism may not be similar to other Enterobacteriaceae since only the two-component regulatory system PhoP/PhoQ (and not PmrA/PmrB) seemed to play a role in resistance regulation. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Isotope effects in the infrared spectra of OCS-He complexes and clusters.

    PubMed

    Abusara, Z; Borvayeh, L; Moazzen-Ahmadi, N; McKellar, A R W

    2006-10-14

    Infrared spectra of the OCS-He van der Waals complex and of OCS-He(N) clusters have been studied in the region of the OCS nu1 fundamental band using a tunable diode laser to probe a pulsed supersonic slit jet. For the complex, the spectrum of the normal isotope, 16O12C32S-4He, has been considerably extended and the 34S- and 13C-substituted forms have been recorded for the first time. The data could be analyzed satisfactorily using a conventional asymmetric rotor Hamiltonian with sextic centrifugal distortion terms. For the clusters, the 34S- and 13C-substituted forms have been observed and assigned for N = 2-7, including some transitions with higher J values than previously reported for the normal isotope, e.g., R5. The observed vibrational shifts, relative to the free OCS molecule, were very similar to those of the normal isotope, and most of the difference could be explained by simple scaling. These results constitute a subtle and precise probe of intermolecular forces and dynamical effects in a system which is of current interest for cluster studies.

  11. A space-time model for carbapenemase-producing Klebsiella pneumoniae (KPC) cluster quantification in a high-complexity hospital.

    PubMed

    Abboud, C S; Monteiro, J; França, J I D; Pignatari, A C; De Souza, E E; Camargo, E C G; Monteiro, A M V; Dos Santos, R G; Kiffer, C R V

    2015-09-01

    A retrospective space-time permutation model with non-Euclidean distance criteria was applied within a high-complexity hospital setting to quantitatively explore cluster patterns of 273 patients infected with or colonized by carbapenemase-producing Klebsiella pneumoniae during 4 years. Results were compared to standard nosocomial active-surveillance methods. Two clusters were identified in the period, suggesting that space-time strategies for cluster quantification within confined environments may be useful.

  12. Copper(II) complexes of salicylic acid combining superoxide dismutase mimetic properties with DNA binding and cleaving capabilities display promising chemotherapeutic potential with fast acting in vitro cytotoxicity against cisplatin sensitive and resistant cancer cell lines.

    PubMed

    O'Connor, Mark; Kellett, Andrew; McCann, Malachy; Rosair, Georgina; McNamara, Mary; Howe, Orla; Creaven, Bernadette S; McClean, Siobhán; Kia, Agnieszka Foltyn-Arfa; O'Shea, Denis; Devereux, Michael

    2012-03-08

    The complexes [Cu(salH)(2)(H(2)O)] (1), [Cu(dipsH)(2)(H(2)O)] (2), {Cu(3-MeOsal)(H(2)O)(0.75)}(n) (3), [Cu(dipsH)(2)(BZDH)(2)] (4), [Cu(dipsH)(2)(2-MeOHBZDH)(2)]·EtOH (5), [Cu(sal)(phen)] (6), [Cu(dips)(phen)]·H(2)O (7), and [Cu(3-MeOsal)(phen)]·H(2)O (8) (salH(2) = salicylic acid; dipsH(2) = 3,5-diisopropylsalicylic acid; 3-MeOsalH(2) = 3-methoxysalicylic acid; BZDH = benzimidazole; 2-MeOHBZDH = 2 methanolbenzimidazole and phen =1,10-phenanthroline) were prepared and characterized. Structures of 4, 5, and 8 were determined by X-ray crystallography. Compounds 1-8 are potent superoxide dismutase mimetics, and they are inactive as inhibitors of COX-2 activity. Compounds 1, 4, and 5 exhibit moderate inhibition of COX-1. Complexes 6-8 display rapid micromolar cytotoxicity against cisplatin sensitive (breast (MCF-7), prostate (DU145), and colon (HT29)) and cisplatin resistant (ovarian (SK-OV-3)) cell lines compared to 1-5, and they exhibit potent in vitro DNA binding and cleavage capabilities.

  13. A Glutaredoxin·BolA Complex Serves as an Iron-Sulfur Cluster Chaperone for the Cytosolic Cluster Assembly Machinery.

    PubMed

    Frey, Avery G; Palenchar, Daniel J; Wildemann, Justin D; Philpott, Caroline C

    2016-10-21

    Cells contain hundreds of proteins that require iron cofactors for activity. Iron cofactors are synthesized in the cell, but the pathways involved in distributing heme, iron-sulfur clusters, and ferrous/ferric ions to apoproteins remain incompletely defined. In particular, cytosolic monothiol glutaredoxins and BolA-like proteins have been identified as [2Fe-2S]-coordinating complexes in vitro and iron-regulatory proteins in fungi, but it is not clear how these proteins function in mammalian systems or how this complex might affect Fe-S proteins or the cytosolic Fe-S assembly machinery. To explore these questions, we use quantitative immunoprecipitation and live cell proximity-dependent biotinylation to monitor interactions between Glrx3, BolA2, and components of the cytosolic iron-sulfur cluster assembly system. We characterize cytosolic Glrx3·BolA2 as a [2Fe-2S] chaperone complex in human cells. Unlike complexes formed by fungal orthologs, human Glrx3-BolA2 interaction required the coordination of Fe-S clusters, whereas Glrx3 homodimer formation did not. Cellular Glrx3·BolA2 complexes increased 6-8-fold in response to increasing iron, forming a rapidly expandable pool of Fe-S clusters. Fe-S coordination by Glrx3·BolA2 did not depend on Ciapin1 or Ciao1, proteins that bind Glrx3 and are involved in cytosolic Fe-S cluster assembly and distribution. Instead, Glrx3 and BolA2 bound and facilitated Fe-S incorporation into Ciapin1, a [2Fe-2S] protein functioning early in the cytosolic Fe-S assembly pathway. Thus, Glrx3·BolA is a [2Fe-2S] chaperone complex capable of transferring [2Fe-2S] clusters to apoproteins in human cells. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Familial clustering of congenital deafness, patent ductus arteriosus, Eisenmenger complex, and differential cyanosis: A case report.

    PubMed

    Lin, Ting-Wei; Tseng, Chih-Wei; Huang, Chi-Yao; Wang, Kuo-Yang; Liang, Kae-Woei

    2017-06-01

    Few studies had reported syndromes that include patent ductus arteriosus (PDA) with Eisenmenger syndrome and congenital deafness clustered in male siblings without facial, skeletal, or mental abnormalities. Two brothers, who were deaf and had PDA with Eisenmenger complex, were first seen at our Cardiology clinic at the ages of 25 and 41, respectively. They presented with progressive dyspnea on exertion. Upon physical examination, both brothers had clubbing and/or cyanotic toes, normal fingers, and without facial, skeletal, ophthalmological, or mental abnormalities. Echocardiography and multidetector computed tomography revealed large PDAs in both brothers. Cardiac catheterization showed bidirectional shunting via the PDA. Familial clustering of Eisenmenger PDA and congenital deafness is rare. Further studies are warranted to define possible genetic links.

  15. High resolution Raman spectroscopy of complexes and clusters in molecular beams. Performance report

    SciTech Connect

    Felker, P.M.

    1991-12-31

    The DOE-sponsored project in this laboratory has two facets. The first is the development of methods of nonlinear Raman spectroscopy for application in studies of sparse samples. The second is the application of such methods to structural and dynamical studies of species in supersonic molecular beams. The progress we have made in both of these areas is described in this paper. The report is divided into five remaining sections. The first pertains to theoretical and experimental developments in Fourier transform stimulated emission spectroscopy and Fourier transform hole-burning spectroscopy. The second deals with progress in the development of ionization-detected stimulated Raman spectroscopies (IDSRS). The third describes results from the application of IDSRS methods to studies of jet-cooled benzene clusters. The fourth describes IDSRS results from studies of hydrogen-bonded complexes containing phenols. The fifth relates to studies of carbazole-(Ar){sub n} clusters.

  16. High resolution Raman spectroscopy of complexes and clusters in molecular beams

    SciTech Connect

    Felker, P.M.

    1991-01-01

    The DOE-sponsored project in this laboratory has two facets. The first is the development of methods of nonlinear Raman spectroscopy for application in studies of sparse samples. The second is the application of such methods to structural and dynamical studies of species in supersonic molecular beams. The progress we have made in both of these areas is described in this paper. The report is divided into five remaining sections. The first pertains to theoretical and experimental developments in Fourier transform stimulated emission spectroscopy and Fourier transform hole-burning spectroscopy. The second deals with progress in the development of ionization-detected stimulated Raman spectroscopies (IDSRS). The third describes results from the application of IDSRS methods to studies of jet-cooled benzene clusters. The fourth describes IDSRS results from studies of hydrogen-bonded complexes containing phenols. The fifth relates to studies of carbazole-(Ar){sub n} clusters.

  17. The impact of polyploidy on the evolution of a complex NB-LRR resistance gene cluster in soybean

    USDA-ARS?s Scientific Manuscript database

    A comparative genomics approach was used to investigate the evolution of a complex NB-LRR gene cluster found in soybean (Glycine max), common bean (Phaseolus vulgaris), and other legumes. In soybean, the cluster is associated with several disease resistance (R) genes of known function including Rpg1...

  18. Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters

    SciTech Connect

    Shen, Chen-Hsiang; Wang, Yuan-Fang; Kovalevsky, Andrey Y.; Harrison, Robert W.; Weber, Irene T.

    2010-10-22

    The structural and kinetic effects of amprenavir (APV), a clinical HIV protease (PR) inhibitor, were analyzed with wild-type enzyme and mutants with single substitutions of V32I, I50V, I54V, I54M, I84V and L90M that are common in drug resistance. Crystal structures of the APV complexes at resolutions of 1.02-1.85 {angstrom} reveal the structural changes due to the mutations. Substitution of the larger side chains in PR{sub V32I}, PR{sub I54M} and PR{sub L90M} resulted in the formation of new hydrophobic contacts with flap residues, residues 79 and 80, and Asp25, respectively. Mutation to smaller side chains eliminated hydrophobic interactions in the PR{sub I50V} and PR{sub I54V} structures. The PR{sub I84V}-APV complex had lost hydrophobic contacts with APV, the PR{sub V32I}-APV complex showed increased hydrophobic contacts within the hydrophobic cluster and the PR{sub I50V} complex had weaker polar and hydrophobic interactions with APV. The observed structural changes in PR{sub I84V}-APV, PR{sub V32I}-APV and PR{sub I50V}-APV were related to their reduced inhibition by APV of six-, 10- and 30-fold, respectively, relative to wild-type PR. The APV complexes were compared with the corresponding saquinavir complexes. The PR dimers had distinct rearrangements of the flaps and 80's loops that adapt to the different P1{prime} groups of the inhibitors, while maintaining contacts within the hydrophobic cluster. These small changes in the loops and weak internal interactions produce the different patterns of resistant mutations for the two drugs.

  19. Chemical Abundances in NGC 5053: A Very Metal Poor and Dynamically Complex Globular Cluster

    NASA Astrophysics Data System (ADS)

    Boberg, Owen; Friel, Eileen D.; Vesperini, Enrico

    2015-01-01

    NGC 5053 provides a rich environment to test our understanding of the complex evolution of globular clusters (GCs). Recent studies have found that this cluster has interesting morphological features beyond the spherical distribution expected from GCs. These features include a ˜6° tidal stream (Lauchner et al. 2006), and a possible, but still debated, bridge-like structure between it and its nearby neighbor NGC 5024 (Chun et al. 2010). These features suggest that the evolution of these clusters has not only been greatly affected by their gravitational interaction with the Galaxy, but possibly each other. Additionally, simulations have shown that NGC 5053 could be a likely candidate to belong to the Sgr dSph stream (Law & Majewski 2010). Using the WIYN-Hydra multi-object spectrograph, we have collected high quality (S/N ˜75-90), medium-resolution spectra for red giant branch (RGB) stars in NGC 5053. Using these spectra we have measured the Fe, Ca, Ti, Ni, Ba, Na, and O abundances in the cluster. We measure an average cluster [Fe/H] abundance of -2.46 with a standard deviation of 0.05 dex, making NGC 5053 one of the most metal poor GCs in the Milky Way. The [Ca/Fe], [Ti/Fe], and [Ba/Fe] we measure are consistent with the abundances of Milky Way halo stars at a similar metallicity, with high alpha values and slightly depleted [Ba/Fe]. The Na and O abundances show the Na-O anti-correlation found in most GCs. From our abundance analysis it appears that NGC 5053 is at least chemically similar to other GCs found in the Milky Way. This does not, however, rule out NGC 5053 being a member of the Sgr dSph stream.

  20. Heptanuclear 3d-4f cluster complexes with a coaxial double-screw-propeller topology and diverse magnetic properties.

    PubMed

    Liu, Cai-Ming; Zhang, De-Qing; Zhu, Dao-Ben

    2010-12-21

    Two novel coaxial double-screw-propeller heptanuclear 3d-4f cluster complexes are ferromagnetic: one exhibits a large magnetocaloric effect while the other a magnetic relaxation behavior, depending on the lanthanoid ions used.

  1. HDV-like self-cleaving ribozymes

    PubMed Central

    Webb, Chiu-Ho T

    2011-01-01

    HDV ribozymes catalyze their own scission from the transcript during rolling circle replication of the hepatitis delta virus. In vitro selection of self-cleaving ribozymes from a human genomic library revealed an HDV-like ribozyme in the second intron of the human CPEB3 gene and recent results suggest that this RNA affects episodic memory performance. Bioinformatic searches based on the secondary structure of the HDV/CPEB3 fold yielded numerous functional ribozymes in a wide variety of organisms. Genomic mapping of these RNAs suggested several biological roles, one of which is the 5′ processing of non-LTR retrotransposons. The family of HDV-like ribozymes thus continues to grow in numbers and biological importance. PMID:21734469

  2. Identifying driving gene clusters in complex diseases through critical transition theory

    NASA Astrophysics Data System (ADS)

    Wolanyk, Nathaniel; Wang, Xujing; Hessner, Martin; Gao, Shouguo; Chen, Ye; Jia, Shuang

    A novel approach of looking at the human body using critical transition theory has yielded positive results: clusters of genes that act in tandem to drive complex disease progression. This cluster of genes can be thought of as the first part of a large genetic force that pushes the body from a curable, but sick, point to an incurable diseased point through a catastrophic bifurcation. The data analyzed is time course microarray blood assay data of 7 high risk individuals for Type 1 Diabetes who progressed into a clinical onset, with an additional larger study requested to be presented at the conference. The normalized data is 25,000 genes strong, which were narrowed down based on statistical metrics, and finally a machine learning algorithm using critical transition metrics found the driving network. This approach was created to be repeatable across multiple complex diseases with only progression time course data needed so that it would be applicable to identifying when an individual is at risk of developing a complex disease. Thusly, preventative measures can be enacted, and in the longer term, offers a possible solution to prevent all Type 1 Diabetes.

  3. The Talin Head Domain Reinforces Integrin-Mediated Adhesion by Promoting Adhesion Complex Stability and Clustering

    PubMed Central

    Ellis, Stephanie J.; Lostchuck, Emily; Goult, Benjamin T.; Bouaouina, Mohamed; Fairchild, Michael J.; López-Ceballos, Pablo; Calderwood, David A.; Tanentzapf, Guy

    2014-01-01

    Talin serves an essential function during integrin-mediated adhesion in linking integrins to actin via the intracellular adhesion complex. In addition, the N-terminal head domain of talin regulates the affinity of integrins for their ECM-ligands, a process known as inside-out activation. We previously showed that in Drosophila, mutating the integrin binding site in the talin head domain resulted in weakened adhesion to the ECM. Intriguingly, subsequent studies showed that canonical inside-out activation of integrin might not take place in flies. Consistent with this, a mutation in talin that specifically blocks its ability to activate mammalian integrins does not significantly impinge on talin function during fly development. Here, we describe results suggesting that the talin head domain reinforces and stabilizes the integrin adhesion complex by promoting integrin clustering distinct from its ability to support inside-out activation. Specifically, we show that an allele of talin containing a mutation that disrupts intramolecular interactions within the talin head attenuates the assembly and reinforcement of the integrin adhesion complex. Importantly, we provide evidence that this mutation blocks integrin clustering in vivo. We propose that the talin head domain is essential for regulating integrin avidity in Drosophila and that this is crucial for integrin-mediated adhesion during animal development. PMID:25393120

  4. Photodissociation of HCl and small (HCl)m complexes in and on large Arn clusters

    NASA Astrophysics Data System (ADS)

    Nahler, N. Hendrik; Fárník, Michal; Buck, Udo; Vach, Holger; Gerber, R. Benny

    2004-07-01

    Photodissociation experiments were carried out at 193 nm for single HCl molecules which are adsorbed on the surface of large Arn clusters and small (HCl)m complexes which are embedded in the interior of these clusters. For the surface case the size dependence is measured for the average sizes =140-1000. No cage exit events are observed in agreement with the substitutional position of the molecule deeply buried in the outermost shell. This result is confirmed by a molecular dynamics simulation of the pickup process under realistic conditions concerning the experiment and the interaction potentials. The calculations of the dissociation process employ the surface hopping model. For the embedded case the average sizes covered are =3 and 6 and =8-248. The kinetic energy of the H atom fragments is measured exhibiting peaks at zero and around 2.0 eV which mark completely caged and unperturbed fragments, respectively. The ratio of theses peaks strongly depends on the cluster size and agrees well with theoretical predictions for one and two closed icosahedral shells, in which the nonadiabatic coupling of all states was accounted for.

  5. Tunable diode laser spectrometer for pulsed supersonic jets: application to weakly-bound complexes and clusters.

    PubMed

    Brookes, Matthew D; Xia, Changhong; Tang, Jian; Anstey, James A; Fulsom, Bryan G; Au Yong, Ke-Xian; King, Jenna M; McKellar, A R W

    2004-12-01

    The design and operation of an apparatus for studying infrared spectra of weakly-bound complexes is described in detail. A pulsed supersonic jet expansion is probed using a tunable Pb-salt diode laser spectrometer operated in a rapid-scan mode. The jet may be fitted with either pinhole or slit shaped nozzles, the former giving lower effective rotational temperatures, and the latter giving sharper spectral lines. Notable features of the apparatus include use of a toroidal multi-pass mirror system to give over 100 passes of the laser through the supersonic jet, use of the normal laser controller for laser sweeping during both setup and data acquisition, and use of a simple semi-automated wavenumber calibration procedure. Performance of the apparatus is illustrated with observed spectra of the van der Waals complex He-OCS, and the seeded helium clusters He(N)-OCS and He(N)-CO.

  6. Communication: Analytic gradients for the complex absorbing potential equation-of-motion coupled-cluster method

    NASA Astrophysics Data System (ADS)

    Benda, Zsuzsanna; Jagau, Thomas-C.

    2017-01-01

    The general theory of analytic energy gradients is presented for the complex absorbing potential equation-of-motion coupled-cluster (CAP-EOM-CC) method together with an implementation within the singles and doubles approximation. Expressions for the CAP-EOM-CC energy gradient are derived based on a Lagrangian formalism with a special focus on the extra terms arising from the presence of the CAP. Our implementation allows for locating minima on high-dimensional complex-valued potential energy surfaces and thus enables geometry optimizations of resonance states of polyatomic molecules. The applicability of our CAP-EOM-CC gradients is illustrated by computations of the equilibrium structures and adiabatic electron affinities of the temporary anions of formaldehyde, formic acid, and ethylene. The results are compared to those obtained from standard EOM-CC calculations and the advantages of CAP methods are emphasized.

  7. Hydrogen activation by unsaturated mixed-metal cluster complexes: new directions.

    PubMed

    Adams, Richard D; Captain, Burjor

    2008-01-01

    There has been a renewed interest in the chemistry of hydrogen as a result of the ever-increasing global demands for energy. Recent studies have revealed new electronically unsaturated polynuclear metal complexes containing bulky ligands that exhibit a variety of reactions with hydrogen, including facile addition and elimination under mild conditions. Materials and molecules that can reversibly absorb large quantities of hydrogen are very attractive for hydrogen storage and hydrogenation catalysis. This Minireview summarizes recent studies of reactions of hydrogen with unsaturated mixed-metal cluster complexes containing platinum and bulky phosphine ligands. Some related studies on bimetallic cooperativity and the synthesis of trimetallic nanoparticles on mesoporous supports that exhibit high activity and selectivity for catalytic hydrogenations are also discussed.

  8. CHEMICAL ABUNDANCES IN NGC 5053: A VERY METAL-POOR AND DYNAMICALLY COMPLEX GLOBULAR CLUSTER

    SciTech Connect

    Boberg, Owen M.; Friel, Eileen D.; Vesperini, Enrico

    2015-05-10

    NGC 5053 provides a rich environment to test our understanding of the complex evolution of globular clusters (GCs). Recent studies have found that this cluster has interesting morphological features beyond the typical spherical distribution of GCs, suggesting that external tidal effects have played an important role in its evolution and current properties. Additionally, simulations have shown that NGC 5053 could be a likely candidate to belong to the Sagittarius dwarf galaxy (Sgr dSph) stream. Using the Wisconsin–Indiana–Yale–NOAO–Hydra multi-object spectrograph, we have collected high quality (signal-to-noise ratio ∼ 75–90), medium-resolution spectra for red giant branch stars in NGC 5053. Using these spectra we have measured the Fe, Ca, Ti, Ni, Ba, Na, and O abundances in the cluster. We measure an average cluster [Fe/H] abundance of −2.45 with a standard deviation of 0.04 dex, making NGC 5053 one of the most metal-poor GCs in the Milky Way (MW). The [Ca/Fe], [Ti/Fe], and [Ba/Fe] we measure are consistent with the abundances of MW halo stars at a similar metallicity, with alpha-enhanced ratios and slightly depleted [Ba/Fe]. The Na and O abundances show the Na–O anti-correlation found in most GCs. From our abundance analysis it appears that NGC 5053 is at least chemically similar to other GCs found in the MW. This does not, however, rule out NGC 5053 being associated with the Sgr dSph stream.

  9. Chemical Abundances in NGC 5053: A Very Metal-poor and Dynamically Complex Globular Cluster

    NASA Astrophysics Data System (ADS)

    Boberg, Owen M.; Friel, Eileen D.; Vesperini, Enrico

    2015-05-01

    NGC 5053 provides a rich environment to test our understanding of the complex evolution of globular clusters (GCs). Recent studies have found that this cluster has interesting morphological features beyond the typical spherical distribution of GCs, suggesting that external tidal effects have played an important role in its evolution and current properties. Additionally, simulations have shown that NGC 5053 could be a likely candidate to belong to the Sagittarius dwarf galaxy (Sgr dSph) stream. Using the Wisconsin-Indiana-Yale-NOAO-Hydra multi-object spectrograph, we have collected high quality (signal-to-noise ratio ˜ 75-90), medium-resolution spectra for red giant branch stars in NGC 5053. Using these spectra we have measured the Fe, Ca, Ti, Ni, Ba, Na, and O abundances in the cluster. We measure an average cluster [Fe/H] abundance of -2.45 with a standard deviation of 0.04 dex, making NGC 5053 one of the most metal-poor GCs in the Milky Way (MW). The [Ca/Fe], [Ti/Fe], and [Ba/Fe] we measure are consistent with the abundances of MW halo stars at a similar metallicity, with alpha-enhanced ratios and slightly depleted [Ba/Fe]. The Na and O abundances show the Na-O anti-correlation found in most GCs. From our abundance analysis it appears that NGC 5053 is at least chemically similar to other GCs found in the MW. This does not, however, rule out NGC 5053 being associated with the Sgr dSph stream.

  10. Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

    PubMed Central

    Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S. P.

    2014-01-01

    Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins. PMID:25340788

  11. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

    PubMed

    Koldsø, Heidi; Shorthouse, David; Hélie, Jean; Sansom, Mark S P

    2014-10-01

    Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

  12. Self-assembly of four new extended architectures based on reduced polyoxometalate clusters and cadmium complexes

    NASA Astrophysics Data System (ADS)

    Ma, Ying; Li, Yangguang; Wang, Enbo; Lu, Ying; Wang, Xinlong; Xu, Xinxin

    2006-08-01

    Four new [P 4Mo 6] cluster-based extended structures containing cadmium complexes, [Cd 3(4,4'-Hbpy) 2(4,4'-bpy) 2(H 2O) 8][Cd(H 2PO 4) 2(HPO 4) 4(PO 4) 2(MoO 2) 12(OH) 6]·7H 2O 1, (4,4'-Hbpy) 2[Cd(4,4'-bpy) 3(H 2O) 3][Cd(4,4'-bpy)(H 2O)] 2[Cd(H 2PO 4) 2(HPO 4) 4 (PO 4) 2(MoO 2) 12(OH) 6]·H 2O 2, [Cd 4(phen) 2(H 2O) 4][Cd(phen)(H 2O)] 2[Cd(HPO 4) 4 (HPO 4) 4(MoO 2) 12(OH) 6]·5H 2O 3 and [Cd 4(2,2'-bpy) 2(H 2O) 4][Cd(2,2'-bpy)(H 2O)] 2 [Cd(HPO 4) 4(HPO 4) 4(MoO 2) 12(OH) 6]·3H 2O 4 (4,4'-bpy=4,4'-bpyridine, phen=1,10-phenanthroline, 2,2'-bpy=2,2'-bpyridine), have been synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. The structure of compound 1 is constructed from the Cd[P 4Mo 6] 2 dimers linked by [Cd 3(4,4'-Hbpy) 2(4,4'-bpy) 2(H 2O) 8] subunits to generate a plane layer. Compound 2 consists of the positive 2D sheets that constructed from Cd[P 4Mo 6] 2 dimers linked by [Cd(4,4'-bpy)(H 2O)] complexes, then the 2D sheets are further linked up together to form a 3D supramolecular framework via extensive hydrogen-bonding interactions among the [P 4Mo 6] clusters, free 4,4'-bpy molecules, dissociated [Cd(4,4'-bpy) 3(H 2O) 3] 2+ complexes and water molecules. Compounds 3 and 4 show new 2D layered structure, with Cd[P 4Mo 6] 2 building blocks connected by tetra-nuclear [Cd 4{(phen) 2/(2,2'-bpy) 2}(H 2O) 4] clusters and [Cd(phen/2,2'-bpy)(H 2O)] complexes. The fluorescent activities of compounds 3 and 4 are reported.

  13. Evidence for iron, copper and zinc complexation as multinuclear sulphide clusters in oxic rivers

    PubMed

    Rozan; Lassman; Ridge; Luther

    2000-08-24

    The availability and toxicity of trace metals in fresh water are known to be regulated by the complexation of free metal ions with dissolved organic matter. The potential role of inorganic sulphides in binding trace metals has been largely ignored because of the reduced persistence of sulphides in these oxic waters. However, nanomolar concentrations of copper and zinc sulphides have been observed in four rivers in Connecticut and Maryland. Here we report dissolved (< 0.2 microm particle diameter) sulphide concentrations ranging up to 600 nM, with more than 90% being complexed by copper, iron and zinc. These complexes account for up to 20% of the total dissolved Fe and Zn and 45% of the total dissolved Cu. Fourier transform mass spectrometry reveals that these complexes are not simple M(HS)+ protonated species but are higher-order unprotonated clusters (M3S3, M4S6, M2S4), similar to those found in laboratory solutions and bio-inorganic molecules. These extended structures have high stability constants and are resistant to oxidation and dissociation, which may help control the toxicity of these and other less abundant, but more toxic, trace metals, such as silver, cadmium and mercury.

  14. STAR CLUSTER COMPLEXES AND THE HOST GALAXY IN THREE H II GALAXIES: Mrk 36, UM 408, AND UM 461

    SciTech Connect

    Lagos, P.; Telles, E.; Nigoche-Netro, A.

    2011-11-15

    We present a stellar population study of three H II galaxies (Mrk 36, UM 408, and UM 461) based on the analysis of new ground-based high-resolution near-infrared J, H, and K{sub p} broadband and Br{gamma} narrowband images obtained with Gemini/NIRI. We identify and determine the relative ages and masses of the elementary star clusters and/or star cluster complexes of the starburst regions in each of these galaxies by comparing the colors with evolutionary synthesis models that include the contribution of stellar continuum, nebular continuum, and emission lines. We found that the current star cluster formation efficiency in our sample of low-luminosity H II galaxies is {approx}10%. Therefore, most of the recent star formation is not in massive clusters. Our findings seem to indicate that the star formation mode in our sample of galaxies is clumpy, and that these complexes are formed by a few massive star clusters with masses {approx}>10{sup 4} M{sub Sun }. The age distribution of these star cluster complexes shows that the current burst started recently and likely simultaneously over short timescales in their host galaxies, triggered by some internal mechanism. Finally, the fraction of the total cluster mass with respect to the low surface brightness (or host galaxy) mass, considering our complete range in ages, is less than 1%.

  15. Self-assembly of four new extended architectures based on reduced polyoxometalate clusters and cadmium complexes

    SciTech Connect

    Ma Ying; Li Yangguang; Wang Enbo . E-mail: wangenbo@public.cc.jl.cn; Lu Ying; Wang Xinlong; Xu Xinxin

    2006-08-15

    Four new [P{sub 4}Mo{sub 6}] cluster-based extended structures containing cadmium complexes, [Cd{sub 3}(4,4'-Hbpy){sub 2}(4,4'-bpy){sub 2}(H{sub 2}O){sub 8}][Cd(H{sub 2}PO{sub 4}){sub 2}(HPO{sub 4}){sub 4}(PO{sub 4}){sub 2}(MoO{sub 2}){sub =} 1{sub 2}(OH){sub 6}].7H{sub 2}O 1 (4,4'-Hbpy){sub 2}[Cd(4,4'-bpy){sub 3}(H{sub 2}O){sub 3}][Cd(4,4'-bpy)(H{sub 2}O)]{sub 2}[Cd(H{sub 2}PO{sub 4}){sub 2}(HPO{sub =} 4){sub 4} (PO{sub 4}){sub 2}(MoO{sub 2}){sub 12}(OH){sub 6}].H{sub 2}O 2, [Cd{sub 4}(phen){sub 2}(H{sub 2}O){sub 4}][Cd(phen)(H{sub 2}O)]{sub 2}[Cd(HPO{sub 4}){sub 4} (HPO{sub 4}){sub 4}(MoO{sub 2}){sub 12}(OH){sub 6}].5H{sub 2}O 3 and [Cd{sub 4}(2,2'-bpy){sub 2}(H{sub 2}O){sub 4}][Cd(2,2'-bpy)(H{sub 2}O)]{sub 2} [Cd(HPO{sub 4}){sub 4}(HPO{sub 4}){sub 4}(MoO{sub 2}){sub 12}(OH){sub 6}].3H{sub 2}O 4 (4,4'-bpy=4,4'-bpyridine, phen=1,10-phenanthroline, 2,2'-bpy=2,2'-bpyridine), have been synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. The structure of compound 1 is constructed from the Cd[P{sub 4}Mo{sub 6}]{sub 2} dimers linked by [Cd{sub 3}(4,4'-Hbpy){sub 2}(4,4'-bpy){sub 2}(H{sub 2}O){sub 8}] subunits to generate a plane layer. Compound 2 consists of the positive 2D sheets that constructed from Cd[P{sub 4}Mo{sub 6}]{sub 2} dimers linked by [Cd(4,4'-bpy)(H{sub 2}O)] complexes, then the 2D sheets are further linked up together to form a 3D supramolecular framework via extensive hydrogen-bonding interactions among the [P{sub 4}Mo{sub 6}] clusters, free 4,4'-bpy molecules, dissociated [Cd(4,4'-bpy){sub 3}(H{sub 2}O){sub 3}]{sup 2+} complexes and water molecules. Compounds 3 and 4 show new 2D layered structure, with Cd[P{sub 4}Mo{sub 6}]{sub 2} building blocks connected by tetra-nuclear [Cd{sub 4}{l_brace}(phen){sub 2}/(2,2'-bpy){sub 2}{r_brace}(H{sub 2}O){sub 4}] clusters and [Cd(phen/2,2'-bpy)(H{sub 2}O)] complexes. The fluorescent activities of compounds 3 and 4 are reported. - Graphical abstract: In this paper, we

  16. Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth.

    PubMed

    Séraphin, Marie Nancy; Lauzardo, Michael; Doggett, Richard T; Zabala, Jose; Morris, J Glenn; Blackburn, Jason K

    2016-01-01

    Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts. We investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan. Among the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (<5 years). Strain allelic diversity (h) ranged from low to medium in most locations and was most diverse in urban centers where foreign-born population density was also high. Overall, 21.5% of cases among U.S.-born persons and 4.6% among foreign-born persons clustered genotypically and spatiotemporally and involved strains of the Haarlem family. One Haarlem space-time cluster identified in the mostly rural northern region of Florida included US/Canada-born individuals incarcerated at the time of diagnosis; two clusters in the mostly urban southern region of Florida were composed predominantly of foreign-born persons. Both groups had HIV prevalence above twenty percent. Almost five percent of TB cases reported in Florida during 2009-2013 were potentially due to recent transmission. Improvements to TB screening practices among the prison population and recent immigrants are likely to impact TB control. Due to the monomorphic nature of

  17. Spatiotemporal Clustering of Mycobacterium tuberculosis Complex Genotypes in Florida: Genetic Diversity Segregated by Country of Birth

    PubMed Central

    Séraphin, Marie Nancy; Lauzardo, Michael; Morris, J. Glenn; Blackburn, Jason K.

    2016-01-01

    Background Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). Although the MTBC is highly clonal, between-strain genetic diversity has been observed. In low TB incidence settings, immigration may facilitate the importation of MTBC strains with a potential to complicate TB control efforts. Methods We investigated the genetic diversity and spatiotemporal clustering of 2,510 MTBC strains isolated in Florida, United States, between 2009 and 2013 and genotyped using spoligotyping and 24-locus MIRU-VNTR. We mapped the genetic diversity to the centroid of patient residential zip codes using a geographic information system (GIS). We assessed transmission dynamics and the influence of immigration on genotype clustering using space-time permutation models adjusted for foreign-born population density and county-level HIV risk and multinomial models stratified by country of birth and timing of immigration in SaTScan. Principal Findings Among the 2,510 strains, 1,245 were reported among foreign-born persons; including 408 recent immigrants (<5 years). Strain allelic diversity (h) ranged from low to medium in most locations and was most diverse in urban centers where foreign-born population density was also high. Overall, 21.5% of cases among U.S.-born persons and 4.6% among foreign-born persons clustered genotypically and spatiotemporally and involved strains of the Haarlem family. One Haarlem space-time cluster identified in the mostly rural northern region of Florida included US/Canada-born individuals incarcerated at the time of diagnosis; two clusters in the mostly urban southern region of Florida were composed predominantly of foreign-born persons. Both groups had HIV prevalence above twenty percent. Conclusions/Significance Almost five percent of TB cases reported in Florida during 2009–2013 were potentially due to recent transmission. Improvements to TB screening practices among the prison population and recent immigrants are

  18. A Single Adaptable Cochaperone-Scaffold Complex Delivers Nascent Iron-Sulfur Clusters to Mammalian Respiratory Chain Complexes I-III.

    PubMed

    Maio, Nunziata; Kim, Ki Soon; Singh, Anamika; Rouault, Tracey A

    2017-04-04

    The iron-sulfur (Fe-S) cluster of the Rieske protein, UQCRFS1, is essential for Complex III (CIII) activity, though the mechanism for Fe-S cluster transfer has not previously been elucidated. Recent studies have shown that the co-chaperone HSC20, essential for Fe-S cluster biogenesis of SDHB, directly binds LYRM7, formerly described as a chaperone that stabilizes UQCRFS1 prior to its insertion into CIII. Here we report that a transient subcomplex involved in CIII assembly, composed of LYRM7 bound to UQCRFS1, interacts with components of an Fe-S transfer complex, consisting of HSC20, its cognate chaperone HSPA9, and the holo-scaffold ISCU. Binding of HSC20 to the LYR motif of LYRM7 in a pre-assembled UQCRFS1-LYRM7 intermediate in the mitochondrial matrix facilitates Fe-S cluster transfer to UQCRFS1. The five Fe-S cluster subunits of Complex I also interact with HSC20 to acquire their clusters, highlighting the crucial role of HSC20 in the assembly of the mitochondrial respiratory chain. Published by Elsevier Inc.

  19. The merger history of the complex cluster Abell 1758: a combined weak lensing and spectroscopic view

    NASA Astrophysics Data System (ADS)

    Monteiro-Oliveira, R.; Cypriano, E. S.; Machado, R. E. G.; Lima Neto, G. B.; Ribeiro, A. L. B.; Sodré, L.; Dupke, R.

    2017-04-01

    We present a weak-lensing and dynamical study of the complex cluster Abell 1758 (A1758, bar{z} = 0.278) supported by hydrodynamical simulations. This cluster is composed of two main structures called A1758N and A1758S. The northern structure is composed of A1758NW and A1758NE, with lensing determined masses of 7.90_{-1.55}^{+1.89} × 1014 M⊙ and 5.49_{-1.33}^{+1.67} × 1014 M⊙, respectively. They show a remarkable feature: while in A1758NW, there is a spatial agreement among weak-lensing mass distribution, intracluster medium and its brightest cluster galaxy (BCG), in A1758NE, the X-ray peak is located 96_{-15}^{+14} arcsec away from the mass peak and BCG positions. Given the detachment between gas and mass, we could use the local surface mass density to estimate an upper limit for the dark matter self-interaction cross-section: σ/m < 5.83 cm2 g-1. Combining our velocity data with hydrodynamical simulations, we have shown that A1758 NW and NE had their closest approach 0.27 Gyr ago and their merger axis is 21° ± 12° from the plane of the sky. In the A1758S system, we have measured a total mass of 4.96_{-1.19}^{+1.08} × 10^{14} M⊙ and, using radial velocity data, we found that the main merger axis is located at 70° ± 4° from the plane of the sky, therefore closest to the line of sight.

  20. New Constraints on a Complex Relation between Globular Cluster Colors and Environment

    NASA Astrophysics Data System (ADS)

    Powalka, Mathieu; Puzia, Thomas H.; Lançon, Ariane; Peng, Eric W.; Schönebeck, Frederik; Alamo-Martínez, Karla; Ángel, Simón; Blakeslee, John P.; Côté, Patrick; Cuillandre, Jean-Charles; Duc, Pierre-Alain; Durrell, Patrick; Ferrarese, Laura; Grebel, Eva K.; Guhathakurta, Puragra; Gwyn, S. D. J.; Kuntschner, Harald; Lim, Sungsoon; Liu, Chengze; Lyubenova, Mariya; Mihos, J. Christopher; Muñoz, Roberto P.; Ordenes-Briceño, Yasna; Roediger, Joel; Sánchez-Janssen, Rubén; Spengler, Chelsea; Toloba, Elisa; Zhang, Hongxin

    2016-09-01

    We present an analysis of high-quality photometry for globular clusters (GCs) in the Virgo cluster core region, based on data from the Next Generation Virgo Cluster Survey (NGVS) pilot field, and in the Milky Way (MW), based on Very Large Telescope/X-Shooter spectrophotometry. We find significant discrepancies in color-color diagrams between sub-samples from different environments, confirming that the environment has a strong influence on the integrated colors of GCs. GC color distributions along a single color are not sufficient to capture the differences we observe in color-color space. While the average photometric colors become bluer with increasing radial distance to the cD galaxy M87, we also find a relation between the environment and the slope and intercept of the color-color relations. A denser environment seems to produce a larger dynamic range in certain color indices. We argue that these results are not due solely to differential extinction, Initial Mass Function variations, calibration uncertainties, or overall age/metallicity variations. We therefore suggest that the relation between the environment and GC colors is, at least in part, due to chemical abundance variations, which affect stellar spectra and stellar evolution tracks. Our results demonstrate that stellar population diagnostics derived from model predictions which are calibrated on one particular sample of GCs may not be appropriate for all extragalactic GCs. These results advocate a more complex model of the assembly history of GC systems in massive galaxies that goes beyond the simple bimodality found in previous decades.

  1. Predicting Water Activity for Complex Wastes with Solvation Cluster Equilibria (SCE) - 12042

    SciTech Connect

    Agnew, S.F.; Reynolds, J.G.; Johnston, C.T.

    2012-07-01

    Predicting an electrolyte mixture's water activity, i.e. the ratio of water vapor pressure over a solution with that of pure water, in principle reveals both boiling point and solubilities for that mixture. Better predictions of these properties helps support the ongoing missions to concentrate complex nuclear waste mixtures in order to conserve tank space and improved predictions of water activity will help. A new approach for predicting water activity, the solvation cluster equilibria (SCE) model, uses pure electrolyte water activities to predict water activity for a complex mixture of those electrolytes. An SCE function based on electrolyte hydration free energy and a standard Debye- Hueckel (DH) charge compression fits each pure electrolyte's water activity with three parameters. Given these pure electrolyte water activities, the SCE predicts any mixture water activity over a large range of concentration with an additional parameter for each mixture vector, the multinarity. In contrast to ionic strength, which scales with concentration, multinarity is related to the relative proportion of electrolytes in a mixture and can either increase or decrease the water activity prediction over a broad range of concentration for that mixture. The SCE model predicts water activity for complex electrolyte mixtures based on the water activities of pure electrolytes. Three parameter SCE functions fit the water activities of pure electrolytes and along with a single multinarity parameter for each mixture vector then predict the mixture water activity. Predictions of water activity can in principle predict solution electrolyte activity and this relationship will be explored in the future. Predicting electrolyte activities for complex mixtures provides a means of determining solubilities for each electrolyte. Although there are a number of reports [9, 10, 11] of water activity models for pure and binary mixtures of electrolytes, none of them compare measured versus calculated

  2. Cluster perturbation theory for the self-assembly of associating fluids into complex structures.

    PubMed

    Marshall, Bennett D

    2014-12-01

    Wertheim's two-density thermodynamic perturbation theory (TPT) has proven to be an indispensable statistical mechanical tool in the description of associating fluids with a single association site. TPT was developed to enforce the monovalence of the hydrogen bond and only recently has been extended to account for divalent association sites. It has been shown through experiment and molecular simulation that certain one-site associating fluids can self-assemble into complex extended supramolecular structures as a result of multiple bonding of association sites. In this paper we reorganize TPT into a form that is more easily applied to complex associated structures. The derived theory is general to all possible self-assemble structures. We obtain the free energy and bonding fractions in a general way in terms of single-cluster partition functions and averages. The new formalism removes any reference to graph theory allowing for the conceptually straightforward application of the two-density formalism to complex self-assembled structures.

  3. Investigating tunnel and above-barrier ionization using complex-scaled coupled-cluster theory

    NASA Astrophysics Data System (ADS)

    Jagau, Thomas-C.

    2016-11-01

    The theory and implementation of the complex-scaled coupled-cluster method with singles and doubles excitations (cs-CCSD) for studying resonances induced by static electric fields are presented. Within this framework, Stark shifts and ionization rates are obtained directly from the real and imaginary parts of the complex energy. The method is applied to the ground states of hydrogen, helium, lithium, beryllium, neon, argon, and carbon at varying field strengths. Complex-scaled Hartree-Fock, second-order many-body perturbation theory, and CCSD results are reported and analyzed with a focus on the impact of electron correlation on the ionization process. cs-CCSD calculations with suitably augmented standard Gaussian basis sets are found to deliver accurate strong-field ionization rates over a range of six orders of magnitude. The field-induced resonances are characterized beyond energy and ionization rate through their dipole moments, second moments, as well as Dyson orbitals and comparisons are drawn to autoionizing and autodetaching resonances. Marked differences are found between the tunneling and above-barrier regimes allowing for a clear distinction of the two mechanisms.

  4. The contribution of cluster and discriminant analysis to the classification of complex aquifer systems.

    PubMed

    Panagopoulos, G P; Angelopoulou, D; Tzirtzilakis, E E; Giannoulopoulos, P

    2016-10-01

    This paper presents an innovated method for the discrimination of groundwater samples in common groups representing the hydrogeological units from where they have been pumped. This method proved very efficient even in areas with complex hydrogeological regimes. The proposed method requires chemical analyses of water samples only for major ions, meaning that it is applicable to most of cases worldwide. Another benefit of the method is that it gives a further insight of the aquifer hydrogeochemistry as it provides the ions that are responsible for the discrimination of the group. The procedure begins with cluster analysis of the dataset in order to classify the samples in the corresponding hydrogeological unit. The feasibility of the method is proven from the fact that the samples of volcanic origin were separated into two different clusters, namely the lava units and the pyroclastic-ignimbritic aquifer. The second step is the discriminant analysis of the data which provides the functions that distinguish the groups from each other and the most significant variables that define the hydrochemical composition of the aquifer. The whole procedure was highly successful as the 94.7 % of the samples were classified to the correct aquifer system. Finally, the resulted functions can be safely used to categorize samples of either unknown or doubtful origin improving thus the quality and the size of existing hydrochemical databases.

  5. Hyperspectral clustering and unmixing for studying the ecology of state formation and complex societies

    NASA Astrophysics Data System (ADS)

    Kwong, Justin D.; Messinger, David W.; Middleton, William D.

    2009-08-01

    This project is an application of hyperspectral classification and unmixing in support of an ongoing archaeological study. The study region is the Oaxaca Valley located in the state of Oaxaca, Mexico on the southern coast. This was the birthplace of the Zapotec civilization which grew into a complex state level society. Hyperion imagery is being collected over a 30,000 km2 area. Classification maps of regions of interest are generated using K-means clustering and a novel algorithm called Gradient Flow. Gradient Flow departs from conventional stochastic or deterministic approaches, using graph theory to cluster spectral data. Spectral unmixing is conducted using the RIT developed algorithm Max-D to automatically find end members. Stepwise unmixing is performed to better model the data using the end members found be Max-D. Data are efficiently shared between imaging scientists and archaeologists using Google Earth to stream images over the internet rather than downloading them. The overall goal of the project is to provide archaeologists with useful information maps without having to interpret the raw data.

  6. MASSIVE STARS IN THE Cl 1813-178 CLUSTER: AN EPISODE OF MASSIVE STAR FORMATION IN THE W33 COMPLEX

    SciTech Connect

    Messineo, Maria; Davies, Ben; Figer, Donald F.; Trombley, Christine; Kudritzki, R. P.; Valenti, Elena; Najarro, F.; Michael Rich, R.

    2011-05-20

    Young massive (M > 10{sup 4} M{sub sun}) stellar clusters are a good laboratory to study the evolution of massive stars. Only a dozen of such clusters are known in the Galaxy. Here, we report about a new young massive stellar cluster in the Milky Way. Near-infrared medium-resolution spectroscopy with UIST on the UKIRT telescope and NIRSPEC on the Keck telescope, and X-ray observations with the Chandra and XMM satellites, of the Cl 1813-178 cluster confirm a large number of massive stars. We detected 1 red supergiant, 2 Wolf-Rayet stars, 1 candidate luminous blue variable, 2 OIf, and 19 OB stars. Among the latter, twelve are likely supergiants, four giants, and the faintest three dwarf stars. We detected post-main-sequence stars with masses between 25 and 100 M{sub sun}. A population with age of 4-4.5 Myr and a mass of {approx}10, 000 M{sub sun} can reproduce such a mixture of massive evolved stars. This massive stellar cluster is the first detection of a cluster in the W33 complex. Six supernova remnants and several other candidate clusters are found in the direction of the same complex.

  7. Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters.

    PubMed

    Kryachko, E S; Remacle, F

    2005-12-08

    The nature of the DNA-gold interaction determines and differentiates the affinity of the nucleobases (adenine, thymine, guanine, and cytosine) to gold. Our preliminary computational study [Kryachko, E. S.; Remacle, F. Nano Lett. 2005, 5, 735] demonstrates that two major bonding factors govern this interaction: the anchoring, either of the Au-N or Au-O type, and the nonconventional N-H...Au hydrogen bonding. In this paper, we offer insight into the nature of nucleobase-gold interactions and provide a detailed characterization of their different facets, i.e., geometrical, energetic, and spectroscopic aspects; the gold cluster size and gold coordination effects; proton affinity; and deprotonation energy. We then investigate how the Watson-Crick DNA pairing patterns are modulated by the nucleobase-gold interaction. We do so in terms of the proton affinities and deprotonation energies of those proton acceptors and proton donors which are involved in the interbase hydrogen bondings. A variety of properties of the most stable Watson-Crick [A x T]-Au3 and [G x C]-Au3 hybridized complexes are described and compared with the isolated Watson-Crick A x T and G x C ones. It is shown that enlarging the gold cluster size to Au6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G x C]-Au6 complex that bridges the G x C pair and thus leads to a significant strengthening of G x C pairing.

  8. Structural oxidation state studies of the manganese cluster in the oxygen evolving complex of photosystem II

    SciTech Connect

    Liang, Wenchuan

    1994-11-01

    X-ray absorption spectroscopy (XAS) was performed on Photosystem II (PSII)-enriched membranes prepared from spinach to explore: (1) the correlation between structure and magnetic spin state of the Mn cluster in the oxygen evolving complex (OEC) in the S2 state; and (2) the oxidation state changes of the Mn cluster in the flash-induced S-states. The structure of the Mn cluster in the S2 state with the g~4 electron paramagnetic resonance (EPR) signal (S2-g4 state) was compared with that in the S2 state with multiline signal (S2-MLS state) and the S1 state. The S2-g4 state has a higher XAS inflection point energy than that of the S1 state, indicating the oxidation of Mn in the advance from the S1 to the S2-g4 state. Differences in the edge shape and in the extended X-ray absorption fine structure (EXAFS) show that the structure of the Mn cluster in the S2-g4 state is different from that in the S2-MLS or the S1 state. In the S2-g4 state, the second shell of backscatterers from the Mn absorber contains two Mn-Mn distances of 2.73 Å and 2.85 Å. Very little distance disorder exists in the second shell of the S1 or S2-MLS states. The third shell of the S2-g4 state at about 3.3 Å also contains increased heterogeneity relative to that of the S2-MLS or the S1 state. Various S-states were prepared at room-temperature by saturating, single-turnover flashes. The flash-dependent oscillation in the amplitude of the MLS was used to characterize the S-state composition and to construct "pure" S-state Mn K-edge spectra. The edge position shifts to higher energy by 1.8 eV upon the S1 → S2 transition.

  9. A functional model of extradiol-cleaving catechol dioxygenases: mimicking the 2-his-1-carboxylate facial triad.

    PubMed

    Paria, Sayantan; Halder, Partha; Paine, Tapan Kanti

    2010-05-17

    The synthesis and characterization of an iron-catecholate model complex of a tridentate 2-N-1-carboxylate ligand derived from L-proline are reported. The X-ray crystal structure of the complex [(L)(3)Fe(3)(DBC)(3)] (1) (where L is 1-(2-pyridylmethyl)pyrrolidine-2-carboxylate and DBC is the dianion of 3,5-di-tert-butyl catechol) reveals that the tridentate ligand binds to the iron center in a facial manner and mimics the 2-his-1-carboxylate facial triad motif observed in extradiol-cleaving catechol dioxygenases. The iron(III)-catecholate complex (1) reacts with dioxygen in acetonitrile in ambient conditions to cleave the C-C bond of catecholate. In the reaction, an equal amount of extra- and intradiol cleavage products are formed without any auto-oxidation product. The iron-catecholate complex is a potential functional model of extradiol-cleaving catechol dioxygenases.

  10. From Cluster to Polymer: Ligand Cone Angle Controlled Syntheses and Structures of Copper(I) Alkynyl Complexes.

    PubMed

    Chang, Xiao-Yong; Low, Kam-Hung; Wang, Juan-Yu; Huang, Jie-Sheng; Che, Chi-Ming

    2016-08-22

    Copper(I) alkynyl complexes have attracted tremendous attention in structural studies, as luminescent materials, and in catalysis, and homoleptic complexes have been reported to form polymers or large clusters. Herein, six unprecedented structures of Cu(I) alkynyl complexes and a procedure to measure the cone angles of alkynyl ligands based on the crystal structures of these complexes are reported. An increase of the alkynyl cone angle in the complexes leads to a modulation of the structures from polymeric [((PhC≡CC≡C)Cu)2 (NH3 )]∞ , to a large cluster [(TripC≡CC≡C)Cu]20 (MeCN)4 , to a relatively small cluster [(TripC≡C)Cu]8 (Trip=2,4,6-iPr3 -C6 H2 ). The complexes exhibit yellow-to-red phosphorescence at ambient temperature in the solid state and the luminescence behavior of the Cu20 cluster is sensitive to acetonitrile. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Synthesis and structural characterization of ruthenium carbonyl cluster complexes containing platinum with a bulky N-heterocyclic carbene ligand.

    PubMed

    Saha, Sumit; Captain, Burjor

    2014-01-21

    The reaction of Ru3(CO)12 with Pt(IMes)2 in benzene solvent at room temperature afforded the monoplatinum-triruthenium cluster complex Ru3Pt(IMes)2(CO)11, 1, in 21% yield and the trigonal bipyramidal cluster complex Ru3Pt2(IMes)2(CO)12, 2, in 26% yield. The reaction of Ru(CO)5 with Pt(IMes)2 in benzene solvent at 0 °C yielded two trinuclear cluster complexes, the monoplatinum-diruthenium Ru2Pt(IMes)(CO)9, 3, and the monoruthenium-diplatinum cluster complex RuPt2(IMes)2(CO)6, 4. The reaction of 2 with hydrogen at 80 °C afforded the tetrahydrido-tetraruthenium complex Ru4(IMes)(CO)11(μ-H)4, 5, and the dihydrido-diruthenium-diplatinum complex Ru2Pt2(IMes)2(CO)8(μ-H)2, 6. All six compounds were structurally characterized by single-crystal X-ray diffraction analyses.

  12. CHIMERA: Top-down model for hierarchical, overlapping and directed cluster structures in directed and weighted complex networks

    NASA Astrophysics Data System (ADS)

    Franke, R.

    2016-11-01

    In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.

  13. Dimeric W3SO3 cluster complexes: synthesis, characterization, and potential applications as X-ray contrast agents.

    PubMed

    Yu, S B; Droege, M; Downey, S; Segal, B; Newcomb, W; Sanderson, T; Crofts, S; Suravajjala, S; Bacon, E; Earley, W; Delecki, D; Watson, A D

    2001-03-26

    Our continued research on the use of heavy metal cluster complexes as a new class of X-ray contrast agents in medical diagnostic imaging is described. A series of 2:3 cluster-ligand complexes, [(W(IV)3SO3)2L3]4- (L = linear polyaminopolycarboxylate ligands), were isolated from the reaction of aqua ion [W(IV)3SO3(H2O)9]4- (prepared in large quantities through an improved literature process) with respective ligands in refluxing DMF. The salts of [(W(IV)3SO3)2L3]4- complex anions were fully characterized using routine techniques such as elemental analysis, MS, HPLC, UV-vis, IR, and NMR. The solid structures of two complex anions, [(W(IV)3SO3)2(PDTA)3]4- and [(W(IV)3SO3)2(HO-PDTA)3]4-, were determined by X-ray crystallography. They are the first examples wherein two W(IV)3SO3 clusters are complexed and linked by three ligands that contain two terminal iminodiacetate (bis-IDA) groups. Complexation of the unstable aqua ion [W(IV)3SO3(H2O)9]4- with ligands has imparted desired biological compatibility to the tungsten metal cluster. These complexes are stable and highly soluble in H2O. The potential utility of such tungsten cluster complexes as X-ray contrast agents was evaluated in both in vitro and in vivo animal studies. In addition, the syntheses of several new linear polyaminopolycarboxylate ligands used in this study are reported.

