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Sample records for 4fe-4s cluster assembly

  1. Electron transfer between [4Fe-4S] clusters

    NASA Astrophysics Data System (ADS)

    Voityuk, Alexander A.

    2010-07-01

    Iron-sulfur clusters [4Fe-4S] are major components in biological electron transport (ET). Using the DFT/B3LYP method, we calculate electronic coupling for low- and high-potential ET between [4Fe-4S] clusters and explore its sensitivity to structural parameters of the system and external electric field. As an example, we consider a model of the bacterial respiratory complex I and estimate the role of neighboring amino acids in facilitating the ET process between the clusters. Our results suggest that the superexchange mechanism rather than hole hopping should be operative in ET between [4Fe-4S] redox centers.

  2. The conserved protein Dre2 uses essential [2Fe-2S] and [4Fe-4S] clusters for its function in cytosolic iron-sulfur protein assembly.

    PubMed

    Netz, Daili J A; Genau, Heide M; Weiler, Benjamin D; Bill, Eckhard; Pierik, Antonio J; Lill, Roland

    2016-07-15

    The cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery comprises 11 essential components and matures Fe-S proteins involved in translation and genome maintenance. Maturation is initiated by the electron transfer chain NADPH-diflavin reductase Tah18-Fe-S protein Dre2 that facilitates the de novo assembly of a [4Fe-4S] cluster on the scaffold complex Cfd1-Nbp35. Tah18-Dre2 also play a critical role in the assembly of the diferric tyrosyl radical cofactor of ribonucleotide reductase. Dre2 contains eight conserved cysteine residues as potential co-ordinating ligands for Fe-S clusters but their functional importance and the type of bound clusters is unclear. In the present study, we use a combination of mutagenesis, cell biological and biochemical as well as UV-visible, EPR and Mössbauer spectroscopic approaches to show that the yeast Dre2 cysteine residues Cys(252), Cys(263), Cys(266) and Cys(268) (motif I) bind a [2Fe-2S] cluster, whereas cysteine residues Cys(311), Cys(314), Cys(322) and Cys(325) (motif II) co-ordinate a [4Fe-4S] cluster. All of these residues with the exception of Cys(252) are essential for cell viability, cytosolic Fe-S protein activity and in vivo (55)Fe-S cluster incorporation. The N-terminal methyltransferase-like domain of Dre2 is important for proper Fe-S cluster assembly at motifs I and II, which occurs in an interdependent fashion. Our findings further resolve why recombinant Dre2 from Arabidopsis, Trypanosoma or humans has previously been isolated with a single [2Fe-2S] instead of native [2Fe-2S] plus [4Fe-4S] clusters. In the presence of oxygen, the motif I-bound [2Fe-2S] cluster is labile and the motif II-bound [4Fe-4S] cluster is readily converted into a [2Fe-2S] cluster. PMID:27166425

  3. Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster.

    PubMed

    Aussignargues, Clément; Pandelia, Maria-Eirini; Sutter, Markus; Plegaria, Jefferson S; Zarzycki, Jan; Turmo, Aiko; Huang, Jingcheng; Ducat, Daniel C; Hegg, Eric L; Gibney, Brian R; Kerfeld, Cheryl A

    2016-04-27

    Bacterial microcompartments (BMCs) are self-assembling organelles composed of a selectively permeable protein shell and encapsulated enzymes. They are considered promising templates for the engineering of designed bionanoreactors for biotechnology. In particular, encapsulation of oxidoreductive reactions requiring electron transfer between the lumen of the BMC and the cytosol relies on the ability to conduct electrons across the shell. We determined the crystal structure of a component protein of a synthetic BMC shell, which informed the rational design of a [4Fe-4S] cluster-binding site in its pore. We also solved the structure of the [4Fe-4S] cluster-bound, engineered protein to 1.8 Å resolution, providing the first structure of a BMC shell protein containing a metal center. The [4Fe-4S] cluster was characterized by optical and EPR spectroscopies; it has a reduction potential of -370 mV vs the standard hydrogen electrode (SHE) and is stable through redox cycling. This remarkable stability may be attributable to the hydrogen-bonding network provided by the main chain of the protein scaffold. The properties of the [4Fe-4S] cluster resemble those in low-potential bacterial ferredoxins, while its ligation to three cysteine residues is reminiscent of enzymes such as aconitase and radical S-adenosymethionine (SAM) enzymes. This engineered shell protein provides the foundation for conferring electron-transfer functionality to BMC shells. PMID:26704697

  4. The [4Fe-4S] cluster of quinolinate synthase from Escherichia coli: investigation of cluster ligands.

    PubMed

    Rousset, Carine; Fontecave, Marc; Ollagnier de Choudens, Sandrine

    2008-08-20

    Nicotinamide adenine dinucleotide (NAD) derives from quinolinic acid which is synthesized in Escherichia coli from l-aspartate and dihydroxyacetone phosphate through the concerted action of l-aspartate oxidase and the [4Fe-4S] quinolinate synthase (NadA). Here, we addressed the question of the identity of the cluster ligands. We performed in vivo complementation experiments as well as enzymatic, spectroscopic and structural in vitro studies using wild-type vs. Cys-to-Ala mutated NadA proteins. These studies reveal that only three cysteine residues, the conserved Cys113, Cys200 and Cys297, are ligands of the cluster. This result is in contrast to the previous proposal that pointed the three cysteines of the C(291)XXC(294)XXC(297) motif. Interestingly, we demonstrated that Cys291 and Cys294 form a disulfide bridge and are important for activity. PMID:18674537

  5. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY.

    PubMed

    Trasviña-Arenas, Carlos H; Lopez-Castillo, Laura M; Sanchez-Sandoval, Eugenia; Brieba, Luis G

    2016-02-01

    7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature. PMID:26613369

  6. Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters

    PubMed Central

    Morris, Wesley D.; Darcy, Julia W.; Mayer, James M.

    2015-01-01

    Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4S4(SAr)4]2- (1, SAr = S-2,4-6-(iPr)3C6H2) leads to thiol dissociation, reversibly forming [Fe4S4(SAr)3L]1- (2) + ArSH (L = solvent, and/or conjugate base). Solutions of 2 + ArSH react with the nitroxyl radical TEMPO to give [Fe4S4(SAr)4]1- (1ox) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4S4(SAr)3(HSAr)]1-(1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

  7. Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters.

    PubMed

    Saouma, Caroline T; Morris, Wesley D; Darcy, Julia W; Mayer, James M

    2015-06-15

    Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4 S4 (SAr)4 ](2-) (1, SAr=S-2,4-6-(iPr)3 C6 H2 ) leads to thiol dissociation, reversibly forming [Fe4 S4 (SAr)3 L](1-) (2) and ArSH (L=solvent, and/or conjugate base). Solutions of 2+ArSH react with the nitroxyl radical TEMPO to give [Fe4 S4 (SAr)4 ](1-) (1ox ) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4 S4 (SAr)3 (HSAr)](1-) (1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

  8. Characterization of [4Fe-4S]-containing and cluster-free forms of Streptomyces WhiD

    PubMed Central

    Crack, Jason C.; den Hengst, Chris D.; Jakimowicz, Piotr; Subramanian, Sowmya; Johnson, Michael K.; Buttner, Mark J.; Thomson, Andrew J.; Le Brun, Nick E.

    2009-01-01

    WhiD, a member of the WhiB-like (Wbl) family of iron-sulfur proteins found exclusively within the actinomycetes, is required for the late stages of sporulation in Streptomyces coelicolor. Like all other Wbl proteins, WhiD has not so far been purified in a soluble form that contains a significant amount of cluster and characterization has relied on cluster-reconstituted protein. Thus, a major goal in Wbl research is to obtain and characterize native protein containing iron-sulfur clusters. Here we report the analysis of S. coelicolor WhiD purified anaerobically from E. coli as a soluble protein containing a single [4Fe-4S]2+ cluster ligated by four cysteines. Upon exposure to oxygen, spectral features associated with the [4Fe-4S] cluster were lost in a slow reaction that unusually yielded apo-WhiD directly without significant concentrations of cluster intermediates. This process was found to be highly pH dependent with an optimal stability observed between pH 7.0 and 8.0. Low molecular weight thiols, including a mycothiol analogue and thioredoxin, exerted a small but significant protective effect against WhiD cluster loss, an activity that could be of physiological importance. [4Fe-4S]2+ WhiD was found to react much more rapidly with superoxide than with either oxygen or hydrogen peroxide, which may also be of physiological significance. Loss of the [4Fe-4S] cluster to form apo-protein destabilized the protein fold significantly, but did not lead to complete unfolding. Finally, apo-WhiD exhibited negligible activity in an insulin-based disulfide reductase assay demonstrating that it does not function as a general protein disulfide reductase. PMID:19954209

  9. AcsF Catalyzes the ATP-dependent Insertion of Nickel into the Ni,Ni-[4Fe4S] Cluster of Acetyl-CoA Synthase.

    PubMed

    Gregg, Christina M; Goetzl, Sebastian; Jeoung, Jae-Hun; Dobbek, Holger

    2016-08-26

    Acetyl-CoA synthase (ACS) catalyzes the reversible condensation of CO, CoA, and a methyl-cation to form acetyl-CoA at a unique Ni,Ni-[4Fe4S] cluster (the A-cluster). However, it was unknown which proteins support the assembly of the A-cluster. We analyzed the product of a gene from the cluster containing the ACS gene, cooC2 from Carboxydothermus hydrogenoformans, named AcsFCh, and showed that it acts as a maturation factor of ACS. AcsFCh and inactive ACS form a stable 2:1 complex that binds two nickel ions with higher affinity than the individual components. The nickel-bound ACS-AcsFCh complex remains inactive until MgATP is added, thereby converting inactive to active ACS. AcsFCh is a MinD-type ATPase and belongs to the CooC protein family, which can be divided into homologous subgroups. We propose that proteins of one subgroup are responsible for assembling the Ni,Ni-[4Fe4S] cluster of ACS, whereas proteins of a second subgroup mature the [Ni4Fe4S] cluster of carbon monoxide dehydrogenases. PMID:27382049

  10. Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin.

    PubMed

    Martins, Berta M; Dobbek, Holger; Cinkaya, Irfan; Buckel, Wolfgang; Messerschmidt, Albrecht

    2004-11-01

    Dehydratases catalyze the breakage of a carbon-oxygen bond leading to unsaturated products via the elimination of water. The 1.6-A resolution crystal structure of 4-hydroxybutyryl-CoA dehydratase from the gamma-aminobutyrate-fermenting Clostridium aminobutyricum represents a new class of dehydratases with an unprecedented active site architecture. A [4Fe-4S](2+) cluster, coordinated by three cysteine and one histidine residues, is located 7 A from the Re-side of a flavin adenine dinucleotide (FAD) moiety. The structure provides insight into the function of these ubiquitous prosthetic groups in the chemically nonfacile, radical-mediated dehydration of 4-hydroxybutyryl-CoA. The substrate can be bound between the [4Fe-4S](2+) cluster and the FAD with both cofactors contributing to its radical activation and catalytic conversion. Our results raise interesting questions regarding the mechanism of acyl-CoA dehydrogenases, which are involved in fatty acid oxidation, and address the divergent evolution of the ancestral common gene. PMID:15496473

  11. (4Fe-4S)-cluster-depleted Azotobacter vinelandii ferredoxin I: a new 3Fe iron-sulfur protein

    SciTech Connect

    Stephens, P.J.; Morgan, T.V.; Devlin, F.; Penner-Hahn, J.E.; Hodgson, K.O.; Scott, R.A.; Stout, C.D.; Burgess, B.K.

    1985-09-01

    Fe(CN)6T oxidation of the aerobically isolated 7Fe Azotobacter vinelandii ferredoxin I, (7Fe)FdI, is a degradative reaction. Destruction of the (4Fe-4S) cluster occurs first, followed by destruction of the (3Fe-3S) cluster. At a Fe(CN)6T /(7Fe)FdI concentration ratio of 20, the product is a mixture of apoprotein and protein containing only a (3Fe-3S) cluster, (3Fe)FdI. This protein mixture, after partial purification, has been characterized by absorption, CD, magnetic CD, and EPR and Fe x-ray absorption spectroscopies. EPR and magnetic CD spectra provide strong evidence that the (3Fe-3S) cluster in (3Fe)FdI is essentially identical in structure to that in (7Fe)FdI. Analysis of the extended x-ray absorption fine structure (EXAFS) of (3Fe)FdI finds Fe scattering at an average Fe...Fe distance of approx. =2.7 A. The structure of the oxidized (3Fe-3S) cluster in solutions of oxidized (3Fe)FdI, and, by extension, of oxidized (7Fe)FdI, is thus different from that obtained by x-ray crystallography on oxidized (7Fe)FdI. Possible interpretations of this result are discussed.

  12. A PAS domain with an oxygen labile [4Fe-4S](2+) cluster in the oxygen sensor kinase NreB of Staphylococcus carnosus.

    PubMed

    Müllner, Martin; Hammel, Oliver; Mienert, Bernd; Schlag, Steffen; Bill, Eckhard; Unden, Gottfried

    2008-12-30

    The cytoplasmic histidine sensor kinase NreB of Staphylococcus carnosus responds to O(2) and controls together with the response regulator NreC the expression of genes of nitrate/nitrite respiration. nreBC homologous genes were found in Staphylococcus strains and Bacillus clausii, and a modified form was found in some Lactobacillus strains. NreB contains a sensory domain with similarity to heme B binding PAS domains. Anaerobically prepared NreB of S. carnosus exhibited a (diamagnetic) [4Fe-4S](2+) cluster when assessed by Mossbauer spectroscopy. Upon reaction with air, the cluster was degraded with a half-life of approximately 2.5 min. No significant amounts of Mossbauer or EPR detectable intermediates were found during the decay, but magnetic Mossbauer spectra revealed formation of diamagnetic [2Fe-2S](2+) clusters. After extended exposure to air, NreB was devoid of a FeS cluster. Photoreduction with deazaflavin produced small amounts of [4Fe-4S](+), which were degraded subsequently. The magnetically perturbed Mossbauer spectrum of the [4Fe-4S](2+) cluster corroborated the S = 0 spin state and revealed uniform electric field gradient tensors of the iron sites, suggesting full delocalization of the valence electrons and binding of each of the Fe ions by four S ligands, including the ligand to the protein. Mutation of each of the four Cys residues inactivated NreB function in vivo in accordance with their role as ligands. [4Fe-4S](2+) cluster-containing NreB had high kinase activity. Exposure to air decreased the kinase activity and content of the [4Fe-4S](2+) cluster with similar half-lives. We conclude that the sensory domain of NreB represents a new type of PAS domain containing a [4Fe-4S](2+) cluster for sensing and function. PMID:19102705

  13. Two [4Fe-4S] clusters containing radical SAM enzyme SkfB catalyze thioether bond formation during the maturation of the sporulation killing factor.

    PubMed

    Flühe, Leif; Burghaus, Olaf; Wieckowski, Beata M; Giessen, Tobias W; Linne, Uwe; Marahiel, Mohamed A

    2013-01-23

    The sporulation killing factor (SKF) is a 26-residue ribosomally assembled and posttranslationally modified sactipeptide. It is produced by Bacillus subtilis 168 and plays a key role in its sporulation. Like all sactipeptides, SKF contains a thioether bond, which links the cysteine residue Cys4 with the α-carbon of the methionine residue Met12. In this study we demonstrate that this bond is generated by the two [4Fe-4S] clusters containing radical SAM enzyme SkfB, which is encoded in the skf operon. By mutational analysis of both cluster-binding sites, we were able to postulate a mechanism for thioether generation which is in agreement with that of AlbA. Furthermore, we were able to show that thioether bond formation is specific toward hydrophobic amino acids at the acceptor site. Additionally we demonstrate that generation of the thioether linkage is leader-peptide-dependent, suggesting that this reaction is the first step in SKF maturation. PMID:23282011

  14. NsrR from Streptomyces coelicolor Is a Nitric Oxide-sensing [4Fe-4S] Cluster Protein with a Specialized Regulatory Function*

    PubMed Central

    Crack, Jason C.; Munnoch, John; Dodd, Erin L.; Knowles, Felicity; Al Bassam, Mahmoud M.; Kamali, Saeed; Holland, Ashley A.; Cramer, Stephen P.; Hamilton, Chris J.; Johnson, Michael K.; Thomson, Andrew J.; Hutchings, Matthew I.; Le Brun, Nick E.

    2015-01-01

    The Rrf2 family transcription factor NsrR controls expression of genes in a wide range of bacteria in response to nitric oxide (NO). The precise form of the NO-sensing module of NsrR is the subject of controversy because NsrR proteins containing either [2Fe-2S] or [4Fe-4S] clusters have been observed previously. Optical, Mössbauer, resonance Raman spectroscopies and native mass spectrometry demonstrate that Streptomyces coelicolor NsrR (ScNsrR), previously reported to contain a [2Fe-2S] cluster, can be isolated containing a [4Fe-4S] cluster. ChIP-seq experiments indicated that the ScNsrR regulon is small, consisting of only hmpA1, hmpA2, and nsrR itself. The hmpA genes encode NO-detoxifying flavohemoglobins, indicating that ScNsrR has a specialized regulatory function focused on NO detoxification and is not a global regulator like some NsrR orthologues. EMSAs and DNase I footprinting showed that the [4Fe-4S] form of ScNsrR binds specifically and tightly to an 11-bp inverted repeat sequence in the promoter regions of the identified target genes and that DNA binding is abolished following reaction with NO. Resonance Raman data were consistent with cluster coordination by three Cys residues and one oxygen-containing residue, and analysis of ScNsrR variants suggested that highly conserved Glu-85 may be the fourth ligand. Finally, we demonstrate that some low molecular weight thiols, but importantly not physiologically relevant thiols, such as cysteine and an analogue of mycothiol, bind weakly to the [4Fe-4S] cluster, and exposure of this bound form to O2 results in cluster conversion to the [2Fe-2S] form, which does not bind to DNA. These data help to account for the observation of [2Fe-2S] forms of NsrR. PMID:25771538

  15. Mutational analysis of the [4Fe-4S]-cluster converting iron regulatory factor from its RNA-binding form to cytoplasmic aconitase.

    PubMed Central

    Hirling, H; Henderson, B R; Kühn, L C

    1994-01-01

    The control of cellular iron homeostasis involves the coordinate post-transcriptional regulation of ferritin mRNA translation and transferring receptor mRNA stability. These regulatory events are mediated by a soluble cytoplasmic protein, iron regulatory factor (IRF), which binds specifically to mRNA hairpin structures, termed iron-responsive elements (IREs), in the respective mRNAs. IRF is modulated by variations of cellular iron levels and exists as either an apo-protein or a [4Fe-4S]-cluster protein. The two conformations show distinct, mutually exclusive functions. High-affinity IRE binding is observed with the apo-form induced by iron deprivation, but is lost under high iron conditions when IRF is converted to the [4Fe-4S]-cluster form which shows cytoplasmic aconitase activity. Moreover, IRE binding is inactivated by the sulfhydryl-oxidizing agent diamide and fully activated in vitro by 2% 2-mercapto-ethanol, whereas alkylation of IRF inhibits IRE binding. In the present study, we analyzed each of the above features using site-directed mutants of recombinant human IRF. The results support the bifunctional nature of IRF. We conclude that cysteines 437, 503 and 506 anchor the [4Fe-4S]-cluster, and are essential to the aconitase activity. Mutagenesis changing any of the cysteines to serine leads to constitutive RNA binding in 0.02% 2-mercaptoethanol. Cysteine 437 is particularly critical to the RNA-protein interaction. The spontaneous or diamide-induced formation of disulfide bonds between cysteines 437 and 503 or 437 and 506, in apo-IRF, as well as its alkylation by N-ethylmaleimide, inhibit binding to the IRE.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:7508861

  16. Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase

    SciTech Connect

    Vaithiyalingam, Sivaraja; Warren, Eric M.; Eichman, Brandt F.; Chazin, Walter J.

    2010-10-19

    DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-{angstrom} resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysis of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C-RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.

  17. 4-Demethylwyosine Synthase from Pyrococcus abyssi Is a Radical-S-adenosyl-l-methionine Enzyme with an Additional [4Fe-4S]+2 Cluster That Interacts with the Pyruvate Co-substrate*

    PubMed Central

    Perche-Letuvée, Phanélie; Kathirvelu, Velavan; Berggren, Gustav; Clemancey, Martin; Latour, Jean-Marc; Maurel, Vincent; Douki, Thierry; Armengaud, Jean; Mulliez, Etienne; Fontecave, Marc; Garcia-Serres, Ricardo; Gambarelli, Serge; Atta, Mohamed

    2012-01-01

    Wybutosine and its derivatives are found in position 37 of tRNA encoding Phe in eukaryotes and archaea. They are believed to play a key role in the decoding function of the ribosome. The second step in the biosynthesis of wybutosine is catalyzed by TYW1 protein, which is a member of the well established class of metalloenzymes called “Radical-SAM.” These enzymes use a [4Fe-4S] cluster, chelated by three cysteines in a CX3CX2C motif, and S-adenosyl-l-methionine (SAM) to generate a 5′-deoxyadenosyl radical that initiates various chemically challenging reactions. Sequence analysis of TYW1 proteins revealed, in the N-terminal half of the enzyme beside the Radical-SAM cysteine triad, an additional highly conserved cysteine motif. In this study we show by combining analytical and spectroscopic methods including UV-visible absorption, Mössbauer, EPR, and HYSCORE spectroscopies that these additional cysteines are involved in the coordination of a second [4Fe-4S] cluster displaying a free coordination site that interacts with pyruvate, the second substrate of the reaction. The presence of two distinct iron-sulfur clusters on TYW1 is reminiscent of MiaB, another tRNA-modifying metalloenzyme whose active form was shown to bind two iron-sulfur clusters. A possible role for the second [4Fe-4S] cluster in the enzyme activity is discussed. PMID:23043105

  18. A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced From Studies With Subunit B of Heterodisulfide Reductase From Methanothermobacter Marburgensis

    SciTech Connect

    Hamann, N.; Mander, G.J.; Shokes, J.E.; Scott, R.A.; Bennati, M.; Hedderich, R.

    2009-06-01

    Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]{sup 3+} cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX{sub 31-39}CCX{sub 35-36}CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusual [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron-sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (g{sub zyx} = 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. {sup 57}Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with {sup 57}Fe hyperfine couplings very similar to that of CoM-HDR. CoM-{sup 33}SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S{sub 3}(O/N){sub 1} geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn

  19. Two EPR-detectable [4Fe-4S] clusters, N2a and N2b, are bound to the NuoI (TYKY) subunit of NADH:ubiquinone oxidoreductase (Complex I) from Rhodobacter capsulatus.

    PubMed

    Chevallet, Mireille; Dupuis, Alain; Issartel, Jean-Paul; Lunardi, Joël; van Belzen, Ronald; Albracht, Simon P J

    2003-03-01

    NADH:ubiquinone oxidoreductases (Complex I) contain a subunit, TYKY in the bovine enzyme and NuoI in the enzyme from Rhodobacter capsulatus, which is assumed to bind two [4Fe-4S] clusters because it contains two sets of conserved cysteine motifs similar to those found in the 2[4Fe-4S] ferredoxins. It was recently shown that the TYKY subunit is not an ordinary 2[4Fe-4S] ferredoxin, but has a unique amino acid sequence, which is only found in NAD(P)H:quinone oxidoreductases and certain membrane-bound [NiFe]-hydrogenases expected to be involved in redox-linked proton translocation [FEBS Lett. 485 (2000) 1]. We have generated a set of R. capsulatus mutants in which five out of the eight conserved cysteine residues in NuoI were replaced by other amino acids. The resulting mutants fell into three categories with virtually no, intermediate or quite normal Complex I activities. EPR-spectroscopic analysis of the membranes of the C67S and C106S mutants, two mutants belonging to the second and third group, respectively, showed a specific 50% decrease of the EPR signal attributed to cluster N2. It is concluded that the NuoI (TYKY) subunit binds two clusters N2, called N2a and N2b, which exhibit very similar spectral features when analyzed by X-band EPR spectroscopy. PMID:12615348

  20. Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations

    PubMed Central

    Mitra, Devrani; Pelmenschikov, Vladimir; Guo, Yisong; Case, David A.; Wang, Hongxin; Dong, Weibing; Tan, Ming-Liang; Ichiye, Toshiko; Jenney, Francis E.; Adams, Michael W. W.; Yoda, Yoshitaka; Zhao, Jiyong; Cramer, Stephen P.

    2011-01-01

    We have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal mode assignments, we recorded the NRVS of D14C ferredoxin samples with 36S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains: (Ph4P)2[Fe4S4Cl4]. Several distinct regions of NRVS intensity are identified, ranging from `protein' and torsional modes below 100 cm−1, through bending and breathing modes near 150 cm−1, to strong bands from Fe-S stretching modes between 250 cm−1 and ~400 cm−1. The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The 57Fe partial vibrational densities of states (PVDOS) for the oxidized samples were interpreted by normal mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe4S4]2+/1+ redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins. PMID:21500788

  1. Evidence That Phosphorylation of Iron Regulatory Protein 1 at Serine 138 Destabilizes the [4Fe-4S] Cluster in Cytosolic Aconitase by Enhancing 4Fe-3Fe Cycling*S⃞

    PubMed Central

    Deck, Kathryn M.; Vasanthakumar, Aparna; Anderson, Sheila A.; Goforth, Jeremy B.; Kennedy, M. Claire; Antholine, William E.; Eisenstein, Richard S.

    2009-01-01

    Iron-sulfur cluster-dependent interconversion of iron regulatory protein 1 (IRP1) between its RNA binding and cytosolic aconitase (c-acon) forms controls vertebrate iron homeostasis. Cluster removal from c-acon is thought to include oxidative demetallation as a required step, but little else is understood about the process of conversion to IRP1. In comparison with c-aconWT, Ser138 phosphomimetic mutants of c-acon contain an unstable [4Fe-4S] cluster and were used as tools to further define the pathway(s) of iron-sulfur cluster disassembly. Under anaerobic conditions cluster insertion into purified IRP1S138E and cluster loss on treatment with NO regulated aconitase and RNA binding activity over a similar range as observed for IRP1WT. However, activation of RNA binding of c-aconS138E was an order of magnitude more sensitive to NO than for c-aconWT. Consistent with this, an altered set point between RNA-binding and aconitase forms was observed for IRP1S138E when expressed in HEK cells. Active c-aconS138E could only accumulate under hypoxic conditions, suggesting enhanced cluster disassembly in normoxia. Cluster disassembly mechanisms were further probed by determining the impact of iron chelation on acon activity. Unexpectedly EDTA rapidly inhibited c-aconS138E activity without affecting c-aconWT. Additional chelator experiments suggested that cluster loss can be initiated in c-aconS138E through a spontaneous nonoxidative demetallation process. Taken together, our results support a model wherein Ser138 phosphorylation sensitizes IRP1/c-acon to decreased iron availability by allowing the [4Fe-4S]2+ cluster to cycle with [3Fe-4S]0 in the absence of cluster perturbants, indicating that regulation can be initiated merely by changes in iron availability. PMID:19269970

  2. Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe-4S] Cluster of the E. coli LytB/IspH Protein.

    PubMed

    Faus, Isabelle; Reinhard, Annegret; Rackwitz, Sergej; Wolny, Juliusz A; Schlage, Kai; Wille, Hans-Christian; Chumakov, Aleksandr; Krasutsky, Sergiy; Chaignon, Philippe; Poulter, C Dale; Seemann, Myriam; Schünemann, Volker

    2015-10-19

    The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate-free LytB has a special [4Fe-4S](2+) cluster with a yet unsolved structure. This motivated us to use synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical-molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate-free LytB. The apical iron atom of the [4Fe-4S](2+) is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) and to the inhibitors (E)-4-amino-3-methylbut-2-en-1-yl diphosphate and (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate. PMID:26118554

  3. Electrochemical Resolution of the [4Fe-4S] Centers of the AdoMet Radical Enzyme BtrN: Evidence of Proton Coupling and an Unusual, Low-Potential Auxiliary Cluster.

    PubMed

    Maiocco, Stephanie J; Grove, Tyler L; Booker, Squire J; Elliott, Sean J

    2015-07-15

    The S-adenosylmethionine (AdoMet) radical superfamily of enzymes includes over 113,500 unique members, each of which contains one indispensable iron-sulfur (FeS) cluster that is required to generate a 5'-deoxyadenosyl 5'-radical intermediate during catalysis. Enzymes within several subgroups of the superfamily, however, have been found to contain one or more additional FeS clusters. While these additional clusters are absolutely essential for enzyme activity, their exact roles in the function and/or mechanism of action of many of the enzymes are at best speculative, indicating a need to develop methods to characterize and study these clusters in more detail. Here, BtrN, an AdoMet radical dehydrogenase that catalyzes the two-electron oxidation of 2-deoxy-scyllo-inosamine to amino-dideoxy-scyllo-inosose, an intermediate in the biosynthesis of 2-deoxystreptamine antibiotics, is examined through direct electrochemistry, where the potential of both its AdoMet radical and auxiliary [4Fe-4S] clusters can be measured simultaneously. We find that the AdoMet radical cluster exhibits a midpoint potential of -510 mV, while the auxiliary cluster exhibits a midpoint potential of -765 mV, to our knowledge the lowest [4Fe-4S](2+/+) potential to be determined to date. The impact of AdoMet binding and the pH dependence of catalysis are also quantitatively observed. These data show that direct electrochemical methods can be used to further elucidate the chemistry of the burgeoning AdoMet radical superfamily in the future. PMID:26088836

  4. sup 17 O, sup 1 H, and sup 2 H electron nuclear double resonance characterization of solvent, substrate, and inhibitor binding to the (4Fe-4S) sup + cluster of aconitase

    SciTech Connect

    Werst, M.M.; Hoffman, B.M. ); Kennedy, M.C.; Beinert, H. )

    1990-11-01

    {sup 17}O electron nuclear double resonance (ENDOR) studies at X-band (9-GHz) and Q-band (35-GHz) microwave frequencies reveal that the (4Fe-4S){sup {plus}} cluster of substrate-free aconitase (citrate (isocitrate) hydro-lyase, EC 4.2.1.3) binds solvent, H{sub x}O (x = 1,2). Previous {sup 17}O ENDOR studies had disclosed that H{sub x}{sup 17}O binds to the enzyme-substrate complex and also to complexes of enzyme with the substrate analogues trans-aconitate and nitroisocitrate (1-hydroxy-2-nitro-1,3-propanedicarboxylate). The authors have used {sup 1}H and {sup 2}H ENDOR to characterize these solvent species. The authors propose that the fourth ligand of Fe{sub a} in substrate-free enzyme is a hydroxyl ion from the solvent; upon binding of substrate or substrate analogues at this Fe{sub a} site, the solvent species becomes protonated to form a water molecule. Previous {sup 17}O and {sup 13}C ENDOR studies showed that only a single carboxyl, at C-2 of the propane backbone of cis-aconitate or at C-1 of the inhibitor nitroisocitrate, coordinates to the cluster. Together, these results imply that enzyme-catalyzed interconversion of citrate and isocitrate does not involve displacement of an endogenous fourth ligand, but rather addition of the anionic carboxylate ligand and a change in protonation state of a solvent species bound to Fe{sub a}. The authors further report the {sup 17}O hyperfine tensor parameters of the C-2 carboxyl oxygen of substrate bound to the cluster as determined by the field dependence of the {sup 17}O ENDOR signals. {sup 17}O ENDOR studies also show that the carboxyl group of the inhibitor trans-aconitate binds similarly to that off substrate.

  5. Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.

    PubMed

    Kuo, C F; McRee, D E; Fisher, C L; O'Handley, S F; Cunningham, R P; Tainer, J A

    1992-10-16

    The crystal structure of the DNA repair enzyme endonuclease III, which recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom resolution with an R factor of 0.185. This iron-sulfur [4Fe-4S] enzyme is elongated and bilobal with a deep cleft separating two similarly sized domains: a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a Greek-key, four-helix domain formed by the amino-terminal and three carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the [4Fe-4S] cluster. The cluster is bound entirely within the carboxyl-terminal loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other known [4Fe-4S] proteins. Sequence conservation and the positive electrostatic potential of conserved regions identify a surface suitable for binding duplex B-DNA across the long axis of the enzyme, matching a 46 angstrom length of protected DNA. The primary role of the [4Fe-4S] cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone. The crystallographically identified inhibitor binding region, which recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin (residues 113 to 119). Location and side chain orientation at the base of the inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and Lys120 in the beta-elimination mechanism. Overall, the structure reveals an unusual fold and a new biological function for [4Fe-4S] clusters and provides a structural basis for studying recognition of damaged DNA and the N-glycosylase and apurinic/apyrimidinic-lyase mechanisms. PMID:1411536

  6. Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase.

    PubMed

    Seiffert, Grazyna B; Ullmann, G Matthias; Messerschmidt, Albrecht; Schink, Bernhard; Kroneck, Peter M H; Einsle, Oliver

    2007-02-27

    The tungsten-iron-sulfur enzyme acetylene hydratase stands out from its class because it catalyzes a nonredox reaction, the hydration of acetylene to acetaldehyde. Sequence comparisons group the protein into the dimethyl sulfoxide reductase family, and it contains a bis-molybdopterin guanine dinucleotide-ligated tungsten atom and a cubane-type [4Fe:4S] cluster. The crystal structure of acetylene hydratase at 1.26 A now shows that the tungsten center binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct, hydrophobic pocket. This mechanism requires a strong shift of pK(a) of the aspartate, caused by a nearby low-potential [4Fe:4S] cluster. To access this previously unrecognized W-Asp active site, the protein evolved a new substrate channel distant from where it is found in other molybdenum and tungsten enzymes. PMID:17360611

  7. Structure and Function of Four Classes of the 4Fe-4S Protein, IspH.

    PubMed

    Rao, Guodong; Oldfield, Eric

    2016-07-26

    IspH, (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate reductase, is an essential enzyme in isoprenoid biosynthesis and an important drug/herbicide target. Using X-ray crystallographic, bioinformatics, mutagenesis/kinetics/stability, and electron paramagnetic resonance (EPR) results, we show that organisms from different environments ultilize one of four main IspH classes. The classes are based on the arrangement of the aromatic residues near the 4Fe-4S cluster and the presence or absence of N- and C-terminal extensions. Class A enzymes are found primarily in anaerobic and microaerophilic bacteria. Class B enzymes are found in aerobic bacteria. Class C enzymes are found in cyanobacteria and plants. Class D enzymes are found in apicomplexan parasites. Using mutagenesis, we show that the cluster-associated aromatic groups in class A and class B IspHs enhance cluster oxidative stability. Y198A, F302A, and a C-terminal truncation mutant of the class B (Escherichia coli) IspH have catalytic activity lower than that of the wild-type protein when using methyl viologen as the electron donor, but higher activity with dithionite as the electron donor, due to ready access of the small reductant to the cluster, consistent with their increased oxygen and H2O2 sensitivity. F302A has the largest effect on the reaction rates, and EPR studies indicate this residue affects Fe-S cluster structure. Similar effects on cluster stability are seen with class A (F14A and Y98A) mutants; however, effects on ET rates are smaller, and there are no differences between the EPR spectra of mutant and wild-type proteins. Overall, the results are of general interest because they show, for the first time, that there are multiple IspH classes that have evolved to allow organisms to survive in diverse oxidative-stress environments. PMID:27357244

  8. Differentiated, Promoter-specific Response of [4Fe-4S] NsrR DNA Binding to Reaction with Nitric Oxide*

    PubMed Central

    Crack, Jason C.; Svistunenko, Dimitri A.; Munnoch, John; Thomson, Andrew J.; Hutchings, Matthew I.; Le Brun, Nick E.

    2016-01-01

    NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ∼2 NO per cluster, although for the hmpA1 and nsrR promoters, ∼4 and ∼8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8–10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ∼2 NO per cluster, along with two further intermediates at ∼4 and ∼6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes. PMID:26887943

  9. Differentiated, Promoter-specific Response of [4Fe-4S] NsrR DNA Binding to Reaction with Nitric Oxide.

    PubMed

    Crack, Jason C; Svistunenko, Dimitri A; Munnoch, John; Thomson, Andrew J; Hutchings, Matthew I; Le Brun, Nick E

    2016-04-15

    NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ∼2 NO per cluster, although for the hmpA1 and nsrR promoters, ∼4 and ∼8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8-10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ∼2 NO per cluster, along with two further intermediates at ∼4 and ∼6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes. PMID:26887943

  10. Copper binding in IscA inhibits iron-sulfur cluster assembly in Escherichia coli

    PubMed Central

    Tan, Guoqiang; Cheng, Zishuo; Pang, Yilin; Landry, Aaron P.; Li, Jianghui; Lu, Jianxin; Ding, Huangen

    2014-01-01

    Among the iron-sulfur cluster assembly proteins encoded by gene cluster iscSUA-hscBA-fdx in Escherichia coli, IscA has a unique and strong iron binding activity and can provide iron for iron-sulfur cluster assembly in proteins in vitro. Deletion of IscA and its paralogue SufA results in an E. coli mutant that fails to assemble [4Fe-4S] clusters in proteins under aerobic conditions, suggesting that IscA has a crucial role for iron-sulfur cluster biogenesis. Here we report that among the iron-sulfur cluster assembly proteins, IscA also has a strong and specific binding activity for Cu(I) in vivo and in vitro. The Cu(I) center in IscA is stable and resistant to oxidation under aerobic conditions. Mutation of the conserved cysteine residues that are essential for the iron binding in IscA abolishes the copper binding activity, indicating that copper and iron may share the same binding site in the protein. Additional studies reveal that copper can compete with iron for the metal binding site in IscA and effectively inhibits the IscA-mediated [4Fe-4S] cluster assembly in E. coli cells. The results suggest that copper may not only attack the [4Fe-4S] clusters in dehydratases, but also block the [4Fe-4S] cluster assembly in proteins by targeting IscA in cells. PMID:24946160

  11. Cloning, expression, and molecular characterization of the gene encoding an extremely thermostable [4Fe-4S] ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus.

    PubMed Central

    Heltzel, A; Smith, E T; Zhou, Z H; Blamey, J M; Adams, M W

    1994-01-01

    The gene for ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus was cloned, sequenced, and expressed in Escherichia coli. The coding region confirmed the determined amino acid sequence. Putative archaeon-type transcriptional regulatory elements were identified. The fdxA gene appears to be an independent transcriptional unit. Recombinant ferredoxin was indistinguishable from the protein purified from P. furiosus in its thermal stability and in the potentiometric and spectroscopic properties of its [4Fe-4S] cluster. PMID:8045914

  12. The reducing component BoxA of benzoyl-coenzyme A epoxidase from Azoarcus evansii is a [4Fe-4S] protein.

    PubMed

    Rather, Liv J; Bill, Eckhard; Ismail, Wael; Fuchs, Georg

    2011-12-01

    BoxA is the reductase component of the benzoyl-coenzyme A (CoA) oxidizing epoxidase enzyme system BoxAB. The enzyme catalyzes the key step of an hitherto unknown aerobic, CoA-dependent pathway of benzoate metabolism, which is the epoxidation of benzoyl-CoA to the non-aromatic 2,3-epoxybenzoyl-CoA. The function of BoxA is the transfer of two electrons from NADPH to the epoxidase component BoxB. We could show recently that BoxB is a diiron enzyme, whereas here we demonstrate that BoxA harbors an FAD and two [4Fe-4S] clusters per protein monomer. The characterization of BoxA was hampered by severe oxygen sensitivity; the cubane [4Fe-4S] clusters degrade already with traces of oxygen. Interestingly, the adventitiously formed [3Fe-4S] centers could be reconstituted in vitro by adding Fe(II) and sulfide to retrieve the native cubane centers. BoxA is the first example of a reductase of this type that has an FAD and two bacterial ferredoxin-type [4Fe-4S] clusters. In other cases within the catalytically versatile family of diiron enzymes, the related reductases have plant-type ferredoxin or Rieske-type [2Fe-2S] centers only. PMID:21672639

  13. Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

    PubMed

    Frazão, Carlos; Aragão, David; Coelho, Ricardo; Leal, Sónia S; Gomes, Cláudio M; Teixeira, Miguel; Carrondo, Maria Arménia

    2008-03-01

    Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn(2+) site and the ferredoxin (betaalphabeta)(2) core, which harbours intact clusters I and II, a [3Fe-4S](1+/0) and a [4Fe-4S](2+/1+) centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe-4S](1+/0) centres and poor definition around cluster II. PMID:18258200

  14. Inhibition of the 4Fe-4S Proteins IspG and IspH: an EPR, ENDOR and HYSCORE Investigation

    PubMed Central

    Guerra, Francisco; Wang, Ke; Li, Jikun; Wang, Weixue; Liu, Yi-Liang; Amin, Shivani

    2014-01-01

    IspG and IspH are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. They contain cubane-type 4Fe-4S clusters that are involved in unusual 2H+/2e− reductions. Here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-HMBPP (HMBPP=E-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) IspH substrate-analog inhibitors to both proteins, as well as the binding of HMBPP and an acetylene diphosphate inhibitor, to IspG. The results show that amino-HMBPP binds to reduced IspH by Fe-C π-bonding with the olefinic carbons interacting with the unique 4th Fe in the 4Fe-4S cluster, quite different to the direct Fe-N ligation seen with the oxidized protein. No such π-complex is observed when amino-HMBPP binds to reduced IspG. No EPR signal is observed with IspH in the presence of dithionite and thiolo-HMBPP, suggesting that the 4Fe-4S cluster is not reduced, consistent with the presence of a 420 nm feature in the absorption spectrum (characteristic of an oxidized cluster). However, with IspG, the EPR spectrum in the presence of dithionite and thiolo-HMBPP is very similar to that seen with HMBPP. The binding of HMBPP to IspG was studied using hyperfine sublevel correlation spectroscopy with 17O and 13C labeled samples: the results rule out direct Fe-O bonding and indicate π-bonding. Finally, the binding to IspG of a potent acetylene diphosphate inhibitor was studied by using electron-nuclear double resonance spectroscopy with 13C labeled ligands: the large hyperfine couplings indicate strong Fe-C π-bonding with the acetylenic group. These results illustrate a remarkable diversity in binding behavior for HMBPP-analog inhibitors, opening up new routes to inhibitor design of interest in the context of anti-bacterial and anti-malarial drug discovery, as well as “cubane-type” metallo-biochemistry, in general. PMID:24999381

  15. Heterologous overproduction of 2[4Fe4S]- and [2Fe2S]-type clostridial ferredoxins and [2Fe2S]-type agrobacterial ferredoxin.

    PubMed

    Huang, Haiyan; Hu, Liejie; Yu, Wenjun; Li, Huili; Tao, Fei; Xie, Huijun; Wang, Shuning

    2016-05-01

    Ferredoxins are small, acidic proteins containing iron-sulfur clusters that are widespread in living organisms. They play key roles as electron carriers in various metabolic processes, including respiration, photosynthesis, fermentation, nitrogen fixation, carbon dioxide fixation, and hydrogen production. However, only several kinds of ferredoxins are commercially available now, greatly limiting the investigation of ferredoxin-related enzymes and metabolic processes. Here we describe the heterologous overproduction of 2[4Fe4S]- and [2Fe2S]-type clostridial ferredoxins and [2Fe2S]-type agrobacterial ferredoxin. Adding extra iron and sulfur sources to the medium in combination with using Escherichia coli C41(DE3) harboring pCodonplus and pRKISC plasmids as host greatly enhanced iron-sulfur cluster synthesis in the three ferredoxins. After induction for 12 h in terrific broth and purification by affinity chromatography and anion exchange chromatography, approximately 3.4 mg of streptavidin (Strep)-tagged and 3.7 mg of polyhistidine (His)-tagged clostridial 2[4Fe4S] ferredoxins were obtained from 1 l of culture. Excitingly, after induction for 24 h in terrific broth, around 40 mg of His-tagged clostridial [2Fe2S] and 23 mg of His-tagged agrobacterial [2Fe2S] ferredoxins were purified from 1 l of culture. The recombinant ferredoxins apparently exhibited identical properties and physiological function to native ferredoxins. No negative impact of two different affinity tags on ferredoxin activity was found. In conclusion, we successfully developed a convenient method for heterologous overproduction of the three kinds of ferredoxins with satisfactory yields and activities, which would be very helpful for the ferredoxin-related researches. PMID:26748213

  16. 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

  17. In Vitro Characterization of AtsB, a Radical SAM Formylglycine-Generating Enzyme That Contains Three [4Fe-4S] Clusters†

    PubMed Central

    Grove, Tyler L.; Lee, Kyung-Hoon; St. Clair, Jennifer; Krebs, Carsten; Booker, Squire J.

    2009-01-01

    Sulfatases catalyze the cleavage of a variety of cellular sulfate esters via a novel mechanism that requires the action of a protein-derived formylglycine cofactor. Formation of the cofactor is catalyzed by an accessory protein and involves the two-electron oxidation of a specific cysteinyl or seryl residue on the relevant sulfatase. Although some sulfatases undergo maturation via mechanisms in which oxygen serves as an electron acceptor, AtsB, the maturase from Klebsiella pneumoniae, catalyzes the oxidation of Ser72 on AtsA, its cognate sulfatase, via an oxygen-independent mechanism. Moreover, it does not make use of pyridine or flavin nucleotide cofactors as direct electron acceptors. In fact, AtsB has been shown to be a member of the radical S-adenosylmethionine superfamily of proteins, suggesting that it catalyzes this oxidation via an intermediate 5′-deoxyadenosyl 5′-radical that is generated by a reductive cleavage of S-adenosyl-L-methionine. In contrast to AtsA, very little in vitro characterization of AtsB has been conducted. Herein we show that coexpression of the K. pneumoniae atsB gene with a plasmid that encodes genes that are known to be involved in iron–sulfur cluster biosynthesis yields soluble protein that can be characterized in vitro. The as-isolated protein contained 8.7 ± 0.4 irons and 12.2 ± 2.6 sulfides per polypeptide, which existed almost entirely in the [4Fe-4S]2+ configuration, as determined by Mössbauer spectroscopy, suggesting that it contained at least two of these clusters per polypeptide. Reconstitution of the as-isolated protein with additional iron and sulfide indicated the presence of 12.3 ± 0.2 irons and 9.9 ± 0.4 sulfides per polypeptide. Subsequent characterization of the reconstituted protein by Mössbauer spectroscopy indicated the presence of only [4Fe-4S] clusters, suggesting that reconstituted AtsB contains three per polypeptide. Consistent with this stoichiometry, an as-isolated AtsB triple variant containing

  18. Structural principles for computational and de novo design of 4Fe-4S metalloproteins.

    PubMed

    Nanda, Vikas; Senn, Stefan; Pike, Douglas H; Rodriguez-Granillo, Agustina; Hansen, Will A; Khare, Sagar D; Noy, Dror

    2016-05-01

    Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed. This article is part of a Special issue entitled Biodesign for Bioenergetics - the design and engineering of electronic transfer cofactors, protein networks, edited by Ronald L. Koder and J.L Ross Anderson. PMID:26449207

  19. Spectroscopic and functional characterization of iron-sulfur cluster-bound forms of Azotobacter vinelandii (Nif)IscA.

    PubMed

    Mapolelo, Daphne T; Zhang, Bo; Naik, Sunil G; Huynh, Boi Hanh; Johnson, Michael K

    2012-10-16

    The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of (Nif)IscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV-visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii(Nif)IscA, and the ability of (Nif)IscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that (Nif)IscA can rapidly and reversibly cycle between forms containing one [2Fe-2S](2+) and one [4Fe-4S](2+) cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S](2+) clusters and O(2)-induced [4Fe-4S](2+) oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S](2+)-(Nif)IscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-(Nif)IscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions. PMID:23003323

  20. Electron spin-lattice relaxation of the (4Fe-4S) ferredoxin from B. stearothermophilus. Comparison with other iron proteins

    NASA Astrophysics Data System (ADS)

    Bertrand, Patrick; Gayda, Jean-Pierre; Rao, K. Krishna

    1982-05-01

    The temperature dependence of the electron spin-lattice relaxation time T1 of the (4Fe-4S) ferredoxin from Bacillus stearothermophilus is studied in the range 1.2 to 40 K. This dependence is similar to that observed for the (2Fe-2S) ferredoxin from Spirulina maxima and can be interpreted with the same relaxation processes [J.P. Gayda, P. Bertrand, A. Deville, C. More, G. Roger, J.F. Gibson, and R. Cammack, Biochim. Biophys. Acta 581, 15 (1979)]. In particular, between 4 and 15 K, the data are well fitted by a second-order Raman process involving three-dimensional phonons, with a Debye temperature of about 60 K (45 cm-1). This would give an estimation of the highest frequency of the vibrations which can propagate through the three-dimensional proteinic medium. In the highest temperature range (T≳30 K) the results are interpreted with an Orbach process involving an excited level of energy 120 cm-1. This process could be induced by the localized vibrations of the active site. Finally, these results are compared to those recently reported for some hemoproteins [H.J. Stapleton, J.P. Allen, C.P. Flynn, D.G. Stinson, and S.R. Kurtz, Phys. Rev. Lett. 45, 1456 (1980)]. Below 15 K, the temperature dependence of T1 for these samples is similar to that observed for the iron-sulfur proteins and may be interpreted in the same way. Our interpretation is compared to the fractal model proposed by Stapleton et al.

  1. X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly

    PubMed Central

    Dinis, Pedro; Suess, Daniel L. M.; Fox, Stephen J.; Harmer, Jenny E.; Driesener, Rebecca C.; De La Paz, Liliana; Swartz, James R.; Essex, Jonathan W.; Britt, R. David; Roach, Peter L.

    2015-01-01

    Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN− ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (βα)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a μ2-sulfide ion to a mononuclear Fe2+ center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly. PMID:25605932

  2. The Human Iron–Sulfur Assembly Complex Catalyzes the Synthesis of [2Fe-2S] Clusters on ISCU2 That Can Be Transferred to Acceptor Molecules

    PubMed Central

    Fox, Nicholas G.; Chakrabarti, Mrinmoy; McCormick, Sean P.; Lindahl, Paul A.; Barondeau, David P.

    2015-01-01

    Iron–sulfur (Fe–S) clusters are essential protein cofactors for most life forms. In human mitochondria, the core Fe–S biosynthetic enzymatic complex (called SDUF) consists of NFS1, ISD11, ISCU2, and frataxin (FXN) protein components. Few mechanistic details about how this complex synthesizes Fe–S clusters and how these clusters are delivered to targets are known. Here circular dichroism and Mössbauer spectroscopies were used to reveal details of the Fe–S cluster assembly reaction on the SDUF complex. SDUF reactions generated [2Fe-2S] cluster intermediates that readily converted to stable [2Fe-2S] clusters bound to uncomplexed ISCU2. Similar reactions that included the apo Fe–S acceptor protein human ferredoxin (FDX1) resulted in formation of [2Fe-2S]-ISCU2 rather than [2Fe-2S]-FDX1. Subsequent addition of dithiothreitol (DTT) induced transfer of the cluster from ISCU2 to FDX1, suggesting that [2Fe-2S]-ISCU2 is an intermediate. Reactions that initially included DTT rapidly generated [2Fe-2S]-FDX1 and bypassed formation of [2Fe-2S]-ISCU2. In the absence of apo-FDX1, incubation of [2Fe-2S]-ISCU2 with DTT generated [4Fe-4S]-ISCU2 species. Together, these results conflict with a recent report of stable [4Fe-4S] cluster formation on the SDUF complex. Rather, they support a model in which SDUF builds transient [2Fe-2S] cluster intermediates that generate clusters on sulfur-containing molecules, including uncomplexed ISCU2. Additional small molecule or protein factors are required for the transfer of these clusters to Fe–S acceptor proteins or the synthesis of [4Fe-4S] clusters. PMID:26016389

  3. Inhibition of IspH, a [4Fe-4S]2+ enzyme involved in the biosynthesis of isoprenoids via the methylerythritol phosphate pathway.