  14. Oxovanadium(V) 1,3-propanediolate chloride complexes: Tetrameric clusters

    SciTech Connect

    Crans, D.C.; Marshman, R.W.; Gottlieb, M.S.; Anderson, O.P.; Miller, M.M. )

    1992-11-25

    Structural, spectroscopic, and catalytic studies of oxovanadium-(V) alkoxide chlorides have shown that these compounds are monomeric and exhibit activities as oxidation catalysts and Lewis acids. The structure of the reaction product of VOCl[sub 3] and various 1,3-propanediol derivatives was characterized in solution at various temperatures using multinuclear NMR spectroscopy. Although oxovanadium dialkoxide chlorides tend to be monomeric, 1,3-propanediol derivatives induce cluster formation generating tetrameric complexes with a molecular formula of (VOC1L)[sub 4] (where L is bidentate). The 1,3-propanediol derivatives preferred to bridge over two (or three) vanadium atoms rather than form a cyclic six-membered ring on one vanadium atom as found with the corresponding phosphorus compounds. When the 1,3-propanediol ligand was asymmetric, several complexes were observed in solution. A hydrolysis product was characterized by X-ray crystallography. The compound crystallizes in the triclinic space group P[bar 1] with a = 10.003 (2) [Angstrom], b = 11.462 (3) [Angstrom], c = 11.699 (2) [Angstrom], [alpha] = 65.72 (2)[degrees], [beta] = 79.81 (2)[degrees], [gamma] = 81.89 (2) [degrees], V = 1199.7 (4) [Angstrom][sup 3], and Z = 1. The correlation between solution and solid-state structure was determined, and a possible pathway to the hydrolysis product was suggested. Vanadium is used as a reagent in organic synthesis; however, these studies suggest that altered reactivities may surface in the presence of 1,3-propanediol ligands or substrates. The studies show that the analogy between phosphorus and vanadium breaks down in complexes containing 1,3-propanediol derivatives, reducing the prospects of chemically preparing vanadium analogs of cAMP.

  15. VizieR Online Data Catalog: Galaxies in the UMa cluster complex (Karachentsev+, 2013)

    NASA Astrophysics Data System (ADS)

    Karachentsev, I. D.; Nasonova, O. G.; Courtois, H. M.

    2015-04-01

    A nearby friable cloud in Ursa Majoris contains 270 galaxies with radial velocities 500complex. According to Makarov & Karachentsev (2011MNRAS.412.2498M, Cat. J/MNRAS/412/2498), most of the UMa galaxies belong to seven bound groups, which have the following median parameters: velocity dispersion of 58k/s, harmonic projected radius of 300kpc, virial mass of 2x1012M⊙ and virial mass-to-K-band luminosity ratio of 27M⊙/L⊙. Almost a half of the UMa cloud population are gas-rich dwarfs (Ir, Im, BCD) with active star formation seen in the GALEX UV-survey. The UMa groups reside within 15-19Mpc from us, being just at the same distance as the Virgo cluster. The total virial mass of the UMa groups is 4x1013M⊙, yielding the average density of dark matter in the UMa cloud to be Ωm=0.08, i.e. a factor of 3 lower than the cosmic average. This is despite the fact that the UMa cloud resides in a region of the Universe that is an apparent overdensity. A possible explanation for this is that most mass in the Universe lies in the empty space between clusters. Herewith, the mean distances and velocities of the UMa groups follow nearly undisturbed Hubble flow without a sign of the 'Z-wave' effect caused by infall towards a massive attractor. This constrains the total amount of dark matter between the UMa groups within the cloud volume. (1 data file).

  16. A Chemical Composition Survey of the Iron-complex Globular Cluster NGC 6273 (M19)

    NASA Astrophysics Data System (ADS)

    Johnson, Christian I.; Caldwell, Nelson; Rich, R. Michael; Mateo, Mario; Bailey, John I., III; Clarkson, William I.; Olszewski, Edward W.; Walker, Matthew G.

    2017-02-01

    Recent observations have shown that a growing number of the most massive Galactic globular clusters contain multiple populations of stars with different [Fe/H] and neutron-capture element abundances. NGC 6273 has only recently been recognized as a member of this “iron-complex” cluster class, and we provide here a chemical and kinematic analysis of >300 red giant branch and asymptotic giant branch member stars using high-resolution spectra obtained with the Magellan-M2FS and VLT-FLAMES instruments. Multiple lines of evidence indicate that NGC 6273 possesses an intrinsic metallicity spread that ranges from about [Fe/H] = -2 to -1 dex, and may include at least three populations with different [Fe/H] values. The three populations identified here contain separate first (Na/Al-poor) and second (Na/Al-rich) generation stars, but a Mg-Al anti-correlation may only be present in stars with [Fe/H] ≳ -1.65. The strong correlation between [La/Eu] and [Fe/H] suggests that the s-process must have dominated the heavy element enrichment at higher metallicities. A small group of stars with low [α/Fe] is identified and may have been accreted from a former surrounding field star population. The cluster’s large abundance variations are coupled with a complex, extended, and multimodal blue horizontal branch (HB). The HB morphology and chemical abundances suggest that NGC 6273 may have an origin that is similar to ω Cen and M54. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program GO-14197. This paper includes data gathered with the 6.5 m Magellan Telescopes located as Las Campanas Observatory, Chile.

  17. Thiophenol and thiophenol radical and their complexes with gold clusters Au 5 and Au 6

    NASA Astrophysics Data System (ADS)

    Remacle, F.; Kryachko, E. S.

    2004-12-01

    The longstanding controversy between experiment and theory regarding which conformer of thiophenol, planar or perpendicular, is the most stable and what is the magnitude of the corresponding rotational barrier of the S-H group is discussed. We propose a variety of rather modest high-level computational methods within the density theory, which corroborate the experimental data. These methods demonstrate that the planar structure of thiophenol is the most stable and the magnitude of the rotational barrier falls within the experimental range of 3.35±0.84 kJ mol -1. However, the barrier is of the order of RT at room temperature, which might prevent to clearly identify the most stable conformer of thiophenol in experiments and leads to a large-amplitude motion of the thiolic hydrogen. On the other hand, such low value of the barrier may lead to some error in evaluating the thermodynamic properties of thiophenol within the rigid-rotor-harmonic oscillator model, in particular for the bond dissociation enthalpy. We also show the existence of a large entropy contribution to the Gibbs free energy difference between the planar and perpendicular conformers which is the order of the rotational barrier (≈4 kJ mol -1). This might be of interest for experimental study. The most stable complexes of thiophenol with the gold clusters Au 5 and Au 6 are also investigated. It is shown that the sulfur atom prefers to anchor to two- and three-coordinated atoms of gold in these clusters to form a strongly directional gold-sulfur bond. The hydrogen abstraction from the S-H group of thiophenol bonded to the two-coordinated gold atom in Au 5 yields the bridging Au-S dibond and results in a spectacular reduction of the bond dissociation energy of thiophenol by nearly a factor of three.

  18. Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension.

    PubMed

    Lynn, Ke-Shiuan; Lu, Chen-Hua; Yang, Han-Ying; Hsu, Wen-Lian; Pan, Wen-Harn

    2013-07-23

    Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous involvement of multiple genes. Rothman's sufficient-cause model, which is well known in epidemiology, provides a framework for such a concept. In the present work, we developed a three-stage algorithm to construct gene clusters resembling Rothman's causal model for a complex disease, starting from finding influential gene pairs followed by grouping homogeneous pairs. The algorithm was trained and tested on 2,772 hypertensives and 6,515 normotensives extracted from four large Caucasian and Taiwanese databases. The constructed clusters, each featured by a major gene interacting with many other genes and identified a distinct group of patients, reproduced in both ethnic populations and across three genotyping platforms. We present the 14 largest gene clusters which were capable of identifying 19.3% of hypertensives in all the datasets and 41.8% if one dataset was excluded for lack of phenotype information. Although a few normotensives were also identified by the gene clusters, they usually carried less risky combinatory genotypes (insufficient causes) than the hypertensive counterparts. After establishing a cut-off percentage for risky combinatory genotypes in each gene cluster, the 14 gene clusters achieved a classification accuracy of 82.8% for all datasets and 98.9% if the information-short dataset was excluded. Furthermore, not only 10 of the 14 major genes but also many other contributing genes in the clusters are associated with either hypertension or hypertension-related diseases or functions. We have shown with the constructed gene clusters that a multi-causal pie-multi-component approach can indeed improve the reproducibility of genetic markers for complex disease. In addition, our novel findings including a major gene in each cluster and sufficient risky

  19. Towards a methodology for cluster searching to provide conceptual and contextual "richness" for systematic reviews of complex interventions: case study (CLUSTER).

    PubMed

    Booth, Andrew; Harris, Janet; Croot, Elizabeth; Springett, Jane; Campbell, Fiona; Wilkins, Emma

    2013-09-28

    Systematic review methodologies can be harnessed to help researchers to understand and explain how complex interventions may work. Typically, when reviewing complex interventions, a review team will seek to understand the theories that underpin an intervention and the specific context for that intervention. A single published report from a research project does not typically contain this required level of detail. A review team may find it more useful to examine a "study cluster"; a group of related papers that explore and explain various features of a single project and thus supply necessary detail relating to theory and/or context.We sought to conduct a preliminary investigation, from a single case study review, of techniques required to identify a cluster of related research reports, to document the yield from such methods, and to outline a systematic methodology for cluster searching. In a systematic review of community engagement we identified a relevant project - the Gay Men's Task Force. From a single "key pearl citation" we conducted a series of related searches to find contextually or theoretically proximate documents. We followed up Citations, traced Lead authors, identified Unpublished materials, searched Google Scholar, tracked Theories, undertook ancestry searching for Early examples and followed up Related projects (embodied in the CLUSTER mnemonic). Our structured, formalised procedure for cluster searching identified useful reports that are not typically identified from topic-based searches on bibliographic databases. Items previously rejected by an initial sift were subsequently found to inform our understanding of underpinning theory (for example Diffusion of Innovations Theory), context or both. Relevant material included book chapters, a Web-based process evaluation, and peer reviewed reports of projects sharing a common ancestry. We used these reports to understand the context for the intervention and to explore explanations for its relative

  20. Nucleophilic ring opening of bridging thietane ligands in trirhenium carbonyl cluster complexes

    SciTech Connect

    Adams, R.D.; Cortopassi, J.E.; Falloon, S.B.

    1992-11-01

    The reactions of 3,3-dimethylthietane, SCH{sub 2}CMe{sub 2}CH{sub 2} (3,3-DMT), and thietane, SCH{sub 2}CH{sub 2}CH{sub 2}, with Re{sub 3}(CO){sub 10}[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}]({mu}-H){sub 3}, 2b. Compound 2a was characterized crystallographically and was found to consist of a trirhenium cluster with three bridging hydride ligands and a bridging thietane ligand coordinated through its sulfur atom. 2a and 2b react with halide ions by ring-opening additions to the 3,3-DMT ligand to yield the complex anions [Re{sub 3}(CO){sub 10}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}x)({mu}-h){sub 3}]{sup -} 3A-6A, X = F (71%), Cl(71%), Br(84%), I(87%) and [Re{sub 3}(CO){sub 10}({mu}-SCH{sub 2}CH{sub 2}CH{sub 2}Cl)({mu}-H){sub 3}]{sup -}, 4b (67%). Similarly, addition of NMe{sub 3} to 2a and 2b yielded the ring-opened zwitterions Re{sub 3}(CO){sub 10}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}NMe{sub 3})({mu}-H){sub 3}, 7 a crystographically. They are zwitterions positively charged at the nitrogen atoms and negatively charged on the trirhenium clusters. Complex 7b was also obtained in a 48% yield from the reaction of Re{sub 3}(C){sub 12}({mu}-H){sub 3} with Me{sub 3}NO in the presence of thietane, but the corresponding reaction using 3,3-DMT yielded only 2a and Re{sub 3}(CO){sub 11}(SCH{sub 2}CMe{sub 2}CH{sub 2})({mu}-H){sub 3}, 8. Attempts to obtain a ring-opening addition to 2a by reaction with PMe{sub 2}Ph yielded only Re{sub 3}(CO){sub 10}(PMe{sub 2}PH){sub 2}({mu}-H){sub 3} by ligand substitution. Attempts to obtain ring opening addition to 8 by reaction with I{sup -} yielded only [Re{sub 3}(CO){sub 11}I({mu}-H){sub 3}]{sup -} by ligand substitution. 20 refs., 3 figs., 10 tabs.

  1. Nucleophilic ring opening of bridging thietanes in open triosmium cluster complexes

    SciTech Connect

    Adams, R.D.; Belinski, J.A.

    1992-07-01

    The complexes Os{sub 3}(CO){sub 9}({mu}{sub 3}-S)[{mu}-SCH{sub 2}CMe{sub 2}CMe{sub 2}CH{sub 2}] (1) and Os{sub 3}(CO){sub 9}({mu}{sub 3}-S)[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}] (2) were obtained from the reactions of Os{sub 3}(CO){sub 10}({mu}{sub 3}-S) with 3,3-dimethylthietane (DMT) and thietane, respectively, at -42 {degree}C in the presence of Me{sub 3}NO. Compound 1 was characterized by a single-crystal X-ray diffraction analysis and was found to contain a DMT group bridging two of the nonbonded metal atoms in the open cluster of three metal atoms by using both lone pairs of electrons on the sulfur atom. Compound 1 reacted with bis(triphenylphosphine)nitrogen(1+) chloride ([PPN]Cl) at 25 {degrees}C to yield the salt [PPN][Os{sub 3}-(CO){sub 9}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}Cl)({mu}{sub 3}-S)] (3; 76%), in which the chloride ion was added to one of the methylene groups of the DMT ring in a process that caused the ring to open by cleavage of one of the carbon-sulfur bonds. A 4-chloro-3,3-dimethylpropanethiolate ligand bridges the open edge of the anionic triosmium cluster. Compound 3 was converted to the neutral complex Os{sub 3}(CO){sub 9}[{mu}-SCH{sub 2}CMe{sub 2}CMe{sub 2}CH{sub 2}Cl]({mu}{sub 3}-S)({mu}-H) (4) by reaction with HCl at 25 {degrees}C. Compound 4 is structurally similar to 3, except that is contains a hydride ligand bridging one of the two metal-metal bonds. Compounds 1 and 2 react with HCl in CH{sub 2}Cl{sub 2} solvent to yield the neutral compounds 4 and Os{sub 3}(CO){sub 9}[{mu}-SCH{sub 2}CH{sub 2}CH{sub 2}Cl]({mu}{sub 3}-S)({mu}-H) (5) in 89% and 90% yields, respectively, in one step. 11 refs., 3 figs., 10 tabs.

  2. Zeolite-supported rhodium complexes and clusters: switching catalytic selectivity by controlling structures of essentially molecular species.

    PubMed

    Serna, Pedro; Gates, B C

    2011-04-06

    Precise synthesis and characterization of site-isolated rhodium complexes and extremely small rhodium clusters supported on zeolite HY allow control of the catalyst selectivity in the conversion of ethene to n-butene or ethane, respectively, as a result of tuning the structure of the active sites at a molecular level.

  3. Carbonyl substitution chemistry of some trimetallic transition metal cluster complexes with polyfunctional ligands

    SciTech Connect

    Byrne, Lindsay T.; Hondow, Nicole S.; Koutsantonis, George A.; Skelton, Brian W.; Torabi, A. Asgar; White, Allan H.; Wild, S. Bruce

    2008-11-03

    The trimetallic clusters [Ru{sub 3}(CO){sub 10}(dppm)], [Ru{sub 3}(CO){sub 12}] and [RuCo{sub 2}(CO){sub 11}] react with a number of multifunctional secondary phosphine and tertiary arsine ligands to give products consequent on carbonyl substitution and, in the case of the secondary phosphines, PH activation. The reaction with the unresolved mixed P/S donor, 1-phenylphosphino-2-thio(ethane), HSCH{sub 2}CH{sub 2}PHPh ({double_bond}LH{sub 2}), gave two products under various conditions which have been characterized by spectroscopic and crystallographic means. These two complexes [Ru{sub 3}({mu}dppm)(H)(CO){sub 7}(LH)] and [Ru{sub 3}({mu}-dppm)(H)(CO){sub 8}(LH)Ru{sub 3}({mu}-dppm)(CO){sub 9}], show the versatility of the ligand, with it chelating in the former and bridging two Ru{sub 3} units in the latter. The stereogenic centres in the molecules gave rise to complicated spectroscopic data which are consistent with the presence of diastereoisomers. In the case of [Ru{sub 3}(CO){sub 12}] the reaction with LH{sub 2} gave a poor yield of a tetranuclear butterfly cluster, [Ru{sub 4}(CO){sub 10}(L){sub 2}], in which two of the ligands bridge opposite hinge wingtip bonds of the cluster. A related ligand, HSCH{sub 2}CH{sub 2}AsMe(C{sub 6}H{sub 4}CH{sub 2}OMe), reacted with [RuCo{sub 2}(CO){sub 11}] to give a low yield of the heterobimetallic Ru-Co adduct, [RuCo(CO){sub 6}(SCH{sub 2}CH{sub 2}AsMe(C{sub 6}H{sub 4}CH{sub 2}OMe))], which appears to be the only one of its type so far structurally characterized. The secondary phosphine, HPMe(C{sub 6}H{sub 4}(CH{sub 2}OMe)) and its oxide HP(O)Me(C{sub 6}H{sub 4}(CH{sub 2}OMe)) also react with the cluster [Ru{sub 3}(CO){sub 10}(dppm)] to give carbonyl substitution products, [Ru{sub 3}(CO){sub 5}(dppm)({mu}{sub 2}-PMe(C{sub 6}H{sub 4}CH{sub 2}OMe)){sub 4}], and [Ru{sub 3}H(CO){sub 7}(dppm)({mu}{sub 2},{eta}{sup 1}P({double_bond}O)Me(C{sub 6}H{sub 4}CH{sub 2}OMe))]. The former consists of an open Ru{sub 3} triangle with four

  4. Ca cofactor of the water-oxidation complex: Evidence for a Mn/Ca heteronuclear cluster

    SciTech Connect

    Cinco, Roehl M.; Robblee, John H.; Messinger, Johannes; Fernandez, Carmen; McFarlane, Karen L.; Pizarro, Shelly A.; Sauer, Ken; Yachandra, Vittal K.

    2001-07-25

    Calcium and chloride are necessary cofactors for the proper function of the oxygen-evolving complex (OEC) of Photosystem II (PS II). Located in the thylakoid membranes of green plants, cyanobacteria and algae, PS II and the OEC catalyze the light-driven oxidation of water into dioxygen (released into the biosphere), protons and electrons for carbon fixation. The actual chemistry of water oxidation is performed by a cluster of four manganese atoms, along with the requisite cofactors Ca{sup 2+} and Cl{sup -}. While the Mn complex has been extensively studied by X-ray absorption techniques, comparatively less is known about the Ca{sup 2+} cofactor. The fewer number of studies on the Ca{sup 2+} cofactor have sometimes relied on substituting the native cofactor with strontium or other metals, and have stirred some debate about the structure of the binding site. past efforts using Mn EXAFS on Sr-substituted PSII are suggestive of a close link between the Mn cluster and Sr, within 3.5 {angstrom}. The most recent published study using Sr EXAFS on similar samples confirms this finding of a 3.5 {angstrom} distance between Mn and Sr. This finding was base3d on a second Fourier peak (R {approx} 3 {angstrom}) in the Sr EXAFS from functional samples, but is absent from inactive, hydroxylamine-treated PS II. This Fourier peak II was found to fit best to two Mn at 3.5 {angstrom} rather than lighter atoms (carbon). Nevertheless, other experiments have given contrary results. They wanted to extend the technique by using polarized Sr EXAFS on layered Sr-substituted samples, to provide important angle information. Polarized EXAFS involves collecting spectra for different incident angles ({theta}) between the membrane normal of the layered sample and the X-ray electric field vector. Dichroism in the EXAFS can occur, depending on how the particular absorber-backscatterer (A-B) vector is aligned with the electric field. Through analysis of the dichroism, they extract the average number

  5. Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering.

    PubMed

    Theofilatos, Konstantinos; Pavlopoulou, Niki; Papasavvas, Christoforos; Likothanassis, Spiros; Dimitrakopoulos, Christos; Georgopoulos, Efstratios; Moschopoulos, Charalampos; Mavroudi, Seferina

    2015-03-01

    Proteins are considered to be the most important individual components of biological systems and they combine to form physical protein complexes which are responsible for certain molecular functions. Despite the large availability of protein-protein interaction (PPI) information, not much information is available about protein complexes. Experimental methods are limited in terms of time, efficiency, cost and performance constraints. Existing computational methods have provided encouraging preliminary results, but they phase certain disadvantages as they require parameter tuning, some of them cannot handle weighted PPI data and others do not allow a protein to participate in more than one protein complex. In the present paper, we propose a new fully unsupervised methodology for predicting protein complexes from weighted PPI graphs. The proposed methodology is called evolutionary enhanced Markov clustering (EE-MC) and it is a hybrid combination of an adaptive evolutionary algorithm and a state-of-the-art clustering algorithm named enhanced Markov clustering. EE-MC was compared with state-of-the-art methodologies when applied to datasets from the human and the yeast Saccharomyces cerevisiae organisms. Using public available datasets, EE-MC outperformed existing methodologies (in some datasets the separation metric was increased by 10-20%). Moreover, when applied to new human datasets its performance was encouraging in the prediction of protein complexes which consist of proteins with high functional similarity. In specific, 5737 protein complexes were predicted and 72.58% of them are enriched for at least one gene ontology (GO) function term. EE-MC is by design able to overcome intrinsic limitations of existing methodologies such as their inability to handle weighted PPI networks, their constraint to assign every protein in exactly one cluster and the difficulties they face concerning the parameter tuning. This fact was experimentally validated and moreover, new

  6. The E. coli Monothiol Glutaredoxin GrxD Forms Homodimeric and Heterodimeric FeS Cluster Containing Complexes

    PubMed Central

    Yeung, N.; Gold, B.; Liu, N. L.; Prathapam, R.; Sterling, H. J.; Willams, E. R.; Butland, G.

    2011-01-01

    Monothiol glutaredoxins (mono-Grx) represent a highly evolutionarily conserved class of proteins present in organisms ranging from prokaryotes to humans. Mono-Grxs have been implicated in iron sulfur (FeS) cluster biosynthesis as potential scaffold proteins and in iron homeostasis via an FeS-containing complex with Fra2p (homolog of E. coli BolA) in yeast, and are linked to signal transduction in mammalian systems. However, the function of the mono-Grx in prokaryotes and the nature of an interaction with BolA-like proteins have not been established. Recent genome-wide screens for E. coli genetic interactions reported the synthetic lethality (combination of mutations leading to cell death; mutation of only one of these genes does not) of a grxD mutation when combined with strains defective in FeS cluster biosynthesis (isc operon) functions [Butland, G. et al. (2008) Nature Methods 5, 789–795]. These data connected the only E. coli mono-Grx, GrxD, to a potential role in FeS cluster biosynthesis. We investigated GrxD to uncover the molecular basis of this synthetic lethality and observed that GrxD can form FeS-bound homodimeric and BolA containing heterodimeric complexes. These complexes display substantially different spectroscopic and functional properties, including the ability to act as scaffold proteins for intact FeS cluster transfer to the model [2Fe-2S] acceptor protein E. coli apo-ferredoxin (Fdx), with the homodimer being significantly more efficient. In this work, we functionally dissect the potential cellular roles of GrxD as a component of both homodimeric and heterodimeric complexes, to ultimately uncover if either of these complexes perform functions linked to FeS cluster biosynthesis. PMID:21899261

  7. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA.

    PubMed

    Fonfara, Ines; Richter, Hagen; Bratovič, Majda; Le Rhun, Anaïs; Charpentier, Emmanuelle

    2016-04-28

    CRISPR-Cas systems that provide defence against mobile genetic elements in bacteria and archaea have evolved a variety of mechanisms to target and cleave RNA or DNA. The well-studied types I, II and III utilize a set of distinct CRISPR-associated (Cas) proteins for production of mature CRISPR RNAs (crRNAs) and interference with invading nucleic acids. In types I and III, Cas6 or Cas5d cleaves precursor crRNA (pre-crRNA) and the mature crRNAs then guide a complex of Cas proteins (Cascade-Cas3, type I; Csm or Cmr, type III) to target and cleave invading DNA or RNA. In type II systems, RNase III cleaves pre-crRNA base-paired with trans-activating crRNA (tracrRNA) in the presence of Cas9 (refs 13, 14). The mature tracrRNA-crRNA duplex then guides Cas9 to cleave target DNA. Here, we demonstrate a novel mechanism in CRISPR-Cas immunity. We show that type V-A Cpf1 from Francisella novicida is a dual-nuclease that is specific to crRNA biogenesis and target DNA interference. Cpf1 cleaves pre-crRNA upstream of a hairpin structure formed within the CRISPR repeats and thereby generates intermediate crRNAs that are processed further, leading to mature crRNAs. After recognition of a 5'-YTN-3' protospacer adjacent motif on the non-target DNA strand and subsequent probing for an eight-nucleotide seed sequence, Cpf1, guided by the single mature repeat-spacer crRNA, introduces double-stranded breaks in the target DNA to generate a 5' overhang. The RNase and DNase activities of Cpf1 require sequence- and structure-specific binding to the hairpin of crRNA repeats. Cpf1 uses distinct active domains for both nuclease reactions and cleaves nucleic acids in the presence of magnesium or calcium. This study uncovers a new family of enzymes with specific dual endoribonuclease and endonuclease activities, and demonstrates that type V-A constitutes the most minimalistic of the CRISPR-Cas systems so far described.

  8. The properties of clusters in the gas phase. IV - Complexes of H2O and HNOx clustering on NOx/-/

    NASA Technical Reports Server (NTRS)

    Lee, N.; Castleman, A. W., Jr.; Keesee, R. G.

    1980-01-01

    Thermodynamic quantities for the gas-phase clustering equilibria of NO2(-) and NO3(-) were determined with high-pressure mass spectrometry. A comparison of values of the free energy of hydration derived from the data shows good agreement with formerly reported values at 296 K. New data for larger NO2(-) and NO3(-) hydrates as well as NO2(-)(HNO2)n were obtained in this study. To aid in understanding the bonding and stability of the hydrates of nitrite and nitrate ions, CNDO/2 calculations were performed, and the results are discussed. A correlation between the aqueous-phase total hydration enthalpy of a single ion and its gas-phase hydration enthalpy was obtained. Atmospheric implications of the data are also briefly discussed.

  9. The properties of clusters in the gas phase. IV - Complexes of H2O and HNOx clustering on NOx/-/

    NASA Technical Reports Server (NTRS)

    Lee, N.; Castleman, A. W., Jr.; Keesee, R. G.

    1980-01-01

    Thermodynamic quantities for the gas-phase clustering equilibria of NO2(-) and NO3(-) were determined with high-pressure mass spectrometry. A comparison of values of the free energy of hydration derived from the data shows good agreement with formerly reported values at 296 K. New data for larger NO2(-) and NO3(-) hydrates as well as NO2(-)(HNO2)n were obtained in this study. To aid in understanding the bonding and stability of the hydrates of nitrite and nitrate ions, CNDO/2 calculations were performed, and the results are discussed. A correlation between the aqueous-phase total hydration enthalpy of a single ion and its gas-phase hydration enthalpy was obtained. Atmospheric implications of the data are also briefly discussed.

  10. Tribological coatings for complex mechanical elements produced by supersonic cluster beam deposition of metal dichalcogenide nanoparticles

    NASA Astrophysics Data System (ADS)

    Piazzoni, C.; Buttery, M.; Hampson, M. R.; Roberts, E. W.; Ducati, C.; Lenardi, C.; Cavaliere, F.; Piseri, P.; Milani, P.

    2015-07-01

    Fullerene-like MoS2 and WS2 nanoparticles can be used as building blocks for the fabrication of fluid and solid lubricants. Metal dichalcogenide films have a very low friction coefficient in vacuum, therefore they have mostly been used as solid lubricants in space and vacuum applications. Unfortunately, their use is significantly hampered by the fact that in the presence of humidity, oxygen and moisture, the low-friction properties of these materials rapidly degrade due to oxidation. The use of closed-cage MoS2 and WS2 nanoparticles may eliminate this problem, although the fabrication of lubricant thin films starting from dichalcogenide nanoparticles is, to date, a difficult task. Here we demonstrate the use of supersonic cluster beam deposition for the coating of complex mechanical elements (angular contact ball bearings) with nanostructured MoS2 and WS2 thin films. We report structural and tribological characterization of the coatings in view of the optimization of tribological performances for aerospace applications.

  11. X-ray observations of complex temperature structure in the cool-core cluster A85

    SciTech Connect

    Schenck, David E.; Datta, Abhirup; Burns, Jack O.; Skillman, Sam

    2014-07-01

    X-ray observations were used to examine the complex temperature structure of A85, a cool-core galaxy cluster. Temperature features can provide evidence of merging events which shock heat the intracluster gas. Temperature maps were made from both Chandra and XMM-Newton observations. The combination of a new, long-exposure XMM observation and an improved temperature map binning technique produced the highest fidelity temperature maps of A85 to date. Hot regions were detected near the subclusters to the south and southwest in both the Chandra and XMM temperature maps. The presence of these structures implies A85 is not relaxed. The hot regions may indicate the presence of shocks. The Mach numbers were estimated to be ∼1.9 at the locations of the hot spots. Observational effects will tend to systematically reduce temperature jumps, so the measured Mach numbers are likely underestimated. Neither temperature map showed evidence for a shock in the vicinity of the presumed radio relic near the southwest subcluster. However, the presence of a weak shock cannot be ruled out. There was tension between the temperatures measured by the two instruments.

  12. Clustered regularly interspaced short palindromic repeats (CRISPRs) analysis of members of the Mycobacterium tuberculosis complex.

    PubMed

    Botelho, Ana; Canto, Ana; Leão, Célia; Cunha, Mónica V

    2015-01-01

    Typical CRISPR (clustered, regularly interspaced, short palindromic repeat) regions are constituted by short direct repeats (DRs), interspersed with similarly sized non-repetitive spacers, derived from transmissible genetic elements, acquired when the cell is challenged with foreign DNA. The analysis of the structure, in number and nature, of CRISPR spacers is a valuable tool for molecular typing since these loci are polymorphic among strains, originating characteristic signatures. The existence of CRISPR structures in the genome of the members of Mycobacterium tuberculosis complex (MTBC) enabled the development of a genotyping method, based on the analysis of the presence or absence of 43 oligonucleotide spacers separated by conserved DRs. This method, called spoligotyping, consists on PCR amplification of the DR chromosomal region and recognition after hybridization of the spacers that are present. The workflow beneath this methodology implies that the PCR products are brought onto a membrane containing synthetic oligonucleotides that have complementary sequences to the spacer sequences. Lack of hybridization of the PCR products to a specific oligonucleotide sequence indicates absence of the correspondent spacer sequence in the examined strain. Spoligotyping gained great notoriety as a robust identification and typing tool for members of MTBC, enabling multiple epidemiological studies on human and animal tuberculosis.

  13. Towards a methodology for cluster searching to provide conceptual and contextual “richness” for systematic reviews of complex interventions: case study (CLUSTER)

    PubMed Central

    2013-01-01

    Background Systematic review methodologies can be harnessed to help researchers to understand and explain how complex interventions may work. Typically, when reviewing complex interventions, a review team will seek to understand the theories that underpin an intervention and the specific context for that intervention. A single published report from a research project does not typically contain this required level of detail. A review team may find it more useful to examine a “study cluster”; a group of related papers that explore and explain various features of a single project and thus supply necessary detail relating to theory and/or context. We sought to conduct a preliminary investigation, from a single case study review, of techniques required to identify a cluster of related research reports, to document the yield from such methods, and to outline a systematic methodology for cluster searching. Methods In a systematic review of community engagement we identified a relevant project – the Gay Men’s Task Force. From a single “key pearl citation” we conducted a series of related searches to find contextually or theoretically proximate documents. We followed up Citations, traced Lead authors, identified Unpublished materials, searched Google Scholar, tracked Theories, undertook ancestry searching for Early examples and followed up Related projects (embodied in the CLUSTER mnemonic). Results Our structured, formalised procedure for cluster searching identified useful reports that are not typically identified from topic-based searches on bibliographic databases. Items previously rejected by an initial sift were subsequently found to inform our understanding of underpinning theory (for example Diffusion of Innovations Theory), context or both. Relevant material included book chapters, a Web-based process evaluation, and peer reviewed reports of projects sharing a common ancestry. We used these reports to understand the context for the intervention and to

  14. FRONTIER FIELDS CLUSTERS: DEEP CHANDRA OBSERVATIONS OF THE COMPLEX MERGER MACS J1149.6+2223

    SciTech Connect

    Ogrean, G. A.; Weeren, R. J. van; Jones, C.; Forman, W.; Andrade-Santos, F.; Murray, S. S.; Nulsen, P.; Bulbul, E.; Kraft, R.; Randall, S.; Dawson, W. A.; Golovich, N.; Roediger, E.; Zitrin, A.; Sayers, J.; Goulding, A.; Umetsu, K.; Mroczkowski, T.; Bonafede, A.; Churazov, E.; and others

    2016-03-10

    The Hubble Space Telescope Frontier Fields cluster MACS J1149.6+2223 is one of the most complex merging clusters, believed to consist of four dark matter halos. We present results from deep (365 ks) Chandra observations of the cluster, which reveal the most distant cold front (z  =  0.544) discovered to date. In the cluster outskirts, we also detect hints of a surface brightness edge that could be the bow shock preceding the cold front. The substructure analysis of the cluster identified several components with large relative radial velocities, thus indicating that at least some collisions occur almost along the line of sight. The inclination of the mergers with respect to the plane of the sky poses significant observational challenges at X-ray wavelengths. MACS J1149.6+2223 possibly hosts a steep-spectrum radio halo. If the steepness of the radio halo is confirmed, then the radio spectrum, combined with the relatively regular ICM morphology, could indicate that MACS J1149.6+2223 is an old merging cluster.

  15. Copper speciation in sulfidic solutions at low sulfur activity: Further evidence for cluster complexes?

    NASA Astrophysics Data System (ADS)

    Thompson, Richard A.; Helz, George R.

    1994-07-01

    The solubility of two as0-buffering assemblages in the Cu-S system have been studied: chalcocite-djurleite (Cc-Dj) and anilite-covellite (An-Cv). Ion activity products, [Cu +]HS -] 1/2[H +] - 1/2 (25°C, I = 0) at equilibrium, derived from solubility measurements in penicillamine solutions, are 10 -17.01 ± 0.05 (Cc-Dj) and 10 -17.14 ± 0.10 (An-Cv), from which ΔG° f = -82.11 kJ/mol for Cc and -74.77 kJ/mol for An. In the An-Cv assemblage, aCu2S = 0.55 (2 σ = 0.2) vs. 1.00 in the Cc-containing assemblage. The difference in aCu2S between the two assemblages is used in a novel way to estimate stoichiometry of Cu-HS complexes. The solubility of both assemblages (0.7-0.01 M NaHS, pH 7-12.5, 25°C) can be fit with a model incorporating the same two chemical species, one containing an odd number of Cu atoms (Cu(HS) 2-3, CU 3S 4H 2-3, or a higher multimer) and the other containing an even number of Cu atoms (Cu 2S(HS) 22-, Cu 4S 4H 22-, etc.). The trimer-tetramer model fits the combined data for the two assemblages distinctly better than the monomer-dimer model, but this result is very sensitive to uncertainty in aCu2S. Along with EXAFS results, the weight of the evidence favors small cluster complexes (2-5 Cu atoms), but is inconclusive at the present level of resolution. Multimers can be rationalized because condensation of metal-centered monomers to clusters provides a means for soft acid/base elements to maintain favored coordination geometries at low ligand to metal ratios. Based on the fitting methods developed here, previous covellite solubility data from this laboratory are reinterpreted in terms of Cu 2S 2(HS) 33-, Cu 2S 3)(S 4) 2-, and Cu(S 9)S 10) 3-; the last of these could also be represented by the trimer, Cu 3(S 7) 33-, which is homologous with a known complex. With the measured equilibrium constants, the speciation of Cu in the sulfidic zone of the Black Sea is calculated. Covellite is the stable Cu-S mineral, but the sulfidic water column is vastly

  16. Ring opening and carbonylation of 3,3-dimethylthietane ligands in ruthenium carbonyl cluster complexes

    SciTech Connect

    Adams, R.D.; Belinski, J.A.; Yamamoto, J.H.

    1992-10-01

    When heated to 97{degrees}C, the complex Ru{sub 4}(CO){sub 12}[{mu}-SCH{sub 2}CMe{sub 2}CH{sub 2}]2 (1) was transformed into two new hexaruthenium cluster complexes, Ru{sub 6}(CO){sub 13}({mu}{sub 3}-SCH{sub 2}CMe{sub 2}CH{sub 2}){sub 4} (2) and Ru{sub 6}(CO){sub 12}({mu}-SCH{sub 2}CMe{sub 2}CH{sub 2})({mu}{sub 3}-SCH{sub 2}CMe{sub 2}CH{sub 2}){sub 3}[{mu}{sub 3}-SCH{sub 2}C(Me)(CH{sub 2})CH{sub 2}] ({mu}-H) (3), that contain four and five ring-opened 3,3-dimethylthietane (3,3-DMT) ligands, respectively. In compound 3 one of the ring-opened DMT ligands has also undergone a CH activation on one of the methyl groups. Compound 2 reacts with additional 3,3-DMT at 97{degrees}C to form 3 in 18% yield. When treated with CO at 95{degrees}C (500 psi), compound 2 yielded 4,4-dimethylthiobutyrolactone and Ru{sub 3}(CO){sub 12}. It was also found that the complex Os{sub 3}(CO){sub 11-}(SCH{sub 2}CMe{sub 2}CH{sub 2}C{double_bond}O) (4) yields 4,4-dimethylthiobutyrolactone when treated with CO at 120{degrees}C (1200 psi). Crystal data for 2: space group P2{sub 1}/n, {alpha} = 22.652 (7) A, {beta} = 11.712 (2) A, c = 19.965 (6) A, {Beta} = 115.75 (2){degrees} Z = 4, 3665 reflections, R = 0.021. Crystal data for 3: space group P2{sub 1}/c, {alpha} = 17.332 (8) A, {Beta} = 14.668 (9) A, c = 19.823 (9) A, {Beta} = 91.27 (4){degrees}, Z = 4, 1875 reflections, R = 0.050. 13 refs., 2 figs., 13 refs.

  17. Unusual structures and reactivity of mixed metal cluster complexes containing the palladium/platinum tri-t-butylphosphine grouping.

    PubMed

    Adams, Richard D; Captain, Burjor

    2009-03-17

    Polynuclear metal carbonyl complexes have a range of applications in chemical research: for example, they can serve as surface models to probe features of heterogeneous catalysis and can perform novel transformations of organic molecules in solutions. Mixed metal complexes can demonstrate bimetallic cooperativity and synergism and can also serve as precursors to multimetallic heterogeneous catalysts that have superior activities and selectivities. This Account describes the results of our recent comprehensive study of the chemistry of mixed metal cluster complexes containing the sterically encumbered M(PBu(t)(3)), M = Pd or Pt, group. This grouping readily adds to the metal-metal bonds of metal carbonyl cluster complexes and modifies their reactivity. We have prepared new, highly electronically unsaturated mixed metal complexes that exhibit unusually high reactivity toward hydrogen. The platinum atom of the Pt(PBu(t)(3)) grouping can bond to as many as five metal atoms, and it can interconvert, sometimes rapidly, between the different bonding modes. The large steric effects of the PBu(t)(3) ligand allowed us to prepare highly unsaturated, stable, mixed-metal complexes, and these complexes react with hydrogen, sometimes reversibly, under very mild conditions to yield polyhydride complexes. Strong evidence suggests that the Pt(PBu(t)(3)) group can also activate metal-hydrogen bonds in other complexes. In the future, we expect that researchers will prepare a greater variety of mixed metal complexes containing the Pd/Pt(PBu(t)(3)) group or other similar bulky groups, and that some of these complexes will exhibit even more unusual chemistry than what we have observed so far.

  18. Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters

    USDA-ARS?s Scientific Manuscript database

    The remarkable conservation of Hox clusters is an accepted but little understood principle of biology. Some organizational constraints have been identified for vertebrate Hox clusters, but most of these are thought to be recent innovations that may not apply to other organisms. Ironically, many mode...

  19. Electronic Structure of Transition Metal Clusters, Actinide Complexes and Their Reactivities

    SciTech Connect

    Krishnan Balasubramanian

    2009-07-18

    methods with all-electron Douglas-Kroll relativistic methods. We have the capabilities for computing full CI extrapolations including spin-orbit effects and several one-electron properties and electron density maps including spin-orbit effects. We are continuously collaborating with several experimental groups around the country and at National Labs to carry out computational studies on the DOE-BES funded projects. The past work in the last 3 years was primarily motivated and driven by the concurrent or recent experimental studies on these systems. We were thus significantly benefited by coordinating our computational efforts with experimental studies. The interaction between theory and experiment has resulted in some unique and exciting opportunities. For example, for the very first time ever, the upper spin-orbit component of a heavy trimer such as Au{sub 3} was experimentally observed as a result of our accurate computational study on the upper electronic states of gold trimer. Likewise for the first time AuH{sub 2} could be observed and interpreted clearly due to our computed potential energy surfaces that revealed the existence of a large barrier to convert the isolated AuH{sub 2} back to Au and H{sub 2}. We have also worked on yet to be observed systems and have made predictions for future experiments. We have computed the spectroscopic and thermodynamic properties of transition metal carbides transition metal clusters and compared our electronic states to the anion photodetachment spectra of Lai Sheng Wang. Prof Mike Morse and coworkers(funded also by DOE-BES) and Prof Stimle and coworkers(also funded by DOE-BES) are working on the spectroscopic properties of transition metal carbides and nitrides. Our predictions on the excited states of transition metal clusters such as Hf{sub 3}, Nb{sub 2}{sup +} etc., have been confirmed experimentally by Prof. Lombardi and coworkers using resonance Raman spectroscopy. We have also been studying larger complexes critical to the

  20. Modeling biological copper clusters: synthesis of a tricopper complex, and its chloride- and sulfide-bridged congeners.

    PubMed

    Di Francesco, Gianna N; Gaillard, Aleth; Ghiviriga, Ion; Abboud, Khalil A; Murray, Leslie J

    2014-05-05

    The synthesis and characterization of a family of tricopper clusters housed within a tris(β-diketimine) cyclophane ligand (H3L) that bear structural similarities to biological copper clusters are reported. In all complexes, each Cu atom is held within the N2-chelate of a single β-diketiminate arm. Reaction of L(3-) with CuCl affords an anionic complex containing a μ3-chloride donor in the central cavity, whereas there is no evidence for bromide incorporation in the product of the reaction of L(3-) with CuBr (Cu3L). Cu3L reacts with elemental sulfur to generate the corresponding air-stable mixed-valent (μ3-sulfido)tricopper complex, Cu3(μ3-S)L, which represents the first example of a sulfide-bridged copper cluster in which each metal center is both coordinatively unsaturated and held within a N-rich environment. The calculated LUMO is predominantly Cu-S π* in character and delocalized over all three metal centers, which is consistent with the isotropic ten-line absorption (g ∼ 2.095, A ∼ 33 G) observed at room temperature in EPR spectra of the one-electron chemically reduced complex, [Cu3(μ3-S)L](-).

  1. A widespread self-cleaving ribozyme class is revealed by bioinformatics

    PubMed Central

    Roth, Adam; Weinberg, Zasha; Chen, Andy G. Y.; Kim, Peter B.; Ames, Tyler D.; Breaker, Ronald R.

    2013-01-01

    Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs. PMID:24240507

  2. Anti-tumor and immunomodulatory activity of iron hepta-tungsten phosphate oxygen clusters complex.

    PubMed

    Zhang, Bisong; Qiu, Jianping; Wu, Changsheng; Li, Yunxia; Liu, Zhenxiang

    2015-12-01

    Polyoxometalates (POMs) have attracted a considerable attention due to their unique structural characteristics, physicochemical properties and biological activities. In this study, iron hepta-tungsten phosphate oxygen clusters complex Na12H[Fe(HPW7O28)2]·44H2O (IHTPO) was synthesized and evaluated for in vitro cytotoxic activities on human hepatoma HepG2, leukemia K562, lung carcinoma A549, and large cell lung cancer NCI-H460 cells, therapeutic efficacies on mice transplantable tumor, and immunomodulatory potentials on the immune response in tumor-bearing mice. IHTPO exhibited lower in vitro cytotoxic activities against four human tumor cell lines, with the IC50 values being higher than 62.5μM (ca. 300μg/ml). IHTPO, however, significantly inhibited the growth of S180 sarcoma transplanted in mice. It was further showed that IHTPO could not only significantly promote splenocytes proliferation, NK cell and CTL activity from splenocytes, but remarkably enhance serum antigen-specific IgG, IgG2a and IgG2b antibody levels in S180-bearing mice. IHTPO also significantly promoted Th1 cytokines IFN-γ and IL-2 production, and up-regulated the mRNA expression levels of IFN-γ, IL-2 and Th1 transcription factors T-bet and STAT-4 in splenocytes from the S180-bearing mice. These results suggested that IHTPO significantly inhibited the growth of mice transplantable tumor, and that its in vivo antitumor activity might be achieved by improving Th1 protective cell-mediated immunity. IHTPO could act as antitumor agent with immunomodulatory activity.

  3. Clustered DNA motifs mark X chromosomes for repression by a dosage compensation complex

    PubMed Central

    McDonel, Patrick; Jans, Judith; Peterson, Brant K.; Meyer, Barbara J.

    2009-01-01

    Gene expression in metazoans is regulated not only at the level of individual genes but also in a coordinated manner across large chromosomal domains (for example centromeres, telomeres and imprinted gene clusters1-3) and along entire chromosomes (for example X-chromosome dosage compensation4-6). The primary DNA sequence usually specifies the regulation of individual genes, but the nature of cis-acting information that controls genes over large regions has been elusive: higher-order DNA structure, specific histone modifications, subnuclear compartmentalization and primary DNA sequence are possibilities. One paradigm of chromosome-wide gene regulation is Caenorhabditis elegans dosage compensation in which a large dosage compensation complex (DCC) is targeted to both X chromosomes of hermaphrodites to repress transcript levels by half6. This essential process equalizes X-linked gene expression between the sexes (XO males and XX hermaphrodites). Here we report the discovery and dissection of cis-acting sites that mark nematode X chromosomes as targets for gene repression by the DCC. These rex (recruitment element on X) sites are widely dispersed along X and reside in promoters, exons and intergenic regions. rex sites share at least two distinct motifs that act in combination to recruit the DCC. Mutating these motifs severely reduces or abolishes DCC binding in vivo, demonstrating the importance of primary DNA sequence in chromosome-wide regulation. Unexpectedly, the motifs are not enriched on X, but altering motif numbers within rex sites demonstrates that motif co-occurrence in unusually high densities is essential for optimal DCC recruitment. Thus, X-specific repression is established through sequences not specific to X. The distribution of common motifs provides the foundation for repression along an entire chromosome. PMID:17122774

  4. Probing the Dragonfish star-forming complex: the ionizing population of the young massive cluster Mercer 30

    NASA Astrophysics Data System (ADS)

    de la Fuente, D.; Najarro, F.; Borissova, J.; Ramírez Alegría, S.; Hanson, M. M.; Trombley, C.; Figer, D. F.; Davies, B.; Garcia, M.; Kurtev, R.; Urbaneja, M. A.; Smith, L. C.; Lucas, P. W.; Herrero, A.

    2016-05-01

    It has recently been claimed that the nebula, Dragonfish, is powered by a superluminous but elusive OB association. However, systematic searches in near-infrared photometric surveys have found many other cluster candidates in this region of the sky. Among these, the first confirmed young massive cluster was Mercer 30, where Wolf-Rayet stars were found.We perform a new characterization of Mercer 30 with unprecedented accuracy, combining NICMOS/HST and VVV photometric data with multi-epoch ISAAC/VLT H- and K-band spectra. Stellar parameters for most of spectroscopically observed cluster members are found through precise non-LTE atmosphere modeling with the CMFGEN code. Our spectrophotometric study for this cluster yields a new, revised distance of d = (12.4 ± 1.7) kpc and a total of QHMc30 ≈ 6.70 × 1050 s-1 Lyman ionizing photons. A cluster age of (4.0 ± 0.8) Myr is found through isochrone fitting, and a total mass of (1.6 ± 0.6) × 104M⊙ is estimated, thanks to our extensive knowledge of the post-main-sequence population. As a consequence, membership of Mercer 30 to the Dragonfish star-forming complex is confirmed, allowing us to use this cluster as a probe for the whole complex, which turns out to be extremely large (~400 pc across) and located at the outer edge of the Sagittarius-Carina spiral arm (~11 kpc from the Galactic center). The Dragonfish complex hosts 19 young clusters or cluster candidates (including Mercer 30 and a new candidate presented in this work) and an estimated minimum of nine field Wolf-Rayet stars. All these contributions account for, at least 73% of the ionization of the Dragonfish nebula and leaves little or no room for the alleged superluminous OB association; alternative explanations are discussed. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, under programs IDs 179.B-2002, 081.D-0471, 083.D-0765, 087.D-0957, and 089.D-0989.

  5. Formation of supported rhodium clusters from mononuclear rhodium complexes controlled by the support and ligands on rhodium.

    PubMed

    Serna, Pedro; Yardimci, Dicle; Kistler, Joseph D; Gates, Bruce C

    2014-01-21

    Extremely small supported rhodium clusters were prepared from rhodium complexes on the surfaces of solids with contrasting electron-donor properties. The samples were characterized by infrared and extended X-ray absorption fine structure spectroscopies to determine the changes occurring in the rhodium species resulting from treatments in hydrogen. Rhodium cluster formation occurred in the presence of H2, and the first steps are controlled by the electron-donor properties of the support--which acts as a ligand--and the other ligands bonded to the rhodium. The cluster formation begins at a lower temperature when the support is zeolite HY than when it is the better electron-donor MgO, provided that the other ligands on rhodium are ethene. In contrast, when these other ligands are CO, the pattern is reversed. The choice of ligands including the support also allows regulation of the stoichiometry of the surface transformations in H2 and the stability of the structures formed in the presence of other reactants. The combination of MgO as the support and ethene as a ligand allows restriction of the rhodium cluster size to the smallest possible-and these were formed in high yields. The data presented here are among the first characterizing the first steps of metal cluster formation.

  6. Metal Sulfide Cluster Complexes and their Biogeochemical Importance in the Environment

    NASA Astrophysics Data System (ADS)

    Luther, George W.; Rickard, David T.

    2005-10-01

    Aqueous clusters of FeS, ZnS and CuS constitute a major fraction of the dissolved metal load in anoxic oceanic, sedimentary, freshwater and deep ocean vent environments. Their ubiquity explains how metals are transported in anoxic environmental systems. Thermodynamic and kinetic considerations show that they have high stability in oxic aqueous environments, and are also a significant fraction of the total metal load in oxic river waters. Molecular modeling indicates that the clusters are very similar to the basic structural elements of the first condensed phase forming from aqueous solutions in the Fe-S, Zn-S and Cu-S systems. The structure of the first condensed phase is determined by the structure of the cluster in solution. This provides an alternative explanation of Ostwald's Rule, where the most soluble, metastable phases form before the stable phases. For example, in the case of FeS, we showed that the first condensed phase is nanoparticulate, metastable mackinawite with a particle size of 2 nm consisting of about 150 FeS subunits, representing the end of a continuum between aqueous FeS clusters and condensed material. These metal sulfide clusters and nanoparticles are significant in biogeochemistry. Metal sulfide clusters reduce sulfide and metal toxicity and help drive ecology. FeS cluster formation drives vent ecology and AgS cluster formation detoxifies Ag in Daphnia magna neonates. We also note a new reaction between FeS and DNA and discuss the potential role of FeS clusters in denaturing DNA.

  7. STS-30 MS Cleave monitors fluids experiment apparatus (FEA) equipment

    NASA Technical Reports Server (NTRS)

    1989-01-01

    STS-30 Mission Specialist (MS) Mary L. Cleave monitors fluids experiment apparatus (FEA) equipment and conducts materials science experiments on Atlantis', Orbiter Vehicle (OV) 104's, middeck. FEA equipment is in configuration for 'Floating Zone Crystal Growth and Purification' experiment. Cleave looks up from portable laptop computer with FEA-2, 35mm camera, and 8mm video camcorder positioned above her in aft locker location. Cleave, wearing polo shirt and light blue flight coveralls, uses knee board note pad to make additional notations. Rockwell International (RI) through its Space Transportation Systems Division, Downey, California, is engaged in a joint endeavor agreement (JEA) with NASA's Office of Commercial Programs in the field for floating zone crystal growth research.

  8. Ligand/cluster/support catalytic complexes in heterogeneous ultrananocatalysis: NO oxidation on Ag3/MgO(100).

    PubMed

    Sementa, Luca; Barcaro, Giovanni; Negreiros, Fabio R; Fortunelli, Alessandro

    2014-12-28

    In the present work we explore via first-principles simulations whether the ligand/cluster/support catalytic complex generated by CO oxidation over silver trimers deposited on the regular MgO(100) surface - i.e. a Ag3/carbonate or Ag3(CO3)/MgO(100) species - can be used as a catalyst in a different reaction: the selective oxidation of NO to NO2 (or NOox). The Ag3(CO3)/MgO(100) complex is first shown to be reasonably stable at room temperature in terms of both disaggregation and sintering, and that it can be generated from Ag3 adsorbed onto an oxygen vacancy defect of the regular MgO(100) surface under oxidation conditions. It is then found that the Ag3(CO3)/MgO(100) species transforms under NOox conditions into an even more complex aggregate, a mixed carbonate/double-nitrite Ag3(CO3)(NO2)2/MgO(100) species, which can then act as an efficient catalyst of NOox. It is noteworthy that under NOox reaction conditions a different ligand/cluster/support catalytic complex is formed with respect to the original COox one. These findings prove the diversity of the catalytic chemistry of subnanometer (or ultranano) metal clusters deposited on oxide substrates, associated with the formation of many different ligand/cluster/support aggregates, the vast amount of combinatorial possibilities thus opening, and the need for computational approaches to perform systematic structural and stoichiometric searches in order to cope with such a multiform diversity.

  9. Porcine Deltacoronavirus Nsp5 Antagonizes Type I Interferon Signaling by Cleaving STAT2.

    PubMed

    Zhu, Xinyu; Wang, Dang; Zhou, Junwei; Pan, Ting; Chen, Jiyao; Yang, Yuting; Lv, Mengting; Ye, Xu; Peng, Guiqing; Fang, Liurong; Xiao, Shaobo

    2017-03-01

    , for the first time, we demonstrate that overexpression of PDCoV nsp5 also antagonizes IFN signaling by cleaving STAT2, an essential component of transcription factor complex ISGF3, and that PDCoV infection reduces the levels of STAT2, which may affect the innate immune response.

  10. The Complexities of Implementing Cluster Supply Chain - Case Study of JCH

    NASA Astrophysics Data System (ADS)

    Xue, Xiao; Zhang, Jibiao; Wang, Yang

    As a new type of management pattern, "cluster supply chain" (CSC) can help SMEs to face the global challenges through all kinds of collaboration. However, a major challenge in implementing CSC is the gap between theory and practice in the field. In an effort to provide a better understanding of this emerging phenomenon, this paper presents the implementation process of CSC in the context of JingCheng Mechanical & Electrical Holding co., ltd.(JCH) as a case study. The cast study of JCH suggests that the key problems in the practice of cluster supply chain: How do small firms use cluster supply chain? Only after we clarify the problem, the actual construction and operation of cluster supply chain does show successful results as it should be.

  11. High speed cleaving of crystals with ultrafast Bessel beams.

    PubMed

    Rapp, L; Meyer, R; Furfaro, L; Billet, C; Giust, R; Courvoisier, F

    2017-04-17

    We develop a novel concept for ultra-high speed cleaving of crystalline materials with femtosecond lasers. Using Bessel beams in single shot, fracture planes can be induced nearly all along the Bessel zone in sapphire. For the first time, we show that only for a pulse duration below 650 fs, a single fracture can be induced in sapphire, while above this duration, cracks appear in all crystallographic orientations. We determine the influential parameters which are polarization direction, crystallographic axes and scanning direction. This is applied to cleave sapphire with a spacing as high as 25 μm between laser impacts.

  12. The complex stellar populations in the background of open clusters in the third Galactic quadrant

    NASA Astrophysics Data System (ADS)

    Carraro, Giovanni; Seleznev, Anton F.; Baume, Gustavo; Turner, David. G.

    2016-02-01

    Multicolour photometry of the stellar populations in five fields in the third Galactic quadrant centred on the clusters NGC 2215, NGC 2354, Haffner 22, Ruprecht 11, and ESO489 SC01 is interpreted in terms of a warped and flared Galactic disc, without resort to an external entity such as the popular Monoceros or Canis Major overdensities. Except for NGC 2215, the clusters are poorly or unstudied previously. The data generate basic parameters for each cluster, including the distribution of stars along the line of sight. We use star counts and photometric analysis, without recourse to Galactic-model-based predictions or interpretations, and confirms earlier results for NGC 2215 and NGC 2354. ESO489 SC01 is not a real cluster, while Haffner 22 is an overlooked cluster aged ˜2.5 Gyr. Conclusions for Ruprecht 11 are preliminary, evidence for a cluster being marginal. Fields surrounding the clusters show signatures of young and intermediate-age stellar populations. The young population background to NGC 2354 and Ruprecht 11 lies ˜8-9 kpc from the Sun and ˜1 kpc below the formal Galactic plane, tracing a portion of the Norma-Cygnus arm, challenging Galactic models that adopt a sharp cut-off of the disc 12-14 kpc from the Galactic Centre. The old population is metal-poor with an age of ˜2-3 Gyr, resembling star clusters like Tombaugh 2 or NGC 2158. It has a large colour spread and is difficult to locate precisely. Young and old populations follow a pattern that depends critically on the vertical location of the thin and/or thick disc, and whether or not a particular line of sight intersects one, both, or none.

  13. Double-layer clustering method to predict protein complexes based on power-law distribution and protein sublocalization.

    PubMed

    Peng, Xiaoqing; Wang, Jianxin; Huan, Jun; Wu, Fang-Xiang

    2016-04-21

    Identifying protein complexes from Protein-protein Interaction Networks (PINs) is fundamental for understanding protein functions and activities in cell. Based on the assumption that protein complexes are highly connected areas in PINs, many algorithms were proposed to identify protein complexes from PINs. However, most of these approaches neglected that not all proteins in complexes are highly connected, and proteins in PINs with different topological properties may form protein complexes in different ways and should be treated differently. In this paper, we proposed a double-layer clustering method based on the power-law distribution (PLCluster). To calculate the centrality scores of nodes, we proposed a Dense-Spread Centrality method. The centrality scores calculated by Dense-Spread Centrality method follow a power-law distribution. Based on the power-law distribution of the centrality scores, PLCluster divides the nodes into two categories: the nodes with very high centrality scores and the nodes with lower centrality scores. Then different strategies are applied to nodes in different categories for detecting protein complexes from the PIN, respectively. Furthermore, the predicted protein complexes, which are inconsistent with the fact that all proteins in a protein complex should be in the same subcellular compartment, are filtered out. Compared with other nine existing methods on a high reliable yeast PIN, PLCluster shows great advantages in terms of the number of known complexes that are identified, Sensitivity, Specificity, f-measure and the number of perfect matches. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. A cluster of basic amino acids in the factor X serine protease mediates surface attachment of adenovirus/FX complexes.

    PubMed

    Duffy, Margaret R; Bradshaw, Angela C; Parker, Alan L; McVey, John H; Baker, Andrew H

    2011-10-01

    Hepatocyte transduction following intravenous administration of adenovirus 5 (Ad5) is mediated by interaction between coagulation factor X (FX) and the hexon. The FX serine protease (SP) domain tethers the Ad5/FX complex to hepatocytes through binding heparan sulfate proteoglycans (HSPGs). Here, we identify the critical HSPG-interacting residues of FX. We generated an FX mutant by modifying seven residues in the SP domain. Surface plasmon resonance demonstrated that mutations did not affect binding to Ad5. FX-mediated, HSPG-associated cell binding and transduction were abolished. A cluster of basic amino acids in the SP domain therefore mediates surface interaction of the Ad/FX complex.

  15. The Ether-Cleaving Methyltransferase System of the Strict Anaerobe Acetobacterium dehalogenans: Analysis and Expression of the Encoding Genes▿

    PubMed Central

    Schilhabel, Anke; Studenik, Sandra; Vödisch, Martin; Kreher, Sandra; Schlott, Bernhard; Pierik, Antonio Y.; Diekert, Gabriele

    2009-01-01

    Anaerobic O-demethylases are inducible multicomponent enzymes which mediate the cleavage of the ether bond of phenyl methyl ethers and the transfer of the methyl group to tetrahydrofolate. The genes of all components (methyltransferases I and II, CP, and activating enzyme [AE]) of the vanillate- and veratrol-O-demethylases of Acetobacterium dehalogenans were sequenced and analyzed. In A. dehalogenans, the genes for methyltransferase I, CP, and methyltransferase II of both O-demethylases are clustered. The single-copy gene for AE is not included in the O-demethylase gene clusters. It was found that AE grouped with COG3894 proteins, the function of which was unknown so far. Genes encoding COG3894 proteins with 20 to 41% amino acid sequence identity with AE are present in numerous genomes of anaerobic microorganisms. Inspection of the domain structure and genetic context of these orthologs predicts that these are also reductive activases for corrinoid enzymes (RACEs), such as carbon monoxide dehydrogenase/acetyl coenzyme A synthases or anaerobic methyltransferases. The genes encoding the O-demethylase components were heterologously expressed with a C-terminal Strep-tag in Escherichia coli, and the recombinant proteins methyltransferase I, CP, and AE were characterized. Gel shift experiments showed that the AE comigrated with the CP. The formation of other protein complexes with the O-demethylase components was not observed under the conditions used. The results point to a strong interaction of the AE with the CP. This is the first report on the functional heterologous expression of acetogenic phenyl methyl ether-cleaving O-demethylases. PMID:19011025

  16. Addition of Cleaved Tail Fragments during Lipid Oxidation Stabilizes Membrane Permeability Behavior.

    PubMed

    Runas, Kristina A; Acharya, Shiv J; Schmidt, Jacob J; Malmstadt, Noah

    2016-01-26

    Lipid oxidation has been linked to plasma membrane damage leading to cell death. In previous work, we examined the effect of oxidation on bilayer permeability by replacing defined amounts of an unsaturated lipid species with the corresponding phospholipid product that would result from oxidative tail scission of that species. This study adds the cleaved tail fragment, better mimicking the chemical results of oxidation. Permeability of PEG12-NBD, a small, uncharged molecule, was measured for vesicles with oxidation concentration corresponding to between 0 and 18 mol % of total lipid content. Permeability was measured using a microfluidic trap to capture the vesicles and spinning disk confocal microscopy (SDCM) to measure the transport of fluorescent PEG12-NBD at the equatorial plane. The thicknesses of lipid bilayers containing oxidized species were estimated by measuring capacitance of a black lipid membrane while simultaneously measuring bilayer area. We found that relative to chemically modeled oxidized bilayers without tail fragments, bilayers containing cleaved tail groups were less permeable for the same degree of oxidation. Curiously, membrane capacitance measurements indicated that the addition of tail fragments to chemically modeled oxidized bilayers also thinned these bilayers relative to samples with no tail fragments; in other words, the more permeable membranes were thicker. Above 12.5% chemically modeled oxidation, compositions both with and without the cleaved tail groups showed pore formation. This work highlights the complexity of the relationship between chemically modeled lipid bilayer oxidation and cell membrane properties.

  17. Formation of rhyolite at the Okataina Volcanic Complex, New Zealand: New insights from analysis of quartz clusters in plutonic lithics

    NASA Astrophysics Data System (ADS)

    Graeter, K.; Beane, R. J.; Deering, C. D.; Gravley, D. M.; Bachmann, O.

    2014-12-01

    Granitoid lithic clasts from the 0.7 ka Kaharoa eruption at the Tarawera volcano (Okataina Volcanic Complex, Taupo Volcanic Zone, New Zealand) - the world's most productive region where rhyolite volcanism is currently active - give insight into the processes of rhyolite formation. The plutonic lithic clasts of the Kaharoa eruption consist of (1) quartz phenocrysts, which are often grouped into clusters of two to eight quartz grains, (2) plagioclase phenocrysts with anorthitic cores and albitic rims, and (3) interstitial potassium feldspar. Quartz orientations obtained through electron backscatter diffraction (EBSD) methods show that 78% of the 82 analyzed clusters have at least one pair of quartz grains with matched dipyramidal faces that are in either parallel or Esterel twin orientation. Variations in cathodoluminescence (CL) zoning patterns of the quartz suggest that quartz clusters in the plutonic lithics formed after initial crystal growth and that many quartz crystals were subject to one or more resorption events. Thus, individual quartz crystals with different magmatic histories came together into preferred orientations to form clusters; this process is indicative of oriented quartz synneusis and suggests a history of crystal accumulation. The quartz clusters are interpreted to have formed as part of a crystal cumulate mush within a shallow magma chamber where quartz crystals rotated into contact along their dipyramidal faces during hindered settling and/or compaction. Therefore, the preservation of oriented quartz clusters from the Kaharoa plutonic lithics provides direct evidence for synchronous, shallow pluton formation from a cumulate mush during active volcanism. This result is consistent with a model whereby melt-rich, high-silica rhyolite formation occurs via interstitial melt extraction from a low-silica rhyolite mush in the shallow crust.

  18. Mössbauer spectroscopy on respiratory complex I: the iron-sulfur cluster ensemble in the NADH-reduced enzyme is partially oxidized.

    PubMed

    Bridges, Hannah R; Bill, Eckhard; Hirst, Judy

    2012-01-10

    In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from Bos taurus have established that five clusters (positions 1, 2, 3, 5, and 7 along the seven-cluster chain extending from the flavin) are (at least partially) reduced by NADH. The other three clusters, positions 4 and 6 plus a cluster on the other side of the flavin, are not observed in EPR spectra from the NADH-reduced enzyme: they may remain oxidized, have unusual or coupled spin states, or their EPR signals may be too fast relaxing. Here, we use Mössbauer spectroscopy on (57)Fe-labeled complex I from the mitochondria of Yarrowia lipolytica to show that the cluster ensemble is only partially reduced in the NADH-reduced enzyme. The three EPR-silent clusters are oxidized, and only the terminal 4Fe cluster (position 7) is fully reduced. Together with the EPR analyses, our results reveal an alternating profile of higher and lower potential clusters between the two active sites in complex I; they are not consistent with the consensus picture of a set of isopotential clusters. The implications for intramolecular electron transfer along the extended chain of cofactors in complex I are discussed.

  19. Mössbauer Spectroscopy on Respiratory Complex I: The Iron–Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized

    PubMed Central

    2011-01-01

    In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron–sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from Bos taurus have established that five clusters (positions 1, 2, 3, 5, and 7 along the seven-cluster chain extending from the flavin) are (at least partially) reduced by NADH. The other three clusters, positions 4 and 6 plus a cluster on the other side of the flavin, are not observed in EPR spectra from the NADH-reduced enzyme: they may remain oxidized, have unusual or coupled spin states, or their EPR signals may be too fast relaxing. Here, we use Mössbauer spectroscopy on 57Fe-labeled complex I from the mitochondria of Yarrowia lipolytica to show that the cluster ensemble is only partially reduced in the NADH-reduced enzyme. The three EPR-silent clusters are oxidized, and only the terminal 4Fe cluster (position 7) is fully reduced. Together with the EPR analyses, our results reveal an alternating profile of higher and lower potential clusters between the two active sites in complex I; they are not consistent with the consensus picture of a set of isopotential clusters. The implications for intramolecular electron transfer along the extended chain of cofactors in complex I are discussed. PMID:22122402

  20. Direct assignment of EPR spectra to structurally defined iron-sulfur clusters in complex I by double electron–electron resonance

    PubMed Central

    Roessler, Maxie M.; King, Martin S.; Robinson, Alan J.; Armstrong, Fraser A.; Harmer, Jeffrey; Hirst, Judy

    2010-01-01

    In oxidative phosphorylation, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. Complex I contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters, in several subunits, to transfer the electrons to quinone. Understanding coupled electron transfer in complex I requires a detailed knowledge of the properties of individual clusters and of the cluster ensemble, and so it requires the correlation of spectroscopic and structural data: This has proved a challenging task. EPR studies on complex I from Bos taurus have established that EPR signals N1b, N2 and N3 arise, respectively, from the 2Fe cluster in the 75 kDa subunit, and from 4Fe clusters in the PSST and 51 kDa subunits (positions 2, 7, and 1 along the seven-cluster chain extending from the flavin). The other clusters have either evaded detection or definitive signal assignments have not been established. Here, we combine double electron-electron resonance (DEER) spectroscopy on B. taurus complex I with the structure of the hydrophilic domain of Thermus thermophilus complex I. By considering the magnetic moments of the clusters and the orientation selectivity of the DEER experiment explicitly, signal N4 is assigned to the first 4Fe cluster in the TYKY subunit (position 5), and N5 to the all-cysteine ligated 4Fe cluster in the 75 kDa subunit (position 3). The implications of our assignment for the mechanisms of electron transfer and energy transduction by complex I are discussed. PMID:20133838

  1. RNA-Cleaving DNA Enzymes with Altered Regio- or Enantioselectivity

    NASA Technical Reports Server (NTRS)

    Ordoukhanian, Phillip; Joyce, Gerald F.

    2002-01-01

    In vitro evolution methods were used to obtain DNA enzymes that cleave either a 2',5' - phosphodiester following a wibonucleotide or a 3',5' -phosphodiester following an L-ribonucleotide. Both enzymes can operate in an intermolecular reaction format with multiple turnover. The DNA enzyme that cleaves a 2',5' -phosphodiester exhibits a k(sub cat) of approx. 0.01/ min and catalytic efficiency, k(sub cat)/k(sub m) of approx. 10(exp 5)/ M min. The enzyme that cleaves an L-ribonudeotide is about 10-fold slower and has a catalytic efficiency of approx. 4 x 10(exp 5)/ M min. Both enzymes require a divalent metal cation for their activity and have optimal catalytic rate at pH 7-8 and 35-50 C. In a comparison of each enzyme s activity with either its corresponding substrate that contains an unnatural ribonudeotide or a substrate that instead contains a standard ribonucleotide, the 2',5' -phosphodiester-deaving DNA enzyme exhibited a regioselectivity of 6000- fold, while the L-ribonucleotide-cleaving DNA enzyme exhibited an enantioselectivity of 50-fold. These molecules demonstrate how in vitro evolution can be used to obtain regio- and enantioselective catalysts that exhibit specificities for nonnatural analogues of biological compounds.

  2. German cockroach frass proteases cleave pro-matrix metalloproteinase-9.

    PubMed

    Hughes, Valerie S; Page, Kristen

    2007-01-01

    Matrix metalloproteinase (MMP)-9, secreted as pro-MMP-9, is cleaved by serine proteases at the N-terminus to generate active MMP-9. Pro-MMP-9 has been found in the bronchoalveolar lavage fluid of patients with asthma. Because many inhaled aeroallergens contain active proteases, the authors sought to determine whether German cockroach (GC) fecal remnants (frass) and house dust mite (HDM) were able to cleave pro-MMP-9. Treatment of recombinant human (rh) pro-MMP-9 with GC frass resulted in a dose- and time-dependent cleavage. This was abrogated by pretreating frass with an inhibitor of serine, but not cysteine protease activity. GC frass also induced cleavage of pro-MMP-9 from primary human neutrophils dependent on the active serine proteases in GC frass. HDM was less potent at cleaving pro-MMP-9. Alpha1-antitrypsin (A1AT), a naturally occurring protease inhibitor, attenuated GC frass-induced cleavage of pro-MMP-9. A1AT partially inactivated the serine protease activity in GC frass, while GC frass cleaved A1AT in a dose- and time-dependent manner. These data suggest that GC frass-derived serine proteases could regulate the activity of MMP-9 and that A1AT may play an important role in modulating GC frass activity in vivo. These data suggest a mechanism by which inhalation of GC frass could regulate airway remodeling through the activation of pro-MMP-9.

  3. From thioxo cluster to dithio cluster: exploring the chemistry of polynuclear zirconium complexes with S,O and S,S ligands.

    PubMed

    Maratini, Federica; Pandolfo, Luciano; Bendova, Maria; Schubert, Ulrich; Bauer, Matthias; Rocchia, Massimiliano; Venzo, Alfonso; Tondello, Eugenio; Gross, Silvia

    2011-01-17

    Three different zirconium thio and oxothio clusters, characterized by different coordination modes of dithioacetate and/or monothioacetate ligands, were obtained by the reaction of monothioacetic acid with zirconium n-butoxide, Zr(O(n)Bu)4, in different experimental conditions. In particular, we isolated the three polynuclear Zr3(μ3-SSSCCH3)2(SSCCH3)6·2(n)BuOH (Zr3), Zr4(μ3-O)2(μ-η(1)-SOCCH3)2(SOCCH3)8(O(n)Bu)2 (Zr4), and Zr6(μ3-O)5(μ-SOCCH3)2(μ-OOCCH3)(SOCCH3)11((n)BuOH) (Zr6) derivatives, presenting some peculiar characteristics. Zr6 has an unusual star-shaped structure. Only sulfur-based ligands, viz., chelating dithioacetate monoanions and an unusual ethane-1,1,1-trithiolate group μ3 coordinating the Zr ions, were observed in the case of Zr3. 1D and 2D NMR analyses confirmed the presence of differently coordinated ligands. Raman spectroscopy was further used to characterize the new polynuclear complexes. Time-resolved extended X-ray absorption fine structure measurements, devoted to unraveling the cluster formation mechanisms, evidenced a fast coordination of sulfur ligands and subsequent relatively rapid rearrangements.

  4. From Thioxo Cluster to Dithio Cluster: Exploring the Chemistry of Polynuclear Zirconium Complexes with S,O and S,S Ligands

    PubMed Central

    2010-01-01

    Three different zirconium thio and oxothio clusters, characterized by different coordination modes of dithioacetate and/or monothioacetate ligands, were obtained by the reaction of monothioacetic acid with zirconium n-butoxide, Zr(OnBu)4, in different experimental conditions. In particular, we isolated the three polynuclear Zr3(μ3-SSSCCH3)2(SSCCH3)6·2nBuOH (Zr3), Zr4(μ3-O)2(μ−η1-SOCCH3)2(SOCCH3)8(OnBu)2 (Zr4), and Zr6(μ3-O)5(μ-SOCCH3)2(μ-OOCCH3)(SOCCH3)11(nBuOH) (Zr6) derivatives, presenting some peculiar characteristics. Zr6 has an unusual star-shaped structure. Only sulfur-based ligands, viz., chelating dithioacetate monoanions and an unusual ethane-1,1,1-trithiolate group μ3 coordinating the Zr ions, were observed in the case of Zr3. 1D and 2D NMR analyses confirmed the presence of differently coordinated ligands. Raman spectroscopy was further used to characterize the new polynuclear complexes. Time-resolved extended X-ray absorption fine structure measurements, devoted to unraveling the cluster formation mechanisms, evidenced a fast coordination of sulfur ligands and subsequent relatively rapid rearrangements. PMID:21141945

  5. Chandra X-ray observation of the young stellar cluster NGC 3293 in the Carina Nebula Complex

    NASA Astrophysics Data System (ADS)

    Preibisch, T.; Flaischlen, S.; Gaczkowski, B.; Townsley, L.; Broos, P.

    2017-09-01

    Context. NGC 3293 is a young stellar cluster at the northwestern periphery of the Carina Nebula Complex that has remained poorly explored until now. Aims: We characterize the stellar population of NGC 3293 in order to evaluate key parameters of the cluster population such as the age and the mass function, and to test claims of an abnormal IMF and a deficit of M ≤ 2.5 M⊙ stars. Methods: We performed a deep (70 ks) X-ray observation of NGC 3293 with Chandra and detected 1026 individual X-ray point sources. These X-ray data directly probe the low-mass (M ≤ 2 M⊙) stellar population by means of the strong X-ray emission of young low-mass stars. We identify counterparts for 74% of the X-ray sources in our deep near-infrared images. Results: Our data clearly show that NGC 3293 hosts a large population of ≈solar-mass stars, refuting claims of a lack of M ≤ 2.5 M⊙ stars. The analysis of the color magnitude diagram suggests an age of 8-10 Myr for the low-mass population of the cluster. There are at least 511 X-ray detected stars with color magnitude positions that are consistent with young stellar members within 7 arcmin of the cluster center. The number ratio of X-ray detected stars in the [1-2 ] M⊙ range versus the M ≥ 5 M⊙ stars (known from optical spectroscopy) is consistent with the expectation from a normal field initial mass function. Most of the early B-type stars and ≈20% of the later B-type stars are detected as X-ray sources. Conclusions: Our data shows that NGC 3293 is one of the most populous stellar clusters in the entire Carina Nebula Complex (very similar to Tr 16 and Tr 15; only Tr 14 is more populous). The cluster probably harbored several O-type stars, whose supernova explosions may have had an important impact on the early evolution of the Carina Nebula Complex. The Chandra data described in this paper have been obtained in the open time project with ObsID 16648 (PI: T. Preibisch) ivo://ADS/Sa.CXO#obs/16648.Tables 1-3 are only

  6. {Ni4O4} Cluster Complex to Enhance the Reductive Photocurrent Response on Silicon Nanowire Photocathodes

    PubMed Central

    Mange, Yatin J.; Chandrasekaran, Soundarrajan; Hollingsworth, Nathan; Voelcker, Nicolas H.; Parkin, Ivan P.; Nann, Thomas; Macdonald, Thomas J.

    2017-01-01

    Metal organic {Ni4O4} clusters, known oxidation catalysts, have been shown to provide a valuable route in increasing the photocurrent response on silicon nanowire (SiNW) photocathodes. {Ni4O4} clusters have been paired with SiNWs to form a new photocathode composite for water splitting. Under AM1.5 conditions, the combination of {Ni4O4} clusters with SiNWs gave a current density of −16 mA/cm2, which corresponds to an increase in current density of 60% when compared to bare SiNWs. The composite electrode was fully characterised and shown to be an efficient and stable photocathode for water splitting. PMID:28336866

  7. Community detection in complex networks using density-based clustering algorithm and manifold learning

    NASA Astrophysics Data System (ADS)

    You, Tao; Cheng, Hui-Min; Ning, Yi-Zi; Shia, Ben-Chang; Zhang, Zhong-Yuan

    2016-12-01

    Like clustering analysis, community detection aims at assigning nodes in a network into different communities. Fdp is a recently proposed density-based clustering algorithm which does not need the number of clusters as prior input and the result is insensitive to its parameter. However, Fdp cannot be directly applied to community detection due to its inability to recognize the community centers in the network. To solve the problem, a new community detection method (named IsoFdp) is proposed in this paper. First, we use IsoMap technique to map the network data into a low dimensional manifold which can reveal diverse pair-wised similarity. Then Fdp is applied to detect the communities in the network. An improved partition density function is proposed to select the proper number of communities automatically. We test our method on both synthetic and real-world networks, and the results demonstrate the effectiveness of our algorithm over the state-of-the-art methods.

  8. Experiments in clustered neuronal networks: A paradigm for complex modular dynamics

    NASA Astrophysics Data System (ADS)

    Teller, Sara; Soriano, Jordi

    2016-06-01

    Uncovering the interplay activity-connectivity is one of the major challenges in neuroscience. To deepen in the understanding of how a neuronal circuit shapes network dynamics, neuronal cultures have emerged as remarkable systems given their accessibility and easy manipulation. An attractive configuration of these in vitro systems consists in an ensemble of interconnected clusters of neurons. Using calcium fluorescence imaging to monitor spontaneous activity in these clustered neuronal networks, we were able to draw functional maps and reveal their topological features. We also observed that these networks exhibit a hierarchical modular dynamics, in which clusters fire in small groups that shape characteristic communities in the network. The structure and stability of these communities is sensitive to chemical or physical action, and therefore their analysis may serve as a proxy for network health. Indeed, the combination of all these approaches is helping to develop models to quantify damage upon network degradation, with promising applications for the study of neurological disorders in vitro.

  9. Cationic cluster formation versus disproportionation of low-valent indium and gallium complexes of 2,2'-bipyridine

    PubMed Central

    Lichtenthaler, Martin R.; Stahl, Florian; Kratzert, Daniel; Heidinger, Lorenz; Schleicher, Erik; Hamann, Julian; Himmel, Daniel; Weber, Stefan; Krossing, Ingo

    2015-01-01

    Group 13 MI compounds often disproportionate into M0 and MIII. Here, however, we show that the reaction of the MI salt of the weakly coordinating alkoxyaluminate [GaI(C6H5F)2]+[Al(ORF)4]− (RF=C(CF3)3) with 2,2'-bipyridine (bipy) yields the paramagnetic and distorted octahedral [Ga(bipy)3]2+•{[Al(ORF)4]−}2 complex salt. While the latter appears to be a GaII compound, both, EPR and DFT investigations assign a ligand-centred [GaIII{(bipy)3}•]2+ radical dication. Surprisingly, the application of the heavier homologue [InI(C6H5F)2]+[Al(ORF)4]− leads to aggregation and formation of the homonuclear cationic triangular and rhombic [In3(bipy)6]3+, [In3(bipy)5]3+ and [In4(bipy)6]4+ metal atom clusters. Typically, such clusters are formed under strongly reductive conditions. Analysing the unexpected redox-neutral cationic cluster formation, DFT studies suggest a stepwise formation of the clusters, possibly via their triplet state and further investigations attribute the overall driving force of the reactions to the strong In−In bonds and the high lattice enthalpies of the resultant ligand stabilized [M3]3+{[Al(ORF)4]−}3 and [M4]4+{[Al(ORF)4]−}4 salts. PMID:26478464

  10. Synthesis of a uranyl persulfide complex and quantum chemical studies of formation and topologies of hypothetical uranyl persulfide cage clusters.

    PubMed

    Grant, Daniel J; Weng, Zhehui; Jouffret, Laurent J; Burns, Peter C; Gagliardi, Laura

    2012-07-16

    The compound Na(4)[(UO(2))(S(2))(3)](CH(3)OH)(8) was synthesized at room temperature in an oxygen-free environment. It contains a rare example of the [(UO(2))(S(2))(3)](4-) complex in which a uranyl ion is coordinated by three bidentate persulfide groups. We examined the possible linkage of these units to form nanoscale cage clusters analogous to those formed from uranyl peroxide polyhedra. Quantum chemical calculations at the density functional and multiconfigurational wave function levels show that the uranyl-persulfide-uranyl, U-(S(2))-U, dihedral angles of model clusters are bent due to partial covalent interactions. We propose that this bent interaction will favor assembly of uranyl ions through persulfide bridges into curved structures, potentially similar to the family of nanoscale cage clusters built from uranyl peroxide polyhedra. However, the U-(S(2))-U dihedral angles predicted for several model structures may be too tight for them to self-assemble into cage clusters with fullerene topologies in the absence of other uranyl-ion bridges that adopt a flatter configuration. Assembly of species such as [(UO(2))(S(2))(SH)(4)](4-) or [(UO(2))(S(2))(C(2)O(4))(4)](4-) into fullerene topologies with ~60 vertices may be favored by use of large counterions.

  11. Three complexes of Cu(I) cluster with flexible and rigid ligands: Synthesis, characterization and photoluminescent properties

    SciTech Connect

    Sun, Shu; Liu, Li-Juan; Ma, Wang-Yang; Zhou, Wei-Xia; Li, Jun; Zhang, Feng-Xing

    2015-05-15

    Three new Cu(I) cluster complexes, viz. [(Cu{sub 4}I{sub 4})(Cu{sub 2}I{sub 2})(dimb){sub 3}]{sub n} (1; dimb=1,4-diimidazol-1-ylbutane), [(Cu{sub 3}I{sub 2})(dimb)(dmtz)]{sub n} (2; dmtz=3,5-dimethyl-1,2,4-triazole), and [Cu{sub 6}(mbt){sub 6}] (3; mbt=2-mercaptobenzothiazole), have been solvothermally synthesized and structurally characterized. In 1, a Cu{sub 4}I{sub 4} cubane core as a 4-connecting node, connects the neighboring nodes either through single dimb or μ{sub 2}-[(Cu{sub 2}I{sub 2})(dimb){sub 2}] linkers, affording an undulated 2D (4,4) net. Parallel interpenetration occurs between the adjacent nets and thus the overall 2D→3D network is formed. Complex 2 is constructed by 2D (4,4) topological plane grid layers of AB stacking. The core, a distorted triangular bipyramidal Cu{sub 3}I{sub 2} cluster, is acted as a 4-connecting node and connected with dimb and μ{sub 3}-dmtz to form the layer. Complex 3 contains a (Cu{sub 6}S{sub 6}) core in discrete paddle-wheel molecule, which serves as a 4-connecting node to link equivalent ones via π···π interaction, forming 2D (4,4) layers. Solid-state luminescence properties and thermogravimetric analyses of 1, 2 and 3 were investigated. - Graphical abstract: Complexes based on Cu(I) clusters possess two-fold 2D→3D parallel interpenetrating (1), triple emissions (2) and near-infrared emission (3). - Highlights: • Complex 1 represents two-fold 2D→3D parallel interpenetrating framework. • Complex 2 shows triple emissions. • Complex 3 displays a quite intense near-infrared (NIR) emission. • These complexes have good thermal stability.

  12. Multilevel Hierarchical Kernel Spectral Clustering for Real-Life Large Scale Complex Networks

    PubMed Central

    Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

    2014-01-01

    Kernel spectral clustering corresponds to a weighted kernel principal component analysis problem in a constrained optimization framework. The primal formulation leads to an eigen-decomposition of a centered Laplacian matrix at the dual level. The dual formulation allows to build a model on a representative subgraph of the large scale network in the training phase and the model parameters are estimated in the validation stage. The KSC model has a powerful out-of-sample extension property which allows cluster affiliation for the unseen nodes of the big data network. In this paper we exploit the structure of the projections in the eigenspace during the validation stage to automatically determine a set of increasing distance thresholds. We use these distance thresholds in the test phase to obtain multiple levels of hierarchy for the large scale network. The hierarchical structure in the network is determined in a bottom-up fashion. We empirically showcase that real-world networks have multilevel hierarchical organization which cannot be detected efficiently by several state-of-the-art large scale hierarchical community detection techniques like the Louvain, OSLOM and Infomap methods. We show that a major advantage of our proposed approach is the ability to locate good quality clusters at both the finer and coarser levels of hierarchy using internal cluster quality metrics on 7 real-life networks. PMID:24949877

  13. Oligomeric rare-earth metal cluster complexes with endohedral transition metal atoms

    NASA Astrophysics Data System (ADS)

    Steinberg, Simon; Zimmermann, Sina; Brühmann, Matthias; Meyer, Eva; Rustige, Christian; Wolberg, Marike; Daub, Kathrin; Bell, Thomas; Meyer, Gerd

    2014-11-01

    Comproportionation reactions of rare-earth metal trihalides (RX3) with the respective rare-earth metals (R) and transition metals (T) led to the formation of 22 oligomeric R cluster halides encapsulating T, in 19 cases for the first time. The structures of these compounds were determined by single-crystal X-ray diffraction and are composed of trimers ({T3R11}X15-type, P63/m), tetramers ({T4R16}X28{R4} (P-43m), {T4R16}X20 (P42/nnm), {T4R16}X24(RX3)4 (I41/a) and {T4R16}X23 (C2/m) types of structure) and pentamers ({Ru5La14}2Br39, Cc) of {TRr}n (n=2-5) clusters. These oligomers are further enveloped by inner (Xi) as well as outer (Xa) halido ligands, which possess diverse functionalities and interconnect like oligomers through i-i, i-a and/or a-i bridges. The general features of the crystal structures for these new compounds are discussed and compared to literature entries as well as different structure types with oligomeric T centered R clusters. Dimers and tetramers originating from the aggregation of {TR6} octahedra via common edges are more frequent than trimers and pentamers, in which the {TRr} clusters share common faces.

  14. Calcium EXAFS establishes the Mn-Ca cluster in the oxygen-evolving complex of photosystem II.

    PubMed

    Cinco, Roehl M; McFarlane Holman, Karen L; Robblee, John H; Yano, Junko; Pizarro, Shelly A; Bellacchio, Emanuele; Sauer, Kenneth; Yachandra, Vittal K

    2002-10-29

    The proximity of Ca to the Mn cluster of the photosynthetic water-oxidation complex is demonstrated by X-ray absorption spectroscopy. We have collected EXAFS data at the Ca K-edge using active PS II membrane samples that contain approximately 2 Ca per 4 Mn. These samples are much less perturbed than previously investigated Sr-substituted samples, which were prepared after Ca depletion. The new Ca EXAFS clearly shows backscattering from Mn at 3.4 A, a distance that agrees with that surmised from previously recorded Mn EXAFS. This result is also consistent with earlier related experiments at the Sr K-edge, using samples that contained functional Sr, that show Mn is approximately 3.5 A distant from Sr. The totality of the evidence clearly advances the notion that the catalytic center of oxygen evolution is a Mn-Ca heteronuclear cluster.

  15. Electrochemical anion sensing using electrodes chemically modified with Au(I)-Cu(I) heterotrimetallic alkynyl cluster complexes containing ferrocenyl groups.

    PubMed

    Doménech, Antonio; Koshevoy, Igor O; Montoya, Noemí; Pakkanen, Tapani A

    2010-07-01

    A novel family of electrochemical anion sensors operating in aqueous media, based on the heterometallic Au(I)-Cu(I) [{Au(3)Cu(2)(C(2)R)(6)}Au(3)(PPh(2)C(6)H(4)PPh(2))(3)](PF(6))(2) (L1, R = Fc; L2, R = C(6)H(4)Fc) alkynyl cluster complexes, is presented. Upon attachment to graphite and gold electrodes, these compounds exhibit a well-defined, essentially reversible, solid-state electrochemistry in contact with aqueous media, based on ferrocenyl-centered oxidation processes involving anion insertion, leading to distinctive pH-independent electrochemical responses for fluoride, chloride, bromide, perchlorate, bicarbonate, carbonate, phosphate, hydrogen phosphate, dihydrogen phosphate, and nitrate anions. Cluster-modified electrodes can be used as potentiometric sensors as a result of the reversible, diffusion-controlled electrochemistry obtained for the anion-assisted electrochemical oxidation of L1 and L2.

  16. Calcium EXAFS establishes the Mn-Ca cluster in the oxygen-evolving complex of Photosystem II

    SciTech Connect

    Cinco, Roehl M.; McFarlane Holman, Karen L.; Robblee, John H.; Yano, Junko; Pizarro, Shelly A.; Bellacchio, Emanuele; Sauer, Kenneth; Yachandra, Vittal K.

    2002-08-02

    The proximity of Ca to the Mn cluster of the photosynthetic water-oxidation complex is demonstrated by X-ray absorption spectroscopy. We have collected EXAFS data at the Ca K-edge using active PS II membrane samples that contain approximately 2 Ca per 4 Mn. These samples are much less perturbed than previously investigated Sr-substituted samples, which were prepared subsequent to Ca depletion. The new Ca EXAFS clearly shows backscattering from Mn at 3.4 angstroms, a distance that agrees with that surmised from previously recorded Mn EXAFS. This result is also consistent with earlier related experiments at the Sr K-edge, using samples that contained functional Sr, that show Mn is {approx}; 3.5 angstroms distant from Sr. The totality of the evidence clearly advances the notion that the catalytic center of oxygen evolution is a Mn-Ca heteronuclear cluster.

  17. Complex Scattered Radiation Fields And Multiple Magnetic Fields In The Protostellar Cluster In NGC 2264

    NASA Astrophysics Data System (ADS)

    KWON, Jungmi; Tamura, M.; Kandori, R.; Kusakabe, N.; Hashimoto, J.; Nakajima, Y.; Nakamura, F.; Nagayama, T.; Nagata, T.; Hough, J. H.; Werner, M. W.; Teixeira, P. S.

    2012-05-01

    Near-infrared imaging polarimetry in the J, H, and Ks bands has been carried out for the protostellar cluster region around NGC 2264 IRS 2 in the Monoceros OB1 molecular cloud. Various infrared reflection nebula clusters (IRNCs) associated with NGC 2264 IRS 2 and the IRAS 12 S1 core, as well as local infrared reflection nebulae (IRNe), were detected. The illuminating sources of the IRNe were identified with known or new near- and mid-infrared sources. In addition, 314 point-like sources were detected in all three bands and their aperture polarimetry was studied. Using a color-color diagram, reddened field stars and diskless pre-main-sequence stars were selected to trace the magnetic field structure of the molecular cloud. The mean polarization position angle of the point-like sources is 80 degrees in the cluster core, and 60 degrees in the perimeter of the cluster core, which is interpreted as the projected direction on the sky of the magnetic field in the observed region of the cloud. The Chandrasekhar-Fermi method gives a rough estimate of the magnetic field strength to be about 100 micro-Gauss. A comparison with recent numerical simulations of the cluster formation implies that the cloud dynamics is controlled by the relatively strong magnetic field. The local magnetic field direction is well associated with that of CO outflow for IRAS 12 S1 and consistent with that inferred from submillimeter polarimetry. In contrast, the local magnetic field direction runs roughly perpendicular to the Galactic magnetic field direction.

  18. Complex Scattered Radiation Fields and Multiple Magnetic Fields in the Protostellar Cluster in NGC 2264

    NASA Astrophysics Data System (ADS)

    Kwon, Jungmi; Tamura, Motohide; Kandori, Ryo; Kusakabe, Nobuhiko; Hashimoto, Jun; Nakajima, Yasushi; Nakamura, Fumitaka; Nagayama, Takahiro; Nagata, Tetsuya; Hough, James H.; Werner, Michael W.; Teixeira, Paula S.

    2011-11-01

    Near-infrared imaging polarimetry in the J, H, and Ks bands has been carried out for the protostellar cluster region around NGC 2264 IRS 2 in the Monoceros OB1 molecular cloud. Various infrared reflection nebula clusters (IRNCs) associated with NGC 2264 IRS 2 and the IRAS 12 S1 core, as well as local infrared reflection nebulae (IRNe), were detected. The illuminating sources of the IRNe were identified with known or new near- and mid-infrared sources. In addition, 314 point-like sources were detected in all three bands and their aperture polarimetry was studied. Using a color-color diagram, reddened field stars and diskless pre-main-sequence stars were selected to trace the magnetic field (MF) structure of the molecular cloud. The mean polarization position angle of the point-like sources is 81° ± 29° in the cluster core, and 58° ± 24° in the perimeter of the cluster core, which is interpreted as the projected direction on the sky of the MF in the observed region of the cloud. The Chandrasekhar-Fermi method gives a rough estimate of the MF strength to be about 100 μG. A comparison with recent numerical simulations of the cluster formation implies that the cloud dynamics is controlled by the relatively strong MF. The local MF direction is well associated with that of CO outflow for IRAS 12 S1 and consistent with that inferred from submillimeter polarimetry. In contrast, the local MF direction runs roughly perpendicular to the Galactic MF direction.

  19. Mathematical modeling of bacterial track-altering motors: Track cleaving through burnt-bridge ratchets

    NASA Astrophysics Data System (ADS)

    Shtylla, Blerta; Keener, James P.

    2015-04-01

    The generation of directed movement of cellular components frequently requires the rectification of Brownian motion. Molecular motor enzymes that use ATP to walk on filamentous tracks are typically involved in cell transport, however, a track-altering motor can arise when an enzyme interacts with and alters its track. In Caulobacter crescentus and other bacteria, an active DNA partitioning (Par) apparatus is employed to segregate replicated chromosome regions to specific locations in dividing cells. The Par apparatus is composed of two proteins: ParA, an ATPase that can form polymeric structures on the nucleoid, and ParB, a protein that can bind and destabilize ParA structures. It has been proposed that the ParB-mediated alteration of ParA structures could be responsible for generating the directed movement of DNA during bacterial division. How precisely these actions are coordinated and translated into directed movement is not clear. In this paper we consider the C. crescentus segregation apparatus as an example of a track altering motor that operates using a so-called burnt-bridge mechanism. We develop and analyze mathematical models that examine how diffusion and ATP-hydrolysis-mediated monomer removal (or cleaving) can be combined to generate directed movement. Using a mean first passage approach, we analytically calculate the effective ParA track-cleaving velocities, effective diffusion coefficient, and other higher moments for the movement a ParB protein cluster that breaks monomers away at random locations on a single ParA track. Our model results indicate that cleaving velocities and effective diffusion constants are sensitive to ParB-induced ATP hydrolysis rates. Our analytical results are in excellent agreement with stochastic simulation results.

  20. Mathematical modeling of bacterial track-altering motors: Track cleaving through burnt-bridge ratchets.

    PubMed

    Shtylla, Blerta; Keener, James P

    2015-04-01

    The generation of directed movement of cellular components frequently requires the rectification of Brownian motion. Molecular motor enzymes that use ATP to walk on filamentous tracks are typically involved in cell transport, however, a track-altering motor can arise when an enzyme interacts with and alters its track. In Caulobacter crescentus and other bacteria, an active DNA partitioning (Par) apparatus is employed to segregate replicated chromosome regions to specific locations in dividing cells. The Par apparatus is composed of two proteins: ParA, an ATPase that can form polymeric structures on the nucleoid, and ParB, a protein that can bind and destabilize ParA structures. It has been proposed that the ParB-mediated alteration of ParA structures could be responsible for generating the directed movement of DNA during bacterial division. How precisely these actions are coordinated and translated into directed movement is not clear. In this paper we consider the C. crescentus segregation apparatus as an example of a track altering motor that operates using a so-called burnt-bridge mechanism. We develop and analyze mathematical models that examine how diffusion and ATP-hydrolysis-mediated monomer removal (or cleaving) can be combined to generate directed movement. Using a mean first passage approach, we analytically calculate the effective ParA track-cleaving velocities, effective diffusion coefficient, and other higher moments for the movement a ParB protein cluster that breaks monomers away at random locations on a single ParA track. Our model results indicate that cleaving velocities and effective diffusion constants are sensitive to ParB-induced ATP hydrolysis rates. Our analytical results are in excellent agreement with stochastic simulation results.

  1. Three complexes of Cu(I) cluster with flexible and rigid ligands: Synthesis, characterization and photoluminescent properties

    NASA Astrophysics Data System (ADS)

    Sun, Shu; Liu, Li-Juan; Ma, Wang-Yang; Zhou, Wei-Xia; Li, Jun; Zhang, Feng-Xing

    2015-05-01

    Three new Cu(I) cluster complexes, viz. [(Cu4I4)(Cu2I2)(dimb)3]n (1; dimb=1,4-diimidazol-1-ylbutane), [(Cu3I2)(dimb)(dmtz)]n (2; dmtz=3,5-dimethyl-1,2,4-triazole), and [Cu6(mbt)6] (3; mbt=2-mercaptobenzothiazole), have been solvothermally synthesized and structurally characterized. In 1, a Cu4I4 cubane core as a 4-connecting node, connects the neighboring nodes either through single dimb or μ2-[(Cu2I2)(dimb)2] linkers, affording an undulated 2D (4,4) net. Parallel interpenetration occurs between the adjacent nets and thus the overall 2D→3D network is formed. Complex 2 is constructed by 2D (4,4) topological plane grid layers of AB stacking. The core, a distorted triangular bipyramidal Cu3I2 cluster, is acted as a 4-connecting node and connected with dimb and μ3-dmtz to form the layer. Complex 3 contains a (Cu6S6) core in discrete paddle-wheel molecule, which serves as a 4-connecting node to link equivalent ones via π···π interaction, forming 2D (4,4) layers. Solid-state luminescence properties and thermogravimetric analyses of 1, 2 and 3 were investigated.

  2. RNA-activated DNA cleavage by the Type III-B CRISPR–Cas effector complex

    PubMed Central

    Estrella, Michael A.; Kuo, Fang-Ting; Bailey, Scott

    2016-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeat) system is an RNA-guided immune system that protects prokaryotes from invading genetic elements. This system represents an inheritable and adaptable immune system that is mediated by multisubunit effector complexes. In the Type III-B system, the Cmr effector complex has been found to cleave ssRNA in vitro. However, in vivo, it has been implicated in transcription-dependent DNA targeting. We show here that the Cmr complex from Thermotoga maritima can cleave an ssRNA target that is complementary to the CRISPR RNA. We also show that binding of a complementary ssRNA target activates an ssDNA-specific nuclease activity in the histidine–aspartate (HD) domain of the Cmr2 subunit of the complex. These data suggest a mechanism for transcription-coupled DNA targeting by the Cmr complex and provide a unifying mechanism for all Type III systems. PMID:26848046

  3. Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs

    DOE PAGES

    Michalska, Karolina; Gucinski, Grant C.; Garza-Sanchez, Fernando; ...

    2017-08-11

    Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxinmore » specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Altogether, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.« less

  4. Functional sulfurtransferase is associated with mitochondrial complex I from Yarrowia lipolytica, but is not required for assembly of its iron-sulfur clusters.

    PubMed

    Abdrakhmanova, Albina; Dobrynin, Krzysztof; Zwicker, Klaus; Kerscher, Stefan; Brandt, Ulrich

    2005-12-19

    Here, we report that in the obligate aerobic yeast Yarrowia lipolytica, a protein exhibiting rhodanese (thiosulfate:cyanide sulfurtransferase) activity is associated with proton pumping NADH:ubiquinone oxidoreductase (complex I). Complex I is a key enzyme of the mitochondrial respiratory chain that contains eight iron-sulfur clusters. From a rhodanese deletion strain, we purified functional complex I that lacked the additional protein but was fully assembled and displayed no functional defects or changes in EPR signature. In contrast to previous suggestions, this indicated that the sulfurtransferase associated with Y. lipolytica complex I is not required for assembly of its iron-sulfur clusters.

  5. Quantum wire structures by MBE overgrowth on a cleaved edge

    NASA Astrophysics Data System (ADS)

    Pfeiffer, Loren; Störmer, H. L.; West, K.; Baldwin, K. W.

    1991-05-01

    We have recently demonstrated the existence of a high mobility (6.1×10 5 cm 2/V·s) two-dimensional electron gas (2DEG) at the (110) vicinal surface formed by cleaving [L. Pfeiffer et al., Appl. Phys. Letters 56 (1990) 1697] a (100) GaAs wafer. We have now expanded this work to modulation-doped overgrowth on the cleaved edge of a multiperiod superlattice. We report here the first observation of the quantum Hall characteristics in such a two-dimensional system containing an atomically precise 71 Å GaAs by 31 Å Al 0.24Ga 0.76As compositional superlattice. The onset of Shubnikov-De Haas oscillations occurs at only 3000 G, implying the Landau cyclotron orbits are phase coherent over diameters as large as 5000 Å, corresponding to more than 200 GaAs/AlGaAs interface crossings.

  6. T. thermophila group I introns that cleave amide bonds

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor)

    1997-01-01

    The present invention relates to nucleic acid enzymes or enzymatic RNA molecules that are capable of cleaving a variety of bonds, including phosphodiester bonds and amide bonds, in a variety of substrates. Thus, the disclosed enzymatic RNA molecules are capable of functioning as nucleases and/or peptidases. The present invention also relates to compositions containing the disclosed enzymatic RNA molecule and to methods of making, selecting, and using such enzymes and compositions.

  7. Quantitative Z-Contrast Imaging of Supported Metal Complexes and Clusters - A Gateway to Understanding Catalysis on the Atomic Scale

    SciTech Connect

    Browning, Nigel D.; Aydin, C.; Lu, Jing; Kulkarni, Apoorva; Okamoto, Norihiko L.; Ortalan, V.; Reed, Bryan W.; Uzun, Alper; Gates, Bruce C.

    2013-09-01

    Z-contrast imaging in an aberration-corrected scanning transmission electron microscope can be used to observe and quantify the sizes, shapes, and compositions of the metal frames in supported mono-, bi-, and multimetallic metal clusters and can even detect the metal atoms in single-metal-atom complexes, as well as providing direct structural information characterizing the metal-support interface. Herein, we assess the major experimental challenges associated with obtaining atomic resolution Z-contrast images of the materials that are highly beam-sensitive, that is, the clusters readily migrate and sinter on support surfaces, and the support itself can drastically change in structure if the experiment is not properly controlled. Calibrated and quantified Z-contrast images are used in conjunction with exsitu analytical measurements and larger-scale characterization methods such as extended X-ray absorption fine structure spectroscopy to generate an atomic-scale understanding of supported catalysts and their function. Examples of the application of these methods include the characterization of a wide range of sizes and compositions of supported clusters, primarily those incorporating Ir, Os, and Au, on highly crystalline supports (zeolites and MgO).

  8. Functional study of elafin cleaved by Pseudomonas aeruginosa metalloproteinases

    PubMed Central

    Guyot, Nicolas; Bergsson, Gudmundur; Butler, Marcus W.; Greene, Catherine M.; Weldon, Sinead; Kessler, Efrat; Levine, Rodney L.; O’Neill, Shane J.; Taggart, Clifford C.; McElvaney, Noel G.

    2012-01-01

    Elafin is a 6 kDa innate immune protein present at several epithelial surfaces including the pulmonary epithelium. It is a canonical protease inhibitor of two neutrophil serine proteases (neutrophil elastase (NE) and proteinase 3) with the capacity to covalently bind extracellular matrix proteins by transglutamination. In addition to these properties, elafin also possesses antimicrobial and immunomodulatory activities. The aim of the present study was to investigate the effect of Pseudomonas aeruginosa proteases on elafin function. We found that P. aeruginosa PAO1-conditioned medium and two purified Pseudomonas metalloproteases, pseudolysin (elastase) and aeruginolysin (alkaline protease), were able to cleave recombinant elafin. Pseudolysin was shown to inactivate the anti-NE activity of elafin by cleaving its protease-binding loop. Interestingly, antibacterial properties of elafin against PAO1 were found to be unaffected after pseudolysin treatment. In contrast to pseudolysin, aeruginolysin failed to inactivate the inhibitory properties of elafin against NE. Aeruginolysin cleaved elafin at the amino-terminal Lys6-Gly7 peptide bond resulting in a decreased ability to covalently bind purified fibronectin following transglutaminase activity. In conclusion, this study provides evidences that elafin is susceptible to proteolytic cleavage at alternative sites by P. aeruginosa metalloproteinases, which can affect different biological functions of elafin. PMID:20370321

  9. Evolutionary origins of the placental expression of chromosome 19 cluster galectins and their complex dysregulation in preeclampsia.

    PubMed

    Than, N G; Romero, R; Xu, Y; Erez, O; Xu, Z; Bhatti, G; Leavitt, R; Chung, T H; El-Azzamy, H; LaJeunesse, C; Wang, B; Balogh, A; Szalai, G; Land, S; Dong, Z; Hassan, S S; Chaiworapongsa, T; Krispin, M; Kim, C J; Tarca, A L; Papp, Z; Bohn, H

    2014-11-01

    placental expression of Chr19 cluster galectins. The complex dysregulation of these genes in preeclampsia may alter immune tolerance mechanisms at the maternal-fetal interface. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Evolutionary origins of the placental expression of Chromosome 19 cluster galectins and their complex dysregulation in preeclampsia

    PubMed Central

    Than, Nandor Gabor; Xu, Yi; Erez, Offer; Xu, Zhonghui; Bhatti, Gaurav; Leavitt, Ron; Chung, Tzu Hung; El-Azzamy, Haidy; LaJeunesse, Christopher; Wang, Bing; Balogh, Andrea; Szalai, Gabor; Land, Susan; Dong, Zhong; Hassan, Sonia S.; Chaiworapongsa, Tinnakorn; Krispin, Manuel; Kim, Chong Jai; Tarca, Adi L.; Papp, Zoltan; Bohn, Hans

    2014-01-01

    . Conclusions These findings reveal the evolutionary origins of the placental expression of Chr19 cluster galectins. The complex dysregulation of these genes in preeclampsia may alter immune tolerance mechanisms at the maternal-fetal interface. PMID:25266889

  11. UV Insights into the Complex Populations of M87 Globular Clusters

    NASA Astrophysics Data System (ADS)

    Bellini, A.; Renzini, A.; Anderson, J.; Bedin, L. R.; Piotto, G.; Soto, M.; Brown, T. M.; Milone, A. P.; Sohn, S. T.; Sweigart, A. V.

    2015-06-01

    We have imaged with Hubble Space Telescope WFC3/UVIS the central 2\\buildrel{ \\prime}\\over{.} 7× 2\\buildrel{ \\prime}\\over{.} 7 region of the giant elliptical galaxy M87, using the ultraviolet filter F275W. In combination with archival ACS/WFC data taken through the F606W and F814W filters, covering the same field, we have constructed integrated-light UV-optical colors and magnitudes for 1460 objects, most of which are believed to be globular clusters (GCs) belonging to M87. The purpose was to ascertain whether the multiple-populations syndrome, ubiquitous among Galactic GCs, also exists among the M87 family of clusters. To achieve this goal, we sought those GCs with exceptionally blue UV-to-optical colors because helium-enriched sub-populations produce a horizontal-branch morphology that is well populated at high effective temperature. For comparison, integrated, synthetic UV-optical and purely optical colors and magnitudes have been constructed for 45 Galactic GCs, starting from individual-star photometry obtained with the same instruments and the same filters. We identify a small group of M87 clusters exhibiting a radial UV-optical color gradient, representing our best candidate GCs hosting multiple populations with extreme helium content. We also find that the central spatial distribution of the bluer GCs is flattened in a direction parallel to the jet, while the distribution of redder GCs is more spherical. We release to the astronomical community our photometric catalog in F275W, F606W, and F814W bands and the high-quality image stacks in the same bands. Based on proprietary and archival observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555.

  12. Cluster agglomeration induced by dust-density waves in complex plasmas.

    PubMed

    Dap, Simon; Lacroix, David; Hugon, Robert; de Poucques, Ludovic; Briancon, Jean-Luc; Bougdira, Jamal

    2012-12-14

    Experimental results showing the agglomeration of large carbonaceous particles in a dusty plasma are reported. Experiments were performed in a capacitively coupled rf argon plasma. Acetylene was injected to produce dust particles. When a sufficient amount of nanoparticles is present in the cathodic sheath, self-excited dust-density waves occur. The latter ones induce the motion of larger clusters, which vertically oscillate with the displacement of wave fronts. In some cases, the relative velocity of large particles was high enough to overcome the Coulomb repulsion forces, and agglomeration can be observed. The mechanisms underlying this process are discussed.

  13. A fluorophore-labelled copper complex: crystal structure, hybrid cyclic water-perchlorate cluster and biological properties.