    PubMed

    Janthawornpong, Karnjapan; Krasutsky, Sergiy; Chaignon, Philippe; Rohmer, Michel; Poulter, C Dale; Seemann, Myriam

    2013-02-01

    The MEP pathway, which is absent in animals but present in most pathogenic bacteria, in the parasite responsible for malaria and in plant plastids, is a target for the development of antimicrobial drugs. IspH, an oxygen-sensitive [4Fe-4S] enzyme, catalyzes the last step of this pathway and converts (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). A crucial step in the mechanism of this enzyme is the binding of the C4 hydroxyl of HMBPP to the unique fourth iron site in the [4Fe-4S](2+) moiety. Here, we report the synthesis and the kinetic investigations of two new extremely potent inhibitors of E. coli IspH where the OH group of HMBPP is replaced by an amino and a thiol group. (E)-4-Mercapto-3-methylbut-2-en-1-yl diphosphate is a reversible tight-binding inhibitor of IspH with K(i) = 20 ± 2 nM. A detailed kinetic analysis revealed that (E)-4-amino-3-methylbut-2-en-1-yl diphosphate is a reversible slow-binding inhibitor of IspH with K(i) = 54 ± 19 nM. The slow binding behavior of this inhibitor is best described by a one-step mechanism with the slow step consisting of the formation of the enzyme-inhibitor (EI) complex. PMID:23316732

  4. Characterization of iron-sulfur cluster assembly protein IscA from Acidithiobacillus ferrooxidans.

    PubMed

    Qian, Lin; Zheng, Chunli; Liu, Jianshe

    2013-03-01

    IscA is a key member of the iron-sulfur cluster assembly machinery found in bacteria and eukaryotes, but the mechanism of its function in the biogenesis of iron-sulfur cluster remains elusive. In this paper, we demonstrate that Acidithiobacillus ferrooxidans IscA is a [4Fe-4S] cluster binding protein, and it can bind iron in the presence of DTT with an apparent iron association constant of 4·10(20) M(-1). The iron binding in IscA can be promoted by oxygen through oxidizing ferrous iron to ferric iron. Furthermore, we show that the iron bound form of IscA can be converted to iron-sulfur cluster bound form in the presence of IscS and L-cysteine in vitro. Substitution of the invariant cysteine residues Cys35, Cys99, or Cys101 in IscA abolishes the iron binding activity of the protein; the IscA mutants that fail to bind iron are unable to assemble the iron-sulfur clusters. Further studies indicate that the iron-loaded IscA could act as an iron donor for the assembly of iron-sulfur clusters in the scaffold protein IscU in vitro. Taken together, these findings suggest that A. ferrooxidans IscA is not only an iron-sulfur protein, but also an iron binding protein that can act as an iron donor for biogenesis of iron-sulfur clusters. PMID:23586717

  5. Role of Nfu1 and Bol3 in iron-sulfur cluster transfer to mitochondrial clients.

    PubMed

    Melber, Andrew; Na, Un; Vashisht, Ajay; Weiler, Benjamin D; Lill, Roland; Wohlschlegel, James A; Winge, Dennis R

    2016-01-01

    Iron-sulfur (Fe-S) clusters are essential for many cellular processes, ranging from aerobic respiration, metabolite biosynthesis, ribosome assembly and DNA repair. Mutations in NFU1 and BOLA3 have been linked to genetic diseases with defects in mitochondrial Fe-S centers. Through genetic studies in yeast, we demonstrate that Nfu1 functions in a late step of [4Fe-4S] cluster biogenesis that is of heightened importance during oxidative metabolism. Proteomic studies revealed Nfu1 physical interacts with components of the ISA [4Fe-4S] assembly complex and client proteins that need [4Fe-4S] clusters to function. Additional studies focused on the mitochondrial BolA proteins, Bol1 and Bol3 (yeast homolog to human BOLA3), revealing that Bol1 functions earlier in Fe-S biogenesis with the monothiol glutaredoxin, Grx5, and Bol3 functions late with Nfu1. Given these observations, we propose that Nfu1, assisted by Bol3, functions to facilitate Fe-S transfer from the biosynthetic apparatus to the client proteins preventing oxidative damage to [4Fe-4S] clusters. PMID:27532773

  6. Role of Nfu1 and Bol3 in iron-sulfur cluster transfer to mitochondrial clients

    PubMed Central

    Melber, Andrew; Na, Un; Vashisht, Ajay; Weiler, Benjamin D; Lill, Roland; Wohlschlegel, James A; Winge, Dennis R

    2016-01-01

    Iron-sulfur (Fe-S) clusters are essential for many cellular processes, ranging from aerobic respiration, metabolite biosynthesis, ribosome assembly and DNA repair. Mutations in NFU1 and BOLA3 have been linked to genetic diseases with defects in mitochondrial Fe-S centers. Through genetic studies in yeast, we demonstrate that Nfu1 functions in a late step of [4Fe-4S] cluster biogenesis that is of heightened importance during oxidative metabolism. Proteomic studies revealed Nfu1 physical interacts with components of the ISA [4Fe-4S] assembly complex and client proteins that need [4Fe-4S] clusters to function. Additional studies focused on the mitochondrial BolA proteins, Bol1 and Bol3 (yeast homolog to human BOLA3), revealing that Bol1 functions earlier in Fe-S biogenesis with the monothiol glutaredoxin, Grx5, and Bol3 functions late with Nfu1. Given these observations, we propose that Nfu1, assisted by Bol3, functions to facilitate Fe-S transfer from the biosynthetic apparatus to the client proteins preventing oxidative damage to [4Fe-4S] clusters. DOI: http://dx.doi.org/10.7554/eLife.15991.001 PMID:27532773

  7. Organometallic mechanism of action and inhibition of the 4Fe-4S isoprenoid biosynthesis protein GcpE (IspG)

    PubMed Central

    Wang, Weixue; Li, Jikun; Wang, Ke; Huang, Cancan; Zhang, Yong; Oldfield, Eric

    2010-01-01

    We report the results of a series of chemical, EPR, ENDOR, and HYSCORE spectroscopic investigations of the mechanism of action (and inhibition) of GcpE, E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) synthase, also known as IspG, an Fe4S4 cluster-containing protein. We find that the epoxide of HMBPP when reduced by GcpE generates the same transient EPR species as observed on addition of the substrate, 2-C-methyl-D-erythritol-2, 4-cyclo-diphosphate. ENDOR and HYSCORE spectra of these transient species (using 2H, 13C and 17O labeled samples) indicate formation of an Fe-C-H containing organometallic intermediate, most likely a ferraoxetane. This is then rapidly reduced to a ferracyclopropane in which the HMBPP product forms an η2-alkenyl π- (or π/σ) complex with the 4th Fe in the Fe4S4 cluster, and a similar “metallacycle” also forms between isopentenyl diphosphate (IPP) and GcpE. Based on this metallacycle concept, we show that an alkyne (propargyl) diphosphate is a good (Ki ∼ 300 nM) GcpE inhibitor, and supported again by EPR and ENDOR results (a 13C hyperfine coupling of ∼7 MHz), as well as literature precedent, we propose that the alkyne forms another π/σ metallacycle, an η2-alkynyl, or ferracyclopropene. Overall, the results are of broad general interest because they provide new mechanistic insights into GcpE catalysis and inhibition, with organometallic bond formation playing, in both cases, a key role. PMID:20534554

  8. Cluster assembly of hierarchical nanostructures

    SciTech Connect

    Siegel, R.W.

    1992-02-01

    In the past few years, atom clusters with diameters in the range of 2--20 nm of a variety of materials, including both metals and ceramics, have been synthesized by evaporation and condensation in high-purity gases and subsequently consolidated in situ under ultrahigh vacuum conditions to create nanophase materials. These new utlrafine-grained materials have properties that are often significantly different and considerably improved relative to those of their coarser-grained counterparts owing to both their small grain-size scale and the large percentage of their atoms in grain boundary environments. Since their properties can be engineered during the synthesis and processing steps, cluster-assembled materials appear to have significant potential for the introduction of a hierarchy of both structure and properties. Some of the recent research on nanophase materials related to properties and scale are reviewed and some of the possibilities for synthesizing hierarchical nanostructures via cluster assembly are considered.

  9. Mitochondrial Bol1 and Bol3 function as assembly factors for specific iron-sulfur proteins

    PubMed Central

    Uzarska, Marta A; Nasta, Veronica; Weiler, Benjamin D; Spantgar, Farah; Ciofi-Baffoni, Simone; Saviello, Maria Rosaria; Gonnelli, Leonardo; Mühlenhoff, Ulrich; Banci, Lucia; Lill, Roland

    2016-01-01

    Assembly of mitochondrial iron-sulfur (Fe/S) proteins is a key process of cells, and defects cause many rare diseases. In the first phase of this pathway, ten Fe/S cluster (ISC) assembly components synthesize and insert [2Fe-2S] clusters. The second phase is dedicated to the assembly of [4Fe-4S] proteins, yet this part is poorly understood. Here, we characterize the BOLA family proteins Bol1 and Bol3 as specific mitochondrial ISC assembly factors that facilitate [4Fe-4S] cluster insertion into a subset of mitochondrial proteins such as lipoate synthase and succinate dehydrogenase. Bol1-Bol3 perform largely overlapping functions, yet cannot replace the ISC protein Nfu1 that also participates in this phase of Fe/S protein biogenesis. Bol1 and Bol3 form dimeric complexes with both monothiol glutaredoxin Grx5 and Nfu1. Complex formation differentially influences the stability of the Grx5-Bol-shared Fe/S clusters. Our findings provide the biochemical basis for explaining the pathological phenotypes of patients with mutations in BOLA3. DOI: http://dx.doi.org/10.7554/eLife.16673.001 PMID:27532772

  10. The Assembly of Galaxy Clusters

    SciTech Connect

    Berrier, Joel C.; Stewart, Kyle R.; Bullock, James S.; Purcell, Chris W.; Barton, Elizabeth J.; Wechsler, Risa H.

    2008-05-16

    We study the formation of fifty-three galaxy cluster-size dark matter halos (M = 10{sup 14.0-14.76} M{sub {circle_dot}}) formed within a pair of cosmological {Lambda}CDM N-body simulations, and track the accretion histories of cluster subhalos with masses large enough to host {approx} 0.1L{sub *} galaxies. By associating subhalos with cluster galaxies, we find the majority of galaxies in clusters experience no 'pre-processing' in the group environment prior to their accretion into the cluster. On average, {approx} 70% of cluster galaxies fall into the cluster potential directly from the field, with no luminous companions in their host halos at the time of accretion; and less than {approx} 12% are accreted as members of groups with five or more galaxies. Moreover, we find that cluster galaxies are significantly less likely to have experienced a merger in the recent past ({approx}< 6 Gyr) than a field halo of the same mass. These results suggest that local, cluster processes like ram-pressure stripping, galaxy harassment, or strangulation play the dominant role in explaining the difference between cluster and field populations at a fixed stellar mass; and that pre-evolution or past merging in the group environment is of secondary importance for setting cluster galaxy properties for most clusters. The accretion times for z = 0 cluster members are quite extended, with {approx} 20% incorporated into the cluster halo more than 7 Gyr ago and {approx} 20% within the last 2 Gyr. By comparing the observed morphological fractions in cluster and field populations, we estimate an approximate time-scale for late-type to early-type transformation within the cluster environment to be {approx} 6 Gyr.

  11. Oriented assembly of polyhedral plasmonic nanoparticle clusters

    PubMed Central

    Henzie, Joel; Andrews, Sean C.; Ling, Xing Yi; Li, Zhiyong; Yang, Peidong

    2013-01-01

    Shaped colloids can be used as nanoscale building blocks for the construction of composite, functional materials that are completely assembled from the bottom up. Assemblies of noble metal nanostructures have unique optical properties that depend on key structural features requiring precise control of both position and connectivity spanning nanometer to micrometer length scales. Identifying and optimizing structures that strongly couple to light is important for understanding the behavior of surface plasmons in small nanoparticle clusters, and can result in highly sensitive chemical and biochemical sensors using surface-enhanced Raman spectroscopy (SERS). We use experiment and simulation to examine the local surface plasmon resonances of different arrangements of Ag polyhedral clusters. High-resolution transmission electron microscopy shows that monodisperse, atomically smooth Ag polyhedra can self-assemble into uniform interparticle gaps that result in reproducible SERS enhancement factors from assembly to assembly. We introduce a large-scale, gravity-driven assembly method that can generate arbitrary nanoparticle clusters based on the size and shape of a patterned template. These templates enable the systematic examination of different cluster arrangements and provide a means of constructing scalable and reliable SERS sensors. PMID:23569275

  12. Nanophase materials assembled from clusters

    SciTech Connect

    Siegel, R.W.

    1992-02-01

    The preparation of metal and ceramic atom clusters by means of the gas-condensation method, followed by their in situ collection and consolidation under high-vacuum conditions, has recently led to the synthesis of a new class of ultrafine-grained materials. These nanophase materials, with typical average grain sizes of 5 to 50 nm and, hence, a large fraction of their atoms in interfaces, exhibit properties that are often considerably improved relative to those of conventional materials. Furthermore, their synthesis and processing characteristics should enable the design of new materials with unique properties. Some examples are ductile ceramics that can be formed and sintered to full density at low temperatures without the need for binding or sintering aids, and metals with dramatically increased strength. The synthesis of these materials is briefly described along with what is presently known of their structure and properties. Their future impact on materials science and technology is also considered.

  13. Formation and Assembly of Massive Star Clusters

    NASA Astrophysics Data System (ADS)

    McMillan, Stephen

    open access to state-of- the-art simulation techniques within a modern, modular software environment. We will follow the gravitational collapse of 0.1-10 million-solar mass gas clouds through star formation and coalescence into a star cluster, modeling in detail the coupling of the gas and the newborn stars. We will study the effects of star formation by detecting accreting regions of gas in self-gravitating, turbulent, MHD, FLASH models that we will translate into collisional dynamical systems of stars modeled with an N-body code, coupled together in the AMUSE framework. Our FLASH models will include treatments of radiative transfer from the newly formed stars, including heating and radiative acceleration of the surrounding gas. Specific questions to be addressed are: (1) How efficiently does the gas in a star forming region form stars, how does this depend on mass, metallicity, and other parameters, and what terminates star formation? What observational predictions can be made to constrain our models? (2) How important are different mechanisms for driving turbulence and removing gas from a cluster: accretion, radiative feedback, and mechanical feedback? (3) How does the infant mortality rate of young clusters depend on the initial properties of the parent cloud? (4) What are the characteristic formation timescales of massive star clusters, and what observable imprints does the assembly process leave on their structure at an age of 10-20 Myr, when formation is essentially complete and many clusters can be observed? These studies are directly relevant to NASA missions at many electromagnetic wavelengths, including Chandra, GALEX, Hubble, and Spitzer. Each traces different aspects of cluster formation and evolution: X-rays trace supernovae, ultraviolet traces young stars, visible colors can distinguish between young blue stars and older red stars, and the infrared directly shows young embedded star clusters.

  14. Key players and their role during mitochondrial iron-sulfur cluster biosynthesis.

    PubMed

    Rawat, Swati; Stemmler, Timothy L

    2011-01-17

    Iron-sulfur clusters are multifaceted iron-containing cofactors coordinated and utilized by numerous proteins in nearly all biological systems. Fe-S-cluster-containing proteins help direct pathways essential for cell viability and participate in biological applications ranging from nucleotide biosynthesis and stability, protein translation, enzyme catalysis, and mitochondrial metabolism. Fe-S-containing proteins function by utilizing the unique electronic and chemical properties inherent in the Fe containing cofactor. Fe-S clusters are constructed of inorganic iron and sulfide arranged in a distinct caged structural makeup ranging from [Fe(2) -S(2) ], [Fe(3) -S(4) ], [Fe(4) -S(4) ], up to [Fe(8) -S(8) ] clusters. In eukaryotes, cluster activity is controlled in part at the assembly level and the major pathway for cluster production exists within the mitochondria. Recent insight into the pathway of mitochondrial cluster assembly has come from new in vivo and in vitro reports that provided direct insight into how all protein partners within the assembly pathway interact. However, we are only just beginning to understand the role of each protein within this complex pageant that is mitochondrial Fe-S cluster assembly. In this report we present results, using the yeast model for mitochondrial assembly, to describe the molecular details of how important proteins in the pathway coordinate for cluster assembly. PMID:21226084

  15. A Redox Active [2Fe-2S] Cluster on the Hydrogenase Maturase HydF.

    PubMed

    Shepard, Eric M; Byer, Amanda S; Betz, Jeremiah N; Peters, John W; Broderick, Joan B

    2016-06-28

    [FeFe]-hydrogenases are nature's most prolific hydrogen catalysts, excelling at facilely interconverting H2 and protons. The catalytic core common to all [FeFe]-hydrogenases is a complex metallocofactor, referred to as the H-cluster, which is composed of a standard [4Fe-4S] cluster linked through a bridging thiolate to a 2Fe subcluster harboring dithiomethylamine, carbon monoxide, and cyanide ligands. This 2Fe subcluster is synthesized and inserted into [FeFe]-hydrogenase by three maturase enzymes denoted HydE, HydF, and HydG. HydE and HydG are radical S-adenosylmethionine enzymes and synthesize the nonprotein ligands of the H-cluster. HydF is a GTPase that functions as a scaffold or carrier for 2Fe subcluster production. Herein, we utilize UV-visible, circular dichroism, and electron paramagnetic resonance spectroscopic studies to establish the existence of redox active [4Fe-4S] and [2Fe-2S] clusters bound to HydF. We have used spectroelectrochemical titrations to assign iron-sulfur cluster midpoint potentials, have shown that HydF purifies with a reduced [2Fe-2S] cluster in the absence of exogenous reducing agents, and have tracked iron-sulfur cluster spectroscopic changes with quaternary structural perturbations. Our results provide an important foundation for understanding the maturation process by defining the iron-sulfur cluster content of HydF prior to its interaction with HydE and HydG. We speculate that the [2Fe-2S] cluster of HydF either acts as a placeholder for HydG-derived Fe(CO)2CN species or serves as a scaffold for 2Fe subcluster assembly. PMID:27232385

  16. Genetics Home Reference: myopathy with deficiency of iron-sulfur cluster assembly enzyme

    MedlinePlus

    ... sulfur cluster assembly enzyme myopathy with deficiency of iron-sulfur cluster assembly enzyme Enable Javascript to view ... All Close All Description Myopathy with deficiency of iron-sulfur cluster assembly enzyme is an inherited disorder ...

  17. Directed Self-Assembly Pathways of Active Colloidal Clusters.

    PubMed

    Zhang, Jie; Yan, Jing; Granick, Steve

    2016-04-18

    Despite the mounting interest in synthetic active particles, too little is known about their assembly into higher-order clusters. Here, mixing bare silica particles with Janus particles that are self-propelled in electric fields, we assemble rotating chiral clusters of various sorts, their structures consisting of active particles wrapped around central "hub" particles. These clusters self-assemble from the competition between standard energetic interactions and the need to be stable as the clusters rotate when the energy source is turned on, and fall apart when the energy input is off. This allows one to guide the formation of intended clusters, as the final structure depends notably on the sequence of steps in which the clusters form. PMID:27010594

  18. IscA, an alternate scaffold for Fe-S cluster biosynthesis.

    PubMed

    Krebs, C; Agar, J N; Smith, A D; Frazzon, J; Dean, D R; Huynh, B H; Johnson, M K

    2001-11-20

    An IscA homologue within the nif regulon of Azotobacter vinelandii, designated (Nif)IscA, was expressed in Escherichia coli and purified to homogeneity. Purified (Nif)IscA was found to be a homodimer of 11-kDa subunits that contained no metal centers or other prosthetic groups in its as-isolated form. Possible roles for (Nif)IscA in Fe-S cluster biosynthesis were assessed by investigating the ability to bind iron and to assemble Fe-S clusters in a NifS-directed process, as monitored by the combination of UV-vis absorption, Mössbauer, resonance Raman, variable-temperature magnetic circular dichroism, and EPR spectroscopies. Although (Nif)IscA was found to bind ferrous ion in a tetrahedral, predominantly cysteinyl-ligated coordination environment, the low-binding affinity argues against a specific role as a metallochaperone for the delivery of ferrous ion to other Fe-S cluster assembly proteins. Rather, a role for (Nif)IscA as an alternate scaffold protein for Fe-S cluster biosynthesis is proposed, based on the NifS-directed assembly of approximately one labile [4Fe-4S](2+) cluster per (Nif)IscA homodimer, via a transient [2Fe-2S](2+) cluster intermediate. The cluster assembly process was monitored temporally using UV-vis absorption and Mössbauer spectroscopy, and the intermediate [2Fe-2S](2+)-containing species was additionally characterized by resonance Raman spectroscopy. The Mössbauer and resonance Raman properties of the [2Fe-2S](2+) center are consistent with complete cysteinyl ligation. The presence of three conserved cysteine residues in all IscA proteins and the observed cluster stoichiometry of approximately one [2Fe-2S](2+) or one [4Fe-4S](2+) per homodimer suggest that both cluster types are subunit bridging. In addition, (Nif)IscA was shown to couple delivery of iron and sulfur by using ferrous ion to reduce sulfane sulfur. The ability of Fe-S scaffold proteins to couple the delivery of these two toxic and reactive Fe-S cluster precursors is likely to

  19. Directed Assembly of Hierarchically Ordered Clusters from Anisotropic Microparticles

    NASA Astrophysics Data System (ADS)

    Han, Koohee; Bharti, Bhuvnesh; Shields, C. Wyatt, IV; Lopez, Gabriel P.; Velev, Orlin D.

    The directed assembly of colloidal particles with specific connectivity, symmetry, and directional response requires controlled interactions and means of programmable binding force. We will show how patchy microparticles can be hierarchically assembled into ordered clusters, resulting from directional interactions between metal-coated facets. First, we introduce lipid mediated capillary bridging as a new class of binding force for directed assembly of metallo-dielectric patchy microspheres. Iron oxide surface patches on latex microspheres were selectively wetted with liquid lipids, guiding the particle assembly into well-defined 2D and 3D clusters. The temperature driven fluid-to-gel phase transition of the fatty acids acts as a thermal switch for cluster assembly and disassembly. Secondly, we used external fields to bind patchy microcubes based on their polarization configuration and interparticle interaction. We present assembled clusters of cobalt-coated patchy microcubes that can be dynamically reconfigured using external magnetic field. The residual polarization of ferromagnetic cobalt patches allows for preserving the assembled sequence even in the absence of the field and drives dynamic reconfiguration of assembled clusters. NSF Grant #DMR-1121107.

  20. Spectromicroscopy of self-assembled protein clusters

    SciTech Connect

    Schonschek, O.; Hormes, J.; Herzog, V.

    1997-04-01

    The aim of this project is to use synchrotron radiation as a tool to study biomedical questions concerned with the thyroid glands. The biological background is outlined in a recent paper. In short, Thyroglobulin (TG), the precursor protein of the hormone thyroxine, forms large (20 - 500 microns in diameter) clusters in the extracellular lumen of thyrocytes. The process of the cluster formation is still not well understood but is thought to be a main storage mechanism of TG and therefore thyroxine inside the thyroid glands. For human thyroids, the interconnections of the proteins inside the clusters are mainly disulfide bondings. Normally, sulfur bridges are catalyzed by an enzyme called Protein Disulfide Bridge Isomerase (PDI). While this enzyme is supposed to be not present in any extracellular space, the cluster formation of TG takes place in the lumen between the thyrocytes. A possible explanation is the autocatalysis of TG.

  1. Controlling the band gap energy of cluster-assembled materials.

    PubMed

    Mandal, Sukhendu; Reber, Arthur C; Qian, Meichun; Weiss, Paul S; Khanna, Shiv N; Sen, Ayusman

    2013-11-19

    Cluster-assembled materials combine the nanoscale size and composition-dependent properties of clusters, which have highly tunable magnetic and electronic properties useful for a great variety of potential technologies. To understand the emergent properties as clusters are assembled into hierarchical materials, we have synthesized 23 cluster-assembled materials composed of As7(3-)-based motifs and different countercations and measured their band gap energies. We found that the band gap energy varies from 1.09 to 2.21 eV. In addition, we have carried out first principles electronic structure studies to identify the physical mechanisms that enable control of the band gap edges of the cluster assemblies. The choice of counterion has a profound effect on the band gap energy in ionic cluster assemblies. The top of the valence band is localized on the arsenic cluster, while the conduction band edge is located on the alkali metal counterions. Changing the counterion changes the position of the conduction band edge, enabling control of the band gap energy. We can also vary the architecture of the ionic solid by incorporating cryptates as counterions, which provide charge but are separated from the clusters by bulky ligands. Higher dimensionality typically decreases the band gap energy through band broadening; however band gap energies increased upon moving from zero-dimensional (0D) to two-dimensional (2D) assemblies. This is because internal electric fields generated by the counterion preferentially stabilize the adjacent lone pair orbitals that mark the top of the valence band. Thus, the choice of the counterion can control the position of the conduction band edge of ionic cluster assemblies. In addition, the dimensionality of the solid via internal electric fields can control the valence band edge. Through covalently linking arsenic clusters into composite building blocks, we have also been able to tune the band gap energy. We used a theoretical description based on

  2. DNA templates silver clusters with magic sizes and colors for multi-cluster fluorescent assemblies

    NASA Astrophysics Data System (ADS)

    Copp, Stacy

    2015-03-01

    The natural inclusion of information in DNA, a vital part of life's rich complexity, can also be exploited to create diverse structures with multiple scales of complexity. Now emerging in novel photonic applications, DNA-stabilized silver clusters (AgN-DNA) are compelling examples of multi-scale DNA-directed assembly: individual fluorescent clusters, each templated by specific DNA base motifs, can then be arranged together in DNA-mediated multi-cluster assemblies with nanoscale precision. We discuss how DNA imbues AgN-DNA with unique features. Our optical data on pure AgN-DNA show that DNA base-cationic silver ligands impose rod-like shapes for neutral silver clusters, whose length primarily determines fluorescence color. This shape anisotropy leads to the aspherical AgN-DNA magic number cluster sizes and ``magic color'' groupings. We exploit DNA's sequence properties to extract multi-base motifs that select certain magic cluster sizes, using machine learning algorithms applied to large data sets. With these base motifs, we design DNA scaffolds to arrange multiple atomically precise AgN together in nanoscale proximity. We demonstrate that clusters are stable when held at separations below 10 nm, both in bicolor, dual cluster DNA clamp assemblies and in one-dimensional assemblies of atomically precise clusters arrayed on DNA nanotubes. Supported by NSF-CHE-1213895 and NSF-DMR-1309410. SMC acknowledges NSF-DGE-1144085, a NSF GRFP.

  3. Rapid Self-Assembly of Uranyl Polyhedra into Crown Clusters

    SciTech Connect

    Sigmon, Ginger E.; Burns, Peter C.

    2011-06-22

    Clusters built from 32 uranyl peroxide polyhedra self-assemble and crystallize within 15 min after combining uranyl nitrate, ammonium hydroxide, and hydrogen peroxide in aqueous solution under ambient conditions. These novel crown-shaped clusters are remarkable in that they form so quickly, have extraordinarily low aqueous solubility, form with at least two distinct peroxide to hydroxyl ratios, and form in very high yield. The clusters, which have outer diameters of 23 Å, topologically consist of eight pentagons and four hexagons. Their rapid formation and low solubility in aqueous systems may be useful properties at various stages in an advanced nuclear energy system.

  4. Nanophase materials assembled from atomic clusters

    SciTech Connect

    Siegel, R.W.

    1989-09-01

    The preparation of atomic clusters of metals and ceramics by means of the gas-condensation method, followed by their in situ consolidation under high-vacuum conditions, has recently led to the synthesis of a new class of ultrafine-grained materials for which their physics is intimately coupled with their application. These nanophase materials, with 2 to 20 nm grain sizes, appear to have properties that are often rather different from conventional materials, and also processing characteristics that are greatly improved. The nanophase synthesis method described here should enable the design of materials heretofore unavailable, with improved or unique properties, based upon an understanding of the physics of these new materials. 23 refs., 8 figs.

  5. Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulfur assembly system, and OxyR induces the Suf system to compensate

    PubMed Central

    Jang, Soojin; Imlay, James A.

    2011-01-01

    Environmental H2O2 creates several injuries in Escherichia coli, including the oxidative conversion of dehydratase [4Fe-4S] clusters to an inactive [3Fe-4S] form. To protect itself, H2O2-stressed E. coli activates the OxyR regulon. This regulon includes the suf operon, which encodes an alternative to the housekeeping Isc iron-sulfur-cluster assembly system. Previously studied [3Fe-4S] clusters are repaired by an Isc/Suf-independent pathway, so the rationale for Suf induction was not obvious. Using strains that cannot scavenge H2O2, we imposed chronic low-grade stress and found that suf mutants could not maintain the activity of isopropylmalate isomerase, a key iron-sulfur dehydratase. Experiments showed that its damaged cluster was degraded in vivo beyond the [3Fe-4S] state, presumably to an apoprotein form, and thus required a de novo assembly system for reactivation. Surprisingly, sub-micromolar H2O2 poisoned the Isc machinery, thereby creating a requirement for Suf both to repair the isomerase and to activate nascent Fe-S enzymes in general. The IscS and IscA components of the Isc system are H2O2-resistant, suggesting that oxidants disrupt Isc by oxidizing clusters as they are assembled on or transferred from the IscU scaffold. Consistent with these results, organisms that are routinely exposed to oxidants rely upon Suf rather than Isc for cluster assembly. PMID:21143317

  6. Stealth Amphiphiles: Self-Assembly of Polyhedral Boron Clusters.

    PubMed

    Ďorďovič, Vladimír; Tošner, Zdeněk; Uchman, Mariusz; Zhigunov, Alexander; Reza, Mehedi; Ruokolainen, Janne; Pramanik, Goutam; Cígler, Petr; Kalíková, Květa; Gradzielski, Michael; Matějíček, Pavel

    2016-07-01

    This is the first experimental evidence that both self-assembly and surface activity are common features of all water-soluble boron cluster compounds. The solution behavior of anionic polyhedral boranes (sodium decaborate, sodium dodecaborate, and sodium mercaptododecaborate), carboranes (potassium 1-carba-dodecaborate), and metallacarboranes {sodium [cobalt bis(1,2-dicarbollide)]} was extensively studied, and it is evident that all the anionic boron clusters form multimolecular aggregates in water. However, the mechanism of aggregation is dependent on size and polarity. The series of studied clusters spans from a small hydrophilic decaborate-resembling hydrotrope to a bulky hydrophobic cobalt bis(dicarbollide) behaving like a classical surfactant. Despite their pristine structure resembling Platonic solids, the nature of anionic boron cluster compounds is inherently amphiphilic-they are stealth amphiphiles. PMID:27287067

  7. On the assembly of dwarf galaxies in clusters and their efficient formation of globular clusters

    NASA Astrophysics Data System (ADS)

    Mistani, Pouria A.; Sales, Laura V.; Pillepich, Annalisa; Sanchez-Janssen, Rubén; Vogelsberger, Mark; Nelson, Dylan; Rodriguez-Gomez, Vicente; Torrey, Paul; Hernquist, Lars

    2016-01-01

    Galaxy clusters contain a large population of low-mass dwarf elliptical galaxies whose exact origin is unclear: their colours, structural properties and kinematics differ substantially from those of dwarf irregulars in the field. We use the Illustris cosmological simulation to study differences in the assembly histories of dwarf galaxies (3 × 108 < M*/M⊙ < 1010) according to their environment. We find that cluster dwarfs achieve their maximum total and stellar mass on average ˜8 and ˜4.5 Gyr ago (or redshifts z = 1.0 and 0.4, respectively), around the time of infall into the clusters. In contrast, field dwarfs not subjected to environmental stripping reach their maximum mass at z = 0. These different assembly trajectories naturally produce a colour bimodality, with blue isolated dwarfs and redder cluster dwarfs exhibiting negligible star formation today. The cessation of star formation happens over median times 3.5-5 Gyr depending on stellar mass, and shows a large scatter (˜1-8 Gyr), with the lower values associated with starburst events that occur at infall through the virial radius or pericentric passages. We argue that such starbursts together with the early assembly of cluster dwarfs can provide a natural explanation for the higher specific frequency of globular clusters (GCs) in cluster dwarfs, as found observationally. We present a simple model for the formation and stripping of GCs that supports this interpretation. The origin of dwarf ellipticals in clusters is, therefore, consistent with an environmentally driven evolution of field dwarf irregulars. However, the z = 0 field analogues of cluster dwarf progenitors have today stellar masses a factor of ˜3 larger - a difference arising from the early truncation of star formation in cluster dwarfs.

  8. Magnetism in nanoclusters and cluster-assembled thin films.

    PubMed

    Binns, C

    2001-09-01

    Increasing attention has been focused on the magnetic behavior of nanoparticles with diameters of 1-5 nm (approximately 50-5000 atoms). In this size range fundamental magnetic parameters such as the orbital and spin magnetic moments per atom deviate significantly from bulk values, and studying clusters addresses fundamental problems in mesoscopic magnetism, which is not as well understood as in either the atomic or the bulk regimes. There is also a growing realization of the enormous industrial potential of materials built by depositing preformed nanoclusters instead of atoms. If the clusters are size-selected and deposited in conjunction with an atomic vapor of a matrix material, it is possible to produce granular films in which there is independent control over the particle size and volume fraction. Using this technique, it also becomes possible to make granular mixtures of miscible materials. This unprecendented degree of control over the properties of the films holds the promise of new magnetic materials with "engineered properties." To fully realize this potential requires a greater understanding of not only the individual particles, but also how they interact in dense assemblies. There has been great progress in understanding some aspects of the magnetic behavior of nanoclusters and cluster-assembled materials. The mechanisms that generate spin and orbital moments that are enhanced by up to 36 and 200%, respectively, relative to the bulk in isolated clusters are well understood as is the dynamical behavior of the magnetic moment. Not so well understood is the observed magnetic anisotropy, which often has a different symmetry than the bulk. In dense assemblies, the nature of the interparticle coupling and the relative importance of dipolar and exchange interactions also require further research. PMID:12914058

  9. Evidence of Halo Assembly Bias in Massive Clusters.

    PubMed

    Miyatake, Hironao; More, Surhud; Takada, Masahiro; Spergel, David N; Mandelbaum, Rachel; Rykoff, Eli S; Rozo, Eduardo

    2016-01-29

    We present significant evidence of halo assembly bias for SDSS redMaPPer galaxy clusters in the redshift range [0.1, 0.33]. By dividing the 8,648 clusters into two subsamples based on the average member galaxy separation from the cluster center, we first show that the two subsamples have very similar halo mass of M_{200m}≃1.9×10^{14}  h^{-1}M_{⊙} based on the weak lensing signals at small radii R≲10  h^{-1}Mpc. However, their halo bias inferred from both the large-scale weak lensing and the projected autocorrelation functions differs by a factor of ∼1.5, which is a signature of assembly bias. The same bias hypothesis for the two subsamples is excluded at 2.5σ in the weak lensing and 4.4σ in the autocorrelation data, respectively. This result could bring a significant impact on both galaxy evolution and precision cosmology. PMID:26871319

  10. Photoelectron spectroscopy of cluster anions: In search of building blocks for cluster-assembled materials

    NASA Astrophysics Data System (ADS)

    Grubisic, Andrej

    A combination of mass spectrometry, anion photoelectron spectroscopy and theory were employed to study the electronic, geometric and reactive properties of a number of different cluster systems. A special emphasis was placed on scouting for those particular cluster compositions that show signs of enhanced stability. Those clusters could potentially be used as building blocks of cluster-assembled materials. The studied systems include aluminum hydrides, lanthanide-silicon mixed cluster, platinum-lead clusters and Al13 -. Among aluminum hydrides an entire family of previously unknown closo-alanes with a general formula AlnHn+2 (4 ≤ n ≤ 8) had been discovered. They exhibit signs of substantial stability and are shown to follow the Wade's rule for closo-alanes (Chapter 3). In the studies of lanthanide-silicon, LnSin- (3 ≤ n ≤ 13) clusters, lanthanide atoms were observed to adopt low oxidation numbers even in the presence of a strongly interacting silicon environment. The implied limited participation of lanthanide atoms' f-electrons in bonding with the silicon stands in stark contrast to the d-electrons of the transition metal atoms. The result raises prospects for magnetic, silicon-based clusters (Chapter 4). A series of reactive studies of Al13- a well-known magic cluster, and Aln- cluster anions in general were conducted to better understand their size-specific behavior. Size-selective etching of Al11- and Al12- by NH3 has been attributed to a diminished barrier for conversion of a physisorbed precursor into the chemisorbed adduct in case of these two clusters. Al13- shows few signs of reactivity. The well-documented inertness of Al13- towards O 2 has been traced back to the triplet state of oxygen. Due to the need to conserve spin along the reaction coordinate, the number of viable reaction channels that have a low barrier is greatly reduced (Chapter 5). Lastly, a building block of a recently synthesized cluster-assembled material, (Pt Pb 12)2-, was studied

  11. The Role of Radiation Pressure in Assembling Super Star Clusters

    NASA Astrophysics Data System (ADS)

    Tsz-Ho Tsang, Benny; Milosavljevic, Milos

    2016-06-01

    Super star clusters are the most extreme star-forming regions of the Universe - they occupy the most massive end of the Kennicutt-Schmidt relation, forming stars at exceptionally high rates and gas surface densities. The radiation feedback from the dense population of massive stars is expected to play a dynamic role during the assembly of the clusters, and represents a potential mechanism for launching large-scale galactic outflows. Observationally, large distances and dust obscuration have been withholding clues about the early stages of massive cluster formation; theoretically, the lack of accurate and efficient radiation transfer schemes in multi-dimensional hydrodynamic simulations has been deterring our understanding of radiative feedback. By extending the adaptive mesh refinement code FLASH with a closure-free, Monte Carlo radiation transport scheme, we perform 3D radiation hydrodynamical simulations of super star cluster formation from the collapse of turbulent molecular clouds. Our simulations probe the star formation in densities typical for starbursts, with both non-ionizing UV and dust-reprocessed IR radiation treated self-consistently. We aim to determine the role of radiation pressure in regulating star formation, and its capacity in driving intense outflows.

  12. Self-assembly of Alkali-uranyl-peroxide Clusters

    SciTech Connect

    Nyman, May; Rodriquez, Mark A.; Campana, Charles F.

    2010-08-11

    The hexavalent uranium specie, uranyl triperoxide, UO2(O2)34-, has been shown recently to behave like high oxidation-state d0 transition-metals, self-assembling into polyoxometalate-like clusters that contain up to 60 uranyl cations bridged by peroxide ligands. There has been much less focus on synthesis and structural characterization of salts of the monomeric UO2(O2)34- building block of these clusters. However, these could serve as water-soluble uranyl precursors for both clusters and materials, and also be used as simple models to study aqueous behavior by experiment and modeling. The countercation is of utmost importance to the assembly of these clusters, and Li+ has proven useful for the crystallization of many of the known cluster geometries to date. We present in this paper synthesis and structural characterization of two monomeric lithium uranyl-peroxide salts, Li4[UO2(O2)3]·10H2O (1) and [UO2(O2)3]12[(UO2(OH)4)Li16(H2O)28]3·Li6[H2O]26 (2). They were obtained from aqueous-alcohol solutions rather than the analogous aqueous solutions from which lithium uranyl-peroxide clusters are crystallized. Rapid introduction of the alcohol gives the structure of (1) whereas slow diffusion of alcohol results in crystallization of (2). (2) is an unusual structure featuring uranyl-centered alkali clusters that are linked into ring and spherical arrangements via [UO2(O2)3] anions. Furthermore, partial substitution of Rb or Cs into the synthesis results in formation of (2) with substitution of these larger alkalis into the uranyl-centered clusters. We surmise that the slow crystallization allows for direct bonding of alkali metals to the

  13. Beyond Clusters: Supramolecular Networks Self-Assembled from Nanosized Silver Clusters and Inorganic Anions.

    PubMed

    Wang, Zhi; Li, Xiao-Yu; Liu, Li-Wei; Yu, Si-Qi; Feng, Zhen-Yu; Tung, Chen-Ho; Sun, Di

    2016-05-10

    Assembly of small clusters into rigid bodies with precise shape and symmetry has been witnessed by the significant advances in cluster-based metal-organic frameworks (MOFs), however, nanosized silver cluster based MOFs remain largely unexplored. Herein, two anion-templated silver clusters, CO3 @Ag20 and SO4 @Ag22 , were ingeniously incorporated into a 2D sql lattice (1, [CO3 @Ag20 (iPrS)10 (NO3 )8 (DMF)2 ]n ) and an unprecedented 3D two-fold interpenetrated dia network (2, [SO4 @Ag22 (iPrS)12 (NO3 )6 ⋅2 NO3 ]n ), respectively, under mild solvothermal conditions. Their atomically precise structures were confirmed by single-crystal X-ray diffraction analysis and further consolidated by IR spectroscopy, thermogravimetric analysis (TGA), and elemental analysis. Each drum-like CO3 @Ag20 cluster is extended by twelve NO3 (-) ions to form the 2D sql lattice of 1, whereas each ball-shaped SO4 @Ag22 cluster with a twisted truncated tetrahedral geometry is pillared by four [Ag6 (NO3 )3 ] triangular prisms to form the 3D interpenetrated dia network of 2. Notably, 2 is the first interpenetrated 3D MOF constructed from silver clusters. These results demonstrate the dual role of the anions, which not only internally act as anion templates to induce the formation of silver thiolate clusters but also externally extend the cluster units into the rigid networks. The photoluminescent and electrochemical properties of 2 are discussed in detail. PMID:27006096

  14. Globular clusters as tracers of the halo assembly of nearby central cluster galaxies

    NASA Astrophysics Data System (ADS)

    Hilker, Michael; Richtler, Tom

    2016-08-01

    The properties of globular cluster systems (GCSs) in the core of the nearby galaxy clusters Fornax and Hydra I are presented. In the Fornax cluster we have gathered the largest radial velocity sample of a GCS system so far, which enables us to identify photometric and kinematic sub-populations around the central galaxy NGC 1399. Moreover, ages, metallicities and [α/Fe] abundances of a sub-sample of 60 bright globular clusters (GCs) with high S/N spectroscopy show a multi-modal distribution in the correlation space of these three parameters, confirming heterogeneous stellar populations in the halo of NGC 1399. In the Hydra I cluster very blue GCs were identified. They are not uniformly distributed around the central galaxies. 3-color photometry including the U-band reveals that some of them are of intermediate age. Their location coincides with a group of dwarf galaxies under disruption. This is evidence of a structurally young stellar halo ``still in formation'', which is also supported by kinematic measurements of the halo light that point to a kinematically disturbed system. The most massive GCs divide into generally more extended ultra-compact dwarf galaxies (UCDs) and genuine compact GCs. In both clusters, the spatial distribution and kinematics of UCDs are different from those of genuine GCs. Assuming that some UCDs represent nuclei of stripped galaxies, the properties of those UCDs can be used to trace the assembly of nucleated dwarf galaxies into the halos of central cluster galaxies. We show via semi-analytical approaches within a cosmological simulation that only the most massive UCDs in Fornax-like clusters can be explained by stripped nuclei, whereas the majority of lower mass UCDs belong to the star cluster family.

  15. Genes for iron-sulphur cluster assembly are targets of abiotic stress in rice, Oryza sativa.

    PubMed

    Liang, Xuejiao; Qin, Lu; Liu, Peiwei; Wang, Meihuan; Ye, Hong

    2014-03-01

    Iron-sulphur (Fe-S) cluster assembly occurs in chloroplasts, mitochondria and cytosol, involving dozens of genes in higher plants. In this study, we have identified 41 putative Fe-S cluster assembly genes in rice (Oryza sativa) genome, and the expression of all genes was verified. To investigate the role of Fe-S cluster assembly as a metabolic pathway, we applied abiotic stresses to rice seedlings and analysed Fe-S cluster assembly gene expression by qRT-PCR. Our data showed that genes for Fe-S cluster assembly in chloroplasts of leaves are particularly sensitive to heavy metal treatments, and that Fe-S cluster assembly genes in roots were up-regulated in response to iron toxicity, oxidative stress and some heavy metal assault. The effect of each stress treatment on the Fe-S cluster assembly machinery demonstrated an unexpected tissue or organelle specificity, suggesting that the physiological relevance of the Fe-S cluster assembly is more complex than thought. Furthermore, our results may reveal potential candidate genes for molecular breeding of rice. PMID:24028141

  16. New redox states observed in [FeFe] hydrogenases reveal redox coupling within the H-cluster.

    PubMed

    Adamska-Venkatesh, Agnieszka; Krawietz, Danuta; Siebel, Judith; Weber, Katharina; Happe, Thomas; Reijerse, Edward; Lubitz, Wolfgang

    2014-08-13

    Active [FeFe] hydrogenases can be obtained by expressing the unmaturated enzyme in Escherichia coli followed by incubation with a synthetic precursor of the binuclear [2Fe] subcluster, namely: [NEt4]2[Fe2(adt)(CO)4(CN)2] (adt = [S-CH2-NH-CH2-S](2-)). The binuclear subsite Fe2(adt)(CO)3(CN)2 is attached through a bridging cysteine side chain to a [4Fe-4S] subcluster already present in the unmaturated enzyme thus yielding the intact native "H-cluster". We present FTIR electrochemical studies of the [FeFe] hydrogenase from Chlamydomonas reinhardtii, CrHydA1, maturated with the precursor of the native cofactor [Fe2(adt)(CO)4(CN)2](2-) as well as a non-natural variant [Fe2(pdt)(CO)4(CN)2](2-) in which the bridging amine functionality is replaced by CH2. The obtained active enzyme CrHydA1(adt) shows the same redox states in the respective potential range as observed for the native system (E(ox/red) = -400 mV, E(red/sred) = -470 mV). For the Hox → Hred transition the reducing equivalent is stored on the binuclear part, ([4Fe-4S](2+)Fe(II)Fe(I) → [4Fe-4S](2+)Fe(I)Fe(I)), while the Hred → Hsred transition is characterized by a reduction of the [4Fe-4S] part of the H-cluster ([4Fe-4S](2+)Fe(I)Fe(I) → [4Fe-4S](+)Fe(I)Fe(I)). A similar transition is reported here for the CO inhibited state of the H-cluster: ([4Fe-4S](2+)Fe(I)Fe(II)CO → [4Fe-4S](+)Fe(I)Fe(II)CO). An FTIR electrochemical study of the inactive variant with the pdt ligand, CrHydA1(pdt), identified two redox states H(pdt)-ox and H(pdt)-"red". Both EPR and FTIR spectra of H(pdt)-ox are virtually identical to those of the H(adt)-ox and the native Hox state. The H(pdt)-"red" state is also characterized by a reduced [4Fe-4S] subcluster. In contrast to CrHydA1(adt), the H(pdt)-ox state of CrHydA1(pdt) is stable up to rather high potentials (+200 mV). This study demonstrates the distinct redox coupling between the two parts of the H-cluster and confirms that the [4Fe-4S]H subsite is also redox active and as

  17. NMR study of cluster-assembled nanophase copper

    SciTech Connect

    Suits, B.H.; Meng, M. . Dept. of Physics); Siegel, R.W.; Liao, Y.X. )

    1992-12-01

    [sup 63]Cu and [sup 65]Cu NMR spectra from cluster-assembled nanophase copper with an average grain size between 5 and 10mn show a broadened peak, at the normal Knight-shifted frequency for copper meta which arises from only the central 1/2 to -1/2 transition. A very broad background is observed on either side of that peak. Some samples exhibit a second broad peak at a position normally associated with non-metallic copper. Pulsed NMR measurements of the central peak show that virtually all the copper signals are significantly broadened and have a spin-spin relaxation time longer than larger grained copper samples. Line shape measurements, using spin echoes, as a function of delay between rf excitation and measurement show there are a number of copper sites with longer relaxation times which have a significantly larger broadening. Those sites are tentatively identified as being at or near a grain boundary or free surface. A small orientation effect is observed indicating an anisotropy within the samples. An isochronal anneal of one sample showed significant, but not complete, line narrowing after an anneal at 450C consistent with other nanophase metals which show grain growth above 40--50% of the melting temperature.

  18. NMR study of cluster-assembled nanophase copper

    SciTech Connect

    Suits, B.H.; Meng, M.; Siegel, R.W.; Liao, Y.X.

    1992-12-01

    {sup 63}Cu and {sup 65}Cu NMR spectra from cluster-assembled nanophase copper with an average grain size between 5 and 10mn show a broadened peak, at the normal Knight-shifted frequency for copper meta which arises from only the central 1/2 to -1/2 transition. A very broad background is observed on either side of that peak. Some samples exhibit a second broad peak at a position normally associated with non-metallic copper. Pulsed NMR measurements of the central peak show that virtually all the copper signals are significantly broadened and have a spin-spin relaxation time longer than larger grained copper samples. Line shape measurements, using spin echoes, as a function of delay between rf excitation and measurement show there are a number of copper sites with longer relaxation times which have a significantly larger broadening. Those sites are tentatively identified as being at or near a grain boundary or free surface. A small orientation effect is observed indicating an anisotropy within the samples. An isochronal anneal of one sample showed significant, but not complete, line narrowing after an anneal at 450C consistent with other nanophase metals which show grain growth above 40--50% of the melting temperature.

  19. Self-Assembly of Hexanuclear Clusters of 4f and 5f Elements with Cation Specificity

    SciTech Connect

    Diwu, J.; Good, Justin J.; DiStefano, Victoria H.; Albrecht-Schmitt, Thomas E.

    2011-02-10

    Six hexanuclear clusters of 4f and 5f elements were synthesized by room-temperature slow concentration experiments. Cerium(IV), thorium(IV), and plutonium(IV) each form two different hexanuclear clusters, among which the cerium and plutonium clusters are isotypic, whereas the thorium clusters show more diversity. The change in ionic radii of approximately 0.08 Å between these different metal ions tunes the cavity size so that NH{sub 4}{sup +} (1.48 Å) has the right dimensions to assemble the cerium and plutonium clusters, whereas Cs{sup +} (1.69 Å) is necessary to assemble the thorium clusters. If these cations are not used in the reactions, only amorphous material is obtained.

  20. Time-resolved assembly of cluster-in-cluster {Ag₁₂}-in-{W₇₆} polyoxometalates under supramolecular control.

    PubMed

    Zhan, Caihong; Cameron, Jamie M; Gao, Jing; Purcell, Jamie W; Long, De-Liang; Cronin, Leroy

    2014-09-22

    We report the time-resolved supramolecular assembly of a series of nanoscale polyoxometalate clusters (from the same one-pot reaction) of the form: [H(10+m)Ag18Cl(Te3W38O134)2]n, where n=1 and m=0 for compound 1 (after 4 days), n=2 and m=3 for compound 2 (after 10 days), and n=∞ and m=5 for compound 3 (after 14 days). The reaction is based upon the self-organization of two {Te3W38} units around a single chloride template and the formation of a {Ag12} cluster, giving a {Ag12}-in-{W76} cluster-in-cluster in compound 1, which further aggregates to cluster compounds 2 and 3 by supramolecular Ag-POM interactions. The proposed mechanism for the formation of the clusters has been studied by ESI-MS. Further, control experiments demonstrate the crucial role that TeO3(2-), Cl(-), and Ag(+) play in the self-assembly of compounds 1-3. PMID:25087861

  1. Synthesis, structure and band gap energy of covalently linked cluster-assembled materials.

    PubMed

    Mandal, Sukhendu; Reber, Arthur C; Qian, Meichun; Liu, Ran; Saavedra, Hector M; Sen, Saikat; Weiss, Paul S; Khanna, Shiv N; Sen, Ayusman

    2012-10-28

    We have synthesized a series of cluster assembled materials in which the building blocks are As(7)(3-) clusters linked by group 12 metals, Zn, Cd and Hg, to investigate the effect of covalent linkers on the band gap energy. The synthesized assemblies include zero dimensional assemblies of [Zn(As(7))(2)](4-), [Cd(As(7))(2)](4-), [Hg(2)(As(7))(2)](4-), and [HgAsAs(14)](3-) in which the clusters are separated by cryptated counterions, and assemblies in which [Zn(As(7))(2)](4-), [Cd(As(7))(2)](4-) are linked by free alkali atoms into unusual three-dimensional structures. These covalently linked cluster-assembled materials have been characterized by elemental analysis, EDX and single-crystal X-ray diffraction. The crystal structure analysis revealed that in the case of Zn and Cd, the two As(7)(3-) units are linked by the metal ion, while in the case of Hg, two As(7)(3-) units are linked by either Hg-Hg or Hg-As dimers. Optical measurements indicate that the band gap energy ranges from 1.62 eV to 2.21 eV. A theoretical description based on cluster orbital theory is used to provide a microscopic understanding of the electronic character of the composite building blocks and the observed variations in the band gap energy. PMID:22940817

  2. ASSEMBLY OF THE RED SEQUENCE IN INFRARED-SELECTED GALAXY CLUSTERS FROM THE IRAC SHALLOW CLUSTER SURVEY

    SciTech Connect

    Snyder, Gregory F.; Brodwin, Mark; Mancone, Conor M.; Gonzalez, Anthony H.; Zeimann, Gregory R.; Stanford, S. A.; Stern, Daniel; Eisenhardt, Peter R. M.; Brown, Michael J. I.; Dey, Arjun; Jannuzi, Buell; Perlmutter, Saul

    2012-09-10

    We present results for the assembly and star formation histories (SFHs) of massive ({approx}L*) red sequence galaxies (RSGs) in 11 spectroscopically confirmed, infrared-selected galaxy clusters at 1.0 < z < 1.5, the precursors to present-day massive clusters with M {approx} 10{sup 15} M{sub Sun }. Using rest-frame optical photometry, we investigate evolution in the color and scatter of the RSG population, comparing with models of possible SFHs. In contrast to studies of central cluster galaxies at lower redshift (z < 1), these data are clearly inconsistent with the continued evolution of stars formed and assembled primarily at a single, much earlier time. Specifically, we find that the colors of massive cluster galaxies at z Almost-Equal-To 1.5 imply that the bulk of star formation occurred at z {approx} 3, whereas by z Almost-Equal-To 1 their colors imply formation at z {approx} 2; therefore these galaxies exhibit approximately the same luminosity-weighted stellar age at 1 < z < 1.5. This likely reflects star formation that occurs over an extended period, the effects of significant progenitor bias, or both. Our results generally indicate that massive cluster galaxy populations began forming a significant mass of stars at z {approx}> 4, contained some red spheroids by z Almost-Equal-To 1.5, and were actively assembling much of their final mass during 1 < z < 2 in the form of younger stars. Qualitatively, the slopes of the cluster color-magnitude relations are consistent with no significant evolution relative to local clusters.