    PubMed

    Bhat, Satish S; Revankar, Vidyanand K; Shivalingegowda, Naveen; Lokanath, N K

    2017-09-01

    A fluorophore-labelled copper(II) complex, aquabis(dimethylformamide-κO)(perchlorato-κO)[2-(quinolin-2-yl)-1,3-oxazolo[4,5-f][1,10]phenanthroline]copper(II) perchlorate monohydrate, [Cu(ClO4)(C22H12N4O)(C3H7NO)2(H2O)]ClO4·H2O, has been synthesized and characterized. A cyclic hydrogen-bonded water-perchlorate anionic cluster, i.e. [(ClO4)2(H2O)2](2-), has been identified within the structure. Each cyclic anionic cluster unit is interconnected by hydrogen bonding to the cation. The cations join into an infinite hydrogen-bonded chain running in the [010] direction. Furthermore, interaction of the complex with calf-thymus DNA (CT-DNA) and cellular localization within the cells was explored. Spectroscopic studies indicate that the compound has a good affinity for DNA and stains the nucleus of the cells.

  14. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

    PubMed Central

    Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-01-01

    Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive. PMID:26078860

  15. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods.

    PubMed

    Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-06-01

    Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60-5068 OTUs) and three orders of magnitude for the natural community (22-22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive.

  16. Mono- and bimetallic manganese-carbonyl complexes and clusters bearing imidazol(in)ium-2-dithiocarboxylate ligands.

    PubMed

    Beltrán, Tomás F; Zaragoza, Guillermo; Delaude, Lionel

    2017-02-14

    Five complexes with the generic formula fac-[MnBr(CO)3(S2C·NHC)] were obtained by reacting [MnBr(CO)5] with a set of representative imidazol(in)ium-2-dithiocarboxylate zwitterions. These ligands are the adducts of N-heterocyclic carbenes (NHCs) and carbon disulfide. The mononuclear Mn(i) derivatives were coupled with Na[Mn(CO)5] to afford bimetallic [Mn2(CO)6(S2C·NHC)] clusters. Yet, the most convenient strategy to access these dinuclear Mn(0) products implied a direct carbonyl substitution from the [Mn2(CO)10] dimer. The molecular structures of three monometallic and four bimetallic compounds were elucidated by single crystal X-ray diffraction analysis. In the monometallic complexes, the NHC·CS2 ligands exhibited a bidentate κ(2)-S,S' coordination mode with an S-C-S bite angle of about 116°. In the dinuclear clusters, the CS2(-) unit acted as a chelate toward one manganese center and as a pseudoallylic ligand toward the other one. The S-C-S bite angle was reduced to ca. 104°. Thus, the zwitterions displayed a remarkable flexibility, which also permitted a staggered arrangement of the carbonyl groups in the bimetallic systems. Examination of the [small nu, Greek, macron]CO absorption bands on IR spectroscopy helped identify the presence of fac-Mn(CO)3 or Mn2(CO)6 motifs, while the (13)C NMR chemical shift of the CS2(-) moiety was a reliable indicator for monitoring its hapticity. Whereas the dinuclear clusters were air- and moisture-stable crystalline solids, mononuclear halido derivatives displayed only a limited stability under aerobic conditions. Both types of compounds underwent rather unselective, extensive fragmentations in the gas phase, in sharp contrast with the analogous rhenium derivatives that led to clean sequential decarbonylation processes upon collision-induced dissociation.

  17. Mesotrypsin has evolved four unique residues to cleave trypsin inhibitors as substrates [Mesotrypsin has evolved to cleave trypsin inhibitors as substrates using four unique residues

    DOE PAGES

    Alloy, Alexandre P.; Kayode, Olumide; Wang, Ruiying; ...

    2015-07-14

    Human mesotrypsin is highly homologous to other mammalian trypsins, and yet it is functionally unique in possessing resistance to inhibition by canonical serine protease inhibitors and in cleaving these inhibitors as preferred substrates. Arg-193 and Ser-39 have been identified as contributors to the inhibitor resistance and cleavage capability of mesotrypsin, but it is not known whether these residues fully account for the unusual properties of mesotrypsin. Here, we use human cationic trypsin as a template for engineering a gain of catalytic function, assessing mutants containing mesotrypsin-like mutations for resistance to inhibition by bovine pancreatic trypsin inhibitor (BPTI) and amyloid precursormore » protein Kunitz protease inhibitor (APPI), and for the ability to hydrolyze these inhibitors as substrates. We find that Arg-193 and Ser-39 are sufficient to confer mesotrypsin-like resistance to inhibition; however, compared with mesotrypsin, the trypsin-Y39S/G193R double mutant remains 10-fold slower at hydrolyzing BPTI and 2.5-fold slower at hydrolyzing APPI. We identify two additional residues in mesotrypsin, Lys-74 and Asp-97, which in concert with Arg-193 and Ser-39 confer the full catalytic capability of mesotrypsin for proteolysis of BPTI and APPI. Novel crystal structures of trypsin mutants in complex with BPTI suggest that these four residues function cooperatively to favor conformational dynamics that assist in dissociation of cleaved inhibitors. Our results reveal that efficient inhibitor cleavage is a complex capability to which at least four spatially separated residues of mesotrypsin contribute. As a result, these findings suggest that inhibitor cleavage represents a functional adaptation of mesotrypsin that may have evolved in response to positive selection pressure.« less

  18. Mesotrypsin has evolved four unique residues to cleave trypsin inhibitors as substrates [Mesotrypsin has evolved to cleave trypsin inhibitors as substrates using four unique residues

    SciTech Connect

    Alloy, Alexandre P.; Kayode, Olumide; Wang, Ruiying; Hockla, Alexandra; Soares, Alexei S.; Radisky, Evette S.

    2015-07-14

    Human mesotrypsin is highly homologous to other mammalian trypsins, and yet it is functionally unique in possessing resistance to inhibition by canonical serine protease inhibitors and in cleaving these inhibitors as preferred substrates. Arg-193 and Ser-39 have been identified as contributors to the inhibitor resistance and cleavage capability of mesotrypsin, but it is not known whether these residues fully account for the unusual properties of mesotrypsin. Here, we use human cationic trypsin as a template for engineering a gain of catalytic function, assessing mutants containing mesotrypsin-like mutations for resistance to inhibition by bovine pancreatic trypsin inhibitor (BPTI) and amyloid precursor protein Kunitz protease inhibitor (APPI), and for the ability to hydrolyze these inhibitors as substrates. We find that Arg-193 and Ser-39 are sufficient to confer mesotrypsin-like resistance to inhibition; however, compared with mesotrypsin, the trypsin-Y39S/G193R double mutant remains 10-fold slower at hydrolyzing BPTI and 2.5-fold slower at hydrolyzing APPI. We identify two additional residues in mesotrypsin, Lys-74 and Asp-97, which in concert with Arg-193 and Ser-39 confer the full catalytic capability of mesotrypsin for proteolysis of BPTI and APPI. Novel crystal structures of trypsin mutants in complex with BPTI suggest that these four residues function cooperatively to favor conformational dynamics that assist in dissociation of cleaved inhibitors. Our results reveal that efficient inhibitor cleavage is a complex capability to which at least four spatially separated residues of mesotrypsin contribute. As a result, these findings suggest that inhibitor cleavage represents a functional adaptation of mesotrypsin that may have evolved in response to positive selection pressure.

  19. Electronic Structure of Transition Metal Clusters and Actinide Complexes and Their Reactivity

    SciTech Connect

    Balasubramanian, K

    2008-10-06

    Our research in this area since October 2007 has resulted in seven completed publications and more papers of the completed work are in progress. Our work during this period principally focused on actinide complexes with secondary emphasis on spectroscopic properties and electronic structure of metal complexes. As the publications are available online with all of the details of the results, tables and figures, we are providing here only a brief summary of major highlights, in each of the categories.

  20. Excited-State Energetics and Dynamics of Large Molecules, Complexes and Clusters.

    DTIC Science & Technology

    1987-04-30

    intramolecular vibrational motion was obtained for the trans-stilbene.Ar complex. 7.P Analogies between Large vanderWaalsMolecules and Microsurfaces . The...of R adsorbates on finite microsurfaces . The elucidation of the structure, energetics and nuclear dynamics of large M.Rn complexes rests on semi...Page 12 (13) Samuel Leutwyler and Joshua Jortner The Adsorption of Rare-Gas on Microsurfaces of Large Aromatic Molecules J. Phys. Chem. (in press) (14

  1. Properties of clusters in the gas phase: V. Complexes of neutral molecules onto negative ions

    SciTech Connect

    Keesee, R.G.; Lee, N.; Castleman, A.W. Jr.

    1980-09-01

    Ion--molecules association reactions of the form A/sup -/(B)/sub n1/-+B=A/sup -/(B)/sub n/ were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl/sup -/, I/sup -/, and NO/sub 2//sup -/ with n ranging from one to three or four, and onto SO/sub 2//sup -/ and SO/sub 3//sup -/ with n equal to one; and (2) carbon dioxide onto Cl/sup -/, I/sup -/, NO/sub 2//sup -/, CO/sub 3//sup -/, and SO/sub 3//sup -/ with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions. For any given ion, the relative order of the addition enthalpies among the neutrals was found to be dependent on the polarizabilities of the neutrals and on the covalency in the ion-neutral bond. Dispersion of charge via covalent bonding was found to affect significantly the succeeding clustering steps.

  2. Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder.

    PubMed

    Frank, René A W; McRae, Allan F; Pocklington, Andrew J; van de Lagemaat, Louie N; Navarro, Pau; Croning, Mike D R; Komiyama, Noboru H; Bradley, Sophie J; Challiss, R A John; Armstrong, J Douglas; Finn, Robert D; Malloy, Mary P; MacLean, Alan W; Harris, Sarah E; Starr, John M; Bhaskar, Sanjeev S; Howard, Eleanor K; Hunt, Sarah E; Coffey, Alison J; Ranganath, Venkatesh; Deloukas, Panos; Rogers, Jane; Muir, Walter J; Deary, Ian J; Blackwood, Douglas H; Visscher, Peter M; Grant, Seth G N

    2011-04-29

    Current models of schizophrenia and bipolar disorder implicate multiple genes, however their biological relationships remain elusive. To test the genetic role of glutamate receptors and their interacting scaffold proteins, the exons of ten glutamatergic 'hub' genes in 1304 individuals were re-sequenced in case and control samples. No significant difference in the overall number of non-synonymous single nucleotide polymorphisms (nsSNPs) was observed between cases and controls. However, cluster analysis of nsSNPs identified two exons encoding the cysteine-rich domain and first transmembrane helix of GRM1 as a risk locus with five mutations highly enriched within these domains. A new splice variant lacking the transmembrane GPCR domain of GRM1 was discovered in the human brain and the GRM1 mutation cluster could perturb the regulation of this variant. The predicted effect on individuals harbouring multiple mutations distributed in their ten hub genes was also examined. Diseased individuals possessed an increased load of deleteriousness from multiple concurrent rare and common coding variants. Together, these data suggest a disease model in which the interplay of compound genetic coding variants, distributed among glutamate receptors and their interacting proteins, contribute to the pathogenesis of schizophrenia and bipolar disorders.

  3. The paracaspase MALT1 cleaves the LUBAC subunit HOIL1 during antigen receptor signaling.

    PubMed

    Douanne, Tiphaine; Gavard, Julie; Bidère, Nicolas

    2016-05-01

    Antigen-receptor-mediated activation of lymphocytes relies on a signalosome comprising CARMA1 (also known as CARD11), BCL10 and MALT1 (the CBM complex). The CBM activates nuclear factor κB (NF-κB) transcription factors by recruiting the 'linear ubiquitin assembly complex' (LUBAC), and unleashes MALT1 paracaspase activity. Although MALT1 enzyme shapes NF-κB signaling, lymphocyte activation and contributes to lymphoma growth, the identity of its substrates continues to be elucidated. Here, we report that the LUBAC subunit HOIL1 (also known as RBCK1) is cleaved by MALT1 following antigen receptor engagement. HOIL1 is also constitutively processed in the 'activated B-cell-like' (ABC) subtype of diffuse large B-cell lymphoma (DLBCL), which exhibits aberrant MALT1 activity. We further show that the overexpression of MALT1-insensitive HOIL1 mitigates T-cell-receptor-mediated NF-κB activation and subsequent cytokine production in lymphocytes. Thus, our results unveil HOIL1 as a negative regulator of lymphocyte activation cleaved by MALT1. This cleavage could therefore constitute an appealing therapeutic target for modulating immune responses.

  4. Assessment of the CCSD and CCSD(T) Coupled-Cluster Methods in Calculating Heats of Formation for Zn Complexes

    PubMed Central

    Weaver, Michael N.; Yang, Yue

    2010-01-01

    Heats of formation were calculated using coupled-cluster methods for a series of zinc complexes. The calculated values were evaluated against previously conducted computational studies using density functional methods as well as experimental values. Heats of formation for nine neutral ZnXn complexes [X = -Zn, -H, -O, -F2, -S, -Cl, -Cl2, -CH3, (-CH3)2] were determined at the CCSD and CCSD(T) levels using the 6–31G** and TZVP basis sets, as well as the LANL2DZ-6–31G** (LACVP**) and LANL2DZ-TZVP hybrid basis sets. The CCSD(T)/6–31G** level of theory was found to predict the heat of formation for the non-alkyl Zn complexes most accurately. The alkyl Zn species were problematic in that none of the methods that were tested accurately predicted the heat of formation for these complexes. For the seven non-alkyl species, the CCSD(T)/6–31G** level of theory was shown to predict the most accurate heat of formation values. In instances where experimental geometric parameters were available, these were most accurately predicted by the CCSD/6–31G** level of theory; going to CCSD(T) did not improve agreement with the experimental values. PMID:19691272

  5. Clustered hydrophobic amino acids in amphipathic helices mediate erlin1/2 complex assembly.

    PubMed

    Pednekar, Deepa; Wang, Yuan; Fedotova, Tatyana V; Wojcikiewicz, Richard J H

    2011-11-11

    Erlin1 and erlin2 are highly homologous, ∼40kDa, endoplasmic reticulum membrane proteins that assemble into a ring-shaped complex with a mass of ∼2 MDa. How this complex is formed is not understood, but appears to involve multiple interactions, including a coiled-coil region that mediates lower-order erlin assembly, and a short hydrophobic region, termed the "assembly domain", that mediates higher-order assembly into ∼2 MDa complexes. Here we have used molecular modeling, mutagenesis and cross-linking to examine the role of the assembly domain in higher-order assembly. We find (i) that the assembly domains of erlin1 and erlin2 are amphipathic helices, (ii) that erlin1 alone and erlin2 alone can assemble into ∼2 MDa complexes, (iii) that higher-order assembly is strongly inhibited by point mutations to the assembly domain, (iv) that three interacting hydrophobic residues in the assembly domain and aromaticity are essential for higher-order assembly, and (iv) that while erlins1 and 2 are equally capable of forming lower-order homo- and hetero-oligomers, hetero-oligomers are the most prevalent form when erlin1 and erlin2 are co-expressed. Overall, we conclude that the ∼2 MDa erlin1/2 complex is composed of an assemblage of lower-order hetero-oligomers, probably heterotrimers, linked together by assembly domain hydrophobic residues. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Cluster analysis in soft x-ray spectromicroscopy : finding the patterns in complex specimens.

    SciTech Connect

    Lerotic, M.; Jacobsen, C.; Gillow, J. B.; Wirick, S.; Vogt, S.; Maser, J.; Experimental Facilities Division; State Univ. of New York at Stony Brook; BNL

    2005-06-01

    Soft X-ray spectromicroscopy provides spectral data on the chemical speciation of light elements at sub-100 nanometer spatial resolution. If all chemical species in a specimen are known and separately characterized, existing approaches can be used to measure the concentration of each component at each pixel. In other situations such as in biology or environmental science, this approach may not be possible. We have previously described the use of principle component analysis (PCA) to orthogonalize and noise-filter spectromicroscopy data, and cluster analysis (CA) to classify the analyzed data and obtain thickness maps of representative spectra. We describe here an extension of that work employing an angle distance measure; this measure provides better classification based on spectral signatures alone in specimens with significant thickness variations. The method is illustrated using simulated data, and also to examine sporulation in the bacterium Clostridium sp.

  7. Properties of clusters in the gas phase. V - Complexes of neutral molecules onto negative ions

    NASA Technical Reports Server (NTRS)

    Keesee, R. G.; Lee, N.; Castleman, A. W., Jr.

    1980-01-01

    Ion-molecules association reactions of the form A(-)(B)n-1 + B = A(-)(B)n were studied over a range of temperatures in the gas phase using high pressure mass spectrometry. Enthalpy and entropy changes were determined for the stepwise clustering reactions of (1) sulfur dioxide onto Cl(-), I(-), and NO2(-) with n ranging from one to three or four, and onto SO2(-) and SO3(-) with n equal to one; and (2) carbon dioxide onto Cl(-), I(-), NO2(-), CO3(-), and SO3(-) with n equal to one. From these data and earlier hydration results, the order of the magnitude of the enthalpy changes on the association of the first neutral for a series of negative ions was found to parallel the gas-phase basicity of those anions.

  8. Communication: Relativistic Fock-space coupled cluster study of small building blocks of larger uranium complexes

    SciTech Connect

    Tecmer, Paweł Visscher, Lucas; Severo Pereira Gomes, André; Knecht, Stefan

    2014-07-28

    We present a study of the electronic structure of the [UO{sub 2}]{sup +}, [UO{sub 2}]{sup 2} {sup +}, [UO{sub 2}]{sup 3} {sup +}, NUO, [NUO]{sup +}, [NUO]{sup 2} {sup +}, [NUN]{sup −}, NUN, and [NUN]{sup +} molecules with the intermediate Hamiltonian Fock-space coupled cluster method. The accuracy of mean-field approaches based on the eXact-2-Component Hamiltonian to incorporate spin–orbit coupling and Gaunt interactions are compared to results obtained with the Dirac–Coulomb Hamiltonian. Furthermore, we assess the reliability of calculations employing approximate density functionals in describing electronic spectra and quantities useful in rationalizing Uranium (VI) species reactivity (hardness, electronegativity, and electrophilicity)

  9. Levels of control exerted by the Isc iron-sulfur cluster system on biosynthesis of the formate hydrogenlyase complex.

    PubMed

    Pinske, Constanze; Jaroschinsky, Monique; Sawers, R Gary

    2013-06-01

    The membrane-associated formate hydrogenlyase (FHL) complex of bacteria like Escherichia coli is responsible for the disproportionation of formic acid into the gaseous products carbon dioxide and dihydrogen. It comprises minimally seven proteins including FdhF and HycE, the catalytic subunits of formate dehydrogenase H and hydrogenase 3, respectively. Four proteins of the FHL complex have iron-sulphur cluster ([Fe-S]) cofactors. Biosynthesis of [Fe-S] is principally catalysed by the Isc or Suf systems and each comprises proteins for assembly and for delivery of [Fe-S]. This study demonstrates that the Isc system is essential for biosynthesis of an active FHL complex. In the absence of the IscU assembly protein no hydrogen production or activity of FHL subcomponents was detected. A deletion of the iscU gene also resulted in reduced intracellular formate levels partially due to impaired synthesis of pyruvate formate-lyase, which is dependent on the [Fe-S]-containing regulator FNR. This caused reduced expression of the formate-inducible fdhF gene. The A-type carrier (ATC) proteins IscA and ErpA probably deliver [Fe-S] to specific apoprotein components of the FHL complex because mutants lacking either protein exhibited strongly reduced hydrogen production. Neither ATC protein could compensate for the lack of the other, suggesting that they had independent roles in [Fe-S] delivery to complex components. Together, the data indicate that the Isc system modulates FHL complex biosynthesis directly by provision of [Fe-S] as well as indirectly by influencing gene expression through the delivery of [Fe-S] to key regulators and enzymes that ultimately control the generation and oxidation of formate.

  10. Two unprecedented inorganic-organic boxlike and chainlike hybrids based on arsenic-vanadium clusters linked by nickel complexes

    SciTech Connect

    Qi Yanfei; Li Yangguang; Wang Enbo Jin Hua; Zhang Zhiming; Wang Xinglong; Chang Song

    2007-01-15

    Two novel organic-inorganic hybrid arsenic-vanadates, [{l_brace}Ni(en){sub 2}{r_brace}{sub 4}(4,4'-bipy){sub 4}{l_brace}Ni(H{sub 2}O){sub 2}{r_brace}]{sub 2}[As{sub 8}V{sub 14}O{sub 42}(NO{sub 3})]{sub 4}.16H{sub 2}O 1 and [Ni(en){sub 2}(H{sub 2}O){sub 2}]{sub 2}[{l_brace}Ni(en){sub 2}(H{sub 2}O){r_brace}{sub 2}As{sub 8}V{sub 14}O{sub 42}(NO{sub 3})][{l_brace}Ni(en){sub 2}{r_brace}As{sub 8}V{sub 14}O{sub 42}(NO{sub 3})] .6H{sub 2}O 2 are reported in this study. Crystal data for compound 1: Tetragonal, I4/m, a=27.507(4) A, b=27.507(4) A, c=22.101(4) A; V=16722(5) A{sup 3}, Z=2, R(final)=0.0508. Crystal data for compound 2: Triclinic, P-1, a=11.530(2) A, b=14.883(3) A, c=21.330(4) A, {alpha}=76.94(3){sup o}, {beta}=76.58(3){sup o}, {gamma}=69.54(3){sup o}, V=3293.4(1) A{sup 3}, Z=1, R(final)=0.0559. The boxlike structure of compound 1 is designed from [{l_brace}Ni(en){sub 2}{r_brace}{sub 4}(4,4'-bipy){sub 4}{l_brace}Ni(H{sub 2}O){sub 2}{r_brace}] sheets pillared by [{alpha}-As{sub 8}V{sub 14}O{sub 42}] clusters, which represents the first mixed-organic ligand-decorated tetrameric As-V-O cluster. Compound 2 is constructed from the rarely [{beta}-As{sub 8}V{sub 14}O{sub 42}] clusters and Ni coordination complex fragments. The electrochemical property and magnetic property of compound 1 have been studied. - Graphical abstract: The boxlike structure of compound 1 with cavity is designed from [{l_brace}Ni(en){sub 2}{r_brace}{sub 4}(4,4'-bipy){sub 4}{l_brace}Ni(H{sub 2}O){sub 2}{r_brace}] sheets pillared by [{alpha}-As{sub 8}V{sub 14}O{sub 42}] clusters, which represents the first mixed-organic ligand-decorated tetrameric As-V-O cluster.

  11. Synthesis of self-assembled large area films of complex hierarchical PZT clusters

    NASA Astrophysics Data System (ADS)

    Pratap Chaudhary, Raghvendra; Saxena, Sumit; Kmar, Amit; Bharadwaj, Rajesh; Shukla, Shobha

    2016-02-01

    The ability to bridge nano-micro interface for applications in functional miniaturized devices is of fundamental interest. We have synthesized novel large area films of complex hierarchical micro-flower morphologies of piezo-ceramics using hydrothermal reactions. The overall size of the samples produced is ∼cm2. The growth morphologies are found to be dependent on concentration and pressure inside the reaction chamber. This can be used to deterministically grow these complex multi-scaled microstructures over a large area. These results outline a strategy for growth of omni-directional microstructures by utilizing self assembly processes.

  12. Iridium Complexes and Clusters in Dealuminated Zeolite HY: Distribution between Crystalline and Impurity Amorphous Regions

    SciTech Connect

    Martinez-Macias, Claudia; Xu, Pinghong; Hwang, Son-Jong; Lu, Jing; Chen, Cong-Yan; Browning, Nigel D.; Gates, Bruce C.

    2014-07-08

    Dealuminated zeolite HY was used to support Ir(CO)2 complexes formed from Ir(CO)2(C5H7O2). Infrared and X-ray absorption spectra and atomic-resolution electron microscopy images identify these complexes, and the images and 27Al NMR spectra identify impurity amorphous regions in the zeolite where the iridium is more susceptible to aggregation than in the crystalline regions. The results indicate a significant stability limitation of metal in amorphous impurity regions of zeolites.

  13. Two new polyoxometalate tri-supported transition metal complexes constructed from bi-capped Keggin molybdenum vanadium clusters and copper complex fragments

    NASA Astrophysics Data System (ADS)

    Cui, Ji-Wen; Cui, Xiao-Bing; Xu, Jia-Ning; Yu, Hai-Hui; Xu, Ji-Qing; Duan, Wei-Jie; Wang, Tie-Gang

    2008-11-01

    Two new molybdenum-vanadium polyoxometalate tri-supported transition metal complexes [Cu(2,2 '-bipy)] [Cu(2,2 '-bipy) 2] 2[PMo 8V 6O 42]· nH 2O ( n = 1.5 ( 1) and n = 2 ( 2); 2,2 '-bipy = 2,2 '-bipyridine) have been hydrothermally synthesized and characterized by elemental analyses, IR, XPS and single-crystal X-ray diffraction analyses. Both compound 1 and compound 2 contain molybdenum-vanadium polyoxometalates, each of which support one [Cu(2,2 '-bipy)] 2+ cation and two [Cu(2,2 '-bipy) 2] 2+ cations, respectively. The difference between compound 1 and compound 2 is that the polyoxoanion of 1 is a bi-capped α-Keggin cluster and that of 2 is a bi-capped pseudo-Keggin one. Studies of magnetic properties indicated the presence of ferromagnetic behaviors for compounds 1 and 2.

  14. An unusual (H(2)O)(20) discrete water cluster in the supramolecular host of a charge transfer platinum(ii) complex: cytotoxicity and DNA cleavage activities.

    PubMed

    Mandal, Sutanuva; Castiñeiras, Alfonso; Mondal, Tapan K; Mondal, Arindam; Chattopadhyay, Dhrubajyoti; Goswami, Sreebrata

    2010-10-28

    The chemical reaction of Pt(II)(L(1))Cl(2) [L(1) = N-4-tolylpyridine-2-aldimine] with a bidentate N,S-donor atom ligand, 2-methylthioaniline, (HL(2)) in alkaline methanolic medium yielded a mixed ligand donor-acceptor complex, [Pt(II)(L(1))(L(2))]Cl, [1]Cl. The complex has been characterized by different spectroscopic and electrochemical techniques. The complex showed intense interligand charge transfer (ILCT) transition in the long wavelength region of UV-vis spectrum (>600 nm). The single-crystal X-ray structure of complex, [1]Cl·3.3H(2)O is reported. The cationic complex upon crystallization from aqueous methanol solvent produces an assembly of discrete, three dimensional (H(2)O)(20) guest moiety within the reference Pt-complex host lattice. The water assembly showed a unique type of aggregation of a distorted cube encapsulated by hydrogen bonded network of a twelve-water ring. The complex displayed one reversible cathodic response at -0.75 V and two irreversible anodic responses at 0.42 and 0.79 V versus Ag/AgCl reference electrode. The redox processes are characterized by EPR and spectroelectrochemistry. Density-functional theory calculations were employed to confirm the structural features and to support the spectral and redox properties of the complex. The square-planar complex has been found to intercalate DNA. Fluorescence spectroscopy, circular dichroism, cyclic voltammetry, viscosity measurements, together with DNA melting studies have been employed to characterize the binding of [1]Cl with calf thymus DNA. Agarose gel electrophoresis indicates that the complex cleaves supercoiled (SC) pUC19 plasmid DNA to its nicked circular (NC) form via singlet oxygen. As determined by a MTT assay, [1]Cl exhibits significant cytotoxicity with IC(50) value 58 μM.

  15. Optical fiber alignment using cleaved-edge diffracted light

    NASA Astrophysics Data System (ADS)

    Brun, Louis C.; Bergeron, Patrick; Duguay, Michel A.; Ouellette, Francois; Tetu, Michel

    1993-08-01

    We describe a simple technique for aligning optical fibers prior to fusion splicing. The technique relies on the fact that well-cleaved fiber ends have extremely sharp edges. By making the narrow pencil of light emerging from one fiber scan laterally over the entrance face of a second fiber, and by monitoring the light diffracted past its sharp edges, we can locate precisely the geometric center of the output fiber. With this technique, we have aligned fiber cores with a mean lateral offset of 0.81 micrometers , the major part of this offset caused by the eccentricity of the core relative to the cladding's circular perimeter.

  16. Surface structure of cleaved (001) USb2 single crystal surface

    SciTech Connect

    Chen, Shao-ping

    2008-01-01

    We have achieved what we believe to be the first atomic resolution scanning tunneling microscopy (STM) images for a uranium compound USb2 taken at room temperature. The a, b, and c lattice parameters in the images confirm that the tetragonal USb2 crystals cleave on the (001) basal plane as expected. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the density of states measured by STM. Since the spacing between Sb atoms and between U atoms is the same, STM topography alone cannot unambiguously identify the surface atom species.

  17. A tray-shaped, Pd(II)-clipped Au₃ complex as a scaffold for the modular assembly of [3×n] Au ion clusters.

    PubMed

    Osuga, Takafumi; Murase, Takashi; Hoshino, Manabu; Fujita, Makoto

    2014-10-13

    A tray-shaped Pd(II)3Au(I)3 complex (1) is prepared from 3,5-bis(3-pyridyl)pyrazole by means of tricyclization with Au(I) followed by Pd(II) clipping. Tray 1 is an efficient scaffold for the modular assembly of [3×n] Au(I) clusters. Treatment of 1 with the Au(I)3 tricyclic guest 2 in H2O/CH3CN (7:3) or H2O results in the selective formation of a [3×2] cluster (1⋅2) or a [3×3] cluster (1⋅2⋅1), respectively. Upon subsequent addition of Ag(I) ions, these complexes are converted to an unprecedented Au3-Au3-Ag-Au3-Au3 metal ion cluster. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Photo-induced transformation process at gold clusters-semiconductor interface: Implications for the complexity of gold clusters-based photocatalysis

    PubMed Central

    Liu, Siqi; Xu, Yi-Jun

    2016-01-01

    The recent thrust in utilizing atomically precise organic ligands protected gold clusters (Au clusters) as photosensitizer coupled with semiconductors for nano-catalysts has led to the claims of improved efficiency in photocatalysis. Nonetheless, the influence of photo-stability of organic ligands protected-Au clusters at the Au/semiconductor interface on the photocatalytic properties remains rather elusive. Taking Au clusters–TiO2 composites as a prototype, we for the first time demonstrate the photo-induced transformation of small molecular-like Au clusters to larger metallic Au nanoparticles under different illumination conditions, which leads to the diverse photocatalytic reaction mechanism. This transformation process undergoes a diffusion/aggregation mechanism accompanied with the onslaught of Au clusters by active oxygen species and holes resulting from photo-excited TiO2 and Au clusters. However, such Au clusters aggregation can be efficiently inhibited by tuning reaction conditions. This work would trigger rational structural design and fine condition control of organic ligands protected-metal clusters-semiconductor composites for diverse photocatalytic applications with long-term photo-stability. PMID:26947754

  19. Characterization of Toxin Complex Gene Clusters and Insect Toxicity of Bacteria Representing Four Subgroups of Pseudomonas fluorescens.

    PubMed

    Rangel, Lorena I; Henkels, Marcella D; Shaffer, Brenda T; Walker, Francesca L; Davis, Edward W; Stockwell, Virginia O; Bruck, Denny; Taylor, Barbara J; Loper, Joyce E

    2016-01-01

    Ten strains representing four lineages of the Pseudomonas fluorescens group (P. chlororaphis, P. corrugata, P. koreensis, and P. fluorescens subgroups) were evaluated for toxicity to the tobacco hornworm Manduca sexta and the common fruit fly Drosophila melanogaster. The three strains within the P. chlororaphis subgroup exhibited both oral and injectable toxicity to the lepidopteran M. sexta. All three strains have the gene cluster encoding the FitD insect toxin and a ΔfitD mutant of P. protegens strain Pf-5 exhibited diminished oral toxicity compared to the wildtype strain. Only one of the three strains, P. protegens Pf-5, exhibited substantial levels of oral toxicity against the dipteran D. melanogaster. Three strains in the P. fluorescens subgroup, which lack fitD, consistently showed significant levels of injectable toxicity against M. sexta. In contrast, the oral toxicity of these strains against D. melanogaster was variable between experiments, with only one strain, Pseudomonas sp. BG33R, causing significant levels of mortality in repeated experiments. Toxin complex (Tc) gene clusters, which encode insecticidal properties in Photorhabdus luminescens, were identified in the genomes of seven of the ten strains evaluated in this study. Within those seven genomes, six types of Tc gene clusters were identified, distinguished by gene content, organization and genomic location, but no correlation was observed between the presence of Tc genes and insect toxicity of the evaluated strains. Our results demonstrate that members of the P. fluorescens group have the capacity to kill insects by both FitD-dependent and independent mechanisms.

  20. Characterization of Toxin Complex Gene Clusters and Insect Toxicity of Bacteria Representing Four Subgroups of Pseudomonas fluorescens

    PubMed Central

    Rangel, Lorena I.; Henkels, Marcella D.; Shaffer, Brenda T.; Walker, Francesca L.; Davis, Edward W.; Stockwell, Virginia O.; Bruck, Denny; Taylor, Barbara J.; Loper, Joyce E.

    2016-01-01

    Ten strains representing four lineages of the Pseudomonas fluorescens group (P. chlororaphis, P. corrugata, P. koreensis, and P. fluorescens subgroups) were evaluated for toxicity to the tobacco hornworm Manduca sexta and the common fruit fly Drosophila melanogaster. The three strains within the P. chlororaphis subgroup exhibited both oral and injectable toxicity to the lepidopteran M. sexta. All three strains have the gene cluster encoding the FitD insect toxin and a ΔfitD mutant of P. protegens strain Pf-5 exhibited diminished oral toxicity compared to the wildtype strain. Only one of the three strains, P. protegens Pf-5, exhibited substantial levels of oral toxicity against the dipteran D. melanogaster. Three strains in the P. fluorescens subgroup, which lack fitD, consistently showed significant levels of injectable toxicity against M. sexta. In contrast, the oral toxicity of these strains against D. melanogaster was variable between experiments, with only one strain, Pseudomonas sp. BG33R, causing significant levels of mortality in repeated experiments. Toxin complex (Tc) gene clusters, which encode insecticidal properties in Photorhabdus luminescens, were identified in the genomes of seven of the ten strains evaluated in this study. Within those seven genomes, six types of Tc gene clusters were identified, distinguished by gene content, organization and genomic location, but no correlation was observed between the presence of Tc genes and insect toxicity of the evaluated strains. Our results demonstrate that members of the P. fluorescens group have the capacity to kill insects by both FitD-dependent and independent mechanisms. PMID:27580176

  1. Excited State Energetics and Dynamics of Large Molecules, Complexes and Clusters

    DTIC Science & Technology

    1988-07-01

    States of Large Molecules 6 .4,,4 7- - . / ,-° - . . - ii - Page No. 7. (cont’d) K) Photoisomerization Dynamics of Trans- Stilbene and 6 of Cis- Stilbene L...Photoisomerization Dynamics of Alkyl Substituted Trans- Stilbene 6 M) Energy-Resolved Photoisomerization Rates 7 N) van der Waals Complexes and... Stilbene andof CisStilbene. Time-resolved fluorescence lifetimes from photoselected states of trans- stilbene were recorded by the techniques of

  2. Synthesis and structural characterization of bimetallic iron-nickel carbido cluster complexes.

    PubMed

    Saha, Sumit; Zhu, Lei; Captain, Burjor

    2010-04-05

    In acetonitrile solvent, Fe(5)(CO)(15)(mu(5)-C), 1, reacts with Ni(COD)(2) at room temperature to afford the iron-nickel complex Fe(5)Ni(NCMe)(CO)(15)(mu(6)-C), 3. The acetonitrile ligand in 3 can be replaced by CO and NH(3) to yield Fe(5)Ni(CO)(16)(mu(6)-C), 4, and Fe(5)Ni(NH(3))(CO)(15)(mu(6)-C), 6, respectively. When refluxed in acetonitrile solvent, compound 3 loses a vertex to form the square pyramidal Fe(4)Ni complex Fe(4)Ni(NCMe)(2)(CO)(12)(mu(5)-C), 7. Compound 7 readily converts to Fe(4)Ni(NCMe)(CO)(13)(mu(5)-C), 8, by losing one of its acetonitrile ligands. Addition of acetonitrile to 8 gives compound 7. When heated to 110 degrees C under an atmosphere of CO, both compounds 7 and 8 furnish the octahedral Fe(4)Ni(2) complex Fe(4)Ni(2)(CO)(15)(mu(6)-C), 9. All six compounds were structurally characterized by single-crystal X-ray diffraction analyses.

  3. The C-type lectin-like receptors of Dectin-1 cluster in natural killer gene complex.

    PubMed

    Xie, Jianhui

    2012-08-01

    Natural killer gene complex (NKC) encodes a group of proteins with a single C-type lectin-like domain, (CTLD) which can be subdivided several subfamilies according to their structures and expression patterns. The receptors containing the conserved calcium binding sites in the CTLD fold belong to group II of C-type lectin superfamily and are expressed on myeloid cells and non- myeloid cells. The receptors lacking conserved calcium binding sites in the CTLD fold have evolved to bind ligands other than carbohydrates independently on calcium and thereby are named as C-type lectin-like receptors. The C-type lectin-like receptors are previously thought to be exclusively expressed on natural killer (NK) cells and enable NK cells to discriminate self, missing self or altered self. However, some C-type lectin-like receptors are identified in myeloid cells and are intensely investigated, recently. These myeloid C-type lectin-like receptors, especially Dectin-1 cluster, have a wide variety of ligands, including those of exogenous origin, and play important roles in the physiological functions and pathological processes including immune homeostasis, immune defenses, and immune surveillance. In this review, we summarize each member of the Dectin-1 cluster, including their structural profiles, expression patterns, signaling properties as well as known physiological functions.

  4. Quick detection of QRS complexes and R-waves using a wavelet transform and K-means clustering.

    PubMed

    Xia, Yong; Han, Junze; Wang, Kuanquan

    2015-01-01

    Based on the idea of telemedicine, 24-hour uninterrupted monitoring on electrocardiograms (ECG) has started to be implemented. To create an intelligent ECG monitoring system, an efficient and quick detection algorithm for the characteristic waveforms is needed. This paper aims to give a quick and effective method for detecting QRS-complexes and R-waves in ECGs. The real ECG signal from the MIT-BIH Arrhythmia Database is used for the performance evaluation. The method proposed combined a wavelet transform and the K-means clustering algorithm. A wavelet transform is adopted in the data analysis and preprocessing. Then, based on the slope information of the filtered data, a segmented K-means clustering method is adopted to detect the QRS region. Detection of the R-peak is based on comparing the local amplitudes in each QRS region, which is different from other approaches, and the time cost of R-wave detection is reduced. Of the tested 8 records (total 18201 beats) from the MIT-BIH Arrhythmia Database, an average R-peak detection sensitivity of 99.72 and a positive predictive value of 99.80% are gained; the average time consumed detecting a 30-min original signal is 5.78s, which is competitive with other methods.

  5. Crystal Structures of the Iron–Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate

    SciTech Connect

    Fenwick, Michael K.; Ealick, Steven E.

    2016-07-12

    The quinolinate synthase of prokaryotes and photosynthetic eukaryotes, NadA, contains a [4Fe-4S] cluster with unknown function. We report crystal structures of Pyrococcus horikoshii NadA in complex with dihydroxyacetone phosphate (DHAP), iminoaspartate analogues, and quinolinate. DHAP adopts a nearly planar conformation and chelates the [4Fe-4S] cluster via its keto and hydroxyl groups. The active site architecture suggests that the cluster acts as a Lewis acid in enediolate formation, like zinc in class II aldolases. The DHAP and putative iminoaspartate structures suggest a model for a condensed intermediate. The ensemble of structures suggests a two-state system, which may be exploited in early steps.

  6. Implementing a Complex Intervention to Support Personal Recovery: A Qualitative Study Nested within a Cluster Randomised Controlled Trial

    PubMed Central

    Leamy, Mary; Clarke, Eleanor; Le Boutillier, Clair; Bird, Victoria; Janosik, Monika; Sabas, Kai; Riley, Genevieve; Williams, Julie; Slade, Mike

    2014-01-01

    Objective To investigate staff and trainer perspectives on the barriers and facilitators to implementing a complex intervention to help staff support the recovery of service users with a primary diagnosis of psychosis in community mental health teams. Design Process evaluation nested within a cluster randomised controlled trial (RCT). Participants 28 interviews with mental health care staff, 3 interviews with trainers, 4 focus groups with intervention teams and 28 written trainer reports. Setting 14 community-based mental health teams in two UK sites (one urban, one semi-rural) who received the intervention. Results The factors influencing the implementation of the intervention can be organised under two over-arching themes: Organisational readiness for change and Training effectiveness. Organisational readiness for change comprised three sub-themes: NHS Trust readiness; Team readiness; and Practitioner readiness. Training effectiveness comprised three sub-themes: Engagement strategies; Delivery style and Modelling recovery principles. Conclusions Three findings can inform future implementation and evaluation of complex interventions. First, the underlying intervention model predicted that three areas would be important for changing practice: staff skill development; intention to implement; and actual implementation behaviour. This study highlighted the importance of targeting the transition from practitioners' intent to implement to actual implementation behaviour, using experiential learning and target setting. Second, practitioners make inferences about organisational commitment by observing the allocation of resources, Knowledge Performance Indicators and service evaluation outcome measures. These need to be aligned with recovery values, principles and practice. Finally, we recommend the use of organisational readiness tools as an inclusion criteria for selecting both organisations and teams in cluster RCTs. We believe this would maximise the likelihood of

  7. Implementing a complex intervention to support personal recovery: a qualitative study nested within a cluster randomised controlled trial.

    PubMed

    Leamy, Mary; Clarke, Eleanor; Le Boutillier, Clair; Bird, Victoria; Janosik, Monika; Sabas, Kai; Riley, Genevieve; Williams, Julie; Slade, Mike

    2014-01-01

    To investigate staff and trainer perspectives on the barriers and facilitators to implementing a complex intervention to help staff support the recovery of service users with a primary diagnosis of psychosis in community mental health teams. Process evaluation nested within a cluster randomised controlled trial (RCT). 28 interviews with mental health care staff, 3 interviews with trainers, 4 focus groups with intervention teams and 28 written trainer reports. 14 community-based mental health teams in two UK sites (one urban, one semi-rural) who received the intervention. The factors influencing the implementation of the intervention can be organised under two over-arching themes: Organisational readiness for change and Training effectiveness. Organisational readiness for change comprised three sub-themes: NHS Trust readiness; Team readiness; and Practitioner readiness. Training effectiveness comprised three sub-themes: Engagement strategies; Delivery style and Modelling recovery principles. Three findings can inform future implementation and evaluation of complex interventions. First, the underlying intervention model predicted that three areas would be important for changing practice: staff skill development; intention to implement; and actual implementation behaviour. This study highlighted the importance of targeting the transition from practitioners' intent to implement to actual implementation behaviour, using experiential learning and target setting. Second, practitioners make inferences about organisational commitment by observing the allocation of resources, Knowledge Performance Indicators and service evaluation outcome measures. These need to be aligned with recovery values, principles and practice. Finally, we recommend the use of organisational readiness tools as an inclusion criteria for selecting both organisations and teams in cluster RCTs. We believe this would maximise the likelihood of adequate implementation and hence reduce waste in research

  8. Two hybrid compounds constructed from Ni-tris(imidazolyl) complexes and Keggin clusters: Syntheses, structures and electrochemical properties

    NASA Astrophysics Data System (ADS)

    Zhang, Zhuanfang; Sun, Xiaojun; Ma, Huiyuan; Pang, Haijun; Li, Shaobin; Zhao, Chunyan

    2016-07-01

    By introducing different polyoxotungstates into the Ni-tib (tib = 1, 3, 5-tris (1-imidazolyl)benzene) system, two new polyoxometalate-based inorganic-organic hybrids with distinct architectures, [Ni(Htib)4][PW12O40]2 (1) and [Nitib]2(H2O)4](GeW12O40)·2H2O (2) have been synthesized under the same hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analyses and characterized by infrared spectra (IR), elemental analyses, powder X-ray diffraction (PXRD) patterns and thermogravimetic (TG) analyses. Structural analyses show that compound 1 is a dimer, in which two neighboring mono-connected [PW12O40]3- (PW12) clusters are linked together by a [Ni(Htib)4] complex cation. In contrast to compound 1, compound 2 presents a 2D grid layer formed by bi-connected [GeW12O40]4- (GeW12) clusters and [Ni2(H2O)4(tib)2] complex cations, and the adjacent layers are further linked together by the hydrogen bondings to form a highly opened 3D framework. The distinct structural features of two hybrids suggest that the charge of the Keggin anions should play a key role in the process of assembly. Additionally, the electrochemical properties of compounds 1 and 2 have been investigated, and the results indicated that 1 and 2 have good electrocatalytic activities towards reduction of nitrite and oxidation of ascorbic acid.

  9. Hydrothermal syntheses and crystal structures of two hybrid materials constructed from polyoxometalate clusters and metal dipyridine complexes

    NASA Astrophysics Data System (ADS)

    Li, Guangzhe; Salim, Chris; Hinode, Hirofumi

    2008-02-01

    Two organic-inorganic hybrid microporous compounds with formulas (4,4'-bipy) 2[Cu(4,4'-bipy) 2{Mo 5P 2O 21(OH) 2}]2(H 3O)·3(H 2O) 1 and (4,4'-bipy) 0.5[Cu 1.5(4,4'-bipy) 4{Mo 5P 2O 21(OH) 2}](H 3O)·2(H 2O) 2 have been hydrothermally prepared and characterized by single-crystal X-ray diffraction. Compound 1 crystallizes in a monoclinic system with space group C2/ c (no. 15), a = 17.667(3) Å, b = 13.669(3) Å, c = 25.067(5) Å, β = 107.479(3)°, V = 5774.2(18) Å 3, and Z = 4. Compound 2 crystallizes in a monoclinic system with space group P2 1/ n (no. 14), a = 13.9590(5) Å, b = 22.4850(7) Å, c = 19.1568(6) Å, β = 97.778(2)°, V = 5957.4(3) Å 3, and Z = 4. Compound 1 is three-dimensional (3D), constructed from {Mo 5P 2O 21(OH) 2} 4- cluster anions bridged through [Cu(4,4'-bipy) 2] n2 n+ layer sheets. In contrast, compound 2 is also three-dimensional, resulting from a complex connectivity pattern among {Mo 5P 2O 21(OH) 2} 4- cluster anions, [Cu(4,4'-bipy) 2] n2 n+ layer sheets and [Cu(4,4'-bipy) 4] n2 n+ complex subunits. Other characterizations by elemental analysis, IR, thermal analysis, and magnetic properties for the compounds are also given.

  10. A highly efficient nano-cluster artificial peroxidase and its direct electrochemistry on a nano complex modified glassy carbon electrode.

    PubMed

    Hong, Jun; Wang, Wei; Huang, Kun; Yang, Wei-Yun; Zhao, Ying-Xue; Xiao, Bao-Lin; Gao, Yun-Fei; Moosavi-Movahedi, Zainab; Ghourchian, Hedayatollah; Moosavi-Movahedi, Ali Akbar

    2012-01-01

    A nano-cluster with highly efficient peroxide activity was constructed based on nafion (NF) and cytochrome c (Cyt c). UV-Vis spectrometry and transmission electron microscopy (TEM) methods were utilized for characterization of the nano-structured enzyme or artificial peroxidase (AP). The nano-cluster was composed of a Chain-Ball structure, with an average ball size of about 40 nm. The Michaelis-Menten (K(m)) and catalytic rate (k(cat)) constants of the AP were determined to be 2.5 ± 0.4 µM and 0.069 ± 0.001 s(-1), respectively, in 50 mM PBS at pH 7.0. The catalytic efficiency of the AP was evaluated to be 0.028 ± 0.005 µM(-1) s(-1), which was 39 ± 5% as efficient as the native horseradish peroxidase (HRP). The AP was also immobilized on a functional multi-wall carbon nanotube (MWNCTs)-gold colloid nanoparticles (AuNPs) nano-complex modified glassy carbon (GC) electrode. The cyclic voltammetry of AP on the nano complex modified GC electrode showed a pair of well-defined redox peaks with a formal potential (E°') of -45 ± 2 mV (vs. Ag/AgCl) at a scan rate of 0.05 V/s. The heterogeneous electron transfer rate constant (k(s)) was evaluated to be 0.65 s(-1). The surface concentration of electroactive AP on GC electrode (Γ) was 7 × 10(-10) mol cm(-2). The apparent Michaelis-Menten constant (K(m)(app)) was 0.23 nM.

  11. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase

    DOE PAGES

    McAndrew, Ryan P.; Sathitsuksanoh, Noppadon; Mbughuni, Michael M.; ...

    2016-11-30

    Stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. Stilbenes are also derived from lignin during kraft pulping. Stilbene cleavage oxygenases (SCOs) cleave the central double bond of stilbenes, forming two phenolic aldehydes. Here in this paper, we report the structure of an SCO. The X-ray structure of NOV1 from Novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 Å), its product vanillin (1.75 Å), and without any bound ligand (1.61 Å). The enzyme is a seven-bladed β-propeller with an iron cofactor coordinated by four histidines. In all three structures,more » dioxygen is observed bound to the iron in a side-on fashion. These structures, along with EPR analysis, allow us to propose a mechanism in which a ferric-superoxide reactswith substrate activated by deprotonation of a phenol group at position 4 of the substrate, which allows movement of electron density toward the central double bond and thus facilitates reaction with the ferric superoxide electrophile. Correspondingly, NOV1 cleaves a wide range of other stilbene-like compounds with a 4'-OH group, offering potential in processing some solubilized fragments of lignin into monomer aromatic compounds.« less

  12. Purification of Escherichia coli RNA polymerase using a self-cleaving elastin-like polypeptide tag

    PubMed Central

    Fong, Baley A; Gillies, Alison R; Ghazi, Iraj; LeRoy, Gary; Lee, Kathleen C; Westblade, Lars F; Wood, David W

    2010-01-01

    A self-cleaving elastin-like polypeptide (ELP) tag was used to purify the multisubunit Escherichia coli RNA polymerase (RNAP) via a simple, nonchromatographic method. To accomplish this, the RNAP α subunit was tagged with a self-cleaving ELP-intein tag and coexpressed with the β, β′, and ω subunits. The assembled RNAP was purified with its associated subunits, and was active and acquired at reasonable yield and purity. To remove residual polynucleotides bound to the purified RNAP, two polymer precipitation methods were investigated: polyethyleneimine (PEI) and polyethylene (PEG) precipitation. The PEG procedure was shown to enhance purity and was compatible with downstream ELP-intein purification. Thus, this simple ELP-based method should be applicable for the nonchromatographic purification of other recombinant, in vivo-assembled multisubunit complexes in a single step. Further, the simplicity and low cost of this method will likely facilitate scale up for large-scale production of additional multimeric protein targets. Finally, this technique may have utility in isolating protein interaction partners that associate with a given target. PMID:20512976

  13. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase

    PubMed Central

    McAndrew, Ryan P.; Sathitsuksanoh, Noppadon; Mbughuni, Michael M.; Heins, Richard A.; Pereira, Jose H.; George, Anthe; Sale, Kenneth L.; Fox, Brian G.; Simmons, Blake A.; Adams, Paul D.

    2016-01-01

    Stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. Stilbenes are also derived from lignin during kraft pulping. Stilbene cleavage oxygenases (SCOs) cleave the central double bond of stilbenes, forming two phenolic aldehydes. Here, we report the structure of an SCO. The X-ray structure of NOV1 from Novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 Å), its product vanillin (1.75 Å), and without any bound ligand (1.61 Å). The enzyme is a seven-bladed β-propeller with an iron cofactor coordinated by four histidines. In all three structures, dioxygen is observed bound to the iron in a side-on fashion. These structures, along with EPR analysis, allow us to propose a mechanism in which a ferric-superoxide reacts with substrate activated by deprotonation of a phenol group at position 4 of the substrate, which allows movement of electron density toward the central double bond and thus facilitates reaction with the ferric superoxide electrophile. Correspondingly, NOV1 cleaves a wide range of other stilbene-like compounds with a 4′-OH group, offering potential in processing some solubilized fragments of lignin into monomer aromatic compounds. PMID:27911781

  14. Recombinant expression of antimicrobial peptides using a novel self-cleaving aggregation tag in Escherichia coli.

    PubMed

    Luan, Chao; Xie, Yong Gang; Pu, Yu Tian; Zhang, Hai Wen; Han, Fei Fei; Feng, Jie; Wang, Yi Zhen

    2014-03-01

    Antimicrobial peptides (AMPs) are part of the innate immune system of complex multicellular organisms. Despite the fact that AMPs show great potential as a novel class of antibiotics, the lack of a cost-effective means for their mass production limits both basic research and clinical use. In this work, we describe a novel expression system for the production of antimicrobial peptides in Escherichia coli by combining ΔI-CM mini-intein with the self-assembling amphipathic peptide 18A to drive the formation of active aggregates. Two AMPs, human β-defensin 2 and LL-37, were fused to the self-cleaving tag and expressed as active protein aggregates. The active aggregates were recovered by centrifugation and the intact antimicrobial peptides were released into solution by an intein-mediated cleavage reaction in cleaving buffer (phosphate-buffered saline supplemented with 40 mmol/L Bis-Tris, 2 mmol/L EDTA, pH 6.2). The peptides were further purified by cation-exchange chromatography. Peptides yields of 0.82 ± 0.24 and 0.59 ± 0.11 mg/L were achieved for human β-defensin 2 and LL-37, respectively, with demonstrated antimicrobial activity. Using our expression system, intact antimicrobial peptides were recovered by simple centrifugation from active protein aggregates after the intein-mediated cleavage reaction. Thus, we provide an economical and efficient way to produce intact antimicrobial peptides in E. coli.

  15. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase.

    PubMed

    McAndrew, Ryan P; Sathitsuksanoh, Noppadon; Mbughuni, Michael M; Heins, Richard A; Pereira, Jose H; George, Anthe; Sale, Kenneth L; Fox, Brian G; Simmons, Blake A; Adams, Paul D

    2016-12-13

    Stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. Stilbenes are also derived from lignin during kraft pulping. Stilbene cleavage oxygenases (SCOs) cleave the central double bond of stilbenes, forming two phenolic aldehydes. Here, we report the structure of an SCO. The X-ray structure of NOV1 from Novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 Å), its product vanillin (1.75 Å), and without any bound ligand (1.61 Å). The enzyme is a seven-bladed β-propeller with an iron cofactor coordinated by four histidines. In all three structures, dioxygen is observed bound to the iron in a side-on fashion. These structures, along with EPR analysis, allow us to propose a mechanism in which a ferric-superoxide reacts with substrate activated by deprotonation of a phenol group at position 4 of the substrate, which allows movement of electron density toward the central double bond and thus facilitates reaction with the ferric superoxide electrophile. Correspondingly, NOV1 cleaves a wide range of other stilbene-like compounds with a 4'-OH group, offering potential in processing some solubilized fragments of lignin into monomer aromatic compounds.

  16. Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme

    PubMed Central

    Kandadai, Srinivas A.; Li, Yingfu

    2005-01-01

    We previously demonstrated—through the isolation of RNA-cleaving deoxyribozymes by in vitro selection that are catalytically active in highly acidic solutions—that DNA, despite its chemical simplicity, could perform catalysis under challenging chemical conditions [Liu,Z., Mei,S.H., Brennan,J.D. and Li,Y. (2003) J. Am. Chem. Soc. 125, 7539–7545]. One remarkable DNA molecule therefrom is pH4DZ1, a self-cleaving deoxyribozyme that exhibits a kobs of ∼1 min−1 at pH 3.8. In this study, we carried out a series of experiments to examine the sequence and catalytic properties of this acidic deoxyribozyme. Extensive nucleotide truncation experiments indicated that pH4DZ1 was a considerably large deoxyribozyme, requiring ∼80 out of the original 123 nt for the optimal catalytic activity. A reselection experiment identified ten absolutely conserved nucleotides that are distributed in three catalytically crucial sequence elements. In addition, a trans deoxyribozyme was successfully designed. Comparison of the observed rate constant of pH4DZ1 with experimentally determined rate constant for the uncatalyzed reaction revealed that pH4DZ1 achieved a rate enhancement of ∼106-fold. This study provides valuable information about this low-pH-functional deoxyribozyme and paves way for further structural and mechanistic characterization of this unique catalytic DNA. PMID:16391005

  17. Cleaving yeast and Escherichia coli genomes at a single site

    SciTech Connect

    Koob, M.; Szybalski, W. )

    1990-10-12

    The 15-megabase pair Saccharomyces cerevisiae and the 4.7-megabase pair Escherichia coli genomes were completely cleaved at a single predetermined site by means of the Achilles' heel cleavage (AC) procedure. The symmetric lac operator (lacO{sub s}) was introduced into the circular Escherichia coli genome and into one of the 16 yeast chromosomes. Intact chromosomes from the resulting strains were prepared in agarose microbeads and methylated with Hha I (5{prime}-GCGC) methyltransferase (M{center dot}Hha I) in the presence of lac repressor (LacI). All Hae II sites ({prime}-{sub G}{sup A}GCGC{sub C}{sup T}) with the exception of the one in lacO{sub s}, which was protected by LacI, were modified and thus no longer recognized by Hae II. After inactivation of M{center dot}Hha I and LacI, Hae II was used to completely cleave the chromosomes specifically at the inserted lacO{sub s}. These experiments demonstrate the feasibility of using the AC approach to efficiently extend the specificity of naturally occurring restriction enzymes and create new tools for the mapping and precise molecular dissection of multimegabase genomes.

  18. Graphene Visualizes the Ion Distribution on Air-Cleaved Mica

    PubMed Central

    Bampoulis, Pantelis; Sotthewes, Kai; Siekman, Martin H.; Zandvliet, Harold J. W.; Poelsema, Bene

    2017-01-01

    The distribution of potassium (K+) ions on air-cleaved mica is important in many interfacial phenomena such as crystal growth, self-assembly and charge transfer on mica. However, due to experimental limitations to nondestructively probe single ions and ionic domains, their exact lateral organization is yet unknown. We show, by the use of graphene as an ultra-thin protective coating and scanning probe microscopies, that single potassium ions form ordered structures that are covered by an ice layer. The K+ ions prefer to minimize the number of nearest neighbour K+ ions by forming row-like structures as well as small domains. This trend is a result of repulsive ionic forces between adjacent ions, weakened due to screening by the surrounding water molecules. Using high resolution conductive atomic force microscopy maps, the local conductance of the graphene is measured, revealing a direct correlation between the K+ distribution and the structure of the ice layer. Our results shed light on the local distribution of ions on the air-cleaved mica, solving a long-standing enigma. They also provide a detailed understanding of charge transfer from the ionic domains towards graphene. PMID:28262710

  19. Graphene Visualizes the Ion Distribution on Air-Cleaved Mica.

    PubMed

    Bampoulis, Pantelis; Sotthewes, Kai; Siekman, Martin H; Zandvliet, Harold J W; Poelsema, Bene

    2017-03-06

    The distribution of potassium (K(+)) ions on air-cleaved mica is important in many interfacial phenomena such as crystal growth, self-assembly and charge transfer on mica. However, due to experimental limitations to nondestructively probe single ions and ionic domains, their exact lateral organization is yet unknown. We show, by the use of graphene as an ultra-thin protective coating and scanning probe microscopies, that single potassium ions form ordered structures that are covered by an ice layer. The K(+) ions prefer to minimize the number of nearest neighbour K(+) ions by forming row-like structures as well as small domains. This trend is a result of repulsive ionic forces between adjacent ions, weakened due to screening by the surrounding water molecules. Using high resolution conductive atomic force microscopy maps, the local conductance of the graphene is measured, revealing a direct correlation between the K(+) distribution and the structure of the ice layer. Our results shed light on the local distribution of ions on the air-cleaved mica, solving a long-standing enigma. They also provide a detailed understanding of charge transfer from the ionic domains towards graphene.

  20. The nature of the air-cleaved mica surface

    NASA Astrophysics Data System (ADS)

    Christenson, Hugo K.; Thomson, Neil H.

    2016-06-01

    The accepted image of muscovite mica is that of an inert and atomically smooth surface, easily prepared by cleavage in an ambient atmosphere. Consequently, mica is extensively used a model substrate in many fundamental studies of surface phenomena and as a substrate for AFM imaging of biomolecules. In this review we present evidence from the literature that the above picture is not quite correct. The mica used in experimental work is almost invariably cleaved in laboratory air, where a reaction between the mica surface, atmospheric CO2 and water occurs immediately after cleavage. The evidence suggests very strongly that as a result the mica surface becomes covered by up to one formula unit of K2CO3 per nm2, which is mobile under humid conditions, and crystallises under drier conditions. The properties of mica in air or water vapour cannot be fully understood without reference to the surface K2CO3, and many studies of the structure of adsorbed water on mica surfaces may need to be revisited. With this new insight, however, the air-cleaved mica should provide exciting opportunities to study phenomena such as two-dimensional ion diffusion, electrolyte effects on surface conductivity, and two-dimensional crystal nucleation.

  1. Graphene Visualizes the Ion Distribution on Air-Cleaved Mica

    NASA Astrophysics Data System (ADS)

    Bampoulis, Pantelis; Sotthewes, Kai; Siekman, Martin H.; Zandvliet, Harold J. W.; Poelsema, Bene

    2017-03-01

    The distribution of potassium (K+) ions on air-cleaved mica is important in many interfacial phenomena such as crystal growth, self-assembly and charge transfer on mica. However, due to experimental limitations to nondestructively probe single ions and ionic domains, their exact lateral organization is yet unknown. We show, by the use of graphene as an ultra-thin protective coating and scanning probe microscopies, that single potassium ions form ordered structures that are covered by an ice layer. The K+ ions prefer to minimize the number of nearest neighbour K+ ions by forming row-like structures as well as small domains. This trend is a result of repulsive ionic forces between adjacent ions, weakened due to screening by the surrounding water molecules. Using high resolution conductive atomic force microscopy maps, the local conductance of the graphene is measured, revealing a direct correlation between the K+ distribution and the structure of the ice layer. Our results shed light on the local distribution of ions on the air-cleaved mica, solving a long-standing enigma. They also provide a detailed understanding of charge transfer from the ionic domains towards graphene.

  2. Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa).

    PubMed

    Christopoulou, Marilena; McHale, Leah K; Kozik, Alex; Reyes-Chin Wo, Sebastian; Wroblewski, Tadeusz; Michelmore, Richard W

    2015-07-01

    Of the over 50 phenotypic resistance genes mapped in lettuce, 25 colocalize to three major resistance clusters (MRC) on chromosomes 1, 2, and 4. Similarly, the majority of candidate resistance genes encoding nucleotide binding-leucine rich repeat (NLR) proteins genetically colocalize with phenotypic resistance loci. MRC1 and MRC4 span over 66 and 63 Mb containing 84 and 21 NLR-encoding genes, respectively, as well as 765 and 627 genes that are not related to NLR genes. Forward and reverse genetic approaches were applied to dissect MRC1 and MRC4. Transgenic lines exhibiting silencing were selected using silencing of β-glucuronidase as a reporter. Silencing of two of five NLR-encoding gene families resulted in abrogation of nine of 14 tested resistance phenotypes mapping to these two regions. At MRC1, members of the coiled coil-NLR-encoding RGC1 gene family were implicated in host and nonhost resistance through requirement for Dm5/8- and Dm45-mediated resistance to downy mildew caused by Bremia lactucae as well as the hypersensitive response to effectors AvrB, AvrRpm1, and AvrRpt2 of the nonpathogen Pseudomonas syringae. At MRC4, RGC12 family members, which encode toll interleukin receptor-NLR proteins, were implicated in Dm4-, Dm7-, Dm11-, and Dm44-mediated resistance to B. lactucae. Lesions were identified in the sequence of a candidate gene within dm7 loss-of-resistance mutant lines, confirming that RGC12G confers Dm7.

  3. The connection between prestellar cores and filaments in cluster-forming clumps of the Aquila Rift complex

    NASA Astrophysics Data System (ADS)

    Könyves, Vera; André, Philippe; Maury, Anaëlle

    2015-08-01

    One of the main goals of the Herschel Gould Belt survey (André et al. 2010) is to elucidate the physicalmechanisms responsible for the formation and evolution of prestellar cores in molecular clouds. In theAquila cloud complex imaged with Herschel/SPIRE-PACS between 70-500 μm, we have recently identifieda complete sample of 651 starless cores, 446 of them are gravitationally-bound prestellar cores, likelyforming stars in the future. We also detected 58 protostellar cores (Könyves et al. 2010 and 2015, subm.- see http://gouldbelt-herschel.cea.fr/archives). This region is dominated by two (proto)clusters which arecurrently active sites of clustered star formation (SF): the filamentary Serpens South cloud and the W40HII region. The latter is powered by massive young stars, and a 2nd-generation SF can be witnessed inthe surroundings (Maury et al. 2011).Our Herschel observations also provide an unprecedented census of filaments in Aquila and suggest aclose connection between them and the formation process of prestellar cores, where both structures arehighly concentrated around the protoclusters. About 10-20% of the gas mass is in the form of filamentsbelow Av~7, while ~50-75% of the dense gas mass above Av~7-10 is in filamentary structures.Furthermore, ~90% of our prestellar cores are located above a background column density correspondingto Av~7, and ~75% of them lie within the densest filamentary structures with supercritical masses per unitlength >16 M⊙/pc. Indeed, a strong correlation is found between the spatial distribution of prestellar coresand the densest filaments.Comparing the statistics of cores and filaments with the number of young stellar objects found by Spitzerin the same complex, we also infer a typical timescale ~1 Myr for the formation and evolution of bothprestellar cores and filaments.In summary, our Herschel findings in Aquila support a filamentary paradigm for the early stages of SF,where the cores result from the gravitational fragmentation

  4. Lessons learnt during a complex, multicentre cluster randomised controlled trial: the ProAct65+ trial

    PubMed Central

    2013-01-01

    Background Failure to recruit to target or schedule is common in randomized controlled trials (RCTs). Innovative interventions are not always fully developed before being tested, and maintenance of fidelity to the intervention during trials can be problematic. Missing data can compromise analyses, and inaccurate capture of risks to participants can influence reporting of intervention harms and benefits. In this paper we describe how challenges of recruitment and retention of participants, standardisation and quality control of interventions and capture of adverse events were overcome in the ProAct65+ cluster RCT. This trial compared class-based and home-based exercise with usual care in people aged 65 years and over, recruited through general practice. The home-based exercise participants were supported by Peer Mentors. Results (1) Organisational factors, including room availability in general practices, slowed participant recruitment so the recruitment period was extended and the number invited to participate increased. (2) Telephone pre-screening was introduced to exclude potential participants who were already very active and those who were frequent fallers. (3) Recruitment of volunteer peer mentors was difficult and time consuming and their acceptable case load less than expected. Lowering the age limit for peer mentors and reducing their contact schedule with participants did not improve recruitment. (4) Fidelity to the group intervention was optimised by introducing quality assurance observation of classes by experienced exercise instructors. (5) Diaries were used to capture data on falls, service use and other exercise-related costs, but completion was variable so their frequency was reduced. (6) Classification of adverse events differed between research sites so all events were assessed by both sites and discrepancies discussed. Conclusions Recruitment rates for trials in general practice may be limited by organisational factors and longer recruitment

  5. Synaptonemal complex extension from clustered telomeres mediates full-length chromosome pairing in Schmidtea mediterranea

    PubMed Central

    Xiang, Youbin; Miller, Danny E.; Ross, Eric J.; Sánchez Alvarado, Alejandro; Hawley, R. Scott

    2014-01-01

    In the 1920s, József Gelei proposed that chromosome pairing in flatworms resulted from the formation of a telomere bouquet followed by the extension of synapsis from telomeres at the base of the bouquet, thus facilitating homolog pairing in a processive manner. A modern interpretation of Gelei’s model postulates that the synaptonemal complex (SC) is nucleated close to the telomeres and then extends progressively along the full length of chromosome arms. We used the easily visible meiotic chromosomes, a well-characterized genome, and RNAi in the sexual biotype of the planarian Schmidtea mediterranea to test that hypothesis. By identifying and characterizing S. mediterranea homologs of genes encoding synaptonemal complex protein 1 (SYCP1), the topoisomerase-like protein SPO11, and RAD51, a key player in homologous recombination, we confirmed that SC formation begins near the telomeres and progresses along chromosome arms during zygotene. Although distal regions pair at the time of bouquet formation, pairing of a unique interstitial locus is not observed until the formation of full-length SC at pachytene. Moreover, neither full extension of the SC nor homologous pairing is dependent on the formation of double-strand breaks. These findings validate Gelei’s speculation that full-length pairing of homologous chromosomes is mediated by the extension of the SC formed near the telomeres. S. mediterranea thus becomes the first organism described (to our knowledge) that forms a canonical telomere bouquet but does not require double-strand breaks for synapsis between homologous chromosomes. However, the initiation of SC formation at the base of the telomere bouquet, which then is followed by full-length homologous pairing in planarian spermatocytes, is not observed in other species and may not be conserved. PMID:25404302

  6. The formation of complex acetylcholine receptor clusters requires MuSK kinase activity and structural information from the MuSK extracellular domain

    PubMed Central

    Mazhar, Sania; Herbst, Ruth

    2012-01-01

    Efficient synaptic transmission at the neuromuscular junction (NMJ) requires the topological maturation of the postsynaptic apparatus from an oval acetylcholine receptor (AChR)-rich plaque into a complex pretzel-shaped array of branches. However, compared to NMJ formation very little is known about the mechanisms that regulate NMJ maturation. Recently the process of in vivo transformation from plaque into pretzel has been reproduced in vitro by culturing myotubes aneurally on laminin-coated substrate. It was proposed that the formation of complex AChR clusters is regulated by a MuSK-dependent muscle intrinsic program. To elucidate the structure–function role of MuSK in the aneural maturation of AChR pretzels, we used muscle cell lines expressing MuSK mutant and chimeric proteins. Here we report, that besides its role during agrin-induced AChR clustering, MuSK kinase activity is also necessary for substrate-dependent cluster formation. Constitutive-active MuSK induces larger AChR clusters, a faster cluster maturation on laminin and increases the anchorage of AChRs to the cytoskeleton compared to MuSK wild-type. In addition, we find that the juxtamembrane region of MuSK, which has previously been shown to regulate agrin-induced AChR clustering, is unable to induce complex AChR clusters on laminin substrate. Most interestingly, MuSK kinase activity is not sufficient for laminin-dependent AChR cluster formation since the MuSK ectodomain is also required suggesting a so far undiscovered instructive role for the extracellular domain of MuSK. PMID:22210232

  7. The formation of complex acetylcholine receptor clusters requires MuSK kinase activity and structural information from the MuSK extracellular domain.

    PubMed

    Mazhar, Sania; Herbst, Ruth

    2012-04-01

    Efficient synaptic transmission at the neuromuscular junction (NMJ) requires the topological maturation of the postsynaptic apparatus from an oval acetylcholine receptor (AChR)-rich plaque into a complex pretzel-shaped array of branches. However, compared to NMJ formation very little is known about the mechanisms that regulate NMJ maturation. Recently the process of in vivo transformation from plaque into pretzel has been reproduced in vitro by culturing myotubes aneurally on laminin-coated substrate. It was proposed that the formation of complex AChR clusters is regulated by a MuSK-dependent muscle intrinsic program. To elucidate the structure-function role of MuSK in the aneural maturation of AChR pretzels, we used muscle cell lines expressing MuSK mutant and chimeric proteins. Here we report, that besides its role during agrin-induced AChR clustering, MuSK kinase activity is also necessary for substrate-dependent cluster formation. Constitutive-active MuSK induces larger AChR clusters, a faster cluster maturation on laminin and increases the anchorage of AChRs to the cytoskeleton compared to MuSK wild-type. In addition, we find that the juxtamembrane region of MuSK, which has previously been shown to regulate agrin-induced AChR clustering, is unable to induce complex AChR clusters on laminin substrate. Most interestingly, MuSK kinase activity is not sufficient for laminin-dependent AChR cluster formation since the MuSK ectodomain is also required suggesting a so far undiscovered instructive role for the extracellular domain of MuSK. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. A CEP215–HSET complex links centrosomes with spindle poles and drives centrosome clustering in cancer

    PubMed Central

    Chavali, Pavithra L.; Chandrasekaran, Gayathri; Barr, Alexis R.; Tátrai, Péter; Taylor, Chris; Papachristou, Evaggelia K.; Woods, C. Geoffrey; Chavali, Sreenivas; Gergely, Fanni

    2016-01-01

    Numerical centrosome aberrations underlie certain developmental abnormalities and may promote cancer. A cell maintains normal centrosome numbers by coupling centrosome duplication with segregation, which is achieved through sustained association of each centrosome with a mitotic spindle pole. Although the microcephaly- and primordial dwarfism-linked centrosomal protein CEP215 has been implicated in this process, the molecular mechanism responsible remains unclear. Here, using proteomic profiling, we identify the minus end-directed microtubule motor protein HSET as a direct binding partner of CEP215. Targeted deletion of the HSET-binding domain of CEP215 in vertebrate cells causes centrosome detachment and results in HSET depletion at centrosomes, a phenotype also observed in CEP215-deficient patient-derived cells. Moreover, in cancer cells with centrosome amplification, the CEP215–HSET complex promotes the clustering of extra centrosomes into pseudo-bipolar spindles, thereby ensuring viable cell division. Therefore, stabilization of the centrosome–spindle pole interface by the CEP215–HSET complex could promote survival of cancer cells containing supernumerary centrosomes. PMID:26987684

  9. Small-volume potentiometric titrations: EPR investigations of Fe-S cluster N2 in mitochondrial complex I.

    PubMed

    Wright, John J; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

    2016-09-01

    EPR-based potentiometric titrations are a well-established method for determining the reduction potentials of cofactors in large and complex proteins with at least one EPR-active state. However, such titrations require large amounts of protein. Here, we report a new method that requires an order of magnitude less protein than previously described methods, and that provides EPR samples suitable for measurements at both X- and Q-band microwave frequencies. We demonstrate our method by determining the reduction potential of the terminal [4Fe-4S] cluster (N2) in the intramolecular electron-transfer relay in mammalian respiratory complex I. The value determined by our method, Em7=-158mV, is precise, reproducible, and consistent with previously reported values. Our small-volume potentiometric titration method will facilitate detailed investigations of EPR-active centres in non-abundant and refractory proteins that can only be prepared in small quantities. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Synthesis and Characterization of Bioinspired [Mo2 Fe2 ]-Hydride Cluster Complexes and Their Application in the Catalytic Silylation of N2.

    PubMed

    Ohki, Yasuhiro; Araki, Yuna; Tada, Mizuki; Sakai, Yoichi

    2017-09-21

    The hydride-supported [Mo2 Fe2 ] cluster complex {Cp*Mo(PMe3 )}2 {FeN(SiMe3 )2 }2 (H)8 (2 a; Cp*=η(5) -C5 Me5 ) and its [Mo2 Mn2 ] congener 2 b were synthesized from the reactions of Cp*Mo(PMe3 )(H)5 (1) with M{N(SiMe3 )2 }2 (M=Fe, Mn). The amide-to-thiolate ligand-exchange reactions of complex 2 a with bulky thiol reagents (HSR; R=2,4,6-iPr3 C6 H2 (Tip), 2,6-(SiMe3 )2 C6 H3 (Btp)) furnished the corresponding hydride-supported [Mo2 Fe2 ](SR)2 cluster complexes. The [Mo2 Fe2 ] clusters served as catalyst precursors for the reductive silylation of N2 and yielded ≈65-69 equivalents of N(SiMe3 )3 relative to the [Mo2 Fe2 ] clusters. Treatment of complexes 2 a and b with an excess of CNtBu resulted in the formation of dinuclear Mo-Fe and Mo-Mn complexes, which indicated that the [Mo2 M2 ] cores (M=Fe, Mn) split into two dinuclear species upon accommodation of substrates. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Clustering dynamics of the metal-benzene sandwich complex: the role of microscopic structure of the solute in the bis(eta6-benzene)chromium .Arn Clusters (n = 1-15).

    PubMed

    Choi, Kyo-Won; Choi, Sunyoung; Ahn, Doo-Sik; Han, Songhee; Kang, Tae Yeon; Baek, Sun Jong; Kim, Sang Kyu

    2008-08-07

    Ar clustering dynamics around the metal-benzene sandwich complex, bis(eta (6)-benzene)chromium: Cr(Bz) 2, is found to occur in two distinct regimes. The shift of the ionization potential (IP) upon the addition of Ar is measured to be 151 cm (-1), and it is constant until the number of Ar solvents ( n) becomes 6. The IP shift per Ar is found to be suddenly decreased to 82 cm (-1) for the clusters of n = 7-12. The cluster distribution indicates that the n = 6 cluster is most populated in the molecular beam. These experimental findings with the aid of ab initio calculation indicate that the first six Ar solvent molecules are attached to top and bottom of Cr(Bz) 2 to give the robust structure for the Cr(Bz) 2-Ar 6 cluster whereas the next six Ar molecules are gathered on the side of the solute core to give the highly symmetric structure of the Cr(Bz) 2-Ar 12 cluster.

  12. Complex magnetic structure of clusters and chains of Ni and Fe on Pt(111)

    PubMed Central

    Bezerra-Neto, Manoel M.; Ribeiro, Marcelo S.; Sanyal, Biplab; Bergman, Anders; Muniz, Roberto B.; Eriksson, Olle; Klautau, Angela B.

    2013-01-01

    We present an approach to control the magnetic structure of adatoms adsorbed on a substrate having a high magnetic susceptibility. Using finite Ni-Pt and Fe-Pt nanowires and nanostructures on Pt(111) surfaces, our ab initio results show that it is possible to tune the exchange interaction and magnetic configuration of magnetic adatoms (Fe or Ni) by introducing different numbers of Pt atoms to link them, or by including edge effects. The exchange interaction between Ni (or Fe) adatoms on Pt(111) can be considerably increased by introducing Pt chains to link them. The magnetic ordering can be regulated allowing for ferromagnetic or antiferromagnetic configurations. Noncollinear magnetic alignments can also be stabilized by changing the number of Pt-mediated atoms. An Fe-Pt triangularly-shaped nanostructure adsorbed on Pt(111) shows the most complex magnetic structure of the systems considered here: a spin-spiral type of magnetic order that changes its propagation direction at the triangle vertices. PMID:24165828

  13. Metal-sulfide species in oxic waters: Complexes, clusters, or colloids?

    NASA Astrophysics Data System (ADS)

    Wang, F.; Sukola, K.; Tessier, A.

    2003-12-01

    A weight-of-evidence approach is employed to characterize metal-sulfide species that have recently been suggested to be present in oxic waters. Sulfide in synthetic Cd-, Zn-, Pb-, Cu-sulfide solutions persists in oxic waters for a prolonged period of time (2 to more than 10 weeks) whereas it is oxidized rapidly in Fe-, Mn- and Ni-sulfide solutions. Direct mass spectrometric (MS) analysis and transmission electron microscopic (TEM) analysis revealed that the metal-sulfide species resistant to oxidation in oxic waters are not soluble molecular nanoclusters as suggested previously; instead, they are a mixture of truly dissolved metal-sulfide complexes and dynamic metal-sulfide colloids. The morphology and size of the colloids change significantly with time. Nanomolar to sub-micromolar levels of acid-volatile sulfide (AVS) and chromous-volatile sulfide (CVS) were measured in oxic surface waters of 6 lakes located on the Canadian Shield and nearby areas. Thermodynamic calculations indicated that at the AVS levels measured, the dissolved metal-sulfide species play a minor role in the speciation of Class B metal ions such as Pb, Cd, Cu, Hg.

  14. STS-30 MS Cleave monitors fluids experiment apparatus (FEA) equipment

    NASA Image and Video Library

    1989-05-08

    STS030-02-018 (4-8 May 1989) --- A 35mm overall scene of the operations devoted to the fluids experiment apparatus (FEA) aboard Atlantis for NASA’s STS-30 mission. Astronaut Mary L. Cleave, mission specialist, is seen with the computer which is instrumental in the carrying out of a variety of materials science experiments. Rockwell International is engaged in a joint endeavor agreement with NASA’s Office of Commercial Programs in the field of floating zone crystal growth and purification research. The March 1987 agreement provides for microgravity experiments to be performed in the company’s Microgravity Laboratory, the FEA. An 8 mm camcorder which documented details inside the apparatus is visible at bottom of the frame.

  15. Chemistry and biology of self-cleaving ribozymes

    PubMed Central

    Jimenez, Randi M.; Polanco, Julio A.; Lupták, Andrej

    2015-01-01

    Self-cleaving ribozymes were discovered thirty years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be employed as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered. PMID:26481500

  16. Evolution of a Complex Disease Resistance Gene Cluster in Diploid Phaseolus and Tetraploid Glycine1[W][OA

    PubMed Central

    Ashfield, Tom; Egan, Ashley N.; Pfeil, Bernard E.; Chen, Nicolas W.G.; Podicheti, Ram; Ratnaparkhe, Milind B.; Ameline-Torregrosa, Carine; Denny, Roxanne; Cannon, Steven; Doyle, Jeff J.; Geffroy, Valérie; Roe, Bruce A.; Saghai Maroof, M.A.; Young, Nevin D.; Innes, Roger W.

    2012-01-01

    We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay. PMID:22457424

  17. piRNA clusters and open chromatin structure

    PubMed Central

    2014-01-01

    Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evolved genetic and epigenetic mechanisms that keep TEs silenced. One such mechanism involves the Piwi-piRNA complex, which represses TEs in animal gonads either by cleaving TE transcripts in the cytoplasm or by directing specific chromatin modifications at TE loci in the nucleus. Most Piwi-interacting RNAs (piRNAs) are derived from genomic piRNA clusters. There has been remarkable progress in our understanding of the mechanisms underlying piRNA biogenesis. However, little is known about how a specific locus in the genome is converted into a piRNA-producing site. In this review, we will discuss a possible link between chromatin boundaries and piRNA cluster formation. PMID:25126116

  18. The Resistance of Electron Transport Chain Fe-S Clusters to Oxidative Damage during the Reaction of Peroxynitrite with Mitochondrial Complex II and Rat Heart Pericardium

    PubMed Central

    Pearce, Linda L.; Martinez-Bosch, Sandra; Manzano, Elisenda Lopez; Winnica, Daniel E.; Epperly, Michael W.; Peterson, Jim

    2009-01-01

    The effects of peroxynitrite and nitric oxide on the iron-sulfur clusters in complex II (succinate dehydrogenase) isolated from bovine heart have been studied primarily by EPR spectroscopy and no measurable damage to the constitutive 2Fe-2S, 3Fe-4S, or 4Fe-4S clusters was observed. The enzyme can be repeatedly oxidized with a slight excess of peroxynitrite and then quantitatively re-reduced with succinate. When added in large excess, peroxynitrite reacted with at least one tyrosine in each subunit of complex II to form 3-nitrotyrosines, but activity was barely compromised. Examination of rat-heart pericardium subjected to conditions leading to peroxynitrite production showed a small inhibition of complex II (16%) and a greater inhibition of aconitase (77%). In addition, experiments performed with excesses of sodium citrate and sodium succinate on rat-heart pericardium indicated that the “g ~2.01” EPR signal observed immediately following the beginning of conditions modeling oxidative/nitrosative stress, could be a consequence of both reversible oxidation of the constitutive 3Fe-4S cluster in complex II and degradation of the 4Fe-4S cluster in aconitase. However, the net signal envelope, which becomes apparent in less than one minute following the start of oxidative/nitrosative conditions, is dominated by the component arising from complex II. Taking into account the findings of a previous study concerning complexes I and III [L.L. Pearce, A.J. Kanai, M.W. Epperly, J. Peterson (2005) Nitric Oxide 13, 254-63] it is now apparent that, with the exception of the cofactor in aconitase, mammalian (mitochondrial) iron-sulfur clusters are surprisingly resistant to degradation stemming from oxidative/nitrosative stress. PMID:19118636

  19. Three tetranuclear copper(II) cluster-based complexes constructed from 4-amino-1,2,4-triazole and different aromatic carboxylates: Assembly, structures, electrochemical and magnetic properties

    SciTech Connect

    Wang, Xiu-Li; Zhao, Wei; Zhang, Ju-Wen; Lu, Qi-Lin

    2013-02-15

    Three new tetranuclear copper(II) cluster-based complexes constructed from 4-amino-1,2,4-triazole (atrz) and three types of aromatic carboxylates, [Cu{sub 4}({mu}{sub 3}-OH){sub 2}(atrz){sub 2}(DNBA){sub 6}] (1), [Cu{sub 4}({mu}{sub 3}-OH){sub 2}(atrz){sub 2}(1,3-BDC){sub 3}]{center_dot}2H{sub 2}O (2) and [Cu{sub 4}({mu}{sub 3}-OH){sub 2}(atrz){sub 2}(SIP){sub 2}]{center_dot}4H{sub 2}O (3) (HDNBA=3,5-dinitrobenzoic acid, 1,3-H{sub 2}BDC=1,3-benzenedicarboxylic acid and NaH{sub 2}SIP=sodium 5-sulfoisophthalate), have been hydrothermally synthesized and structurally characterized. Complex 1 displays a single-molecular Cu{sup II}{sub 4} cluster structure, which is further connected by the intermolecular hydrogen-bonding interactions to form a 2D supramolecular layer. In 2, there also exist tetranuclear Cu{sup II}{sub 4} clusters, which are linked by the 1,3-BDC anions to give a 3D NaCl-type framework. In 3, the Cu{sup II}{sub 4} clusters are connected by the carboxyl and sulfo groups of SIP anions to generate 3D (4,8)-connected framework with a (4{sup 10}{center_dot}6{sup 14}{center_dot}8{sup 4})(4{sup 5}{center_dot}6){sub 2} topology. The atrz ligand conduces to the construction of tetranuclear copper(II) clusters and the carboxylates with different non-carboxyl substituent show important effects on the final structures of the title complexes. The electrochemical and magnetic properties of 1-3 have been investigated. - Graphical abstract: Three tetranuclear copper(II) cluster-based complexes based on different carboxylates have been synthesized under hydrothermal conditions. The carboxylate anions play a key role in the formation of three different structures. Highlights: Black-Right-Pointing-Pointer Three new tetranuclear copper(II) cluster-based complexes have been obtained. Black-Right-Pointing-Pointer The atrz conduces to the construction of tetranuclear copper(II) clusters. Black-Right-Pointing-Pointer Carboxylates show important effect on the structures of

  20. Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection.

    PubMed

    Beattie, T L; Collins, R A

    1997-04-11

    Varkud Satellite (VS) RNA contains a small self-cleaving RNA motif that is distinct in its sequence and secondary structure from the hammerhead, hairpin, and hepatitis delta virus ribozymes, which are found in other natural RNAs. We have used a base specific chemical damage selection (modification interference) assay to identify functionally important nucleotides and structural elements in VS RNA. Many modified bases interfered with self-cleavage and most of these clustered at helix junctions, certain internal loops, and in a long-range pseudoknot; these correspond to previously determined sites of magnesium-dependent protection from chemical modification. The clustering suggests that these bases are important not only for a large number of individual interactions, but because they form a smaller number of structural elements that are important for activity. Modification of bases in other single-stranded regions, which did not exhibit magnesium-dependent protection, generally did not interfere with activity, suggesting that some of these regions might be dispensable for function. Surprisingly, we found a separate cluster of bases whose modification significantly enhanced cleavage. These bases appear to form a structural element that naturally attenuates the self-cleavage reaction. In natural VS RNA this attenuator structure may affect the cleavage/ligation equilibrium by inhibiting circle re-opening, thereby helping to maintain the RNA in a circular form, which is the predominant form of VS RNA in vivo. Taken together, the results of the damage selection experiments localize the catalytic core of VS RNA to a small subset of the previously determined minimal contiguous sequence.

  1. Packing of Russian doll clusters to form a nanometer-scale CsCl-type compound in a Cr–Zn–Sn complex metallic alloy

    DOE PAGES

    Xie, Weiwei; Cava, Robert J.; Miller, Gordon J.

    2017-07-03

    A new cubic complex metallic alloy phase, Cr22Zn72Sn24, with a lattice parameter near 2.5 nm was discovered in crystals grown using a Zn/Sn flux. The structure consists of Russian doll clusters or a 3-d network of Cr-centered icosahedra (shown) with bcc-metal fragments in void spaces.

  2. Synthesis, structural and magnetic characterisation of iron(II/III), cobalt(II) and copper(II) cluster complexes of the polytopic ligand: N-(2-pyridyl)-3-carboxypropanamide.

    PubMed

    Russell, Mark E; Hawes, Chris S; Ferguson, Alan; Polson, Matthew I J; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S; Kruger, Paul E

    2013-10-07

    Herein we describe the synthesis, structural and magnetic characterisation of three transition metal cluster complexes that feature the polytopic ligand N-(2-pyridyl)-3-carboxypropanamide (H2L): [Fe3(III)Fe2(II)(HL)6(O)(H2O)3][ClO4]5·3MeCN·4H2O, 1, [Co8(HL)8(O)(OH)4(MeOH)3(H2O)]-[ClO4]3·5MeOH·2H2O, 2, and [Cu6(L(ox))4(MeOH)(H2O)3]·MeOH, 3. Complex 1 is a mixed valence penta-nuclear iron cluster containing the archetypal {Fe3(III)O} triangular basic carboxylate cluster at its core, with two Fe(II) ions above and below the core coordinated to three bidentate pyridyl-amide groups. The structure of the octanuclear Co(II) complex, 2, is based upon a central Co4 square with the remaining four Co(II) centres at the 'wing-tips' of the complex. The cluster core is replete with bridging oxide, hydroxide and carboxylate groups. Cluster 3 contains an oxidised derivative of the ligand, L(ox), generated in situ through hydroxylation of an α-carbon atom. This hexanuclear cluster has a 'barrel-like' core and contains Cu(II) ions in both square planar and square-based pyramidal geometries. Bridging between Cu(II) centres is furnished by alkoxide and carboxylate groups. Magnetic studies on 1-3 reveals dominant antiferro-magnetic interactions for 1 and 2, leading to small non-zero spin ground states, while 3 shows ferro-magnetic exchange between the Cu(II) centres to give an S = 3 spin ground state.

  3. Fabrication of submicron devices on the (011) cleave surface of a cleaved-edge-overgrowth GaAs/AlGaAs crystal

    NASA Astrophysics Data System (ADS)

    Chang, A. M.; Zhang, Hao; Pfeiffer, L. N.; West, K. W.

    2012-03-01

    We describe the fabrication of submicron devices on the (011) cleave surface of a GaAs heterostructure crystal, in which this surface is extremely narrow. Special purpose devices are produced, which take advantage of the unique characteristics of cleaved-edge-overgrowth. The successful fabrication relies on understanding the surface tension of the electron beam polymethyl methacrylate resist, the workable degree of variation in resist thickness, and on gluing the crystal onto a backing substrate to increase structural strength. We demonstrate functional gate-controlled quantum point contact constrictions placed 9 μm from one edge of the cleave surface.

  4. Laser fiber cleaving techniques: effects on tip morphology and power output.

    PubMed

    Vassantachart, Janna M; Lightfoot, Michelle; Yeo, Alexander; Maldonado, Jonathan; Li, Roger; Alsyouf, Muhannad; Martin, Jacob; Lee, Michael; Olgin, Gaudencio; Baldwin, D Duane

    2015-01-01

    Proper cleaving of reusable laser fibers is needed to maintain optimal functionality. This study quantifies the effect of different cleaving tools on power output of the holmium laser fiber and demonstrates morphologic changes using microscopy. The uncleaved tips of new 272 μm reusable laser fibers were used to obtain baseline power transmission values at 3 W (0.6 J, 5 Hz). Power output for each of four cleaving techniques-11-blade scalpel, scribe pen cleaving tool, diamond cleaving wheel, and suture scissors-was measured in a single-blinded fashion. Dispersion of light from the fibers was compared with manufacturer specifications and rated as "ideal," "acceptable," or "unacceptable" by blinded reviewers. The fiber tips were also imaged using confocal and scanning electron microscopy. Independent samples Kruskal-Wallis test and chi square were used for statistical analysis (α<0.05). New uncleaved fiber tips transmitted 3.04 W of power and were used as a reference (100%). The scribe pen cleaving tool produced the next highest output (97.1%), followed by the scalpel (83.4%), diamond cleaving wheel (77.1%), and suture scissors (61.7%), a trend that was highly significant (P<0.001). On pairwise comparison, no difference in power output was seen between the uncleaved fiber tips and those cleaved with the scribe pen (P=1.0). The rating of the light dispersion patterns from the different cleaving methods followed the same trend as the power output results (P<0.001). Microscopy showed that the scribe pen produced small defects along the fiber cladding but maintained a smooth, flat core surface. The other cleaving techniques produced defects on both the core and cladding. Cleaving techniques produce a significant effect on the initial power transmitted by reusable laser fibers. The scribe pen cleaving tool produced the most consistent and highest average power output.

  5. Detecting hidden spatial and spatio-temporal structures in glasses and complex physical systems by multiresolution network clustering.

    PubMed

    Ronhovde, P; Chakrabarty, S; Hu, D; Sahu, M; Sahu, K K; Kelton, K F; Mauro, N A; Nussinov, Z

    2011-09-01

    We elaborate on a general method that we recently introduced for characterizing the "natural" structures in complex physical systems via multi-scale network analysis. The method is based on "community detection" wherein interacting particles are partitioned into an "ideal gas" of optimally decoupled groups of particles. Specifically, we construct a set of network representations ("replicas") of the physical system based on interatomic potentials and apply a multiscale clustering ("multiresolution community detection") analysis using information-based correlations among the replicas. Replicas may i) be different representations of an identical static system, ii) embody dynamics by considering replicas to be time separated snapshots of the system (with a tunable time separation), or iii) encode general correlations when different replicas correspond to different representations of the entire history of the system as it evolves in space-time. Inputs for our method are the inter-particle potentials or experimentally measured two (or higher order) particle correlations. We apply our method to computer simulations of a binary Kob-Andersen Lennard-Jones system in a mixture ratio of A(80)B(20) , a ternary model system with components "A", "B", and "C" in ratios of A(88)B(7)C(5) (as in Al(88)Y(7)Fe(5) , and to atomic coordinates in a Zr(80)Pt(20) system as gleaned by reverse Monte Carlo analysis of experimentally determined structure factors. We identify the dominant structures (disjoint or overlapping) and general length scales by analyzing extrema of the information theory measures. We speculate on possible links between i) physical transitions or crossovers and ii) changes in structures found by this method as well as phase transitions associated with the computational complexity of the community detection problem. We also briefly consider continuum approaches and discuss rigidity and the shear penetration depth in amorphous systems; this latter length scale increases as

  6. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB

    PubMed Central

    Khara, Pratick; Roy, Madhumita; Chakraborty, Joydeep; Ghosal, Debajyoti; Dutta, Tapan K.

    2014-01-01

    Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO) genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET) proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads. PMID:24918041

  7. Structure of cleaved (001) USb2 single crystal

    SciTech Connect

    Chen, Shao-ping; Hawley, Marilyn; Bauer, Eric D; Stockum, Phil B; Manoharan, Hari C

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features observed in the STM will be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites) and the presence of contaminants

  8. Deficiency of the iron-sulfur clusters of mitochondrial reduced nicotinamide-adenine dinucleotide-ubiquinone oxidoreductase (complex I) in an infant with congenital lactic acidosis.

    PubMed Central

    Moreadith, R W; Batshaw, M L; Ohnishi, T; Kerr, D; Knox, B; Jackson, D; Hruban, R; Olson, J; Reynafarje, B; Lehninger, A L

    1984-01-01

    We report the case of an infant with hypoglycemia, progressive lactic acidosis, an increased serum lactate/pyruvate ratio, and elevated plasma alanine, who had a moderate to profound decrease in the ability of mitochondria from four organs to oxidize pyruvate, malate plus glutamate, citrate, and other NAD+-linked respiratory substrates. The capacity to oxidize the flavin adenine dinucleotide-linked substrate, succinate, was normal. The most pronounced deficiency was in skeletal muscle, the least in kidney mitochondria. Enzymatic assays on isolated mitochondria ruled out defects in complexes II, III, and IV of the respiratory chain. Further studies showed that the defect was localized in the inner membrane mitochondrial NADH-ubiquinone oxidoreductase (complex I). When ferricyanide was used as an artificial electron acceptor, complex I activity was normal, indicating that electrons from NADH could reduce the flavin mononucleotide cofactor. However, electron paramagnetic resonance spectroscopy performed on liver submitochondrial particles showed an almost total loss of the iron-sulfur clusters characteristic of complex I, whereas normal signals were noted for other mitochondrial iron-sulfur clusters. This infant is presented as the first reported case of congenital lactic acidosis caused by a deficiency of the iron-sulfur clusters of complex I of the mitochondrial electron transport chain. Images PMID:6432847

  9. Deficiency of the iron-sulfur clusters of mitochondrial reduced nicotinamide-adenine dinucleotide-ubiquinone oxidoreductase (complex I) in an infant with congenital lactic acidosis.

    PubMed

    Moreadith, R W; Batshaw, M L; Ohnishi, T; Kerr, D; Knox, B; Jackson, D; Hruban, R; Olson, J; Reynafarje, B; Lehninger, A L

    1984-09-01

    We report the case of an infant with hypoglycemia, progressive lactic acidosis, an increased serum lactate/pyruvate ratio, and elevated plasma alanine, who had a moderate to profound decrease in the ability of mitochondria from four organs to oxidize pyruvate, malate plus glutamate, citrate, and other NAD+-linked respiratory substrates. The capacity to oxidize the flavin adenine dinucleotide-linked substrate, succinate, was normal. The most pronounced deficiency was in skeletal muscle, the least in kidney mitochondria. Enzymatic assays on isolated mitochondria ruled out defects in complexes II, III, and IV of the respiratory chain. Further studies showed that the defect was localized in the inner membrane mitochondrial NADH-ubiquinone oxidoreductase (complex I). When ferricyanide was used as an artificial electron acceptor, complex I activity was normal, indicating that electrons from NADH could reduce the flavin mononucleotide cofactor. However, electron paramagnetic resonance spectroscopy performed on liver submitochondrial particles showed an almost total loss of the iron-sulfur clusters characteristic of complex I, whereas normal signals were noted for other mitochondrial iron-sulfur clusters. This infant is presented as the first reported case of congenital lactic acidosis caused by a deficiency of the iron-sulfur clusters of complex I of the mitochondrial electron transport chain.

  10. Perturbation of the Quinone-binding Site of Complex II Alters the Electronic Properties of the Proximal [3Fe-4S] Iron-Sulfur Cluster*

    PubMed Central

    Ruprecht, Jonathan; Iwata, So; Rothery, Richard A.; Weiner, Joel H.; Maklashina, Elena; Cecchini, Gary

    2011-01-01

    Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis. PMID:21310949

  11. Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.

    PubMed

    Ruprecht, Jonathan; Iwata, So; Rothery, Richard A; Weiner, Joel H; Maklashina, Elena; Cecchini, Gary

    2011-04-08

    Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis.

  12. A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin

    PubMed Central

    Liu, Yao; Zhu, Wenhan; Tan, Yunhao; Nakayasu, Ernesto S.; Staiger, Christopher J.

    2017-01-01

    Legionella pneumophila, the etiological agent of Legionnaires’ disease, replicates intracellularly in protozoan and human hosts. Successful colonization and replication of this pathogen in host cells requires the Dot/Icm type IVB secretion system, which translocates approximately 300 effector proteins into the host cell to modulate various cellular processes. In this study, we identified RavK as a Dot/Icm substrate that targets the host cytoskeleton and reduces actin filament abundance in mammalian cells upon ectopic expression. RavK harbors an H95EXXH99 motif associated with diverse metalloproteases, which is essential for the inhibition of yeast growth and for the induction of cell rounding in HEK293T cells. We demonstrate that the actin protein itself is the cellular target of RavK and that this effector cleaves actin at a site between residues Thr351 and Phe352. Importantly, RavK-mediated actin cleavage also occurs during L. pneumophila infection. Cleavage by RavK abolishes the ability of actin to form polymers. Furthermore, an F352A mutation renders actin resistant to RavK-mediated cleavage; expression of the mutant in mammalian cells suppresses the cell rounding phenotype caused by RavK, further establishing that actin is the physiological substrate of RavK. Thus, L. pneumophila exploits components of the host cytoskeleton by multiple effectors with distinct mechanisms, highlighting the importance of modulating cellular processes governed by the actin cytoskeleton in the intracellular life cycle of this pathogen. PMID:28129393

  13. Hausdorff clustering

    NASA Astrophysics Data System (ADS)

    Basalto, Nicolas; Bellotti, Roberto; de Carlo, Francesco; Facchi, Paolo; Pantaleo, Ester; Pascazio, Saverio

    2008-10-01

    A clustering algorithm based on the Hausdorff distance is analyzed and compared to the single, complete, and average linkage algorithms. The four clustering procedures are applied to a toy example and to the time series of financial data. The dendrograms are scrutinized and their features compared. The Hausdorff linkage relies on firm mathematical grounds and turns out to be very effective when one has to discriminate among complex structures.

  14. The Yeast Iron Regulatory Proteins Grx3/4 and Fra2 Form Heterodimeric Complexes Containing a [2Fe-2S] Cluster with Cysteinyl and Histidyl Ligation†

    PubMed Central

    Li, Haoran; Mapolelo, Daphne T.; Dingra, Nin N.; Naik, Sunil G.; Lees, Nicolas S.; Hoffman, Brian M.; Riggs-Gelasco, Pamela J.; Huynh, Boi Hanh; Johnson, Michael K.; Outten, Caryn E.

    2009-01-01

    The transcription of iron uptake and storage genes in S. cerevisiae is primarily regulated by the transcription factor Aft1. Nucleocytoplasmic shuttling of Aft1 is dependent upon mitochondrial Fe-S cluster biosynthesis via a signaling pathway that includes the cytosolic monothiol glutaredoxins (Grx3 and Grx4) and the BolA homologue Fra2. However the interactions between these proteins and the iron-dependent mechanism by which they control Aft1 localization are unclear. To reconstitute and characterize components of this signaling pathway in vitro, we have overexpressed yeast Fra2 and Grx3/4 in E. coli. We have shown that co-expression of recombinant Fra2 with Grx3 or Grx4 allows purification of a stable [2Fe-2S]2+ cluster-containing Fra2-Grx3 or Fra2-Grx4 heterodimeric complex. Reconstitution of a [2Fe-2S] cluster on Grx3 or Grx4 without Fra2 produces a [2Fe-2S]-bridged homodimer. UV-visible absorption and CD, resonance Raman, EPR, ENDOR, Mössbauer, and EXAFS studies of [2Fe-2S] Grx3/4 homodimers and the [2Fe-2S] Fra2-Grx3/4 heterodimers indicate that inclusion of Fra2 in the Grx3/4 Fe-S complex causes a change in the cluster stability and coordination environment. Taken together, our analytical, spectroscopic, and mutagenesis data indicate that Grx3/4 and Fra2 form a Fe-S-bridged heterodimeric complex with Fe ligands provided by the active site cysteine of Grx3/4, glutathione, and a histidine residue. Overall, these results suggest that the ability of the Fra2-Grx3/4 complex to assemble a [2Fe-2S] cluster may act as a signal to control the iron regulon in response to cellular iron status in yeast. PMID:19715344

  15. Structural diversity of copper-CO2 complexes: infrared spectra and structures of [Cu(CO2)n]- clusters.

    PubMed

    Knurr, Benjamin J; Weber, J Mathias

    2014-11-06

    We  present infrared spectra of  [Cu(CO2)n](-) (n = 2-9) clusters in the wavenumber range 1600-2400 cm(-1). The CO stretching modes in this region encode the structural nature of the cluster core and are interpreted with the aid of density functional theory. We find a variety of core species in [Cu(CO2)n](-) clusters, but the dominant core structure is a [Cu(CO2)2](-) core where the two CO2 ligands are bound to the Cu atom in a bidentate fashion. We compare the results of [Cu(CO2)n](-) clusters to those of other [M(CO2)n](-) clusters (M = Au, Ag, Co, Ni) to establish trends of how the metal-CO2 interaction depends on the metal partner.

  16. Infrared and electronic spectroscopy of benzene-ammonia cluster radical cations [C(6)H(6)(NH(3))(1,2)](+): observation of isolated and microsolvated σ-complexes.

    PubMed

    Mizuse, Kenta; Hasegawa, Hayato; Mikami, Naohiko; Fujii, Asuka

    2010-10-28

    We report infrared (IR) and electronic spectra of benzene-ammonia cluster radical cations [C(6)H(6)(NH(3))(n)](+) (n = 1 and 2) in the gas phase to explore cluster structures and chemical reactivity of the simplest aromatic radical cation with base (nucleophile) molecules. The electronic spectra in the visible region indicate that these cluster cations no longer have the benzene cation chromophore as a result of an intracluster reaction. Analyses of the IR spectra, on the basis quantum chemical calculations and the vibration-internal rotation analysis, reveal that both [C(6)H(6)(NH(3))(1,2)](+) form σ-complex structures, in which the ammonia moiety is covalently bonded to the benzene moiety due to the intracluster nucleophilic addition. For [C(6)H(6)(NH(3))(2)](+), it is also shown that the second ammonia molecule solvates the σ-complex core via a N-H···N hydrogen bond. Such σ-complex structures are generally supposed to be a key intermediate of aromatic substitution reactions. The observed mass spectra and energetics calculations, however, show that [C(6)H(6)(NH(3))(n)](+) systems are inert for aromatic substitutions. The present experimental observations indicate the inherent stability of these σ-complex structures, even though they do not show the aromatic substitution reactivity.

  17. Role of Caspase-3-Mediated Apoptosis in Chronic Caspase-3-Cleaved Tau Accumulation and Blood-Brain Barrier Damage in the Corpus Callosum after Traumatic Brain Injury in Rats.

    PubMed

    Glushakova, Olena Y; Glushakov, Andriy O; Borlongan, Cesar V; Valadka, Alex B; Hayes, Ronald L; Glushakov, Alexander V

    2017-07-21

    Traumatic brain injury (TBI) may be a significant risk factor for development of neurodegenerative disorders such as chronic traumatic encephalopathy (CTE), post-traumatic epilepsy (PTE), and Alzheimer's (AD) and Parkinson's (PD) diseases. Chronic TBI is associated with several pathological features that are also characteristic of neurodegenerative diseases, including tau pathologies, caspase-3-mediated apoptosis, neuroinflammation, and microvascular alterations. The goal of this study was to evaluate changes following TBI in cleaved-caspase-3 and caspase-3-cleaved tau truncated at Asp421, and their relationships to cellular markers potentially associated with inflammation and blood-brain (BBB) barrier damage. We studied astrocytes (glial fibrillary acidic protein [GFAP]), microglia (ionized calcium-binding adapter molecule 1 [Iba1]), BBB (endothelial barrier antigen [EBA]), and activated microglia/macrophages (cluster of differentiation 68 [CD68]). We employed immunohistochemistry at different time points from 24 h to 3 months after controlled cortical impact (CCI) injury in rats, with particular interest in white matter. The study demonstrated that CCI caused chronic upregulation of cleaved-caspase-3 in the white matter of the corpus callosum. Increases in cleaved-caspase-3 in the corpus callosum were accompanied by accumulation of caspase-3-cleaved tau, with increasing perivascular aggregation 3 months after CCI. Immunofluorescence experiments further showed cellular co-localization of cleaved-caspase-3 with GFAP and CD68 and its adjacent localization with EBA, suggesting involvement of apoptosis and neuroinflammation in mechanisms of delayed BBB and microvascular damage that could contribute to white matter changes. This study also provides the first evidence that evolving upregulation of cleaved-caspase-3 is associated with accumulation of caspase-3-cleaved tau following experimental TBI, thus providing new insights into potential common mechanisms mediated

  18. A structure-based analysis of the vibrational spectra of nitrosyl ligands in transition-metal coordination complexes and clusters.

    PubMed

    De La Cruz, Carlos; Sheppard, Norman

    2011-01-01

    The vibrational spectra of nitrogen monoxide or nitric oxide (NO) bonded to one or to several transition-metal (M) atom(s) in coordination and cluster compounds are analyzed in relation to the various types of such structures identified by diffraction methods. These structures are classified in: (a) terminal (linear and bent) nitrosyls, [M(σ-NO)] or [M(NO)]; (b) twofold nitrosyl bridges, [M2(μ2-NO)]; (c) threefold nitrosyl bridges, [M3(μ3-NO)]; (d) σ/π-dihaptonitrosyls or "side-on" nitrosyls; and (e) isonitrosyls (oxygen-bonded nitrosyls). Typical ranges for the values of internuclear N-O and M-N bond-distances and M-N-O bond-angles for linear nitrosyls are: 1.14-1.20 Å/1.60-1.90 Å/180-160° and for bent nitrosyls are 1.16-1.22 Å/1.80-2.00 Å/140-110°. The [M2(μ2-NO)] bridges have been divided into those that contain one or several metal-metal bonds and those without a formal metal/metal bond (M⋯M). Typical ranges for the M-M, N-O, M-N bond distances and M-N-M bond angles for the normal twofold NO bridges are: 2.30-3.00 Å/1.18-1.22 Å/1.80-2.00 Å/90-70°, whereas for the analogous ranges of the long twofold NO bridges these are 3.10-3.40 Å/1.20-1.24 Å/1.90-2.10 Å/130-110°. In both situations the N-O vector is approximately at right angle to the M-M (or M⋯M) vector within the experimental error; i.e. the NO group is symmetrical bonded to the two metal atoms. In contrast the threefold NO bridges can be symmetrically or unsymmetrically bonded to an M3-plane of a cluster compound. Characteristic values for the N-O and M-N bond-distances of these NO bridges are: 1.24-1.28 Å/1.80-1.90 Å, respectively. As few dihaptonitrosyl and isonitrosyl complexes are known, the structural features of these are discussed on an individual basis. The very extensive vibrational spectroscopy literature considered gives emphasis to the data from linearly bonded NO ligands in stable closed-shell metal complexes; i.e. those which are consistent with the

  19. A structure-based analysis of the vibrational spectra of nitrosyl ligands in transition-metal coordination complexes and clusters

    NASA Astrophysics Data System (ADS)

    De La Cruz, Carlos; Sheppard, Norman

    2011-01-01

    The vibrational spectra of nitrogen monoxide or nitric oxide (NO) bonded to one or to several transition-metal (M) atom(s) in coordination and cluster compounds are analyzed in relation to the various types of such structures identified by diffraction methods. These structures are classified in: (a) terminal (linear and bent) nitrosyls, [M(σ-NO)] or [M(NO)]; (b) twofold nitrosyl bridges, [M 2(μ 2-NO)]; (c) threefold nitrosyl bridges, [M 3(μ 3-NO)]; (d) σ/π-dihaptonitrosyls or " side-on" nitrosyls; and (e) isonitrosyls (oxygen-bonded nitrosyls). Typical ranges for the values of internuclear N-O and M-N bond-distances and M-N-O bond-angles for linear nitrosyls are: 1.14-1.20 Å/1.60-1.90 Å/180-160° and for bent nitrosyls are 1.16-1.22 Å/1.80-2.00 Å/140-110°. The [M 2(μ 2-NO)] bridges have been divided into those that contain one or several metal-metal bonds and those without a formal metal/metal bond (M⋯M). Typical ranges for the M-M, N-O, M-N bond distances and M-N-M bond angles for the normal twofold NO bridges are: 2.30-3.00 Å/1.18-1.22 Å/1.80-2.00 Å/90-70°, whereas for the analogous ranges of the long twofold NO bridges these are 3.10-3.40 Å/1.20-1.24 Å/1.90-2.10 Å/130-110°. In both situations the N-O vector is approximately at right angle to the M-M (or M⋯M) vector within the experimental error; i.e. the NO group is symmetrical bonded to the two metal atoms. In contrast the threefold NO bridges can be symmetrically or unsymmetrically bonded to an M 3-plane of a cluster compound. Characteristic values for the N-O and M-N bond-distances of these NO bridges are: 1.24-1.28 Å/1.80-1.90 Å, respectively. As few dihaptonitrosyl and isonitrosyl complexes are known, the structural features of these are discussed on an individual basis. The very extensive vibrational spectroscopy literature considered gives emphasis to the data from linearly bonded NO ligands in stable closed-shell metal complexes; i.e. those which are consistent with the

  20. A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin

    DOE PAGES

    Liu, Yao; Zhu, Wenhan; Tan, Yunhao; ...