  3. Dynamic Expression of DNA Complexation with Self-assembled Biomolecular Clusters.

    PubMed

    Bartolami, Eline; Bessin, Yannick; Gervais, Virginie; Dumy, Pascal; Ulrich, Sébastien

    2015-08-24

    We report herein the implementation of a dynamic covalent chemistry approach to the generation of multivalent clusters for DNA recognition. We show that biomolecular clusters can be expressed in situ by a programmed self-assembly process using chemoselective ligations. The cationic clusters are shown, by fluorescence displacement assay, gel electrophoresis and isothermal titration calorimetry, to effectively complex DNA through multivalent interactions. The reversibility of the ligation was exploited to demonstrate that template effects occur, whereby DNA imposes component selection in order to favor the most active DNA-binding clusters. Furthermore, we show that a chemical effector can be used to trigger DNA release through component exchange reactions. PMID:26177835

  4. Chair like NiAu6: Clusters assemblies and CO oxidation study by ab initio methods

    NASA Astrophysics Data System (ADS)

    Nigam, Sandeep; Sahoo, Suman Kalyan; Sarkar, Pranab; Majumder, Chiranjib

    2013-10-01

    Based on the first-principles approach, this Letter reports that the ground state geometry of the Ni@Au6 cluster forms chair-like conformation, which is distinctly different than the Pd@Au6 and Pt@Au6 clusters, where hexagonal planar structure is favored over non-planar isomers. The higher stability of the chair-like conformation has been verified through various complementary basis sets and methodologies. Further investigations were carried out to show the stability of a cluster assembled material (CAM) based on these small clusters and the CO oxidation reaction was carried out to establish their uses as an industrial catalyst.

  5. Identification of FeS clusters in the glycyl-radical enzyme benzylsuccinate synthase via EPR and Mössbauer spectroscopy.

    PubMed

    Hilberg, Markus; Pierik, Antonio J; Bill, Eckhard; Friedrich, Thorsten; Lippert, Marie-Luise; Heider, Johann

    2012-01-01

    The anaerobic degradation pathway of toluene is initiated by the addition of the methyl group of toluene to the double bond of fumarate. This reaction is catalyzed by a novel glycyl-radical enzyme, (R)-benzylsuccinate synthase (BSS). The enzyme consists of three subunits, α, β, and γ, and differs from most other glycyl-radical enzymes in having additional cofactors. We have purified a Strep-tagged nonactivated BSS from recombinant Escherichia coli and identified the additional cofactors as FeS clusters by UV/vis, EPR, and Mössbauer spectroscopy. Analysis of the metal content as well as the EPR and Mössbauer spectra indicated that BSS contains magnetically coupled low-potential [4Fe-4S] clusters. Several enzyme preparations showed differing amounts of [3Fe-4S] clusters that could be reconstituted to [4Fe-4S] clusters, indicating that they arise from partial decay of the initial [4Fe-4S] clusters. The most likely location of these FeS clusters in the enzyme are the small β and γ subunits, which are unique for the BSS subfamily of glycyl-radical enzymes and contain conserved cysteines as potential ligands. PMID:21837540

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

    PubMed

    Fenwick, Michael K; Ealick, Steven E

    2016-08-01

    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. PMID:27404889

  7. Designed Assembly of Heterometallic Cluster Organic Frameworks Based on Anderson-Type Polyoxometalate Clusters.

    PubMed

    Li, Xin-Xiong; Wang, Yang-Xin; Wang, Rui-Hu; Cui, Cai-Yan; Tian, Chong-Bin; Yang, Guo-Yu

    2016-05-23

    A new approach to prepare heterometallic cluster organic frameworks has been developed. The method was employed to link Anderson-type polyoxometalate (POM) clusters and transition-metal clusters by using a designed rigid tris(alkoxo) ligand containing a pyridyl group to form a three-fold interpenetrated anionic diamondoid structure and a 2D anionic layer, respectively. This technique facilitates the integration of the unique inherent properties of Anderson-type POM clusters and cuprous iodide clusters into one cluster organic framework. PMID:27061042

  8. Self-Assembly of One-Dimensional Nanocrystal Superlattice Chains Mediated by Molecular Clusters.

    PubMed

    Zhang, Xianfeng; Lv, Longfei; Ji, Li; Guo, Guannan; Liu, Limin; Han, Dandan; Wang, Biwei; Tu, Yaqi; Hu, Jianhua; Yang, Dong; Dong, Angang

    2016-03-16

    Self-assembly of nanocrystal (NC) building blocks into mesoscopic superstructures with well-defined symmetry and geometry is essential for creating new materials with rationally designed properties. Despite the tremendous progress in colloidal assembly, it remains a fundamental challenge to assemble isotropic spherical NCs into one-dimensional (1D) ordered superstructures. Here, we report a new and general methodology that utilizes molecular clusters to induce the anisotropic assembly of NCs in solution, yielding polymer-like, single-NC-wide linear chains comprising as many as ∼1000 close-packed NCs. This cluster-assisted assembly process is applicable to various metallic, semiconductor, and magnetic NCs of different sizes and shapes. Mechanistic investigation reveals that the solvent-induced association of clusters plays a key role in driving the anisotropic assembly of NCs. Our work opens a solution-based route for linearly assembling NCs and represents an important step toward the bottom-up construction of 1D ordered NC superstructures. PMID:26936281

  9. The formation of NGC 3603 young starburst cluster: `prompt' hierarchical assembly or monolithic starburst?

    NASA Astrophysics Data System (ADS)

    Banerjee, Sambaran; Kroupa, Pavel

    2015-02-01

    The formation of very young massive clusters or `starburst' clusters is currently one of the most widely debated topic in astronomy. The classical notion dictates that a star cluster is formed in situ in a dense molecular gas clump. The stellar radiative and mechanical feedback to the residual gas energizes the latter until it escapes the system. The newly born gas-free young cluster eventually readjusts with the corresponding mass-loss. Based on the observed substructured morphologies of many young stellar associations, it is alternatively suggested that even the smooth-profiled massive clusters are also assembled from migrating less massive subclusters. A very young (age ≈ 1 Myr), massive (>104 M⊙) star cluster like the Galactic NGC 3603 young cluster (HD 97950) is an appropriate testbed for distinguishing between the above `monolithic' and `hierarchical' formation scenarios. A recent study by Banerjee & Kroupa demonstrates that the monolithic scenario remarkably reproduces the HD 97950 cluster. In particular, its shape, internal motion and the mass distribution of stars are found to follow naturally and consistently from a single model calculation undergoing ≈70 per cent by mass gas dispersal. In this work, we explore the possibility of the formation of the above cluster via hierarchical assembly of subclusters. These subclusters are initially distributed over a wide range of spatial volumes and have various modes of subclustering in both absence and presence of a background gas potential. Unlike the above monolithic initial system that reproduces HD 97950 very well, the same is found to be prohibitive with hierarchical assembly alone (with/without a gas potential). Only those systems which assemble promptly into a single cluster (in ≲1 Myr) from a close separation (all within ≲2 pc) could match the observed density profile of HD 97950 after a similar gas removal. These results therefore suggest that the NGC 3603 young cluster has formed essentially

  10. Keplerate cluster (Mo-132) mediated electrostatic assembly of nanoparticles.

    PubMed

    Gooch, Jonathan; Jalan, Abhishek A; Jones, Stephanie; Hine, Corey R; Alam, Rabeka; Garai, Somenath; Maye, Mathew M; Müller, Achim; Zubieta, Jon

    2014-10-15

    The electrostatic assembly between a series of differently charged Mo-132-type Keplerates present in the compounds (NH4)42[{(Mo(VI))Mo(VI)5O21(H2O)6}12 {Mo(V)2O4(CH3COO)}30].ca. {300 H2O+10 CH3COONH4} (Mo-132a), (NH4)72-n[{(H2O)81-n+(NH4)n} {(Mo(VI))Mo(VI)5O21(H2O)6}12 {Mo(V)2O4(SO4)}30].ca. 200 H2O (Mo-132b), and Na10(NH4)62[{(Mo(VI))Mo(VI)5O21(H2O)6}12 {Mo(V)2O4(HPO4)}30]. ca. {300H2O+2Na(+)+2NH4(+)+4H2PO4(-)} (Mo-132c) with cationic gold nanoparticles (AuNPs) was investigated for the first time. The rapid electrostatic assembly from nanoscopic entities to micron scale aggregates was observed upon precipitation, which closely matched the point of aggregate electroneutrality. Successful assembly was demonstrated using UV-vis, DLS, TEM, and zeta-potential analysis. Results indicate that the point at which precipitation occurs is related to charge balance or electroneutrality, and that counterions at both the Mo-132 and AuNP play a significant role in assembly. PMID:25086388

  11. Influence of cluster-assembly parameters on the field emission properties of nanostructured carbon films

    NASA Astrophysics Data System (ADS)

    Ducati, C.; Barborini, E.; Piseri, P.; Milani, P.; Robertson, J.

    2002-11-01

    Supersonic cluster beam deposition has been used to produce films with different nanostructures by controlling the deposition parameters such as the film thickness, substrate temperature and cluster mass distribution. The field emission properties of cluster-assembled carbon films have been characterized and correlated to the evolution of the film nanostructure. Threshold fields ranging between 4 and 10 V/mum and saturation current densities as high as 0.7 mA have been measured for samples heated during deposition. A series of voltage ramps, i.e., a conditioning process, was found to initiate more stable and reproducible emission. It was found that the presence of graphitic particles (onions, nanotube embryos) in the films substantially enhances the field emission performance. Films patterned on a micrometer scale have been conditioned spot by spot by a ball-tip anode, showing that a relatively high emission site density can be achieved from the cluster-assembled material.

  12. Detection of the Splashback Radius and Halo Assembly Bias of Massive Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    More, Surhud; Miyatake, Hironao; Takada, Masahiro; Diemer, Benedikt; Kravtsov, Andrey V.; Dalal, Neal K.; More, Anupreeta; Murata, Ryoma; Mandelbaum, Rachel; Rozo, Eduardo; Rykoff, Eli S.; Oguri, Masamune; Spergel, David N.

    2016-07-01

    We show that the projected number density profiles of Sloan Digital Sky Survey photometric galaxies around galaxy clusters display strong evidence for the splashback radius, a sharp halo edge corresponding to the location of the first orbital apocenter of satellite galaxies after their infall. We split the clusters into two subsamples with different mean projected radial distances of their members, < {R}{{mem}}> , at fixed richness and redshift. The sample with smaller < {R}{{mem}}> has a smaller ratio of the splashback radius to the traditional halo boundary {R}{{200m}} than the subsample with larger < {R}{{mem}}> , indicative of different mass accretion rates for these subsamples. The same subsamples were recently used by Miyatake et al. to show that their large-scale clustering differs despite their similar weak lensing masses, demonstrating strong evidence for halo assembly bias. We expand on this result by presenting a 6.6σ difference in the clustering amplitudes of these samples using cluster–photometric galaxy cross-correlations. This measurement is a clear indication that halo clustering depends on parameters other than halo mass. If < {R}{{mem}}> is related to the mass assembly history of halos, the measurement is a manifestation of the halo assembly bias. However, our measured splashback radii are smaller, while the strength of the assembly bias signal is stronger, than the predictions of collisionless Λ cold dark matter simulations. We show that dynamical friction, cluster mis-centering, or projection effects are not likely to be the sole source of these discrepancies. However, further investigations regarding unknown catastrophic weak lensing or cluster identification systematics are warranted.

  13. Crystal structure of an Fe-S cluster-containing fumarate hydratase enzyme from Leishmania major reveals a unique protein fold.

    PubMed

    Feliciano, Patricia R; Drennan, Catherine L; Nonato, M Cristina

    2016-08-30

    Fumarate hydratases (FHs) are essential metabolic enzymes grouped into two classes. Here, we present the crystal structure of a class I FH, the cytosolic FH from Leishmania major, which reveals a previously undiscovered protein fold that coordinates a catalytically essential [4Fe-4S] cluster. Our 2.05 Å resolution data further reveal a dimeric architecture for this FH that resembles a heart, with each lobe comprised of two domains that are arranged around the active site. Besides the active site, where the substrate S-malate is bound bidentate to the unique iron of the [4Fe-4S] cluster, other binding pockets are found near the dimeric enzyme interface, some of which are occupied by malonate, shown here to be a weak inhibitor of this enzyme. Taken together, these data provide a framework both for investigations of the class I FH catalytic mechanism and for drug design aimed at fighting neglected tropical diseases. PMID:27528683

  14. Assembly of open clusters of colloidal dumbbells via droplet evaporation

    NASA Astrophysics Data System (ADS)

    Pham Van, Hai; Fortini, Andrea; Schmidt, Matthias

    2016-05-01

    We investigate the behavior of a mixture of asymmetric colloidal dumbbells and emulsion droplets by means of kinetic Monte Carlo simulations. The evaporation of the droplets and the competition between droplet-colloid attraction and colloid-colloid interactions lead to the formation of clusters built up of colloid aggregates with both closed and open structures. We find that stable packings and hence complex colloidal structures can be obtained by changing the relative size of the colloidal spheres and/or their interfacial tension with the droplets.

  15. The Effects of Halo Assembly Bias on Self-Calibration in Galaxy Cluster Surveys

    SciTech Connect

    Wu, Hao-Yi; Rozo, Eduardo; Wechsler, Risa H.

    2008-08-07

    Self-calibration techniques for analyzing galaxy cluster counts utilize the abundance and the clustering amplitude of dark matter halos. These properties simultaneously constrain cosmological parameters and the cluster observable-mass relation. It was recently discovered that the clustering amplitude of halos depends not only on the halo mass, but also on various secondary variables, such as the halo formation time and the concentration; these dependences are collectively termed 'assembly bias'. Applying modified Fisher matrix formalism, we explore whether these secondary variables have a significant impact on the study of dark energy properties using the self-calibration technique in current (SDSS) and the near future (DES, SPT, and LSST) cluster surveys. The impact of the secondary dependence is determined by (1) the scatter in the observable-mass relation and (2) the correlation between observable and secondary variables. We find that for optical surveys, the secondary dependence does not significantly influence an SDSS-like survey; however, it may affect a DES-like survey (given the high scatter currently expected from optical clusters) and an LSST-like survey (even for low scatter values and low correlations). For an SZ survey such as SPT, the impact of secondary dependence is insignificant if the scatter is 20% or lower but can be enhanced by the potential high scatter values introduced by a highly-correlated background. Accurate modeling of the assembly bias is necessary for cluster self-calibration in the era of precision cosmology.

  16. Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

    SciTech Connect

    Cook, J.; Kondapalli, K; Rawat, S; Childs, W; Murugesan, Y; Dancis, A; Stemmler, T

    2010-01-01

    Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

  17. Ionic self-assembly affords mesoporous ionic networks by crosslinking linear polyviologens with polyoxometalate clusters.

    PubMed

    Chen, Guojian; Hou, Wei; Li, Jing; Wang, Xiaochen; Zhou, Yu; Wang, Jun

    2016-03-21

    Ionic-bonded mesoporous ionic networks were prepared by the ionic self-assembly of polyoxometalate (POM) clusters with linear cationic polyviologens in water. The POM-enriched PMIN-2(V) possesses a high surface area up to 120 m(2) g(-1), exhibiting superior non-noble metal heterogeneous catalytic performance in the ambient aerobic selective oxidation of 5-hydroxymethylfurfural. PMID:26898883

  18. Multistep assembly of DNA condensation clusters by SMC

    PubMed Central

    Kim, HyeongJun; Loparo, Joseph J.

    2016-01-01

    SMC (structural maintenance of chromosomes) family members play essential roles in chromosome condensation, sister chromatid cohesion and DNA repair. It remains unclear how SMCs structure chromosomes and how their mechanochemical cycle regulates their interactions with DNA. Here we used single-molecule fluorescence microscopy to visualize how Bacillus subtilis SMC (BsSMC) interacts with flow-stretched DNAs. We report that BsSMC can slide on DNA, switching between static binding and diffusion. At higher concentrations, BsSMCs form clusters that condense DNA in a weakly ATP-dependent manner. ATP increases the apparent cooperativity of DNA condensation, demonstrating that BsSMC can interact cooperatively through their ATPase head domains. Consistent with these results, ATPase mutants compact DNA more slowly than wild-type BsSMC in the presence of ATP. Our results suggest that transiently static BsSMC molecules can nucleate the formation of clusters that act to locally condense the chromosome while forming long-range DNA bridges. PMID:26725510

  19. Multistep assembly of DNA condensation clusters by SMC.

    PubMed

    Kim, HyeongJun; Loparo, Joseph J

    2016-01-01

    SMC (structural maintenance of chromosomes) family members play essential roles in chromosome condensation, sister chromatid cohesion and DNA repair. It remains unclear how SMCs structure chromosomes and how their mechanochemical cycle regulates their interactions with DNA. Here we used single-molecule fluorescence microscopy to visualize how Bacillus subtilis SMC (BsSMC) interacts with flow-stretched DNAs. We report that BsSMC can slide on DNA, switching between static binding and diffusion. At higher concentrations, BsSMCs form clusters that condense DNA in a weakly ATP-dependent manner. ATP increases the apparent cooperativity of DNA condensation, demonstrating that BsSMC can interact cooperatively through their ATPase head domains. Consistent with these results, ATPase mutants compact DNA more slowly than wild-type BsSMC in the presence of ATP. Our results suggest that transiently static BsSMC molecules can nucleate the formation of clusters that act to locally condense the chromosome while forming long-range DNA bridges. PMID:26725510

  20. Probing transition pathways of self-assembled colloidal clusters

    NASA Astrophysics Data System (ADS)

    Perry, Rebecca W.; Holmes-Cerfon, Miranda; Brenner, Michael P.; Manoharan, Vinothan N.

    2013-03-01

    Clusters of colloidal particles bound by weak interactions explore rich energy landscapes characterized by a few minima and many higher-energy, non-rigid configurations. To investigate how such systems transit through their energy landscapes, we designed a two-dimensional system that lends itself to simple observations with brightfield video microscopy. In our aqueous system, a short-range depletion interaction strongly confines the diffusion of the spherical polystyrene colloids to a shallow volume close to a glass cover slip. The same depletion interaction provides reversible bonds between the spheres. Analyzing time series of clusters of 3, 4, and 6 spheres allows us to compare the free energy of rigid configurations to that of the transition states and to measure the kinetics of the transitions. Combining experimental measurements of the kinetics with a recent theory using a geometrical approach for calculating energy landscapes leads to a new understanding of how hydrodynamics effect transitions rates between energy minima. We acknowledge support from the NSF Graduate Research Fellowship Program

  1. Stepwise Assembly and Characterization of DNA Linked Two-Color Quantum Dot Clusters.

    PubMed

    Coopersmith, Kaitlin; Han, Hyunjoo; Maye, Mathew M

    2015-07-14

    The DNA-mediated self-assembly of multicolor quantum dot (QD) clusters via a stepwise approach is described. The CdSe/ZnS QDs were synthesized and functionalized with an amphiphilic copolymer, followed by ssDNA conjugation. At each functionalization step, the QDs were purified via gradient ultracentrifugation, which was found to remove excess polymer and QD aggregates, allowing for improved conjugation yields and assembly reactivity. The QDs were then assembled and disassembled in a stepwise manner at a ssDNA functionalized magnetic colloid, which provided a convenient way to remove unreacted QDs and ssDNA impurities. After assembly/disassembly, the clusters' optical characteristics were studied by fluorescence spectroscopy and the assembly morphology and stoichiometry was imaged via electron microscopy. The results indicate that a significant amount of QD-to-QD energy transfer occurred in the clusters, which was studied as a function of increasing acceptor-to-donor ratios, resulting in increased QD acceptor emission intensities compared to controls. PMID:26086169

  2. Shearing Janus Nanoparticles Confined in Two-Dimensional Space: Reshaped Cluster Configurations and Defined Assembling Kinetics.

    PubMed

    Huang, Zihan; Chen, Pengyu; Yang, Ye; Yan, Li-Tang

    2016-06-01

    The self-assembly of anisotropic nanoparticles (ANPs) possesses a wide array of potential applications in various fields, ranging from nanotechnology to material science. Despite intense research of the thermodynamic self-assembly of ANPs, elucidating their nonequilibrium behaviors under confinement still remains an urgent issue. Here, by performing simulation and theoretical justification, we present for the first time a study of the shear-induced behaviors of Janus spheres (the most elementary ANPs) confined in two-dimensional space. Our results demonstrate that the collective effects of shear and bonding structures can give rise to reshaped cluster configurations, featured by the chiral transition of clusters. Scaling analysis and numerical modeling are performed to quantitatively capture the assembling kinetics of dispersed Janus spheres, thereby suggesting an exotic way to bridge the gap between anisotropic and isotropic particles. The findings highlight confinement and shearing engineering as a versatile strategy to tailor the superstructures formed by ANPs toward unique properties. PMID:27164289

  3. Synthesis of LECBD grown cluster assembled SeO 2 thin films

    NASA Astrophysics Data System (ADS)

    Rath, S.; Das, K.; Sarangi, S. N.; Dash, A. K.; Ray, S. K.; Sahu, S. N.

    2006-12-01

    Cluster assembled selenium oxide (SeO 2) thin films, as a function of oxygen flow pressure (OFP) have been synthesized by a low energy cluster beam deposition (LECBD) technique. The OFP dependent surface morphology leading to well separated nanoclusters (size ranging from 50 to 200 nm) and fractal features are confirmed from transmission electron microscopic (TEM) measurements. A diffusion limited aggregation (DLA) mediated fractal growth with dimension as 1.71 ± 0.01 has been observed for high OFP (60 mbar). Structural analysis by glancing angle X-ray diffraction (GXRD) and selected area diffraction (SAD) studies identify the presence of tetragonal phase SeO 2 in the deposit. Micro-Raman studies indicate the shifts in bending and stretching vibrational phonon modes in cluster assembled SeO 2 as compared to their bulk counter part due to the phonon confinement effect.

  4. Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus

    PubMed Central

    Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Lubitz, Wolfgang

    2011-01-01

    Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron “wires” form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O2 to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of 57Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S]3+ state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress. PMID:21444783

  5. Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

    DOE PAGESBeta

    Yin, Panchao; Wu, Bin; Li, Tao; Bonnesen, Peter V.; Hong, Kunlun; Seifert, Soenke; Porcar, Lionel; Do, Changwoo; Keum, Jong Kahk

    2016-07-26

    A 2.9 nm molybdenum oxide cluster {Mo132} (Formula: [MoVI72MoV60O372(CH3COO)30(H2O)72]42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH3COOH/CH3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value,more » it triggers the assembly of MoV and MoVI species into {Mo132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo132} (formula: [MoVI72MoV60O372(CH3COO)30(H2O)72]42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a

  6. Selective self-assembly of molecular clusters with designed sizes on metal surfaces

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Li, Qing; Fuentes-Cabrera, Miguel; Sumpter, Bobby G.; Baddorf, Arthur P.; Pan, Minghu

    2014-03-01

    The self-assembly of ``magic'' molecular clusters on various substrates provides a new arena for studies of surface nanocatalysis and molecular electronics. Here we present the self-assembly of phenylacetylene molecules on Cu(100) by a combined low-temperature STM and in-depth density functional theory investigation. We observe the molecules form distinct tetramer clusters on Cu(100) at 40 K. Each cluster has a four-fold symmetry and consists of four molecules. A delicate balance of intramolecular and dipole-dipole interactions between clusters maintains this magic tetramer configuration on Cu(100). The strong interaction between the molecules and the copper surface creates an anchor at each adsorption site. Through comparison with our previous observed hexamer (six-molecule) clusters on Au(111), we conclude that the epitaxial relationship between the molecules and metal surfaces is crucial in defining magic numbers of surface-supported molecular clusters under weak intermolecular interaction. This research was conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

  7. Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters.

    PubMed

    Yin, Panchao; Wu, Bin; Li, Tao; Bonnesen, Peter V; Hong, Kunlun; Seifert, Soenke; Porcar, Lionel; Do, Changwoo; Keum, Jong Kahk

    2016-08-24

    Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo132} (formula: [Mo(VI)72Mo(V)60O372(CH3COO)30(H2O)72](42-)), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial Mo(VI) centers of molybdate precursors are reduced to form {Mo(V)2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {Mo(V)2(acetate)} reaches a critical value, it triggers the co-assembly of Mo(V) and Mo(VI) species into the giant clusters. PMID:27459601

  8. Spectroscopic changes during a single turnover of biotin synthase: destruction of a [2Fe-2S] cluster accompanies sulfur insertion.

    PubMed

    Ugulava, N B; Sacanell, C J; Jarrett, J T

    2001-07-27

    Biotin synthase catalyzes the insertion of a sulfur atom between the saturated C6 and C9 carbons of dethiobiotin. Catalysis requires AdoMet and flavodoxin and generates 5'-deoxyadenosine and methionine, suggesting that biotin synthase is an AdoMet-dependent radical enzyme. Biotin synthase (BioB) is aerobically purified as a dimer of 38.4 kDa monomers that contains 1-1.5 [2Fe-2S](2+) clusters per monomer and can be reconstituted with exogenous iron, sulfide, and reductants to contain up to two [4Fe-4S] clusters per monomer. The iron-sulfur clusters may play a dual role in biotin synthase: a reduced iron-sulfur cluster is probably involved in radical generation by mediating the reductive cleavage of AdoMet, while recent in vitro labeling studies suggest that an iron-sulfur cluster also serves as the immediate source of sulfur for the biotin thioether ring. Consistent with this dual role for iron-sulfur clusters in biotin synthase, we have found that the protein is stable, containing one [2Fe-2S](2+) cluster and one [4Fe-4S](2+) cluster per monomer. In the present study, we demonstrate that this mixed cluster state is essential for optimal activity. We follow changes in the Fe and S content and UV/visible and EPR spectra of the enzyme during a single turnover and conclude that during catalysis the [4Fe-4S](2+) cluster is preserved while the [2Fe-2S](2+) cluster is destroyed. We propose a mechanism for incorporation of sulfur into dethiobiotin in which a sulfur atom is oxidatively extracted from the [2Fe-2S](2+) cluster. PMID:11444982

  9. THE XMM CLUSTER SURVEY: THE STELLAR MASS ASSEMBLY OF FOSSIL GALAXIES

    SciTech Connect

    Harrison, Craig D.; Miller, Christopher J.; Richards, Joseph W.; Deadman, Paul-James; Lloyd-Davies, E. J.; Kathy Romer, A.; Mehrtens, Nicola; Liddle, Andrew R.; Hoyle, Ben; Hilton, Matt; Stott, John P.; Capozzi, Diego; Collins, Chris A.; Sahlen, Martin; Stanford, S. Adam; Viana, Pedro T. P.

    2012-06-10

    This paper presents both the result of a search for fossil systems (FSs) within the XMM Cluster Survey and the Sloan Digital Sky Survey and the results of a study of the stellar mass assembly and stellar populations of their fossil galaxies. In total, 17 groups and clusters are identified at z < 0.25 with large magnitude gaps between the first and fourth brightest galaxies. All the information necessary to classify these systems as fossils is provided. For both groups and clusters, the total and fractional luminosity of the brightest galaxy is positively correlated with the magnitude gap. The brightest galaxies in FSs (called fossil galaxies) have stellar populations and star formation histories which are similar to normal brightest cluster galaxies (BCGs). However, at fixed group/cluster mass, the stellar masses of the fossil galaxies are larger compared to normal BCGs, a fact that holds true over a wide range of group/cluster masses. Moreover, the fossil galaxies are found to contain a significant fraction of the total optical luminosity of the group/cluster within 0.5 R{sub 200}, as much as 85%, compared to the non-fossils, which can have as little as 10%. Our results suggest that FSs formed early and in the highest density regions of the universe and that fossil galaxies represent the end products of galaxy mergers in groups and clusters.

  10. THE IMACS CLUSTER BUILDING SURVEY. II. SPECTRAL EVOLUTION OF GALAXIES IN THE EPOCH OF CLUSTER ASSEMBLY

    SciTech Connect

    Dressler, Alan; Oemler, Augustus Jr.; Poggianti, Bianca M.; Vulcani, Benedetta; Gladders, Michael D.; Abramson, Louis

    2013-06-10

    The IMACS Cluster Building Survey (ICBS) provides spectra of {approx}2200 galaxies 0.31 < z < 0.54 in five rich clusters (R {approx}< 5 Mpc) and the field. Infalling, dynamically cold groups with tens of members account for approximately half of the supercluster population, contributing to a growth in cluster mass of {approx}100% by the present day. The ICBS spectra distinguish non-star-forming (PAS) and poststarburst (PSB) from star-forming galaxies-continuously star-forming (CSF) or starbursts (SBH or SBO), identified by anomalously strong H{delta} absorption or [O II] emission. For the infalling cluster groups and similar field groups, we find a correlation between PAS+PSB fraction and group mass, indicating substantial ''preprocessing'' through quenching mechanisms that can turn star-forming galaxies into passive galaxies without the unique environment of rich clusters. SBH + SBO starburst galaxies are common, and they maintain an approximately constant ratio (SBH+SBO)/CSF Almost-Equal-To 25% in all environments-from field, to groups, to rich clusters. Similarly, while PSB galaxies strongly favor denser environments, PSB/PAS Almost-Equal-To 10%-20% for all environments. This result, and their timescale {tau} {approx} 500 Myr, indicates that starbursts are not signatures of a quenching mechanism that produces the majority of passive galaxies. We suggest instead that starbursts and poststarbursts signal minor mergers and accretions, in star-forming and passive galaxies, respectively, and that the principal mechanisms for producing passive systems are (1) early major mergers, for elliptical galaxies, and (2) later, less violent processes-such as starvation and tidal stripping, for S0 galaxies.

  11. Growth of cluster assembled ZnO film by nanocluster beam deposition technique

    SciTech Connect

    Halder, Nilanjan

    2015-06-24

    ZnO is considered as one of the most promising material for optoelectronic devices. The present work emphasizes production of cluster assembled ZnO films by a UHV nanocluster beam deposition technique where the nanoclusters were produced in a laser vaporization cluster source. The microstructural and the optical properties of the ZnO nanocluster film deposited were investigated. As the wet chemical processes are not compatible with current solid state methods of device fabrication, therefore alternative UHV technique described in the paper is the need of the hour.

  12. Cluster-assembled cubic zirconia films with tunable and stable nanoscale morphology against thermal annealing

    NASA Astrophysics Data System (ADS)

    Borghi, F.; Sogne, E.; Lenardi, C.; Podestà, A.; Merlini, M.; Ducati, C.; Milani, P.

    2016-08-01

    Nanostructured zirconium dioxide (zirconia) films are very promising for catalysis and biotechnological applications: a precise control of the interfacial properties of the material at different length scales and, in particular, at the nanoscale, is therefore necessary. Here, we present the characterization of cluster-assembled zirconia films produced by supersonic cluster beam deposition possessing cubic structure at room temperature and controlled nanoscale morphology. We characterized the effect of thermal annealing in reducing and oxidizing conditions on the crystalline structure, grain dimensions, and topography. We highlight the mechanisms of film growth and phase transitions, which determine the observed interfacial morphological properties and their resilience against thermal treatments.

  13. Galaxy Luminosity Function of the Dynamically Young Abell 119 Cluster: Probing the Cluster Assembly

    NASA Astrophysics Data System (ADS)

    Lee, Youngdae; Rey, Soo-Chang; Hilker, Michael; Sheen, Yun-Kyeong; Yi, Sukyoung K.

    2016-05-01

    We present the galaxy luminosity function (LF) of the Abell 119 cluster down to {M}r∼ -14 mag based on deep images in the u, g, and r bands taken by using MOSAIC II CCD mounted on the Blanco 4 m telescope at the CTIO. The cluster membership was accurately determined based on the radial velocity information and on the color–magnitude relation for bright galaxies and the scaling relation for faint galaxies. The overall LF exhibits a bimodal behavior with a distinct dip at r∼ 18.5 mag ({M}r∼ -17.8 mag), which is more appropriately described by a two-component function. The shape of the LF strongly depends on the clustercentric distance and on the local galaxy density. The LF of galaxies in the outer, low-density region exhibits a steeper slope and more prominent dip compared with that of counterparts in the inner, high-density region. We found evidence for a substructure in the projected galaxy distribution in which several overdense regions in the Abell 119 cluster appear to be closely associated with the surrounding, possible filamentary structure. The combined LF of the overdense regions exhibits a two-component function with a distinct dip, while the LF of the central region is well described by a single Schechter function. We suggest that, in the context of the hierarchical cluster formation scenario, the observed overdense regions are the relics of galaxy groups, retaining their two-component LFs with a dip, which acquired their shapes through a galaxy merging process in group environments, before they fall into a cluster.

  14. Magnetic self-assembly of microparticle clusters in an aqueous two-phase microfluidic cross-flow

    NASA Astrophysics Data System (ADS)

    Abbasi, Niki; Jones, Steven G.; Moon, Byeong-Ui; Tsai, Scott S. H.

    2015-11-01

    We present a technique that self-assembles paramagnetic microparticles on the interface of aqueous two-phase system (ATPS) fluids in a microfluidic cross-flow. A co-flow of the ATPS is formed in the microfluidic cross channel as the flows of a dilute dextran (DEX) phase, along with a flow-focused particle suspension, converges with a dilute polyethylene glycol (PEG) phase. The microparticles arrive at the liquid-liquid interface and self-assemble into particle clusters due to forces on the particles from an applied external magnetic field gradient, and the interfacial tension of the ATPS. The microparticles form clusters at the interface, and once the cluster size grows to a critical value, the cluster passes through the interface. We control the size of the self-assembled clusters, as they pass through the interface, by varying the strength of the applied magnetic field gradient and the ATPS interfacial tension. We observe rich assembly dynamics, from the formation of Pickering emulsions to clusters that are completely encapsulated inside DEX phase droplets. We anticipate that this microparticle self-assembly method may have important biotechnological applications that require the controlled assembly of cells into clusters.

  15. Studies of cluster-assembled materials: From gas phase to condensed phase

    NASA Astrophysics Data System (ADS)

    Gao, Lin

    . After being mass gated in a reflectron equipped time-of-flight mass spectrometer (TOF-MS) and deposited onto TEM grids, the resultant specimens can be loaded onto high-resolution TEM investigation via electron diffraction. In conclusion, soft-landing of mass selected clusters has been shown to be a successful approach to obtain structural information on Zr-Met-Car cluster-assembled materials collected from the gas phase. TEM images indicate the richness of the morphologies associated with these cluster crystals. However, passivation methods are expected to be examined further to overcome the limited stabilities of these novel clusters. From this initial study, it's shown the promising opportunity to study other Met-Cars species and more cluster-based materials. Experimental results of reactions run with a solvothermal synthesis method obtained while searching for new Zr-C cluster assembled materials, are reported. One unexpected product in single crystal form was isolated and tentatively identified by X-ray diffraction to be [Zr6i O(OH)O12·2(Bu)4], with space group P2 1/n and lattice parameters of a = 12.44 A, b = 22.06 A, c = 18.40 A, alpha = 90°, beta = 105°, gamma = 90°, V = 4875 A3 and R 1 = 3.15% for the total observed data (I ≥ 2 sigma I) and oR2 = 2.82%. This novel hexanuclear Zr(IV)-oxo-hydroxide cluster anion may be the first member in polyoxometalates class with metal atoms from the IVB group and having Oh symmetry. Alternatively, it may be the first member in {[(Zr6Z)X 12]X6}m- class with halides replaced by oxo- and hydroxyl groups and with an increased oxidation state of Zr. It is predicted to bear application potentials directed by both families. This work could suggest a direction in which the preparation of Zr-C cluster-assembled materials in a liquid environment may be eventually fulfilled. 1,3-Bis(diethylphosphino)propane (depp) protected small gold clusters are studied via multiple techniques, including Electrospray Ionization Mass Spectrometry

  16. Thermodynamic-Driven Self-Assembly: Heterochiral Self-Sorting and Structural Reconfiguration in Gold(I)-Sulfido Cluster System.

    PubMed

    Yao, Liao-Yuan; Lee, Terence Kwok-Ming; Yam, Vivian Wing-Wah

    2016-06-15

    By employing chiral precursors, a new class of chiral gold(I)-sulfido clusters with unique structures has been constructed. Interestingly, pure enantiomers of the precursors are found to self-assemble into chiral hexa- and decanuclear clusters sequentially, while a racemic mixture of them has resulted in heterochiral self-sorting of an achiral meso decanuclear cluster. Chirality has determined not only the symmetry and structures but also the photophysical behaviors of these clusters. The racemic mixture of decanuclear clusters undergoes rearrangement and heterochiral self-sorting to give a meso decanuclear cluster. The thermodynamic-driven heterochiral self-sorting of gold(I) clusters provides a means to develop controlled self-assembly that may be of relevance to the understanding of chirality in nature. PMID:27248613

  17. Active photosynthesis in cyanobacterial mutants with directed modifications in the ligands for two iron-sulfur clusters on the PsaC protein of photosystem I.

    PubMed Central

    Mannan, R M; He, W Z; Metzger, S U; Whitmarsh, J; Malkin, R; Pakrasi, H B

    1996-01-01

    The PsaC protein of the Photosystem I (PSI) complex in thylakoid membranes coordinates two [4Fe-4S] clusters, FA and FB. Although it is known that PsaC participates in electron transfer to ferredoxin, the pathway of electrons through this protein is unknown. To elucidate the roles of FA and FB, we created two site-directed mutant strains of the cyanobacterium Anabaena variabilis ATCC 29413. In one mutant, cysteine 13, a ligand for FB was replaced by an aspartic acid (C13D); in the other mutant, cysteine 50, a ligand for FA was modified similarly (C50D). Low-temperature electron paramagnetic resonance studies demonstrated that the C50D mutant has a normal FB center and a modified FA center. In contrast, the C13D strain has normal FA, but failed to reveal any signal from FB. Room-temperature optical studies showed that C13D has only one functional electron acceptor in PsaC, whereas two such acceptors are functional in the C50D and wild-type strains. Although both mutants grow under photoautotrophic conditions, the rate of PSI-mediated electron transfer in C13D under low light levels is about half that of C50D or wild type. These data show that (i) FB is not essential for the assembly of the PsaC protein in PSI and (ii) FB is not absolutely required for electron transfer from the PSI reaction center to ferredoxin. PMID:8617228

  18. Dimensional scale effects on surface enhanced Raman scattering efficiency of self-assembled silver nanoparticle clusters

    SciTech Connect

    Fasolato, C.; Domenici, F. E-mail: paolo.postorino@roma1.infn.it; De Angelis, L.; Luongo, F.; Postorino, P. E-mail: paolo.postorino@roma1.infn.it; Sennato, S.; Mura, F.; Costantini, F.; Bordi, F.

    2014-08-18

    A study of the Surface Enhanced Raman Scattering (SERS) from micrometric metallic nanoparticle aggregates is presented. The sample is obtained from the self-assembly on glass slides of micro-clusters of silver nanoparticles (60 and 100 nm diameter), functionalized with the organic molecule 4-aminothiophenol in water solution. For nanoparticle clusters at the micron scale, a maximum enhancement factor of 10{sup 9} is estimated from the SERS over the Raman intensity ratio normalized to the single molecule contribution. Atomic force microscopy, correlated to spatially resolved Raman measurements, allows highlighting the connection between morphology and efficiency of the plasmonic system. The correlation between geometric features and SERS response of the metallic structures reveals a linear trend of the cluster maximum scattered intensity as a function of the surface area of the aggregate. On given clusters, the intensity turns out to be also influenced by the number of stacking planes of the aggregate, thus suggesting a plasmonic waveguide effect. The linear dependence results weakened for the largest area clusters, suggesting 30 μm{sup 2} as the upper limit for exploiting the coherence over large scale of the plasmonic response.

  19. Electric-field–induced assembly and propulsion of chiral colloidal clusters

    PubMed Central

    Ma, Fuduo; Wang, Sijia; Wu, David T.; Wu, Ning

    2015-01-01

    Chiral molecules with opposite handedness exhibit distinct physical, chemical, or biological properties. They pose challenges as well as opportunities in understanding the phase behavior of soft matter, designing enantioselective catalysts, and manufacturing single-handed pharmaceuticals. Microscopic particles, arranged in a chiral configuration, could also exhibit unusual optical, electric, or magnetic responses. Here we report a simple method to assemble achiral building blocks, i.e., the asymmetric colloidal dimers, into a family of chiral clusters. Under alternating current electric fields, two to four lying dimers associate closely with a central standing dimer and form both right- and left-handed clusters on a conducting substrate. The cluster configuration is primarily determined by the induced dipolar interactions between constituent dimers. Our theoretical model reveals that in-plane dipolar repulsion between petals in the cluster favors the achiral configuration, whereas out-of-plane attraction between the central dimer and surrounding petals favors a chiral arrangement. It is the competition between these two interactions that dictates the final configuration. The theoretical chirality phase diagram is found to be in excellent agreement with experimental observations. We further demonstrate that the broken symmetry in chiral clusters induces an unbalanced electrohydrodynamic flow surrounding them. As a result, they rotate in opposite directions according to their handedness. Both the assembly and propulsion mechanisms revealed here can be potentially applied to other types of asymmetric particles. Such kinds of chiral colloids will be useful for fabricating metamaterials, making model systems for both chiral molecules and active matter, or building propellers for microscale transport. PMID:25941383

  20. Electric-field-induced assembly and propulsion of chiral colloidal clusters.

    PubMed

    Ma, Fuduo; Wang, Sijia; Wu, David T; Wu, Ning

    2015-05-19

    Chiral molecules with opposite handedness exhibit distinct physical, chemical, or biological properties. They pose challenges as well as opportunities in understanding the phase behavior of soft matter, designing enantioselective catalysts, and manufacturing single-handed pharmaceuticals. Microscopic particles, arranged in a chiral configuration, could also exhibit unusual optical, electric, or magnetic responses. Here we report a simple method to assemble achiral building blocks, i.e., the asymmetric colloidal dimers, into a family of chiral clusters. Under alternating current electric fields, two to four lying dimers associate closely with a central standing dimer and form both right- and left-handed clusters on a conducting substrate. The cluster configuration is primarily determined by the induced dipolar interactions between constituent dimers. Our theoretical model reveals that in-plane dipolar repulsion between petals in the cluster favors the achiral configuration, whereas out-of-plane attraction between the central dimer and surrounding petals favors a chiral arrangement. It is the competition between these two interactions that dictates the final configuration. The theoretical chirality phase diagram is found to be in excellent agreement with experimental observations. We further demonstrate that the broken symmetry in chiral clusters induces an unbalanced electrohydrodynamic flow surrounding them. As a result, they rotate in opposite directions according to their handedness. Both the assembly and propulsion mechanisms revealed here can be potentially applied to other types of asymmetric particles. Such kinds of chiral colloids will be useful for fabricating metamaterials, making model systems for both chiral molecules and active matter, or building propellers for microscale transport. PMID:25941383

  1. SOS System Induction Inhibits the Assembly of Chemoreceptor Signaling Clusters in Salmonella enterica

    PubMed Central

    Irazoki, Oihane; Mayola, Albert; Campoy, Susana; Barbé, Jordi

    2016-01-01

    Swarming, a flagellar-driven multicellular form of motility, is associated with bacterial virulence and increased antibiotic resistance. In this work we demonstrate that activation of the SOS response reversibly inhibits swarming motility by preventing the assembly of chemoreceptor-signaling polar arrays. We also show that an increase in the concentration of the RecA protein, generated by SOS system activation, rather than another function of this genetic network impairs chemoreceptor polar cluster formation. Our data provide evidence that the molecular balance between RecA and CheW proteins is crucial to allow polar cluster formation in Salmonella enterica cells. Thus, activation of the SOS response by the presence of a DNA-injuring compound increases the RecA concentration, thereby disturbing the equilibrium between RecA and CheW and resulting in the cessation of swarming. Nevertheless, when the DNA-damage decreases and the SOS response is no longer activated, basal RecA levels and thus polar cluster assembly are reestablished. These results clearly show that bacterial populations moving over surfaces make use of specific mechanisms to avoid contact with DNA-damaging compounds. PMID:26784887

  2. Exchange variation of zero-field splittings in [Fe 4S 4] + clusters of ferredoxins with high-spin S=3/2 ground state

    NASA Astrophysics Data System (ADS)

    Belinsky, Moisey I.

    2000-04-01

    The spin-coupling model of zero-field splitting (ZFS) of tetrameric mixed-valent and monovalent clusters is developed. The <| ŝi0(2)|> matrix elements of the individual ZFS tensor operator of the second rank were calculated for tetramers of the general type in the representation of the total and intermediate spins. The spin-dependent correlations between ZFS parameters D S of the cluster states S and D i of individual ions s i were obtained for [4Fe-4S] + centers of native systems and synthetic model compounds with the high-spin Sgr=3/2 ground state. It was shown that the single-particle spin parameters f i=<| ŝiz2-s i(s i+1)/3|>/<| Ŝz2-S(S+1)/3|> of the [Fe 3(II)Fe(III)] center essentially depend on the total, intermediate and local spins and on the exchange parameters. In the spin schemes with fixed intermediate spins, the correlation between the cluster total spin ZFS parameters, D S, and the individual ZFS parameters, D i, are determined by the total, intermediate and individual spins. Anisotropic cluster ZFS parameters D S strongly depend on isotropic Heisenberg exchange and double exchange inter-ion interactions due to exchange mixing of the states with different intermediate spins. It was shown that the cluster ZFS parameters D S, for the states with S=3/2, change their values and sign under the variation of the Heisenberg exchange and double exchange parameters during the cluster deformation. The single-particle ZFS parameters D i and the exchange effects determine the observed strong positive ( DS=1.5-6 cm -1) and negative ( DS=-1.7 to -5 cm -1) cluster ZFS splittings of the ground Sgr=3/2 states of the [4Fe-4S] + clusters. Positive (negative) cluster ZFS parameters D S correspond to negative (positive) individual ZFS parameters D1-3 [Fe(II)]. The theory explains the observation of small negative effective hyperfine constants A i for the Sgr=3/2 clusters with positive and negative cluster ZFS parameters D S. The correlations between the individual and

  3. Magnetic Assembly of Superparamagnetic Iron Oxide Nanoparticle Clusters into Nanochains and Nanobundles.

    PubMed

    Kralj, Slavko; Makovec, Darko

    2015-10-27

    We report on the syntheses of magnetoresponsive, superparamagnetic nanostructures with highly anisotropic shapes, i.e., nanochains of controlled length and their bundles (nanobundles). These nanochains and nanobundles were obtained by the simultaneous magnetic assembly of superparamagnetic nanoparticle clusters (SNCs) and the fixation of the assembled SNCs with an additional layer of deposited silica, produced by a sol-gel process. This low-cost approach provides excellent length control of the short nanochains (approximately 6 or 14 SNCs per nanochain) and fine-tuning of the spacing between the neighboring SNCs inside an individual nanochain. Our magnetically responsive superparamagnetic nanostructures have a controlled aspect ratio, a uniform size, and a well-defined shape, and they express good colloidal stability. This general approach should lead to new, advanced applications of the nanochains and nanobundles in the treatment of cancer and in the ability to magnetically manipulate liquid and photonic crystals. PMID:26394039

  4. Nanoscale control of polyoxometalate assembly: a {Mn8W4} cluster within a {W36Si4Mn10} cluster showing a new type of isomerism.

    PubMed

    Winter, Ross S; Yan, Jun; Busche, Christoph; Mathieson, Jennifer S; Prescimone, Alessandro; Brechin, Euan K; Long, De-Liang; Cronin, Leroy

    2013-02-25

    Two near isomeric clusters containing a novel {Mn(8)W(4)} Keggin cluster within a [W(36)Mn(10)Si(4)O(136)(OH)(4)(H(2)O)8](24-) cluster are reported: K(10)Li(14)[W(36)Si(4)O(136)Mn(II)(10)(OH)(4)(H(2)O)(8)] (1) and K(10)Li1(3.5)Mn(0.25)[W(36)Si(4)O(136)Mn(II)(10)(OH)(4)(H(2)O)(8) ] (1'). Bulk characterization of the clusters has been carried out by single crystal X-ray structure analysis, ICP-MS, TGA, ESI-MS, CV and SQUID-magnetometer analysis. X-ray analysis revealed that 1' has eight positions within the central Keggin core that were disordered W/Mn whereas 1 contained no such disorder. This subtle difference is due to a differences is how the two clusters assemble and recrystallize from the same mother liquor and represents a new type of isomerism. The rapid recrystallization process was captured via digital microscopy and this uncovered two "intermediate" types of crystal which formed temporarily and provided nucleation sites for the final clusters to assemble. The intermediates were investigated by single crystal X-ray analysis and revealed to be novel clusters K(4)Li(22)[W(36)Si(4)Mn(7)O(136)(H(2)O)(8)]·56H(2)O (2) and Mn(2)K(8)Li(14)[W(36)Si(4)Mn(7)O(136)(H(2)O)(8)]·45H(2)O (3). The intermediate clusters contained different yet related building blocks to the final clusters which allowed for the postulation of a mechanism of assembly. This demonstrates a rare example where the use X-ray crystallography directly facilitated understanding the means by which a POM assembled. PMID:23362186

  5. Human Mitochondrial Chaperone (mtHSP70) and Cysteine Desulfurase (NFS1) Bind Preferentially to the Disordered Conformation, Whereas Co-chaperone (HSC20) Binds to the Structured Conformation of the Iron-Sulfur Cluster Scaffold Protein (ISCU)*

    PubMed Central

    Cai, Kai; Frederick, Ronnie O.; Kim, Jin Hae; Reinen, Nichole M.; Tonelli, Marco; Markley, John L.

    2013-01-01

    Human ISCU is the scaffold protein for mitochondrial iron-sulfur (Fe-S) cluster biogenesis and transfer. NMR spectra have revealed that ISCU populates two conformational states; that is, a more structured state (S) and a partially disordered state (D). We identified two single amino acid substitutions (D39V and N90A) that stabilize the S-state and two (D39A and H105A) that stabilize the D-state. We isolated the two constituent proteins of the human cysteine desulfurase complex (NFS1 and ISD11) separately and used NMR spectroscopy to investigate their interaction with ISCU. We found that ISD11 does not interact directly with ISCU. By contrast, NFS1 binds preferentially to the D-state of ISCU as does the NFS1-ISD11 complex. An in vitro Fe-S cluster assembly assay showed that [2Fe-2S] and [4Fe-4S] clusters are assembled on ISCU when catalyzed by NFS1 alone and at a higher rate when catalyzed by the NFS1-ISD11 complex. The DnaK-type chaperone (mtHSP70) and DnaJ-type co-chaperone (HSC20) are involved in the transfer of clusters bound to ISCU to acceptor proteins in an ATP-dependent reaction. We found that the ATPase activity of mtHSP70 is accelerated by HSC20 and further accelerated by HSC20 plus ISCU. NMR studies have shown that mtHSP70 binds preferentially to the D-state of ISCU and that HSC20 binds preferentially to the S-state of ISCU. PMID:23940031

  6. High throughput assembly of spatially controlled 3D cell clusters on a micro/nanoplatform.

    PubMed

    Gallego-Perez, Daniel; Higuita-Castro, Natalia; Sharma, Sadhana; Reen, Rashmeet K; Palmer, Andre F; Gooch, Keith J; Lee, L James; Lannutti, John J; Hansford, Derek J

    2010-03-21

    Guided assembly of microscale tissue subunits (i.e. 3D cell clusters/aggregates) has found applications in cell therapy/tissue engineering, cell and developmental biology, and drug discovery. As cluster size and geometry are known to influence cellular responses, the ability to spatially control cluster formation in a high throughput manner could be advantageous for many biomedical applications. In this work, a micro- and nanofabricated platform was developed for this purpose, consisting of a soft-lithographically fabricated array of through-thickness microwells structurally bonded to a sheet of electrospun fibers. The microwells and fibers were manufactured from several polymers of biomedical interest. Human hepatocytes were used as model cells to demonstrate the ability of the platform to allow controlled cluster formation. In addition, the ability of the device to support studies on semi-controlled heterotypic interactions was demonstrated by co-culturing hepatocytes and fibroblasts. Preliminary experiments with other cells of interest (pancreatic cells, embryonic stem cells, and cardiomyocytes) were also conducted. Our platform possesses several advantages over previously developed microwell arrays: a more in vivo-like topographical stimulation of cells; better nutrient/waste exchange through the underlying nanofiber mat; and easy integration into standard two-chamber cell culture well systems. PMID:20221567

  7. Assembly of iron-sulfur clusters. Identification of an iscSUA-hscBA-fdx gene cluster from Azotobacter vinelandii.

    PubMed

    Zheng, L; Cash, V L; Flint, D H; Dean, D R

    1998-05-22

    An enzyme having the same L-cysteine desulfurization activity previously described for the NifS protein was purified from a strain of Azotobacter vinelandii deleted for the nifS gene. This protein was designated IscS to indicate its proposed role in iron-sulfur cluster assembly. Like NifS, IscS is a pyridoxal-phosphate containing homodimer. Information gained from microsequencing of oligopeptides obtained by tryptic digestion of purified IscS was used to design a strategy for isolation and DNA sequence analysis of a 7,886-base pair A. vinelandii genomic segment that includes the iscS gene. The iscS gene is contained within a gene cluster that includes homologs to nifU and another gene contained within the major nif cluster of A. vinelandii previously designated orf6. These genes have been designated iscU and iscA, respectively. Information available from complete genome sequences of Escherichia coli and Hemophilus influenzae reveals that they also encode iscSUA gene clusters. A wide conservation of iscSUA genes in nature and evidence that NifU and NifS participate in the mobilization of iron and sulfur for nitrogenase-specific iron-sulfur cluster formation suggest that the products of the iscSUA genes could play a general role in the formation or repair of iron-sulfur clusters. The proposal that IscS is involved in mobilization of sulfur for iron-sulfur cluster formation in A. vinelandii is supported by the presence of a cysE-like homolog in another gene cluster located immediately upstream from the one containing the iscSUA genes. O-Acetylserine synthase is the product of the cysE gene, and it catalyzes the rate-limiting step in cysteine biosynthesis. A similar cysE-like gene is also located within the nif gene cluster of A. vinelandii. The likely role of such cysE-like gene products is to increase the cysteine pool needed for iron-sulfur cluster formation. Another feature of the iscSUA gene cluster region from A. vinelandii is that E. coli genes previously

  8. The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions

    PubMed Central

    Couturier, Jérémy; Touraine, Brigitte; Briat, Jean-François; Gaymard, Frédéric; Rouhier, Nicolas

    2013-01-01

    Many metabolic pathways and cellular processes occurring in most sub-cellular compartments depend on the functioning of iron-sulfur (Fe-S) proteins, whose cofactors are assembled through dedicated protein machineries. Recent advances have been made in the knowledge of the functions of individual components through a combination of genetic, biochemical and structural approaches, primarily in prokaryotes and non-plant eukaryotes. Whereas most of the components of these machineries are conserved between kingdoms, their complexity is likely increased in plants owing to the presence of additional assembly proteins and to the existence of expanded families for several assembly proteins. This review focuses on the new actors discovered in the past few years, such as glutaredoxin, BOLA and NEET proteins as well as MIP18, MMS19, TAH18, DRE2 for the cytosolic machinery, which are integrated into a model for the plant Fe-S cluster biogenesis systems. It also discusses a few issues currently subjected to an intense debate such as the role of the mitochondrial frataxin and of glutaredoxins, the functional separation between scaffold, carrier and iron-delivery proteins and the crosstalk existing between different organelles. PMID:23898337

  9. Combinatorial and topological modeling of cluster self-assembly of the crystal structure of zeolites

    NASA Astrophysics Data System (ADS)

    Ilyushin, G. D.; Blatov, V. A.