    2017-01-27

    Legionella pneumophila, the etiological agent of Legionnaires' disease, replicates intracellularly in protozoan and human hosts. Successful colonization and replication of this pathogen in host cells requires the Dot/Icm type IVB secretion system, which translocates approximately 300 effector proteins into the host cell to modulate various cellular processes. In this study, we identified RavK as a Dot/Icm substrate that targets the host cytoskeleton and reduces actin filament abundance in mammalian cells upon ectopic expression. RavK harbors an H95EXXH99 motif associated with diverse metalloproteases, which is essential for the inhibition of yeast growth and for the induction of cell rounding in HEK293Tmore » cells. We demonstrate that the actin protein itself is the cellular target of RavK and that this effector cleaves actin at a site between residues Thr351 and Phe352. Importantly, RavK-mediated actin cleavage also occurs during L. pneumophila infection. Cleavage by RavK abolishes the ability of actin to form polymers. Furthermore, an F352A mutation renders actin resistant to RavK-mediated cleavage; expression of the mutant in mammalian cells suppresses the cell rounding phenotype caused by RavK, further establishing that actin is the physiological substrate of RavK. Furthermore, L. pneumophila exploits components of the host cytoskeleton by multiple effectors with distinct mechanisms, highlighting the importance of modulating cellular processes governed by the actin cytoskeleton in the intracellular life cycle of this pathogen.« less

  1. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA

    PubMed Central

    Silverman, Scott K.

    2005-01-01

    Over the last decade, many catalytically active DNA molecules (deoxyribozymes; DNA enzymes) have been identified by in vitro selection from random-sequence DNA pools. This article focuses on deoxyribozymes that cleave RNA substrates. The first DNA enzyme was reported in 1994 and cleaves an RNA linkage. Since that time, many other RNA-cleaving deoxyribozymes have been identified. Most but not all of these deoxyribozymes require a divalent metal ion cofactor such as Mg2+ to catalyze attack by a specific RNA 2′-hydroxyl group on the adjacent phosphodiester linkage, forming a 2′,3′-cyclic phosphate and a 5′-hydroxyl group. Several deoxyribozymes that cleave RNA have utility for in vitro RNA biochemistry. Some DNA enzymes have been applied in vivo to degrade mRNAs, and others have been engineered into sensors. The practical impact of RNA-cleaving deoxyribozymes should continue to increase as additional applications are developed. PMID:16286368

  2. Complexes of DNA Bases and Watson-Crick Base Pairs Interaction with Neutral Silver Agn (n = 8, 10, 12) Clusters: A DFT and TDDFT Study.

    PubMed

    Srivastava, Ruby

    2017-03-21

    We study the binding of the neutral Agn (n = 8, 10, 12) to the DNA base- adenine (A), guanine (G) and Watson-Crick -adenine-thymine (AT), guanine-cytosine (GC) pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential (ECP) was used for silver and 6-31+G(**) was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Agn-A,G/WC complexes were also studied using time-dependent density functional theory (TDDFT). The absorption spectra for these complexes show wavelength in the visible region. It was revealed that silver clusters interact more strongly with WC pairs than with isolated DNA complexes. Furthermore, it was found that the electronic charge transferred from silver to isolated DNA clusters are less than the electronic charge transferred from silver to the Agn-WC complexes. The vertical ionization potential, vertical electron affinity, hardness and electrophilicity index of Agn-DNA/WC complexes have also been discussed.

  3. Hydrothermal syntheses, crystal structures of three new organic-inorganic hybrids constructed from Keggin-type [BW 12O 40] 5- clusters and transition metal complexes

    NASA Astrophysics Data System (ADS)

    Wang, Jing-Ping; Guo, Gui-Ling; Niu, Jing-Yang

    2008-08-01

    Three new organic-inorganic hybrid compounds constructed from Keggin-type polyanions and transition metal complexes, [Mn(2,2'-bipy) 3] 1.5[BW 12O 40Mn(2,2'-bipy) 2(H 2O)]·0.25H 2O ( 1), [Fe(2,2'-bipy) 3] 1.5[BW 12O 40Fe(2,2'-bipy) 2(H 2O)]·0.5H 2O ( 2) and [Cu 2(phen) 2(OH) 2] 2H[Cu(H 2O) 2{BW 12O 40Cu 0.75(phen)(H 2O)} 2]·1.5H 2O ( 3), have been hydrothermally synthesized and characterized by elemental analyses, IR, TGA and single-crystal X-ray diffraction. Compounds 1 and 2 are isostructural and both exhibit monosupporting polyoxometalate cluster structure, each of which contains a [BW 12O 40] 5- cluster decorated by one transition metal complex. Compound 3 contains a bisupporting polyoxometalate cluster anion where two {Cu 0.75(phen)(H 2O)} 0.75+ fragments are supported on the polyoxometalate dimer {Cu(H 2O) 2(BW 12O 40) 2} 8-, this represents the first bisupporting polyoxometalate cluster based on a Keggin-type polyoxometalate dimer, which are further packed together via π-π stacking contacts into an extended 1-D chain.

  4. Differentiation of the gene clusters encoding botulinum neurotoxin type A complexes in Clostridium botulinum type A, Ab, and A(B) strains.

    PubMed

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-12-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained.

  5. Differentiation of the Gene Clusters Encoding Botulinum Neurotoxin Type A Complexes in Clostridium botulinum Type A, Ab, and A(B) Strains

    PubMed Central

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-01-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained. PMID:15574917

  6. Path-integral molecular dynamics simulations of BeO embedded in helium clusters: Formation of the stable HeBeO complex

    NASA Astrophysics Data System (ADS)

    Motegi, Haruki; Kakizaki, Akira; Takayanagi, Toshiyuki; Taketsugu, Yuriko; Taketsugu, Tetsuya; Shiga, Motoyuki

    2008-12-01

    Path-integral molecular dynamics simulations have been performed to understand the quantum helium solvation structures in the He nBeO cluster up to n = 100. Our simulations show that one helium atom is strongly bound to BeO to form HeBeO and that the first solvation shell around the HeBeO complex includes roughly 12-14 helium atoms. The second solvation structure was also observed for n > 20. Both the first and second solvation shells show an anisotropic behavior but the anisotropy for the second solvation shell was found to be much weaker than that for the first solvation shell, as expected. The present simulations suggest that the HeBeO complex may be formed in large helium clusters.

  7. Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB)

    PubMed Central

    Thiaville, Jennifer J.; Frelin, Océane; García-Salinas, Carolina; Harrison, Katherine; Hasnain, Ghulam; Horenstein, Nicole A.; Díaz de la Garza, Rocio I.; Henry, Christopher S.; Hanson, Andrew D.; de Crécy-Lagard, Valérie

    2016-01-01

    Tetrahydrofolate (THF) and its one-carbon derivatives, collectively termed folates, are essential cofactors, but are inherently unstable. While it is clear that chemical oxidation can cleave folates or damage their pterin precursors, very little is known about enzymatic damage to these molecules or about whether the folate biosynthesis pathway responds adaptively to damage to its end-products. The presence of a duplication of the gene encoding the folate biosynthesis enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (FolK) in many sequenced bacterial genomes combined with a strong chromosomal clustering of the folK gene with panB, encoding the 5,10-methylene-THF-dependent enzyme ketopantoate hydroxymethyltransferase, led us to infer that PanB has a side activity that cleaves 5,10-methylene-THF, yielding a pterin product that is recycled by FolK. Genetic and metabolic analyses of Escherichia coli strains showed that overexpression of PanB leads to accumulation of the likely folate cleavage product 6-hydroxymethylpterin and other pterins in cells and medium, and—unexpectedly—to a 46% increase in total folate content. In silico modeling of the folate biosynthesis pathway showed that these observations are consistent with the in vivo cleavage of 5,10-methylene-THF by a side-activity of PanB, with FolK-mediated recycling of the pterin cleavage product, and with regulation of folate biosynthesis by folates or their damage products. PMID:27065985

  8. Human MUS81-EME2 can cleave a variety of DNA structures including intact Holliday junction and nicked duplex.

    PubMed

    Amangyeld, Tamir; Shin, Yong-Keol; Lee, Miju; Kwon, Buki; Seo, Yeon-Soo

    2014-05-01

    MUS81 shares a high-degree homology with the catalytic XPF subunit of the XPF-ERCC1 endonuclease complex. It is catalytically active only when complexed with the regulatory subunits Mms4 or Eme1 in budding and fission yeasts, respectively, and EME1 or EME2 in humans. Although Mus81 complexes are implicated in the resolution of recombination intermediates in vivo, recombinant yeast Mus81-Mms4 and human MUS81-EME1 isolated from Escherichia coli fail to cleave intact Holliday junctions (HJs) in vitro. In this study, we show that human recombinant MUS81-EME2 isolated from E. coli cleaves HJs relatively efficiently, compared to MUS81-EME1. Furthermore, MUS81-EME2 catalyzed cleavage of nicked and gapped duplex deoxyribonucleic acids (DNAs), generating double-strand breaks. The presence of a 5' phosphate terminus at nicks and gaps rendered DNA significantly less susceptible to the cleavage by MUS81-EME2 than its absence, raising the possibility that this activity could play a role in channeling damaged DNA duplexes that are not readily repaired into the recombinational repair pathways. Significant differences in substrate specificity observed with unmodified forms of MUS81-EME1 and MUS81-EME2 suggest that they play related but non-overlapping roles in DNA transactions. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Friedreich's Ataxia Variants I154F and W155R Diminish Frataxin-Based Activation of the Iron-Sulfur Cluster Assembly Complex

    SciTech Connect

    Tsai, Chi-Lin; Bridwell-Rabb, Jennifer; Barondeau, David P

    2011-11-07

    Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease that has been linked to defects in the protein frataxin (Fxn). Most FRDA patients have a GAA expansion in the first intron of their Fxn gene that decreases protein expression. Some FRDA patients have a GAA expansion on one allele and a missense mutation on the other allele. Few functional details are known for the ~15 different missense mutations identified in FRDA patients. Here in vitro evidence is presented that indicates the FRDA I154F and W155R variants bind more weakly to the complex of Nfs1, Isd11, and Isu2 and thereby are defective in forming the four-component SDUF complex that constitutes the core of the Fe-S cluster assembly machine. The binding affinities follow the trend Fxn ~ I154F > W155F > W155A ~ W155R. The Fxn variants also have diminished ability to function as part of the SDUF complex to stimulate the cysteine desulfurase reaction and facilitate Fe-S cluster assembly. Four crystal structures, including the first for a FRDA variant, reveal specific rearrangements associated with the loss of function and lead to a model for Fxn-based activation of the Fe-S cluster assembly complex. Importantly, the weaker binding and lower activity for FRDA variants correlate with the severity of disease progression. Together, these results suggest that Fxn facilitates sulfur transfer from Nfs1 to Isu2 and that these in vitro assays are sensitive and appropriate for deciphering functional defects and mechanistic details for human Fe-S cluster biosynthesis.

  10. Semiquinone and Cluster N6 Signals in His-tagged Proton-translocating NADH:Ubiquinone Oxidoreductase (Complex I) from Escherichia coli*

    PubMed Central

    Narayanan, Madhavan; Gabrieli, David J.; Leung, Steven A.; Elguindy, Mahmoud M.; Glaser, Carl A.; Saju, Nitha; Sinha, Subhash C.; Nakamaru-Ogiso, Eiko

    2013-01-01

    NADH:ubiquinone oxidoreductase (complex I) pumps protons across the membrane using downhill redox energy. The Escherichia coli complex I consists of 13 different subunits named NuoA-N coded by the nuo operon. Due to the low abundance of the protein and some difficulty with the genetic manipulation of its large ∼15-kb operon, purification of E. coli complex I has been technically challenging. Here, we generated a new strain in which a polyhistidine sequence was inserted upstream of nuoE in the operon. This allowed us to prepare large amounts of highly pure and active complex I by efficient affinity purification. The purified complex I contained 0.94 ± 0.1 mol of FMN, 29.0 ± 0.37 mol of iron, and 1.99 ± 0.07 mol of ubiquinone/1 mol of complex I. The extinction coefficient of isolated complex I was 495 mm−1 cm−1 at 274 nm and 50.3 mm−1 cm−1 at 410 nm. NADH:ferricyanide activity was 219 ± 9.7 μmol/min/mg by using HEPES-Bis-Tris propane, pH 7.5. Detailed EPR analyses revealed two additional iron-sulfur cluster signals, N6a and N6b, in addition to previously assigned signals. Furthermore, we found small but significant semiquinone signal(s), which have been reported only for bovine complex I. The line width was ∼12 G, indicating its neutral semiquinone form. More than 90% of the semiquinone signal originated from the single entity with P½ (half-saturation power level) = 1.85 milliwatts. The semiquinone signal(s) decreased by 60% when with asimicin, a potent complex I inhibitor. The functional role of semiquinone and the EPR assignment of clusters N6a/N6b are discussed. PMID:23543743

  11. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA.

    PubMed

    Haurwitz, Rachel E; Sternberg, Samuel H; Doudna, Jennifer A

    2012-06-13

    CRISPR-Cas adaptive immune systems protect prokaryotes against foreign genetic elements. crRNAs derived from CRISPR loci base pair with complementary nucleic acids, leading to their destruction. In Pseudomonas aeruginosa, crRNA biogenesis requires the endoribonuclease Csy4, which binds and cleaves the repetitive sequence of the CRISPR transcript. Biochemical assays and three co-crystal structures of wild-type and mutant Csy4/RNA complexes reveal a substrate positioning and cleavage mechanism in which a histidine deprotonates the ribosyl 2'-hydroxyl pinned in place by a serine, leading to nucleophilic attack on the scissile phosphate. The active site catalytic dyad lacks a general acid to protonate the leaving group and positively charged residues to stabilize the transition state, explaining why the observed catalytic rate constant is ∼10(4)-fold slower than that of RNase A. We show that this RNA cleavage step is essential for assembly of the Csy protein-crRNA complex that facilitates target recognition. Considering that Csy4 recognizes a single cellular substrate and sequesters the cleavage product, evolutionary pressure has likely selected for substrate specificity and high-affinity crRNA interactions at the expense of rapid cleavage kinetics.

  12. Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe–2S] cluster

    PubMed Central

    Abdalla, Mohnad; Dai, Ya-Nan; Chi, Chang-Biao; Cheng, Wang; Cao, Dong-Dong; Zhou, Kang; Ali, Wafa; Chen, Yuxing; Zhou, Cong-Zhao

    2016-01-01

    Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe–2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe–2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe–2S] cluster-incorporated dithiol Grxs, which share a highly conserved [2Fe–2S] cluster-binding pattern and dimeric conformation that is distinct from the previously identified [2Fe–2S] cluster-ligated monothiol Grxs. PMID:27710937

  13. Histidine 129 in the 75-kDa subunit of mitochondrial complex I from Yarrowia lipolytica is not a ligand for [Fe4S4] cluster N5 but is required for catalytic activity.

    PubMed

    Waletko, Antje; Zwicker, Klaus; Abdrakhmanova, Albina; Zickermann, Volker; Brandt, Ulrich; Kerscher, Stefan

    2005-02-18

    Respiratory chain complex I contains 8-9 iron-sulfur clusters. In several cases, the assignment of these clusters to subunits and binding motifs is still ambiguous. To test the proposed ligation of the tetranuclear iron-sulfur cluster N5 of respiratory chain complex I, we replaced the conserved histidine 129 in the 75-kDa subunit from Yarrowia lipolytica with alanine. In the mutant strain, reduced amounts of fully assembled but destabilized complex I could be detected. Deamino-NADH: ubiquinone oxidoreductase activity was abolished completely by the mutation. However, EPR spectroscopic analysis of mutant complex I exhibited an unchanged cluster N5 signal, excluding histidine 129 as a cluster N5 ligand.

  14. Properties of clusters in the gas phase. IV. Complexes of H/sub 2/O and HNO/sub x/ clustering on NO/sub x//sup -/

    SciTech Connect

    Lee, N.; Keesee, R.G.; Castleman, A.W. Jr.

    1980-01-15

    Thermodynamic quantities for the gas-phase clustering equilibria of NO/sub 2//sup -/ and NO/sub 3//sup -/ were determined with high-pressure mass spectrometry. Comparison of ..delta..G/sup 0//sub n/,n+1 values derived from our data shows good agreement with formerly reported values at 296 /sup 0/K. New data for larger NO/sub 2//sup -/ and NO/sub 3//sup -/ hydrates as well as NO/sub 2//sup -/(HNO/sub 2/) were obtained in this study. To aid in understanding the bonding and stability of the hydrates of nitrite and nitrate ions, CNDO/2 calculations were performed, and the results are discussed herein. A correlation between the aqueous phase total hydration enthalpy of a single ion and its gas-phase hydration enthalpy was obtained. Atmoshperic implications of the data are also briefly discussed.

  15. Lifetime of Major Histocompatibility Complex Class-I Membrane Clusters Is Controlled by the Actin Cytoskeleton

    PubMed Central

    Lavi, Yael; Gov, Nir; Edidin, Michael; Gheber, Levi A.

    2012-01-01

    Lateral heterogeneity of cell membranes has been demonstrated in numerous studies showing anomalous diffusion of membrane proteins; it has been explained by models and experiments suggesting dynamic barriers to free diffusion, that temporarily confine membrane proteins into microscopic patches. This picture, however, comes short of explaining a steady-state patchy distribution of proteins, in face of the transient opening of the barriers. In our previous work we directly imaged persistent clusters of MHC-I, a type I transmembrane protein, and proposed a model of a dynamic equilibrium between proteins newly delivered to the cell surface by vesicle traffic, temporary confinement by dynamic barriers to lateral diffusion, and dispersion of the clusters by diffusion over the dynamic barriers. Our model predicted that the clusters are dynamic, appearing when an exocytic vesicle fuses with the plasma membrane and dispersing with a typical lifetime that depends on lateral diffusion and the dynamics of barriers. In a subsequent work, we showed this to be the case. Here we test another prediction of the model, and show that changing the stability of actin barriers to lateral diffusion changes cluster lifetimes. We also develop a model for the distribution of cluster lifetimes, consistent with the function of barriers to lateral diffusion in maintaining MHC-I clusters. PMID:22500754

  16. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

    PubMed Central

    2012-01-01

    Background Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection of arCOGs is expected to

  17. Density-based clustering: A ‘landscape view’ of multi-channel neural data for inference and dynamic complexity analysis

    PubMed Central

    Gigante, Guido; Del Giudice, Paolo

    2017-01-01

    Two, partially interwoven, hot topics in the analysis and statistical modeling of neural data, are the development of efficient and informative representations of the time series derived from multiple neural recordings, and the extraction of information about the connectivity structure of the underlying neural network from the recorded neural activities. In the present paper we show that state-space clustering can provide an easy and effective option for reducing the dimensionality of multiple neural time series, that it can improve inference of synaptic couplings from neural activities, and that it can also allow the construction of a compact representation of the multi-dimensional dynamics, that easily lends itself to complexity measures. We apply a variant of the ‘mean-shift’ algorithm to perform state-space clustering, and validate it on an Hopfield network in the glassy phase, in which metastable states are largely uncorrelated from memories embedded in the synaptic matrix. In this context, we show that the neural states identified as clusters’ centroids offer a parsimonious parametrization of the synaptic matrix, which allows a significant improvement in inferring the synaptic couplings from the neural activities. Moving to the more realistic case of a multi-modular spiking network, with spike-frequency adaptation inducing history-dependent effects, we propose a procedure inspired by Boltzmann learning, but extending its domain of application, to learn inter-module synaptic couplings so that the spiking network reproduces a prescribed pattern of spatial correlations; we then illustrate, in the spiking network, how clustering is effective in extracting relevant features of the network’s state-space landscape. Finally, we show that the knowledge of the cluster structure allows casting the multi-dimensional neural dynamics in the form of a symbolic dynamics of transitions between clusters; as an illustration of the potential of such reduction, we define

  18. Altered Structure of the Mn4Ca Cluster in the Oxygen-evolving Complex of Photosystem II by a Histidine Ligand Mutation*

    PubMed Central

    Yano, Junko; Walker, Lee M.; Strickler, Melodie A.; Service, Rachel J.; Yachandra, Vittal K.; Debus, Richard J.

    2011-01-01

    The effect of replacing a histidine ligand on the properties of the oxygen-evolving complex (OEC) and the structure of the Mn4Ca cluster in Photosystem II (PSII) is studied by x-ray absorption spectroscopy using PSII core complexes from the Synechocystis sp. PCC 6803 D1 polypeptide mutant H332E. In the x-ray crystallographic structures of PSII, D1-His332 has been assigned as a direct ligand of a manganese ion, and the mutation of this histidine ligand to glutamate has been reported to prevent the advancement of the OEC beyond the S2Yz• intermediate state. The manganese K-edge (1s core electron to 4p) absorption spectrum of D1-H332E shifts to a lower energy compared with that of the native WT samples, suggesting that the electronic structure of the manganese cluster is affected by the presence of the additional negative charge on the OEC of the mutant. The extended x-ray absorption spectrum shows that the geometric structure of the cluster is altered substantially from that of the native WT state, resulting in an elongation of manganese-ligand and manganese-manganese interactions in the mutant. The strontium-H332E mutant, in which calcium is substituted by strontium, confirms that strontium (calcium) is a part of the altered cluster. The structural perturbations caused by the D1-H332E mutation are much larger than those produced by any biochemical treatment or mutation examined previously with x-ray absorption spectroscopy. The substantial structural changes provide an explanation not only for the altered properties of the D1-H332E mutant but also the importance of the histidine ligand for proper assembly of the Mn4Ca cluster. PMID:21233216

  19. Altered structure of the Mn4Ca cluster in the oxygen-evolving complex of photosystem II by a histidine ligand mutation.

    PubMed

    Yano, Junko; Walker, Lee M; Strickler, Melodie A; Service, Rachel J; Yachandra, Vittal K; Debus, Richard J

    2011-03-18

    The effect of replacing a histidine ligand on the properties of the oxygen-evolving complex (OEC) and the structure of the Mn(4)Ca cluster in Photosystem II (PSII) is studied by x-ray absorption spectroscopy using PSII core complexes from the Synechocystis sp. PCC 6803 D1 polypeptide mutant H332E. In the x-ray crystallographic structures of PSII, D1-His(332) has been assigned as a direct ligand of a manganese ion, and the mutation of this histidine ligand to glutamate has been reported to prevent the advancement of the OEC beyond the S(2)Yz(•) intermediate state. The manganese K-edge (1s core electron to 4p) absorption spectrum of D1-H332E shifts to a lower energy compared with that of the native WT samples, suggesting that the electronic structure of the manganese cluster is affected by the presence of the additional negative charge on the OEC of the mutant. The extended x-ray absorption spectrum shows that the geometric structure of the cluster is altered substantially from that of the native WT state, resulting in an elongation of manganese-ligand and manganese-manganese interactions in the mutant. The strontium-H332E mutant, in which calcium is substituted by strontium, confirms that strontium (calcium) is a part of the altered cluster. The structural perturbations caused by the D1-H332E mutation are much larger than those produced by any biochemical treatment or mutation examined previously with x-ray absorption spectroscopy. The substantial structural changes provide an explanation not only for the altered properties of the D1-H332E mutant but also the importance of the histidine ligand for proper assembly of the Mn(4)Ca cluster.

  20. CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases.

    PubMed

    Toliusis, Paulius; Zaremba, Mindaugas; Silanskas, Arunas; Szczelkun, Mark D; Siksnys, Virginijus

    2017-08-21

    The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric 5'-GCCGC-3' site and cleaves the DNA 7 and 6/7 nucleotides downstream on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent reaction. CglI is composed of two different proteins: an endonuclease (R.CglI) and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a heterotetrameric complex with R2H2 stoichiometry. However, the R2H2·CglI complex has only one nuclease active site sufficient to cut one DNA strand suggesting that two complexes are required to introduce a double strand break. Here, we report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and two-site circular DNA substrates we show that CglI does not require two sites on the same DNA for optimal catalytic activity. However, one-site linear DNA is a poor substrate, supporting a mechanism where CglI complexes must communicate along the one-dimensional DNA contour before cleavage is activated. Based on experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by CglI produces translocation on DNA preferentially in a downstream direction from the target, although upstream translocation is also possible. Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. The neuronal protein Neurexin directly interacts with the Scribble-Pix complex to stimulate F-actin assembly for synaptic vesicle clustering.

    PubMed

    Rui, Menglong; Qian, Jinjun; Liu, Lijuan; Cai, Yihan; Lv, Huihui; Han, Junhai; Jia, Zhengping; Xie, Wei

    2017-09-01

    Synaptic vesicles (SVs) form distinct pools at synaptic terminals, and this well-regulated separation is necessary for normal neurotransmission. However, how the SV cluster, in particular synaptic compartments, maintains normal neurotransmitter release remains a mystery. The presynaptic protein Neurexin (NRX) plays a significant role in synaptic architecture and function, and some evidence suggests that NRX is associated with neurological disorders, including autism spectrum disorders. However, the role of NRX in SV clustering is unclear. Here, using the neuromuscular junction at the 2-3 instar stages of Drosophila larvae as a model and biochemical imaging and electrophysiology techniques, we demonstrate that Drosophila NRX (DNRX) plays critical roles in regulating synaptic terminal clustering and release of SVs. We found that DNRX controls the terminal clustering and release of SVs by stimulating presynaptic F-actin. Furthermore, our results indicate that DNRX functions through the scaffold protein Scribble and the GEF protein DPix to activate the small GTPase Ras-related C3 Botulinum toxin substrate 1 (Rac1). We observed a direct interaction between the C-terminal PDZ-binding motif of DNRX and the PDZ domains of Scribble and that Scribble bridges DNRX to DPix, forming a DNRX-Scribble-DPix complex that activates Rac1 and subsequently stimulates presynaptic F-actin assembly and SV clustering. Taken together, our work provides important insights into the function of DNRX in regulating SV clustering, which could help inform further research into pathological neurexin-mediated mechanisms in neurological disorders such as autism. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Fabrication of Submicron Devices on the (011) Cleave Surface of a Cleaved-Edge-Overgrowth GaAs/AlGaAs Crystal

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Pfeiffer, Loren; West, Kenneth; Chang, Albert

    2013-03-01

    We describe the fabrication of submicron devices on the (011)cleave surface of a GaAs heterostructure crystal, in which this surface is extremely narrow. Special purpose devices are produced, which take advantage of the unique characteristics of Cleaved-Edge-Overgrowth. The successful fabrication relies on understanding the surface tension of the electron beam PMMA resist, the workable degree of variation in resist thickness, and on gluing the crystal onto a backing substrate to increase structural strength. We demonstrate a functional gate-controlled point contact constriction placed 9 um from one edge of the cleave surface. This technique may enable the study of fractional quantum Hall fluid in a novel structure. Work supported by NSFDMR-0701948

  3. A new quantum chemical approach to the magnetic properties of oligonuclear transition-metal complexes: application to a model for the tetranuclear manganese cluster of photosystem II.

    PubMed

    Pantazis, Dimitrios A; Orio, Maylis; Petrenko, Taras; Zein, Samir; Bill, Eckhard; Lubitz, Wolfgang; Messinger, Johannes; Neese, Frank

    2009-01-01

    The reliable correlation of structural features and magnetic or spectroscopic properties of oligonuclear transition-metal complexes is a critical requirement both for research into innovative magnetic materials and for elucidating the structure and function of many metalloenzymes. We have developed a novel method that for the first time enables the extraction of hyperfine coupling constants (HFCs) from broken-symmetry density functional theory (BS-DFT) calculations on clusters. Using the geometry-optimized tetranuclear manganese complex [Mn(4)O(6)(bpy)(6)](4+/3+) as a model, we first examine in detail the calculation of exchange coupling constants J through the BS-DFT approach. Complications arising from the indeterminacy of experimentally fitted J constants are identified and analyzed. It is found that only the energy levels derived from Hamiltonian diagonalization are a physically meaningful basis for comparing theory and experiment. Subsequently, the proposed theoretical scheme is applied to the calculation of (55)Mn HFCs of the Mn(III,IV,IV,IV) state of the complex, which is similar to the S(2) state of the oxygen-evolving complex (OEC) in photosystem II of oxygenic photosynthesis. The new approach performs reliably and accurately, and yields calculated HFCs that can be directly compared with experimental data. Finally, we carefully examine the dependence of HFC on the J value and draw attention to the sensitivity of the calculated values to the exchange coupling parameters. The proposed strategy extends naturally to hetero-oligonuclear clusters of arbitrary shape and nuclearity, and hence is of general validity and usefulness in the study of magnetic metal clusters. The successful application of the new approach presented here is a first step in the effort to establish correlations between the available spectroscopic information and the structural features of complex metalloenzymes like OEC.

  4. HIGH-RESOLUTION STUDY OF THE CLUSTER COMPLEXES IN A LENSED SPIRAL AT REDSHIFT 1.5: CONSTRAINTS ON THE BULGE FORMATION AND DISK EVOLUTION

    SciTech Connect

    Adamo, Angela; Oestlin, G.; Zackrisson, E.; Guaita, L.; Bastian, N.; Livermore, R. C.

    2013-04-01

    We analyze the clump population of the spiral galaxy Sp 1149 at redshift 1.5. Located behind the galaxy cluster MACS J1149.5+2223, Sp 1149 has been significantly magnified allowing us to study the galaxy on physical scales down to {approx}100 pc. The galaxy cluster frame is among the targets of the Cluster Lensing And Supernova survey with Hubble (CLASH), an ongoing Hubble Space Telescope (HST) Multi-Cycle Treasury program. We have used the publicly available multi-band imaging data set to reconstruct the spectral energy distributions of the clumps in Sp 1149, and derive, by means of stellar evolutionary models, their physical properties. We found that 40% of the clumps observed in Sp 1149 are older than 30 Myr and can be as old as 300 Myr. These are also the more massive (luminous) clumps in the galaxy. Among the complexes in the local reference sample, the star-forming knots in luminous blue compact galaxies could be considered progenitor analogs of these long-lived clumps. The remaining 60% of clumps have colors comparable to local cluster complexes, suggesting a similar young age. We observe that the Sp 1149 clumps follow the M{proportional_to}R {sup 2} relation similar to local cluster complexes, suggesting similar formation mechanisms although they may have different initial conditions (e.g., higher gas surface densities). We suggest that the galaxy is experiencing a slow decline in star formation rate and a likely transitional phase toward a more quiescent star formation mode. The older clumps have survived between 6 and 20 dynamical times and are all located at projected distances smaller than 4 kpc from the center. Their current location suggests migration toward the center and the possibility of being the building blocks of the bulge. On the other hand, the dynamical timescale of the younger clumps is significantly shorter, meaning that they are quite close to their birthplace. We show that the clumps of Sp 1149 may account for the expected metal

  5. High-resolution Study of the Cluster Complexes in a Lensed Spiral at Redshift 1.5: Constraints on the Bulge Formation and Disk Evolution

    NASA Astrophysics Data System (ADS)

    Adamo, Angela; Östlin, G.; Bastian, N.; Zackrisson, E.; Livermore, R. C.; Guaita, L.

    2013-04-01

    We analyze the clump population of the spiral galaxy Sp 1149 at redshift 1.5. Located behind the galaxy cluster MACS J1149.5+2223, Sp 1149 has been significantly magnified allowing us to study the galaxy on physical scales down to ~100 pc. The galaxy cluster frame is among the targets of the Cluster Lensing And Supernova survey with Hubble (CLASH), an ongoing Hubble Space Telescope (HST) Multi-Cycle Treasury program. We have used the publicly available multi-band imaging data set to reconstruct the spectral energy distributions of the clumps in Sp 1149, and derive, by means of stellar evolutionary models, their physical properties. We found that 40% of the clumps observed in Sp 1149 are older than 30 Myr and can be as old as 300 Myr. These are also the more massive (luminous) clumps in the galaxy. Among the complexes in the local reference sample, the star-forming knots in luminous blue compact galaxies could be considered progenitor analogs of these long-lived clumps. The remaining 60% of clumps have colors comparable to local cluster complexes, suggesting a similar young age. We observe that the Sp 1149 clumps follow the MvpropR 2 relation similar to local cluster complexes, suggesting similar formation mechanisms although they may have different initial conditions (e.g., higher gas surface densities). We suggest that the galaxy is experiencing a slow decline in star formation rate and a likely transitional phase toward a more quiescent star formation mode. The older clumps have survived between 6 and 20 dynamical times and are all located at projected distances smaller than 4 kpc from the center. Their current location suggests migration toward the center and the possibility of being the building blocks of the bulge. On the other hand, the dynamical timescale of the younger clumps is significantly shorter, meaning that they are quite close to their birthplace. We show that the clumps of Sp 1149 may account for the expected metal-rich globular cluster population

  6. Effect of the Keggin anions on assembly of CuI-bis(tetrazole) thioether complexes containing multinuclear CuI-cluster

    NASA Astrophysics Data System (ADS)

    Wang, Xiu-Li; Gao, Qiang; Tian, Ai-Xiang; Hu, Hai-Liang; Liu, Guo-Cheng

    2012-03-01

    In order to investigate the effect of polyoxometalate (POM) on the assembly of transition metal-bis(tetrazole) thioether complexes, three new complexes based on different Keggin anions and multinuclear CuI-cluster [CuI12(bmtr)9(HSiMo12O40)4] (1), [CuI3(bmtr)3(PM12O40)] (M=W for 2; Mo for 3) (bmtr=1,3-bis(1-methyl-5-mercapto-1,2,3,4-tetrazole)propane), have been hydrothermally synthesized and characterized by routine physical methods and single crystal X-ray diffraction. In compound 1, two kinds of nanometer-scale tetranuclear subunits linked by [SiMo12O40]4- polyanions assemble a (3, 4)-connected three-dimensional (3D) self-penetrating framework. Compounds 2 and 3 are isostructural, exhibiting a 1D chain with [PW12O40]3-/[PMo12O40]3- polyanions and trinuclear clusters arranging alternately. The distinct structural differences between these POM-based CuI-bmtr complexes of 1 and 2/3 maybe rest on the contrast of Keggin-type polyoxometalate with different central heteroatoms, which have been discussed in detail. In addition, the electrochemical properties of the title complexes have been investigated.

  7. Protons bound to the Mn cluster in photosystem II oxygen evolving complex detected by proton matrix ENDOR.

    PubMed

    Yamada, Hiroiku; Mino, Hiroyuki; Itoh, Shigeru

    2007-03-01

    Protons in the vicinity of the oxygen-evolving manganese cluster in photosystem II were studied by proton matrix ENDOR. Six pairs of proton ENDOR signals were detected in both the S(0) and S(2) states of the Mn-cluster. Two pairs of signals that show hyperfine constants of 2.3/2.2 and 4.0 MHz, respectively, disappeared after D(2)O incubation in both states. The signals with 2.3/2.2 MHz hyperfine constants in S(0) and S(2) state multiline disappeared after 3 h of D(2)O incubation in the S(0) and S(1) states, respectively. The signal with 4.0 MHz hyperfine constants in S(0) state multiline disappeared after 3 h of D(2)O incubation in the S(0) state, while the similar signal in S(2) state multiline disappeared only after 24 h of D(2)O incubation in the S(1) state. The different proton exchange rates seem to be ascribable to the change in affinities of water molecules to the variation in oxidation state of the Mn cluster during the water oxidation cycle. Based on the point dipole approximation, the distances between the center of electronic spin of the Mn cluster and the exchangeable protons were estimated to be 3.3/3.2 and 2.7 A, respectively. These short distances suggest the protons belong to the water molecules ligated to the manganese cluster. We propose a model for the binding of water to the manganese cluster based on these results.

  8. Electron Transfer and Proton-Coupled Electron Transfer Reactivity and Self-Exchange of Synthetic [2Fe–2S] Complexes: Models for Rieske and mitoNEET Clusters

    PubMed Central

    2015-01-01

    This report describes the thermochemistry, proton-coupled electron transfer (PCET) reactions and self-exchange rate constants for a set of bis-benzimidazolate-ligated [2Fe–2S] clusters. These clusters serve as a model for the chemistry of biological Rieske and mitoNEET clusters. PCET from [Fe2S2(Prbbim)(PrbbimH)]2– (4) and [Fe2S2(Prbbim)(PrbbimH2)]1– (5) to TEMPO occurs via concerted proton–electron transfer (CPET) mechanisms (PrbbimH2 = 4,4-bis-(benzimidazol-2-yl)heptane). Intermolecular electron transfer (ET) self-exchange between [Fe2S2(Prbbim)2]2– (1) and [Fe2S2(Prbbim)2]3– (2) occurs with a rate constant of (1.20 ± 0.06) × 105 M–1 s–1 at 26 °C. A similar self-exchange rate constant is found for the related [2Fe–2S] cluster [Fe2S2(SArO)2]2–/3–, SArO2– = thiosalicylate. These are roughly an order of magnitude slower than that reported for larger [4Fe–4S] clusters and 1 order of magnitude faster than that reported for N-ligated high-spin iron complexes. These results suggest that the rate of intermolecular ET to/from [Fe–S] clusters is modulated by cluster size. The measured PCET self-exchange rate constant for 1 and 4 at −30 °C is (3.8 ± 0.7) × 104 M–1 s–1. Analysis of rate constants using the Marcus cross-relation suggests that this process likely occurs via a concerted proton–electron transfer (CPET) mechanism. The implications of these findings to biological systems are also discussed, including the conclusion that histidine-ligated [2Fe–2S] clusters should not have a strong bias to undergo concerted e–/H+ transfers. PMID:24592857

  9. A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex from natural MnO2 precipitates in the early ocean

    SciTech Connect

    Sauer, Kenneth; Yachandra, Vittal K.

    2002-04-30

    The photosynthetic water oxidation complex consists of a cluster of 4 Mn atoms bridged by O atoms, associated with Ca2+ and Cl- and incorporated into protein. The structure is similar in higher plants and algae, as well as in cyanobacteria of more ancient lineage, dating back more than 2.5 Ga on Earth. It has been proposed that the proto-enzyme derived from a component of a natural early marine manganese precipitate that contained a CaMn4O9 cluster. A variety of MnO2 minerals is found in nature. Three major classes are spinels, sheet-like layered structures and 3-dimensional networks that contain parallel tunnels. These relatively open structures readily incorporate cations (Na+, Li+, Mg2+, Ca2+, Ba2+, H+ and even Mn2+) and water. The minerals have different ratios of Mn(III) and Mn(IV) octahedrally coordinated to oxygens. Using X-ray spectroscopy we compare the chemical structures of Mn in the minerals with what is known about the arrangement in the water-oxidation complex to define the parameters of a structural model for the photosynthetic catalytic site. This comparison provides for the structural model a set of candidate Mn4 clusters -- some previously proposed and considered and others entirely novel.

  10. A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex from natural MnO2 precipitates in the early ocean.

    PubMed

    Sauer, Kenneth; Yachandra, Vittal K

    2002-06-25

    The photosynthetic water oxidation complex consists of a cluster of four Mn atoms bridged by O atoms, associated with Ca2+ and Cl-, and incorporated into protein. The structure is similar in higher plants and algae, as well as in cyanobacteria of more ancient lineage, dating back more than 2.5 billion years ago on Earth. It has been proposed that the proto-enzyme derived from a component of a natural early marine manganese precipitate that contained a CaMn4O9 cluster. A variety of MnO2 minerals are found in nature. Three major classes are spinels, sheet-like layered structures, and three-dimensional networks that contain parallel tunnels. These relatively open structures readily incorporate cations (Na+, Li+, Mg2+, Ca2+, Ba2+, H+, and even Mn2+) and water. The minerals have different ratios of Mn(III) and Mn(IV) octahedrally coordinated to oxygens. Using x-ray spectroscopy we compare the chemical structures of Mn in the minerals with what is known about the arrangement in the water oxidation complex to define the parameters of a structural model for the photosynthetic catalytic site. This comparison provides for the structural model a set of candidate Mn(4) clusters-some previously proposed and considered and others entirely novel.

  11. ADAM17 cleaves CD16b (FcγRIIIb) in human neutrophils

    PubMed Central

    Wang, Yue; Wu, Jianming; Newton, Robert; Bahaie, Nooshin S.; Long, Chunmei; Walcheck, Bruce

    2012-01-01

    CD16b (FcγRIIIb) is exclusively expressed by human neutrophils and binds IgG in immune complexes. Cell surface CD16b undergoes efficient ectodomain shedding upon neutrophil activation and apoptosis. Indeed, soluble CD16b is present at high levels in the plasma of healthy individuals, which appears to be maintained by the daily turnover of apoptotic neutrophils. At this time, the principal protease responsible for CD16b shedding is not known. We show that CD16b plasma levels were significantly decreased in patients administered a selective inhibitor targeting the metalloproteases ADAM10 and ADAM17. Additional analysis with inhibitors selective for ADAM10 or ADAM17 revealed that only inhibition of ADAM17 significantly blocked the cleavage of CD16b following neutrophil activation and apoptosis. CD16b shedding by ADAM17 was further demonstrated using a unique ADAM17 function-blocking mAb and a cell-based ADAM17 reconstitution assay. Unlike human CD16, however, mouse CD16 did not undergo efficient ectodomain shedding upon neutrophil stimulation or apoptosis, indicating that this mechanism cannot be modeled in normal mice. Taken together, our findings are the first to directly demonstrate that ADAM17 cleaves CD16 in human leukocytes. PMID:23228566

  12. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway.

    PubMed

    Saito, Yuichiro; Takeda, Jun; Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V; Taoka, Masato; Isobe, Toshiaki

    2014-01-01

    Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA(Ser-Met). To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA(Ser-Met), suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry-based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute "Domain 1" in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.

  13. The fluence effect in hydrogen-ion cleaving of silicon at the sub-100-nm scale

    NASA Astrophysics Data System (ADS)

    Moutanabbir, O.; Terreault, B.; Chicoine, M.; Schiettekatte, F.

    2005-04-01

    The implementation at the sub-100-nm scale of ion cleaving requires ion beams of ˜5 keV/amu or less. The blistering efficiency in 5-keV H-ion-implanted and annealed Si has been found to peak and vanish in a narrow range of ion fluence of (1.5-3.5)×1016 H/cm2. In order to understand this effect, the defect profiles in 5-keV H-irradiated Si were studied by Rutherford backscattering/channelling, while the Si-H bonding configurations during annealing were investigated by Raman scattering spectroscopy. Three types of defects play major roles: the `broad-band' monohydride multivacancy complexes, the fully or partially passivated monovacancy VHn, and H-terminated internal surfaces Si(100):H. Blister absence at high fluence is characterised by the persistence up to 550 °C of the Si(100):H structures, which are blister embryos that failed to coalesce and grow. Radiation-induced stresses and fracture toughening may play roles in inhibiting cleavage at high fluence; however, widening towards the surface of the zone of high H and defect concentration is the likely major factor.

  14. Cleaving for growth: threonine aspartase 1--a protease relevant for development and disease.

    PubMed

    Stauber, Roland H; Hahlbrock, Angelina; Knauer, Shirley K; Wünsch, Désirée

    2016-03-01

    From the beginning of life, proteases are key to organismal development comprising morphogenesis, cellular differentiation, and cell growth. Regulated proteolytic activity is essential for the orchestration of multiple developmental pathways, and defects in protease activity can account for multiple disease patterns. The highly conserved protease threonine aspartase 1 is a member of such developmental proteases and critically involved in the regulation of complex processes, including segmental identity, head morphogenesis, spermatogenesis, and proliferation. Additionally, threonine aspartase 1 is overexpressed in numerous liquid as well as in solid malignancies. Although threonine aspartase 1 is able to cleave the master regulator mixed lineage leukemia protein as well as other regulatory proteins in humans, our knowledge of its detailed pathobiological function and the underlying molecular mechanisms contributing to development and disease is still incomplete. Moreover, neither effective genetic nor chemical inhibitors for this enzyme are available so far precluding the detailed dissection of the pathobiological functions of threonine aspartase 1. Here, we review the current knowledge of the structure-function relationship of threonine aspartase 1 and its mechanistic impact on substrate-mediated coordination of the cell cycle and development. We discuss threonine aspartase 1-mediated effects on cellular transformation and conclude by presenting a short overview of recent interference strategies. © FASEB.

  15. Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

    DOE PAGES

    White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; ...

    2017-06-21

    The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies. Furthermore, themore » ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

  16. Mixed-metal chloro sulfido cluster complex of molybdenum and platinum, (Mo sub 3 Pt sub 2 S sub 4 Cl sub 4 (PEt sub 3 ) sub 6 )

    SciTech Connect

    Saito, Taro; Tsuboi, Toshio; Kajitani, Yoshimichi; Yamagata, Tsuneaki; Imoto, Hideo )

    1991-09-04

    In the authors recent publication, syntheses of mixed-metal chloro sulfido and chloro selenido complexes of molybdenum and nickel were reported. They were prepared by the reaction of (Mo{sub 3}X{sub 4}Cl{sub 4}(PEt{sub 3}){sub 3}(MeOH){sub 2}) (X = S, Se){sup 2} with Ni(cod){sub 2} (cod = 1,5-cyclooctadiene). In the present study, another excellent building block compound, Pt(cot){sub 2}, was reacted with the same trinuclear molybdenum complex, and the mixed-metal cluster complex (Mo{sub 3}Pt{sub 2}S{sub 4}Cl{sub 4}(PEt{sub 3}){sub 6}) (1) with an unexpected structure was obtained.

  17. Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

    NASA Astrophysics Data System (ADS)

    White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; Head-Gordon, Martin

    2017-06-01

    The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N2-, CO-, CO2-, and CH2O-. Analytic continuation of complex 𝜃 -trajectories is used to compute Siegert energies, and the 𝜃 -trajectories of energy differences are found to yield more consistent results than those of total energies. The ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.

  18. Surface Structure of Azotobacter vinelandii Cysts as Revealed by Freeze-Cleaving1

    PubMed Central

    Koo, Victoria M.; Lin, L. P.; Sadoff, H. L.

    1969-01-01

    Micrographs of freeze-cleaved Azotobacter vinelandii cysts reveal that the surface is composed of several overlapping layers. This observation is consistent with the previously proposed structure of the outer cyst coat. Images PMID:5359611

  19. Electron gas quality at various (110)-GaAs interfaces as benchmark for cleaved edge overgrowth

    NASA Astrophysics Data System (ADS)

    Riedi, S.; Reichl, C.; Berl, M.; Alt, L.; Maier, A.; Wegscheider, W.

    2016-12-01

    We study molecular beam epitaxial growth on the unusual (110) surface of GaAs substrates as prerequisite for cleaved edge overgrown structures. We present the first systematic comparison of the quality of two dimensional electron systems on simultaneously overgrown (110) GaAs monitor wafers with ex situ as well as in situ cleaved (110) facets. Our study confirms that characterization of the monitor wafer is a valid benchmark for the magnetotransport characteristics of structures grown on cleaved facets. We show that deviating results can be traced back to (110) substrates of lower quality. We also demonstrate that the roughness of the in situ cleaved facets is decisive for the quality of the induced electron gas.

  20. Extensive Variation in the O-Antigen Gene Cluster within One Salmonella enterica Serogroup Reveals an Unexpected Complex History

    PubMed Central

    Wang, Lei; Andrianopoulos, Kanella; Liu, Dan; Popoff, Michel Y.; Reeves, Peter R.

    2002-01-01

    The 46 serogroups of Salmonella enterica have different O-antigens, and each is thought to have a specific form of the O-antigen cluster. Comparison of the 145 serovars of serogroup B revealed much more intraserogroup genetic diversity than expected. The O27 factor, due to an α 1-6 linkage between O units in place of the more common α 1-2 linkage and previously thought to be due to a converting bacteriophage, is now shown to be due to a wzyα(1-6) gene located within the major gene cluster. Surprisingly a remnant of this gene in all O27− serovars shows that the ancestor was O27+. There are six distinct gene cluster forms, five apparently derived by a series of deletions and one by an insertion from an ancestral O27+ form present in 57 serovars. The history of the gene cluster and movement between subspecies I and II can be traced. Two of the derivative forms still have a functional wzyα(1-6) gene, while in three it has been inactivated by deletion or insertion. Two of the forms lacking a functional wzyα(1-6) gene have the wzyα(1-2) gene first described for strain LT2 as rfc, whereas for the third the wzy gene has not been located. PMID:11872718

  1. Complex-to-Predict Generational Shift between Nested and Clustered Organization of Individual Prey Networks in Digger Wasps

    PubMed Central

    Ballesteros, Yolanda; Polidori, Carlo; Tormos, José; Baños-Picón, Laura; Asís, Josep Daniel

    2014-01-01

    Although diet has traditionally been considered to be a property of the species or populations as a whole, there is nowadays extensive knowledge that individual specialization is widespread among animal populations. Nevertheless, the factors determining the shape of interactions within food webs remain largely undiscovered, especially in predatory insects. We used an aggregation of the digger wasp Bembix merceti to 1) analyse patterns of individual prey use across three flying seasons in a network–based context; and 2) test the effect of four potential factors that might explain network topologies (wasp mass, nest spatial distribution, simultaneous nest-provisioning, prey availability). Inter-individual diet variation was found in all three years, under different predator-prey network topologies: Individuals arranged in dietary clusters and displayed a checkerboard pattern in 2009, but showed nestedness in 2008 and 2010. Network topologies were not fully explained by the tested factors. Larger females consumed a higher proportion of the total number of prey species captured by the population as a whole, in such a way that nested patterns may arise from mass-dependent prey spectrum width. Conversely, individuals with similar body mass didn’t form clusters. Nested patterns seemed to be associated with a greater availability of the main prey species (a proxy for reduced intra-specific competition). Thus, according with theory, clusters seemed to appear when competition increased. On the other hand, the nests of the individuals belonging to a given cluster were not more closely located, and neither did individuals within a cluster provision their nests simultaneously. Thus, a female-female copying behaviour during foraging was unlikely. In conclusion, wasp populations can maintain a considerable individual variation across years under different food web organizations. The tested factors only partially accounted for the shift in network properties, and new analyses

  2. Improved fabrication of HgI/sub 2/ nuclear radiation detectors by machine-cleaving

    SciTech Connect

    Levi, A.; Burger, A.; Schieber, M.; Vandenberg, L.; Yellon, W.B.; Alkire, R.W.

    1982-01-01

    The perfection of machine-cleaved sections from HgI/sub 2/ bulk crystals was examined. The perfection of the machine-cleaved sections as established by gamma diffraction rocking curves was found to be much better than the perfection of hand-cleaved sections or as grown thin platelets, reaching a perfection similar to that of the wire-sawn sections of HgI/sub 2/. A correlation between the perfection and the thickness of the machine-cleaved section was also found, i.e., the thicker the cleaved-section the more perfect it is. The reproducibility of the fabrication was significantly improved by using machine cleaving in the process of fabrication. Large single crystals of HgI/sub 2/ weighing 20 to 200 g, can be grown from the vapor phase using the TOM Technique. In order to fabricate nuclear radiation detectors from these single crystals, thin sections of about 0.4 to 0.8 mm thickness have to be prepared. Up till now, the state-of-the-art of fabricating HgI/sub 2/ nuclear radiation detectors involved two methods to get thin sections from the large single crystals: (1) hand-cleaving using a razor-blade and (2) solution wire sawing. The chemical wire sawing method involves a loss of about 50% of the crystal volume and is usually followed by a chemical polishing process which involves a significant loss of volume of the original volume. This procedure is complicated and wasteful. The traditional fabrication method, i.e., hand-cleaving followed by rapid nonselective chemical etching, is simpler and less wasteful.

  3. Bacillus cereus Fnr binds a [4Fe-4S] cluster and forms a ternary complex with ResD and PlcR

    PubMed Central

    2012-01-01

    Background Bacillus cereus is a facultative anaerobe that causes diarrheal disease in humans. Diarrheal syndrome may result from the secretion of various virulence factors including hemolysin BL and nonhemolytic enterotoxin Nhe. Expression of genes encoding Hbl and Nhe is regulated by the two redox systems, ResDE and Fnr, and the virulence regulator PlcR. B. cereus Fnr is a member of the Crp/Fnr family of iron-sulfur (Fe-S) proteins. Only its apo-form has so far been studied. A major goal in deciphering the Fnr-dependent regulation of enterotoxin genes is thus to obtain and characterize holoFnr. Results Fnr has been subjected to in vitro Fe-S cluster reconstitution under anoxic conditions. UV-visible and EPR spectroscopic analyses together with the chemical estimation of the iron content indicated that Fnr binds one [4Fe-4S]2+ cluster per monomer. Atmospheric O2 causes disassembly of the Fe-S cluster, which exhibited a half-life of 15 min in air. Holo- and apoFnr have similar affinities for the nhe and hbl promoter regions, while holoFnr has a higher affinity for fnr promoter region than apoFnr. Both the apo- and holo-form of Fnr interact with ResD and PlcR to form a ternary complex. Conclusions Overall, this work shows that incorporation of the [4Fe-4S]2+ cluster is not required for DNA binding of Fnr to promoter regions of hbl and nhe enterotoxin genes or for the formation of a ternary complex with ResD and PlcR. This points to some new unusual properties of Fnr that may have physiological relevance in the redox regulation of enterotoxin gene regulation. PMID:22731107

  4. Malfunctioning of the Iron–Sulfur Cluster Assembly Machinery in Saccharomyces cerevisiae Produces Oxidative Stress via an Iron-Dependent Mechanism, Causing Dysfunction in Respiratory Complexes

    PubMed Central

    Gomez, Mauricio; Pérez-Gallardo, Rocío V.; Sánchez, Luis A.; Díaz-Pérez, Alma L.; Cortés-Rojo, Christian; Meza Carmen, Victor; Saavedra-Molina, Alfredo; Lara-Romero, Javier; Jiménez-Sandoval, Sergio; Rodríguez, Francisco; Rodríguez-Zavala, José S.; Campos-García, Jesús

    2014-01-01

    Biogenesis and recycling of iron–sulfur (Fe–S) clusters play important roles in the iron homeostasis mechanisms involved in mitochondrial function. In Saccharomyces cerevisiae, the Fe–S clusters are assembled into apoproteins by the iron–sulfur cluster machinery (ISC). The aim of the present study was to determine the effects of ISC gene deletion and consequent iron release under oxidative stress conditions on mitochondrial functionality in S. cerevisiae. Reactive oxygen species (ROS) generation, caused by H2O2, menadione, or ethanol, was associated with a loss of iron homeostasis and exacerbated by ISC system dysfunction. ISC mutants showed increased free Fe2+ content, exacerbated by ROS-inducers, causing an increase in ROS, which was decreased by the addition of an iron chelator. Our study suggests that the increment in free Fe2+ associated with ROS generation may have originated from mitochondria, probably Fe–S cluster proteins, under both normal and oxidative stress conditions, suggesting that Fe–S cluster anabolism is affected. Raman spectroscopy analysis and immunoblotting indicated that in mitochondria from SSQ1 and ISA1 mutants, the content of [Fe–S] centers was decreased, as was formation of Rieske protein-dependent supercomplex III2IV2, but this was not observed in the iron-deficient ATX1 and MRS4 mutants. In addition, the activity of complexes II and IV from the electron transport chain (ETC) was impaired or totally abolished in SSQ1 and ISA1 mutants. These results confirm that the ISC system plays important roles in iron homeostasis, ROS stress, and in assembly of supercomplexes III2IV2 and III2IV1, thus affecting the functionality of the respiratory chain. PMID:25356756

  5. Size evolution relativistic DFT-QTAIM study on the gold cluster complexes Au4-S-CnH2n-S‧-Au4‧ (n = 2-5)

    NASA Astrophysics Data System (ADS)

    Rodríguez, Juan I.; Uribe, Emilbus A.; Baltazar-Méndez, María I.; Autschbach, Jochen; Castillo-Alvarado, F. L.; Gutiérrez-González, Israel

    2016-09-01

    We introduce relativistic density functional theory (DFT) calculations on the gold cluster complexes (cluster-molecule-cluster) Au4-S-CnH2n-S‧-Au4‧ (n = 2-5). The structural, electronic and relativistic (ZORA) Bader's quantum theory of atoms in molecules (QTAIM) properties of the two lowest-energy complex isomers were computed as a function of the alkanedithiol size (n). The lowest-energy isomer is a triplet spin state independently of the complex size. According to QTAIM, the Au-Au and S-Au bonds are classified as closed shell (non-covalent) type. The HOMO-LUMO gap of the cluster complexes shows a zigzag behavior typical of gold nanoclusters with respect to the size of the alkanedithiol chain (n).