    2015-07-01

    Combinatorial and topological modeling of packings of symmetrically connected polyhedral T12 clusters (hexagonal prisms), which are most widespread in crystal structures of zeolites, has been performed. Packings of T12 clusters are periodic 1D chains (11 types) and 2D microlayers (15 types). 2D microlayers that can be involved in the self-assembly of 3D zeolite structures described by tetracoordinated T nets are selected. Computer methods (the ToposPro program package) have been used to establish a correspondence with zeolites CHA (Chabazite, Ca6(H2O)40Al12Si24O72), AEI (AlPO-18, Al24P24O96), SAV ((C18H42N6)2(H2O)7Mg5Al19P24O96), KFI (Na30(H2O)98Al30Si66O192), GME (Gmelinite, (Ca,Na)4(H2O)24Al8Si16O48), AFX (SAPO-56, H3Al23Si5P20O96), and AFT (AlPO-52, Al36P36O144) for 7 out of 11 obtained models of 3D frameworks. Modeling of 3D polytypes of the GME (1L type)- AFX (2L type)- AFT (3L type) family has resulted in a new 3L polytype with the following crystallographic parameters: a =13.75 Å, c = 30.00 Å, V = 4912.0 Å3, sp. gr. P m2 (no. 187). It is established that the 2D self-assembly of known zeolite structures is accompanied by pairwise binding of all (T12 + T12) clusters with the formation of 4C rings, and the number of bonds between complementary chains during the formation of microlayers is maximum. Three types of obtained frameworks, which have no analogs among zeolites, exhibit low chain connectivity during microlayer formation in all cases.

  10. Assembly of a Highly Stable Luminescent Zn5 Cluster and Application to Bio-Imaging.

    PubMed

    Zeng, Ming-Hua; Yin, Zheng; Liu, Ze-Hui; Xu, Hai-Bing; Feng, Ying-Chun; Hu, Yue-Qiao; Chang, Li-Xian; Zhang, Yue-Xing; Huang, Jin; Kurmoo, Mohamedally

    2016-09-12

    The assembly sequence of the coordination cluster [Zn5 (H2 L(n) )6 ](NO3 )4 ]⋅8 H2 O⋅2 CH3 OH (Zn5 , H3 L(n) =(1,2-bis(benzo[d]imidazol-2-yl)-ethenol) involves in situ dehydration of 1,2-bis(benzo[d]imidazol-2-yl)-1,2-ethanediol (H4 L) through the formation of the [Zn(H3 L)2 ](+) monomer, dimerization to [Zn2 (H3 L)2 ](+) , dehydration of the ligand to [Zn2 (H2 L(n) )2 ](+) , and the final formation of the pentanuclear cluster. The cluster has the following special characteristics: 1) high stability in both refluxing 37 % HCl and 27 % NH3 , 2) low cytotoxicity, and 3) pH-sensitive fluorescence in the visible-to-near-infrared (Vis/NIR) region in the solid state and in solution. We have applied it as a fluorescent probe both in vivo and in vitro. Its H-bonding ability is the key to its affinity and selectivity for imaging lysosomes in HeLa cells and tumors in male BALB/C mice. It provides a new type of sensitive and biocompatible fluorescent probe for detecting small tumors (13.5 mm(3) ). PMID:27529333

  11. Mössbauer studies of frataxin role in iron-sulfur cluster assembly and dysfunction-related disease

    NASA Astrophysics Data System (ADS)

    Garcia-Serres, Ricardo; Clémancey, Martin; Oddou, Jean-Louis; Pastore, Annalisa; Lesuisse, Emmanuel; Latour, Jean-Marc

    2012-03-01

    Friedreich ataxia is a disease that is associated with defects in the gene coding for a small protein frataxin. Several different roles have been proposed for the protein, including iron chaperoning and iron storage. Mössbauer spectroscopy was used to probe these hypotheses. Iron accumulation in mutant mitochondria unable to assemble iron sulfur clusters proved to be insensitive to overexpression of frataxin, ruling out its potential involvement as an iron storage protein similar to ferritin. Rather, it was found that frataxin negatively regulates iron sulfur cluster assembly.

  12. Self-assembly of methanethiol on cluster arrays of Co/Au(111)

    NASA Astrophysics Data System (ADS)

    Nenchev, Georgi; Diaconescu, Bogdan; Pohl, Karsten

    2007-03-01

    Self-assembly on strained metallic interfaces is an attractive option for growing highly ordered multi-functional nanopatterns. We present a Variable Temperature STM and Auger Electron Spectroscopy study of selective adsorption of sulfur-terminated CH3SH molecules on the lattice of Co clusters on Au(111). We investigate the growth of a uniform network of Co on the reconstructed Au(111) surface, the temperature evolution of the island height and the termination, and the onset of surface alloying. Further we will show the evolution of morphology of the CH3SH film on Au (111) as a function of coverage and temperature, and the importance of the herringbone reconstruction for the SAM formation and orientation. Successful combination and control of these two processes leads to the creation of an ordered, stable patterned Co/CH3SH heterostructure with nanometer-sized unit cell.

  13. Bacterial iron-sulfur cluster sensors in mammalian pathogens

    PubMed Central

    Miller, Halie K.; Auerbuch, Victoria

    2015-01-01

    Iron-sulfur clusters act as important cofactors for a number of transcriptional regulators in bacteria, including many mammalian pathogens. The sensitivity of iron-sulfur clusters to iron availability, oxygen tension, and reactive oxygen and nitrogen species enables bacteria to use such regulators to adapt their gene expression profiles rapidly in response to changing environmental conditions. In this review, we discuss how the [4Fe-4S] or [2Fe-2S] cluster-containing regulators FNR, Wbl, aconitase, IscR, NsrR, SoxR, and AirSR contribute to bacterial pathogenesis through control of both metabolism and classical virulence factors. In addition, we briefly review mammalian iron homeostasis as well as oxidative/nitrosative stress to provide context for understanding the function of bacterial iron-sulfur cluster sensors in different niches within the host. PMID:25738802

  14. Iron-sulfur clusters as biological sensors: the chemistry of reactions with molecular oxygen and nitric oxide.

    PubMed

    Crack, Jason C; Green, Jeffrey; Thomson, Andrew J; Le Brun, Nick E

    2014-10-21

    Iron-sulfur cluster proteins exhibit a range of physicochemical properties that underpin their functional diversity in biology, which includes roles in electron transfer, catalysis, and gene regulation. Transcriptional regulators that utilize iron-sulfur clusters are a growing group that exploit the redox and coordination properties of the clusters to act as sensors of environmental conditions including O2, oxidative and nitrosative stress, and metabolic nutritional status. To understand the mechanism by which a cluster detects such analytes and then generates modulation of DNA-binding affinity, we have undertaken a combined strategy of in vivo and in vitro studies of a range of regulators. In vitro studies of iron-sulfur cluster proteins are particularly challenging because of the inherent reactivity and fragility of the cluster, often necessitating strict anaerobic conditions for all manipulations. Nevertheless, and as discussed in this Account, significant progress has been made over the past decade in studies of O2-sensing by the fumarate and nitrate reduction (FNR) regulator and, more recently, nitric oxide (NO)-sensing by WhiB-like (Wbl) and FNR proteins. Escherichia coli FNR binds a [4Fe-4S] cluster under anaerobic conditions leading to a DNA-binding dimeric form. Exposure to O2 converts the cluster to a [2Fe-2S] form, leading to protein monomerization and hence loss of DNA binding ability. Spectroscopic and kinetic studies have shown that the conversion proceeds via at least two steps and involves a [3Fe-4S](1+) intermediate. The second step involves the release of two bridging sulfide ions from the cluster that, unusually, are not released into solution but rather undergo oxidation to sulfane (S(0)) subsequently forming cysteine persulfides that then coordinate the [2Fe-2S] cluster. Studies of other [4Fe-4S] cluster proteins that undergo oxidative cluster conversion indicate that persulfide formation and coordination may be more common than previously

  15. Exploring DNA assembler, a synthetic biology tool for characterizing and engineering natural product gene clusters

    PubMed Central

    Shao, Zengyi; Zhao, Huimin

    2015-01-01

    The majority of existing antibacterial and anticancer drugs are natural products or their derivatives. However, the characterization and engineering of these compounds are often hampered by limited ability to manipulate the corresponding biosynthetic pathways. Recently, we developed a genomics-driven, synthetic biology-based method, DNA assembler, for discovery, characterization, and engineering of natural product biosynthetic pathways (Shao et al., 2011). By taking advantage of the highly efficient yeast in vivo homologous recombination mechanism, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the genetic elements needed for DNA maintenance and replication in individual hosts in a single-step manner. In this chapter, we describe the general guidelines for construct design. By using two distinct biosynthetic pathways, we demonstrate that DNA assembler can perform multiple tasks, including heterologous expression, introduction of single or multiple point mutations, scar-less gene deletion, generation of product derivatives and creation of artificial gene clusters. As such, this method offers unprecedented flexibility and versatility in pathway manipulations. PMID:23084940

  16. Evolution and cellular function of monothiol glutaredoxins: involvement in iron-sulphur cluster assembly.

    PubMed

    Vilella, Felipe; Alves, Rui; Rodríguez-Manzaneque, María Teresa; Bellí, Gemma; Swaminathan, Swarna; Sunnerhagen, Per; Herrero, Enrique

    2004-01-01

    A number of bacterial species, mostly proteobacteria, possess monothiol glutaredoxins homologous to the Saccharomyces cerevisiae mitochondrial protein Grx5, which is involved in iron-sulphur cluster synthesis. Phylogenetic profiling is used to predict that bacterial monothiol glutaredoxins also participate in the iron-sulphur cluster (ISC) assembly machinery, because their phylogenetic profiles are similar to the profiles of the bacterial homologues of yeast ISC proteins. High evolutionary co-occurrence is observed between the Grx5 homologues and the homologues of the Yah1 ferredoxin, the scaffold proteins Isa1 and Isa2, the frataxin protein Yfh1 and the Nfu1 protein. This suggests that a specific functional interaction exists between these ISC machinery proteins. Physical interaction analyses using low-definition protein docking predict the formation of strong and specific complexes between Grx5 and several components of the yeast ISC machinery. Two-hybrid analysis has confirmed the in vivo interaction between Grx5 and Isa1. Sequence comparison techniques and cladistics indicate that the other two monothiol glutaredoxins of S. cerevisiae, Grx3 and Grx4, have evolved from the fusion of a thioredoxin gene with a monothiol glutaredoxin gene early in the eukaryotic lineage, leading to differential functional specialization. While bacteria do not contain these chimaeric glutaredoxins, in many eukaryotic species Grx5 and Grx3/4-type monothiol glutaredoxins coexist in the cell. PMID:18629168

  17. Silver(I), Mercury(II), Cadmium(II), and Zinc(II) Target Exposed Enzymic Iron-Sulfur Clusters when They Toxify Escherichia coli

    PubMed Central

    Xu, Fang Fang

    2012-01-01

    The toxicity of soft metals is of broad interest to microbiologists, both because such metals influence the community structures in natural environments and because several metals are used as antimicrobial agents. Their potency roughly parallels their thiophilicity, suggesting that their primary biological targets are likely to be enzymes that contain key sulfhydryl moieties. A recent study determined that copper poisons Escherichia coli in part by attacking the exposed [4Fe-4S] clusters of dehydratases. The present investigation sought to test whether other soft metals also target these enzymes. In vitro experiments revealed that low-micromolar concentrations of Ag(I) and Hg(II) directly inactivated purified fumarase A, a member of the dehydratase family. The enzyme was also poisoned by higher levels of Cd(II) and Zn(II), but it was unaffected by even millimolar concentrations of Mn(II), Co(II), Ni(II), and Pb(II). Electron paramagnetic resonance analysis and measurements of released iron confirmed that damage was associated with destruction of the [4Fe-4S] cluster, and indeed, the reconstruction of the cluster fully restored activity. Growth studies were then performed to test whether dehydratase damage might underlie toxicity in vivo. Barely toxic doses of Ag(I), Hg(II), Cd(II), and Zn(II) inactivated all tested members of the [4Fe-4S] dehydratase family. Again, activity was recovered when the clusters were rebuilt. The metals did not diminish the activities of other sampled enzymes, including NADH dehydrogenase I, an iron-sulfur protein whose clusters are shielded by polypeptide. Thus, the data indicate that dehydratases are damaged by the concentrations of metals that initiate bacteriostasis. PMID:22344668

  18. Structural and functional characterization of an iron-sulfur cluster assembly scaffold protein-SufA from Plasmodium vivax.

    PubMed

    Pala, Zarna Rajeshkumar; Saxena, Vishal; Saggu, Gagandeep Singh; Yadav, Sushil Kumar; Pareek, R P; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Garg, Shilpi

    2016-07-01

    Iron-sulfur (Fe-S) clusters are utilized as prosthetic groups in all living organisms for diverse range of cellular processes including electron transport in respiration and photosynthesis, sensing of ambient conditions, regulation of gene expression and catalysis. In Plasmodium, two Fe-S cluster biogenesis pathways are reported, of which the Suf pathway in the apicoplast has been shown essential for the erythrocytic stages of the parasite. While the initial components of this pathway detailing the sulfur mobilization have been elucidated, the components required for the assembly and transfer of Fe-S clusters are not reported from the parasite. In Escherichia coli, SufB acts as a scaffold protein and SufA traffics the assembled Fe-S cluster from SufB to target apo-proteins. However, in Plasmodium, the homologs of these proteins are yet to be characterized for their function. Here, we report a putative SufA protein from Plasmodium vivax with signature motifs of A-type scaffold proteins, which is evolutionarily conserved. The presence of the [Fe4S4](3+) cluster under reduced conditions was confirmed by UV-visible and EPR spectroscopy and the interaction of these clusters with the conserved cysteine residues of chains A and B of PvSufA, validates its existence as a dimer, similar to that in E. coli. The H-bond interactions at the PvSufA-SufB interface demonstrate SufA as a scaffold protein in conjunction with SufB for the pre-assembly of Fe-S clusters and their transfer to the target proteins. Co-localization of the protein to the apicoplast further provides an experimental evidence of a functional scaffold protein SufA for the biogenesis of Fe-S clusters in apicoplast of Plasmodium. PMID:27033210

  19. Cluster self-organization of silicate and germanate systems: Invariant suprapolyhedral cluster precursors and self-assembly of the crystal structures of Li,TR silicates (germanates)

    SciTech Connect

    Ilyushin, G. D. Dem'yanets, L. N.

    2008-05-15

    The initial stages of formation of suprapolyhedral clusters (containing polyhedra of different types) in an evolving chemical system are considered. The suprapolyhedral clusters of the chain and cyclic types are used for modeling two-dimensional periodic structures. The developed model is used to search for cluster precursors in the structures of Li,TR silicates (germanates) of the known structure types. The complete threedimensional reconstruction of the self-assembly of Li,TR silicates (germanates) is performed using computer methods (with the TOPOS program package) according to the following scheme: cluster precursor {sup {yields}} primary chain {sup {yields}} microlayer {sup {yields}} microframework (supraprecursor) {sup {yields}} ... framework. Two types of invariant cyclic cluster precursors composed of the TR polyhedra linked by tetrahedra and the TR polyhedra joined by diorthotetrahedra are identified in five and two structures, respectively. It is revealed that the lithium atoms are located at the centers of all clusters. New types of two-dimensional nets with a hierarchical structure formed as a result of the packing of cyclic four-, six-, and eight-node clusters are described.

  20. O2 Reactions at the Six-iron Active Site (H-cluster) in [FeFe]-Hydrogenase*

    PubMed Central

    Lambertz, Camilla; Leidel, Nils; Havelius, Kajsa G. V.; Noth, Jens; Chernev, Petko; Winkler, Martin; Happe, Thomas; Haumann, Michael

    2011-01-01

    Irreversible inhibition by molecular oxygen (O2) complicates the use of [FeFe]-hydrogenases (HydA) for biotechnological hydrogen (H2) production. Modification by O2 of the active site six-iron complex denoted as the H-cluster ([4Fe4S]-2FeH) of HydA1 from the green alga Chlamydomonas reinhardtii was characterized by x-ray absorption spectroscopy at the iron K-edge. In a time-resolved approach, HydA1 protein samples were prepared after increasing O2 exposure periods at 0 °C. A kinetic analysis of changes in their x-ray absorption near edge structure and extended X-ray absorption fine structure spectra revealed three phases of O2 reactions. The first phase (τ1 ≤ 4 s) is characterized by the formation of an increased number of Fe–O,C bonds, elongation of the Fe–Fe distance in the binuclear unit (2FeH), and oxidation of one iron ion. The second phase (τ2 ≈ 15 s) causes a ∼50% decrease of the number of ∼2.7-Å Fe–Fe distances in the [4Fe4S] subcluster and the oxidation of one more iron ion. The final phase (τ3 ≤ 1000 s) leads to the disappearance of most Fe–Fe and Fe–S interactions and further iron oxidation. These results favor a reaction sequence, which involves 1) oxygenation at 2FeH+ leading to the formation of a reactive oxygen species-like superoxide (O2−), followed by 2) H-cluster inactivation and destabilization due to ROS attack on the [4Fe4S] cluster to convert it into an apparent [3Fe4S]+ unit, leading to 3) complete O2-induced degradation of the remainders of the H-cluster. This mechanism suggests that blocking of ROS diffusion paths and/or altering the redox potential of the [4Fe4S] cubane by genetic engineering may yield improved O2 tolerance in [FeFe]-hydrogenase. PMID:21930709

  1. Nanoparticle cluster arrays for high-performance SERS through directed self-assembly on flat substrates and on optical fibers.

    PubMed

    Yap, Fung Ling; Thoniyot, Praveen; Krishnan, Sathiyamoorthy; Krishnamoorthy, Sivashankar

    2012-03-27

    We demonstrate template-guided self-assembly of gold nanoparticles into ordered arrays of uniform clusters suitable for high-performance SERS on both flat (silicon or glass) chips and an optical fiber faucet. Cluster formation is driven by electrostatic self-assembly of anionic citrate-stabilized gold nanoparticles (~11.6 nm diameter) onto two-dimensionally ordered polyelectrolyte templates realized by self-assembly of polystyrene-block-poly(2-vinylpyridine). A systematic variation is demonstrated for the number of particles (N ≈ 5, 8, 13, or 18) per cluster as well as intercluster separations (S(c) ≈ 37-10 nm). Minimum interparticle separations of <5 nm, intercluster separations of ~10 nm, and nanoparticle densities on surfaces as high as ~7 × 10(11)/in.(2) are demonstrated. Geometric modeling is used to support experimental data toward estimation of interparticle and intercluster separations in cluster arrays. Optical modeling and simulations using the finite difference time domain method are used to establish the influence of cluster size, shape, and intercluster separations on the optical properties of the cluster arrays in relation to their SERS performance. Excellent SERS performance, as evidenced by a high enhancement factor, >10(8) on flat chips and >10(7) for remote sensing, using SERS-enabled optical fibers is demonstrated. The best performing cluster arrays in both cases are achievable without the use of any expensive equipment or clean room processing. The demonstrated approach paves the way to significantly low-cost and high-throughput production of sensor chips or 3D-configured surfaces for remote sensing applications. PMID:22332718

  2. Mitochondrial Hspa9/Mortalin regulates erythroid differentiation via iron-sulfur cluster assembly.

    PubMed

    Shan, Yuxi; Cortopassi, Gino

    2016-01-01

    Mitochondrial iron-sulfur cluster (ISC) biogenesis provides iron-sulfur cofactors to several mitochondrial proteins, but the extent to which ISC biogenesis regulates hematopoiesis has been unclear. The blood disease Myelodysplastic syndrome (MDS) is characterized by ineffective hematopoiesis, and the disease overlaps with the gene Hspa9/Mortalin in multiple ways: the HSPA9 locus maps to 5q31.2 that is frequently deleted in human MDS; mutant Hspa9 causes zebrafish MDS; and Hspa9 knockdown mice have decreased hematopoiesis. We show here that HSPA9 functions in mitochondrial ISC biogenesis, and is required for erythroid differentiation. HSPA9 interacts with and stabilizes the mitochondrial ISC biogenesis proteins frataxin, Nfs1, ISCU, and Nfu. MDS-causing mutations in HSPA9 protein change its interactions with ISC biogenesis proteins. Depletion of HSPA9 decreases aconitase activity, which requires an ISC at its active site, but not that of the non-ISC requiring malate dehydrogenase, and increases IRP1 binding activity. In erythroid cell lines, Hspa9 depletion inhibited erythroid differentiation, post-transcriptionally regulating the expression of Alas2 and FeCH, as expected through known ISC control of the IRE response elements in these genes. By contrast, the Alas2 open reading frame rescued the Hspa9-dependent defect in erythroid differentiation, but not when uncoupled from its 5'-IRE sequence. Thus, Hspa9 depletion causes a mitochondrial ISC deficit, altering IRP1-IRE binding and FeCH stability, which consequently inhibits Alas2 translation, heme synthesis, and erythroid differentiation, i.e.: Hspa9->ISC->IRP/IRE->Alas2->heme synthesis->erythroid differentiation. Thus Hspa9 regulates erythroid differentiation through ISC cluster assembly, providing a pathophysiological mechanism for an MDS subtype characterized by HSPA9 haploinsufficiency, and suggests hemin and other pharmacological stimulators of ISC synthesis as potential routes to therapy. PMID:26702583

  3. Ongoing assembly of massive galaxies by major merging in large groups and clusters from the SDSS

    NASA Astrophysics Data System (ADS)

    McIntosh, Daniel H.; Guo, Yicheng; Hertzberg, Jen; Katz, Neal; Mo, H. J.; van den Bosch, Frank C.; Yang, Xiaohu

    2008-08-01

    We investigate the incidence of major mergers creating massive (Mstar > 1011Msolar) galaxies in present-day (z <= 0.12) groups and clusters. Using a volume-limited sample of 845 groups with dark matter halo masses above 2.5 × 1013Msolar, we isolate 221 galaxy pairs with <=1.5r-band magnitude differences, <=30 kpc projected separations and combined masses above 1011Msolar. We fit the r-band images of each pair as the line-of-sight projection of symmetric models and identify 38 mergers by the presence of residual asymmetric structure associated with both progenitors, such as non-concentric isophotes, broad and diffuse tidal tails and dynamical friction wakes. In other words, at the resolution and sensitivity of the Sloan Digital Sky Survey (SDSS), 16 per cent of massive major pairs in dense environments have mutual tidal interaction signatures; relying on automated searches of major pairs from the SDSS spectroscopic galaxy sample will result in missing 70 per cent of these mergers owing to spectroscopic incompleteness in high-density regions. We find that 90 per cent of these mergers are between two nearly equal-mass progenitors with red-sequence colours and centrally concentrated morphologies, in agreement with numerical simulations that predict that an important mechanism for the formation of massive elliptical galaxies is the dissipationless (gas-poor or so-called dry) major merging of spheroid-dominated galaxies. We identify seven additional massive mergers with disturbed morphologies and semiresolved double nuclei; thus, 1.5 +/- 0.2 per cent of Mstar >= 5 × 1010Msolar galaxies in large groups are involved in the major merger assembly of massive galaxies. Mergers at the centres of these groups are more common than between two satellites, but both types are morphologically indistinguishable and we tentatively conclude that the latter are likely located at the dynamical centres of large subhaloes that have recently been accreted by their host halo. Based on

  4. How chain plasmons govern the optical response in strongly interacting self-assembled metallic clusters of nanoparticles.

    PubMed

    Esteban, Ruben; Taylor, Richard W; Baumberg, Jeremy J; Aizpurua, Javier

    2012-06-19

    Self-assembled clusters of metallic nanoparticles separated by nanometric gaps generate strong plasmonic modes that support both intense and localized near fields. These find use in many ultrasensitive chemical and biological sensing applications through surface enhanced Raman scattering (SERS). The inability to control at the nanoscale the structure of the clusters on which the optical response crucially depends, has led to the development of general descriptions to model the various morphologies fabricated. Here, we use rigorous electrodynamic calculations to study clusters formed by a hundred nanospheres that are separated by ∼1 nm distance, set by the dimensions of the macrocyclic molecular linker employed experimentally. Three-dimensional (3D) cluster structures of moderate compactness are of special interest since they resemble self-assembled clusters grown under typical diffusion-limited aggregation conditions. We find very good agreement between the simulated and measured far-field extinction spectra, supporting the equivalence of the assumed and experimental morphologies. From these results we argue that the main features of the optical response of two- and three-dimensional clusters can be understood in terms of the excitation of simple units composed of different length resonant chains. Notably, we observe a qualitative difference between short- and long-chain modes in both spectral response and spatial distribution: dimer and short-chain modes are observed in the periphery of the cluster at higher energies, whereas inside the structure longer chain excitation occurs at lower energies. We study in detail different configurations of isolated one-dimensional chains as prototypical building blocks for large clusters, showing that the optical response of the chains is robust to disorder. This study provides an intuitive understanding of the behavior of very complex aggregates and may be generalized to other types of aggregates and systems formed by large

  5. New Family of Octagonal-Prismatic Lanthanide Coordination Cages Assembled from Unique Ln17 Clusters and Simple Cliplike Dicarboxylate Ligands.

    PubMed

    Zhou, Yuan-Yuan; Geng, Bing; Zhang, Zhen-Wei; Guan, Qun; Lu, Jun-Ling; Bo, Qi-Bing

    2016-03-01

    Novel high-nuclearity lanthanide clusters (Ln17) are generated in situ in the coordination-driven self-assembly. A metal-cluster-directed symmetry strategy for building metal coordination cages is successfully applied to a lanthanide system for the first time. A new family of octagonal-prismatic lanthanide coordination cages UJN-Ln, formulated as [Ln(μ3-OH)8][Ln16(μ4-O)(μ4-OH)(μ3-OH)8(H2O)8(μ4-dcd)8][(μ3-dcd)8]·22H2O (Ln = Gd, Tb, Dy, Ho, and Er; dcd = 3,3-dimethylcyclopropane-1,2-dicarboxylate dianion), have been assembled from the unique Ln17 clusters and simple cliplike ligand H2dcd. Apart from featuring aesthetically charming structures, all of the compounds present predominantly antiferromagnetic coupling between the corresponding lanthanide ions. Additionally, the intense-green photoluminescence for UJN-Tb and magnetic relaxation behavior for UJN-Dy have been observed. Remarkably, UJN-Gd shows a large magnetocaloric effect (MCE) with an impressive entropy change value of 42.3 J kg(-1) K(-1) for ΔH = 7.0 T at 2.0 K due to the high-nuclearity cluster and the lightweight ligand. The studies highlight the structural diversity of multigonal-prismatic metal coordination cages and provide a new direction in the design of cagelike multifunctional materials by the introduction of lanthanide clusters and other suitable cliplike ligands. PMID:26894272

  6. Distinct Roles of the Salmonella enterica Serovar Typhimurium CyaY and YggX Proteins in the Biosynthesis and Repair of Iron-Sulfur Clusters

    PubMed Central

    Velayudhan, Jyoti; Karlinsey, Joyce E.; Frawley, Elaine R.; Becker, Lynne A.; Nartea, Margaret

    2014-01-01

    Labile [4Fe-4S]2+ clusters found at the active sites of many dehydratases are susceptible to damage by univalent oxidants that convert the clusters to an inactive [3Fe-4S]1+ form. Bacteria repair damaged clusters in a process that does not require de novo protein synthesis or the Isc and Suf cluster assembly pathways. The current study investigates the participation of the bacterial frataxin ortholog CyaY and the YggX protein, which are proposed to play roles in iron trafficking and iron-sulfur cluster repair. Previous reports found that individual mutations in cyaY or yggX were not associated with phenotypic changes in Escherichia coli and Salmonella enterica serovar Typhimurium, suggesting that CyaY and YggX might have functionally redundant roles. However, we have found that individual mutations in cyaY or yggX confer enhanced susceptibility to hydrogen peroxide in Salmonella enterica serovar Typhimurium. In addition, inactivation of the stm3944 open reading frame, which is located immediately upstream of cyaY and which encodes a putative inner membrane protein, dramatically enhances the hydrogen peroxide sensitivity of a cyaY mutant. Overexpression of STM3944 reduces the elevated intracellular free iron levels observed in an S. Typhimurium fur mutant and also reduces the total cellular iron content under conditions of iron overload, suggesting that the stm3944-encoded protein may mediate iron efflux. Mutations in cyaY and yggX have different effects on the activities of the iron-sulfur cluster-containing aconitase, serine deaminase, and NADH dehydrogenase I enzymes of S. Typhimurium under basal conditions or following recovery from oxidative stress. In addition, cyaY and yggX mutations have additive effects on 6-phosphogluconate dehydratase-dependent growth during nitrosative stress, and a cyaY mutation reduces Salmonella virulence in mice. Collectively, these results indicate that CyaY and YggX play distinct supporting roles in iron-sulfur cluster biosynthesis

  7. Witnessing the Hierarchical Assembly of the Brightest Cluster Galaxy in a Cluster at z=1.26

    NASA Astrophysics Data System (ADS)

    Yamada, Toru; Koyama, Yohei; Nakata, Fumiaki; Kajisawa, Masaru; Tanaka, Ichi; Kodama, Tadayuki; Okamura, Sadanori; De Propris, Roberto

    2002-10-01

    We have obtained a new high-resolution K'-band image of the central region of the rich X-ray cluster RX J0848.9+4452 at z=1.26. We found that the brightest cluster galaxy (BCG) in the cluster is clearly separated into two distinct objects. Whereas the optical to near-infrared colors of the objects are consistent with the predictions of passive evolution models for galaxies formed at high redshift, the luminosities of the two galaxies are both considerably fainter than predicted by passive evolution of BCGs in low- and intermediate-redshift clusters. We argue that this is evidence of an ongoing merger of normal cluster elliptical galaxies to form the dominant galaxy in the core of RX J0848.9+4452. The two galaxies appear to point toward the nearby cluster ClG J0848+4453 and are aligned with the outer X-ray contour of their parent cluster, supporting a model of BCG formation by collimated infall along the surrounding large-scale structure.

  8. Magnetism, structures and stabilities of cluster assembled TM@Si nanotubes (TM = Cr, Mn and Fe): a density functional study.

    PubMed

    Dhaka, Kapil; Bandyopadhyay, Debashis

    2016-08-01

    The present study reports transition metal (TM = Cr, Mn and Fe) doped silicon nanotubes with tunable band structures and magnetic properties by careful selection of cluster assemblies as building blocks using the first-principles density functional theory. We found that the transition metal doping and in addition, the hydrogen termination process can stabilize the pure silicon nanoclusters or cluster assemblies and then it could be extended as magnetic nanotubes with finite magnetic moments. Study of the band structures and density of states (DOS) of different empty and TM doped nanotubes (Type 1 to Type 4) show that these nanotubes are useful as metals, semiconductors, semi-metals and half-metals. These designer magnetic materials could be useful in spintronics and magnetic devices of nanoscale order. PMID:27430742

  9. The cluster-assembled nanowires based on M12N12 (M = Al and Ga) clusters as potential gas sensors for CO, NO, and NO2 detection.

    PubMed

    Yong, Yongliang; Jiang, Huai; Li, Xiaohong; Lv, Shijie; Cao, Jingxiao

    2016-08-01

    The advances in cluster-assembled materials where clusters serve as building blocks have opened new opportunities to develop ever more sensitive gas sensors. Here, using density functional theory calculations, the structural and electronic properties of cluster-assembled nanowires based on M12N12 (M = Al and Ga) clusters and their application as gas sensors have been investigated. Our results show that the nanowires can be produced via the coalescence of stable M12N12 fullerene-like clusters. The M12N12-based nanowires have semiconducting electrical properties with direct energy gaps, and are particularly stable at room temperature for long enough to allow for their characterization and applications. Furthermore, we found that the CO, NO, and NO2 molecules are chemisorbed on the M12N12-based nanowires with reasonable adsorption energies and apparent charge transfer. The electronic properties of the M12N12-based nanowires present dramatic changes after the adsorption of the CO, NO, and NO2 molecules, especially their electric conductivity. However, the adsorption of NO2 on the Al12N12-based nanowire is too strong, indicating an impractical recovery time as NO2 sensors. In addition to this, due to reasonable adsorption energies, apparent charge transfer, change in the electric conductivity, and the short recovery time, the Al12N12-based nanowire should be a good CO and NO sensor with quick response as well as short recovery time, while the Ga12N12-based nanowire should be a promising gas sensor for CO, NO, and NO2 detection. PMID:27424739

  10. Slow formation of [3Fe-4S](1+) clusters in mutant forms of Desulfovibrio africanus ferredoxin III.

    PubMed

    Hannan, J P; Busch, J L; James, R; Thomson, A J; Moore, G R; Davy, S L

    2000-02-25

    Desulfovibrio africanus ferredoxin III (Da FdIII) readily interconverts between a 7Fe and an 8Fe form with Asp-14 believed to provide a cluster ligand in the latter form. To investigate the factors important for cluster interconversion in Fe/S cluster-containing proteins we have studied two variants of Da FdIII produced by site-directed mutagenesis, Asp14Glu and Asp14His, with cluster incorporation performed in vitro. Characterisation of these proteins by UV/visible, EPR and (1)H NMR spectroscopies revealed that the formation of the stable 7Fe form of these proteins takes some time to occur. Evidence is presented which indicates the [4Fe-4S](2+) cluster is incorporated prior to the [3Fe-4S](1+) cluster. PMID:10692579

  11. Diblock-copolymer-mediated self-assembly of protein-stabilized iron oxide nanoparticle clusters for magnetic resonance imaging.

    PubMed

    Tähkä, Sari; Laiho, Ari; Kostiainen, Mauri A

    2014-03-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) can be used as efficient transverse relaxivity (T2 ) contrast agents in magnetic resonance imaging (MRI). Organizing small (D<10 nm) SPIONs into large assemblies can considerably enhance their relaxivity. However, this assembly process is difficult to control and can easily result in unwanted aggregation and precipitation, which might further lead to lower contrast agent performance. Herein, we present highly stable protein-polymer double-stabilized SPIONs for improving contrast in MRI. We used a cationic-neutral double hydrophilic poly(N-methyl-2-vinyl pyridinium iodide-block-poly(ethylene oxide) diblock copolymer (P2QVP-b-PEO) to mediate the self-assembly of protein-cage-encapsulated iron oxide (γ-Fe2 O3 ) nanoparticles (magnetoferritin) into stable PEO-coated clusters. This approach relies on electrostatic interactions between the cationic N-methyl-2-vinylpyridinium iodide block and magnetoferritin protein cage surface (pI≈4.5) to form a dense core, whereas the neutral ethylene oxide block provides a stabilizing biocompatible shell. Formation of the complexes was studied in aqueous solvent medium with dynamic light scattering (DLS) and cryogenic transmission electron microcopy (cryo-TEM). DLS results indicated that the hydrodynamic diameter (Dh ) of the clusters is approximately 200 nm, and cryo-TEM showed that the clusters have an anisotropic stringlike morphology. MRI studies showed that in the clusters the longitudinal relaxivity (r1 ) is decreased and the transverse relaxivity (r2 ) is increased relative to free magnetoferritin (MF), thus indicating that clusters can provide considerable contrast enhancement. PMID:24523066

  12. Assembly history of subhalo populations in galactic and cluster sized dark haloes

    NASA Astrophysics Data System (ADS)

    Xie, Lizhi; Gao, Liang

    2015-12-01

    We make use of two suits of ultrahigh resolution N-body simulations of individual dark matter haloes from the Phoenix and the Aquarius Projects to investigate systematics of assembly history of subhaloes in dark matter haloes differing by a factor of 1000 in the halo mass. We have found that real progenitors which built up present-day subhalo population are relatively more abundant for high-mass haloes, in contrast to previous studies claiming a universal form independent of the host halo mass. That is mainly because of repeated counting of the `re-accreted' (progenitors passed through and were later re-accreted to the host more than once) and inclusion of the `ejected' progenitor population (progenitors were accreted to the host in the past but no longer members at present day) in previous studies. The typical accretion time for all progenitors vary strongly with the host halo mass, which is typical about z ˜ 5 for the galactic Aquarius and about z ˜ 3 for the cluster sized Phoenix haloes. Once these progenitors start to orbit their parent haloes, they rapidly lose their original mass but not their identifiers, more than 55 (50) per cent of them survive to present day for the Phoenix (Aquarius) haloes. At given redshift, survival fraction of the accreted subhalo is independent of the parent halo mass, whilst the mass-loss of the subhalo is more efficient in high-mass haloes. These systematics results in similarity and difference in the subhalo population in dark matter haloes of different masses at present day.

  13. Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001).

    PubMed

    Pandey, Puran; Sui, Mao; Li, Ming-Yu; Zhang, Quanzhen; Kim, Eun-Soo; Lee, Jihoon

    2015-01-01

    Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots. PMID:26285135

  14. Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001)

    PubMed Central

    Pandey, Puran; Sui, Mao; Li, Ming-Yu; Zhang, Quanzhen; Kim, Eun-Soo; Lee, Jihoon

    2015-01-01

    Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots. PMID:26285135

  15. Assembling Fe/S-clusters and modifying tRNAs: ancient co-factors meet ancient adaptors.

    PubMed

    Alfonzo, Juan D; Lukeš, Julius

    2011-06-01

    Trypanosoma brucei undergoes two clearly distinct develomental stages: in the insect vector (procyclic stage) the cells generate the bulk of their energy through respiration, whereas in the bloodstream of the mammalian host (bloodstream stage) they grow mostly glycolytically. Several mitochondrial respiratory proteins require iron-sulfur clusters for activity, and their activation coincides with developmental changes. Likewise some tRNA modification enzymes either require iron-sulfur clusters or use components of the iron-sulfur cluster assembly pathway for activity. These enzymes affect the anticodon loop of various tRNAs and can impact protein synthesis. Herein, the possibility of these pathways being integrated and exploited by T. brucei to carefully coordinate energy demands to translational rates in response to enviromental changes is examined. PMID:21419700

  16. Assembling Fe/S-clusters and modifying tRNAs: ancient co-factors meet ancient adaptors

    PubMed Central

    Alfonzo, Juan D.; Lukeš, Julius

    2011-01-01

    Trypanosoma brucei undergoes two clearly distinct develomental stages: in the insect vector (procyclic stage) the cells generate the bulk of their energy through respiration, while in the bloodstream of the mammalian host (bloodstream stage) they grow mostly glycolytically. Several mitochondrial respiratory proteins require iron-sulfur clusters for activity, and their activation coincides with developmental changes. Likewise some tRNA modification enzymes either require iron-sulfur clusters or use components of the iron-sulfur cluster assembly pathway for activity. These enzymes affect the anticodon loop of various tRNAs and may impact protein synthesis. Herein, the possibility of these pathways being integrated and exploited by T. brucei to carefully coordinate energy demands to translational rates in response to enviromental changes is examined. PMID:21419700

  17. Dark matter and the assembly history of massive galaxies and clusters

    NASA Astrophysics Data System (ADS)

    Newman, Andrew B.

    In Part I of this thesis we study the distribution of dark matter and baryons in a sample of seven massive, relaxed galaxy clusters by combining multiple observational tools. Our aim is to make comprehensive mass profile measurements and compare these to the form of the universal density profile derived in numerical cold dark matter (CDM) simulations. By joining weak and strong gravitational lensing observations with resolved stellar kinematic data within the central brightest cluster galaxy (BCG), we constrain the density profile over the wide dynamic range of 3-3000 kpc in radius for the first time. We first compare lensing- and X-ray-derived mass measures to constrain the line-of-sight geometry of the clusters in our sample. We then show that the logarithmic slope of the total density profile -- comprising both stars and dark matter -- agrees closely with numerical simulations containing only dark matter down to radii of ˜ 7 kpc, despite the significant contribution of stellar material on such small scales. Our unique stellar kinematic data allow us to constrain two-component models of the stellar and dark matter distributions in the cluster cores. We find a mean logarithmic slope for the dark matter density of beta = 0.50 +/- 0.10 (random) +0.14, -0.13 (systematic) at small radii, where rho DM ˜ r-beta. This is significantly shallower than a canonical CDM cusp having beta = 1. Alternatively, a cored dark matter profile with log rcore / kpc = 1.14 +/- 0.13 (random) +0.14,-0.22 (systematic) provides an equally good description. The mean mass-to-light ratio of the stars in the BCGs, derived from lensing and dynamics, is found to be consistent with estimates from stellar population synthesis modeling provided that a Salpeter initial mass function (IMF), or one with a similarly high mass-to-light ratio, is adopted. We find some evidence for a correlation between the inner dark matter profile and the size or luminosity of the BCG, which suggests a connection

  18. Oxidative dehydrogenation of cyclohexene on size selected subnanometer cobalt clusters: improved catalytic performance via evolution of cluster-assembled nanostructures.

    PubMed

    Lee, Sungsik; Di Vece, Marcel; Lee, Byeongdu; Seifert, Sönke; Winans, Randall E; Vajda, Stefan

    2012-07-14

    The catalytic activity of oxide-supported metal nanoclusters strongly depends on their size and support. In this study, the origin of morphology transformation and chemical state changes during the oxidative dehydrogenation of cyclohexene was investigated in terms of metal-support interactions. Model catalyst systems were prepared by deposition of size selected subnanometer Co(27±4) clusters on various metal oxide supports (Al(2)O(3), ZnO and TiO(2) and MgO). The oxidation state and reactivity of the supported cobalt clusters were investigated by temperature programmed reaction (TPRx) and in situ grazing incidence X-ray absorption (GIXAS) during oxidative dehydrogenation of cyclohexene, while the sintering resistance monitored with grazing incidence small angle X-ray scattering (GISAXS). The activity and selectivity of cobalt clusters shows strong dependence on the support. GIXAS reveals that metal-support interaction plays a key role in the reaction. The most pronounced support effect is observed for MgO, where during the course of the reaction in its activity, composition and size dynamically evolving nanoassembly is formed from subnanometer cobalt clusters. PMID:22419008

  19. Clustering and Mobility of HIV-1 Env at Viral Assembly Sites Predict Its Propensity To Induce Cell-Cell Fusion

    PubMed Central

    Roy, Nathan H.; Chan, Jany; Lambelé, Marie

    2013-01-01

    HIV-1 Env mediates virus attachment to and fusion with target cell membranes, and yet, while Env is still situated at the plasma membrane of the producer cell and before its incorporation into newly formed particles, Env already interacts with the viral receptor CD4 on target cells, thus enabling the formation of transient cell contacts that facilitate the transmission of viral particles. During this first encounter with the receptor, Env must not induce membrane fusion, as this would prevent the producer cell and the target cell from separating upon virus transmission, but how Env's fusion activity is controlled remains unclear. To gain a better understanding of the Env regulation that precedes viral transmission, we examined the nanoscale organization of Env at the surface of producer cells. Utilizing superresolution microscopy (stochastic optical reconstruction microscopy [STORM]) and fluorescence recovery after photobleaching (FRAP), we quantitatively assessed the clustering and dynamics of Env upon its arrival at the plasma membrane. We found that Gag assembly induced the aggregation of small Env clusters into larger domains and that these domains were completely immobile. Truncation of the cytoplasmic tail (CT) of Env abrogated Gag's ability to induce Env clustering and restored Env mobility at assembly sites, both of which correlated with increased Env-induced fusion of infected and uninfected cells. Hence, while Env trapping by Gag secures Env incorporation into viral particles, Env clustering and its sequestration at assembly sites likely also leads to the repression of its fusion function, and thus, by preventing the formation of syncytia, Gag helps to secure efficient transfer of viral particles to target cells. PMID:23637402

  20. Inclusion of Cu nano-cluster 1D arrays inside a C3-symmetric artificial oligopeptide via co-assembly

    NASA Astrophysics Data System (ADS)

    Gong, Ruiying; Li, Fei; Yang, Chunpeng; Wan, Xiaobo

    2015-12-01

    supplementary information (ESI) available: Detailed synthesis, gel preparation, general methods for characterization, and the characterisation of BTA-C3-GVGVOMe assembly including or not including Cu nano-cluster arrays. See DOI: 10.1039/c5nr06095h

  1. Self-assembly of Fe 3 O 4 nanocrystal-clusters into cauliflower-like architectures: Synthesis and characterization

    NASA Astrophysics Data System (ADS)

    Zhu, Lu-Ping; Liao, Gui-Hong; Bing, Nai-Ci; Wang, Lin-Lin; Xie, Hong-Yong

    2011-09-01

    Large-scale cauliflower-like Fe 3O 4 architectures consist of well-assembled magnetite nanocrystal clusters have been synthesized by a simple solvothermal process. The as-synthesized Fe 3O 4 samples were characterized by XRD, XPS, FT-IR, SEM, TEM, etc. The results show that the samples exhibit cauliflower-like hierarchical microstructures. The influences of synthesis parameters on the morphology of the samples were experimentally investigated. Magnetic properties of the Fe 3O 4 cauliflower-like hierarchical microstructures have been detected by VSM at room temperature, showing a relatively low saturation magnetization of 65 emu/g and an enhanced coercive force of 247 Oe.

  2. Near-Infrared Emitters: Stepwise Assembly of Two Heteropolynuclear Clusters with Tunable Ag(I):Zn(II) Ratio.

    PubMed

    Wang, Zhi; Zhuang, Gui-Lin; Deng, Yong-Kai; Feng, Zhen-Yu; Cao, Zhao-Zhen; Kurmoo, Mohamedally; Tung, Chen-Ho; Sun, Di

    2016-05-16

    Two 3d-4d heteropolynuclear clusters with Ag-Zn ratios of 9:2 and 9:4 were stepwise constructed from a robust nonanuclear silver cluster. Their crystal structures consist of a common bucket-shaped [Ag9(mba)9](9-) (H2mba = 2-mercaptobenzoic acid) core with different numbers of Zn(II) connected by different exo-oriented carboxylates. Most fascinating is the observation of emission (∼703 nm) in the near-infrared (NIR) region at 300 K that may be compared to the related Ag9Zn3 cluster with aliphatic polyamine as auxiliary ligand that emits from the visible (∼580 nm). The shift is associated with the change of ligand field of the 2,2'-bipyridine. The emission intensity and lifetime were dramatically enhanced along with the slight bathochromic shift upon cooling from 300 K to 80 K. The results raise two significant issues: (a) the structural and electronic effects of the secondary metal binding to the metalloligand and the factors influencing the heteropolynuclear cluster assembly and (b) the use of NIR fluorescence, introduced by integrating two luminophores into one heteropolynuclear entity, in detecting free-moving zinc in biological systems both in vivo and in vitro. PMID:27110839

  3. Globular Clusters, Dwarf Galaxies, and the Assembly of the M87 Halo

    NASA Astrophysics Data System (ADS)

    Peng, Eric W.; Zhang, Hong-Xin; Liu, Chengze; Liu, Yiqing

    2016-08-01

    At the center of the nearest galaxy cluster, the Virgo cluster, lies the massive cD galaxy, M87 (NGC 4486). Using data from the Next Generation Virgo Cluster Survey, we investigate the relationship between M87, its globular clusters (GCs), and satellite dwarf galaxies. We find that the kinematics of GCs and ultra-compact dwarfs (UCDs) are different, indicating that UCDs are not simply massive GCs. We also identify a morphological sequence of envelope fraction around UCDs correlated with cluster-centric distance that suggest UCDs are the result of tidal stripping. Lastly, we find that the [α/Fe] abundance ratios of low-mass early-type galaxies in Virgo exhibit a strong negative gradient within ~ 400 kpc of M87, where the galaxies closest to M87 have the highest values. These satellite galaxies are likely the surviving counterparts of accreted dwarfs that contribute stars to the metal-poor, α-rich stellar halos of massive galaxies. Together, these results describe a dense environment that has had a strong and continuing impact on the evolution of its low-mass neighbors.

  4. Accurate determination of the magnetic anisotropy in cluster-assembled nanostructures

    NASA Astrophysics Data System (ADS)

    Tamion, Alexandre; Hillenkamp, Matthias; Tournus, Florent; Bonet, Edgar; Dupuis, Véronique

    2009-08-01

    The simultaneous triple adjustment of experimental magnetization curves under different conditions is shown to allow the unambiguous and consistent determination of both the magnetic particle size distribution and anisotropy for granular nanostructures of Co clusters embedded in protective matrices. The importance of interface effects resulting in magnetically dead layers is demonstrated.

  5. Polymer Grafted Nanoparticle Assemblies: From Optical to Mechanical Performance through Clusters, Monolayers and Monoliths

    NASA Astrophysics Data System (ADS)

    Vaia, Richard

    Solution or melt-based fabrication of large area, matrix-free, ordered assemblies of polymer grafted nanoparticles (PGN) will enable additive manufacturing of novel membrane, electronic, and photonic elements. Due to the single component nature of these hybrids, aggregation and phase separation common in blended polymer nanocomposites are avoided. Architecturally, PGNs combine characteristics of colloids, brushes and high molecular weight polymers. Thus the processing-structure-property relationship of the entangled PGN assembly is unique from analogous condensed nano-structures, such as ligand stabilized nanoparticles, hard-sphere colloids, star macromolecules and linear chain - nanoparticle blends. Here in, we will discuss the intermediate character of PGNs with respect to deformability, physical aging, and rapid fabrication of stable, large-area, ordered PGN monolayers. For example, processing via flow coating follows that of classic colloids; however local structure and order within the PGN assembly is determined by the canopy architecture and substrate interactions. From this insight, large-area (cm2), highly-ordered, monolayer polystyrene-Au nanoparticle films that are resistant to de-wetting can be fabricated on substrates with high interface energy (80 mN/m) within seconds using flow-coating and a volatile solvent (THF). Overall these findings imply intriguing parallels between PGN assemblies and other mesoscale ordered polymeric systems including hard-soft block copolymers and semi-crystalline polymers. With the appropriate corona architecture, PGNs afford opportunities to design high inorganic fraction hybrids that retain processibility and enable the creation of films and fibers for next generation optoelectronic applications. Aknowledgement: Justin Che, Christopher A. Grabowski, Yang Jiao, Ming-Siao Hsiao, Kyoungweon Park, Lawrence Drummy.

  6. Diverse Tp*-Capped W-Cu-S Clusters from One-Pot Assembly Involving in Situ Thiolation of Phosphines.

    PubMed

    Zhao, Xin; Zhou, Feng; Liu, Quan; Chen, Qiu-Fang; Yang, Jun-Yi; Zhang, Wen-Hua; Song, Ying-Lin; Lang, Jian-Ping

    2016-02-15

    In the absence/presence of S8, the one-pot assembly of [Et4N][Tp*WS3] [1; Tp* = hydridotris(3,5-dimethylpyrazol-1-yl)borate] with [Cu(MeCN)4]PF6 and bis- or tetraphosphine ligands 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,4-bis(diphenylphosphino)butane (dppb), and N,N,N',N'-tetrakis(diphenylphosphinomethyl)ethylenediamine (dppeda) produces six W-Cu-S clusters, namely, [(Tp*WS3Cu2Cl)2(dppe)] (2), [Tp*WS3Cu4(dppp)2(μ4-Cl)(μ-Cl)]PF6·MeCN (3·MeCN), [(Tp*WS3Cu3)2(μ4-Cl)(μ-Cl)2(dpppS2)] (4), [(Tp*WS3Cu2Cl)2(dppbS2)]·2MeCN·2H2O (5·2MeCN·2H2O), [(Tp*WS3Cu3Cl2)2(dppbS2)] (6), and [(Tp*WS3Cu3)2(Ph2PS2)3(μ6-Cl)0.5](PF6)0.5·0.75CH2Cl2 (7·0.75CH2Cl2). Compounds 2-7 are characterized by elemental analysis, IR, UV-vis, (1)H and (31)P{(1)H} NMR, electrospray ionization mass spectrometry, and X-ray crystallography. For 2, the dppe ligand bridges a pair of butterfly-shaped [Tp*WS3Cu2] cores to form a double-butterfly-shaped structure. For 4, the dppp ligand is susceptible toward S association and forms an in situ generated dpppS2 ligand, supporting an octanuclear double-half-open-cubane structure and contrasting an analogous system wherein a pentanuclear motorcycle-shaped cationic cluster 3 is formed with the absence of S8. A longer dppb ligand readily converts to S-based ligands in 5 and 6, subsequently serving as bridges between a pair of a butterfly-shaped (5) and nest-shaped (6) clusters. Further use of a tetraphosphine ligand, dppeda, in the cluster formation, with the presence of S8, leads to an unexpected ligand degradation to give the [Ph2PS2](-) anions. Three [Ph2PS2](-) anions juxtapose a pair of nest-shaped cluster cores to yield an octanuclear cluster, 7, featuring a cage to encapsulate μ6-Cl(-). The third-order nonlinear-optical (NLO) properties of 2-7 in N,N-dimethylformamide, investigated using a Z-scan technique at 532 nm, show that 2-6 have a reverse saturable absorption, while 7 has a notable saturable

  7. Pores of the toxin FraC assemble into 2D hexagonal clusters in both crystal structures and model membranes.

    PubMed

    Mechaly, Ariel E; Bellomio, Augusto; Morante, Koldo; Agirre, Jon; Gil-Cartón, David; Valle, Mikel; González-Mañas, Juan Manuel; Guérin, Diego M A

    2012-11-01

    The recent high-resolution structure of the toxin FraC derived from the sea anemone Actinia fragacea has provided new insight into the mechanism of pore formation by actinoporins. In this work, we report two new crystal forms of FraC in its oligomeric prepore conformation. Together with the previously reported structure, these two new structures reveal that ring-like nonamers of the toxin assemble into compact two-dimensional hexagonal arrays. This supramolecular organization is maintained in different relative orientations adopted by the oligomers within the crystal layers. Analyses of the aggregation of FraC pores in both planar and curved (vesicles) model membranes show similar 2D hexagonal arrangements. Our observations support a model in which hexagonal pore-packing is a clustering mechanism that maximizes toxin-driven membrane damage in the target cell. PMID:22728830

  8. A flexible toolbox to study protein-assisted metalloenzyme assembly in vitro.

    PubMed

    Schiffels, Johannes; Selmer, Thorsten

    2015-11-01

    strong indications for the presence of a putative [4Fe-4S]-cluster, which is unique among this class of maturases. Results are discussed in the context of [NiFe]-hydrogenase maturation, and in light of the capacity of the novel toolbox. PMID:25994231

  9. 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.

  10. Experimental and theoretical photoluminescence studies in nucleic acid assembled gold-upconverting nanoparticle clusters

    NASA Astrophysics Data System (ADS)

    He, Liangcan; Mao, Chenchen; Cho, Suehyun; Ma, Ke; Xi, Weixian; Bowman, Christopher N.; Park, Wounjhang; Cha, Jennifer N.

    2015-10-01

    Combinations of rare earth doped upconverting nanoparticles (UCNPs) and gold nanostructures are sought as nanoscale theranostics due to their ability to convert near infrared (NIR) photons into visible light and heat, respectively. However, because the large NIR absorption cross-section of the gold coupled with their thermo-optical properties can significantly hamper the photoluminescence of UCNPs, methods to optimize the ratio of gold nanostructures to UCNPs must be developed and studied. We demonstrate here nucleic acid assembly methods to conjugate spherical gold nanoparticles (AuNPs) and gold nanostars (AuNSs) to silica-coated UCNPs and probe the effect on photoluminescence. These studies showed that while UCNP fluorescence enhancement was observed from the AuNPs conjugated UCNPs, AuNSs tended to quench fluorescence. However, conjugating lower ratios of AuNSs to UCNPs led to reduced quenching. Simulation studies both confirmed the experimental results and demonstrated that the orientation and distance of the UCNP with respect to the core and arms of the gold nanostructures played a significant role in PL. In addition, the AuNS-UCNP assemblies were able to cause rapid gains in temperature of the surrounding medium enabling their potential use as a photoimaging-photodynamic-photothermal agent.Combinations of rare earth doped upconverting nanoparticles (UCNPs) and gold nanostructures are sought as nanoscale theranostics due to their ability to convert near infrared (NIR) photons into visible light and heat, respectively. However, because the large NIR absorption cross-section of the gold coupled with their thermo-optical properties can significantly hamper the photoluminescence of UCNPs, methods to optimize the ratio of gold nanostructures to UCNPs must be developed and studied. We demonstrate here nucleic acid assembly methods to conjugate spherical gold nanoparticles (AuNPs) and gold nanostars (AuNSs) to silica-coated UCNPs and probe the effect on

  11. Self-Assembled Colloidal Particle Clusters from In Situ Pickering-Like Emulsion Polymerization via Single Electron Transfer Mechanism.

    PubMed

    Yuan, Jinfeng; Zhao, Weiting; Pan, Mingwang; Zhu, Lei

    2016-08-01

    A simple route is reported to synthesize colloidal particle clusters (CPCs) from self-assembly of in situ poly(vinylidene fluoride)/poly(styrene-co-tert-butyl acrylate) [PVDF/P(St-co-tBA)] Janus particles through one-pot seeded emulsion single electron transfer radical polymerization. In the in situ Pickering-like emulsion polymerization, the tBA/St/PVDF feed ratio and polymerization temperature are important for the formation of well-defined CPCs. When the tBA/St/PVDF feed ratio is 0.75 g/2.5 g/0.5 g and the reaction temperature is 35 °C, relatively uniform raspberry-like CPCs are obtained. The hydrophobicity of the P(St-co-tBA) domains and the affinity of PVDF to the aqueous environment are considered to be the driving force for the self-assembly of the in situ formed PVDF/P(St-co-tBA) Janus particles. The resultant raspberry-like CPCs with PVDF particles protruding outward may be promising for superhydrophobic smart coatings. PMID:27226331

  12. Hierarchical multiple bit clusters and patterned media enabled by novel nanofabrication techniques -- High resolution electron beam lithography and block polymer self assembly

    NASA Astrophysics Data System (ADS)

    Xiao, Qijun

    This thesis discusses the full scope of a project exploring the physics of hierarchical clusters of interacting nanomagnets. These clusters may be relevant for novel applications such as multilevel data storage devices. The work can be grouped into three main activities: micromagnetic simulation, fabrication and characterization of proof-of-concept prototype devices, and efforts to scale down the structures by creating the hierarchical structures with the aid of diblock copolymer self assembly. Theoretical micromagnetic studies and simulations based on Landau-Lifshitz-Gilbert (LLG) equation were conducted on nanoscale single domain magnetic entities. For the simulated nanomagnet clusters with perpendicular uniaxial anisotropy, the simulation showed the switching field distributions, the stability of the magnetostatic states with distinctive total cluster perpendicular moments, and the stepwise magnetic switching curves. For simulated nanomagnet clusters with in-plane shape anisotropy, the simulation showed the stepwise switching behaviors governed by thermal agitation and cluster configurations. Proof-of-concept cluster devices with three interacting Co nanomagnets were fabricated by e-beam lithography (EBL) and pulse-reverse electrochemical deposition (PRECD). EBL patterning on a suspended 100 nm SiN membrane showed improved lateral lithography resolution to 30 nm. The Co nanomagnets deposited using the PRECD method showed perpendicular anisotropy. The switching experiments with external applied fields were able to switch the Co nanomagnets through the four magnetostatic states with distinctive total perpendicular cluster magnetization, and proved the feasibility of multilevel data storage devices based on the cluster concept. Shrinking the structures size was experimented by the aid of diblock copolymer. Thick poly(styrene)-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer templates aligned with external electrical field were used to fabricate long Ni

  13. MET18 Connects the Cytosolic Iron-Sulfur Cluster Assembly Pathway to Active DNA Demethylation in Arabidopsis

    PubMed Central

    Tang, Kai; Zhang, Huiming; Mangrauthia, Satendra K.; Lei, Mingguang; Hsu, Chuan-Chih; Hou, Yueh-Ju; Wang, Chunguo; Li, Yan; Tao, W. Andy; Zhu, Jian-Kang

    2015-01-01

    DNA demethylation mediated by the DNA glycosylase ROS1 helps determine genomic DNA methylation patterns and protects active genes from being silenced. However, little is known about the mechanism of regulation of ROS1 enzymatic activity. Using a forward genetic screen, we identified an anti-silencing (ASI) factor, ASI3, the dysfunction of which causes transgene promoter hyper-methylation and silencing. Map-based cloning identified ASI3 as MET18, a component of the cytosolic iron-sulfur cluster assembly (CIA) pathway. Mutation in MET18 leads to hyper-methylation at thousands of genomic loci, the majority of which overlap with hypermethylated loci identified in ros1 and ros1dml2dml3 mutants. Affinity purification followed by mass spectrometry indicated that ROS1 physically associates with MET18 and other CIA components. Yeast two-hybrid and split luciferase assays showed that ROS1 can directly interact with MET18 and another CIA component, AE7. Site-directed mutagenesis of ROS1 indicated that the conserved iron-sulfur motif is indispensable for ROS1 enzymatic activity. Our results suggest that ROS1-mediated active DNA demethylation requires MET18-dependent transfer of the iron-sulfur cluster, highlighting an important role of the CIA pathway in epigenetic regulation. PMID:26492035

  14. MET18 Connects the Cytosolic Iron-Sulfur Cluster Assembly Pathway to Active DNA Demethylation in Arabidopsis.

    PubMed

    Duan, Cheng-Guo; Wang, Xingang; Tang, Kai; Zhang, Huiming; Mangrauthia, Satendra K; Lei, Mingguang; Hsu, Chuan-Chih; Hou, Yueh-Ju; Wang, Chunguo; Li, Yan; Tao, W Andy; Zhu, Jian-Kang

    2015-10-01

    DNA demethylation mediated by the DNA glycosylase ROS1 helps determine genomic DNA methylation patterns and protects active genes from being silenced. However, little is known about the mechanism of regulation of ROS1 enzymatic activity. Using a forward genetic screen, we identified an anti-silencing (ASI) factor, ASI3, the dysfunction of which causes transgene promoter hyper-methylation and silencing. Map-based cloning identified ASI3 as MET18, a component of the cytosolic iron-sulfur cluster assembly (CIA) pathway. Mutation in MET18 leads to hyper-methylation at thousands of genomic loci, the majority of which overlap with hypermethylated loci identified in ros1 and ros1dml2dml3 mutants. Affinity purification followed by mass spectrometry indicated that ROS1 physically associates with MET18 and other CIA components. Yeast two-hybrid and split luciferase assays showed that ROS1 can directly interact with MET18 and another CIA component, AE7. Site-directed mutagenesis of ROS1 indicated that the conserved iron-sulfur motif is indispensable for ROS1 enzymatic activity. Our results suggest that ROS1-mediated active DNA demethylation requires MET18-dependent transfer of the iron-sulfur cluster, highlighting an important role of the CIA pathway in epigenetic regulation. PMID:26492035

  15. Syntheses and characterization of two novel tetranuclear lead(II) clusters self-assembled by hydrogen bonded interactions

    PubMed Central

    2014-01-01

    Background The usage of polynuclear metal clusters as secondary building units (SBU’s) in designing of metal organic frameworks (MOF’s) is a field of current interest. These metal clusters have attracted a great deal of attention not only due to their interesting structural topologies but also due to promising physical and chemical properties. In this regard various d,f block (transition and lanthanide) metal clusters have been widely investigated so far. Less attention is paid to construction of heavy p-block Pb(II) clusters. Results Two mixed ligand Pb(II) clusters have been synthesized with bipy(2,2’-Bipyridine), phen(1,10-Phenanthroline), quin (8-Hydroxy quinolinate) and 5-tpc (5-chloro thiophene 2-carboxylate). They have been characterized by elemental analysis, IR, TGA and X-ray crystallography. X-ray diffraction analysis reveals that the complexes [Pb4(quin)4(bipy)2(5-tpc)4] (1) and [Pb4(quin) 4(phen) 2(5-tpc)4] (2) are tetranuclear. The complexes show a slight variation in unit cell parameters, due to the replacement of bipy and the phen ligands. Both complexes contain two types of Pb(II) ions which differ in the coordination geometry around the Pb(II) ion. Conclusions In both complexes the four lead ions Pb1,Pb2, Pb1i and Pb2i lie on the same plane bridged by the 5-tpc anions. Pb1 and Pb2 of both complexes contain a 5-tpc and quin coordinated in a bidentate chelating bridging fashion. In addition the Pb2 and Pb2i ions alone contain a bipy and phen in a bidentate chelating fashion in (1) and (2) respectively. An additional notable feature in both of these complexes are the bridging ability of the quin oxygen which forms a network of coordination bonds in between the four Pb(II) ions. In both complexes the individual units are self-assembled by C-H---Cl/C-H---S hydrogen bonding interactions to generate 2-D aggregates. PMID:24987455

  16. Experimental and theoretical photoluminescence studies in nucleic acid assembled gold-upconverting nanoparticle clusters.

    PubMed

    He, Liangcan; Mao, Chenchen; Cho, Suehyun; Ma, Ke; Xi, Weixian; Bowman, Christopher N; Park, Wounjhang; Cha, Jennifer N

    2015-11-01

    Combinations of rare earth doped upconverting nanoparticles (UCNPs) and gold nanostructures are sought as nanoscale theranostics due to their ability to convert near infrared (NIR) photons into visible light and heat, respectively. However, because the large NIR absorption cross-section of the gold coupled with their thermo-optical properties can significantly hamper the photoluminescence of UCNPs, methods to optimize the ratio of gold nanostructures to UCNPs must be developed and studied. We demonstrate here nucleic acid assembly methods to conjugate spherical gold nanoparticles (AuNPs) and gold nanostars (AuNSs) to silica-coated UCNPs and probe the effect on photoluminescence. These studies showed that while UCNP fluorescence enhancement was observed from the AuNPs conjugated UCNPs, AuNSs tended to quench fluorescence. However, conjugating lower ratios of AuNSs to UCNPs led to reduced quenching. Simulation studies both confirmed the experimental results and demonstrated that the orientation and distance of the UCNP with respect to the core and arms of the gold nanostructures played a significant role in PL. In addition, the AuNS-UCNP assemblies were able to cause rapid gains in temperature of the surrounding medium enabling their potential use as a photoimaging-photodynamic-photothermal agent. PMID:26427014

  17. Lamellipodin promotes actin assembly by clustering Ena/VASP proteins and tethering them to actin filaments

    PubMed Central

    Hansen, Scott D; Mullins, R Dyche

    2015-01-01

    Enabled/Vasodilator (Ena/VASP) proteins promote actin filament assembly at multiple locations, including: leading edge membranes, focal adhesions, and the surface of intracellular pathogens. One important Ena/VASP regulator is the mig-10/Lamellipodin/RIAM family of adaptors that promote lamellipod formation in fibroblasts and drive neurite outgrowth and axon guidance in neurons. To better understand how MRL proteins promote actin network formation we studied the interactions between Lamellipodin (Lpd), actin, and VASP, both in vivo and in vitro. We find that Lpd binds directly to actin filaments and that this interaction regulates its subcellular localization and enhances its effect on VASP polymerase activity. We propose that Lpd delivers Ena/VASP proteins to growing barbed ends and increases their polymerase activity by tethering them to filaments. This interaction represents one more pathway by which growing actin filaments produce positive feedback to control localization and activity of proteins that regulate their assembly. DOI: http://dx.doi.org/10.7554/eLife.06585.001 PMID:26295568

  18. The Cytosolic Iron-Sulfur Cluster Assembly Protein MMS19 Regulates Transcriptional Gene Silencing, DNA Repair, and Flowering Time in Arabidopsis.

    PubMed

    Han, Yong-Feng; Huang, Huan-Wei; Li, Lin; Cai, Tao; Chen, She; He, Xin-Jian

    2015-01-01

    MMS19 is an essential component of the cytoplasmic iron-sulfur (Fe-S) cluster assembly complex in fungi and mammals; the mms19 null mutant alleles are lethal. Our study demonstrates that MMS19/MET18 in Arabidopsis thaliana interacts with the cytoplasmic Fe-S cluster assembly complex but is not an essential component of the complex. We find that MMS19 also interacts with the catalytic subunits of DNA polymerases, which have been demonstrated to be involved in transcriptional gene silencing (TGS), DNA repair, and flowering time regulation. Our results indicate that MMS19 has a similar biological function, suggesting a functional link between MMS19 and DNA polymerases. In the mms19 null mutant, the assembly of Fe-S clusters on the catalytic subunit of DNA polymerase α is reduced but not blocked, which is consistent with the viability of the mutant. Our study suggests that MMS19 assists the assembly of Fe-S clusters on DNA polymerases in the cytosol, thereby facilitating transcriptional gene silencing, DNA repair, and flowering time control. PMID:26053632

  19. Functionalized SPIONs: the surfactant nature modulates the self-assembly and cluster formation.

    PubMed

    Luchini, Alessandra; Heenan, Richard K; Paduano, Luigi; Vitiello, Giuseppe

    2016-07-21

    SuperParamagnetic Iron Oxide Nanoparticles (SPIONs) represent a suitable system for several applications especially in nanomedicine. Great efforts have been made to design stable and biocompatible functionalized SPIONs suitable for diagnostics and drug delivery. In particular, zwitterionic-surfactant functionalized SPIONs, obtained through a coating strategy based on hydrophobic interaction, are promising systems for biomedical applications. The size of functionalized SPIONs has emerged as a crucial parameter determining their fate in living organisms. However, not all the proposed functionalization strategies lead to monodispersed systems and SPION clustering often occurs. In this study, we report a systematic investigation on different surfactant-functionalized SPIONs in order to explore the possibility of tuning the particle size by choosing an appropriate amphiphilic molecule. By combining Small-Angle Neutron Scattering (SANS) and Dynamic Light Scattering (DLS) analysis, we have provided a detailed description of the functionalized SPION structure. Furthermore, we have also related the surfactant aggregation properties, i.e. the Critical Micelle Concentration (CMC), to their efficiency in coating the SPION surface. A lack in the formation of a compact shell leads to a clusters formation. On this basis, the present study contributes to furnishing decisive information to define synthetic strategies able to tune functionalized-SPION design. PMID:27338137

  20. General Assembly of Twisted Trigonal-Prismatic Nonanuclear Silver(I) Clusters.

    PubMed

    Li, Xiao-Yu; Su, Hai-Feng; Zhou, Rui-Qi; Feng, Sheng; Tan, Yuan-Zhi; Wang, Xing-Po; Jia, Jiong; Kurmoo, Mohamedally; Sun, Di; Zheng, Lan-Sun

    2016-02-24

    A general class of C3 -symmetric Ag9 clusters, [Ag9 S(tBuC6 H4 S)6 (dpph)3 (CF3 SO3 )] (1), [Ag9 (tBuC6 H4 S)6 (dpph)3 (CF3 SO3 )2 ]⋅CF3 SO3 (2), [Ag9 (tBuC6 H4 S)6 (dpph)3 (NO3 )2 ] ⋅NO3 (3), and [Ag9 (tBuC6 H4 S)7 (dpph)3 (Mo2 O7 )0.5 ]2 ⋅2 CF3 COO (4) (dpph=1,6-bis(diphenylphosphino)hexane), with a twisted trigonal-prism geometry was isolated by the reaction of polymeric {(HNEt3 )2 [Ag10 (tBuC6 H4 S)12 ]}n , 1,6-bis(diphenylphosphino)hexane, and various silver salts under solvothermal conditions. The structures consist of discrete clusters constructed from a girdling Ag9 twisted trigonal prism with the top and bottom trigonal faces capped by diverse anions (i.e., S(2-) and CF3 SO3 (-) for compound 1, 2×CF3 SO3 (-) for compound 2, 2×NO3 (-) for compound 3, and tBuC6 H4 S(-) and Mo2 O7 (2-) for compound 4). This trigonal prism is bisected by another shrunken Ag3 trigon at its waist position. Interestingly, two inversion-related Ag9 trigonal-prismatic clusters are dimerized by the Mo2 O7 (2-) ion in compound 4. The twist is amplified by the bulkier thiolate, which also introduces high steric-hindrance for the capping ligand, that is, the longer dpph ligand. Four more silver-sulfur clusters (namely, compounds 5-8) with their nuclearity ranging from 6-10 were solely characterized by single-crystal X-ray diffraction to verify the above-described synergetic effect of mixed ligands in the construction of Ag9 twisted trigonal prisms. Surprisingly, only cluster 1 emits yellow luminescence at λ=584 nm at room temperature, which may be attributed to a charge transfer from the S 3p orbital to the Ag 5s orbital, or mixed with metal-centered (MC) d(10) →d(9) s(1) transitions. Upon cooling from 300 to 80 K, the emission intensity was enhanced along with a hypsochromic shift. The good linear relationship between the maximum emission intensity and the temperature for compound 1 in the range of 180-300 K indicates that this is a promising molecular luminescent

  1. Mycobacterium tuberculosis WhiB1 is an essential DNA-binding protein with a nitric oxide-sensitive iron-sulfur cluster.

    PubMed

    Smith, Laura J; Stapleton, Melanie R; Fullstone, Gavin J M; Crack, Jason C; Thomson, Andrew J; Le Brun, Nick E; Hunt, Debbie M; Harvey, Evelyn; Adinolfi, Salvatore; Buxton, Roger S; Green, Jeffrey

    2010-12-15

    Mycobacterium tuberculosis is a major pathogen that has the ability to establish, and emerge from, a persistent state. Wbl family proteins are associated with developmental processes in actinomycetes, and M. tuberculosis has seven such proteins. In the present study it is shown that the M. tuberculosis H37Rv whiB1 gene is essential. The WhiB1 protein possesses a [4Fe-4S]2+ cluster that is stable in air but reacts rapidly with eight equivalents of nitric oxide to yield two dinuclear dinitrosyl-iron thiol complexes. The [4Fe-4S] form of WhiB1 did not bind whiB1 promoter DNA, but the reduced and oxidized apo-WhiB1, and nitric oxide-treated holo-WhiB1 did bind to DNA. Mycobacterium smegmatis RNA polymerase induced transcription of whiB1 in vitro; however, in the presence of apo-WhiB1, transcription was severely inhibited, irrespective of the presence or absence of the CRP (cAMP receptor protein) Rv3676, which is known to activate whiB1 expression. Footprinting suggested that autorepression of whiB1 is achieved by apo-WhiB1 binding at a region that overlaps the core promoter elements. A model incorporating regulation of whiB1 expression in response to nitric oxide and cAMP is discussed with implications for sensing two important signals in establishing M. tuberculosis infections. PMID:20929442

  2. Periodic fluorescent silver clusters assembled by rolling circle amplification and their sensor application.

    PubMed

    Ye, Tai; Chen, Jinyang; Liu, Yufei; Ji, Xinghu; Zhou, Guohua; He, Zhike

    2014-09-24

    A simple method for preparing DNA-stabilized Ag nanoclusters (NCs) nanowires is presented. To fabricate the Ag NCs nanowires, we use just two unmodified component strands and a long enzymatically produced scaffold. These nanowires form at room temperature and have periodic sequence units that are available for fluorescence Ag NCs assembled which formed three-way junction (TWJ) structure. These Ag NCs nanowires can be clearly visualized by confocal microscopy. Furthermore, due to the high efficiency of rolling circle amplification reaction in signal amplification, the nanowires exhibit high sensitivity for the specific DNA detection with a wide linear range from 6 to 300 pM and a low detection limit of 0.84 pM, which shows good performance in the complex serum samples. Therefore, these Ag NCs nanowires might have great potential in clinical and imaging applications in the future. PMID:25116051

  3. De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters.

    PubMed

    Chiara, Matteo; Horner, David S; Spada, Alberto

    2013-01-01

    De novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Indeed, closely related paralogous transcripts are often merged into single clusters by current approaches. Here, a novel heuristic method for locus-specific clustering is compared to that implemented in the de novo assembler Oases, using the same initial transcript collections, derived from Arabidopsis thaliana and the developmental model Streptocarpus rexii. We show that the proposed approach improves cluster specificity in the A. thaliana dataset for which the reference genome is available. Furthermore, for the S. rexii data our filtered transcript collection matches a larger number of distinct annotated loci in reference genomes than the Oases set, while containing a reduced overall number of loci. A detailed discussion of advantages and limitations of our approach in processing de novo transcriptome reconstructions is presented. The proposed method should be widely applicable to other organisms, irrespective of the transcript assembly method employed. The S. rexii transcriptome is available as a sophisticated and augmented publicly available online database. PMID:24324652

  4. De Novo Assembly of the Transcriptome of the Non-Model Plant Streptocarpus rexii Employing a Novel Heuristic to Recover Locus-Specific Transcript Clusters

    PubMed Central

    Chiara, Matteo; Horner, David S.; Spada, Alberto

    2013-01-01

    De novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Indeed, closely related paralogous transcripts are often merged into single clusters by current approaches. Here, a novel heuristic method for locus-specific clustering is compared to that implemented in the de novo assembler Oases, using the same initial transcript collections, derived from Arabidopsis thaliana and the developmental model Streptocarpus rexii. We show that the proposed approach improves cluster specificity in the A. thaliana dataset for which the reference genome is available. Furthermore, for the S. rexii data our filtered transcript collection matches a larger number of distinct annotated loci in reference genomes than the Oases set, while containing a reduced overall number of loci. A detailed discussion of advantages and limitations of our approach in processing de novo transcriptome reconstructions is presented. The proposed method should be widely applicable to other organisms, irrespective of the transcript assembly method employed. The S. rexii transcriptome is available as a sophisticated and augmented publicly available online database. PMID:24324652

  5. Cluster-Expanded Solids: A Strategy for Assembling Functional Porous Materials

    SciTech Connect

    Long, Jeffrey R.

    2008-10-31

    This grant provided (partial) support for the research efforts of three graduate students and two undergraduate students. The intention of the program was to explore the use of molecular precursors in generating functional porous materials with precisely tailored structures and properties. Prior work in our laboratory had demonstrated the feasibility of employing face-capped octahedral clusters of the type [Re{sub 6}Q{sub 8}(CN){sub 6}]{sup 3-/4-} (Q = S, Se, Te) in the expansion of known metal-cyanide frameworks. For example, the use of [Re{sub 6}Se{sub 8}(CN){sub 6}]{sup 4-} as a reactant in place of [Fe(CN){sub 6}]{sup 4-} resulted in formation of Fe{sub 4}[Re{sub 6}Se{sub 8}(CN){sub 6}]{sub 3}·36H{sub 2}O, featuring an expanded form of the porous three-dimensional framework of Prussian blue (Fe{sub 4}[Fe(CN){sub 6}]{sub 3}·14H{sub 2}O). This compound could be dehydrated without loss of integrity, and the increase in void volume significantly enhances its capacity as a molecular sieve, enabling absorption of larger molecules. For this project, we continued with our efforts to devise new routes to microporous coordination solids that function as molecular sieves, sensors, or catalysts. In particular, our focus was on: (i) the synthesis of new molecular precursors of specific utility for such purposes, and (ii) attempts to incorporate these and existing molecular precursors into new coordination solids. Investigations of the terminal ligand substitution chemistry of the carbon-centered, trigonal prismatic cluster [W{sub 6}CCl{sub 18}]{sup 2-} generated the solvated species [W{sub 6}CCl{sub 12}(DMF){sub 6}]{sup 2+} and [W{sub 6}CCl{sub 12}(py){sub 6}]{sup 2+}, as well as the potential framework building units [W{sub 6}C(CN){sub 18}]{sup 3-}, [W6CCl{sub 12}(pyrazine){sub 6}]{sup 2+}, [W6CCl{sub 12}(4-cyanopyridine){sub 6}]{sup 2+}, and [W{sub 6}CCl{sub 12}(4,4ʹ′-bipyridine){sub 6}]{sup 2+}. Efforts to produce microporous magnets capable of performing magnetic

  6. Tenascin-R promotes assembly of the extracellular matrix of perineuronal nets via clustering of aggrecan

    PubMed Central

    Morawski, Markus; Dityatev, Alexander; Hartlage-Rübsamen, Maike; Blosa, Maren; Holzer, Max; Flach, Katharina; Pavlica, Sanja; Dityateva, Galina; Grosche, Jens; Brückner, Gert; Schachner, Melitta

    2014-01-01

    Perineuronal nets (PNs) in the brains of tenascin-R-deficient (tn-r−/−) mice develop in temporal concordance with those of wild-type (tn-r+/+) mice. However, the histological appearance of PNs is abnormal in adult tn-r−/− mice. Here, we investigated whether similar defects are also seen in dissociated and organotypic cultures from hippocampus and forebrain of tn-r−/− mice and whether the structure of PNs could be normalized. In tn-r−/− cultures, accumulations of several extracellular matrix molecules were mostly associated with somata, whereas dendrites were sparsely covered, compared with tn-r+/+ mice. Experiments to normalize the structure of PNs in tn-r−/− organotypic slice cultures by depolarization of neurons, or by co-culturing tn-r+/+ and tn-r−/− brain slices failed to restore a normal PN phenotype. However, formation of dendritic PNs in cultures was improved by the application of tenascin-R protein and rescued by polyclonal antibodies to aggrecan and a bivalent, but not monovalent form of the lectin Wisteria floribunda agglutinin. These results show that tenascin-R and aggrecan are decisive contributors to formation and stabilization of PNs and that tenascin-R may implement these functions by clustering of aggrecan. Proposed approaches for restoration of normal PN structure are noteworthy in the context of PN abnormalities in neurological disorders, such as epilepsy, schizophrenia and addiction. PMID:25225104

  7. Formation and Attachment of the Deoxysugar Moiety and Assembly of the Gene Cluster for Caprazamycin Biosynthesis▿ †

    PubMed Central

    Kaysser, Leonard; Wemakor, Emmanuel; Siebenberg, Stefanie; Salas, Jose A.; Sohng, Jae Kyung; Kammerer, Bernd; Gust, Bertolt

    2010-01-01

    Caprazamycins are antimycobacterials produced by Streptomyces sp. MK730-62F2. Previously, cosmid cpzLK09 was shown to direct the biosynthesis of caprazamycin aglycones, but not of intact caprazamycins. Sequence analysis of cpzLK09 identified 23 genes involved in the formation of the caprazamycin aglycones and the transfer and methylation of the sugar moiety, together with genes for resistance, transport, and regulation. In this study, coexpression of cpzLK09 in Streptomyces coelicolor M512 with pRHAM, containing all the required genes for dTDP-l-rhamnose biosynthesis, led to the production of intact caprazamycins. In vitro studies showed that Cpz31 is responsible for the attachment of the l-rhamnose to the caprazamycin aglycones, generating a rare acylated deoxyhexose. An l-rhamnose gene cluster was identified elsewhere on the Streptomyces sp. MK730-62F2 genome, and its involvement in caprazamycin formation was demonstrated by insertional inactivation of cpzDIII. The l-rhamnose subcluster was assembled with cpzLK09 using Red/ET-mediated recombination. Heterologous expression of the resulting cosmid, cpzEW07, led to the production of caprazamycins, demonstrating that both sets of genes are required for caprazamycin biosynthesis. Knockouts of cpzDI and cpzDV in the l-rhamnose subcluster confirmed that four genes, cpzDII, cpzDIII, cpzDIV, and cpzDVI, are sufficient for the biosynthesis of the deoxysugar moiety. The presented recombineering strategy may provide a useful tool for the assembly of biosynthetic building blocks for heterologous production of microbial compounds. PMID:20418426

  8. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    DOE PAGESBeta

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, whichmore » is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.« less

  9. Phosphatidylinositol 4,5-Bisphosphate Clusters the Cell Adhesion Molecule CD44 and Assembles a Specific CD44-Ezrin Heterocomplex, as Revealed by Small Angle Neutron Scattering*

    PubMed Central

    Chen, Xiaodong; Khajeh, Jahan Ali; Ju, Jeong Ho; Gupta, Yogesh K.; Stanley, Christopher B.; Do, Changwoo; Heller, William T.; Aggarwal, Aneel K.; Callaway, David J. E.; Bu, Zimei

    2015-01-01

    The cell adhesion molecule CD44 regulates diverse cellular functions, including cell-cell and cell-matrix interaction, cell motility, migration, differentiation, and growth. In cells, CD44 co-localizes with the membrane-cytoskeleton adapter protein Ezrin that links the CD44 assembled receptor signaling complexes to the cytoskeletal actin network, which organizes the spatial and temporal localization of signaling events. Here we report that the cytoplasmic tail of CD44 (CD44ct) is largely disordered. Upon binding to the signaling lipid phosphatidylinositol 4,5-bisphosphate (PIP2), CD44ct clusters into aggregates. Further, contrary to the generally accepted model, CD44ct does not bind directly to the FERM domain of Ezrin or to the full-length Ezrin but only forms a complex with FERM or with the full-length Ezrin in the presence of PIP2. Using contrast variation small angle neutron scattering, we show that PIP2 mediates the assembly of a specific heterotetramer complex of CD44ct with Ezrin. This study reveals the role of PIP2 in clustering CD44 and in assembling multimeric CD44-Ezrin complexes. We hypothesize that polyvalent electrostatic interactions are responsible for the assembly of CD44 clusters and the multimeric PIP2-CD44-Ezrin complexes. PMID:25572402

  10. Multimolecular Analysis of Stable Immunological Synapses Reveals Sustained Recruitment and Sequential Assembly of Signaling Clusters*

    PubMed Central

    Philipsen, Lars; Engels, Thomas; Schilling, Kerstin; Gurbiel, Slavyana; Fischer, Klaus-Dieter; Tedford, Kerry; Schraven, Burkhart; Gunzer, Matthias; Reichardt, Peter

    2013-01-01

    The formation of the immunological synapse between T cells and antigen-presenting cells (APC) begins within minutes of contact and can take hours for full T-cell activation. Although early phases of the synapse have been extensively studied for a select number of proteins, later phases have not yet been examined in detail. We studied the signaling network in stable synapses by measuring the simultaneous localization of 25 signaling and structural molecules over 2 h at the level of individual synapses using multi-epitope ligand cartography (MELC). Signaling proteins including phospho(p)ZAP70, pSLP76, pCD3ζ, and pLAT, along with proteins that influence synapse structure such as F-actin, tubulin, CD45, and ICAM-1, were localized in images of synapses and revealed the multidimensional construction of a mature synapse. The construction of the stable synapse included intense early TCR signaling, a phase of recruitment of structural proteins, and a sustained increase in signaling molecules and colocalization of TCR and pLAT signaling clusters in the center of the synapse. Consolidation of TCR and associated proteins resulted in formation of a small number of discrete synaptic microclusters. Development of synapses and cSMAC composition was greatly affected by the absence of Vav1, with an associated loss in PLCγ1 recruitment, pSLP76, and increased CXCR4. Together, these data demonstrate the use of multi-epitope ligand cartography to quantitatively analyze synapse formation and reveal successive recruitment of structural and signaling proteins and sustained phosphorylation at the mature synapse. PMID:23754785

  11. Compact Stellar Binary Assembly in the First Nuclear Star Clusters and r-process Synthesis in the Early Universe

    NASA Astrophysics Data System (ADS)

    Ramirez-Ruiz, Enrico; Trenti, Michele; MacLeod, Morgan; Roberts, Luke F.; Lee, William H.; Saladino-Rosas, Martha I.

    2015-04-01

    Investigations of elemental abundances in the ancient and most metal deficient stars are extremely important because they serve as tests of variable nucleosynthesis pathways and can provide critical inferences of the type of stars that lived and died before them. The presence of r-process elements in a handful of carbon-enhanced metal-poor (CEMP-r) stars, which are assumed to be closely connected to the chemical yield from the first stars, is hard to reconcile with standard neutron star mergers. Here we show that the production rate of dynamically assembled compact binaries in high-z nuclear star clusters can attain a sufficient high value to be a potential viable source of heavy r-process material in CEMP-r stars. The predicted frequency of such events in the early Galaxy, much lower than the frequency of Type II supernovae but with significantly higher mass ejected per event, can naturally lead to a high level of scatter of Eu as observed in CEMP-r stars.

  12. Self-assembling of impurity clusters in AlN:(Ga, BV, CV), (BV, CV = P, As; P, Sb; As, Sb)

    NASA Astrophysics Data System (ADS)

    Elyukhin, V. A.

    2015-11-01

    The self-assembling conditions of arrays of tetrahedral impurity clusters of two types in zinc blende AlN:(Ga, BV, CV), (BV, CV = P, As; P, Sb; As, Sb) are represented. Doping with one cation and two anion isoelectronic impurities transforms AlN into AlN-rich GaxAl1-xBVyCVzN1-y-z alloy of GaBV, GaCV, GaN, AlBV, AlCV and AlN. The cause of self-assembling is the preference of GaBV, GaCV and AlN bonding over that of GaN, AlBV, AlCV. The conditions are considered from 0 °C to 1000 °C in the dilute and ultra dilute limits for the cation and anion impurities, correspondingly. The temperature ranges between the cluster occurrence and self-assembling completion when the same anion impurities are in clusters are very small. 1P4Ga and 1As4Ga cluster occurrence temperatures are equal, correspondingly, to 797 °C and 736 °C at Ga content 2% and P and As contents 0.01%. 1P4Ga and 1Sb4Ga cluster occurrence temperatures are equal, correspondingly, to 976 °C and 736 °C at the same impurity contents. The cluster densities in AlN:(Ga, As, Sb) are close to those in AlN:(Ga, P, Sb). The results demonstrate that studied semiconductors are promising materials to produce arrays of identical ∼1 nm low band gap objects of two types embedded in the wide band gap matrix.

  13. Tangled web of interactions among proteins involved in iron–sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies☆

    PubMed Central

    Kim, Jin Hae; Bothe, Jameson R.; Alderson, T. Reid; Markley, John L.

    2014-01-01

    Proteins containing iron–sulfur (Fe–S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe–S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins and small-angle X-ray scattering (SAXS), chemical crosslinking experiments, and functional assays, we have constructed working models for Fe–S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe–S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases. PMID:25450980

  14. The electronic structure of the H-cluster in the [FeFe]-hydrogenase from Desulfovibrio desulfuricans: a Q-band 57Fe-ENDOR and HYSCORE study.

    PubMed

    Silakov, Alexey; Reijerse, Eduard J; Albracht, Simon P J; Hatchikian, E Claude; Lubitz, Wolfgang

    2007-09-19

    The active site of the (57)Fe-enriched [FeFe]-hydrogenase (i.e., the "H-cluster") from Desulfovibrio desulfuricans has been examined using advanced pulse EPR methods at X- and Q-band frequencies. For both the active oxidized state (H(ox)) and the CO inhibited form (H(ox)-CO) all six (57)Fe hyperfine couplings were detected. The analysis shows that the apparent spin density extends over the whole H-cluster. The investigations revealed different hyperfine couplings of all six (57)Fe nuclei in the H-cluster of the H(ox)-CO state. Four large 57Fe hyperfine couplings in the range 20-40 MHz were found (using pulse ENDOR and TRIPLE methods) and were assigned to the [4Fe-4S](H) (cubane) subcluster. Two weak (57)Fe hyperfine couplings below 5 MHz were identified using Q-band HYSCORE spectroscopy and were assigned to the [2Fe](H) subcluster. For the H(ox) state only two different 57Fe hyperfine couplings in the range 10-13 MHz were detected using pulse ENDOR. An (57)Fe line broadening analysis of the X-band CW EPR spectrum indicated, however, that all six (57)Fe nuclei in the H-cluster are contributing to the hyperfine pattern. It is concluded that in both states the binuclear subcluster [2Fe](H) assumes a [Fe(I)Fe(II)] redox configuration where the paramagnetic Fe(I) atom is attached to the [4Fe-4S](H) subcluster. The (57)Fe hyperfine interactions of the formally diamagnetic [4Fe-4S](H) are due to an exchange interaction between the two subclusters as has been discussed earlier by Popescu and Münck [Popescu, C.V.; Münck, E., J. Am. Chem. Soc. 1999, 121, 7877-7884]. This exchange coupling is strongly enhanced by binding of the extrinsic CO ligand. Binding of the dihydrogen substrate may induce a similar effect, and it is therefore proposed that the observed modulation of the electronic structure by the changing ligand surrounding plays an important role in the catalytic mechanism of [FeFe]-hydrogenase. PMID:17722921

  15. Inter-cluster distance dependence of electrical conduction in nanocluster assembled films of silver: a new paradigm for design of nanostructures

    PubMed Central

    Bansal, Chandrahas; Praveen, S. G.; Kumaran, J. T. T.; Chatterjee, Ashok

    2015-01-01

    The transport properties of films assembled from metal nanoclusters can be significantly different from the metals in their bulk or thin film forms due to quantum confinement effects and several competing energy and length scales. For a film composed of metal nanoclusters as its building blocks, the cluster size and the inter-cluster separation are parameters that can be varied experimentally. Here we show that the electrical conductivity of a film composed of silver nanoclusters can be changed by 9 orders of magnitude as a function of the average inter-cluster separation while keeping the average cluster size same. For inter-cluster separations of 9 nanometres or more the conductivity is insulating type whereas for lesser inter-cluster separations the conductivity behaviour is metallic type with a positive temperature coefficient of resistance. In the intermediate range between the two regions, a very interesting temperature-independent conductivity is seen. Our work provides a new paradigm for design of artificial solid structures composed of nanoclusters. The properties of these nanostructures could be tuned by varying the inter-cluster distances to get the desired properties in the same material. PMID:25566690

  16. 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

    Pearce, Linda L; Martinez-Bosch, Sandra; Manzano, Elisenda Lopez; Winnica, Daniel E; Epperly, Michael W; Peterson, Jim

    2009-05-01

    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 approximately 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 1min 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, Nitrosative stress results in irreversible inhibition of purified mitochondrial complexes I and III without modification of cofactors, Nitric Oxide 13 (2005) 254-263) 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

  17. Triplet energy transfers in electrostatic host-guest assemblies of unsaturated organometallic cluster cations and carboxylate-containing porphyrin pigments.

    PubMed

    Aly, Shawkat M; Ayed, Charfedinne; Stern, Christine; Guilard, Roger; Abd-El-Aziz, Alaa S; Harvey, Pierre D

    2008-11-01

    The unsaturated cyclic [M3(dppm)3(CO)](2+) clusters (M = Pt, Pd; dppm = Ph2PCH2PPh2; such as PF6(-) salt) exhibit a cavity formed by the six dppm-phenyl groups placed like a picket fence above the unsaturated triangular M3 dicationic center. Electrostatic interactions of the M(3+) units inside this cavity with the carboxylate anion RCO2(-) [R = tetraphenylporphyrinatozinc(II), ZnTPP; p-phenyltritolylporphyrinatozinc(II), ZnTTPP; p-phenyltritolylporphyrinatopalladium(II), PdTTPP] form dyads for through-space triplet energy transfers. The binding constants are on the order of 20,000 M(-1) in all six cases (298 K). The energy diagram built upon absorption and emission spectra at 298 and 77 K places the [Pt3(dppm)3(CO)](2+) and [Pd3(dppm)3(CO)](2+) as triplet energy donors, respectively, with respect to the ZnTPPCO2(-), ZnTTPPCO2(-), and PdTTPPCO2(-) pigments, which act as acceptors. Evidence for energy transfer is provided by the transient absorption spectra at 298 K, where triplet-triplet absorption bands of the metalloporphyrin chromophores are depicted at all time (at 298 K) with total absence of the charge-separated state in the nanosecond to microsecond time scale. Rates for energy transfer (ranging in the 10(4) s(-1) time scale) are extracted from the emission lifetimes of the [Pt3(dppm)3(CO)](2+) donor in the free chromophore and the host-guest assemblies. The emission intensity of [Pd3(dppm)3(CO)](2+) is too weak to measure its spectrum and emission lifetime in the presence of the strongly luminescent metalloporphyrin-containing materials. For the [Pd3(dppm)3(CO)](2+)...metalloporphyrin dyads, evidence for fluorescence and phosphorescence lifetime quenching of the porphyrin chromophore at 298 K is provided. These quenchings, exhibiting rates of 10(4) (triplet) and 10(8) s(-1) (singlet), are attributed to a photoinduced electron transfer from the metalloporphyrin to the cluster due to the low reduction potential. PMID:18844340

  18. Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA.

    PubMed

    Miggiano, Riccardo; Perugino, Giuseppe; Ciaramella, Maria; Serpe, Mario; Rejman, Dominik; Páv, Ondřej; Pohl, Radek; Garavaglia, Silvia; Lahiri, Samarpita; Rizzi, Menico; Rossi, Franca

    2016-01-15

    Mycobacterium tuberculosis O(6)-methylguanine-DNA methyltransferase (MtOGT) contributes to protect the bacterial GC-rich genome against the pro-mutagenic potential of O(6)-methylated guanine in DNA. Several strains of M. tuberculosis found worldwide encode a point-mutated O(6)-methylguanine-DNA methyltransferase (OGT) variant (MtOGT-R37L), which displays an arginine-to-leucine substitution at position 37 of the poorly functionally characterized N-terminal domain of the protein. Although the impact of this mutation on the MtOGT activity has not yet been proved in vivo, we previously demonstrated that a recombinant MtOGT-R37L variant performs a suboptimal alkylated-DNA repair in vitro, suggesting a direct role for the Arg(37)-bearing region in catalysis. The crystal structure of MtOGT complexed with modified DNA solved in the present study reveals details of the protein-protein and protein-DNA interactions occurring during alkylated-DNA binding, and the protein capability also to host unmodified bases inside the active site, in a fully extrahelical conformation. Our data provide the first experimental picture at the atomic level of a possible mode of assembling three adjacent MtOGT monomers on the same monoalkylated dsDNA molecule, and disclose the conformational flexibility of discrete regions of MtOGT, including the Arg(37)-bearing random coil. This peculiar structural plasticity of MtOGT could be instrumental to proper protein clustering at damaged DNA sites, as well as to protein-DNA complexes disassembling on repair. PMID:26512127

  19. Response of Fe-S cluster assembly machinery of Escherichia coli to mechanical stress in a model of amino-acid crystal fermentation.

    PubMed

    Okutani, Satoshi; Iwai, Takayoshi; Iwatani, Shintaro; Matsuno, Kiyoshi; Takahashi, Yasuhiro; Hase, Toshiharu

    2015-09-01

    During amino-acid crystal fermentation, mechanical stress on bacterial cells caused by crystal collision often impacts negatively on bacterial growth and amino-acid production. When Escherichia coli cells were cultivated under mechanical stress of polyvinyl chloride particles as a model of the crystal fermentation, activities of iron-sulfur (Fe-S) cluster-containing enzymes were apparently decreased. Based on an assumption that function of Fe-S cluster assembly machinery would be elevated to recover the enzyme activities in such stressed cells, we analyzed levels of various components of Fe-S cluster assembly machinery by western blotting. It was found that the expression of HscA, a chaperon component of the machinery, was up-regulated and that shorter forms of HscA with the N-terminal region truncated were accumulated, suggesting an important role of HscA against the mechanical stress. An overexpression of HscA gene in E. coli cells gave a positive effect on rescue of the stress-induced decrease of the activity of Fe-S cluster-containing enzyme. These results may provide a new strategy to alleviate the mechanical stress during the amino-acid crystal fermentation. PMID:25682519

  20. Ferredoxin, in conjunction with NADPH and ferredoxin-NADP reductase, transfers electrons to the IscS/IscU complex to promote iron-sulfur cluster assembly.

    PubMed

    Yan, Robert; Adinolfi, Salvatore; Pastore, Annalisa

    2015-09-01

    Fe-S cluster biogenesis is an essential pathway coordinated by a network of protein-protein interactions whose functions include desulfurase activity, substrate delivery, electron transfer and product transfer. In an effort to understand the intricacies of the pathway, we have developed an in vitro assay to follow the ferredoxin role in electron transfer during Fe-S cluster assembly. Previously, assays have relied upon the non-physiological reducing agents dithionite and dithiothreitol to assess function. We have addressed this shortcoming by using electron transfer between NADPH and ferredoxin-NADP-reductase to reduce ferredoxin. Our results show that this trio of electron transfer partners are sufficient to sustain the reaction in in vitro studies, albeit with a rate slower compared with DTT-mediated cluster assembly. We also show that, despite overlapping with the CyaY protein in binding to IscS, Fdx does not interfere with the inhibitory activity of this protein. We suggest explanations for these observations which have important consequences for understanding the mechanism of cluster formation. Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. PMID:25688831

  1. THE METALLICITY BIMODALITY OF GLOBULAR CLUSTER SYSTEMS: A TEST OF GALAXY ASSEMBLY AND OF THE EVOLUTION OF THE GALAXY MASS-METALLICITY RELATION

    SciTech Connect

    Tonini, Chiara

    2013-01-01

    We build a theoretical model to study the origin of the globular cluster metallicity bimodality in the hierarchical galaxy assembly scenario. The model is based on empirical relations such as the galaxy mass-metallicity relation [O/H]-M {sub star} as a function of redshift, and on the observed galaxy stellar mass function up to redshift z {approx} 4. We make use of the theoretical merger rates as a function of mass and redshift from the Millennium simulation to build galaxy merger trees. We derive a new galaxy [Fe/H]-M {sub star} relation as a function of redshift, and by assuming that globular clusters share the metallicity of their original parent galaxy at the time of their formation, we populate the merger tree with globular clusters. We perform a series of Monte Carlo simulations of the galaxy hierarchical assembly, and study the properties of the final globular cluster population as a function of galaxy mass, assembly and star formation history, and under different assumptions for the evolution of the galaxy mass-metallicity relation. The main results and predictions of the model are the following. (1) The hierarchical clustering scenario naturally predicts a metallicity bimodality in the galaxy globular cluster population, where the metal-rich subpopulation is composed of globular clusters formed in the galaxy main progenitor around redshift z {approx} 2, and the metal-poor subpopulation is composed of clusters accreted from satellites, and formed at redshifts z {approx} 3-4. (2) The model reproduces the observed relations by Peng et al. for the metallicities of the metal-rich and metal-poor globular cluster subpopulations as a function of galaxy mass; the positions of the metal-poor and metal-rich peaks depend exclusively on the evolution of the galaxy mass-metallicity relation and the [O/Fe], both of which can be constrained by this method. In particular, we find that the galaxy [O/Fe] evolves linearly with redshift from a value of {approx}0.5 at redshift

  2. Bottom-Up Self-Assembly of the Sphere-Shaped Icosametallic Oxo Clusters {Cu20} and {Cu12Zn8}.

    PubMed

    Chen, Juan; Zhou, Hulan; Xu, Feng

    2016-05-16

    A discrete nanospheric icosametallic cluster comprised of 20 Cu ions (1) was self-assembled from facile synthesis. Adjustment of the synthesis by the choice of ligands gave rise to another cluster (2) with an intact icosacupric core and improved stability. Referring to the synthesis of 1 and 2, a heterometallic cluster (3), which contains 12 Cu(II) and 8 Zn(II), was designed and characterized by single-crystal X-ray diffraction, combined with elemental analysis, energy-dispersive X-ray, X-ray photoelectron spectroscopy, thermogravimetric analysis, and element mapping. The magnetic measurements of 2 and 3 and the scanning electron microscopy images and UV-visible diffuse-reflectance measurements of metal oxides from 2 and 3 indicate that isolation of {Cu12M8} is a new synthetic route to materials with engineered properties. PMID:27116596

  3. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    SciTech Connect

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.

  4. 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.

  5. 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

  6. Iron-sulfur cluster damage by the superoxide radical in neural tissues of the SOD1(G93A) ALS rat model.

    PubMed

    Popović-Bijelić, Ana; Mojović, Miloš; Stamenković, Stefan; Jovanović, Miloš; Selaković, Vesna; Andjus, Pavle; Bačić, Goran

    2016-07-01

    Extensive clinical investigations, in hand with biochemical and biophysical research, have associated brain iron accumulation with the pathogenesis of the amyotrophic lateral sclerosis (ALS) disease. The origin of iron is still not identified, but it is proposed that it forms redox active complexes that can participate in the Fenton reaction generating the toxic hydroxyl radical. In this paper, the state of iron in the neural tissues isolated from SOD1(G93A) transgenic rats was investigated using low temperature EPR spectroscopy and is compared with that of nontransgenic (NTg) littermates. The results showed that iron in neural tissues is present as high- and low-spin, heme and non-heme iron. It appears that the SOD1(G93A) rat neural tissues were most likely exposed in vivo to higher amounts of reactive oxygen species when compared to the corresponding NTg tissues, as they showed increased oxidized [3Fe-4S](1+) cluster content relative to [4Fe-4S](1+). Also, the activity of cytochrome c oxidase (CcO) was found to be reduced in these tissues, which may be associated with the observed uncoupling of heme a3 Fe and CuB in the O2-reduction site of the enzyme. Furthermore, the SOD1(G93A) rat spinal cords and brainstems contained more manganese, presumably from MnSOD, than those of NTg rats. The addition of potassium superoxide to all neural tissues ex vivo, led to the [4Fe-4S]→[3Fe-4S] cluster conversion and concurrent release of Fe. These results suggest that the superoxide anion may be the cause of the observed oxidative damage to SOD1(G93A) rat neural tissues and that the iron-sulfur clusters may be the source of poorly liganded redox active iron implicated in ALS pathogenesis. Low temperature EPR spectroscopy appears to be a valuable tool in assessing the role of metals in neurodegenerative diseases. PMID:27130034

  7. Self-assembled mesoporous Co and Ni-ferrite spherical clusters consisting of spinel nanocrystals prepared using a template-free approach.