  6. Delta ribozyme has the ability to cleave in transan mRNA.

    PubMed Central

    Roy, G; Ananvoranich, S; Perreault, J P

    1999-01-01

    We report here the first demonstration of the cleavage of an mRNA in trans by delta ribozyme derived from the antigenomic version of the human hepatitis delta virus (HDV). We characterized potential delta ribozyme cleavage sites within HDV mRNA sequence (i.e. C/UGN6), using oligonucleotide binding shift assays and ribonuclease H hydrolysis. Ribozymes were synthesized based on the structural data and then tested for their ability to cleave the mRNA. Of the nine ribozymes examined, three specifically cleaved a derivative HDV mRNA. All three active ribozymes gave consistent indications that they cleaved single-stranded regions. Kinetic characterization of the ability of ribozymes to cleave both the full-length mRNA and either wild-type or mutant small model substrate suggests: (i) delta ribozyme has turnovers, that is to say, several mRNA molecules can be successively cleaved by one ribozyme molecule; and (ii) the substrate specificity of delta ribozyme cleavage is not restricted to C/UGN6. Specifically, substrates with a higher guanosine residue content upstream of the cleavage site (i.e. positions -4 to -2) were always cleaved more efficiently than wild-type substrate. This work shows that delta ribozyme constitutes a potential catalytic RNA for further gene-inactivation therapy. PMID:9927724

  7. Interaction between Nbp35 and Cfd1 Proteins of Cytosolic Fe-S Cluster Assembly Reveals a Stable Complex Formation in Entamoeba histolytica

    PubMed Central

    Anwar, Shadab; Dikhit, Manas Ranjan; Singh, Krishn Pratap; Kar, Rajiv Kumar; Zaidi, Amir; Sahoo, Ganesh Chandra; Roy, Awadh Kishore; Nozaki, Tomoyoshi; Das, Pradeep; Ali, Vahab

    2014-01-01

    Iron-Sulfur (Fe-S) proteins are involved in many biological functions such as electron transport, photosynthesis, regulation of gene expression and enzymatic activities. Biosynthesis and transfer of Fe-S clusters depend on Fe-S clusters assembly processes such as ISC, SUF, NIF, and CIA systems. Unlike other eukaryotes which possess ISC and CIA systems, amitochondriate Entamoeba histolytica has retained NIF & CIA systems for Fe-S cluster assembly in the cytosol. In the present study, we have elucidated interaction between two proteins of E. histolytica CIA system, Cytosolic Fe-S cluster deficient 1 (Cfd1) protein and Nucleotide binding protein 35 (Nbp35). In-silico analysis showed that structural regions ranging from amino acid residues (P33-K35, G131-V135 and I147-E151) of Nbp35 and (G5-V6, M34-D39 and G46-A52) of Cfd1 are involved in the formation of protein-protein complex. Furthermore, Molecular dynamic (MD) simulations study suggested that hydrophobic forces surpass over hydrophilic forces between Nbp35 and Cfd1 and Van-der-Waal interaction plays crucial role in the formation of stable complex. Both proteins were separately cloned, expressed as recombinant fusion proteins in E. coli and purified to homogeneity by affinity column chromatography. Physical interaction between Nbp35 and Cfd1 proteins was confirmed in vitro by co-purification of recombinant Nbp35 with thrombin digested Cfd1 and in vivo by pull down assay and immunoprecipitation. The insilico, in vitro as well as in vivo results prove a stable interaction between these two proteins, supporting the possibility of its involvement in Fe-S cluster transfer to target apo-proteins through CIA machinery in E. histolytica. Our study indicates that initial synthesis of a Fe-S precursor in mitochondria is not necessary for the formation of Cfd1-Nbp35 complex. Thus, Cfd1 and Nbp35 with the help of cytosolic NifS and NifU proteins can participate in the maturation of non-mitosomal Fe-S proteins without any

  8. Interaction between Nbp35 and Cfd1 proteins of cytosolic Fe-S cluster assembly reveals a stable complex formation in Entamoeba histolytica.

    PubMed

    Anwar, Shadab; Dikhit, Manas Ranjan; Singh, Krishn Pratap; Kar, Rajiv Kumar; Zaidi, Amir; Sahoo, Ganesh Chandra; Roy, Awadh Kishore; Nozaki, Tomoyoshi; Das, Pradeep; Ali, Vahab

    2014-01-01

    Iron-Sulfur (Fe-S) proteins are involved in many biological functions such as electron transport, photosynthesis, regulation of gene expression and enzymatic activities. Biosynthesis and transfer of Fe-S clusters depend on Fe-S clusters assembly processes such as ISC, SUF, NIF, and CIA systems. Unlike other eukaryotes which possess ISC and CIA systems, amitochondriate Entamoeba histolytica has retained NIF & CIA systems for Fe-S cluster assembly in the cytosol. In the present study, we have elucidated interaction between two proteins of E. histolytica CIA system, Cytosolic Fe-S cluster deficient 1 (Cfd1) protein and Nucleotide binding protein 35 (Nbp35). In-silico analysis showed that structural regions ranging from amino acid residues (P33-K35, G131-V135 and I147-E151) of Nbp35 and (G5-V6, M34-D39 and G46-A52) of Cfd1 are involved in the formation of protein-protein complex. Furthermore, Molecular dynamic (MD) simulations study suggested that hydrophobic forces surpass over hydrophilic forces between Nbp35 and Cfd1 and Van-der-Waal interaction plays crucial role in the formation of stable complex. Both proteins were separately cloned, expressed as recombinant fusion proteins in E. coli and purified to homogeneity by affinity column chromatography. Physical interaction between Nbp35 and Cfd1 proteins was confirmed in vitro by co-purification of recombinant Nbp35 with thrombin digested Cfd1 and in vivo by pull down assay and immunoprecipitation. The insilico, in vitro as well as in vivo results prove a stable interaction between these two proteins, supporting the possibility of its involvement in Fe-S cluster transfer to target apo-proteins through CIA machinery in E. histolytica. Our study indicates that initial synthesis of a Fe-S precursor in mitochondria is not necessary for the formation of Cfd1-Nbp35 complex. Thus, Cfd1 and Nbp35 with the help of cytosolic NifS and NifU proteins can participate in the maturation of non-mitosomal Fe-S proteins without any

  9. Comprehensive study of hexarhenium cluster complex Na4[{Re6Te8}(CN)6] - In terms of a new promising luminescent and X-ray contrast agent.

    PubMed

    Krasilnikova, Anna A; Solovieva, Anastasiya O; Ivanov, Anton A; Trifonova, Kristina E; Pozmogova, Tatiana N; Tsygankova, Alphiya R; Smolentsev, Anton I; Kretov, Evgeniy I; Sergeevichev, David S; Shestopalov, Michael A; Mironov, Yuri V; Shestopalov, Alexander M; Poveshchenko, Alexander F; Shestopalova, Lidiya V

    2017-02-01

    Octahedral rhenium cluster complexes may have considerable potential as therapeutic and diagnostic drugs due to their luminescent and X-ray contrast properties, as well as their ability to generate singlet oxygen upon photoirradiation. However, their potential biological effects and toxicity in vitro and in vivo are rather far from being understood. Thus, the aim of our research was to study cytotoxicity, intracellular localization and cellular uptake/elimination kinetics in vitro, biodistribution and acute intravenous toxicity in vivo of a complex Na4[{Re6Te8}(CN)6] as the promising compound for biomedical application. The results have demonstrated that the complex penetrates through cell membranes with the maximum accumulation in cells in 24h of incubation and have low toxic effects in vitro and in vivo. The median lethal dose (LD50) of intravenously administrated Na4[{Re6Te8}(CN)6] is equal to 1082±83mg/kg. These findings will be useful for future development of cluster-based agents for different biomedical applications. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Cu(II)-azide polynuclear complexes of Cu4 building clusters with Schiff-base co-ligands: synthesis, structures, magnetic behavior and DFT studies.

    PubMed

    Mukherjee, Sandip; Mukherjee, Partha Sarathi

    2013-03-21

    Three new copper-azido complexes [Cu(4)(N(3))(8)(L(1))(2)](n) (1), [Cu(4)(N(3))(6)(L(2))(2)(H(2)O)(2)] (2), and [Cu(4)(N(3))(6)(L(3))(2)](n) (3) [L(1) is the imine resulting from the condensation of pyridine-2-carboxaldehyde with N-methylethylenediamine, HL(2) and HL(3) are the condensation products of 2-hydroxy-3-methoxybenzaldehyde with N,N-diethylethylenediamine and N-ethylethylenediamine respectively] have been synthesized by using 0.5 molar equivalents of the Schiff base ligands with Cu(NO(3))(2)·3H(2)O and an excess of NaN(3). Single crystal X-ray structures show that the basic unit of these complexes contains very similar Cu(II)(4) building blocks. While 1 and 3 have overall 1D structures, 2 forms discrete tetranuclear clusters due to blocking of two coordination sites on the tetranuclear cluster by water molecules. Magnetic susceptibility measurements over a wide range of temperatures exhibit the presence of both antiferromagnetic and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional and two different basis sets) have been performed on the complexes 1-3 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

  11. Hydrido-ruthenium cluster complexes as models for reactive surface hydrogen species of ruthenium nanoparticles. Solid-state 2H NMR and quantum chemical calculations.

    PubMed

    Gutmann, Torsten; Walaszek, Bernadeta; Yeping, Xu; Wächtler, Maria; del Rosal, Iker; Grünberg, Anna; Poteau, Romuald; Axet, Rosa; Lavigne, Guy; Chaudret, Bruno; Limbach, Hans-Heinrich; Buntkowsky, Gerd

    2010-08-25

    The (2)H quadrupolar interaction is a sensitive tool for the characterization of deuterium-metal binding states. In the present study, experimental solid-state (2)H MAS NMR techniques are used in the investigations of two ruthenium clusters, D(4)Ru(4)(CO)(12) (1) and D(2)Ru(6)(CO)(18) (2), which serve as model compounds for typical two-fold, three-fold, and octahedral coordination sites on metal surfaces. By line-shape analysis of the (2)H MAS NMR measurements of sample 1, a quadrupolar coupling constant of 67 +/- 1 kHz, an asymmetry parameter of 0.67 +/- 0.1, and an isotropic chemical shift of -17.4 ppm are obtained. In addition to the neutral complex, sample 2 includes two ionic clusters, identified as anionic [DRu(6)(CO)(18)](-) (2(-)) and cationic [D(3)Ru(6)(CO)(18)](+) (2(+)). By virtue of the very weak quadrupolar interaction (<2 kHz) and the strong low-field shift (+16.8 ppm) of 2(-), it is shown that the deuteron is located in the symmetry center of the octahedron spanned by the six ruthenium atoms. For the cationic 2(+), the quadrupolar interaction is similar to that of the neutral 2. Quantum chemical DFT calculations at different model structures for these ruthenium clusters were arranged in order to help in the interpretation of the experimental results. It is shown that the (2)H nuclear quadrupolar interaction is a sensitive tool for distinguishing the binding state of the deuterons to the transition metal. Combining the data from the polynuclear complexes with the data from mononuclear complexes, a molecular ruler for quadrupolar interactions is created. This ruler now permits the solid-state NMR spectroscopic characterization of deuterium adsorbed on the surfaces of catalytically active metal nanoparticles.

  12. Ortho-para interconversion in cation-water complexes: The case of V+(H2O) and Nb+(H2O) clusters

    NASA Astrophysics Data System (ADS)

    Ward, T. B.; Miliordos, E.; Carnegie, P. D.; Xantheas, S. S.; Duncan, M. A.

    2017-06-01

    Vanadium and niobium cation-water complexes, V+(H2O) and Nb+(H2O), are produced by laser vaporization in a pulsed supersonic expansion, mass selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy using rare gas atom (Ar, Ne) complex predissociation. The vibrational bands measured in the O-H stretching region contain K-type rotational sub-band structure, which provides insight into the structures of these complexes. However, rotational sub-bands do not exhibit the simple patterns seen previously for other metal ion-water complexes. The A rotational constants are smaller than expected and the normal 3:1 intensity ratios for K = odd:even levels for independent ortho:para nuclear spin states are missing for some complexes. We relied on highly correlated internally contracted multi-reference configuration interaction and Coupled Cluster [CCSD(T)] electronic structure calculations of those complexes with and without the rare gas atoms to investigate these anomalies. Rare gas atoms were found to bind via asymmetric motifs to the hydrated complexes undergoing large amplitude motions that vibrationally average to the quasi-C2v symmetry with a significant probability off the C2 axis, thus explaining the reduced A values. Both vanadium and niobium cations exhibit unusually strong nuclear spin coupling to the hydrogen atoms of water, the values of which vary with their electronic state. This catalyzes ortho-para interconversion in some complexes and explains the rotational patterns. The rate of ortho-para relaxation in the equilibrated complexes must therefore be greater than the collisional cooling rate in the supersonic expansion (about 106 s-1).

  13. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  14. A Chandra Study of the Rosette Star-Forming Complex. II. Clusters in the Rosette Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Wang, Junfeng; Feigelson, Eric D.; Townsley, Leisa K.; Román-Zúñiga, Carlos G.; Lada, Elizabeth; Garmire, Gordon

    2009-05-01

    We explore here the young stellar populations in the Rosette Molecular Cloud (RMC) region with high spatial resolution X-ray images from the Chandra X-ray Observatory, which are effective in locating weak-lined T Tauri stars as well as disk-bearing young stars. A total of 395 X-ray point sources are detected, 299 of which (76%) have an optical or near-infrared (NIR) counterpart identified from deep FLAMINGOS images. From X-ray and mass sensitivity limits, we infer a total population of ~1700 young stars in the survey region. Based on smoothed stellar surface density maps, we investigate the spatial distribution of the X-ray sources and define three distinctive structures and substructures within them. Structures B and C are associated with previously known embedded IR clusters, while structure A is a new X-ray-identified unobscured cluster. A high-mass protostar RMCX #89 = IRAS 06306+0437 and its associated sparse cluster are studied. The different subregions are not coeval but do not show a simple spatial-age pattern. Disk fractions vary between subregions and are generally lsim20% of the total stellar population inferred from the X-ray survey. The data are consistent with speculations that triggered star formation around the H II region is present in the RMC, but do not support a simple sequential triggering process through the cloud interior. While a significant fraction of young stars are located in a distributed population throughout the RMC region, it is not clear if they originated in clustered environments.

  15. A CHANDRA STUDY OF THE ROSETTE STAR-FORMING COMPLEX. II. CLUSTERS IN THE ROSETTE MOLECULAR CLOUD

    SciTech Connect

    Wang Junfeng; Feigelson, Eric D.; Townsley, Leisa K.; Garmire, Gordon; Roman-Zuniga, Carlos G.; Lada, Elizabeth E-mail: edf@astro.psu.edu

    2009-05-01

    We explore here the young stellar populations in the Rosette Molecular Cloud (RMC) region with high spatial resolution X-ray images from the Chandra X-ray Observatory, which are effective in locating weak-lined T Tauri stars as well as disk-bearing young stars. A total of 395 X-ray point sources are detected, 299 of which (76%) have an optical or near-infrared (NIR) counterpart identified from deep FLAMINGOS images. From X-ray and mass sensitivity limits, we infer a total population of {approx}1700 young stars in the survey region. Based on smoothed stellar surface density maps, we investigate the spatial distribution of the X-ray sources and define three distinctive structures and substructures within them. Structures B and C are associated with previously known embedded IR clusters, while structure A is a new X-ray-identified unobscured cluster. A high-mass protostar RMCX no. 89 = IRAS 06306+0437 and its associated sparse cluster are studied. The different subregions are not coeval but do not show a simple spatial-age pattern. Disk fractions vary between subregions and are generally {approx}<20% of the total stellar population inferred from the X-ray survey. The data are consistent with speculations that triggered star formation around the H II region is present in the RMC, but do not support a simple sequential triggering process through the cloud interior. While a significant fraction of young stars are located in a distributed population throughout the RMC region, it is not clear if they originated in clustered environments.

  16. MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G

    PubMed Central

    Arfi, Yonathan; Minder, Laetitia; Di Primo, Carmelo; Le Roy, Aline; Ebel, Christine; Coquet, Laurent; Claverol, Stephane; Vashee, Sanjay; Jores, Joerg; Blanchard, Alain; Sirand-Pugnet, Pascal

    2016-01-01

    Mycoplasmas are “minimal” bacteria able to infect humans, wildlife, and a large number of economically important livestock species. Mycoplasma infections include a spectrum of clinical manifestations ranging from simple fever to fulminant inflammatory diseases with high mortality rates. These infections are mostly chronic, suggesting that mycoplasmas have developed means to evade the host immune response. Here we present and functionally characterize a two-protein system from Mycoplasma mycoides subspecies capri that is involved in the capture and cleavage of IgG. The first component, Mycoplasma Ig binding protein (MIB), is an 83-kDa protein that is able to tightly bind to the Fv region of a wide range of IgG. The second component, Mycoplasma Ig protease (MIP), is a 97-kDa serine protease that is able to cleave off the VH domain of IgG. We demonstrate that MIB is necessary for the proteolytic activity of MIP. Cleavage of IgG requires a sequential interaction of the different partners of the system: first MIB captures the IgG, and then MIP is recruited to the MIB–IgG complex, enabling protease activity. MIB and MIP are encoded by two genes organized in tandem, with homologs found in the majority of pathogenic mycoplasmas and often in multiple copies. Phylogenetic studies suggest that genes encoding the MIB–MIP system are specific to mycoplasmas and have been disseminated by horizontal gene transfer. These results highlight an original and complex system targeting the host immunoglobulins, playing a potentially key role in the immunity evasion by mycoplasmas. PMID:27114507

  17. Crystal Structure of Human Arginase l Complexed with Thiosemicarbazide Reveals an Unusual Thiocarbonly u-Sulfide Ligand in the Binuclear Manganese Cluster

    SciTech Connect

    Di Costanzo,L.; Pique, M.; Christianson, D.

    2007-01-01

    The crystal structure of the human arginase I-thiosemicarbazide complex reveals an unusual thiocarbonyl {mu}-sulfide ligand in the binuclear manganese cluster. The CS moiety of thiosemicarbazide bridges Mn2+A and Mn2+B with coordination distances of 2.6 and 2.4 Angstroms, respectively. Otherwise, the binding of thiosemicarbazide to human arginase I does not cause any significant structural changes in the active site. The crystal structure of the unliganded enzyme reveals a hydrogen-bonded water molecule that could support proton transfer between a {mu}-water molecule and H141 to regenerate the nucleophilic {mu}-hydroxide ion in the final step of catalysis.

  18. Cellular internalization and morphological analysis after intravenous injection of a highly hydrophilic octahedral rhenium cluster complex - a new promising X-ray contrast agent.

    PubMed

    Krasilnikova, Anna A; Solovieva, Anastasiya O; Trifonova, Kristina E; Brylev, Konstantin A; Ivanov, Anton A; Kim, Sung-Jin; Shestopalov, Michael A; Fufaeva, Maria S; Shestopalov, Alexander M; Mironov, Yuri V; Poveshchenko, Alexander F; Shestopalova, Lidia V

    2016-11-01

    The octahedral cluster compound Na2 H8 [{Re6 Se8 }(P(C2 H4 CONH2 )(C2 H4 COO)2 )6 ] has been shown to be highly radio dense, thus becoming a promising X-ray contrast agent. It was also shown that this compound had low cytotoxic effect in vitro, low acute toxicity in vivo and was eliminated rapidly from the body through the urinary tract. The present contribution describes a more detailed cellular internalization assay and morphological analysis after intravenous injection of this hexarhenium cluster compound at different doses. The median lethal dose (LD50 ) of intravenously administrated compound was calculated (4.67 ± 0.69 g/kg). Results of the study clearly indicated that the cluster complex Hn [{Re6 Se8 }(P(C2 H4 CONH2 )(C2 H4 COO)2 )6 ](n-10) was not internalized into cells in vitro and induced only moderate morphological alterations of kidneys at high doses without any changes in morphology of liver, spleen, duodenum, or heart of mice. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  19. Bismuth(III) complexes derived from α-amino acids: the impact of hydrolysis and oxido-cluster formation on their activity against Helicobacter pylori.

    PubMed

    Busse, Madleen; Border, Emily; Junk, Peter C; Ferrero, Richard L; Andrews, Philip C

    2014-12-28

    Eight bismuth(III) complexes derived from a variety of α-amino acids covering a range of physico-chemical properties (L-phenylalanine (Phe), L-proline (Pro), L-methionine (Met), L-cysteine (Cys), D,L-serine (Ser), L-tyrosine (Tyr), l-aspartic acid (Asp) and L-glutamic acid (Glu)) have been synthesised, characterised, and evaluated for their activity against Helicobacter pylori. The optimal synthetic procedure utilises [Bi(O(t)Bu)3], giving the complexes [BiL3] (L = Phe 1, Pro 2, Met 3, Ser 5, Tyr 6) and [Bi2L3] (L = Cys 4, Asp 7, Glu 8) cleanly and in good yield. However, the synthesis is sensitive to both temperature and moisture. The solubility and stability of the bismuth(III) complexes was investigated using ESI-MS. Almost all compounds (except for [Bi(Phe)3] and [Bi(Pro)3]) were found to be partially or completely soluble in aqueous solution giving a pH 2.5-5.0, indicating the presence of free α-amino acid and hydrolysis of the bismuth(III) complexes to polynuclear bismuth oxido-clusters. The results of the bactericidal studies against Helicobacter pylori demonstrate that this hydrolysis process impacts significantly on the observed Minimum Inhibitory Concentration (MICs) which are increased substantially, often by many orders of magnitude, when the complexes are initially prepared in water rather than DMSO.

  20. Total and caspase-cleaved cytokeratin 18 in chronic cholecystitis: A prospective study

    PubMed Central

    Simopoulos, Constantinos; Tsaroucha, Alexandra K; Asimakopoulos, Byron; Giatromanolaki, Alexandra; Gavriilidis, Paschalis; Polychronidis, Alexandros; Karayiannakis, Anastasios

    2008-01-01

    Background Cell death mode has been studied in cancer, autoimmune, and neurodegenerative diseases. In this study, apoptosis and necrosis are investigated for the first time in patients with chronic calculous cholecystitis. Methods and materials Thirty five (35) patients (27 women and 8 men, aged 55.65 ± 13.48 years) with symptomatic chronic calculous cholecystitis underwent laparoscopic cholecystectomy. The early specific apoptotic tendency (caspase-cleaved cytokeratin 18) was studied in these patients with M30 Apoptosense ELISA and the total cytokerarin 18 (both derived from apoptosis and necrosis) with M65 ELISA. The ratio M30/M65 (caspase-cleaved to total cytokeratin 18) was also computed. According to the histopathological examination, the patients were divided in two groups: group A included patients with chronic inactive cholecystitis (n = 10), and group B those with chronic active cholecystitis (n = 25). Results The concentrations of caspase-cleaved cytokerarin 18 (CK18), and especially those of total CK18, were higher in bile samples than in serum samples. In group B, there were significant differences between serum and bile samples regarding both caspase-cleaved CK18 and total CK18. Cells staining positive for caspase-cleaved CK18 were present in the epithelial cells of the mucosa of the gallbladder. Conclusion CK18 is expressed in the gallbladder epithelial cells. The concentrations of both caspase-cleaved CK18 and total CK18 were higher in bile samples than in serum samples. The levels of total CK18, as well as caspase-cleaved CK18, do not seem to differ between active and inactive chronic cholecystitis. PMID:18460214

  1. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states.

    PubMed

    Godtliebsen, Ian H; Christiansen, Ove

    2015-10-07

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  2. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states

    NASA Astrophysics Data System (ADS)

    Godtliebsen, Ian H.; Christiansen, Ove

    2015-10-01

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  3. Effect of the Keggin anions on assembly of Cu{sup I}-bis(tetrazole) thioether complexes containing multinuclear Cu{sup I}-cluster

    SciTech Connect

    Wang Xiuli; Gao Qiang; Tian Aixiang; Hu Hailiang; Liu Guocheng

    2012-03-15

    In order to investigate the effect of polyoxometalate (POM) on the assembly of transition metal-bis(tetrazole) thioether complexes, three new complexes based on different Keggin anions and multinuclear Cu{sup I}-cluster [Cu{sup I}{sub 12}(bmtr){sub 9}(HSiMo{sub 12}O{sub 40}){sub 4}] (1), [Cu{sup I}{sub 3}(bmtr){sub 3}(PM{sub 12}O{sub 40})] (M=W for 2; Mo for 3) (bmtr=1,3-bis(1-methyl-5-mercapto-1,2,3,4-tetrazole)propane), have been hydrothermally synthesized and characterized by routine physical methods and single crystal X-ray diffraction. In compound 1, two kinds of nanometer-scale tetranuclear subunits linked by [SiMo{sub 12}O{sub 40}]{sup 4-} polyanions assemble a (3, 4)-connected three-dimensional (3D) self-penetrating framework. Compounds 2 and 3 are isostructural, exhibiting a 1D chain with [PW{sub 12}O{sub 40}]{sup 3-}/[PMo{sub 12}O{sub 40}]{sup 3-} polyanions and trinuclear clusters arranging alternately. The distinct structural differences between these POM-based Cu{sup I}-bmtr complexes of 1 and 2/3 maybe rest on the contrast of Keggin-type polyoxometalate with different central heteroatoms, which have been discussed in detail. In addition, the electrochemical properties of the title complexes have been investigated. - Graphical abstract: Three new complexes based on different Keggin anions and multinuclear Cu{sup I}-cluster have been synthesized under hydrothermal conditions. The Keggin polyanions with different central heteroatoms play a key role. Highlights: Black-Right-Pointing-Pointer The flexible bis(tetrazole)-based thioether ligand with some advantages have been used. Black-Right-Pointing-Pointer The effect of Keggin anions with different central heteroatoms has been discussed in detail. Black-Right-Pointing-Pointer The electrochemical behaviors and electrocatalysis property have been investigated.

  4. Spindle-to-cortex communication in cleaving, polyspermic Xenopus eggs

    PubMed Central

    Field, Christine M.; Groen, Aaron C.; Nguyen, Phuong A.; Mitchison, Timothy J.

    2015-01-01

    Mitotic spindles specify cleavage planes in early embryos by communicating their position and orientation to the cell cortex using microtubule asters that grow out from the spindle poles during anaphase. Chromatin also plays a poorly understood role. Polyspermic fertilization provides a natural experiment in which aster pairs from the same spindle (sister asters) have chromatin between them, whereas asters pairs from different spindles (nonsisters) do not. In frogs, only sister aster pairs induce furrows. We found that only sister asters recruited two conserved furrow-inducing signaling complexes, chromosome passenger complex (CPC) and Centralspindlin, to a plane between them. This explains why only sister pairs induce furrows. We then investigated factors that influenced CPC recruitment to microtubule bundles in intact eggs and a cytokinesis extract system. We found that microtubule stabilization, optimal starting distance between asters, and proximity to chromatin all favored CPC recruitment. We propose a model in which proximity to chromatin biases initial CPC recruitment to microtubule bundles between asters from the same spindle. Next a positive feedback between CPC recruitment and microtubule stabilization promotes lateral growth of a plane of CPC-positive microtubule bundles out to the cortex to position the furrow. PMID:26310438

  5. Energy transfer efficiency based on one-and two-photon FRET microscopy differentiates between clustered and random distribution of membrane-bound receptor-ligand complexes

    NASA Astrophysics Data System (ADS)

    Wallrabe, Horst; Elangovan, Masilamani; Burchard, Almut; Barroso, Margarida

    2002-06-01

    We are investigating membrane-based sorting processes in polarized epithelial MDCK cells, which most likely involves membrane microdomains. We have postulated that proteins contained in these microdomains, cluster, and to prove this, we have internalized differently fluorophore labeled pIgA-R ligands in MDCK cells, stably transfected with polymeric IgA receptors (pIgA-R), from opposite plasma membranes. Our previous work showed that these receptor-ligand complexes colocalize in the apical recycling endosome (ARE), underneath the apical plasma membrane. Quantitative one-photon confocal and 2-photon (2-P) FRET microscopy allowed us to calculate energy transfer efficiency (E%). Unquenched donor levels where established based on a novel algorithm, which corrects the FRET contamination of acceptor bleed-through and donor crosstalk. Using different emission filters also confirmed the veracity of the algorithm. 2-P FRET allows the selection of a specific donor wavelength, which does not precipitate acceptor bleed-through, a clear advantage over 1-P confocal microscopy. Results show that E% is independent of acceptor levels, an indication of a clustered distribution, as in random distribution E% rises with increasing acceptor levels. However, E% decreases with increasing donor and donor:acceptor ratio levels, which we have termed 'donor geometric exclusion', where some donors in a cluster block others from interacting with an acceptor. We submit that this is a second indicator for a clustered pattern, because in a random, dispersed situation donors are not likely to be in close proximity to have such an effect. We have developed a model explaining this phenomenon.

  6. Calculation of Heats of Formation for Zn Complexes: Comparison of Density Functional Theory, Second Order Perturbation Theory, Coupled-Cluster and Complete Active Space Methods

    PubMed Central

    Weaver, Michael N.; Ma, Dongxia; Kim, Hyun Jung

    2013-01-01

    Heats of formation were predicted for nine ZnX complexes (X= Zn, H, O, F2, S, Cl, Cl2, CH3, (CH3)2) using fourteen density functionals, MP2 calculations and the CCSD and CCSD(T) coupled-cluster methods. Calculations utilized the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Heats of formation were most accurately predicted by the TPSSTPSS and TPSSKCIS density functionals, and the BLYP, B3LYP, MP2, CCSD and CCSD(T) levels were among the poorest performing methods based on accuracy. A wide range of Zn2 equilibrium bond distances were predicted, indicating that many of the studied levels of theory may be unable to adequately describe this transition metal dimer. To further benchmark the accuracy of the density functional methods, high-level CASSCF and CASPT2 calculations were performed to estimate bond dissociation energies, equilibrium bond lengths and heats of formation for the diatomic Zn complexes and the latter two quantities were compared with the results of DFT, MP2 and coupled-cluster calculations as well as experimental values. PMID:24409106

  7. Furrow microtubules and localized exocytosis in cleaving Xenopus laevis embryos

    NASA Technical Reports Server (NTRS)

    Danilchik, Michael V.; Bedrick, Steven D.; Brown, Elizabeth E.; Ray, Kimberly

    2003-01-01

    In dividing Xenopus eggs, furrowing is accompanied by expansion of a new domain of plasma membrane in the cleavage plane. The source of the new membrane is known to include a store of oogenetically produced exocytotic vesicles, but the site where their exocytosis occurs has not been described. Previous work revealed a V-shaped array of microtubule bundles at the base of advancing furrows. Cold shock or exposure to nocodazole halted expansion of the new membrane domain, which suggests that these microtubules are involved in the localized exocytosis. In the present report, scanning electron microscopy revealed collections of pits or craters, up to approximately 1.5 micro m in diameter. These pits are evidently fusion pores at sites of recent exocytosis, clustered in the immediate vicinity of the deepening furrow base and therefore near the furrow microtubules. Confocal microscopy near the furrow base of live embryos labeled with the membrane dye FM1-43 captured time-lapse sequences of individual exocytotic events in which irregular patches of approximately 20 micro m(2) of unlabeled membrane abruptly displaced pre-existing FM1-43-labeled surface. In some cases, stable fusion pores, approximately 2 micro m in diameter, were seen at the surface for up to several minutes before suddenly delivering patches of unlabeled membrane. To test whether the presence of furrow microtubule bundles near the surface plays a role in directing or concentrating this localized exocytosis, membrane expansion was examined in embryos exposed to D(2)O to induce formation of microtubule monasters randomly under the surface. D(2)O treatment resulted in a rapid, uniform expansion of the egg surface via random, ectopic exocytosis of vesicles. This D(2)O-induced membrane expansion was completely blocked with nocodazole, indicating that the ectopic exocytosis was microtubule-dependent. Results indicate that exocytotic vesicles are present throughout the egg subcortex, and that the presence of

  8. Furrow microtubules and localized exocytosis in cleaving Xenopus laevis embryos

    NASA Technical Reports Server (NTRS)

    Danilchik, Michael V.; Bedrick, Steven D.; Brown, Elizabeth E.; Ray, Kimberly

    2003-01-01

    In dividing Xenopus eggs, furrowing is accompanied by expansion of a new domain of plasma membrane in the cleavage plane. The source of the new membrane is known to include a store of oogenetically produced exocytotic vesicles, but the site where their exocytosis occurs has not been described. Previous work revealed a V-shaped array of microtubule bundles at the base of advancing furrows. Cold shock or exposure to nocodazole halted expansion of the new membrane domain, which suggests that these microtubules are involved in the localized exocytosis. In the present report, scanning electron microscopy revealed collections of pits or craters, up to approximately 1.5 micro m in diameter. These pits are evidently fusion pores at sites of recent exocytosis, clustered in the immediate vicinity of the deepening furrow base and therefore near the furrow microtubules. Confocal microscopy near the furrow base of live embryos labeled with the membrane dye FM1-43 captured time-lapse sequences of individual exocytotic events in which irregular patches of approximately 20 micro m(2) of unlabeled membrane abruptly displaced pre-existing FM1-43-labeled surface. In some cases, stable fusion pores, approximately 2 micro m in diameter, were seen at the surface for up to several minutes before suddenly delivering patches of unlabeled membrane. To test whether the presence of furrow microtubule bundles near the surface plays a role in directing or concentrating this localized exocytosis, membrane expansion was examined in embryos exposed to D(2)O to induce formation of microtubule monasters randomly under the surface. D(2)O treatment resulted in a rapid, uniform expansion of the egg surface via random, ectopic exocytosis of vesicles. This D(2)O-induced membrane expansion was completely blocked with nocodazole, indicating that the ectopic exocytosis was microtubule-dependent. Results indicate that exocytotic vesicles are present throughout the egg subcortex, and that the presence of

  9. A multifunctional lipoxygenase with fatty acid hydroperoxide cleaving activity from the moss Physcomitrella patens.

    PubMed

    Senger, Toralf; Wichard, Thomas; Kunze, Susan; Göbel, Cornelia; Lerchl, Jens; Pohnert, Georg; Feussner, Ivo

    2005-03-04

    A complex mixture of fatty acid-derived aldehydes, ketones, and alcohols is released upon wounding of the moss Physcomitrella patens. To investigate the formation of these oxylipins at the molecular level we isolated a lipoxygenase from P. patens, which was identified in an EST library by sequence homology to lipoxygenases from plants. Sequence analysis of the cDNA showed that it exhibits a domain structure similar to that of type2 lipoxygenases from plants, harboring an N-terminal import signal for chloroplasts. The recombinant protein was identified as arachidonate 12-lipoxygenase and linoleate 13-lipoxygenase with a preference for arachidonic acid and eicosapentaenoic acid. In contrast to any other lipoxygenase cloned so far, this enzyme exhibited in addition an unusual high hydroperoxidase and also a fatty acid chain-cleaving lyase activity. Because of these unique features the pronounced formation of (2Z)-octen-1-ol, 1-octen-3-ol, the dienal (5Z,8Z,10E)-12-oxo-dodecatrienoic acid and 12-keto eicosatetraenoic acid was observed when arachidonic acid was administered as substrate. 12-Hydroperoxy eicosatetraenoic acid was found to be only a minor product. Moreover, the P. patens LOX has a relaxed substrate tolerance accepting C(18)-C(22) fatty acids giving rise to even more LOX-derived products. In contrast to other lipoxygenases a highly diverse product spectrum is formed by a single enzyme accounting for most of the observed oxylipins produced by the moss. This single enzyme might, in a fast and effective way, be involved in the formation of signal and/or defense molecules thus contributing to the broad resistance of mosses against pathogens.

  10. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

    PubMed

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

    2011-06-17

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

  11. High-throughput assay and engineering of self-cleaving ribozymes by sequencing

    PubMed Central

    Kobori, Shungo; Nomura, Yoko; Miu, Anh; Yokobayashi, Yohei

    2015-01-01

    Self-cleaving ribozymes are found in all domains of life and are believed to play important roles in biology. Additionally, self-cleaving ribozymes have been the subject of extensive engineering efforts for applications in synthetic biology. These studies often involve laborious assays of multiple individual variants that are either designed rationally or discovered through selection or screening. However, these assays provide only a limited view of the large sequence space relevant to the ribozyme function. Here, we report a strategy that allows quantitative characterization of greater than 1000 ribozyme variants in a single experiment. We generated a library of predefined ribozyme variants that were converted to DNA and analyzed by high-throughput sequencing. By counting the number of cleaved and uncleaved reads of every variant in the library, we obtained a complete activity profile of the ribozyme pool which was used to both analyze and engineer allosteric ribozymes. PMID:25829176

  12. Enterovirus 71 Infection Cleaves a Negative Regulator for Viral Internal Ribosomal Entry Site-Driven Translation

    PubMed Central

    Chen, Li-Lien; Kung, Yu-An; Weng, Kuo-Feng; Lin, Jing-Yi; Horng, Jim-Tong

    2013-01-01

    Far-upstream element-binding protein 2 (FBP2) is an internal ribosomal entry site (IRES) trans-acting factor (ITAF) that negatively regulates enterovirus 71 (EV71) translation. This study shows that EV71 infection cleaved FBP2. Live EV71 and the EV71 replicon (but not UV-inactivated virus particles) induced FBP2 cleavage, suggesting that viral replication results in FBP2 cleavage. The results also showed that virus-induced proteasome, autophagy, and caspase activity co-contribute to EV71-induced FBP2 cleavage. Using FLAG-fused FBP2, we mapped the potential cleavage fragments of FBP2 in infected cells. We also found that FBP2 altered its function when its carboxyl terminus was cleaved. This study presents a mechanism for virus-induced cellular events to cleave a negative regulator for viral IRES-driven translation. PMID:23345520

  13. Cleaved caspase-3 in lung epithelium of children who died with acute respiratory distress syndrome.

    PubMed

    Bem, Reinout A; van der Loos, Chris M; van Woensel, Job B M; Bos, Albert P

    2010-09-01

    To investigate the extent of cleaved caspase-3 immunostaining in lung epithelial cells in children with acute respiratory distress syndrome. Observational study in sixteen children who died with acute respiratory distress syndrome and diffuse alveolar damage. Pediatric intensive care unit. Sixteen children with fatal acute respiratory distress syndrome and diffuse alveolar damage. None. Double immunohistochemistry for cleaved caspase-3 and (pan)cytokeratin in lung tissues obtained at autopsy. Spectral imaging was used for the quantification of immunohistochemistry colocalization of these markers. We found a wide range in the percentage of alveolar epithelial cell surface area with positive cleaved caspase-3 staining in the lungs of children with acute respiratory distress syndrome (from 1% to almost 20%). The degree of caspase-3 immunostaining in epithelial cells positively correlated with age. There is a high variability in the extent of classic apoptosis in lung epithelial cells in pediatric acute respiratory distress syndrome, potentially in part dependent on age.

  14. Complexation of the vulcanization accelerator tetramethylthiuram disulfide and related molecules with zinc compounds including zinc oxide clusters (Zn4O4).

    PubMed

    Steudel, Ralf; Steudel, Yana; Wong, Ming Wah

    2008-01-01

    Zinc chemicals are used as activators in the vulcanization of organic polymers with sulfur to produce elastic rubbers. In this work, the reactions of Zn(2+), ZnMe(2), Zn(OMe)(2), Zn(OOCMe)(2), and the heterocubane cluster Zn(4)O(4) with the vulcanization accelerator tetramethylthiuram disulfide (TMTD) and with the related radicals and anions Me(2)NCS(2)(*), Me(2)NCS(3)(*), Me(2)NCS(2)(-), and Me(2)NCS(3)(-) have been studied by quantum chemical methods at the MP2/6-31+G(2df,p)//B3LYP/6-31+G* level of theory. More than 35 zinc complexes have been structurally characterized and the energies of formation from their components calculated for the first time. The binding energy of TMTD as a bidendate ligand increases in the order ZnMe(2)complexes with the radicals Me(2)NCS(2)(*) and Me(2)NCS(3)(*). Dissociation of the TMTD molecule at the S-S bond on reaction with the Zn(4)O(4) cluster is predicted to be strongly exothermic, in sharp contrast to the endothermic S-S bond dissociation of the free molecule. The same holds for tetramethylthiuram trisulfide (TMTT). Surprisingly, the resulting complexes contain Zn-S as well as S-O bonds. The Zn(4)O(4) nanocluster serves here as a model for bulk zinc oxide used as an activator in rubber vulcanization by sulfur. The further uptake of sulfur atoms by the various complexes from S(8) or TMTD with formation of species derived from the radical Me(2)NCS(3)(*) or the trithiocarbamate anion Me(2)NCS(3)(-) is endothermic for mono- and dinuclear zinc dithiocarbamate (dtc) complexes such as [Zn(dtc)(2)] and [Zn(2)(dtc)(4)], but exothermic in the case of polynuclear zinc oxide species containing bridging ligands as in [Zn(4)O(4)(mu-S(2)CNMe(2))] and [Zn(4)O(4)(mu-dtc)]. Therefore, zinc oxide as a polynuclear species is predicted to promote the formation of trisulfido complexes, which are generally assumed to serve as catalysts for the transfer of

  15. Edge-bridging and face-capping coordination of alkenyl ligands in triruthenium carbonyl cluster complexes derived from hydrazines: synthetic, structural, theoretical, and kinetic studies.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; Fernández-Colinas, José M; García-Granda, Santiago; Martínez-Méndez, Lorena; Pérez-Carreño, Enrique

    2004-12-03

    The reactions of the triruthenium cluster complex [Ru3(mu-H)(mu3-eta2-HNNMe2)(CO)9] (1; H2NNMe2=1,1-dimethylhydrazine) with alkynes (PhC triple bond CPh, HC triple bond CH, MeO2CC triple bond CCO2Me, PhC triple bond CH, MeO2CC triple bond CH, HOMe2CC triple bond CH, 2-pyC triple bond CH) give trinuclear complexes containing edge-bridging and/or face-capping alkenyl ligands. Whereas the edge-bridged products are closed triangular species (three Ru-Ru bonds), the face-capped products are open derivatives (two Ru-Ru bonds). For terminal alkynes, products containing gem (RCCH2) and/or trans (RHCCH) alkenyl ligands have been identified in both edge-bridging and face-capping positions, except for the complex [Ru3(mu3-eta2-HNNMe2)(mu3-eta3-HCCH-2-py)(mu-CO)(CO)7], which has the two alkenyl H atoms in a cis arrangement. Under comparable reaction conditions (1:1 molar ratio, THF at reflux, time required for the consumption of complex 1), some reactions give a single product, but most give mixtures of isomers (not all the possible ones), which were separated. To determine the effect of the hydrazido ligand, the reactions of [Ru3(mu-H)(mu3-eta2-MeNNHMe)(CO)9] (2; HMeNNHMe=1,2-dimethylhydrazine) with PhC triple bond CPh, PhC triple bond CH, and HC triple bond CH were also studied. For edge-bridged alkenyl complexes, the Ru--Ru edge that is spanned by the alkenyl ligand depends on the position of the methyl groups on the hydrazido ligand. For face-capped alkenyl complexes, the relative orientation of the hydrazido and alkenyl ligands also depends on the position of the methyl groups on the hydrazido ligand. A kinetic analysis of the reaction of 1 with PhC[triple chemical bond]CPh revealed that the reaction follows an associative mechanism, which implies that incorporation of the alkyne in the cluster is rate-limiting and precedes the release of a CO ligand. X-ray diffraction, IR and NMR spectroscopy, and calculations of minimum-energy structures by DFT methods were used to

  16. Raman study of in vivo synthesized Zn(II)-metallothionein complexes: structural insight into metal clusters and protein folding.

    PubMed

    Torreggiani, Armida; Domènech, Jordi; Atrian, Sílvia; Capdevila, Mercè; Tinti, Anna

    2008-12-01

    Metallothioneins (MTs) are metal-chelating peptides that play an active role in zinc homeostasis. The participation of metal ligands other than cysteines and the presence of secondary structure elements in metal-MT complexes are fairly unknown, especially in nonvertebrate MTs. Here, four Zn(II) complexes of invertebrate MTs (mollusc, insect, nematode, and echinoderm) and the Zn(II)-MT complex of the mammalian MT1 isoform, heterologously synthesized in E. coli, were studied by analytic and spectroscopic techniques. By Raman and circular dichroism spectroscopy, new structural informations were obtained. The five analyzed MT isoforms consist largely of beta-turns with the near exclusion of alpha-helical segments. Raman spectroscopy was revealed as an useful tool, providing information about the state of the cysteine sulfur atoms (metal coordinated and oxidized), the participation of histidine in metal coordination, and the molecular environment of tyrosine residues. In all the five Zn(II)-MT studied samples, acid-labile sulfide anions were found as nonproteic ligands, since sulfide-containing and sulfide-devoid species coexisted in the corresponding preparations. Significantly, Raman bands useful as markers of sulfide bridging ligands were identified. Overall, this work illustrates how the combination of analytical and spectroscopic techniques can be a very informative approach for the analysis of in vivo-synthesized metal-MT complexes, providing new data on the metal binding behavior of MTs from the most diverse organisms.

  17. Method for assaying clustered DNA damages

    DOEpatents

    Sutherland, Betsy M.

    2004-09-07

    Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (.PHI..sub.c) in the DNA is then calculated.

  18. Characterizing the intrinsic stability of gas-phase clusters of transition metal complex dianions with alkali metal counterions: counterion perturbation of multiply charged anions.

    PubMed

    Burke, Ruth M; Boxford, William E; Dessent, Caroline E H

    2007-02-14

    The authors report the gas-phase generation and characterization of a series of cation-dianion clusters, e.g., M(+).PtCl(6) (2-), M(+).PtCl(4) (2-), M(+).Pt(CN)(6) (2-), and M(+).Pd(CN)(4) (2-), where M(+)=Na(+),K(+),Rb(+), as model systems for investigating gas-phase contact ionpairs. Low-energy collisional excitation of these systems isolated within a quadrupole ion trap reveals that the fragmentation products are determined by the dianion and are independent of the counterion. This indicates that cation-dianion clusters represent gaseous ion-pair complexes, in line with recent findings for K(+).Pt(CN)(n) (2-), n=4,6 [Burke et al., J. Chem. Phys. 125, 021105 (2006)]. The relative fragmentation energies of several cation-dianion systems are obtained as a function of the counterion to explore the nature of ion-pair binding. For most of the systems studied, e.g., M(+).PtCl(6) (2-), the fragmentation energy increases as the cation size decreases, in line with a simple electrostatic description of the cation-dianion binding. However, the M(+).Pt(CN)(4) (2-) clusters displayed the reverse trend with the fragmentation energy increasing as the cation size increases. Density functional theory calculations of the cation-dianion fragmentation potential energy surfaces reveal the existence of a novel double-minima surface, separated by a repulsive Coulomb barrierlike feature at short range. The experimentally observed trends in the fragmentation energies can be fully understood with reference to the computed surfaces, hence providing strong support for the existence of the double-minima surface.

  19. σ-Aromatic cyclic M3(+) (M = Cu, Ag, Au) clusters and their complexation with dimethyl imidazol-2-ylidene, pyridine, isoxazole, furan, noble gases and carbon monoxide.

    PubMed

    Pan, Sudip; Saha, Ranajit; Mandal, Subhajit; Chattaraj, Pratim K

    2016-04-28

    The σ-aromaticity of M3(+) (M = Cu, Ag, Au) is analyzed and compared with that of Li3(+) and a prototype σ-aromatic system, H3(+). Ligands (L) like dimethyl imidazol-2-ylidene, pyridine, isoxazole and furan are employed to stabilize these monocationic M3(+) clusters. They all bind M3(+) with favorable interaction energy. Dimethyl imidazol-2-ylidene forms the strongest bond with M3(+) followed by pyridine, isoxazole and furan. Electrostatic contribution is considerably more than that of orbital contribution in these M-L bonds. The orbital interaction arises from both L → M σ donation and L ← M back donation. M3(+) clusters also bind noble gas atoms and carbon monoxide effectively. In general, among the studied systems Au3(+) binds a given L most strongly followed by Cu3(+) and Ag3(+). Computation of the nucleus-independent chemical shift (NICS) and its different extensions like the NICS-rate and NICS in-plane component vs. NICS out-of-plane component shows that the σ-aromaticity in L bound M3(+) increases compared to that of bare clusters. The aromaticity in pyridine, isoxazole and furan bound Au3(+) complexes is quite comparable with that in the recently synthesized Zn3(C5(CH3)5)3(+). The energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital also increases upon binding with L. The blue-shift and red-shift in the C-O stretching frequency of M3(CO)3(+) and M3(OC)3(+), respectively, are analyzed through reverse polarization of the σ- and π-orbitals of CO as well as the relative amount of OC → M σ donation and M → CO π back donation. The electron density analysis is also performed to gain further insight into the nature of interaction.

  20. Kinetics of excited states of pigment clusters in solubilized light-harvesting complex II: photon density-dependent fluorescence yield and transmittance.

    PubMed Central

    Schödel, R; Hillmann, F; Schrötter, T; Voigt, J; Irrgang, K D; Renger, G

    1996-01-01

    Relative fluorescence yield, phi F, and transmittance, T, were measured in solubilized light-harvesting complex II (LHCII) as a function of photon density, Ip, of monochromatic 645-nm laser pulses (duration: approximately 2.5 ns). Special efforts were made in constructing an optical set-up that allows the accurate determination of the fluorescence from an area of constant Ip, phi F(Ip) starts to decline at approximately 10(14) and drops to values below 0.01% at maximum Ip (approximately 10(19) photons cm-2 pulse-1). T(Ip) decreases only slightly at photon densities of approximately 10(15) but increases steeply at values of > 10(17) photons cm-2 pulse-1. The interpretation of the phi F(Ip) data using the saturation limit of Mauzerall's multiple hit model leads to a unit size of about 10-15 chlorophyll molecules. One interpretation is to attribute this result to a very fast exciton-exciton annihilation of multiple excited states generated within this small domain. Alternatively, based on the assumption that delocalized cluster states within the monomeric/trimeric subunit of LHCII exist, the results can be consistently described by a kinetic model comprising ground, monoexcitonic, and biexcitonic states of clusters and a triplet state that is quenched by carotenoids in LHCII. Within the framework of this model the annihilation of multiple excitations is explained as ultrafast radiationless relaxation of higher excited cluster states. Comparative measurements in diluted acetonic Chl a solution are consistently described by the depletion of the ground state, taking the absorption cross section at the used wavelength. Images FIGURE 1 PMID:8968606

  1. Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: theory, implementation, and examples.

    PubMed

    Bravaya, Ksenia B; Zuev, Dmitry; Epifanovsky, Evgeny; Krylov, Anna I

    2013-03-28

    Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e., excited states that are metastable with respect to electron ejection. The method is applied to Feshbach resonances in atomic systems (He, H(-), and Be). The dependence of the results on one-electron basis set is quantified and analyzed. Energy decomposition and wave function analysis reveal that the origin of the dependence is in electron correlation, which is essential for the lifetime of Feshbach resonances. It is found that one-electron basis should be sufficiently flexible to describe radial and angular electron correlation in a balanced fashion and at different values of the scaling parameter, θ. Standard basis sets that are optimized for not-complex-scaled calculations (θ = 0) are not sufficiently flexible to describe the θ-dependence of the wave functions even when heavily augmented by additional sets.

  2. Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: Theory, implementation, and examples

    SciTech Connect

    Bravaya, Ksenia B.; Zuev, Dmitry; Epifanovsky, Evgeny; Krylov, Anna I.

    2013-03-28

    Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e., excited states that are metastable with respect to electron ejection. The method is applied to Feshbach resonances in atomic systems (He, H{sup -}, and Be). The dependence of the results on one-electron basis set is quantified and analyzed. Energy decomposition and wave function analysis reveal that the origin of the dependence is in electron correlation, which is essential for the lifetime of Feshbach resonances. It is found that one-electron basis should be sufficiently flexible to describe radial and angular electron correlation in a balanced fashion and at different values of the scaling parameter, {theta}. Standard basis sets that are optimized for not-complex-scaled calculations ({theta} = 0) are not sufficiently flexible to describe the {theta}-dependence of the wave functions even when heavily augmented by additional sets.

  3. Genetic manipulation of the Fusarium fujikuroi fusarin gene cluster yields insight into the complex regulation and fusarin biosynthetic pathway.

    PubMed

    Niehaus, Eva-Maria; Kleigrewe, Karin; Wiemann, Philipp; Studt, Lena; Sieber, Christian M K; Connolly, Lanelle R; Freitag, Michael; Güldener, Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich

    2013-08-22

    In this work, the biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunoprecipitation revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. We provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with nuclear magnetic resonance and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, we indicate that PKS/NRPS releases its product with an open ring structure, probably as an alcohol. Our data indicate that 2-pyrrolidone ring closure, oxidation at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Accounting for interactions and complex inter-subject dependency in estimating treatment effect in cluster randomized trials with missing outcomes

    PubMed Central

    Prague, Melanie; Wang, Rui; Stephens, Alisa; Tchetgen Tchetgen, Eric; DeGruttola, Victor

    2016-01-01

    Summary Semi-parametric methods are often used for the estimation of intervention effects on correlated outcomes in cluster-randomized trials (CRTs). When outcomes are missing at random (MAR), Inverse Probability Weighted (IPW) methods incorporating baseline covariates can be used to deal with informative missingness. Also, augmented generalized estimating equations (AUG) correct for imbalance in baseline covariates but need to be extended for MAR outcomes. However, in the presence of interactions between treatment and baseline covariates, neither method alone produces consistent estimates for the marginal treatment effect if the model for interaction is not correctly specified. We propose an AUG-IPW estimator that weights by the inverse of the probability of being a complete case and allows different outcome models in each intervention arm. This estimator is doubly robust (DR), it gives correct estimates whether the missing data process or the outcome model is correctly specified. We consider the problem of covariate interference which arises when the outcome of an individual may depend on covariates of other individuals. When interfering covariates are not modeled, the DR property prevents bias as long as covariate interference is not present simultaneously for the outcome and the missingness. An R package is developed implementing the proposed method. An extensive simulation study and an application to a CRT of HIV risk reduction-intervention in South Africa illustrate the method. PMID:27060877

  5. Cancer Clusters

    MedlinePlus

    ... Genetics Services Directory Cancer Prevention Overview Research Cancer Clusters On This Page What is a cancer cluster? ... the number of cancer cases in the suspected cluster Many reported clusters include too few cancer cases ...