    PubMed

    Yu, Byong Yong; Kwak, Seung-Yeop

    2011-10-21

    Based on a self-assembly strategy, spherical mesoporous cobalt and nickel ferrite nanocrystal clusters with a large surface area and narrow size distribution were successfully synthesized for the first time via a template-free solvothermal process in ethylene glycol and subsequent heat treatment. In this work, the mesopores in the ferrite clusters were derived mainly from interior voids between aggregated primary nanoparticles (with crystallite size of less than 7 nm) and disordered particle packing domains. The concentration of sodium acetate is shown herein to play a crucial role in the formation of mesoporous ferrite spherical clusters. These ferrite clusters were characterized in detail using wide-angle X-ray diffraction, thermogravimetric-differential thermal analysis, (57)Fe Mössbauer spectroscopy, X-ray photoelectron spectroscopy, field-emission scanning electron microscopy, standard and high-resolution transmission electron microscopy, and other techniques. The results confirmed the formation of both pure-phase ferrite clusters with highly crystalline spinel structure, uniform size (about 160 nm) and spherical morphology, and worm-like mesopore structures. The BET specific surface areas and mean pore sizes of the mesoporous Co and Ni-ferrite clusters were as high as 160 m(2) g(-1) and 182 m(2) g(-1), and 7.91 nm and 6.87 nm, respectively. A model for the formation of the spherical clusters in our system is proposed on the basis of the results. The magnetic properties of both samples were investigated at 300 K, and it was found that these materials are superparamagnetic. PMID:21904731

  8. Proteus mirabilis fimbriae- and urease-dependent clusters assemble in an extracellular niche to initiate bladder stone formation.

    PubMed

    Schaffer, Jessica N; Norsworthy, Allison N; Sun, Tung-Tien; Pearson, Melanie M

    2016-04-19

    The catheter-associated uropathogenProteus mirabilisfrequently causes urinary stones, but little has been known about the initial stages of bladder colonization and stone formation. We found thatP. mirabilisrapidly invades the bladder urothelium, but generally fails to establish an intracellular niche. Instead, it forms extracellular clusters in the bladder lumen, which form foci of mineral deposition consistent with development of urinary stones. These clusters elicit a robust neutrophil response, and we present evidence of neutrophil extracellular trap generation during experimental urinary tract infection. We identified two virulence factors required for cluster development: urease, which is required for urolithiasis, and mannose-resistantProteus-like fimbriae. The extracellular cluster formation byP. mirabilisstands in direct contrast to uropathogenicEscherichia coli, which readily formed intracellular bacterial communities but not luminal clusters or urinary stones. We propose that extracellular clusters are a key mechanism ofP. mirabilissurvival and virulence in the bladder. PMID:27044107

  9. Surface-induced assembly of apolipoprotein A-I: Implications for symmetry-driven non-cooperative clustering

    NASA Astrophysics Data System (ADS)

    Winford, Sidney; Tobin, Moriah; Gross, Eitan

    2012-03-01

    In condensed matter physics the geometry of a crystal is determined by the mechanism of condensation. In biology, the link between clustering mechanisms and the shape of a protein crystal is not well defined. To gain more insight into the problem, we studied clustering of apolipoprotein A-I (apo A-I) on a solid surface using AFM. The amyloidogenic protein apo A-I is the main protein component of high density lipoprotein and thus reduces the risk of atherosclerosis. We found that apo A-I clustered to form nano-scale, symmetrical clusters on mica. Statistical analysis of size distribution for several thousand clusters suggested that the clustering reaction followed a non-cooperative kinetic scheme characterized by a single equilibrium constant of 0.92·106 M-1 and a change in free energy (ΔG) of -0.03 kJ mole-1/residue. This is close to ΔG of-0.04 kJ mole-1/residue for apo A-I binding to phospholipid membrane; and 30-fold smaller than ΔG for β-amyloid formation by apo A-I. The high symmetry of the clusters is consistent with an isotropic diffusion coefficient of protein monomers on the surface of the substrate. This previously unrecognized link between protein clustering mechanism and the symmetry of the growth pattern may have important implications in medicine, pharmaceutics and polymer science.

  10. Multiple Metal-rich Sub-populations in Galaxies: the Star Formation/Assembly History of Galaxies Probed by Globular Clusters

    NASA Astrophysics Data System (ADS)

    Kissler-Patig, Markus

    Extragalactic globular clusters are used since a decade to probe the star formation and assembly history of nearby galaxies. In the early 90's, Zepf & Ashman (1993, MNRAS 264, 611) showed that several galaxies host at least two sub-populations of globular clusters. This fact was reinforced by subsequent studies (e. g. Gebhardt & Kissler-Patig 1999, AJ 118, 1526; Kundu 1999, PhD thesis), and many following studies dealt with the interpretation of the two main sub-populations (e. g. Kissler-Patig 2000, Reviews in Modern Astronomy, Vol. 13, p. 13 for a recent review) and their implications for galaxy formation scenarios. The nature of the metal-poor sub-populations is slowly understood as being a very uniform population in the nearby universe and most probably having formed in small fragments at the very beginning of galaxy formation and assembly. The nature of the metal-rich sub-populations is still hotly debated. It remains unclear whether its origin it mostly due to major mergers, whether it formed in situ during a monolithic bulge collapse, or whether it was accreted or cannibalized. The key to the answer lies in a more detailed analysis of the metal-rich sub-population. Is it itself composed by several sub-components? And can these sub-components tell us which mechanism dominated? First studies of extragalactic globular clusters in the optical and near-infrared show that the metal-rich sub-population might indeed be composed of several components. If confirmed, it would point to a significant contribution of hierarchical-like processes (accretion or mergers) to the metal-rich cluster and stellar component of galaxies.

  11. DNA mediated wire-like clusters of self-assembled TiO₂ nanomaterials: supercapacitor and dye sensitized solar cell applications.

    PubMed

    Nithiyanantham, U; Ramadoss, Ananthakumar; Ede, Sivasankara Rao; Kundu, Subrata

    2014-07-21

    A new route for the formation of wire-like clusters of TiO₂ nanomaterials self-assembled in DNA scaffold within an hour of reaction time is reported. TiO₂ nanomaterials are synthesized by the reaction of titanium-isopropoxide with ethanol and water in the presence of DNA under continuous stirring and heating at 60 °C. The individual size of the TiO₂ NPs self-assembled in DNA and the diameter of the wires can be tuned by controlling the DNA to Ti-salt molar ratios and other reaction parameters. The eventual diameter of the individual particles varies between 15 ± 5 nm ranges, whereas the length of the nanowires varies in the 2-3 μm range. The synthesized wire-like DNA-TiO₂ nanomaterials are excellent materials for electrochemical supercapacitor and DSSC applications. From the electrochemical supercapacitor experiment, it was found that the TiO₂ nanomaterials showed different specific capacitance (Cs) values for the various nanowires, and the order of Cs values are as follows: wire-like clusters (small size) > wire-like clusters (large size). The highest Cs of 2.69 F g(-1) was observed for TiO₂ having wire-like structure with small sizes. The study of the long term cycling stability of wire-like clusters (small size) electrode were shown to be stable, retaining ca. 80% of the initial specific capacitance, even after 5000 cycles. The potentiality of the DNA-TiO₂ nanomaterials was also tested in photo-voltaic applications and the observed efficiency was found higher in the case of wire-like TiO₂ nanostructures with larger sizes compared to smaller sizes. In future, the described method can be extended for the synthesis of other oxide based materials on DNA scaffold and can be further used in other applications like sensors, Li-ion battery materials or treatment for environmental waste water. PMID:24905088

  12. THE HERSCHEL FILAMENT: A SIGNATURE OF THE ENVIRONMENTAL DRIVERS OF GALAXY EVOLUTION DURING THE ASSEMBLY OF MASSIVE CLUSTERS AT z = 0.9

    SciTech Connect

    Coppin, K. E. K.; Geach, J. E.; Webb, T. M. A.; Faloon, A.; O'Donnell, D.; Yan, R.; Ouellette, N.; Egami, E.; Ellingson, E.; Gilbank, D.; Hicks, A.; Barrientos, L. F.; Yee, H. K. C.; Gladders, M.

    2012-04-20

    We have discovered a 2.5 Mpc (projected) long filament of infrared-bright galaxies connecting two of the three {approx}5 Multiplication-Sign 10{sup 14} M{sub Sun} clusters making up the RCS 2319+00 supercluster at z = 0.9. The filament is revealed in a deep Herschel Spectral and Photometric Imaging REceiver (SPIRE) map that shows 250-500 {mu}m emission associated with a spectroscopically identified filament of galaxies spanning two X-ray bright cluster cores. We estimate that the total (8-1000 {mu}m) infrared luminosity of the filament is L{sub IR} {approx_equal} 5 Multiplication-Sign 10{sup 12} L{sub Sun }, which, if due to star formation alone, corresponds to a total SFR {approx_equal} 900 M{sub Sun} yr{sup -1}. We are witnessing the scene of the buildup of a >10{sup 15} M{sub Sun} cluster of galaxies, seen prior to the merging of three massive components, each of which already contains a population of red, passive galaxies that formed at z > 2. The infrared filament demonstrates that significant stellar mass assembly is taking place in the moderate density, dynamically active circumcluster environments of the most massive clusters at high redshift, and this activity is concomitant with the hierarchical buildup of large-scale structure.

  13. Oxidative dehydrogenation of cyclohexene on size selected subnanometer cobalt clusters: improved catalytic performance via structural fluxionality of cluster-assembled nanostructures.

    SciTech Connect

    Lee, S.; Di Vece, M.; Lee, B.; Seifert, S.; Winans, R. E.; Vajda, S.

    2012-01-01

    The catalytic activity of oxide-supported metal nanoclusters strongly depends on their size and support. In this study, the origin of morphology transformation and chemical state changes during the oxidative dehydrogenation of cyclohexene was investigated in terms of metal-support interactions. Model catalyst systems were prepared by deposition of size selected subnanometer Co{sub 27{+-}4} clusters on various metal oxide supports (Al{sub 2}O{sub 3}, ZnO and TiO{sub 2} and MgO). The oxidation state and reactivity of the supported cobalt clusters were investigated by temperature programmed reaction (TPRx) and in situ grazing incidence X-ray absorption (GIXAS) during oxidative dehydrogenation of cyclohexene, while the sintering resistance monitored with grazing incidence small angle X-ray scattering (GISAXS). The activity and selectivity of cobalt clusters shows strong dependence on the support. GIXAS reveals that metal-support interaction plays a key role in the reaction. The most pronounced support effect is observed for MgO, where during the course of the reaction in its activity, composition and size dynamically evolving nanoassembly is formed from subnanometer cobalt clusters.

  14. [FeFe]-hydrogenase oxygen inactivation is initiated at the H cluster 2Fe subcluster.

    PubMed

    Swanson, Kevin D; Ratzloff, Michael W; Mulder, David W; Artz, Jacob H; Ghose, Shourjo; Hoffman, Andrew; White, Spencer; Zadvornyy, Oleg A; Broderick, Joan B; Bothner, Brian; King, Paul W; Peters, John W

    2015-02-11

    The [FeFe]-hydrogenase catalytic site H cluster is a complex iron sulfur cofactor that is sensitive to oxygen (O2). The O2 sensitivity is a significant barrier for production of hydrogen as an energy source in water-splitting, oxygenic systems. Oxygen reacts directly with the H cluster, which results in rapid enzyme inactivation and eventual degradation. To investigate the progression of O2-dependent [FeFe]-hydrogenase inactivation and the process of H cluster degradation, the highly O2-sensitive [FeFe]-hydrogenase HydA1 from the green algae Chlamydomonas reinhardtii was exposed to defined concentrations of O2 while monitoring the loss of activity and accompanying changes in H cluster spectroscopic properties. The results indicate that H cluster degradation proceeds through a series of reactions, the extent of which depend on the initial enzyme reduction/oxidation state. The degradation process begins with O2 interacting and reacting with the 2Fe subcluster, leading to degradation of the 2Fe subcluster and leaving an inactive [4Fe-4S] subcluster state. This final inactive degradation product could be reactivated in vitro by incubation with 2Fe subcluster maturation machinery, specifically HydF(EG), which was observed by recovery of enzyme activity. PMID:25579778

  15. Two Fe-S clusters catalyse sulfur insertion by Radical-SAM methylthiotransferases

    PubMed Central

    Forouhar, Farhad; Arragain, Simon; Atta, Mohamed; Gambarelli, Serge; Mouesca, Jean-Marie; Hussain, Munif; Xiao, Rong; Kieffer-Jaquinod, Sylvie; Seetharaman, Jayaraman; Acton, Thomas B.; Montelione, Gaetano T.

    2014-01-01

    How living organisms create carbon-sulfur bonds during biosynthesis of critical sulphur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a sub-group of Radical-SAM enzymes that bear two [4Fe-4S] clusters. One cluster binds S-Adenosylmethionine and generates an Ado• radical via a well- established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting Radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur co-substrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction. PMID:23542644

  16. A density functional study of silver clusters on a stepped graphite surface: formation of self-assembled nano-wires.

    PubMed

    Singh, Akansha; Sen, Prasenjit

    2015-05-21

    Adsorption and diffusion of silver adatoms and clusters containing up to eight atoms on an HOPG substrate with an armchair step are studied using density functional methods. Step edges act as attractive sinks for adatoms and clusters. The diffusion barrier of an Ag adatom along the step edge is much larger than that on a clean terrace. At zero temperature, Ag clusters either distort or dissociate by forming covalent bonds with the edge C atoms. At 600 K, Ag5 and Ag8 clusters diffuse to the step edges, and then break up so as to maximize Ag-C bonds. The Ag atoms try to form a nanowire structure along the step edge. At such high temperatures, diffusion of clusters along the step edge involves diffusion of individual Ag atoms not bonded to the edge C atoms. Assumption of complete immobility of clusters trapped at step edges in the Gates-Robins model is not valid at high temperatures in this particular system. PMID:25903308

  17. The role of Arabidopsis thaliana NAR1, a cytosolic iron-sulfur cluster assembly component, in gametophytic gene expression and oxidative stress responses in vegetative tissue.

    PubMed

    Nakamura, Miyuki; Buzas, Diana Mihaela; Kato, Akira; Fujita, Masahiro; Kurata, Nori; Kinoshita, Tetsu

    2013-09-01

    Iron-sulfur proteins have iron-sulfur clusters as a prosthetic group and are responsible for various cellular processes, including general transcriptional regulation, photosynthesis and respiration. The cytosolic iron-sulfur assembly (CIA) pathway of yeast has been shown to be responsible for regulation of iron-sulfur cluster assembly in both the cytosol and the nucleus. However, little is known about the roles of this pathway in multicellular organisms. In a forward genetic screen, we identified an Arabidopsis thaliana mutant with impaired expression of the endosperm-specific gene Flowering Wageningen (FWA). To characterize this mutant, we carried out detailed phenotypic and genetic analyses during reproductive and vegetative development. The mutation affects NAR1, which encodes a homolog of a yeast CIA pathway component. Comparison of embryo development in nar1-3 and other A. thaliana mutants affected in the CIA pathway showed that the embryos aborted at a similar stage, suggesting that this pathway potentially functions in early seed development. Transcriptome analysis of homozygous viable nar1-4 seedlings showed transcriptional repression of a subset of genes involved in 'iron ion transport' and 'response to nitrate'. nar1-4 also exhibited resistance to the herbicide paraquat. Our results indicate that A. thaliana NAR1 has various functions including transcriptional regulation in gametophytes and abiotic stress responses in vegetative tissues. PMID:23734982

  18. Structural Basis for Fe-S Cluster Assembly and tRNA Thiolation Mediated by IscS Protein-Protein Interactions

    SciTech Connect

    Shi, Rong; Proteau, Ariane; Villarroya, Magda; Moukadiri, Ismaïl; Zhang, Linhua; Trempe, Jean-François; Matte, Allan; Armengod, M Eugenia; Cygler, Miroslaw

    2010-05-04

    The cysteine desulfurase IscS is a highly conserved master enzyme initiating sulfur transfer via persulfide to a range of acceptor proteins involved in Fe-S cluster assembly, tRNA modifications, and sulfur-containing cofactor biosynthesis. Several IscS-interacting partners including IscU, a scaffold for Fe-S cluster assembly; TusA, the first member of a sulfur relay leading to sulfur incorporation into the wobble uridine of several tRNAs; ThiI, involved in tRNA modification and thiamine biosynthesis; and rhodanese RhdA are sulfur acceptors. Other proteins, such as CyaY/frataxin and IscX, also bind to IscS, but their functional roles are not directly related to sulfur transfer. We have determined the crystal structures of IscS-IscU and IscS-TusA complexes providing the first insight into their different modes of binding and the mechanism of sulfur transfer. Exhaustive mutational analysis of the IscS surface allowed us to map the binding sites of various partner proteins and to determine the functional and biochemical role of selected IscS and TusA residues. IscS interacts with its partners through an extensive surface area centered on the active site Cys328. The structures indicate that the acceptor proteins approach Cys328 from different directions and suggest that the conformational plasticity of a long loop containing this cysteine is essential for the ability of IscS to transfer sulfur to multiple acceptor proteins. The sulfur acceptors can only bind to IscS one at a time, while frataxin and IscX can form a ternary complex with IscU and IscS. Our data support the role of frataxin as an iron donor for IscU to form the Fe-S clusters.

  19. 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

  20. Synthesis, properties and surface self-assembly of a pentanuclear cluster based on the new π-conjugated TTF-triazole ligand

    PubMed Central

    Cui, Long; Geng, Yan-Fang; Leong, Chanel F.; Ma, Qian; D’Alessandro, Deanna M.; Deng, Ke; Zeng, Qing-Dao; Zuo, Jing-Lin

    2016-01-01

    The new π-extended redox-active ligand with both TTF and triazole units, 6-(4,5-bis(propylthio)-1,3-dithiol-2-ylidene)-1H-[1,3]dithiolo[4′,5′:4,5]benzo [1,2-d] [1–3]triazole, has been successfully prepared. Based on the versatile ligand and Cu(tta)2 precursors (tta− = 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione), a TTF-based pentanuclear CuII cluster (Cu5(tta)4(TTFN3)6) is synthesized and structurally characterized. Their absorption and electrochemical properties are investigated. Antiferromagnetic couplings are operative between metal ion centers bridged by triazoles in the complex. The self-assembled structure of the cluster complex on a highly oriented pyrolytic graphite (HOPG) surface was observed using scanning tunneling microscopy and density functional theory (DFT) calculations have been performed to provide insight into the formation mechanism. The introduction of the redox-active TTF unit into the cluster complexes with interesting magnetic properties renders them promising candidates for new multifunctional materials. PMID:27150720

  1. De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster

    PubMed Central

    Kumar, Abhishek; Henrissat, Bernard; Arvas, Mikko; Syed, Muhammad Fahad; Thieme, Nils; Benz, J. Philipp; Sørensen, Jens Laurids; Record, Eric; Pöggeler, Stefanie; Kempken, Frank

    2015-01-01

    The marine-derived Scopulariopsis brevicaulis strain LF580 produces scopularides A and B, which have anticancerous properties. We carried out genome sequencing using three next-generation DNA sequencing methods. De novo hybrid assembly yielded 621 scaffolds with a total size of 32.2 Mb and 16298 putative gene models. We identified a large non-ribosomal peptide synthetase gene (nrps1) and supporting pks2 gene in the same biosynthetic gene cluster. This cluster and the genes within the cluster are functionally active as confirmed by RNA-Seq. Characterization of carbohydrate-active enzymes and major facilitator superfamily (MFS)-type transporters lead to postulate S. brevicaulis originated from a soil fungus, which came into contact with the marine sponge Tethya aurantium. This marine sponge seems to provide shelter to this fungus and micro-environment suitable for its survival in the ocean. This study also builds the platform for further investigations of the role of life-style and secondary metabolites from S. brevicaulis. PMID:26505484

  2. Synthesis, properties and surface self-assembly of a pentanuclear cluster based on the new π-conjugated TTF-triazole ligand

    NASA Astrophysics Data System (ADS)

    Cui, Long; Geng, Yan-Fang; Leong, Chanel F.; Ma, Qian; D’Alessandro, Deanna M.; Deng, Ke; Zeng, Qing-Dao; Zuo, Jing-Lin

    2016-05-01

    The new π-extended redox-active ligand with both TTF and triazole units, 6-(4,5-bis(propylthio)-1,3-dithiol-2-ylidene)-1H-[1,3]dithiolo[4‧,5‧:4,5]benzo [1,2-d] [1–3]triazole, has been successfully prepared. Based on the versatile ligand and Cu(tta)2 precursors (tta‑ = 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione), a TTF-based pentanuclear CuII cluster (Cu5(tta)4(TTFN3)6) is synthesized and structurally characterized. Their absorption and electrochemical properties are investigated. Antiferromagnetic couplings are operative between metal ion centers bridged by triazoles in the complex. The self-assembled structure of the cluster complex on a highly oriented pyrolytic graphite (HOPG) surface was observed using scanning tunneling microscopy and density functional theory (DFT) calculations have been performed to provide insight into the formation mechanism. The introduction of the redox-active TTF unit into the cluster complexes with interesting magnetic properties renders them promising candidates for new multifunctional materials.

  3. Cooperative phenomena in self-assembled nucleation of 3 × 4-In/Si(100) surface magic clusters

    NASA Astrophysics Data System (ADS)

    Utas, O. A.; Denisov, N. V.; Kotlyar, V. G.; Zotov, A. V.; Saranin, A. A.; Chou, J. P.; Lai, M. Y.; Wei, C. M.; Wang, Y. L.

    2010-07-01

    Using statistical analysis of the scanning tunneling microscopy images of the 3 × 4-In surface magic cluster (SMC) arrays on Si(100)1 × 2 substrate at low In coverages, the main regularities of the space distribution of the nucleated SMCs have been established. It has been found that a nucleated SMC perturbs the surface potential relief within a limited zone around itself in a way that some of the sites in the zone demonstrate a great preference for nucleating a new cluster, while in the other sites the nucleation is greatly suppressed. Outside the zone, the nucleation probability is close to that of the random nucleation simulated using Monte-Carlo technique. Energetic background of the observed phenomena has been proved using density-functional theory calculations, which clearly demonstrate that the lower the formation energy the higher the occurrence probability of a given cluster-pair configuration.

  4. Low-energy spectrum of iron-sulfur clusters directly from many-particle quantum mechanics

    NASA Astrophysics Data System (ADS)

    Sharma, Sandeep; Sivalingam, Kantharuban; Neese, Frank; Chan, Garnet Kin-Lic

    2014-10-01

    Iron-sulfur clusters are a universal biological motif. They carry out electron transfer, redox chemistry and even oxygen sensing, in diverse processes including nitrogen fixation, respiration and photosynthesis. Their low-lying electronic states are key to their remarkable reactivity, but they cannot be directly observed. Here, we present the first ever quantum calculation of the electronic levels of [2Fe-2S] and [4Fe-4S] clusters free from any model assumptions. Our results highlight the limitations of long-standing models of their electronic structure. In particular, we demonstrate that the widely used Heisenberg double exchange model underestimates the number of states by one to two orders of magnitude, which can conclusively be traced to the absence of Fe dd excitations, thought to be important in these clusters. Furthermore, the electronic energy levels of even the same spin are dense on the scale of vibrational fluctuations and this provides a natural explanation for the ubiquity of these clusters in catalysis in nature.

  5. Unanticipated coordination of tris buffer to the Radical SAM cluster of the RimO methylthiotransferase.

    PubMed

    Molle, Thibaut; Clémancey, Martin; Latour, Jean-Marc; Kathirvelu, Velavan; Sicoli, Giuseppe; Forouhar, Farhad; Mulliez, Etienne; Gambarelli, Serge; Atta, Mohamed

    2016-07-01

    Radical SAM enzymes generally contain a [4Fe-4S](2+/1+) (RS cluster) cluster bound to the protein via the three cysteines of a canonical motif CxxxCxxC. The non-cysteinyl iron is used to coordinate SAM via its amino-carboxylate moiety. The coordination-induced proximity between the cluster acting as an electron donor and the adenosyl-sulfonium bond of SAM allows for the homolytic cleavage of the latter leading to the formation of the reactive 5'-deoxyadenosyl radical used for substrate activation. Most of the structures of Radical SAM enzymes have been obtained in the presence of SAM, and therefore, little is known about the situation when SAM is not present. In this report, we show that RimO, a methylthiotransferase belonging to the radical SAM superfamily, binds a Tris molecule in the absence of SAM leading to specific spectroscopic signatures both in Mössbauer and pulsed EPR spectroscopies. These data provide a cautionary note for researchers who work with coordinative unsaturated iron sulfur clusters. PMID:27259294

  6. Assembly of Fe-substituted Dawson-type nanoscale selenotungstate clusters with photocatalytic H2 evolution activity.

    PubMed

    Chen, Wei-Chao; Qin, Chao; Wang, Xin-Long; Li, Yang-Guang; Zang, Hong-Ying; Jiao, Yan-Qing; Huang, Peng; Shao, Kui-Zhan; Su, Zhong-Min; Wang, En-Bo

    2014-11-11

    Two Fe-substituted Dawson-type nanoscale selenotungstate clusters, {Fe6Se6W34} and {Fe10Se8W62} involving {α-Se2W14} and {γ-Se2W14} building blocks, have been isolated, which exhibit photocatalytic H2 evolution activity. Their electrochemical behaviours and magnetic properties were also investigated. PMID:25232933

  7. Plasmon resonance hybridization in self-assembled copper nanoparticle clusters: efficient and precise localization of surface plasmon resonance (LSPR) sensing based on Fano resonances.

    PubMed

    Ahmadivand, Arash; Pala, Nezih

    2015-01-01

    In this work, we have investigated the hybridization of plasmon resonance modes in completely copper (Cu)-based subwavelength nanoparticle clusters from simple symmetric dimers to complex asymmetric self-assembled structures. The quality of apparent bonding and antibonding plasmon resonance modes for all of the clusters has been studied, and we examined the spectral response of each one of the proposed configurations numerically using the finite-difference time domain (FDTD) method. The effect of the geometric sizes of nanoparticles used and substrate refractive index on the cross-sectional profiles of each of the studied structures has been calculated and drawn. We proved that Fano-like resonance can be formed in Cu-based heptamer clusters as in analogous noble metallic particles (e.g., Au and Ag) by determining the coupling strength and interference between sub-radiant and super-radiant resonance modes. Employing certain Cu nanodiscs in designing an octamer structure, we measured the quality of the Fano dip formation along the scattering diagram. Accurate tuning of the geometric sizes for the Cu-based octamer yields an opportunity to observe isotropic, deep, and narrow Fano minima along the scattering profile that are in comparable condition with the response of other plasmonic metallic substances. Immersing investigated final Cu-based octamer in various liquids with different refractive indices, we determined the sensing accuracy of the cluster based on the performance of the Fano dip. Plotting a linear diagram of plasmon energy differences over the refractive index variations as a figure of merit (FoM), which we have quantified as 13.25. With this method, the precision of the completely Cu-based octamer is verified numerically using the FDTD tool. This study paves the way toward the use of Cu as an efficient, low-cost, and complementary metal-oxide semiconductor (CMOS)-compatible plasmonic material with optical properties that are similar to analogous plasmonic

  8. Spatial Association of Signaling Proteins and F-Actin Effects on Cluster Assembly Analyzed via Photoactivation Localization Microscopy in T Cells

    PubMed Central

    Hsu, Chih-Jung; Baumgart, Tobias

    2011-01-01

    Recognition of antigens by T cell receptors (TCRs) triggers cellular signaling cascades initiated by recruitment to the plasma membrane of numerous effector molecules to form signaling microclusters (MCs). Here we show that the method of high-resolution photoactivation localization microscopy (PALM) imaging can be used to analyze the spatial correlation between kinase ZAP70 and adaptor SLP76 MCs at the cell periphery and the effects of F-actin on MC assembly. We first determined the photophysical rate constants of Dronpa and tdEos fluorescence probes, which allowed us to optimize our dual-color PALM imaging method. We next analyzed the degrees of spatial association through determination of Mander's colocalization coefficients from PALM images, which revealed increasing spatial segregation of ZAP70 and SLP76 MCs at the cell periphery after initiation of signaling. We showed that this spatial segregation at the cell periphery occurred in parallel with the reduction of MC phosphorylation levels. Furthermore, we used Ripley's K function to analyze spatial randomness, and determined average radii of clusters as a function of activation time. The average radii of SLP76 and LAT MCs were found to decrease, whereas ZAP70 MC radii remained relatively constant. Finally, effects of F-actin depolymerization on MC morphology were studied by determining radial distributions of cluster circularity. Our data suggest that MC morphology is affected by actin polymerization. The quantitative analysis of sub-diffraction PALM images may provide a starting point for a molecular interpretation of cluster-cluster interactions and of the regulation of T cell signaling MCs by the cytoskeleton. PMID:21887278

  9. A review of immune amplification via ligand clustering by self-assembled liquid-crystalline DNA complexes.

    PubMed

    Lee, Ernest Y; Lee, Calvin K; Schmidt, Nathan W; Jin, Fan; Lande, Roberto; Curk, Tine; Frenkel, Daan; Dobnikar, Jure; Gilliet, Michel; Wong, Gerard C L

    2016-06-01

    We examine how the interferon production of plasmacytoid dendritic cells is amplified by the self-assembly of liquid-crystalline antimicrobial peptide/DNA complexes. These specialized dendritic cells are important for host defense because they quickly release large quantities of type I interferons in response to infection. However, their aberrant activation is also correlated with autoimmune diseases such as psoriasis and lupus. In this review, we will describe how polyelectrolyte self-assembly and the statistical mechanics of multivalent interactions contribute to this process. In a more general compass, we provide an interesting conceptual corrective to the common notion in molecular biology of a dichotomy between specific interactions and non-specific interactions, and show examples where one can construct exquisitely specific interactions using non-specific interactions. PMID:26956527

  10. Computation of neutron fluxes in clusters of fuel pins arranged in hexagonal assemblies (2D and 3D)

    SciTech Connect

    Prabha, H.; Marleau, G.

    2012-07-01

    For computations of fluxes, we have used Carvik's method of collision probabilities. This method requires tracking algorithms. An algorithm to compute tracks (in 2D and 3D) has been developed for seven hexagonal geometries with cluster of fuel pins. This has been implemented in the NXT module of the code DRAGON. The flux distribution in cluster of pins has been computed by using this code. For testing the results, they are compared when possible with the EXCELT module of the code DRAGON. Tracks are plotted in the NXT module by using MATLAB, these plots are also presented here. Results are presented with increasing number of lines to show the convergence of these results. We have numerically computed volumes, surface areas and the percentage errors in these computations. These results show that 2D results converge faster than 3D results. The accuracy on the computation of fluxes up to second decimal is achieved with fewer lines. (authors)

  11. Self-assembled semi-crystallinity at parallel β-sheet nanocrystal interfaces in clustered MaSp1 (spider silk) proteins.

    PubMed

    Sintya, Erly; Alam, Parvez

    2016-01-01

    In this communication, we use molecular dynamics methods to model the self-assembly of semi-crystalline domains at β-sheet nanocrystal interfaces in clusters of spider silk (MaSp1) proteins. Our research elucidates that the energetics at interfaces between crystalline and amorphous domains control effectively, the extent to which semi-crystalline domains can form at interfaces. Stability at nanocrystal interfaces is not linearly related to the internal (bulk) stability of the β-sheet nanocrystal. Rather, interfacial stability is found to be highly sensitive to the number of alanine repeat units that make up each sheet. Intriguingly, the most stable interface for the development of semi-crystallinity is built up of polyalanine β-sheets of a length similar to that which is spun naturally in spider dragline silk. PMID:26478322

  12. Self-assembly of Fe{sub 3}O{sub 4} nanocrystal-clusters into cauliflower-like architectures: Synthesis and characterization

    SciTech Connect

    Zhu Luping; Liao Guihong; Bing Naici; Wang Linlin; Xie Hongyong

    2011-09-15

    Large-scale cauliflower-like Fe{sub 3}O{sub 4} architectures consist of well-assembled magnetite nanocrystal clusters have been synthesized by a simple solvothermal process. The as-synthesized Fe{sub 3}O{sub 4} samples were characterized by XRD, XPS, FT-IR, SEM, TEM, etc. The results show that the samples exhibit cauliflower-like hierarchical microstructures. The influences of synthesis parameters on the morphology of the samples were experimentally investigated. Magnetic properties of the Fe{sub 3}O{sub 4} cauliflower-like hierarchical microstructures have been detected by VSM at room temperature, showing a relatively low saturation magnetization of 65 emu/g and an enhanced coercive force of 247 Oe. - Graphical Abstract: Cauliflower-like Fe{sub 3}O{sub 4} architectures consist of well-assembled magnetite nanocrystal clusters have been synthesized by a simple solvothermal process, using FeCl{sub 3}.6H{sub 2}O and EDA as the starting materials. Highlights: > Cauliflower-like Fe{sub 3}O{sub 4} architectures were successfully prepared by a simple solvothermal route. > The cauliflower-like Fe{sub 3}O{sub 4} architectures have a size in the range of 200-300 nm. > They show a low saturation magnetization of 65 emu/g and an enhanced coercive force of 247 Oe. > These Fe{sub 3}O{sub 4} architectures may have potential applications in catalysis and biological fields.

  13. Fluorescent probes for tracking the transfer of iron-sulfur cluster and other metal cofactors in biosynthetic reaction pathways.

    PubMed

    Vranish, James N; Russell, William K; Yu, Lusa E; Cox, Rachael M; Russell, David H; Barondeau, David P

    2015-01-14

    Iron-sulfur (Fe-S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe-S cluster synthesis and transfer reactions. Here we present fusion protein- and intein-based fluorescent labeling strategies that can probe Fe-S cluster binding. The fluorescence is sensitive to different cluster types ([2Fe-2S] and [4Fe-4S] clusters), ligand environments ([2Fe-2S] clusters on Rieske, ferredoxin (Fdx), and glutaredoxin), and cluster oxidation states. The power of this approach is highlighted with an extreme example in which the kinetics of Fe-S cluster transfer reactions are monitored between two Fdx molecules that have identical Fe-S spectroscopic properties. This exchange reaction between labeled and unlabeled Fdx is catalyzed by dithiothreitol (DTT), a result that was confirmed by mass spectrometry. DTT likely functions in a ligand substitution reaction that generates a [2Fe-2S]-DTT species, which can transfer the cluster to either labeled or unlabeled Fdx. The ability to monitor this challenging cluster exchange reaction indicates that real-time Fe-S cluster incorporation can be tracked for a specific labeled protein in multicomponent assays that include several unlabeled Fe-S binding proteins or other chromophores. Such advanced kinetic experiments are required to untangle the intricate networks of transfer pathways and the factors affecting flux through branch points. High sensitivity and suitability with high-throughput methodology are additional benefits of this approach. We anticipate that this cluster detection methodology will transform the study of Fe-S cluster pathways and potentially other metal cofactor biosynthetic pathways. PMID:25478817

  14. The cytosolic Fe-S cluster assembly component MET18 is required for the full enzymatic activity of ROS1 in active DNA demethylation

    PubMed Central

    Wang, Xiaokang; Li, Qi; Yuan, Wei; Cao, Zhendong; Qi, Bei; Kumar, Suresh; Li, Yan; Qian, Weiqiang

    2016-01-01

    DNA methylation patterns in plants are dynamically regulated by DNA methylation and active DNA demethylation in response to both environmental changes and development of plant. Beginning with the removal of methylated cytosine by ROS1/DME family of 5-methylcytosine DNA glycosylases, active DNA demethylation in plants occurs through base excision repair. So far, many components involved in active DNA demethylation remain undiscovered. Through a forward genetic screening of Arabidopsis mutants showing DNA hypermethylation at the EPF2 promoter region, we identified the conserved iron-sulfur cluster assembly protein MET18. MET18 dysfunction caused DNA hypermethylation at more than 1000 loci as well as the silencing of reporter genes and some endogenous genes. MET18 can directly interact with ROS1 in vitro and in vivo. ROS1 activity was reduced in the met18 mutant plants and point mutation in the conserved Fe-S cluster binding motif of ROS1 disrupted its biological function. Interestingly, a large number of DNA hypomethylated loci, especially in the CHH context, were identified from the met18 mutants and most of the hypo-DMRs were from TE regions. Our results suggest that MET18 can regulate both active DNA demethylation and DNA methylation pathways in Arabidopsis. PMID:27193999

  15. Polydentate-ligand-supported self-assembly of heterometallic T-shaped Co4RE (RE = Gd, Tb, Y) clusters: synthesis, structure and magnetism.

    PubMed

    Ke, Hongshan; Zhao, Lang; Guo, Yang; Tang, Jinkui

    2012-08-28

    A series of mixed-valent heterometallic pentanuclear Co(III)(3)Co(II)RE(III) (RE = Gd (1), Tb (2), Y (3)) clusters have been rationally assembled by taking advantage of a bifunctional ligand with o-vanillin and tripodal tris(hydroxymethyl)aminomethane units. Structural determinations reveal that all compounds are isomorphous and possess a T-shaped Co(4)RE core, which comprises two nearly linear Co(2)RE subunits sharing a common RE ion. Their magnetic properties were thoroughly studied. The static magnetic susceptibility studies of 1 demonstrate the presence of weak ferromagnetic interactions between the magnetic centres and magnetic anisotropy reflected by the single ion zero-field splitting (ZFS) D term. Both 1 and 2 behave magnetically as heterodinuclear metal systems, while the magnetic behaviour of 3 is identical to an isolated Co(II) ion. Moreover, alternating-current susceptibility measurements did not exhibit any out-of-phase signal, suggesting that slow magnetic relaxation is absent above 2 K within them. These isomorphous Co(4)RE clusters offer an opportunity to systematically probe the contribution of different metal ions to the overall magnetic behaviour in Co(II)-RE(III) systems. PMID:22767361

  16. The cytosolic Fe-S cluster assembly component MET18 is required for the full enzymatic activity of ROS1 in active DNA demethylation.

    PubMed

    Wang, Xiaokang; Li, Qi; Yuan, Wei; Cao, Zhendong; Qi, Bei; Kumar, Suresh; Li, Yan; Qian, Weiqiang

    2016-01-01

    DNA methylation patterns in plants are dynamically regulated by DNA methylation and active DNA demethylation in response to both environmental changes and development of plant. Beginning with the removal of methylated cytosine by ROS1/DME family of 5-methylcytosine DNA glycosylases, active DNA demethylation in plants occurs through base excision repair. So far, many components involved in active DNA demethylation remain undiscovered. Through a forward genetic screening of Arabidopsis mutants showing DNA hypermethylation at the EPF2 promoter region, we identified the conserved iron-sulfur cluster assembly protein MET18. MET18 dysfunction caused DNA hypermethylation at more than 1000 loci as well as the silencing of reporter genes and some endogenous genes. MET18 can directly interact with ROS1 in vitro and in vivo. ROS1 activity was reduced in the met18 mutant plants and point mutation in the conserved Fe-S cluster binding motif of ROS1 disrupted its biological function. Interestingly, a large number of DNA hypomethylated loci, especially in the CHH context, were identified from the met18 mutants and most of the hypo-DMRs were from TE regions. Our results suggest that MET18 can regulate both active DNA demethylation and DNA methylation pathways in Arabidopsis. PMID:27193999

  17. Electric bistability induced by incorporating self-assembled monolayers/aggregated clusters of azobenzene derivatives in pentacene-based thin-film transistors.

    PubMed

    Tseng, Chiao-Wei; Huang, Ding-Chi; Tao, Yu-Tai

    2012-10-24

    Composite films of pentacene and a series of azobenzene derivatives are prepared and used as the active channel material in top-contact, bottom-gate field-effect transistors. The transistors exhibit high field-effect mobility as well as large I-V hysteresis as a function of the gate bias history. The azobenzene moieties, incorporated either in the form of self-assembled monolayer or discrete multilayer clusters at the dielectric surface, result in electric bistability of the pentacene-based transistor either by photoexcitation or gate biasing. The direction of threshold voltage shifts, size of hysteresis, response time, and retention characteristics all strongly depend on the substituent on the benzene ring. The results show that introducing a monolayer of azobenzene moieties results in formation of charge carrier traps responsible for slower switching between the bistable states and longer retention time. With clusters of azobenzene moieties as the trap sites, the switching is faster but the retention is shorter. Detailed film structure analyses and correlation with the transistor/memory properties of these devices are provided. PMID:22974132

  18. DNA mediated wire-like clusters of self-assembled TiO2 nanomaterials: supercapacitor and dye sensitized solar cell applications

    NASA Astrophysics Data System (ADS)

    Nithiyanantham, U.; Ramadoss, Ananthakumar; Ede, Sivasankara Rao; Kundu, Subrata

    2014-06-01

    A new route for the formation of wire-like clusters of TiO2 nanomaterials self-assembled in DNA scaffold within an hour of reaction time is reported. TiO2 nanomaterials are synthesized by the reaction of titanium-isopropoxide with ethanol and water in the presence of DNA under continuous stirring and heating at 60 °C. The individual size of the TiO2 NPs self-assembled in DNA and the diameter of the wires can be tuned by controlling the DNA to Ti-salt molar ratios and other reaction parameters. The eventual diameter of the individual particles varies between 15 +/- 5 nm ranges, whereas the length of the nanowires varies in the 2-3 μm range. The synthesized wire-like DNA-TiO2 nanomaterials are excellent materials for electrochemical supercapacitor and DSSC applications. From the electrochemical supercapacitor experiment, it was found that the TiO2 nanomaterials showed different specific capacitance (Cs) values for the various nanowires, and the order of Cs values are as follows: wire-like clusters (small size) > wire-like clusters (large size). The highest Cs of 2.69 F g-1 was observed for TiO2 having wire-like structure with small sizes. The study of the long term cycling stability of wire-like clusters (small size) electrode were shown to be stable, retaining ca. 80% of the initial specific capacitance, even after 5000 cycles. The potentiality of the DNA-TiO2 nanomaterials was also tested in photo-voltaic applications and the observed efficiency was found higher in the case of wire-like TiO2 nanostructures with larger sizes compared to smaller sizes. In future, the described method can be extended for the synthesis of other oxide based materials on DNA scaffold and can be further used in other applications like sensors, Li-ion battery materials or treatment for environmental waste water.A new route for the formation of wire-like clusters of TiO2 nanomaterials self-assembled in DNA scaffold within an hour of reaction time is reported. TiO2 nanomaterials are

  19. 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.

  20. Electrical conductivity of cluster-assembled carbon/titania nanocomposite films irradiated by highly focused vacuum ultraviolet photon beams

    SciTech Connect

    Amati, M.; Lenardi, C.; Agostino, R. G.; Caruso, T.; Ducati, C.; La Rosa, S.; Bongiorno, G.; Cassina, V.; Podesta, P.; Ravagnan, L.; Piseri, P.; Milani, P.

    2007-03-15

    We investigated the electrical transport properties of nanostructured carbon and carbon/titanium oxide nanocomposite films produced by supersonic cluster beam deposition and irradiated by highly focused vacuum UV photon beam. We have observed a relevant increase of the density of states at Fermi level, suggesting that the films acquire a 'metallic' character. This is confirmed by the increment of the conductivity of four orders of magnitude for pure nanostructured carbon films and at least eight orders of magnitude for films containing 9 at. % of titanium. A partial reversibility of the process is observed by exposing the modified films to molecular oxygen or directly to air. We demonstrate the capability of writing micrometric conductive strips (2-3 {mu}m width and 60 {mu}m length) and controlling the variation of the conductivity as a function of the titanium concentration.

  1. THE ONGOING ASSEMBLY OF A CENTRAL CLUSTER GALAXY: PHASE-SPACE SUBSTRUCTURES IN THE HALO OF M87

    SciTech Connect

    Romanowsky, Aaron J.; Brodie, Jean P.; Arnold, Jacob A.; Strader, Jay; Mihos, J. Christopher; Spitler, Lee R.; Forbes, Duncan A.; Foster, Caroline

    2012-03-20

    The halos of galaxies preserve unique records of their formation histories. We carry out the first combined observational and theoretical study of phase-space halo substructure in an early-type galaxy: M87, the central galaxy in the Virgo cluster. We analyze an unprecedented wide-field, high-precision photometric and spectroscopic data set for 488 globular clusters (GCs), which includes new, large-radius Subaru/Suprime-Cam and Keck/DEIMOS observations. We find signatures of two substructures in position-velocity phase space. One is a small, cold stream associated with a known stellar filament in the outer halo; the other is a large shell-like pattern in the inner halo that implies a massive, hitherto unrecognized accretion event. We perform extensive statistical tests and independent metallicity analyses to verify the presence and characterize the properties of these features, and to provide more general methodologies for future extragalactic studies of phase-space substructure. The cold outer stream is consistent with a dwarf galaxy accretion event, while for the inner shell there is tension between a low progenitor mass implied by the cold velocity dispersion, and a high mass from the large number of GCs, which might be resolved by a {approx}0.5 L* E/S0 progenitor. We also carry out proof-of-principle numerical simulations of the accretion of smaller galaxies in an M87-like gravitational potential. These produce analogous features to the observed substructures, which should have observable lifetimes of {approx}1 Gyr. The shell and stream GCs together support a scenario where the extended stellar envelope of M87 has been built up by a steady rain of material that continues until the present day. This phase-space method demonstrates unique potential for detailed tests of galaxy formation beyond the Local Group.

  2. A kinetic model for impact/sliding wear of pressurized water reactor internal components: Application to rod cluster control assemblies

    SciTech Connect

    Zbinden, M.; Durbec, V.

    1996-12-01

    Certain internal components of Pressurized Water Reactors are damaged by wear when subjected to vibration induced by flow. In order to enable predictive calculation of such wear, one must have a model which takes account reliably of real damages. The modelling of wear represents a final link in a succession of numerical calculations which begins by the determination of hydraulic excitations induced by the flow. One proceeds, then, in the dynamic response calculation of the structure to finish up with an estimation of volumetric wear and of the depth of wear scars. A new concept of industrial wear model adapted to components of nuclear plants is proposed. Its originality is to be supported, on one hand, by experimental results obtained via wear machines of relatively short operational times, and, on the other hand, by the information obtained from the operating feedback over real wear kinetics of the reactors components. The proposed model is illustrated by an example which correspond to a specific real situation. The determination of the coefficients permitting to cover all assembly of configurations and the validation of the model in these configurations have been the object of the most recent work.

  3. Fast assembling microarrays of superparamagnetic Fe3O4@Au nanoparticle clusters as reproducible substrates for surface-enhanced Raman scattering

    NASA Astrophysics Data System (ADS)

    Ye, Min; Wei, Zewen; Hu, Fei; Wang, Jianxin; Ge, Guanglu; Hu, Zhiyuan; Shao, Mingwang; Lee, Shuit-Tong; Liu, Jian

    2015-08-01

    It is currently a very active research area to develop new types of substrates which integrate various nanomaterials for surface-enhanced Raman scattering (SERS) techniques. Here we report a unique approach to prepare SERS substrates with reproducible performance. It features silicon mold-assisted magnetic assembling of superparamagnetic Fe3O4@Au nanoparticle clusters (NCs) into arrayed microstructures on a wafer scale. This approach enables the fabrication of both silicon-based and hydrogel-based substrates in a sequential manner. We have demonstrated that strong SERS signals can be harvested from these substrates due to an efficient coupling effect between Fe3O4@Au NCs, with enhancement factors >106. These substrates have been confirmed to provide reproducible SERS signals, with low variations in different locations or batches of samples. We investigate the spatial distributions of electromagnetic field enhancement around Fe3O4@Au NCs assemblies using finite-difference-time-domain (FDTD) simulations. The procedure to prepare the substrates is straightforward and fast. The silicon mold can be easily cleaned out and refilled with Fe3O4@Au NCs assisted by a magnet, therefore being re-useable for many cycles. Our approach has integrated microarray technologies and provided a platform for thousands of independently addressable SERS detection, in order to meet the requirements of a rapid, robust, and high throughput performance.It is currently a very active research area to develop new types of substrates which integrate various nanomaterials for surface-enhanced Raman scattering (SERS) techniques. Here we report a unique approach to prepare SERS substrates with reproducible performance. It features silicon mold-assisted magnetic assembling of superparamagnetic Fe3O4@Au nanoparticle clusters (NCs) into arrayed microstructures on a wafer scale. This approach enables the fabrication of both silicon-based and hydrogel-based substrates in a sequential manner. We have

  4. Sulfur Mobilization for Fe-S Cluster Assembly by the Essential SUF Pathway in the Plasmodium falciparum Apicoplast and Its Inhibition

    PubMed Central

    Charan, Manish; Singh, Nidhi; Kumar, Bijay; Srivastava, Kumkum; Siddiqi, Mohammad Imran

    2014-01-01

    The plastid of the malaria parasite, the apicoplast, is essential for parasite survival. It houses several pathways of bacterial origin that are considered attractive sites for drug intervention. Among these is the sulfur mobilization (SUF) pathway of Fe-S cluster biogenesis. Although the SUF pathway is essential for apicoplast maintenance and parasite survival, there has been limited biochemical investigation of its components and inhibitors of Plasmodium SUFs have not been identified. We report the characterization of two proteins, Plasmodium falciparum SufS (PfSufS) and PfSufE, that mobilize sulfur in the first step of Fe-S cluster assembly and confirm their exclusive localization to the apicoplast. The cysteine desulfurase activity of PfSufS is greatly enhanced by PfSufE, and the PfSufS-PfSufE complex is detected in vivo. Structural modeling of the complex reveals proximal positioning of conserved cysteine residues of the two proteins that would allow sulfide transfer from the PLP (pyridoxal phosphate) cofactor-bound active site of PfSufS. Sulfide release from the l-cysteine substrate catalyzed by PfSufS is inhibited by the PLP inhibitor d-cycloserine, which forms an adduct with PfSufS-bound PLP. d-Cycloserine is also inimical to parasite growth, with a 50% inhibitory concentration close to that reported for Mycobacterium tuberculosis, against which the drug is in clinical use. Our results establish the function of two proteins that mediate sulfur mobilization, the first step in the apicoplast SUF pathway, and provide a rationale for drug design based on inactivation of the PLP cofactor of PfSufS. PMID:24709262

  5. SHORT GAMMA-RAY BURSTS FROM DYNAMICALLY ASSEMBLED COMPACT BINARIES IN GLOBULAR CLUSTERS: PATHWAYS, RATES, HYDRODYNAMICS, AND COSMOLOGICAL SETTING

    SciTech Connect

    Lee, William H.; Ramirez-Ruiz, Enrico; Van de Ven, Glenn E-mail: enrico@ucolick.or

    2010-09-01

    We present a detailed assessment of the various dynamical pathways leading to the coalescence of compact objects in globular clusters (GCs) and Short Gamma-ray Burst (SGRB) production. We consider primordial binaries, dynamically formed binaries (through tidal two-body and three-body exchange interactions), and direct impacts of compact objects (WD/NS/BH). Here, we show that if the primordial binary fraction is small, close encounters dominate the production rate of coalescing compact systems. We find that the two dominant channels are the interaction of field neutron stars (NSs) with dynamically formed binaries and two-body encounters. Under such conditions, we estimate the redshift distribution and host galaxy demographics of SGRB progenitors, and find that GCs can provide a significant contribution to the overall observed rate. Regarding the newly identified channel of close stellar encounters involving WD/NS/BH, we have carried out precise modeling of the hydrodynamical evolution, giving us a detailed description of the resulting merged system. Our calculations show that there is in principle no problem in accounting for the global energy budget of a typical SGRB. The particulars of each encounter, however, are variable in several aspects and can lead to interesting diversity. First and most importantly, the characteristics of the encounter are highly dependent on the impact parameter. This is in contrast to the merger scenario, where the masses of the compact objects dictate a typical length and luminosity scale for SGRB activity. Second, the nature of the compact star itself can produce very different outcomes. Finally, the presence of tidal tails in which material will fall back onto the central object at a later time is a robust feature of the present set of calculations. The mass involved in these structures is considerably larger than for binary mergers. It is thus possible to account generically in this scenario for a prompt episode of energy release, as

  6. VIMOS Ultra-Deep Survey (VUDS): Witnessing the assembly of a massive cluster at z ~ 3.3

    NASA Astrophysics Data System (ADS)

    Lemaux, B. C.; Cucciati, O.; Tasca, L. A. M.; Le Fèvre, O.; Zamorani, G.; Cassata, P.; Garilli, B.; Le Brun, V.; Maccagni, D.; Pentericci, L.; Thomas, R.; Vanzella, E.; Zucca, E.; Amorín, R.; Bardelli, S.; Capak, P.; Cassarà, L. P.; Castellano, M.; Cimatti, A.; Cuby, J. G.; de la Torre, S.; Durkalec, A.; Fontana, A.; Giavalisco, M.; Grazian, A.; Hathi, N. P.; Ilbert, O.; Moreau, C.; Paltani, S.; Ribeiro, B.; Salvato, M.; Schaerer, D.; Scodeggio, M.; Sommariva, V.; Talia, M.; Taniguchi, Y.; Tresse, L.; Vergani, D.; Wang, P. W.; Charlot, S.; Contini, T.; Fotopoulou, S.; Gal, R. R.; Kocevski, D. D.; López-Sanjuan, C.; Lubin, L. M.; Mellier, Y.; Sadibekova, T.; Scoville, N.

    2014-12-01

    Using new spectroscopic observations obtained as part of the VIMOS Ultra-Deep Survey (VUDS), we performed a systematic search for overdense environments in the early universe (z> 2) and report here on the discovery of Cl J0227-0421, a massive protocluster at z = 3.29. This protocluster is characterized by both the large overdensity of spectroscopically confirmed members, δgal = 10.5 ± 2.8, and a significant overdensity in photometric redshift members. The halo mass of this protocluster is estimated by a variety of methods to be ~3 × 1014ℳ⊙ at z ~ 3.3, which, evolved to z = 0 results in a halo mass rivaling or exceeding that of the Coma cluster. The properties of 19 spectroscopically confirmed member galaxies are compared with a large sample of VUDS/VVDS galaxies in lower density field environments at similar redshifts. We find tentative evidence for an excess of redder, brighter, and more massive galaxies within the confines of the protocluster relative to the field population, which suggests that we may be observing the beginning ofenvironmentally induced quenching. The properties of these galaxies are investigated, including a discussion of the brightest protocluster galaxy, which appears to be undergoing vigorous coeval nuclear and starburst activity. The remaining member galaxies appear to have characteristics that are largely similar to the field population. Though we find weaker evidence of the suppression of the median star formation rates among and differences in the stacked spectra of member galaxies with respect to the field, we defer any conclusions about these trends to future work with the ensemble of protostructures that are found in the full VUDS sample. Based on data obtained with the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Program 185.A-0791.Appendices are available in electronic form at http://www.aanda.orgData are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130

  7. The iron uptake repressor Fep1 in the fission yeast binds Fe-S cluster through conserved cysteines.

    PubMed

    Kim, Hyo-Jin; Lee, Kang-Lok; Kim, Kyoung-Dong; Roe, Jung-Hye

    2016-09-01

    Iron homeostasis is tightly regulated since iron is an essential but toxic element in the cell. The GATA-type transcription factor Fep1 and its orthologs contribute to iron homeostasis in many fungi by repressing genes for iron uptake when intracellular iron is high. Even though the function and interaction partners of Fep1 have been elucidated extensively In Schizosaccharomyces pombe, the mechanism behind iron-sensing by Fep1 remains elusive. It has been reported that Fep1 interacts with Fe-S-containing monothiol glutaredoxin Grx4 and Grx4-Fra2 complex. In this study, we demonstrate that Fep1 also binds iron, in the form of Fe-S cluster. Spectroscopic and biochemical analyses of as isolated and reconstituted Fep1 suggest that the dimeric Fep1 binds Fe-S clusters. The mutation study revealed that the cluster-binding depended on the conserved cysteines located between the two zinc fingers in the DNA binding domain. EPR analyses revealed [Fe-S]-specific peaks indicative of mixed presence of [2Fe-2S], [3Fe-4S], or [4Fe-4S]. The finding that Fep1 is an Fe-S protein fits nicely with the model that the Fe-S-trafficking Grx4 senses intracellular iron environment and modulates the activity of Fep1. PMID:27444384

  8. Incorporation of [35S]sulfide into the Fe-S cluster of aconitase.

    PubMed

    Kennedy, M C; Emptage, M H; Beinert, H

    1984-03-10

    Exchange of sulfide into the iron-sulfur cluster of beef heart aconitase was investigated using Na235S. After anaerobic incubation for minutes and up to 24 h, samples were freed of substances of low Mr by Sephadex G-50 and analyzed for protein, protein-bound Fe, S2-, total Fe-S cluster by EPR, and for radioactivity. The activated and the inactive enzyme exchange three S2- ions within 1-2 h at essentially equal rates. No further exchange is observed with the activated enzyme within 24 h, whereas with the inactive enzyme, (partial) exchange of one more S2- occurs slowly within 5-10 h. Exchange is facilitated at elevated pH, but then destruction of clusters also increases. During incubation of inactive enzyme with S2-, partial activation may occur because S2- can act as reductant. Thus, depending on conditions, we observed very low to substantial activities. There is a linear, positive correlation between activity developed and ratio of cluster bound Fe to S2-. When Fe and dithiothreitol are present together with S2- during incubation, the extent of S2-exchange generally is between 10 and 25%. Fe incorporation exceeds S2- exchange, with the difference between Fe and S2- incorporation consistently amounting to one Fe/cluster. It is suggested that this excess Fe represents the Fe ion taken up on completion of the [4Fe-4S] from the [3Fe-4S] structure. The ease of S2-exchange suggests that the Fe-S cluster of aconitase is readily accessible to solvent. PMID:6699009

  9. CRITICAL CONFIGURATION FOR BERYLLIUM REFLECTED ASSEMBLIES OF U(93.15)O2 FUEL RODS (1.506-CM PITCH AND 7-TUBE CLUSTERS)

    SciTech Connect

    Margaret A. Marshall

    2012-05-01

    A series of critical experiments were completed in 1962-1965 at Oak Ridge National Laboratory’s Critical Experiments Facility in support of the Medium-Power Reactor Experiments (MPRE) program. In the late 1950’s efforts were made to study “power plants for the production of electrical power in space vehicles”. The MPRE program was a part of those efforts and studied the feasibility of a stainless steel system, boiling potassium 1 MW(t), or about 140 kW(e), reactor. The program was carried out in [fiscal years] 1964, 1965, and 1966. A summary of the program’s effort was compiled in 1967. The delayed critical experiments were a mockup of a small, potassium-cooled space power reactor for validation of reactor calculations and reactor physics methods. Initial experiments, performed in November and December of 1962, consisted of a core of 253 unmoderated stainless steel tubes, each containing 26 UO2 fuel pellets, surrounded by a graphite reflector. Measurements were made to determine critical reflector arrangements, fission-rate distributions, and cadmium ratio distributions. “The [assemblies were built] on [a] vertical assembly machine so that the movable part was the core and bottom reflector.” The first two experiments in the series were evaluated in HEU-COMP-FAST-001 (SCCA-FUND-EXP-001) and HEU-COMP-FAST-002 (SCCA-FUND-EXP-002). The first experiment had the 253 fuel tubes packed tightly into a 22.87 cm outside diameter (OD) core tank (References 1 and 2). The second experiment in the series, performed in early 1963, had the 253 fuel tubes at a 1.506-cm triangular lattice in a 25.96 cm OD core tank and graphite reflectors on all sides. The third set of experiments in the series, performed in mid-1963, which is studied in this evaluation, used beryllium reflectors. The beryllium reflected system was the preferred reactor configuration for this application because of the small thickness of the reflector. The two core configurations had the 253 fuel tubes

  10. Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima.

    PubMed

    Birrell, James A; Laurich, Christoph; Reijerse, Edward J; Ogata, Hideaki; Lubitz, Wolfgang

    2016-08-01

    Iron-sulfur clusters form one of the largest and most diverse classes of enzyme cofactors in nature. They may serve as structural factors, form electron transfer chains between active sites and external redox partners, or form components of enzyme active sites. Their specific role is a consequence of the cluster type and the surrounding protein environment. The relative effects of these factors are not completely understood, and it is not yet possible to predict the properties of iron-sulfur clusters based on amino acid sequences or rationally tune their properties to generate proteins with new desirable functions. Here, we generate mutations in a [2Fe-2S] cluster protein, the TmHydC subunit of the trimeric [FeFe]-hydrogenase from Thermotoga maritima, to study the factors that affect its redox potential. Saturation mutagenesis of Val131 was used to tune the redox potential over a 135 mV range and revealed that cluster redox potential and electronic properties correlate with amino acid hydrophobicity and the ability to form hydrogen bonds to the cluster. Proline scanning mutagenesis between pairs of ligating cysteines was used to remove backbone amide hydrogen bonds to the cluster and decrease the redox potential by up to 132 mV, without large structural changes in most cases. However, substitution of Gly83 with proline caused a change of HydC to a [4Fe-4S] cluster protein with a redox potential of -526 mV. Together, these results confirm the importance of hydrogen bonding in tuning cluster redox potentials and demonstrate the versatility of iron-sulfur cluster protein folds at binding different types of clusters. PMID:27396836

  11. Assembly of juxtaparanodes in myelinating DRG culture: Differential clustering of the Kv1/Caspr2 complex and scaffolding protein 4.1B.

    PubMed

    Hivert, Bruno; Pinatel, Delphine; Labasque, Marilyne; Tricaud, Nicolas; Goutebroze, Laurence; Faivre-Sarrailh, Catherine

    2016-05-01

    The precise distribution of ion channels at the nodes of Ranvier is essential for the efficient propagation of action potentials along myelinated axons. The voltage-gated potassium channels Kv1.1/1.2 are clustered at the juxtaparanodes in association with the cell adhesion molecules, Caspr2 and TAG-1 and the scaffolding protein 4.1B. In the present study, we set up myelinating cultures of DRG neurons and Schwann cells to look through the formation of juxtaparanodes in vitro. We showed that the Kv1.1/Kv1.2 channels were first enriched at paranodes before being restricted to distal paranodes and juxtaparanodes. In addition, the Kv1 channels displayed an asymmetric expression enriched at the distal juxtaparanodes. Caspr2 was strongly co-localized with Kv1.2 whereas the scaffolding protein 4.1B was preferentially recruited at paranodes while being present at juxtaparanodes too. Kv1.2/Caspr2 but not 4.1B, also transiently accumulated within the nodal region both in myelinated cultures and developing sciatic nerves. Studying cultures and sciatic nerves from 4.1B KO mice, we further showed that 4.1B is required for the proper targeting of Caspr2 early during myelination. Moreover, using adenoviral-mediated expression of Caspr-GFP and photobleaching experiments, we analyzed the stability of paranodal junctions and showed that the lateral stability of paranodal Caspr was not altered in 4.1B KO mice indicating that 4.1B is not required for the assembly and stability of the paranodal junctions. Thus, developing an adapted culture paradigm, we provide new insights into the dynamic and differential distribution of Kv1 channels and associated proteins during myelination. GLIA 2016;64:840-852. PMID:26840208

  12. Characterization of two dissimilatory sulfite reductases from sulfate-reducing bacteria

    NASA Astrophysics Data System (ADS)

    Huynh, B. H.; Moura, I.; Lino, A. R.; Moura, J. J. G.; Legall, J.

    1988-02-01

    Mössbauer, EPR, and biochemical techniques were used to characterize two dissimilatory sulfite reductases: desulforubidin from Desulfovibrio baculatus strain DSM 1743 and desulfoviridin from Desulfovibrio gigas. For each molecule of desulforubidin, there are two sirohemes and four [4Fe-4S] clusters. The [4Fe-4S] clusters are in the diamagnetic 2+ oxidation state. The sirohemes are high-spin ferric (S=5/2) and each siroheme is exchanged-coupled to a [4Fe-4S]2+ cluster. Such an exchange-coupled siroheme-[4Fe-4S] unit has also been found in the assimilatory sulfite reductase from Escherichia coli/1/ and in a low-molecular weight sulfite reductase from Desulfovibrio vulgaris/2/. For each molecule of defulfoviridin, there are two tetrahydroporphyrin groups and four [4Fe-4S]2+ clusters. To our surprise, we discovered that about 80% of the tetrahydroporphyrin groups, however, do not bind iron.

  13. Dark-operative protochlorophyllide oxidoreductase generates substrate radicals by an iron-sulphur cluster in bacteriochlorophyll biosynthesis

    PubMed Central

    Nomata, Jiro; Kondo, Toru; Mizoguchi, Tadashi; Tamiaki, Hitoshi; Itoh, Shigeru; Fujita, Yuichi

    2014-01-01

    Photosynthesis converts solar energy to chemical energy using chlorophylls (Chls). In a late stage of biosynthesis of Chls, dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR), a nitrogenase-like enzyme, reduces the C17 = C18 double bond of Pchlide and drastically changes the spectral properties suitable for photosynthesis forming the parental chlorin ring for Chl a. We previously proposed that the spatial arrangement of the proton donors determines the stereospecificity of the Pchlide reduction based on the recently resolved structure of the DPOR catalytic component, NB-protein. However, it was not clear how the two-electron and two-proton transfer events are coordinated in the reaction. In this study, we demonstrate that DPOR initiates a single electron transfer reaction from a [4Fe-4S]-cluster (NB-cluster) to Pchlide, generating Pchlide anion radicals followed by a single proton transfer, and then, further electron/proton transfer steps transform the anion radicals into chlorophyllide (Chlide). Thus, DPOR is a unique iron-sulphur enzyme to form substrate radicals followed by sequential proton- and electron-transfer steps with the protein folding very similar to that of nitrogenase. This novel radical-mediated reaction supports the biosynthesis of Chl in a wide variety of photosynthetic organisms. PMID:24965831

  14. Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: THE SUB-COMPLEX FORMED BY THE IRON DONOR, Yfh1 PROTEIN, AND THE SCAFFOLD, Isu1 PROTEIN.

    PubMed

    Ranatunga, Wasantha; Gakh, Oleksandr; Galeano, Belinda K; Smith, Douglas Y; Söderberg, Christopher A G; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

    2016-05-01

    The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24 Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly. PMID:26941001

  15. Cluster self-organization of TR-containing germanate systems: Suprapolyhedral precursors and self-assembly of the crystal structures of the LiNdGeO{sub 4} and CeGeO{sub 4} compounds

    SciTech Connect

    Ilyushin, G. D. Dem'yanets, L. N.

    2007-07-15

    A combinatorial-topological analysis of the orthogermanates LiNdGeO{sub 4} (space group Pbcn) and CeGeO{sub 4} (space group I 4{sub 1}/a, the scheelite structure type), which have MT frameworks composed of polyhedral structural units in the form of M dodecahedra (NdO{sub 8} and CeO{sub 8}) and T tetrahedra (GeO{sub 4}), is performed using the method of coordination sequences with the TOPOS program package. It is established that the structures of both orthogermanates are characterized by equivalent crystal-forming nets 4444. The cluster precursors of the M{sub 2}T{sub 2} cyclic type are identified by the method of two-color decomposition. The local symmetry of four-polyhedral clusters corresponds to the point group 2. In the precursor of the LiNdGeO{sub 4} orthogermanate, the Li atom is located above the M{sub 2}T{sub 2} ring. The number of Li-O bonds in this precursor is 4. The cluster precursors M{sub 2}T{sub 2} and LiM{sub 2}T{sub 2} are responsible for the formation of crystal-forming clusters of a higher level according to the mechanism of matrix self-assembly. The coordination numbers of the cluster precursors in two-dimensional nets for these structures are found to be equal to 4. The equivalent bilayer TR,Ge stacks that consist of eight cluster precursors are revealed in the structures under investigation. It is demonstrated that there exist three types of translational interlayer arrangements of cluster precursors upon the formation of macrostructures of the orthogermanates.

  16. Simulation of self-organization processes in crystal-forming systems: Supramolecular cyclic R6 cluster precursors and self-assembly of TeO2- TEL ( Tellurite) and TeO2- PAR ( Paratellurite) structures

    NASA Astrophysics Data System (ADS)

    Ilyushin, G. D.

    2014-11-01

    The supramolecular chemistry of oxides of sp elements (SO2, SeO2, and TeO2) is considered. The self-assembly of TeO2- TEL ( Tellurite) and TeO2- PAR ( Paratellurite) crystal structures is simulated. Methods of combinatorial and topological analysis (TOPOS program package) are applied which are based on constructing a basis 3D network of the structure in the form of a graph, the sites of which correspond to the positions of centroids of TeO2 molecules and the edges characterize bonds between them. The topological type of the basis 2D network in the TeO2- TEL structure corresponds to graphite (C- GRA), while in the TeO2- PAR structure the basis network corresponds to the 3D diamond network (C- DIA). A nanocluster precursor of cyclic type ( R6) composed of six covalently bound TeO2 molecules (chair conformation) is established for both structures. The desymmetrization of the cyclic structure of the R6 cluster in TeO2- PAR is related to the formation of Te-Te bonds with lengths of 3.824 and 4.062 Å. The symmetry and topology code of the processes of self-assembly of 3D structures from nanocluster precursors is completely reconstructed into the form "primary chain → microlayer → microframework." In both structures R6 clusters form 2D packings with a coordination number of 6. The cluster self-assembly model explains the specific features of the morphogenesis of TeO2- TEL and TeO2- PAR (phases with low and high crystallization temperatures, respectively): platelike shape, perfect cleavage in the (110) plane, and preferred growth in the primar-chain direction [100] in the former case and growth in the direction of the primary [001] axis with the preferred formation of tetragonal prism faces (110) in the latter case.

  17. Role of the carboxy terminus of polypeptide D1 in the assembly of a functional water-oxidizing manganese cluster in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803: assembly requires a free carboxyl group at C-terminal position 344.

    PubMed

    Nixon, P J; Trost, J T; Diner, B A

    1992-11-10

    The D1 polypeptide of the photosystem II (PSII) reaction center is synthesized as a precursor polypeptide which is posttranslationally processed at the carboxy terminus. It has been shown in spinach that such processing removes nine amino acids, leaving Ala344 as the C-terminal residue [Takahashi, M., Shiraishi, T., & Asada, K. (1988) FEBS Lett. 240, 6-8; Takahashi, Y., Nakane, H., Kojima, H., & Satoh, K. (1990) Plant Cell Physiol. 31, 273-280]. We show here that processing on the carboxy side of Ala344 also occurs in the cyanobacterium Synechocystis 6803, resulting in the removal of 16 amino acids. By constructing a deletion strain of Synechocystis 6803 that lacks the three copies of the psbA gene encoding D1, we have developed a system for generating psbA mutants. Using this system, we have constructed mutants of Synechocystis 6803 that are modified in the region of the C-terminus of the D1 polypeptide. Characterization of these mutants has revealed that (1) processing of the D1 polypeptide is blocked when the residue after the cleavage site is changed from serine to proline (mutant Ser345Pro) with the result that the manganese cluster is unable to assemble correctly; (2) the C-terminal extension of 16 amino acid residues can be deleted with little consequence either for insertion of D1 into the thylakoid membrane or for assembly of D1 into a fully active PSII complex; (3) removal of only one more residue (mutant Ala344stop) results in a loss of assembly of the manganese cluster; and (4) the ability of detergent-solubilized PSII core complexes (lacking the manganese cluster) to bind and oxidize exogenous Mn2+ by the secondary donor, Z+, is largely unaffected in the processing mutants (the Ser345Pro mutant of Synechocystis 6803 and the LF-1 mutant of Scenedesmus obliquus) and the truncation mutant Ala344stop. Our results are consistent with a role for processing in regulating the assembly of the photosynthetic manganese cluster and a role for the free carboxy

  18. A thermostable hybrid cluster protein from Pyrococcus furiosus: effects of the loss of a three helix bundle subdomain.

    PubMed

    Overeijnder, Marieke L; Hagen, Wilfred R; Hagedoorn, Peter-Leon

    2009-06-01

    Pyrococcus furiosus hybrid cluster protein (HCP) was expressed in Escherichia coli, purified, and characterized. This is the first archaeal and thermostable HCP to be isolated. Compared with the protein sequences of previously characterized HCPs from mesophiles, the protein sequence of P. furiosus HCP exhibits a deletion of approximately 13 kDa as a single amino acid stretch just after the N-terminal cysteine motif, characteristic for class-III HCPs from (hyper)thermophilic archaea and bacteria. The protein was expressed as a thermostable, soluble homodimeric protein. Hydroxylamine reductase activity of P. furiosus HCP showed a K(m) value of 0.40 mM and a k(cat) value of 3.8 s(-1) at 70 degrees C and pH 9.0. Electron paramagnetic resonance spectroscopy showed evidence for the presence of a spin-admixed, S = 3/2 [4Fe-4S](+) cubane cluster and of the hybrid cluster. The cubane cluster of P. furiosus HCP is presumably coordinated by a CXXC-X(7)-C-X(5)-C motif close to the N-terminus, which is similar to the CXXC-X(8)-C-X(5)-C motif of the Desulfovibrio desulfuricans and Desulfovibrio vulgaris HCPs. Amino acid sequence alignment and homology modeling of P. furiosus HCP reveal that the deletion results in a loss of one of the two three-helix bundles of domain 1. Clearly the loss of one of the three-helix bundles of domain 1 does not diminish the hydroxylamine reduction activity and the incorporation of the iron-sulfur clusters. PMID:19241093

  19. Electronic structure of the unique [4Fe-3S] cluster in O2-tolerant hydrogenases characterized by 57Fe Mossbauer and EPR spectroscopy.

    PubMed

    Pandelia, Maria-Eirini; Bykov, Dmytro; Izsak, Robert; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Neese, Frank; Lubitz, Wolfgang

    2013-01-01

    Iron-sulfur clusters are ubiquitous electron transfer cofactors in hydrogenases. Their types and redox properties are important for H(2) catalysis, but, recently, their role in a protection mechanism against oxidative inactivation has also been recognized for a [4Fe-3S] cluster in O(2)-tolerant group 1 [NiFe] hydrogenases. This cluster, which is uniquely coordinated by six cysteines, is situated in the proximity of the catalytic [NiFe] site and exhibits unusual redox versatility. The [4Fe-3S] cluster in hydrogenase (Hase) I from Aquifex aeolicus performs two redox transitions within a very small potential range, forming a superoxidized state above +200 mV vs. standard hydrogen electrode (SHE). Crystallographic data has revealed that this state is stabilized by the coordination of one of the iron atoms to a backbone nitrogen. Thus, the proximal [4Fe-3S] cluster undergoes redox-dependent changes to serve multiple purposes beyond classical electron transfer. In this paper, we present field-dependent (57)Fe-Mössbauer and EPR data for Hase I, which, in conjunction with spectroscopically calibrated density functional theory (DFT) calculations, reveal the distribution of Fe valences and spin-coupling schemes for the iron-sulfur clusters. The data demonstrate that the electronic structure of the [4Fe-3S] core in its three oxidation states closely resembles that of corresponding conventional [4Fe-4S] cubanes, albeit with distinct differences for some individual iron sites. The medial and distal iron-sulfur clusters have similar electronic properties as the corresponding cofactors in standard hydrogenases, although their redox potentials are higher. PMID:23267108

  20. Modeling of the self-organization processes in crystal-forming systems: Symmetry and topological code of cluster self-assembly of molecular (island) and framework MT structures of vanadyl sulfates

    NASA Astrophysics Data System (ADS)

    Ilyushin, G. D.; Pisarevskii, Yu. V.

    2015-11-01

    The supramolecular chemistry of vanadyl sulfates, consisting of polyhedral clusters V(O, OH, H2O)6 with octahedral O coordination (M polyhedra) and SO4 tetrahedra (T polyhedra) and forming molecular (island) and framework 3D MT structures, is considered. Algorithms of combinatorial and topological analysis are developed that make it possible to reconstruct (based on known structural data) the symmetry and topological code of the matrix convergent self-assembly of crystal structure. Cluster modeling of the selfassembly of molecular (island) MT structures of the V2O2(H2O)6(SO4)2 · 4H2O (anorthominasragrite (ANM)) and V2O2(H2O)6(SO4)2 (bobjonesite (BBN)) compositions and topologically different framework 3D MT structures with covalent bonds, V2O2(SO4)2 (pauflerite (PAF) and synthetic phase (SYN)), is performed. A 3D reconstruction of the self-assembly mechanism in the form nanocluster precursor S 0 3 → primary chain → S 1 3 microlayer S 2 3 → microframework S 3 3 has revealed an invariant type of cyclic cluster precursor M2T2 (with a symmetry g = overline 1 ) for all compounds; differences in the self-assembly mechanisms are found for ANM and BBN in the stage of formation of primary chain S 1 3 and for PAF and SYN in the stage of formation of microlayer S 2 3. Basic 2D and 3D nets are presented in the form of graphs, the sites of which correspond to the positions of centroids of cluster precursors M2T2. The same topological type of basic 2D nets (4.4.4.4) is ascertained for all compounds. A basic 3D net corresponding to a simple cubic structure of Po (coordination number (CN) = 6) is established for ANM, SYN, and PAF; the basic 3D net for BBN corresponds to the cubic F structure of Cu (CN = 12).

  1. Communication: The cluster vapor to cluster solid transition

    NASA Astrophysics Data System (ADS)

    Sweatman, Martin B.; Lue, Leo

    2016-05-01

    Until now, depletion induced transitions have been the hallmark of multicomponent systems only. Monte Carlo simulations reveal a depletion-induced phase transition from cluster vapor to cluster solid in a one-component fluid with competing short range and long range interactions. This confirms a prediction made by earlier theoretical work. Analysis of renormalized cluster-cluster and cluster-vapor interactions suggests that a cluster liquid is also expected within a very narrow range of model parameters. These insights could help identify the mechanisms of clustering in experiments and assist the design of colloidal structures through engineered self-assembly.

  2. Assemblies based on the directing effect of non-classical W{sub 18} anionic clusters and the rod-like trans-1,2-di-(4-pyridyl)-ethylen (bpe)

    SciTech Connect

    Han, Zhangang; Wang, Yanna; Song, Xuejun; Huang, Jiao; Zhai, Xueliang

    2011-03-15

    Two polyoxometalate (POM) supramolecular assemblies based on W{sub 18} clusters and the rigid organic trans-1,2-di-(4-pyridyl)-ethylen (bpe) have been synthesized and fully characterized, namely (H{sub 2}bpe)3.5H{sub 2}[SbW{sub 18}O{sub 60}].5H{sub 2}O (1), and (H{sub 2}bpe)5[Ni{sub 4}(AsW{sub 9}O{sub 34}){sub 2}(H{sub 2}O){sub 2}].3H2O (2). Compounds 1-2 are formed from organic bpe cations and different polytungstate anions: pseudo-Dawson-type [SbW{sub 18}O{sub 60}]{sup 9-} in 1 and sandwich-type [Ni{sub 4}(H{sub 2}O){sub 2}(AsW{sub 9}O{sub 34}){sub 2}]{sup 10-} in 2. Both of compounds 1-2 crystallize in a low-symmetrical space group of P-1 and consist of a complicated supramolecular network based on non-covalent intermolecular weak interactions, including hydrogen bonding and {pi}...{pi} stacking. The multipoint hydrogen bonding interactions constitute the structural feature in two supramolecular frameworks. The UV-vis, fluorescence and electrochemistry properties are also studied. -- Graphical abstract: Two polyoxometalate-based supramolecular assemblies built upon W{sub 18} clusters and the rigid organic trans-1,2-di-(4-pyridyl)-ethylen (bpe) have been synthesized and characterized. Research highlights: > Sb{sup 3+} has a larger ionic radius to prevent the formation of the sandwich-type polyoxometalate cluster. > Non-covalent interactions play important roles in the self-organization process. > Polyanion can structure the conjugated organic molecule into a parallel and ordered arrangement. > Polyanion-based hybrid is a potential candidate in the modified material for electrode.

  3. 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

  4. Phosphatidylinositol 4,5-Bisphosphate Clusters the Cell Adhesion Molecule CD44 and Assembles a Specific CD44-Ezrin Heterocomplex, as Revealed by Small Angle Neutron Scattering

    DOE PAGESBeta

    Khajeh, Jahan Ali; Ju, Jeong Ho; Gupta, Yogesh K.; Stanley, Christopher B.; Do, Changwoo; Heller, William T.; Aggarwal, Aneel K.; Callaway, David J.E.; Bu, Zimei

    2015-01-08

    The cell adhesion molecule CD44 regulates diverse cellular functions, including cell-cell and cell-matrix interaction, cell motility, migration, differentiation, and growth. In cells, CD44 co-localizes with the membrane-cytoskeleton adapter protein Ezrin, which links the CD44 assembled receptor signaling complexes to the cytoskeletal actin and organizes the spatial and temporal localization of signaling events. Here we report that the cytoplasmic tail of CD44 (CD44ct) is largely disordered and adopts an autoinhibited conformation, which prevents CD44ct from binding directly to activated Ezrin in solution. Binding to the signaling lipid phosphatidylinositol 4,5-biphosphlate (PIP2) disrupts autoinhibition in CD44ct, and activates CD44ct to associate with Ezrin.more » Further, using contrast variation small angle neutron scattering, we show that PIP2 mediates the assembly of a specific hetero-tetramer complex of CD44ct with Ezrin. This study reveals a novel autoregulation mechanism in the cytoplasmic tail of CD44 and the role of PIP2 in mediating the assembly of multimeric CD44ct-Ezrin complexes. We hypothesize that polyvalent electrostatic interactions are responsible for the assembly of multimeric PIP2-CD44-Ezrin complexes.« less

  5. Phosphatidylinositol 4,5-Bisphosphate Clusters the Cell Adhesion Molecule CD44 and Assembles a Specific CD44-Ezrin Heterocomplex, as Revealed by Small Angle Neutron Scattering

    SciTech Connect

    Khajeh, Jahan Ali; Ju, Jeong Ho; Gupta, Yogesh K.; Stanley, Christopher B.; Do, Changwoo; Heller, William T.; Aggarwal, Aneel K.; Callaway, David J.E.; Bu, Zimei

    2015-01-08

    The cell adhesion molecule CD44 regulates diverse cellular functions, including cell-cell and cell-matrix interaction, cell motility, migration, differentiation, and growth. In cells, CD44 co-localizes with the membrane-cytoskeleton adapter protein Ezrin, which links the CD44 assembled receptor signaling complexes to the cytoskeletal actin and organizes the spatial and temporal localization of signaling events. Here we report that the cytoplasmic tail of CD44 (CD44ct) is largely disordered and adopts an autoinhibited conformation, which prevents CD44ct from binding directly to activated Ezrin in solution. Binding to the signaling lipid phosphatidylinositol 4,5-biphosphlate (PIP2) disrupts autoinhibition in CD44ct, and activates CD44ct to associate with Ezrin. Further, using contrast variation small angle neutron scattering, we show that PIP2 mediates the assembly of a specific hetero-tetramer complex of CD44ct with Ezrin. This study reveals a novel autoregulation mechanism in the cytoplasmic tail of CD44 and the role of PIP2 in mediating the assembly of multimeric CD44ct-Ezrin complexes. We hypothesize that polyvalent electrostatic interactions are responsible for the assembly of multimeric PIP2-CD44-Ezrin complexes.

  6. Universal Cluster Deposition System

    NASA Astrophysics Data System (ADS)

    Qiang, You; Sun, Zhiguang; Sellmyer, David J.

    2001-03-01

    We have developed a universal cluster deposition system (UCDS), which combines a new kind of sputtering-gas-aggregation (SGA) cluster beam source with two atom beams from magnetron sputtering. A highly intense, very stable beam of nanoclusters (like Co, Fe, Ni, Si, CoSm or CoPt) are produced. A quadrupole and/or a new high transmission infinite range mass selector have been designed for the cluster beam. The size distribution (Δd/d) is between 0.05+/-0.10, measured in situ by TOF. A range of mean cluster size is 2 to 10 nm. Usually the deposition rate is about 5 deg/s. The cluster concentration in the film is adjusted through the ratio of cluster and atomic beam deposition rates, as measured in situ with a rotatable quartz microbalance. The UCDS can be used to prepare coated clusters. After exiting from the cluster source, the clusters can be coated first with an atomic or molecular species in an evaporation chamber, and deposited alone or co-deposited with another material. This system is used to deposit simultaneously or alternately mesoscopic thin films or multilayers, and offers the possibility to control independently the incident cluster size and concentration, and thereby the interaction between clusters and cluster-matrix material which is of interest for fundamental research and industry applications. Magnetic properties of Co cluster-assembled materials will be discussed. * Research supported by NSF, DARPA through ARO, and CMRA

  7. Biochemical and spectroscopic studies of epoxyqueuosine reductase: A novel iron-sulfur cluster and cobalamin containing protein involved in the biosynthesis of queuosine

    PubMed Central

    Miles, Zachary D.; Myers, William K.; Kincannon, William M.; Britt, R. David; Bandarian, Vahe

    2015-01-01

    Queuosine is a hypermodified nucleoside present in the wobble position of tRNAs with a 5′-GUN-3′ sequence in their anticodon (His, Asp, Asn, and Tyr). The 7-deazapurine core of the base is synthesized de novo in prokaryotes from guanosine-5′-triphosphate in a series of eight sequential enzymatic transformations, the final three occurring on tRNA. Epoxyqueuosine reductase (QueG), catalyzes the final step in the pathway, which entails the 2-electron reduction of epoxyqueuosine to form queuosine. Biochemical analyses reveal that this enzyme requires cobalamin and two [4Fe-4S] clusters for catalysis. Spectroscopic studies show that the cobalamin appears to bind in a base-off conformation, whereby the dimethylbenzimidazole moiety of the cofactor is removed from the coordination sphere of the cobalt but not replaced by an imidazole sidechain, which is a hallmark of many cobalamin-dependent enzymes. The bioinformatically-identified residues are shown to have a role in modulating the primary coordination sphere of cobalamin. These studies provide the first demonstration of the cofactor requirements for QueG. PMID:26230193

  8. Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore

    PubMed Central

    Zhang, Fan; Scheerer, Patrick; Oberpichler, Inga; Lamparter, Tilman; Krauß, Norbert

    2013-01-01

    The (6-4) photolyases use blue light to reverse UV-induced (6-4) photoproducts in DNA. This (6-4) photorepair was thought to be restricted to eukaryotes. Here we report a prokaryotic (6-4) photolyase, PhrB from Agrobacterium tumefaciens, and propose that (6-4) photolyases are broadly distributed in prokaryotes. The crystal structure of photolyase related protein B (PhrB) at 1.45 Å resolution suggests a DNA binding mode different from that of the eukaryotic counterparts. A His-His-X-X-Arg motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. The PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore and a [4Fe-4S] cluster bound to the catalytic domain. A significant part of the Fe-S fold strikingly resembles that of the large subunit of eukaryotic and archaeal primases, suggesting that the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. Our study presents a unique prokaryotic (6-4) photolyase and proposes that the prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family. PMID:23589886

  9. The FX iron-sulfur cluster serves as the terminal bound electron acceptor in heliobacterial reaction centers.

    PubMed

    Romberger, Steven P; Golbeck, John H

    2012-03-01

    Phototrophs of the family Heliobacteriaceae contain the simplest known Type I reaction center (RC), consisting of a homodimeric (PshA)(2) core devoid of bound cytochromes and antenna proteins. Unlike plant and cyanobacterial Photosystem I in which the F(A)/F(B) protein, PsaC, is tightly bound to P(700)-F(X) cores, the RCs of Heliobacterium modesticaldum contain two F(A)/F(B) proteins, PshBI and PshBII, which are loosely bound to P(800)-F(X) cores. These two 2[4Fe-4S] ferredoxins have been proposed to function as mobile redox proteins, reducing downstream metabolic partners much in the same manner as does [2Fe-2S] ferredoxin or flavodoxin (Fld) in PS I. Using P(800)-F(X) cores devoid of PshBI and PshBII, we show that iron-sulfur cluster F(X) directly reduces Fld without the involvement of F(A) or F(B) (Fld is used as a proxy for soluble redox proteins even though a gene encoding Fld is not identified in the H. modesticaldum genome). The reduction of Fld is suppressed by the addition of PshBI or PshBII, an effect explained by competition for the electron on F(X). In contrast, P(700)-F(X) cores require the presence of the PsaC, and hence, the F(A)/F(B) clusters for Fld (or ferredoxin) reduction. Thus, in H. modesticaldum, the interpolypeptide F(X) cluster serves as the terminal bound electron acceptor. This finding implies that the homodimeric (PshA)(2) cores should be capable of donating electrons to a wide variety of yet-to-be characterized soluble redox partners. PMID:22297911

  10. Self-Assembled Multimetallic/Peptide Complexes: Structures and Unimolecular Reactions of [Mn (GlyGly-H)2n-1 ](+) and Mn+1 (GlyGly-H2n ](2+) Clusters in the Gas Phase.

    PubMed

    Moghaddam, Maryam B; Jami-Alahmadi, Yasaman; Fridgen, Travis D

    2015-10-26

    The unimolecular chemistry and structures of self-assembled complexes containing multiple alkaline-earth-metal dications and deprotonated GlyGly ligands are investigated. Singly and doubly charged ions [Mn (GlyGly-H)n-1 ](+) (n=2-4), [Mn+1 (GlyGly-H)2n ](2+) (n=2,4,6), and [M(GlyGly-H)GlyGly](+) were observed. The losses of 132 Da (GlyGly) and 57 Da (determined to be aminoketene) were the major dissociation pathways for singly charged ions. Doubly charged Mg(2+) clusters mainly lost GlyGly, whereas those containing Ca(2+) or Sr(2+) also underwent charge separation. Except for charge separation, no loss of metal cations was observed. Infrared multiple photon dissociation spectra were the most consistent with the computed IR spectra for the lowest energy structures, in which deprotonation occurs at the carboxyl acid groups and all amide and carboxylate oxygen atoms are complexed to the metal cations. The N-H stretch band, observed at 3350 cm(-1) , is indicative of hydrogen bonding between the amine nitrogen atoms and the amide hydrogen atom. This study represents the first into large self-assembled multimetallic complexes bound by peptide ligands. PMID:26279054

  11. Interaction with DNA of a heteronuclear [Na2Cu4] coordination cluster obtained from the assembly of two hydroxo-bridged [Cu(II)2] units by a dimeric sodium nitrate template.

    PubMed

    Mandal, Debashree; Chauhan, Mala; Arjmand, Farukh; Aromí, Guillem; Ray, Debashis

    2009-11-14

    The heteronuclear [Na(2)Cu(4)(bemp)(2)(OH)(2)(NO(3))(2)(OH(2))(4)] x 5 H(2)O (1 x 5H(2)O; H(3)bemp: 2,6-bis-[(2-hydroxyethylimino)-methyl]-4-methyl-phenol) cluster has been synthesized in aqueous-methanol at room temperature and structurally characterized. The water soluble complex is obtained from the template assembly of two [Cu(2)(bemp)(OH)] neutral fragments through their weak oxophillic interactions with two interconnected NaNO(3) units as core. Four [Na(2)Cu(4)] units form a metal-organic cage arrangement in the crystal lattice that traps a (H(2)O)(7) cluster. Variable-temperature magnetic susceptibility measurements (2-300 K) reveals a strong antiferromagnetic coupling between the Cu(II) ions within the dimers with J = -124.1 cm(-1) (in the H = -2JS(1)S(2) convention). The interaction of complex 1 x 3H(2)O with calf thymus DNA (binding constant K(b), 4.6 x 10(4) M(-1)) in Tris buffer was studied by UV-visible and emission titration, and cyclic voltammetry. The hexanuclear Na(2)Cu(4) complex also binds double-stranded supercoiled plasmid pBR322 DNA and displays efficient hydrolytic cleavage. The hydrolytic mechanism is supported by evidence from DNA relegation employing T4 ligase assay and reactive oxygen species (ROS) quenching cleavage experiments. PMID:20449195

  12. Planetary Nebulae and their parent stellar populations. Tracing the mass assembly of M87 and Intracluster light in the Virgo cluster core

    NASA Astrophysics Data System (ADS)

    Arnaboldi, Magda; Longobardi, Alessia; Gerhard, Ortwin

    2016-08-01

    The diffuse extended outer regions of galaxies are hard to study because they are faint, with typical surface brightness of 1% of the dark night sky. We can tackle this problem by using resolved star tracers which remain visible at large distances from the galaxy centers. This article describes the use of Planetary Nebulae as tracers and the calibration of their properties as indicators of the star formation history, mean age and metallicity of the parent stars in the Milky Way and Local Group galaxies. We then report on the results from a deep, extended, planetary nebulae survey in a 0.5 deg2 region centered on the brightest cluster galaxy NGC 4486 (M87) in the Virgo cluster core, carried out with SuprimeCam@Subaru and FLAMES-GIRAFFE@VLT. Two planetary nebulae populations are identified out to 150 kpc distance from the center of M87. One population is associated with the M87 halo and the second one with the intracluster light in the Virgo cluster core. They have different line-of-sight velocity and spatial distributions, as well as different planetary nebulae specific frequencies and luminosity functions. The intracluster planetary nebulae in the surveyed region correspond to a luminosity of four times the luminosity of the Large Magellanic Cloud. The M87 halo planetary nebulae trace an older, more metal-rich, parent stellar population. A substructure detected in the projected phase-space of the line-of-sight velocity vs. major axis distance for the M87 halo planetary nebulae provides evidence for the recent accretion event of a satellite galaxy with luminosity twice that of M33. The satellite stars were tidally stripped about 1 Gyr ago, and reached apocenter at a major axis distance of 60-90 kpc from the center of M87. The M87 halo is still growing significantly at the distances where the substructure is detected.

  13. Respiratory chain complex I is essential for sexual development in neurospora and binding of iron sulfur clusters are required for enzyme assembly.

    PubMed Central

    Duarte, M; Videira, A

    2000-01-01

    We have cloned and disrupted in vivo, by repeat-induced point mutations, the nuclear gene coding for an iron sulfur subunit of complex I from Neurospora crassa, homologue of the mammalian TYKY protein. Analysis of the obtained mutant nuo21.3c revealed that complex I fails to assemble. The peripheral arm of the enzyme is disrupted while its membrane arm accumulates. Furthermore, mutated 21.3c-kD proteins, in which selected cysteine residues were substituted with alanines or serines, were expressed in mutant nuo21. 3c. The phenotypes of these strains regarding the formation of complex I are similar to that of the original mutant, indicating that binding of iron sulfur centers to protein subunits is a prerequisite for complex I assembly. Homozygous crosses of nuo21.3c strain, and of other complex I mutants, are unable to complete sexual development. The crosses are blocked at an early developmental stage, before fusion of the nuclei of opposite mating types. This phenotype can be rescued only by transformation with the intact gene. Our results suggest that this might be due to the compromised capacity of complex I-defective strains in energy production. PMID:11014810

  14. Oil Phase Evaporation Induced Self-Assembly of Hydrophobic Nanoparticles into Spherical Clusters with Controlled Surface Chemistry in an Oil-in-Water Dispersion and Comparison of Behaviors of Individual and Clustered Iron Oxide Nanoparticles

    PubMed Central

    Qiu, Penghe; Jensen, Christina; Charity, Njoku; Towner, Rheal; Mao, Chuanbin

    2010-01-01

    We report a general method for preparing nanoparticle clusters (NPCs) in an oil-in-water emulsion system mediated by cetyl trimethylammonium bromide (CTAB) where previously, only individual nanoparticles were obtained. NPCs of magnetic, metallic and semiconductor nanoparticles have been prepared to demonstrate the generality of the method. The NPCs were spherical and composed of densely packed individual nanoparticles. The number density of nanoparticles in the oil phase was found to be critical for the formation, morphology and yield of NPCs. The method developed here is scalable and can produce NPCs in nearly 100% yield at a concentration of 5 mg/ml in water which is approximately 5 times higher than the highest value reported in literature. The surface chemistry of NPCs can also be controlled by replacing CTAB with polymers containing different functional groups via a similar procedure. The reproducible production of NPCs with well defined shapes has allowed us to compare the properties of individual and clustered iron oxide nanoparticles including magnetization, magnetic moments and contrast enhancement in magnetic resonance imaging (MRI). We found that due to their collective properties, NPCs are more responsive to an external magnetic field and can potentially serve as better contrast enhancement agents than individually dispersed magnetic NPs in MRI. PMID:21117657

  15. Synergistic Assembly of Heavy Metal Clusters and Luminescent Organic Bridging Ligands in Metal–Organic Frameworks for Highly Efficient X-ray Scintillation

    PubMed Central

    2015-01-01

    We have designed two metal–organic frameworks (MOFs) to efficiently convert X-ray to visible-light luminescence. The MOFs are constructed from M6(μ3-O)4(μ3-OH)4(carboxylate)12 (M = Hf or Zr) secondary building units (SBUs) and anthracene-based dicarboxylate bridging ligands. The high atomic number of Zr and Hf in the SBUs serves as effective X-ray antenna by absorbing X-ray photons and converting them to fast electrons through the photoelectric effect. The generated electrons then excite multiple anthracene-based emitters in the MOF through inelastic scattering, leading to efficient generation of detectable photons in the visible spectrum. The MOF materials thus serve as efficient X-ray scintillators via synergistic X-ray absorption by the metal-cluster SBUs and optical emission by the bridging ligands. PMID:24730683

  16. Synergistic assembly of heavy metal clusters and luminescent organic bridging ligands in metal-organic frameworks for highly efficient X-ray scintillation.

    PubMed

    Wang, Cheng; Volotskova, Olga; Lu, Kuangda; Ahmad, Moiz; Sun, Conroy; Xing, Lei; Lin, Wenbin

    2014-04-30

    We have designed two metal-organic frameworks (MOFs) to efficiently convert X-ray to visible-light luminescence. The MOFs are constructed from M6(μ3-O)4(μ3-OH)4(carboxylate)12 (M = Hf or Zr) secondary building units (SBUs) and anthracene-based dicarboxylate bridging ligands. The high atomic number of Zr and Hf in the SBUs serves as effective X-ray antenna by absorbing X-ray photons and converting them to fast electrons through the photoelectric effect. The generated electrons then excite multiple anthracene-based emitters in the MOF through inelastic scattering, leading to efficient generation of detectable photons in the visible spectrum. The MOF materials thus serve as efficient X-ray scintillators via synergistic X-ray absorption by the metal-cluster SBUs and optical emission by the bridging ligands. PMID:24730683

  17. Metal-binding properties and structural characterization of a self-assembled coiled coil: formation of a polynuclear Cd-thiolate cluster.

    PubMed

    Zaytsev, Daniil V; Morozov, Vasily A; Fan, Jiufeng; Zhu, Xianchun; Mukherjee, Madhumita; Ni, Shuisong; Kennedy, Michael A; Ogawa, Michael Y

    2013-02-01

    This paper describes the design, characterization, and metal-binding properties of a 32-residue polypeptide called AQ-C16C19. The sequence of this peptide is composed of four repeats of the seven residue sequence Ile-Ala-Ala-Leu-Glu-Gln-Lys but with a Cys-X-X-Cys metal-binding motif substituted at positions 16-19. Size exclusion chromatography with multiangle light scattering detection (SEC-MALS) and circular dichroism (CD) spectroscopy studies showed that the apo peptide exhibits a pH-dependent oligomerization state in which a three-stranded α-helical coiled coil is dominant between pH5.4 and 8.5. The Cd(2+)-binding properties of the AQ-C16C19 peptide were studied by ultraviolet-visible spectroscopy (UV-vis), electrospray ionization mass spectrometry (ESI MS), and (113)Cd NMR techniques. The holoprotein was found to contain a polynuclear cadmium-thiolate center formed within the hydrophobic core of the triple-stranded α-helical coiled-coil structure. The X-ray crystal structure of the Cd-loaded peptide, resolved at 1.85Å resolution, revealed an adamantane-like configuration of the polynuclear metal center consisting of four cadmium ions, six thiolate sulfur ligands from cysteine residues and four oxygen-donor ligands. Three of these are from glutamic acid residues and one is from an exogenous water molecule. Thus, each cadmium ion is coordinated in a distorted tetrahedral S(3)O geometry. The metal cluster was found to form cooperatively at pH5.4 but in a stepwise fashion at pH>7. The results demonstrate that synthetic coiled-coils can be designed to incorporate multinuclear metal clusters, a proof-of-concept for their potential use in developing synthetic metalloenzymes and multi-electron redox agents. PMID:23160144

  18. Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63.

    PubMed

    Habe, H; Miyakoshi, M; Chung, J; Kasuga, K; Yoshida, T; Nojiri, H; Omori, T

    2003-03-01

    Phthalate is a metabolic intermediate of the pathway of fluorene (FN) degradation via angular dioxygenation. A gene cluster responsible for the conversion of phthalate to protocatechuate was cloned from the dibenzofuran (DF)- and FN-degrading bacterium Terrabacter sp. strain DBF63 and sequenced. The genes encoding seven catabolic enzymes, oxygenase large subunit of phthalate 3,4-dioxygenase (phtA1), oxygenase small subunit of phthalate 3,4-dioxygenase (phtA2), cis-3,4-dihydroxy-3,4-dihydrophthalate dehydrogenase (phtB), [3Fe-4S] or [4Fe-4S] type of ferredoxin (phtA3), ferredoxin reductase (phtA4), 3,4-dihydroxyphthalate decarboxylase (phtC) and putative regulatory protein (phtR), were found in the upstream region of the angular dioxygenase gene (dbfA1A2), encoded in this order. Escherichia coli carrying phtA1A2BA3A4 genes converted phthalate to 3,4-dihydroxyphthalate, and the 3,4-dihydroxyphthalate decarboxylase activity by E. coli cells carrying phtC was finally detected with the introduction of a Shine-Dalgarno sequence in the upstream region of its initiation codon. Homology analysis on the upstream region of the pht gene cluster revealed that there was an insertion sequence (IS) (ISTesp2; ORF14 and its flanking region), part of which was almost 100% identical to the orf1 and its flanking region adjacent to the extradiol dioxygenase gene ( bphC1) involved in the DF degradation of Terrabacter sp. strain DPO360 [Schmid et al. (1997) J Bacteriol 179:53-62]. This suggests that ISTesp2 plays a role in the metabolism of aromatic compounds in Terrabacter sp. strains DBF63 and DPO360. PMID:12658514

  19. Metal-induced self-assembly of peroxiredoxin as a tool for sorting ultrasmall gold nanoparticles into one-dimensional clusters

    NASA Astrophysics Data System (ADS)

    Ardini, Matteo; Giansanti, Francesco; di Leandro, Luana; Pitari, Giuseppina; Cimini, Annamaria; Ottaviano, Luca; Donarelli, Maurizio; Santucci, Sandro; Angelucci, Francesco; Ippoliti, Rodolfo

    2014-06-01

    Nanomanipulation of matter to create responsive, ordered materials still remains extremely challenging. Supramolecular chemistry has inspired new strategies by which such nanomaterials can be synthesized step by step by exploiting the self-recognition properties of molecules. In this work, the ring-shaped architecture of the 2-Cys peroxiredoxin I protein from Schistosoma mansoni, engineered to have metal ion-binding sites, is used as a template to build up 1D nanoscopic structures through metal-induced self-assembly. Chromatographic and microscopic analyses demonstrate the ability of the protein rings to stack directionally upon interaction with divalent metal ions and form well-defined nanotubes by exploiting the intrinsic recognition properties of the ring surfaces. Taking advantage of such behavior, the rings are then used to capture colloidal Ni2+-functionalized ultrasmall gold nanoparticles and arrange them into 1D arrays through stacking into peapod-like complexes. Finally, as the formation of such nano-peapods strictly depends on nanoparticle dimensions, the peroxiredoxin template is used as a colloidal cut-off device to sort by size the encapsulated nanoparticles. These results open up possibilities in developing Prx-based methods to synthesize new advanced functional materials.Nanomanipulation of matter to create responsive, ordered materials still remains extremely challenging. Supramolecular chemistry has inspired new strategies by which such nanomaterials can be synthesized step by step by exploiting the self-recognition properties of molecules. In this work, the ring-shaped architecture of the 2-Cys peroxiredoxin I protein from Schistosoma mansoni, engineered to have metal ion-binding sites, is used as a template to build up 1D nanoscopic structures through metal-induced self-assembly. Chromatographic and microscopic analyses demonstrate the ability of the protein rings to stack directionally upon interaction with divalent metal ions and form well

  20. Energies and spin states of FeS(0/-), FeS2(0/-), Fe2S2(0/-), Fe3S4(0/-), and Fe4S4(0/-) clusters.

    PubMed

    Li, Yan-Ni; Wang, Shengguang; Wang, Tao; Gao, Rui; Geng, Chun-Yu; Li, Yong-Wang; Wang, Jianguo; Jiao, Haijun

    2013-04-15

    The structures and energies of the electronic ground states of the FeS(0/-), FeS2(0/-), Fe2S2(0/-), Fe3S4(0/-), and Fe4S4(0/-) neutral and anionic clusters have been computed systematically with nine computational methods in combination with seven basis sets. The computed adiabatic electronic affinities (AEA) have been compared with available experimental data. Most reasonable agreements between theory and experiment have been found for both hybrid B3LYP and B3PW91 functionals in conjugation with 6-311+G* and QZVP basis sets. Detailed comparisons between the available experimental and computed AEA data at the B3LYP/6-311+G* level identified the electronic ground state of (5)Δ for FeS, (4)Δ for FeS(-), (5)B2 for FeS2, (6)A1 for FeS2(-), (1)A1 for Fe2S2, (8)A' for Fe2S2(-), (5)A'' for Fe3S4, (6)A'' for Fe3S4(-), (1)A1 for Fe4S4, and (1)A2 for Fe4S4(-). In addition, Fe2S2, Fe3S4, Fe3S4(-), Fe4S4, and Fe4S4(-) are antiferromagnetic at the B3LYP/6-311+G* level. The magnetic properties are discussed on the basis of natural bond orbital analysis. PMID:23471871

  1. CRITICAL CONFIGURATION AND PHYSICS MEASUREMENTS FOR BERYLLIUM REFLECTED ASSEMBLIES OF U(93.15)O2 FUEL RODS (1.506-CM PITCH AND 7-TUBE CLUSTERS)

    SciTech Connect

    Margaret A. Marshall

    2014-03-01

    Cadmium ratios were measured with enriched uranium metal foils at various locations in the assembly with the fuel tube at the 1.506-cm spacing. They are described in the following subsections. The experiment configuration was the same as the first critical configuration described in HEU-COMP-FAST-004 (Case 1). The experimenter placed 0.75-cm-diameter × 0.010-cm-thick 93.15%-235U-enriched uranium metal foils with and without 0.051-cm-thick cadmium covers at various locations in the core and top reflector. One part of the cadmium cover was cupshape and contained the uranium foil. The other part was a lid that fit over the exposed side of the foil when it was in the cup shaped section of the cover. As can be seen in the logbook, two runs were required to obtain all the measurements necessary for the cadmium ratio. The bare foil measurements within the top reflector were run first as part of the axial foil activation measurements. The results of this run are used for both the axial activation results and the cadmium ratios. Cadmium covered foils were then placed at the same location through the top reflector in a different run. Three pairs of bare and cadmium covered foils were also placed through the core tank. One pair was placed at the axial center of a fuel tube 11.35 cm from the center of the core. Two pairs of foils were placed on top of fuel tubes 3.02 and 12.06 cm from the center of the core. The activation of the uranium metal foils was measured after removal from the assembly using two lead shielded NaI scintillation detectors as follows. The NaI scintillators were carefully matched and had detection efficiencies for counting delayed-fission-product gamma rays with energies above 250 KeV within 5%. In all foil activation measurements, one foil at a specific location was used as a normalizing foil to remove the effects of the decay of fission products during the counting measurements with the NaI detectors. The normalization foil was placed on one Na

  2. Critical Configuration and Physics Measurements for Beryllium Reflected Assemblies of U(93.15)O₂ Fuel Rods (1.506-cm Pitch and 7-Tube Clusters)

    SciTech Connect

    Marshall, Margaret A.; Bess, John D.; Briggs, J. Blair; Murphy, Michael F.; Mihalczo, John T.