  6. Influence of Single Skimmer Versus Dual Funnel Transfer on the Appearance of ESI-Generated LiCl Cluster/ß-Cyclodextrin Inclusion Complexes

    NASA Astrophysics Data System (ADS)

    Kellner, Ina D.; Drewello, Thomas

    2015-08-01

    Singly and doubly charged adducts of LiCl with β-cyclodextrin (βCD) of the type (βCD)(LiCl)nLi+ and (βCD)2(LiCl)pLi2 2+ were studied using electrospray ionization mass spectrometry (ESI-MS). Insight into their structural composition was gained by analysis of their collision-induced dissociation (CID) mass spectra. The conditions the ions experience in the transfer region interfacing the ESI source and the mass analyzer were found to have a marked influence on the nature of the detected ions. In one instrument incorporating a single skimmer, individually attached LiCl ion pairs were observed, whereas the dual funnel ion guides of the second instrument allow the detection of previously unknown labile inclusion complexes of (LiCl)n clusters in βCD.

  7. High-nuclearity ruthenium carbonyl cluster complexes derived from 2-amino-6-methylpyridine: synthesis of nonanuclear derivatives containing mu4- and mu5-oxo ligands.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; García-Alvarez, Pablo; Miguel, Daniel

    2006-07-24

    Nonanuclear cluster complexes [Ru9(mu3-H)2(mu-H)(mu5-O)(mu4-ampy)(mu3-Hampy)(CO)21] (4) (H2ampy = 2-amino-6-methylpyridine), [Ru9(mu5-O)2(mu4-ampy)(mu3-Hampy)2(mu-CO)(CO)20] (5), [Ru9(mu5-O)2(mu4-ampy)(mu3-Hampy)2(mu-CO)2(CO)19] (6), and [Ru9(mu4-O)(mu5-O)(mu4-ampy)(mu3-Hampy)(mu-Hampy)(mu-CO)(CO)19] (7), together with the known hexanuclear [Ru6(mu3-H)2(mu5-ampy)(mu-CO)2(CO)14] (2) and the novel pentanuclear [Ru5(mu4-ampy)(2)(mu-CO)(CO)12] (3) complexes, are products of the thermolysis of [Ru3(mu-H)(mu3-Hampy)(CO)9] (1) in decane at 150 degrees C. Two different and very unusual quadruply bridging coordination modes have been observed for the ampy ligand. Compounds 4-7 also feature one (4) or two (5-7) bridging oxo ligands. With the exception of one of the oxo ligands of 7, which is in a distorted tetrahedral environment, the remaining oxo ligands of 4-7 are surrounded by five metal atoms. In carbonyl metal clusters, quadruply bridging oxo ligands are very unusual, whereas quintuply bridging oxo ligands are unprecedented. By using 18O-labeled water, we have unambiguously established that these oxo ligands arise from water.

  8. In vitro reconstitution of the ordered assembly of the endosomal sorting complex required for transport at membrane-bound HIV-1 Gag clusters.

    PubMed

    Carlson, Lars-Anders; Hurley, James H

    2012-10-16

    Most membrane-enveloped viruses depend on host proteins of the endosomal sorting complex required for transport (ESCRT) machinery for their release. HIV-1 is the prototypic ESCRT-dependent virus. The direct interactions between HIV-1 and the early ESCRT factors TSG101 and ALIX have been mapped in detail. However, the full pathway of ESCRT recruitment to HIV-1 budding sites, which culminates with the assembly of the late-acting CHMP4, CHMP3, CHMP2, and CHMP1 subunits, is less completely understood. Here, we report the biochemical reconstitution of ESCRT recruitment to viral assembly sites, using purified proteins and giant unilamellar vesicles. The myristylated full-length Gag protein of HIV-1 was purified to monodispersity. Myr-Gag forms clusters on giant unilamellar vesicle membranes containing the plasma membrane lipid PI(4,5)P(2). These Gag clusters package a fluorescent oligonucleotide, and recruit early ESCRT complexes ESCRT-I or ALIX with the appropriate dependence on the Gag PTAP and LYP(X)(n)L motifs. ALIX directly recruits the key ESCRT-III subunit CHMP4. ESCRT-I can only recruit CHMP4 when ESCRT-II and CHMP6 are present as intermediary factors. Downstream of CHMP4, CHMP3 and CHMP2 assemble synergistically, with the presence of both subunits required for efficient recruitment. The very late-acting factor CHMP1 is not recruited unless the pathway is completed through CHMP3 and CHMP2. These findings define the minimal sets of components needed to complete ESCRT assembly at HIV-1 budding sites, and provide a starting point for in vitro structural and biophysical dissection of the system.

  9. In vitro reconstitution of the ordered assembly of the endosomal sorting complex required for transport at membrane-bound HIV-1 Gag clusters

    PubMed Central

    Carlson, Lars-Anders; Hurley, James H.

    2012-01-01

    Most membrane-enveloped viruses depend on host proteins of the endosomal sorting complex required for transport (ESCRT) machinery for their release. HIV-1 is the prototypic ESCRT-dependent virus. The direct interactions between HIV-1 and the early ESCRT factors TSG101 and ALIX have been mapped in detail. However, the full pathway of ESCRT recruitment to HIV-1 budding sites, which culminates with the assembly of the late-acting CHMP4, CHMP3, CHMP2, and CHMP1 subunits, is less completely understood. Here, we report the biochemical reconstitution of ESCRT recruitment to viral assembly sites, using purified proteins and giant unilamellar vesicles. The myristylated full-length Gag protein of HIV-1 was purified to monodispersity. Myr-Gag forms clusters on giant unilamellar vesicle membranes containing the plasma membrane lipid PI(4,5)P2. These Gag clusters package a fluorescent oligonucleotide, and recruit early ESCRT complexes ESCRT-I or ALIX with the appropriate dependence on the Gag PTAP and LYP(X)nL motifs. ALIX directly recruits the key ESCRT-III subunit CHMP4. ESCRT-I can only recruit CHMP4 when ESCRT-II and CHMP6 are present as intermediary factors. Downstream of CHMP4, CHMP3 and CHMP2 assemble synergistically, with the presence of both subunits required for efficient recruitment. The very late-acting factor CHMP1 is not recruited unless the pathway is completed through CHMP3 and CHMP2. These findings define the minimal sets of components needed to complete ESCRT assembly at HIV-1 budding sites, and provide a starting point for in vitro structural and biophysical dissection of the system. PMID:23027949

  10. Simple bioseparations using self-cleaving elastin-like polypeptide tags.

    PubMed

    Banki, Mahmoud Reza; Feng, Liang; Wood, David W

    2005-09-01

    We introduce a new method for the purification of recombinant proteins expressed in Escherichia coli using self-cleaving elastin-like polypeptide (ELP) fusion tags without the need for affinity chromatography or proteolytic tag removal. Using this method we obtained high purity, activity and reasonable yields for ten diverse target proteins.

  11. Localization of two post-proline cleaving peptidases in the midgut of Tenebrio molitor larvae

    USDA-ARS?s Scientific Manuscript database

    Two soluble post-proline cleaving peptidase activities, PPCP1 and PPCP2, were demonstrated in the midgut of Tenebrio molitor larvae with the substrate benzyloxycarbonyl-L-alanyl-L-proline p-nitroanilide. Both activities were serine peptidases. PPCP1 was active in acidic buffers, with maximum activit...

  12. FeCl3-catalyzed self-cleaving deprotection of methoxyphenylmethyl-protected alcohols.

    PubMed

    Sawama, Yoshinari; Masuda, Masahiro; Asai, Shota; Goto, Ryota; Nagata, Saori; Nishimura, Shumma; Monguchi, Yasunari; Sajiki, Hironao

    2015-02-06

    4-Methoxyphenylmethyl ethers are widely utilized as alcohol protecting groups. FeCl3 effectively catalyzes the deprotection of methoxyphenylmethyl-type ethers in a self-cleaving manner to produce oligomeric derivatives and alcohols. Remarkably, the highly pure mother alcohols can be obtained without silica gel column chromatography by using the 2,4-dimethoxyphenylmethyl group as a protective group.

  13. Generation and characterization of antibodies specific for caspase-cleaved neo-epitopes: a novel approach.

    PubMed

    Ai, X; Butts, B; Vora, K; Li, W; Tache-Talmadge, C; Fridman, A; Mehmet, H

    2011-09-01

    Apoptosis research has been significantly aided by the generation of antibodies against caspase-cleaved peptide neo-epitopes. However, most of these antibodies recognize the N-terminal fragment and are specific for the protein in question. The aim of this project was to create antibodies, which could identify caspase-cleaved proteins without a priori knowledge of the cleavage sites or even the proteins themselves. We hypothesized that many caspase-cleavage products might have a common antigenic shape, given that they must all fit into the same active site of caspases. Rabbits were immunized with the eight most prevalent exposed C-terminal tetrapeptide sequences following caspase cleavage. After purification of the antibodies we demonstrated (1) their specificity for exposed C-terminal (but not internal) peptides, (2) their ability to detect known caspase-cleaved proteins from apoptotic cell lysates or supernatants from apoptotic cell culture and (3) their ability to detect a caspase-cleaved protein whose tetrapeptide sequence differs from the eight tetrapeptides used to generate the antibodies. These antibodies have the potential to identify novel neo-epitopes produced by caspase cleavage and so can be used to identify pathway-specific caspase cleavage events in a specific cell type. Additionally this methodology may be applied to generate antibodies against products of other proteases, which have a well-defined and non-promiscuous cleavage activity.

  14. Generation and characterization of antibodies specific for caspase-cleaved neo-epitopes: a novel approach

    PubMed Central

    Ai, X; Butts, B; Vora, K; Li, W; Tache-Talmadge, C; Fridman, A; Mehmet, H

    2011-01-01

    Apoptosis research has been significantly aided by the generation of antibodies against caspase-cleaved peptide neo-epitopes. However, most of these antibodies recognize the N-terminal fragment and are specific for the protein in question. The aim of this project was to create antibodies, which could identify caspase-cleaved proteins without a priori knowledge of the cleavage sites or even the proteins themselves. We hypothesized that many caspase-cleavage products might have a common antigenic shape, given that they must all fit into the same active site of caspases. Rabbits were immunized with the eight most prevalent exposed C-terminal tetrapeptide sequences following caspase cleavage. After purification of the antibodies we demonstrated (1) their specificity for exposed C-terminal (but not internal) peptides, (2) their ability to detect known caspase-cleaved proteins from apoptotic cell lysates or supernatants from apoptotic cell culture and (3) their ability to detect a caspase-cleaved protein whose tetrapeptide sequence differs from the eight tetrapeptides used to generate the antibodies. These antibodies have the potential to identify novel neo-epitopes produced by caspase cleavage and so can be used to identify pathway-specific caspase cleavage events in a specific cell type. Additionally this methodology may be applied to generate antibodies against products of other proteases, which have a well-defined and non-promiscuous cleavage activity. PMID:21881607

  15. Cysteine digestive peptidases function as post-glutamine cleaving enzymes in tenebrionid stored product pests

    USDA-ARS?s Scientific Manuscript database

    Cereals have storage proteins with high amounts of the amino acids glutamine and proline. Therefore, storage pests need to have digestive enzymes that are efficient in hydrolyzing these types of proteins. Post-glutamine cleaving peptidases (PGP) were isolated from the midgut of the stored product pe...

  16. CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

    PubMed Central

    Kumar, Sonu; Ratnikov, Boris I.; Kazanov, Marat D.; Smith, Jeffrey W.; Cieplak, Piotr

    2015-01-01

    CleavPredict (http://cleavpredict.sanfordburnham.org) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required. PMID:25996941

  17. STS-30 Mission Specialists Cleave, Thagard, Lee at preflight press conference

    NASA Technical Reports Server (NTRS)

    1989-01-01

    During preflight press conference, STS-30 Mission Specialists (left to right) Mary L. Cleave, Norman E. Thagard, and Mark C. Lee ponder a question from the news media. The event was held in the JSC Auditorium and Public Affairs Facility Bldg 2 briefing room. STS-30 mission will fly onboard Atlantis, Orbiter Vehicle (OV) 104, and is scheduled for an April 28 liftoff.

  18. The effect of complex workplace dietary interventions on employees' dietary intakes, nutrition knowledge and health status: a cluster controlled trial.

    PubMed

    Geaney, Fiona; Kelly, Clare; Di Marrazzo, Jessica Scotto; Harrington, Janas M; Fitzgerald, Anthony P; Greiner, Birgit A; Perry, Ivan J

    2016-08-01

    Evidence on effective workplace dietary interventions is limited. The comparative effectiveness of a workplace environmental dietary modification and an educational intervention both alone and in combination was assessed versus a control workplace on employees' dietary intakes, nutrition knowledge and health status. In the Food Choice at Work cluster controlled trial, four large, purposively selected manufacturing workplaces in Ireland were allocated to control (N=111), nutrition education (Education) (N=226), environmental dietary modification (Environment) (N=113) and nutrition education and environmental dietary modification (Combined) (N=400) in 2013. Nutrition education included group presentations, individual consultations and detailed nutrition information. Environmental dietary modification included menu modification, fruit price discounts, strategic positioning of healthier alternatives and portion size control. Data on dietary intakes, nutrition knowledge and health status were obtained at baseline and follow-up at 7-9months. Multivariate analysis of covariance compared changes across the four groups with adjustment for age, gender, educational status and other baseline characteristics. Follow-up data at 7-9months were obtained for 541 employees (64% of 850 recruited) aged 18-64years: control: 70 (63%), Education: 113 (50%), 74 (65%) and Combined: 284 (71%). There were significant positive changes in intakes of saturated fat (p=0.013), salt (p=0.010) and nutrition knowledge (p=0.034) between baseline and follow-up in the combined intervention versus the control. Small but significant changes in BMI (-1.2kg/m(2) (95% CI -2.385, -0.018, p=0.047) were observed in the combined intervention. Effects in the education and environment alone workplaces were smaller and generally non-significant. Combining nutrition education and environmental dietary modification may be an effective approach for promoting a healthy diet and weight loss at work. Copyright © 2016

  19. Comparison of flat cleaved and cylindrical diffusing fibers as treatment sources for interstitial photodynamic therapy.

    PubMed

    Baran, Timothy M; Foster, Thomas H

    2014-02-01

    For interstitial photodynamic therapy (iPDT) of bulky tumors, careful treatment planning is required in order to ensure that a therapeutic dose is delivered to the tumor, while minimizing damage to surrounding normal tissue. In clinical contexts, iPDT has typically been performed with either flat cleaved or cylindrical diffusing optical fibers as light sources. Here, the authors directly compare these two source geometries in terms of the number of fibers and duration of treatment required to deliver a prescribed light dose to a tumor volume. Treatment planning software for iPDT was developed based on graphics processing unit enhanced Monte Carlo simulations. This software was used to optimize the number of fibers, total energy delivered by each fiber, and the position of individual fibers in order to deliver a target light dose (D90) to 90% of the tumor volume. Treatment plans were developed using both flat cleaved and cylindrical diffusing fibers, based on tissue volumes derived from CT data from a head and neck cancer patient. Plans were created for four cases: fixed energy per fiber, fixed number of fibers, and in cases where both or neither of these factors were fixed. When the number of source fibers was fixed at eight, treatment plans based on flat cleaved fibers required each to deliver 7180-8080 J in order to deposit 90 J/cm(2) in 90% of the tumor volume. For diffusers, each fiber was required to deliver 2270-2350 J (333-1178 J/cm) in order to achieve this same result. For the case of fibers delivering a fixed 900 J, 13 diffusers or 19 flat cleaved fibers at a spacing of 1 cm were required to deliver the desired dose. With energy per fiber fixed at 2400 J and the number of fibers fixed at eight, diffuser fibers delivered the desired dose to 93% of the tumor volume, while flat cleaved fibers delivered this dose to 79%. With both energy and number of fibers allowed to vary, six diffusers delivering 3485-3600 J were required, compared to ten flat cleaved

  20. Comparison of flat cleaved and cylindrical diffusing fibers as treatment sources for interstitial photodynamic therapy

    SciTech Connect

    Baran, Timothy M. Foster, Thomas H.

    2014-02-15

    Purpose: For interstitial photodynamic therapy (iPDT) of bulky tumors, careful treatment planning is required in order to ensure that a therapeutic dose is delivered to the tumor, while minimizing damage to surrounding normal tissue. In clinical contexts, iPDT has typically been performed with either flat cleaved or cylindrical diffusing optical fibers as light sources. Here, the authors directly compare these two source geometries in terms of the number of fibers and duration of treatment required to deliver a prescribed light dose to a tumor volume. Methods: Treatment planning software for iPDT was developed based on graphics processing unit enhanced Monte Carlo simulations. This software was used to optimize the number of fibers, total energy delivered by each fiber, and the position of individual fibers in order to deliver a target light dose (D{sub 90}) to 90% of the tumor volume. Treatment plans were developed using both flat cleaved and cylindrical diffusing fibers, based on tissue volumes derived from CT data from a head and neck cancer patient. Plans were created for four cases: fixed energy per fiber, fixed number of fibers, and in cases where both or neither of these factors were fixed. Results: When the number of source fibers was fixed at eight, treatment plans based on flat cleaved fibers required each to deliver 7180–8080 J in order to deposit 90 J/cm{sup 2} in 90% of the tumor volume. For diffusers, each fiber was required to deliver 2270–2350 J (333–1178 J/cm) in order to achieve this same result. For the case of fibers delivering a fixed 900 J, 13 diffusers or 19 flat cleaved fibers at a spacing of 1 cm were required to deliver the desired dose. With energy per fiber fixed at 2400 J and the number of fibers fixed at eight, diffuser fibers delivered the desired dose to 93% of the tumor volume, while flat cleaved fibers delivered this dose to 79%. With both energy and number of fibers allowed to vary, six diffusers delivering 3485–3600 J

  1. Cyclically amplified fluorescent detection of theophylline and thiamine pyrophosphate by coupling self-cleaving RNA ribozyme with endonuclease.

    PubMed

    Li, Xuemei; Song, Jian; Wang, Yan; Cheng, Tao

    2013-10-03

    A structure-switching-based approach for the design of fluorescent biosensors from known RNA aptazymes were demonstrated for the detection of theophylline and thiamine pyrophosphate (TPP). Taking advantages of the ability of graphene oxide (GO) to protect ssDNA from nuclease cleavage and the cyclic amplification induced by deoxyribonuclease I (DNase I), the amplified assay showed high sensitivity. In the presence of target, the target-dependent hammerhead aptazyme cleaves off. The released Shine-Dalgarno (SD) sequence was introduced into the detection system, in which a FAM labeled probe ssDNA was noncovalently assembled on GO, and the fluorescence of the dye was completely quenched. In the presence of the released sequence, the binding between the dye-labeled DNA and the SD sequence alter the conformation of dye-labeled DNA, and disturb the interaction between the dye-labeled DNA and GO, liberating dye-labeled DNA from GO. The fluorescent intensity was increased, whereupon the DNase I can cleave the free DNA in the DNA/RNA complex, thereby liberating the fluorophore and ultimately releasing the SD RNA sequence. The released SD RNA sequence then binds another DNA probe, and the cycle starts anew, which leads to significant amplification of the fluorescent signal. The strategy showed good sensitivity and the dynamic ranges were of 0.1-10 μM and 0.5-100 μM for theophylline and TPP, respectively. The approach opens up a wide range of possibilities for sensing of other small molecules in biological entities.

  2. A multifrequency study of the active star-forming complex NGC 6357 - I. Interstellar structures linked to the open cluster Pis 24

    NASA Astrophysics Data System (ADS)

    Cappa, C. E.; Barbá, R.; Duronea, N. U.; Vasquez, J.; Arnal, E. M.; Goss, W. M.; Fernández Lajús, E.

    2011-08-01

    We investigate the distribution of gas (ionized, neutral atomic and molecular) and interstellar dust in the complex star-forming region NGC 6357 with the goal of studying the interplay between the massive stars in the open cluster Pis 24 and the surrounding interstellar matter. Our study of the distribution of the ionized gas is based on narrow-band Hα, [S II]and [O III] images obtained with the Curtis-Schmidt Camera at CTIO, Chile, and on radio continuum observations at 1465 MHz taken with the VLA with a synthesized beam of 40 arcsec. The distribution of the molecular gas is analysed using 12CO(1-0) data obtained with the NANTEN radiotelescope, Chile (angular resolution = 2.7 arcmin). The interstellar dust distribution was studied using mid-infrared data from the GLIMPSE survey and far-infrared observations from IRAS. NGC 6357 consists of a large ionized shell and a number of smaller optical nebulosities. The optical, radio continuum, and near- and mid-IR images delineate the distributions of the ionized gas and interstellar dust in the H II regions and in previously unknown wind-blown bubbles linked to the massive stars in Pis 24 revealing surrounding photodissociation regions. The CO line observations allowed us to identify the molecular counterparts of the ionized structures in the complex and to confirm the presence of photodissociation regions. The action of the WR star HD 157504 on the surrounding gas was also investigated. The molecular mass in the complex is estimated to be (4 ± 2) × 105 M⊙. The mean electron densities derived from the radio data suggest electron densities >200 cm-3, indicating that NGC 6357 is a complex formed in a region of high ambient density. The known massive stars in Pis 24 and a number of newly inferred massive stars are mainly responsible for the excitation and photodissociation of the parental molecular cloud.

  3. A rare tetranuclear thorium(IV) μ4 -oxo cluster and dinuclear thorium(IV) complex assembled by carbon-oxygen bond activation of 1,2-dimethoxyethane (DME).

    PubMed

    Travia, Nicholas E; Scott, Brian L; Kiplinger, Jaqueline L

    2014-12-15

    The synthesis and X-ray crystal structure of two new multinuclear thorium complexes are reported. The tetranuclear μ4 -oxo cluster complex Th4 (μ4 -O)(μ-Cl)2 I6 [κ(2) (O,O')-μ-O(CH2 )2 OCH3 ]6 and the dinuclear complex Th2 I5 [κ(2) (O,O')-μ-O(CH2 )2 OCH3 ]3 (DME) (DME=dimethoxyethane) are formed by CO bond activation of 1,2-dimethoxyethane (DME) mediated by thorium iodide complexes.

  4. Comparison of CBS-QB3, CBS-APNO, G2, and G3 thermochemical predictions with experiment for formation of ionic clusters of hydronium and hydroxide ions complexed with water.

    PubMed

    Pickard, Frank C; Pokon, Emma K; Liptak, Matthew D; Shields, George C

    2005-01-08

    The GAUSSIAN 2, GAUSSIAN 3, complete basis set-QB3, and complete basis set-APNO methods have been used to calculate DeltaH( composite function) and DeltaG( composite function) values for ionic clusters of hydronium and hydroxide ions complexed with water. Results for the clusters H3O+(H2O)n and OH-(H2O)n, where n=1-4 are reported in this paper, and compared against experimental values contained in the National Institutes of Standards and Technology (NIST) database. Agreement with experiment is excellent for the three ab initio methods for formation of these clusters. The high accuracy of these methods makes them reliable for calculating energetics for the formation of ionic clusters containing water. In addition this allows them to serve as a valuable check on the accuracy of experimental data reported in the NIST database, and makes them useful tools for addressing unresolved issues in atmospheric chemistry.

  5. Electronic Structure of the Mn(4)Ca Cluster in the Oxygen-Evolving Complex of Photosystem Ii Studied By Resonant Inelastic X-Ray Scattering

    SciTech Connect

    Yano, J.; Pushkar, Y.; Messinger, J.; Bergmann, U.; Glatzel, P.; Yachandra, V.K.

    2009-06-04

    Oxygen-evolving complex (Mn{sub 4}Ca cluster) of Photosystem II cycles through five intermediate states (S{sub i}-states, i=0--4) before a molecule of dioxygen is released. During the S-state transitions, electrons are extracted from the OEC, either from Mn or alternatively from a Mn ligand. The oxidation state of Mn is widely accepted as Mn{sub 4}(III{sub 2},IV{sub 2}) and Mn{sub 4}(III,IV{sub 3}) for S{sub 1} and S{sub 2} states, while it is still controversial for the S{sub 0} and S{sub 3} states. We used resonant inelastic X-ray scattering (RIXS) to study the electronic structure of Mn{sub 4}Ca complex in the OEC. The RIXS data yield two-dimensional plots that provide a significant advantage by obtaining both K-edge pre-edge and L-edge-like spectra simultaneously. The second energy dimension separates the pre-edge (1s to 3d) transitions from the main K-edge (1s to 4p), and thus more precise analysis is possible. The 1s2p RIXS final state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy and the RIXS spectra are therefore sensitive to the metal spin state. We have collected data from PS II samples in the each of the S-states and compared them with data from various inorganic Mn complexes. The spectral changes in the Mn 1s2p{sub 3/2} RIXS spectra between the S-states are small compared to those of the oxides of Mn and coordination complexes. The results indicate strong covalency for the electronic configuration in the OEC, and we conclude that the electron is transferred from a strongly delocalized orbital, compared to those in Mn oxides or coordination complexes. The magnitude for the S{sub 0} to S{sub 1}, and S{sub 1} to S{sub 2} transitions is twice as large as that during the S{sub 2} to S{sub 3} transition, indicating that the electron for this transition is extracted from a highly delocalized orbital with little change in charge density at the Mn atoms. The RIXS spectra of S{sub 0} and S{sub 3

  6. Electronic Structure of the Mn[subscript 4]Ca Cluster in the Oxygen-Evolving Complex of Photosystem II Studied by Resonant Inelastic X-Ray Scattering

    SciTech Connect

    Yano, Junko; Pushkar, Yulia; Messinger, Johannes; Bergmann, Uwe; Glatzel, Pieter; Yachandra, Vittal K.

    2007-11-12

    Oxygen-evolving complex (Mn{sub 4}Ca cluster) of Photosystem II cycles through five intermediate states (S{sub i}-states, i = 0-4) before a molecule of dioxygen is released. During the S-state transitions, electrons are extracted from the OEC, either from Mn or alternatively from a Mn ligand. The oxidation state of Mn is widely accepted as Mn{sub 4}(III{sub 2},IV{sub 2}) and Mn{sub 4}(III,IV{sub 3}) for S{sub 1} and S{sub 2} states, while it is still controversial for the S{sub 0} and S{sub 3} states. We used resonant inelastic X-ray scattering (RIXS) to study the electronic structure of Mn{sub 4}Ca complex in the OEC. The RIXS data yield two-dimensional plots that provide a significant advantage by obtaining both K-edge pre-edge and L-edge-like spectra simultaneously. The second energy dimension separates the pre-edge (1s to 3d) transitions from the main K-edge (1s to 4p), and thus more precise analysis is possible. The 1s2p RIXS final state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy and the RIXS spectra are therefore sensitive to the metal spin state. We have collected data from PS II samples in the each of the S-states and compared them with data from various inorganic Mn complexes. The spectral changes in the Mn 1s2p{sub 3/2} RIXS spectra between the S-states are small compared to those of the oxides of Mn and coordination complexes. The results indicate strong covalency for the electronic configuration in the OEC, and we conclude that the electron is transferred from a strongly delocalized orbital, compared to those in Mn oxides or coordination complexes. The magnitude for the S{sub 0} to S{sub 1}, and S{sub 1} to S{sub 2} transitions is twice as large as that during the S{sub 2} to S{sub 3} transition, indicating that the electron for this transition is extracted from a highly delocalized orbital with little change in charge density at the Mn atoms. The RIXS spectra of S{sub 0} and S{sub 3

  7. Barriers to and facilitators of implementing complex workplace dietary interventions: process evaluation results of a cluster controlled trial.

    PubMed

    Fitzgerald, Sarah; Geaney, Fiona; Kelly, Clare; McHugh, Sheena; Perry, Ivan J

    2016-04-21

    Ambiguity exists regarding the effectiveness of workplace dietary interventions. Rigorous process evaluation is vital to understand this uncertainty. This study was conducted as part of the Food Choice at Work trial which assessed the comparative effectiveness of a workplace environmental dietary modification intervention and an educational intervention both alone and in combination versus a control workplace. Effectiveness was assessed in terms of employees' dietary intakes, nutrition knowledge and health status in four large manufacturing workplaces. The study aimed to examine barriers to and facilitators of implementing complex workplace interventions, from the perspectives of key workplace stakeholders and researchers involved in implementation. A detailed process evaluation monitored and evaluated intervention implementation. Interviews were conducted at baseline (27 interviews) and at 7-9 month follow-up (27 interviews) with a purposive sample of workplace stakeholders (managers and participating employees). Topic guides explored factors which facilitated or impeded implementation. Researchers involved in recruitment and data collection participated in focus groups at baseline and at 7-9 month follow-up to explore their perceptions of intervention implementation. Data were imported into NVivo software and analysed using a thematic framework approach. Four major themes emerged; perceived benefits of participation, negotiation and flexibility of the implementation team, viability and intensity of interventions and workplace structures and cultures. The latter three themes either positively or negatively affected implementation, depending on context. The implementation team included managers involved in coordinating and delivering the interventions and the researchers who collected data and delivered intervention elements. Stakeholders' perceptions of the benefits of participating, which facilitated implementation, included managers' desire to improve company

  8. Empower multiplex cell and tissue-specific CRISPR-mediated gene manipulation with self-cleaving ribozymes and tRNA

    PubMed Central

    Xu, Li; Zhao, Lixia; Gao, Yandi; Xu, Jing

    2017-01-01

    Abstract Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) system has emerged in recent years as a highly efficient RNA-guided gene manipulation platform. Simultaneous editing or transcriptional activation/suppression of different genes becomes feasible with the co-delivery of multiple guide RNAs (gRNAs). Here, we report that multiple gRNAs linked with self-cleaving ribozymes and/or tRNA could be simultaneously expressed from a single U6 promoter to exert genome editing of dystrophin and myosin binding protein C3 in human and mouse cells. Moreover, this strategy allows the expression of multiple gRNAs for synergistic transcription activation of follistatin when used with catalytically inactive dCas9-VP64 or dCas9-p300core fusions. Finally, the gRNAs linked by the self-cleaving ribozymes and tRNA could be expressed from RNA polymerase type II (pol II) promoters such as generic CMV and muscle/heart-specific MHCK7. This is particularly useful for in vivo applications when the packaging capacity of recombinant adeno-associated virus is limited while tissue-specific delivery of gRNAs and Cas9 is desired. Taken together, this study provides a novel strategy to enable tissue-specific expression of more than one gRNAs for multiplex gene editing from a single pol II promoter. PMID:27799472

  9. Intensity-modulated lateral microdisplacement sensor enabled by cleaved tapered fiber tips

    NASA Astrophysics Data System (ADS)

    Liu, Yan; Wang, Weiwei; Li, Yang

    2017-02-01

    A lateral microdisplacement sensor based on tapered fiber tips, which is suitable for measuring lateral displacement with high sensitivity, is proposed. A jacket-off single-mode fiber (SMF) is tapered down to tens of microns and then cleaved in the middle of the waist region to get two identical tapered fiber tips. The lateral microdisplacement can be measured by monitoring the transmission intensity of a tip-tip structure. The beam propagation characteristics of such tapered fiber tips with different waist diameters are analyzed in detail. The tip-tip structure, together with the structure composed by one tip and one cleaved SMF, is investigated both experimentally and numerically. Experimental and numerical results show that this kind of lateral microdisplacement sensing structure can provide remarkable performance. A sensitivity of about -1.0 dB/μm with a measuring range of 28 μm is obtained experimentally.

  10. Immune evasion by pathogenic Leptospira strains: the secretion of proteases that directly cleave complement proteins.

    PubMed

    Fraga, Tatiana Rodrigues; Courrol, Daniella Dos Santos; Castiblanco-Valencia, Mónica Marcela; Hirata, Izaura Yoshico; Vasconcellos, Sílvio Arruda; Juliano, Luiz; Barbosa, Angela Silva; Isaac, Lourdes

    2014-03-01

    Leptospirosis is an infectious disease of public health importance. To successfully colonize the host, pathogens have evolved multiple strategies to escape the complement system. Here we demonstrate that the culture supernatant of pathogenic but not saprophytic Leptospira inhibit the three complement pathways. We showed that the proteolytic activity in the supernatants of pathogenic strains targets the central complement molecule C3 and specific proteins from each pathway, such as factor B, C2, and C4b. The proteases cleaved α and β chains of C3 and work in synergy with host regulators to inactivate C3b. Proteolytic activity was inhibited by 1,10-phenanthroline, suggesting the participation of metalloproteases. A recombinant leptospiral metalloprotease from the thermolysin family cleaved C3 in serum and could be one of the proteases responsible for the supernatant activity. We conclude that pathogenic leptospiral proteases can deactivate immune effector molecules and represent potential targets to the development of new therapies in leptospirosis.

  11. Human dipeptidyl peptidase III acts as a post-proline-cleaving enzyme on endomorphins.

    PubMed

    Barsun, Marina; Jajcanin, Nina; Vukelić, Bojana; Spoljarić, Jasminka; Abramić, Marija

    2007-03-01

    Dipeptidyl peptidase III (DPP III) is a zinc exopeptidase with an implied role in the mammalian pain-modulatory system owing to its high affinity for enkephalins and localisation in the superficial laminae of the spinal cord dorsal horn. Our study revealed that this human enzyme hydrolyses opioid peptides belonging to three new groups, endomorphins, hemorphins and exorphins. The enzymatic hydrolysis products of endomorphin-1 were separated and quantified by capillary electrophoresis and the kinetic parameters were determined for human DPP III and rat DPP IV. Both peptidases cleave endomorphin-1 at comparable rates, with liberation of the N-terminal Tyr-Pro. This is the first evidence of DPP III acting as an endomorphin-cleaving enzyme.

  12. Friction imprint effect in mechanically cleaved BaTiO{sub 3} (001)

    SciTech Connect

    Long, Christian J.; Ebeling, Daniel; Solares, Santiago D.; Cannara, Rachel J.

    2014-09-28

    Adsorption, chemisorption, and reconstruction at the surfaces of ferroelectric materials can all contribute toward the pinning of ferroelectric polarization, which is called the electrical imprint effect. Here, we show that the opposite is also true: freshly cleaved, atomically flat surfaces of (001) oriented BaTiO{sub 3} exhibit a persistent change in surface chemistry that is driven by ferroelectric polarization. This surface modification is explored using lateral force microscopy (LFM), while the ferroelectric polarization is probed using piezoresponse force microscopy. We find that immediately after cleaving BaTiO{sub 3}, LFM reveals friction contrast between ferroelectric domains. We also find that this surface modification remains after the ferroelectric domain distribution is modified, resulting in an imprint of the original ferroelectric domain distribution on the sample surface. This friction imprint effect has implications for surface patterning as well as ferroelectric device operation and failure.

  13. A density functional investigation of thiolate-protected bimetal PdAu(24)(SR)(18)(z) clusters: doping the superatom complex.

    PubMed

    Kacprzak, Katarzyna A; Lehtovaara, Lauri; Akola, Jaakko; Lopez-Acevedo, Olga; Häkkinen, Hannu

    2009-09-07

    Structure, electronic properties, optical absorption and charging properties of methylthiolate-protected bimetal PdAu(24)(SR)(18)(z) (R = Me) clusters with various charge states (-3 complex Au(25)(SR)(18)((-1)) [J. Akola, M. Walter, H. Häkkinen and H. Grönbeck, J. Am. Chem. Soc., 2008, 130, 3756]. The atomic structure of this all-gold complex can be written in a "divide-and-protect" way [H. Häkkinen, M. Walter and H. Grönbeck, J. Phys. Chem. B, 2006, 110, 9927] as Au(13)[Au(2)(SR)(3)](6)((-1)) where 6 v-shaped Au(2)(SR)(3) ligands protect the close-to-icosahedral Au(13) core and where eight delocalized metal electrons, derived from Au(6s) electrons, comprise a stable closed-shell 1S(2)1P(6)"superatom" configuration in the core. We show that the di-anion PdAu(24)(SR)(18)((-2)) is a corresponding eight-electron closed-shell species whereas the clusters PdAu(24)(SR)(18)(z), -1

  14. Cluster headache

    MedlinePlus

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... Doctors do not know exactly what causes cluster headaches. They ... (chemical in the body released during an allergic response) or ...

  15. Recess integration of micro-cleaved laser diode platelets with dielectric waveguides on silicon

    NASA Astrophysics Data System (ADS)

    Fonstad, Clifton G., Jr.; Rumpler, Joseph J.; Barkley, Edward R.; Perkins, James M.; Famenini, Shaya

    2008-02-01

    Ongoing research directed at integrating 1.55 μm III-V ridge waveguide gain elements (i.e. diode lasers and semiconductor optical amplifiers) co-axially aligned with, and coupled to, silicon oxy-nitride waveguides on silicon substrates is presented. The integration techniques used are highly modular and consistent with fabricating waveguides on Si-CMOS wafers and doing the integration of the III-V gain elements after all standard front- and back-end Si processing has been completed. A novel micro-cleaving technique is used to produce active ridge waveguide platelets on the order of 6 µm thick and 100 μm wide, with precisely controlled lengths, in the current work 300 +/- 1 μm, and cleaved end facets. Typical ridge guide micro-cleaved platelet lasers have thresholds under 30 mA. Micro-cleaved platelets are bonded within dielectric recesses etched through the oxy-nitride (SiO xN y) waveguides on a wafer so the ridge and SiO xN y waveguides are co-axially aligned. Transmission measurements indicate coupling losses are as low as 5 db with air filling the gaps between the waveguide ends, and measurements made through filled gaps indicate that the coupling losses can be reduced to below 1.5 dB with a high index (n = 2.2) dielectric fill. Simulations indicate that with further optimization of the mode profile in the III-V waveguide the loss can be reduced to below 1 dB. The paper concludes with a discussion of device design and optimization for co-axial recess integration, and with a comparison of co-axial coupling with the hybrid evanescent vertical coupling III-V/Si integration approach recently introduced by researchers at UCSB and Intel.

  16. Identification of ribozymes within a ribozyme library that efficiently cleave a long substrate RNA.

    PubMed Central

    Campbell, T B; Cech, T R

    1995-01-01

    Positions 2-6 of the substrate-binding internal guide sequence (IGS) of the L-21 Sca I form of the Tetrahymena thermophila intron were mutagenized to produce a GN5 IGS library. Ribozymes within the GN5 library capable of efficient cleavage of an 818-nt human immunodeficiency virus type 1 vif-vpr RNA, at 37 degrees C, were identified by ribozyme-catalyzed guanosine addition to the 3' cleavage product. Three ribozymes (IGS = GGGGCU, GGCUCC, and GUGGCU) within the GN5 library that actively cleaved the long substrate were characterized kinetically and compared to the wild-type ribozyme (GGAGGG) and two control ribozymes (GGAGUC and GGAGAU). The two control ribozymes have specific sites within the long substrate, but were not identified during screening of the library. Under single-turnover conditions, ribozymes GGGGCU, GGCUCC, and GUGGCU cleaved the 818-nt substrate 4- to 200-fold faster than control ribozymes. Short cognate substrates, which should be structureless and therefore accessible to ribozyme binding, were cleaved at similar rates by all ribozymes except GGGGCU, which showed a fourfold rate enhancement. The rate of cleavage of long relative to short substrate under single-turnover conditions suggests that GGCUCC and GUGGCU were identified because of accessibility to their specific cleavage sites within the long substrate (substrate-specific effects), whereas GGGGCU was identified because of an enhanced rate of substrate binding despite a less accessible site in the long substrate. Even though screening was performed with 100-fold excess substrate (relative to total ribozyme), the rate of multiple-turnover catalysis did not contribute to identification of trans-cleaving ribozymes in the GN5 library. PMID:7489519

  17. INACTIVATION OF SEXUAL AGGLUTINATION IN HANSENULA WINGEI AND SACCHAROMYCES KLUYVERI BY DISULFIDE-CLEAVING AGENTS.

    PubMed

    TAYLOR, N W

    1964-10-01

    Taylor, Neil W. (Northern Regional Research Laboratory, Peoria, Ill.). Inactivation of sexual agglutination in Hansenula wingei and Saccharomyces kluyveri by disulfide-cleaving agents. J. Bacteriol. 88:929-936. 1964.-Mating types of both Hansenula wingei and Saccharomyces kluyveri can be activated to produce uniformly strong sexual agglutination by treatments with various solvents, such as 8 m LiBr. The strongly agglutinative mating-type preparations were irreversibly inactivated for sexual agglutination by various chemical treatments. Type 5 of H. wingei was inactivated by disulfide-cleaving reagents, but type 21 of H. wingei was not. Type 3 of S. kluyveri was more sensitive than type 26 of S. kluyveri to inactivation by disulfide-cleaving reagents. Comparison of sensitivities to these and other treatments, plus a moderately strong cross-agglutination between type 3 and type 21, indicated that the sexually agglutinative elements on type 3 are similar to type 5, and those of type 21 are similar to those of type 26. Inactivation-rate experiments showed a loss of agglutinative ability according to a sigmoid decrement with time for both types 5 and 21. The apparent extent of inactivation depended markedly on agglutination test conditions. Results of these experiments were interpreted to indicate tentatively, first, that the agglutinative elements of both types of a species are proteins and, second, that several agglutinating linkages are formed between any two cells in sexual agglutination.

  18. Chloridazon-catechol dioxygenases, a distinct group of meta-cleaving enzymes.

    PubMed

    Schmitt, S; Müller, R; Wegst, W; Lingens, F

    1984-02-01

    We previously described a new meta-cleaving enzyme, termed chloridazon-catechol dioxygenase. The present paper describes the comparison of this enzyme with the meta-cleaving enzymes of eighteen strains of soil bacteria isolated with various aromatic compounds. Four of these strains were isolated with the herbicide chloridazon, six with the analgeticum aminopyrine and one with the analgeticum antipyrine as sole carbon source. These strains all belonged to a new type of bacteria, called Phenylobacteria. The seven other strains were isolated with aromatic compounds such as toluene, 3-phenylpropionate, benzoate, papaverine and 4-chlorobenzoate, and belonged to various species including Pseudomonas, Acinetobacter and Nocardia. In double diffusion experiments with antibodies, prepared against chloridazon-catechol dioxygenase, extracts from the eleven strains of Phenylobacteria gave a cross reaction, whereas the extracts of the seven other strains showed no reaction. The enzymes of the eleven positive strains showed the same characteristic kinetic behaviour as the previously described enzyme. In contrast to catechol 2, 3-dioxygenase they needed the addition of exogenous Fe2+ ions for activity. On ion-exchange chromatography they emerged at the same buffer concentration as chloridazon-catechol dioxygenase. In polyacrylamide electrophoresis they migrated identically. The linkage map derived from the activities of the various enzymes with 10 different substrates revealed an identity of more than 80% for these eleven enzymes. So the meta-cleaving enzymes of the Phenylobacteria seem to form a distinct group among the non-heme iron-containing dioxygenases.

  19. Post-proline cleaving enzyme. Purification of this endopeptidase by affinity chromatography.

    PubMed

    Koida, M; Walter, R

    1976-12-10

    The endopeptidase, post-proline cleaving enzyme, has been purified 10,500-fold in an overall yield of 18% from lamb kidney. The enzyme possesses a specific activity of 45 mumol/mg/min as tested with the substrate Z-Gly-Pro-Leu-Gly (Km = 6.0 X 10(-5)), has a molecular weight of 115,000, is comprised of two subunits with a molecular weight of 57,000, and exhibits maximal activity at pH 7.5 to 8.0. With the exception of the -Pro-Pro linkage, the -Pro-X-peptide bond (X equals L- and D-amino acid residues) located internally in the peptide sequence can be hydrolyzed (cleavage occurs faster when X = lipophilic side chain as compared to X = acidic side chain). The appropriate -Pro-X- bonds in zinc-free porcine insulin, oxytocin, arginine vasopressin, angiotensin II, bradykinin-potentiating factor were cleaved. Human gastrin, adrenocorticotropic hormone, denatured guinea pig skin collagen, and ascaris cuticle collagen were not degraded. Dipeptides with the structure Z-Pro-LD-X competitively inhibit post-proline cleaving enzyme.

  20. Ovastacin, a cortical granule protease, cleaves ZP2 in the zona pellucida to prevent polyspermy.

    PubMed

    Burkart, Anna D; Xiong, Bo; Baibakov, Boris; Jiménez-Movilla, Maria; Dean, Jurrien

    2012-04-02

    The mouse zona pellucida is composed of three glycoproteins (ZP1, ZP2, and ZP3), of which ZP2 is proteolytically cleaved after gamete fusion to prevent polyspermy. This cleavage is associated with exocytosis of cortical granules that are peripherally located subcellular organelles unique to ovulated eggs. Based on the cleavage site of ZP2, ovastacin was selected as a candidate protease. Encoded by the single-copy Astl gene, ovastacin is an oocyte-specific member of the astacin family of metalloendoproteases. Using specific antiserum, ovastacin was detected in cortical granules before, but not after, fertilization. Recombinant ovastacin cleaved ZP2 in native zonae pellucidae, documenting that ZP2 was a direct substrate of this metalloendoprotease. Female mice lacking ovastacin did not cleave ZP2 after fertilization, and mouse sperm bound as well to Astl-null two-cell embryos as they did to normal eggs. Ovastacin is a pioneer component of mouse cortical granules and plays a definitive role in the postfertilization block to sperm binding that ensures monospermic fertilization and successful development.

  1. INACTIVATION OF SEXUAL AGGLUTINATION IN HANSENULA WINGEI AND SACCHAROMYCES KLUYVERI BY DISULFIDE-CLEAVING AGENTS

    PubMed Central

    Taylor, Neil W.

    1964-01-01

    Taylor, Neil W. (Northern Regional Research Laboratory, Peoria, Ill.). Inactivation of sexual agglutination in Hansenula wingei and Saccharomyces kluyveri by disulfide-cleaving agents. J. Bacteriol. 88:929–936. 1964.—Mating types of both Hansenula wingei and Saccharomyces kluyveri can be activated to produce uniformly strong sexual agglutination by treatments with various solvents, such as 8 m LiBr. The strongly agglutinative mating-type preparations were irreversibly inactivated for sexual agglutination by various chemical treatments. Type 5 of H. wingei was inactivated by disulfide-cleaving reagents, but type 21 of H. wingei was not. Type 3 of S. kluyveri was more sensitive than type 26 of S. kluyveri to inactivation by disulfide-cleaving reagents. Comparison of sensitivities to these and other treatments, plus a moderately strong cross-agglutination between type 3 and type 21, indicated that the sexually agglutinative elements on type 3 are similar to type 5, and those of type 21 are similar to those of type 26. Inactivation-rate experiments showed a loss of agglutinative ability according to a sigmoid decrement with time for both types 5 and 21. The apparent extent of inactivation depended markedly on agglutination test conditions. Results of these experiments were interpreted to indicate tentatively, first, that the agglutinative elements of both types of a species are proteins and, second, that several agglutinating linkages are formed between any two cells in sexual agglutination. PMID:14219056

  2. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity

    PubMed Central

    Zhang, Jing; Rouillon, Christophe; Kerou, Melina; Reeks, Judith; Brugger, Kim; Graham, Shirley; Reimann, Julia; Cannone, Giuseppe; Liu, Huanting; Albers, Sonja-Verena; Naismith, James H; Spagnolo, Laura; White, Malcolm F

    2012-01-01

    Summary The prokaryotic Clusters of Regularly Interspaced Palindromic Repeats (CRISPR) system utilizes genomically-encoded CRISPR RNA (crRNA), derived from invading viruses and incorporated into ribonucleoprotein complexes with CRISPR-associated (CAS) proteins, to target and degrade viral DNA or RNA on subsequent infection. RNA is targeted by the CMR complex. In Sulfolobus solfataricus, this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse “payload” of targeting crRNA. The crystal structure of Cmr7 and low resolution structure of the complex are presented. S. solfataricus CMR cleaves RNA targets in an endonucleolytic reaction at UA dinucleotides. This activity is dependent on the 8-nucleotide repeat-derived 5′ sequence in the crRNA, but not on the presence of a proto-spacer associated motif (PAM) in the target. Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets. PMID:22227115

  3. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  4. Shaping a high-mass star-forming cluster through stellar feedback. The case of the NGC 7538 IRS 1-3 complex

    NASA Astrophysics Data System (ADS)

    Frau, P.; Girart, J. M.; Zhang, Q.; Rao, R.

    2014-07-01

    Context. NGC 7538 IRS 1-3 is a high-mass star-forming cluster with several detected dust cores, infrared sources, (ultra)compact H II regions, molecular outflows, and masers. In such a complex environment, interactions and feedback among the embedded objects are expected to play a major role in the evolution of the region. Aims: We study the dust, kinematic, and polarimetric properties of the NGC 7538 IRS 1-3 region to investigate the role of the different forces in the formation and evolution of high-mass star-forming clusters. Methods: We performed SMA high angular resolution observations at 880 μm with the compact configuration. We developed the RATPACKS code to generate synthetic velocity cubes from models of choice to be compared to the observational data. To quantify the stability against gravitational collapse we developed the "mass balance" analysis that accounts for all the energetics on core scales. Results: We detect 14 dust cores from 3.5 M⊙ to 37 M⊙ arranged in two larger scale structures: a central bar and a filamentary spiral arm. The spiral arm presents large-scale velocity gradients in H13CO+ 4-3 and C17O 3-2, and magnetic field segments aligned well to the dust main axis. The velocity gradient is reproduced well by a spiral arm expanding at 9 km s-1 with respect to the central core MM1, which is known to power a large precessing outflow. The energy of the outflow is comparable to the spiral-arm kinetic energy, which dominates gravitational and magnetic energies. In addition, the dynamical ages of the outflow and spiral arm are comparable. On core scales, those embedded in the central bar seem to be unstable against gravitational collapse and prone to forming high-mass stars, while those in the spiral arm have lower masses that seem to be supported by non-thermal motions and magnetic fields. Conclusions: The NGC 7538 IRS 1-3 cluster seems to be dominated by protostellar feedback. The dusty spiral arm appears to be formed in a snowplow fashion

  5. Effectiveness of a complex intervention in reducing the prevalence of smoking among adolescents: study design of a cluster-randomized controlled trial

    PubMed Central

    2014-01-01

    Background The likelihood of an adolescent taking up smoking may be influenced by his or her society, school and family. Thus, changes in the immediate environment may alter a young person’s perception of smoking. Methods/Design The proposed multi-center, cluster-randomized controlled trial will be stratified by the baseline prevalence of smoking in schools. Municipalities with fewer than 100,000 inhabitants will be randomly assigned to a control or intervention group. One secondary school will be randomly selected from each municipality. These schools will be randomized to two groups: the students of one will receive any existing educational course regarding smoking, while those of the other school will receive a four-year, class-based curriculum intervention (22 classroom lessons) aimed at reinforcing a smoke-free school policy and encouraging smoking cessation in parents, pupils, and teachers. The intervention will also include annual meetings with parents and efforts to empower adolescents to change the smoking-related attitudes and behaviors in their homes, classrooms and communities. We will enroll children aged 12-13 years as they enter secondary school during two consecutive school years (to obtain sufficient enrolled subjects). We will follow them for five years, until two years after they leave secondary school. All external evaluators and analysts will be blinded to school allocation. The aim of this study is to analyze the effectiveness of a complex intervention in reducing the prevalence of smoking in the third year of compulsory secondary education (ESO) and two years after secondary school, when the participants are 14-15 and 17-18 years old, respectively. Discussion Most interventions aimed at preventing smoking among adolescents yield little to no positive long-term effects. This clinical trial will analyze the effectiveness of a complex intervention aimed at reducing the incidence and prevalence of smoking in this vulnerable age group. Trial

  6. Increasing chlamydia screening tests in general practice: a modified Zelen prospective Cluster Randomised Controlled Trial evaluating a complex intervention based on the Theory of Planned Behaviour.

    PubMed

    McNulty, Cliodna A M; Hogan, Angela H; Ricketts, Ellie J; Wallace, Louise; Oliver, Isabel; Campbell, Rona; Kalwij, Sebastian; O'Connell, Elaine; Charlett, Andre

    2014-05-01

    To determine if a structured complex intervention increases opportunistic chlamydia screening testing of patients aged 15-24 years attending English general practitioner (GP) practices. A prospective, Cluster Randomised Controlled Trial with a modified Zelen design involving 160 practices in South West England in 2010. The intervention was based on the Theory of Planned Behaviour (TPB). It comprised of practice-based education with up to two additional contacts to increase the importance of screening to GP staff and their confidence to offer tests through skill development (including videos). Practical resources (targets, posters, invitation cards, computer reminders, newsletters including feedback) aimed to actively influence social cognitions of staff, increasing their testing intention. Data from 76 intervention and 81 control practices were analysed. In intervention practices, chlamydia screening test rates were 2.43/100 15-24-year-olds registered preintervention, 4.34 during intervention and 3.46 postintervention; controls testing rates were 2.61/100 registered patients prior intervention, 3.0 during intervention and 2.82 postintervention. During the intervention period, testing in intervention practices was 1.76 times as great (CI 1.24 to 2.48) as controls; this persisted for 9 months postintervention (1.57 times as great, CI 1.27 to 2.30). Chlamydia infections detected increased in intervention practices from 2.1/1000 registered 15-24-year-olds prior intervention to 2.5 during the intervention compared with 2.0 and 2.3/1000 in controls (Estimated Rate Ratio intervention versus controls 1.4 (CI 1.01 to 1.93). This complex intervention doubled chlamydia screening tests in fully engaged practices. The modified Zelen design gave realistic measures of practice full engagement (63%) and efficacy of this educational intervention in general practice; it should be used more often. The trial was registered on the UK Clinical Research Network Study Portfolio database

  7. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363.

    PubMed

    Peters, Daniel T; Fung, Herman K H; Levdikov, Vladimir M; Irmscher, Tobias; Warrander, Fiona C; Greive, Sandra J; Kovalevskiy, Oleg; Isaacs, Harry V; Coles, Mark; Antson, Alfred A

    2016-09-13

    Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein-RNA complex are unknown. Characterization of human Lin28's interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions.

  8. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363

    PubMed Central

    2016-01-01

    Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein–RNA complex are unknown. Characterization of human Lin28’s interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions. PMID:27559824

  9. An unsupervised two-stage clustering approach for forest structure classification based on X-band InSAR data - A case study in complex temperate forest stands

    NASA Astrophysics Data System (ADS)

    Abdullahi, Sahra; Schardt, Mathias; Pretzsch, Hans

    2017-05-01

    Forest structure at stand level plays a key role for sustainable forest management, since the biodiversity, productivity, growth and stability of the forest can be positively influenced by managing its structural diversity. In contrast to field-based measurements, remote sensing techniques offer a cost-efficient opportunity to collect