    2015-03-01

    Cadmium ratios were measured with enriched uranium metal foils at various locations in the assembly with the fuel tube at the 1.506-cm spacing. They are described in the following subsections. The experiment configuration was the same as the first critical configuration described in HEU-COMP-FAST-004 (Case 1). The experimenter placed 0.75-cm-diameter × 0.010-cm-thick 93.15%-235U-enriched uranium metal foils with and without 0.051-cm-thick cadmium covers at various locations in the core and top reflector. One part of the cadmium cover was cupshape and contained the uranium foil. The other part was a lid that fit over the exposed side of the foil when it was in the cup shaped section of the cover. As can be seen in the logbook, two runs were required to obtain all the measurements necessary for the cadmium ratio. The bare foil measurements within the top reflector were run first as part of the axial foil activation measurements. The results of this run are used for both the axial activation results and the cadmium ratios. Cadmium covered foils were then placed at the same location through the top reflector in a different run. Three pairs of bare and cadmium covered foils were also placed through the core tank. One pair was placed at the axial center of a fuel tube 11.35 cm from the center of the core. Two pairs of foils were placed on top of fuel tubes 3.02 and 12.06 cm from the center of the core. The activation of the uranium metal foils was measured after removal from the assembly using two lead shielded NaI scintillation detectors as follows. The NaI scintillators were carefully matched and had detection efficiencies for counting delayed-fission-product gamma rays with energies above 250 KeV within 5%. In all foil activation measurements, one foil at a specific location was used as a normalizing foil to remove the effects of the decay of fission products during the counting measurements with the NaI detectors. The normalization foil was placed on one Na

  3. Galaxy population properties of the massive X-ray luminous galaxy cluster XDCP J0044.0-2033 at z = 1.58. Red-sequence formation, massive galaxy assembly, and central star formation activity

    NASA Astrophysics Data System (ADS)

    Fassbender, R.; Nastasi, A.; Santos, J. S.; Lidman, C.; Verdugo, M.; Koyama, Y.; Rosati, P.; Pierini, D.; Padilla, N.; Romeo, A. D.; Menci, N.; Bongiorno, A.; Castellano, M.; Cerulo, P.; Fontana, A.; Galametz, A.; Grazian, A.; Lamastra, A.; Pentericci, L.; Sommariva, V.; Strazzullo, V.; Šuhada, R.; Tozzi, P.

    2014-08-01

    Context. Recent observational progress has enabled the detection of galaxy clusters and groups out to very high redshifts and for the first time allows detailed studies of galaxy population properties in these densest environments in what was formerly known as the "redshift desert" at z> 1.5. Aims: We aim to investigate various galaxy population properties of the massive X-ray luminous galaxy cluster XDCP J0044.0-2033 at z = 1.58, which constitutes the most extreme currently known matter-density peak at this redshift. Methods: We analyzed deep VLT/HAWK-I near-infrared data with an image quality of 0.5'' and limiting Vega magnitudes (50% completeness) of 24.2 in J- and 22.8 in the Ks band, complemented by similarly deep Subaru imaging in i and V, Spitzer observations at 4.5 μm, and new spectroscopic observations with VLT/FORS 2. Results: We detect a cluster-associated excess population of about 90 galaxies, most of them located within the inner 30'' (250 kpc) of the X-ray centroid, which follows a centrally peaked, compact NFW galaxy surface-density profile with a concentration of c200 ≃ 10. Based on the Spitzer 4.5 μm imaging data, we measure a total enclosed stellar mass of M∗500 ≃ (6.3 ± 1.6) × 1012 M⊙ and a resulting stellar mass fraction of f∗,500 = M∗,500/M500 = (3.3 ± 1.4)%, consistent with local values. The total J- and Ks-band galaxy luminosity functions of the core region yield characteristic magnitudes J* and Ks* consistent with expectations from simple zf = 3 burst models. However, a detailed look at the morphologies and color distributions of the spectroscopically confirmed members reveals that the most massive galaxies are undergoing a very active mass-assembly epoch through merging processes. Consequently, the bright end of the cluster red sequence is not in place, while a red-locus population is present at intermediate magnitudes [Ks*, Ks* + 1.6], which is then sharply truncated at magnitudes fainter than Ks* + 1.6. The dominant

  4. Identification of the iron-sulfur clusters in a ferredoxin from the archaeon Sulfolobus acidocaldarius. Evidence for a reduced [3Fe-4S] cluster with pH-dependent electronic properties.

    PubMed

    Breton, J L; Duff, J L; Butt, J N; Armstrong, F A; George, S J; Pétillot, Y; Forest, E; Schäfer, G; Thomson, A J

    1995-11-01

    A ferredoxin isolated from the archaeon Sulfolobus acidocaldarius strain DSM 639 has been shown to contain one [3Fe-4S]1 + 10 cluster with a reduction potential of -275 mV and one [4Fe-4S]2+/1+ cluster with a reduction potential of -529 mV at pH 6.4, in the temperature range 0-50 degrees C. The monomer molecular mass was confirmed to be 10907.5 +/- 1.0 Da by electrospray mass spectrometry, as calculated from the published amino acid sequence [Minami, Y. Wakabayashi. S., Wada, K., Matsubara, H., Kerscher, L. & Oesterhelt, D. (1985) J. Biochem. (Tokyo) 97, 745-751], while the holoprotein molecular mass was found to be 11,550 +/- 1.0 Da. The reduced [3Fe-4S]0 cluster was also shown by direct electrochemistry and magnetic circular dichroic spectroscopy to undergo a one-proton uptake reaction as first observed for Azotobacter chroococcum ferredoxin I [George, S. J., Richards, A. J. M., Thomson, A. J. & Yates, M. G. (1984) Biochem. J. 224, 247-251]. The pKa of the protonation step has been determined by a novel thin film electrochemical method to be 5.8. This is significantly different from the pKa of 7.7 determined for A. vinelandii ferredoxin I [Shen, B., Martin, L. L., Butt, J. N., Armstrong, F. A., Stout, C. D., Jensen, J. M., Stephens, P. J., LaMar, G. N., Gorst, C. M. & Burgess, B. K. (1993) J. Biol. Chem. 268, 25928-25939] and indicates that the polypeptide chain around the [3Fe-4S] cluster controls this reaction. Although this appears to be only the second reported case of protonation at or near the reduced [3Fe-4S]0 cluster, its observation in S. acidocaldarius ferredoxin raises the question of the generality of this chemistry for 3Fe clusters. The similarity of the pKa to the estimated intracellular pH of S. acidocaldarius strongly suggests a physiological role for this process. PMID:8521862

  5. Joint assembly

    NASA Technical Reports Server (NTRS)

    Wilson, Andrew (Inventor); Punnoose, Andrew (Inventor); Strausser, Katherine (Inventor); Parikh, Neil (Inventor)

    2010-01-01

    A joint assembly is provided which includes a drive assembly and a swivel mechanism. The drive assembly features a motor operatively associated with a plurality of drive shafts for driving auxiliary elements, and a plurality of swivel shafts for pivoting the drive assembly. The swivel mechanism engages the swivel shafts and has a fixable element that may be attached to a foundation. The swivel mechanism is adapted to cooperate with the swivel shafts to pivot the drive assembly with at least two degrees of freedom relative to the foundation. The joint assembly allows for all components to remain encased in a tight, compact, and sealed package, making it ideal for space, exploratory, and commercial applications.

  6. The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium.

    PubMed

    Volbeda, Anne; Darnault, Claudine; Renoux, Oriane; Nicolet, Yvain; Fontecilla-Camps, Juan C

    2015-12-01

    The structure of the dimeric holo-fumarate and nitrate reduction regulator (FNR) from Aliivibrio fischeri has been solved at 2.65 Å resolution. FNR globally controls the transition between anaerobic and aerobic respiration in facultative anaerobes through the assembly/degradation of its oxygen-sensitive [4Fe-4S] cluster. In the absence of O2, FNR forms a dimer and specifically binds to DNA, whereas in its presence, the cluster is degraded causing FNR monomerization and DNA dissociation. We have used our crystal structure and the information previously gathered from numerous FNR variants to propose that this process is governed by extremely fine-tuned interactions, mediated by two salt bridges near the amino-terminal cluster-binding domain and an "imperfect" coiled-coil dimer interface. [4Fe-4S] to [2Fe-2S] cluster degradation propagates a conformational signal that indirectly causes monomerization by disrupting the first of these interactions and unleashing the "unzipping" of the FNR dimer in the direction of the carboxyl-terminal DNA binding domain. PMID:26665177

  7. The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium

    PubMed Central

    Volbeda, Anne; Darnault, Claudine; Renoux, Oriane; Nicolet, Yvain; Fontecilla-Camps, Juan C.

    2015-01-01

    The structure of the dimeric holo–fumarate and nitrate reduction regulator (FNR) from Aliivibrio fischeri has been solved at 2.65 Å resolution. FNR globally controls the transition between anaerobic and aerobic respiration in facultative anaerobes through the assembly/degradation of its oxygen-sensitive [4Fe-4S] cluster. In the absence of O2, FNR forms a dimer and specifically binds to DNA, whereas in its presence, the cluster is degraded causing FNR monomerization and DNA dissociation. We have used our crystal structure and the information previously gathered from numerous FNR variants to propose that this process is governed by extremely fine-tuned interactions, mediated by two salt bridges near the amino-terminal cluster-binding domain and an “imperfect” coiled-coil dimer interface. [4Fe-4S] to [2Fe-2S] cluster degradation propagates a conformational signal that indirectly causes monomerization by disrupting the first of these interactions and unleashing the “unzipping” of the FNR dimer in the direction of the carboxyl-terminal DNA binding domain. PMID:26665177

  8. Cluster self-organization of inorganic crystal-forming systems: Templated nanocluster precursors and self-assembly of framework MT structures of A/B,Zr silicates (A = Na, K; B = Ca, Sr)

    SciTech Connect

    Ilyushin, G. D.

    2012-03-15

    The basic concepts that are used to describe crystallization as a phenomenon of the hierarchical (cluster) self-organization of a chemical system are considered. The templation of theoretically possible nan-ocluster precursors composed of M octahedra and T tetrahedra by atoms of (A) alkaline and (B) alkaline earth metals is considered for the first time. A relationship between the A/B,M,T composition of templated nanocluster precursors with the composition of A/B,M silicates is established. The model that is developed is used to search for nanocluster precursors in framework MT structures of A/B,Zr silicates. Computer methods (TOPOS 4.0 program package) were used to perform complete 3D reconstruction of the self-assembly of all (four) structural types of A/B,Zr silicates (A = Na, K; B = Ca, Sr) with frameworks of the MT{sub 2}O{sub 7} type: nan-ocluster precursor S{sub 3}{sup 0}-primary chain S{sub 3}{sup 1}-microlayer S{sub 3}{sup 2}-microframework S{sub 3}{sup 3}. The invariant type of mono-cyclic nanocluster precursor M{sub 2}T{sub 4} (with the point symmetries 1-bar and 2), stabilized by one or two template cations (A and B), is determined. Bifurcations of the paths of evolution at the S{sub 3}{sup 1} level (structural branching point) are established for the self-assembly of the following frameworks: MT-1 in CaZrSi{sub 2}O{sub 7} (gittinsite, C2), MT-2 in SrZrSi{sub 2}O{sub 7} (P2{sub 1}/c); MT-3 in Na{sub 2}ZrSi{sub 2}O{sub 7} (parakeldyshite,), K{sub 2}ZrSi{sub 2}O{sub 7} (khibinskite, P2{sub 1}/b), and K{sub 2}ZrGe{sub 2}O{sub 7} (C2/c); and MT-4 in Na{sub 2}ZrSi{sub 2}O{sub 7} (H{sub 2}O)(C2/c), Na{sub 3}ScSi{sub 2}O{sub 7} (Pbnm), and K{sub 3}ScSi{sub 2}O{sub 7} (P6{sub 3}/mmc).

  9. Cluster self-organization of inorganic crystal-forming systems: Templated nanocluster precursors and self-assembly of framework MT structures of A/B,Zr silicates ( A = Na, K; B = Ca, Sr)

    NASA Astrophysics Data System (ADS)

    Ilyushin, G. D.

    2012-03-01

    The basic concepts that are used to describe crystallization as a phenomenon of the hierarchical (cluster) self-organization of a chemical system are considered. The templation of theoretically possible nan-ocluster precursors composed of M octahedra and T tetrahedra by atoms of ( A) alkaline and ( B) alkaline earth metals is considered for the first time. A relationship between the A/B,M,T composition of templated nanocluster precursors with the composition of A/B,M silicates is established. The model that is developed is used to search for nanocluster precursors in framework MT structures of A/B,Zr silicates. Computer methods (TOPOS 4.0 program package) were used to perform complete 3 D reconstruction of the self-assembly of all (four) structural types of A/B,Zr silicates ( A = Na, K; B = Ca, Sr) with frameworks of the MT 2O7 type: nan-ocluster precursor S {3/0}-primary chain S {3/1}-microlayer S {3/2}-microframework S {3/3}. The invariant type of mono-cyclic nanocluster precursor M 2 T 4 (with the point symmetries bar 1 and 2), stabilized by one or two template cations ( A and B), is determined. Bifurcations of the paths of evolution at the S {3/1} level (structural branching point) are established for the self-assembly of the following frameworks: MT-1 in CaZrSi2O7 (gittinsite, C2), MT-2 in SrZrSi2O7 ( P21/ c); MT-3 in Na2ZrSi2O7 (parakeldyshite,), K2ZrSi2O7 (khibinskite, P21/ b), and K2ZrGe2O7 ( C2/ c); and MT-4 in Na2ZrSi2O7 (H2O)( C2/ c), Na3ScSi2O7 ( Pbnm), and K3ScSi2O7 ( P63/ mmc).

  10. Cyclostomes Lack Clustered Protocadherins.

    PubMed

    Ravi, Vydianathan; Yu, Wei-Ping; Pillai, Nisha E; Lian, Michelle M; Tay, Boon-Hui; Tohari, Sumanty; Brenner, Sydney; Venkatesh, Byrappa

    2016-02-01

    The brain, comprising billions of neurons and intricate neural networks, is arguably the most complex organ in vertebrates. The diversity of individual neurons is fundamental to the neuronal network complexity and the overall function of the vertebrate brain. In jawed vertebrates, clustered protocadherins provide the molecular basis for this neuronal diversity, through stochastic and combinatorial expression of their various isoforms in individual neurons. Based on analyses of transcriptomes from the Japanese lamprey brain and sea lamprey embryos, genome assemblies of the two lampreys, and brain expressed sequence tags of the inshore hagfish, we show that extant jawless vertebrates (cyclostomes) lack the clustered protocadherins. Our findings indicate that the clustered protocadherins originated from a nonclustered protocadherin in the jawed vertebrate ancestor, after the two rounds of whole-genome duplication. In the absence of clustered protocadherins, cyclostomes might have evolved novel molecules or mechanisms for generating neuronal diversity which remains to be discovered. PMID:26545918

  11. 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.

  12. A mixed-ligand iron-sulfur cluster (C556SPaB or C565SPsaB) in the Fx-binding site leads to a decreased quantum efficiency of electron transfer in photosystem I.

    PubMed Central

    Vassiliev, I R; Jung, Y S; Smart, L B; Schulz, R; McIntosh, L; Golbeck, J H

    1995-01-01

    The proposed structure of Photosystem I depicts two cysteines on the PsaA polypeptide and two cysteines on the PsaB polypeptide in a symmetrical environment, each providing ligands for the interpolypeptide Fx cluster. We studied the role of Fx in electron transfer by substituting serine for cysteine (C565SPsaB and C556SPsaB), thereby introducing the first example of a genetically engineered, mixed-ligand [4Fe-4S] cluster into a protein. Optical kinetic spectroscopy shows that after a single-turnover flash at 298 K, the contribution of A1- (lifetime of 10 microseconds, 40% of total and lifetime of 100 microseconds, 20% of total) and Fx- (lifetime of 500-800 microseconds, 10-15% of total) to the overall P700+ back reaction have increased in C565SPsaB and C556SPsaB at the expense of the back reaction from [FA/FB]-. The electron paramagnetic resonance spectrum of Fx shows g-values of 2.04, 1.94, and 1.81 in both mutants and a similarly decreased amount of FA and FB reduced at 15 K after a single-turnover flash. These results indicate that the mixed-ligand (3 cysteines, 1 serine) Fx cluster is an inefficient electron carrier, but that a small leak through Fx still permits FA and FB to be reduced quantitatively when the samples are frozen during continuous illumination. The data confirm that Fx is a necessary intermediate in the electron transfer pathway from A1 to FA and FB in Photosystem I. PMID:8534825

  13. Rod cluster having improved vane configuration

    SciTech Connect

    Shockling, L.A.; Francis, T.A.

    1989-09-05

    This patent describes a pressurized water reactor vessel, the vessel defining a predetermined axial direction of the flow of coolant therewithin and having plural spider assemblies supporting, for vertical movement within the vessel, respective clusters of rods in spaced, parallel axial relationship, parallel to the predetermined axial direction of coolant flow, and a rod guide for each spider assembly and respective cluster of rods. The rod guide having horizontally oriented support plates therewithin, each plate having an interior opening for accommodating axial movement therethrough of the spider assembly and respective cluster of rods. The opening defining plural radially extending channels and corresponding parallel interior wall surfaces of the support plate.

  14. Nondeterministic self-assembly with asymmetric interactions.

    PubMed

    Tesoro, S; Göpfrich, K; Kartanas, T; Keyser, U F; Ahnert, S E

    2016-08-01

    We investigate general properties of nondeterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides insights into the study of diseases caused by protein aggregation. PMID:27627332

  15. Nondeterministic self-assembly with asymmetric interactions

    NASA Astrophysics Data System (ADS)

    Tesoro, S.; Göpfrich, K.; Kartanas, T.; Keyser, U. F.; Ahnert, S. E.

    2016-08-01

    We investigate general properties of nondeterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides insights into the study of diseases caused by protein aggregation.

  16. Crew Assembly

    NASA Video Gallery

    Train to improve your dexterity and hand-eye coordination by assembling a puzzle.The Train Like an Astronaut project uses the excitement of exploration to challenge students to set goals, practice ...

  17. F-1 Engine Assembly

    NASA Technical Reports Server (NTRS)

    1968-01-01

    A complete F-1 engine assembly is shown in this photograph. Designed and developed by Rocketdye under the direction of the Marshall Space Flight Center, the engine measured 19-feet tall by 12.5 feet at the nozzle exit, and each engine produced a 1,500,000-pound thrust using liquid oxygen and kerosene as the propellant. A cluster of five F-1 engines was mounted on the Saturn V S-IC (first) stage and burned 15 tons of liquid oxygen and kerosene each second to produce 7,500,000 pounds of thrust.

  18. Seal assembly

    SciTech Connect

    Johnson, Roger Neal; Longfritz, William David

    2001-01-01

    A seal assembly that seals a gap formed by a groove comprises a seal body, a biasing element, and a connection that connects the seal body to the biasing element to form the seal assembly. The seal assembly further comprises a concave-shaped center section and convex-shaped contact portions at each end of the seal body. The biasing element is formed from an elastic material and comprises a convex-shaped center section and concave-shaped biasing zones that are opposed to the convex-shaped contact portions. The biasing element is adapted to be compressed to change a width of the seal assembly from a first width to a second width that is smaller than the first width. In the compressed state, the seal assembly can be disposed in the groove. After release of the compressing force, the seal assembly expands. The contact portions will move toward a surface of the groove and the biasing zones will move into contact with another surface of the groove. The biasing zones will bias the contact portions of the seal body against the surface of the groove.

  19. Manipulating Natural Product Biosynthetic Pathways via DNA Assembler

    PubMed Central

    Shao, Zengyi; Zhao, Huimin

    2014-01-01

    DNA assembler is an efficient synthetic biology method for constructing and manipulating biochemical pathways. The rapidly increasing number of sequenced genomes provides a rich source for discovery of gene clusters involved in synthesizing new natural products. However, both discovery and economical production are hampered by our limited knowledge in manipulating most organisms and the corresponding pathways. By taking advantage of yeast in vivo homologous recombination, DNA assembler synthesizes an entire expression vector containing the target biosynthetic pathway and the genetic elements needed for DNA maintenance and replication. Here we use the spectinabilin clusters originated from two hosts as examples to illustrate the guidelines of using DNA assembler for cluster characterization and silent cluster activation. Such strategies offer unprecedented versatility in cluster manipulation, bypass the traditional laborious strategies to elicit pathway expression, and provide a new platform for de novo cluster assembly and genome mining for discovering new natural products. PMID:24903884

  20. Architecture of Eph receptor clusters

    SciTech Connect

    Himanen, Juha P.; Yermekbayeva, Laila; Janes, Peter W.; Walker, John R.; Xu, Kai; Atapattu, Lakmali; Rajashankar, Kanagalaghatta R.; Mensinga, Anneloes; Lackmann, Martin; Nikolov, Dimitar B.; Dhe-Paganon, Sirano

    2010-10-04

    Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bidirectional signaling in interacting cells. However, the structural and mechanistic details of this assembly remained undefined. Here we present high-resolution structures of the complete EphA2 ectodomain and complexes with ephrin-A1 and A5 as the base unit of an Eph cluster. The structures reveal an elongated architecture with novel Eph/Eph interactions, both within and outside of the Eph ligand-binding domain, that suggest the molecular mechanism underlying Eph/ephrin clustering. Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering.

  1. Re-shaping colloidal clusters

    NASA Astrophysics Data System (ADS)

    Kraft, Daniela

    2015-03-01

    Controlling the geometry and yield of anisotropic colloidal particles remains a challenge for hierarchical self-assembly. I will discuss a synthetic strategy for fabricating colloidal clusters by creating order in randomly aggregated polymer spheres using surface tension and geometrical constraints. The technique can be extended to a variety of charge-stabilized polymer spheres and offers control over the cluster size distribution. VENI grant from The Netherlands Organization for Scientific Research (NWO).

  2. Probe assembly

    SciTech Connect

    Avera, C.J.

    1981-01-06

    A hand-held probe assembly, suitable for monitoring a radioactive fibrinogen tracer, is disclosed comprising a substantially cylindrically shaped probe handle having an open end. The probe handle is adapted to be interconnected with electrical circuitry for monitoring radioactivity that is sensed or detected by the probe assembly. Mounted within the probe handle is a probe body assembly that includes a cylindrically shaped probe body inserted through the open end of the probe handle. The probe body includes a photomultiplier tube that is electrically connected with a male connector positioned at the rearward end of the probe body. Mounted at the opposite end of the probe body is a probe head which supports an optical coupler therewithin. The probe head is interconnected with a probe cap which supports a detecting crystal. The probe body assembly, which consists of the probe body, the probe head, and the probe cap is supported within the probe handle by means of a pair of compressible o-rings which permit the probe assembly to be freely rotatable, preferably through 360*, within the probe handle and removable therefrom without requiring any disassembly.

  3. Hinge assembly

    DOEpatents

    Vandergriff, D.H.

    1999-08-31

    A hinge assembly is disclosed having a first leaf, a second leaf and linking member. The first leaf has a contact surface. The second leaf has a first contact surface and a second contact surface. The linking member pivotally connects to the first leaf and to the second leaf. The hinge assembly is capable of moving from a closed position to an open position. In the closed position, the contact surface of the first leaf merges with the first contact surface of the second leaf. In the open position, the contact surface of the first leaf merges with the second contact surface of the second leaf. The hinge assembly can include a seal on the contact surface of the first leaf. 8 figs.

  4. Hinge assembly

    DOEpatents

    Vandergriff, David Houston

    1999-01-01

    A hinge assembly having a first leaf, a second leaf and linking member. The first leaf has a contact surface. The second leaf has a first contact surface and a second contact surface. The linking member pivotally connects to the first leaf and to the second leaf. The hinge assembly is capable of moving from a closed position to an open position. In the closed position, the contact surface of the first leaf merges with the first contact surface of the second leaf. In the open position, the contact surface of the first leaf merges with the second contact surface of the second leaf. The hinge assembly can include a seal on the contact surface of the first leaf.

  5. Latch assembly

    DOEpatents

    Frederickson, J.R.; Harper, W.H.; Perez, R.

    1984-08-17

    A latch assembly for releasably securing an article in the form of a canister within a container housing. The assembly includes a cam pivotally mounted on the housing wall and biased into the housing interior. The cam is urged into a disabled position by the canister as it enters the housing and a latch release plate maintains the cam disabled when the canister is properly seated in the housing. Upon displacement of the release plate, the cam snaps into latching engagement against the canister for securing the same within the housing. 2 figs.

  6. Latch assembly

    SciTech Connect

    Frederickson, James R.; Harper, William H.; Perez, Raymond

    1986-01-01

    A latch assembly for releasably securing an article in the form of a canister within a container housing. The assembly includes a cam pivotally mounted on the housing wall and biased into the housing interior. The cam is urged into a disabled position by the canister as it enters the housing and a latch release plate maintains the cam disabled when the canister is properly seated in the housing. Upon displacement of the release plate, the cam snaps into latching engagement against the canister for securing the same within the housing.

  7. Computer modeling of self-assembly of the crystal structure of zeolite Na{sub 384}[Al{sub 384}Si{sub 384}O{sub 1536}] (H{sub 2}O){sub 422} (LTN, cF4080) from suprapolyhedral cluster precursors AB{sub 2} (A-K{sub 48}, B-K{sub 24})

    SciTech Connect

    Blatov, V. A.; Ilyushin, G. D.

    2012-05-15

    Combinatorial and topological analyses and a simulation of the self-assembly of zeolite crystal structure Na{sub 384}Al{sub 384}Si{sub 384}O{sub 1536} {center_dot} 422H{sub 2}O (LTN, sp. gr. Fd3 bar) have been performed using computer methods (TOPOS program package). A cubic cell with the parameters a = 36.95 Angstrom-Sign and V = 50 449 Angstrom-Sign {sup 3} contains 768 framework-forming AlO{sub 4}- and SiO{sub 4} tetrahedra (T tetrahedra). The method of complete expansion of a 3D factor graph in nonintersecting cluster substructures in the tetrahedral T framework was used to reveal nanocluster precursors: A composed of 48 T tetrahedra (A-K{sub 48}) and B composed of 24 T tetrahedra (B-K{sub 24}). The nanocluster precursors A and B correspond to the polyhedral T clusters (tiles) 48T-grc and 24T-toc; they are involved in the matrix self-assembly of the crystal structure within the supracluster AB{sub 2}. The centers of clusters A and B occupy the positions of Mg and Cu atoms in the Laves net AB{sub 2} = MgCu{sub 2}; i.e., the zeolite structure is a suprapolyhedral analog of an intermetallic compound. The self-assembly code of a 3D structure from complementary bound nanocluster precursors is completely reconstuctured in the following form: supracluster {yields} primary chain {yields} microlayer {yields} microframework {yields} ...framework. The localization of the Na{sup +} template cations in the 6T- and 8T rings of nanocluster precursors A and B and Na{sup +} spacer cations in the 28T-ltn tile with the formation of tetrahedral configuration and in the center of 6-ring, which arises as a result of bonding two B nanoclusters, is established.

  8. Meaningful Clusters

    SciTech Connect

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  9. Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly.

    PubMed

    Ghosh, Tarini Shankar; Mehra, Varun; Mande, Sharmila S

    2015-06-01

    Metagenomics approach involves extraction, sequencing and characterization of the genomic content of entire community of microbes present in a given environment. In contrast to genomic data, accurate assembly of metagenomic sequences is a challenging task. Given the huge volume and the diverse taxonomic origin of metagenomic sequences, direct application of single genome assembly methods on metagenomes are likely to not only lead to an immense increase in requirements of computational infrastructure, but also result in the formation of chimeric contigs. A strategy to address the above challenge would be to partition metagenomic sequence datasets into clusters and assemble separately the sequences in individual clusters using any single-genome assembly method. The current study presents such an approach that uses tetranucleotide usage patterns to first represent sequences as points in a three dimensional (3D) space. The 3D space is subsequently partitioned into "Grids". Sequences within overlapping grids are then progressively assembled using any available assembler. We demonstrate the applicability of the current Grid-Assembly method using various categories of assemblers as well as different simulated metagenomic datasets. Validation results indicate that the Grid-Assembly approach helps in improving the overall quality of assembly, in terms of the purity and volume of the assembled contigs. PMID:25790784

  10. Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases.

    PubMed

    Evans, Rhiannon M; Parkin, Alison; Roessler, Maxie M; Murphy, Bonnie J; Adamson, Hope; Lukey, Michael J; Sargent, Frank; Volbeda, Anne; Fontecilla-Camps, Juan C; Armstrong, Fraser A

    2013-02-20

    "Hyd-1", produced by Escherichia coli , exemplifies a special class of [NiFe]-hydrogenase that can sustain high catalytic H(2) oxidation activity in the presence of O(2)-an intruder that normally incapacitates the sulfur- and electron-rich active site. The mechanism of "O(2) tolerance" involves a critical role for the Fe-S clusters of the electron relay, which is to ensure the availability-for immediate transfer back to the active site-of all of the electrons required to reduce an attacking O(2) molecule completely to harmless H(2)O. The unique [4Fe-3S] cluster proximal to the active site is crucial because it can rapidly transfer two of the electrons needed. Here we investigate and establish the equally crucial role of the high potential medial [3Fe-4S] cluster, located >20 Å from the active site. A variant, P242C, in which the medial [3Fe-4S] cluster is replaced by a [4Fe-4S] cluster, is unable to sustain steady-state H(2) oxidation activity in 1% O(2). The [3Fe-4S] cluster is essential only for the first stage of complete O(2) reduction, ensuring the supply of all three electrons needed to form the oxidized inactive state "Ni-B" or "Ready" (Ni(III)-OH). Potentiometric titrations show that Ni-B is easily reduced (E(m) ≈ +0.1 V at pH 6.0); this final stage of the O(2)-tolerance mechanism regenerates active enzyme, effectively completing a competitive four-electron oxidase cycle and is fast regardless of alterations at the proximal or medial clusters. As a consequence of all these factors, the enzyme's response to O(2), viewed by its electrocatalytic activity in protein film electrochemistry (PFE) experiments, is merely to exhibit attenuated steady-state H(2) oxidation activity; thus, O(2) behaves like a reversible inhibitor rather than an agent that effectively causes irreversible inactivation. The data consolidate a rich picture of the versatile role of Fe-S clusters in electron relays and suggest that Hyd-1 can function as a proficient hydrogen oxidase. PMID

  11. A GMBCG galaxy cluster catalog of 55,880 rich clusters from SDSS DR7

    SciTech Connect

    Hao, Jiangang; McKay, Timothy A.; Koester, Benjamin P.; Rykoff, Eli S.; Rozo, Eduardo; Annis, James; Wechsler, Risa H.; Evrard, August; Siegel, Seth R.; Becker, Matthew; Busha, Michael; /Fermilab /Michigan U. /Chicago U., Astron. Astrophys. Ctr. /UC, Santa Barbara /KICP, Chicago /KIPAC, Menlo Park /SLAC /Caltech /Brookhaven

    2010-08-01

    We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red sequence plus Brightest Cluster Galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 square degrees of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.

  12. A GMBCG Galaxy Cluster Catalog of 55,424 Rich Clusters from SDSS DR7

    SciTech Connect

    Hao, Jiangang; McKay, Timothy A.; Koester, Benjamin P.; Rykoff, Eli S.; Rozo, Eduardo; Annis, James; Wechsler, Risa H.; Evrard, August; Siegel, Seth R.; Becker, Matthew; Busha, Michael; Gerdes, David; Johnston, David E.; Sheldon, Erin; /Brookhaven

    2011-08-22

    We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red sequence plus Brightest Cluster Galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 square degrees of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.

  13. Furnace assembly

    DOEpatents

    Panayotou, Nicholas F.; Green, Donald R.; Price, Larry S.

    1985-01-01

    A method of and apparatus for heating test specimens to desired elevated temperatures for irradiation by a high energy neutron source. A furnace assembly is provided for heating two separate groups of specimens to substantially different, elevated, isothermal temperatures in a high vacuum environment while positioning the two specimen groups symmetrically at equivalent neutron irradiating positions.

  14. Furnace assembly

    DOEpatents

    Panayotou, N.F.; Green, D.R.; Price, L.S.

    A method of and apparatus for heating test specimens to desired elevated temperatures for irradiation by a high energy neutron source. A furnace assembly is provided for heating two separate groups of specimens to substantially different, elevated, isothermal temperatures in a high vacuum environment while positioning the two specimen groups symmetrically at equivalent neutron irradiating positions.

  15. Active matter clusters at interfaces.

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    2016-03-01

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor formation and metastasis, colonies of bacteria in a biofilm, or even flocks of birds and schools of fish at the macro-scale. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit that moves in two dimensions by exerting a force/torque per unit area whose magnitude depends on the nature of the local environment. We find that low speed (overdamped) clusters encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds (underdamped), where inertia dominates, the clusters show more complex behaviors crossing the interface multiple times and deviating from the predictable refraction and reflection for the low velocity clusters. We then present an extreme limit of the model in the absence of rotational damping where clusters can become stuck spiraling along the interface or move in large circular trajectories after leaving the interface. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  16. Cartwheel assembly

    PubMed Central

    Hirono, Masafumi

    2014-01-01

    The cartwheel is a subcentriolar structure consisting of a central hub and nine radially arranged spokes, located at the proximal end of the centriole. It appears at the initial stage of the centriole assembly process as the first ninefold symmetrical structure. The cartwheel was first described more than 50 years ago, but it is only recently that its pivotal role in establishing the ninefold symmetry of the centriole was demonstrated. Significant progress has since been made in understanding its fine structure and assembly mechanism. Most importantly, the central part of the cartwheel, from which the ninefold symmetry originates, is shown to form by self-association of nine dimers of the protein SAS-6. This finding, together with emerging data on other components of the cartwheel, has opened new avenues in centrosome biology. PMID:25047612

  17. Sensor assembly

    DOEpatents

    Bennett, Thomas E.; Nelson, Drew V.

    2004-04-13

    A ribbon-like sensor assembly is described wherein a length of an optical fiber embedded within a similar lengths of a prepreg tow. The fiber is ""sandwiched"" by two layers of the prepreg tow which are merged to form a single consolidated ribbon. The consolidated ribbon achieving a generally uniform distribution of composite filaments near the embedded fiber such that excess resin does not ""pool"" around the periphery of the embedded fiber.

  18. pH-Controlled assembly of two novel Dawson-sandwiched clusters involving the in situ reorganization of trivacant α-[P2W15O56](12-) into divacant α-[P2W16O57](8.).

    PubMed

    Guo, Ling-Yu; Jagodič, Marko; Zeng, Su-Yuan; Wang, Zhi; Shi, Zhi-Qiang; Wang, Xing-Po; Tung, Chen-Ho; Sun, Di

    2016-05-28

    Modified classical trivacant Wells-Dawson α-[P2W15O56](12-) and the assembly of related sandwiched transition metal clusters are of interest, but surprisingly few reports of these materials exist because of the sensitivity of α-[P2W15O56](12-) to the assembly environment. Herein, we describe the pH-controlled assembly of two novel Dawson-sandwiched clusters, (H2bpz)6[Co2(P2W16O57)2]·22H2O (1, bpz = 3,3',5,5'-tetramethyl-4,4'-bipyrazole) and (H2bpz)6[Co3H2(P2W16O57)(P2W15O56)(H2O)]·12H2O (2), involving the in situ transformation of α-[P2W15O56](12-). Both clusters were characterized by X-ray single-crystal diffraction, FT-IR spectroscopy, UV-Visible spectroscopy, thermogravimetric analysis, powder X-ray diffraction, and elemental analyses. X-ray crystallography showed that both heteropolytungstates become divacant α-[P2W16O57](8-) and symmetrically encapsulate two edge-shared CoO6 octahedra in the interior in 1, while only one divacant α-[P2W16O57](8-) is observed in 2, which combined with another trivacant α-[P2W15O56](12-) to asymmetrically clamp three edge-shared CoO6 octahedra. The α-[P2W16O57](8-) heteropolytungstate should be generated in situ from α-[P2W15O56](12-)via self-decomposition equilibria in solution. Their electrochemical behaviors reveal characteristic multi-electron redox processes related to W(VI) centers. The electrocatalytic reduction performances toward nitrite, hydrogen peroxide, chlorate, bromate and iodate were fully measured and discussed; among these species, both clusters exhibit the best electrocatalytic activity towards the reduction of bromate. Magnetic measurements indicate weak ferromagnetic exchange interactions between Co atoms sandwiched by vacant polyoxometalates. PMID:27108482

  19. Early assembly of the most massive galaxies.

    PubMed

    Collins, Chris A; Stott, John P; Hilton, Matt; Kay, Scott T; Stanford, S Adam; Davidson, Michael; Hosmer, Mark; Hoyle, Ben; Liddle, Andrew; Lloyd-Davies, Ed; Mann, Robert G; Mehrtens, Nicola; Miller, Christopher J; Nichol, Robert C; Romer, A Kathy; Sahlén, Martin; Viana, Pedro T P; West, Michael J

    2009-04-01

    The current consensus is that galaxies begin as small density fluctuations in the early Universe and grow by in situ star formation and hierarchical merging. Stars begin to form relatively quickly in sub-galactic-sized building blocks called haloes which are subsequently assembled into galaxies. However, exactly when this assembly takes place is a matter of some debate. Here we report that the stellar masses of brightest cluster galaxies, which are the most luminous objects emitting stellar light, some 9 billion years ago are not significantly different from their stellar masses today. Brightest cluster galaxies are almost fully assembled 4-5 billion years after the Big Bang, having grown to more than 90 per cent of their final stellar mass by this time. Our data conflict with the most recent galaxy formation models based on the largest simulations of dark-matter halo development. These models predict protracted formation of brightest cluster galaxies over a Hubble time, with only 22 per cent of the stellar mass assembled at the epoch probed by our sample. Our findings suggest a new picture in which brightest cluster galaxies experience an early period of rapid growth rather than prolonged hierarchical assembly. PMID:19340075

  20. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-08-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-[3-(triethoxysilyl)propyl]-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  1. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-01-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-(3-(triethoxysilyl)propyl)-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  2. Dump assembly

    DOEpatents

    Goldmann, L.H.

    1984-12-06

    This is a claim for a dump assembly having a fixed conduit and a rotatable conduit provided with overlapping plates, respectively, at their adjacent ends. The plates are formed with openings, respectively, normally offset from each other to block flow. The other end of the rotatable conduit is provided with means for securing the open end of a filled container thereto. Rotation of the rotatable conduit raises and inverts the container to empty the contents while concurrently aligning the conduit openings to permit flow of material therethrough. 4 figs.

  3. Pushrod assembly

    DOEpatents

    Potter, Jerry D.

    1987-01-01

    A pushrod assembly including a carriage mounted on a shaft for movement therealong and carrying a pushrod engageable with a load to be moved. A magnet is mounted on a supporting bracket for movement along such shaft. Means are provided for adjustably spacing said magnet away from said carriage to obtain a selected magnetic attractive or coupling force therebetween. Movement of the supporting bracket and the magnet carried thereby pulls the carriage along with it until the selected magnetic force is exceeded by a resistance load acting on the carriage.

  4. Shingle assembly

    DOEpatents

    Dinwoodie, Thomas L.

    2007-02-20

    A barrier, such as a PV module, is secured to a base by a support to create a shingle assembly with a venting region defined between the barrier and base for temperature regulation. The first edge of one base may be interengageable with the second edge of an adjacent base to be capable of resisting first and second disengaging forces oriented perpendicular to the edges and along planes oriented parallel to and perpendicular to the base. A deflector may be used to help reduce wind uplift forces.

  5. Active matter clusters at interfaces

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development and flocks of birds. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit whose movement depends on the nature of the local environment. We find that low speed clusters which exert forces but no active torques, encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds and clusters with active torques, they show more complex behaviors crossing the interface multiple times, becoming trapped at the interface and deviating from the predictable refraction and reflection of the low velocity clusters. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  6. DNA Enabled Self-Assembly of Plasmonic Nanoclusters

    PubMed Central

    Fan, Jonathan A.; He, Yu; Bao, Kui; Wu, Chihhui; Bao, Jiming; Schade, Nicholas B.; Manoharan, Vinothan N.; Shvets, Gennady; Nordlander, Peter; Liu, David R.; Capasso, Federico

    2012-01-01

    DNA nanotechnology provides a versatile foundation for the chemical assembly of nanostructures. Plasmonic nanoparticle assemblies are of particular interest because they can be tailored to exhibit a broad range of electromagnetic phenomena. In this Letter, we report the assembly of DNA-functionalized nanoparticles into pentamer clusters, which consist of a smaller gold sphere surrounded by a ring of four larger spheres. Magnetic and Fano-like resonances are observed in individual clusters. The DNA plays a dual role: it selectively assembles the clusters in solution and functions as an insulating spacer between the conductive nanoparticles. These particle assemblies can be generalized to a new class of DNA-enabled plasmonic heterostructures that comprise various active and passive materials and other forms of DNA scaffolding. PMID:22007607

  7. First assembly times and equilibration in stochastic coagulation-fragmentation

    SciTech Connect

    D’Orsogna, Maria R.; Lei, Qi; Chou, Tom

    2015-07-07

    We develop a fully stochastic theory for coagulation and fragmentation (CF) in a finite system with a maximum cluster size constraint. The process is modeled using a high-dimensional master equation for the probabilities of cluster configurations. For certain realizations of total mass and maximum cluster sizes, we find exact analytical results for the expected equilibrium cluster distributions. If coagulation is fast relative to fragmentation and if the total system mass is indivisible by the mass of the largest allowed cluster, we find a mean cluster-size distribution that is strikingly broader than that predicted by the corresponding mass-action equations. Combinations of total mass and maximum cluster size under which equilibration is accelerated, eluding late-stage coarsening, are also delineated. Finally, we compute the mean time it takes particles to first assemble into a maximum-sized cluster. Through careful state-space enumeration, the scaling of mean assembly times is derived for all combinations of total mass and maximum cluster size. We find that CF accelerates assembly relative to monomer kinetic only in special cases. All of our results hold in the infinite system limit and can be only derived from a high-dimensional discrete stochastic model, highlighting how classical mass-action models of self-assembly can fail.

  8. Quintuplet Cluster

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.

  9. Swivel assembly

    DOEpatents

    Hall, David R.; Pixton, David S.; Briscoe, Michael; Bradford, Kline; Rawle, Michael; Bartholomew, David B.; McPherson, James

    2007-03-20

    A swivel assembly for a downhole tool string comprises a first and second coaxial housing cooperatively arranged. The first housing comprises a first transmission element in communication with surface equipment. The second housing comprises a second transmission element in communication with the first transmission element. The second housing further comprises a third transmission element adapted for communication with a network integrated into the downhole tool string. The second housing may be rotational and adapted to transmit a signal between the downhole network and the first housing. Electronic circuitry is in communication with at least one of the transmission elements. The electronic circuitry may be externally mounted to the first or second housing. Further, the electronic circuitry may be internally mounted in the second housing. The electronic circuitry may be disposed in a recess in either first or second housing of the swivel.

  10. RETORT ASSEMBLY

    DOEpatents

    Loomis, C.C.; Ash, W.J.

    1957-11-26

    An improved retort assembly useful in the thermal reduction of volatilizable metals such as magnesium and calcium is described. In this process a high vacuum is maintained in the retort, however the retort must be heated to very high temperatures while at the same time the unloading end must bo cooled to condense the metal vapors, therefore the retention of the vacuum is frequently difficult due to the thermal stresses involved. This apparatus provides an extended condenser sleeve enclosed by the retort cover which forms the vacuum seal. Therefore, the seal is cooled by the fluid in the condenser sleeve and the extreme thermal stresses found in previous designs together with the deterioration of the sealing gasket caused by the high temperatures are avoided.

  11. Thermocouple assembly

    DOEpatents

    Thermos, Anthony Constantine; Rahal, Fadi Elias

    2002-01-01

    A thermocouple assembly includes a thermocouple; a plurality of lead wires extending from the thermocouple; an insulating jacket extending along and enclosing the plurality of leads; and at least one internally sealed area within the insulating jacket to prevent fluid leakage along and within the insulating jacket. The invention also provides a method of preventing leakage of a fluid along and through an insulating jacket of a thermocouple including the steps of a) attaching a plurality of lead wires to a thermocouple; b) adding a heat sensitive pseudo-wire to extend along the plurality of lead wires; c) enclosing the lead wires and pseudo-wire inside an insulating jacket; d) locally heating axially spaced portions of the insulating jacket to a temperature which melts the pseudo-wire and fuses it with an interior surface of the jacket.

  12. Uranyl peroxide closed clusters containing topological squares

    SciTech Connect

    Unruh, Daniel K.; Burtner, Alicia; Pressprich, Laura; Sigmon, Ginger E.; Burns, Peter C

    2010-01-01

    Four self-assembling clusters of uranyl peroxide polyhedra have been formed in alkaline aqueous solutions and structurally characterized. These clusters consist of 28, 30, 36 and 44 uranyl polyhedra and exhibit complex new topologies. Each has a structure that contains topological squares, pentagons and hexagons. Analysis of possible topologies within boundary constraints indicates a tendency for adoption of higher symmetry topologies in these cases. Small angle X-ray scattering data demonstrated that crystals of one of these clusters can be dissolved in ultrapure water and that the clusters remain intact for at least several days.

  13. Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Miller, Christopher J. Miller

    2012-03-01

    There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

  14. SACS: Spitzer Archival Cluster Survey

    NASA Astrophysics Data System (ADS)

    Stern, Daniel

    Emerging from the cosmic web, galaxy clusters are the most massive gravitationally bound structures in the universe. Thought to have begun their assembly at z > 2, clusters provide insights into the growth of large-scale structure as well as the physics that drives galaxy evolution. Understanding how and when the most massive galaxies assemble their stellar mass, stop forming stars, and acquire their observed morphologies in these environments remain outstanding questions. The redshift range 1.3 < z < 2 is a key epoch in this respect: elliptical galaxies start to become the dominant population in cluster cores, and star formation in spiral galaxies is being quenched. Until recently, however, this redshift range was essentially unreachable with available instrumentation, with clusters at these redshifts exceedingly challenging to identify from either ground-based optical/nearinfrared imaging or from X-ray surveys. Mid-infrared (MIR) imaging with the IRAC camera on board of the Spitzer Space Telescope has changed the landscape. High-redshift clusters are easily identified in the MIR due to a combination of the unique colors of distant galaxies and a negative k-correction in the 3-5 μm range which makes such galaxies bright. Even 90-sec observations with Spitzer/IRAC, a depth which essentially all extragalactic observations in the archive achieve, is sufficient to robustly detect overdensities of L* galaxies out to z~2. Here we request funding to embark on a ambitious scientific program, the “SACS: Spitzer Archival Cluster Survey”, a comprehensive search for the most distant galaxy clusters in all Spitzer/IRAC extragalactic pointings available in the archive. With the SACS we aim to discover ~2000 of 1.3 < z < 2.5 clusters, thus provide the ultimate catalog for high-redshift MIR selected clusters: a lasting legacy for Spitzer. The study we propose will increase by more than a factor of 10 the number of high-redshift clusters discovered by all previous surveys

  15. Occupational Clusters.

    ERIC Educational Resources Information Center

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  16. Data Clustering

    NASA Astrophysics Data System (ADS)

    Wagstaff, Kiri L.

    2012-03-01

    On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained

  17. Cluster generator

    DOEpatents

    Donchev, Todor I.; Petrov, Ivan G.

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  18. Nanoparticle Array Assembly Using Chemical Templates

    NASA Astrophysics Data System (ADS)

    Adams, Sarah Marie

    This dissertation demonstrates chemically-driven self-assembly techniques to produce assemblies of closely-spaced metal nanoparticles from colloidal nanoparticle solution in order to engineer enhanced optical fields. Planar nanoparticle assemblies provide a platform for a multitude of applications and material architectures. With nanoscale inter-particle spacing, metallic nanoparticles enable increased efficiency of photovoltaic devices due to light focusing and enhancement of electromagnetic fields useful for optical sensing of molecules due to coupling of the plasmon resonance in nanoparticle gaps. For molecular sensors, development of self-assembled two-dimensional assemblies of closely-spaced nanoparticles is useful for producing surface plasmon resonance sensors and surface-enhanced Raman spectroscopy (SERS) based sensing. Using chemical self-assembly, monodisperse, colloidal gold nanoparticles were attached on self-organized polymer templates in order to pattern assemblies of nanoparticle clusters with sub-10 nanometer inter-particle spacing. First citrate-stabilized Au nanoparticles were functionalized with thioctic acid ligands in solution. Then poly(methyl methacrylate) domains in phase-separated poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films were chemically modified with surface amine functional groups. Au nanoparticles were preferentially attached to the functionalized PMMA surface domains using cross-linking chemistry. This method allows for versatility of size, shape, and composition. In this dissertation, we demonstrated attachment of 5, 10, and 20 nm Au and 20 nm Ag nanoparticles. PS-b-PMMA thin films also exhibit versatility of domain size and morphology by varying polymer molecular weights. The nanoparticle diameter to PMMA domain size ratio influenced the cluster size. As the ratio decreased, larger clusters were observed on PMMA domains with increased frequency. SERS measurement of nanoparticle assemblies showed uniform signal

  19. Nanobiocatalytic assemblies for artificial photosynthesis.

    PubMed

    Kim, Jae Hong; Nam, Dong Heon; Park, Chan Beum

    2014-08-01

    Natural photosynthesis, a solar-to-chemical energy conversion process, occurs through a series of photo-induced electron transfer reactions in nanoscale architectures that contain light-harvesting complexes, protein-metal clusters, and many redox biocatalysts. Artificial photosynthesis in nanobiocatalytic assemblies aims to reconstruct man-made photosensitizers, electron mediators, electron donors, and redox enzymes for solar synthesis of valuable chemicals through visible light-driven cofactor regeneration. The key requirement in the design of biocatalyzed artificial photosynthetic process is an efficient and forward electron transfer between each photosynthetic component. This review describes basic principles in combining redox biocatalysis with photocatalysis, and highlights recent research outcomes in the development of nanobiocatalytic assemblies that can mimic natural photosystems I and II, respectively. Current issues in biocatalyzed artificial photosynthesis and future perspectives will be briefly discussed. PMID:24832068

  20. Construction and engineering of large biochemical pathways via DNA assembler

    PubMed Central

    Shao, Zengyi; Zhao, Huimin

    2015-01-01

    Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442

  1. Au20: A Tetrahedral Cluster

    SciTech Connect

    Li, Jun; Li, Xi; Zhai, Hua Jin; Wang, Lai S.

    2003-02-07

    Photoelectron spectroscopy revealed that a 20 atom gold cluster has an extremely large energy gap, which is even greater than that of C60, and an electron affinity comparable with that of C60. This observation suggests that the Au20 cluster must be extremely stable and chemically inert. Using relativistic density functional calculations, we found that Au20 possesses a remarkable tetrahedral structure, which is a fragment of the bulk face-centered cubic lattice of gold with a small structural relaxation. Au20 is thus a true cluster molecule, while at the same time it is exactly part of the bulk, but with very different properties. The tetrahedral Au20 may possess interesting catalytic properties and may be synthesized in bulk quantity or assembled on non-interacting surfaces.

  2. Amphoteric Aqueous Hafnium Cluster Chemistry.

    PubMed

    Goberna-Ferrón, Sara; Park, Deok-Hie; Amador, Jenn M; Keszler, Douglas A; Nyman, May

    2016-05-17

    Selective dissolution of hafnium-peroxo-sulfate films in aqueous tetramethylammonium hydroxide enables extreme UV lithographic patterning of sub-10 nm HfO2 structures. Hafnium speciation under these basic conditions (pH>10), however, is unknown, as studies of hafnium aqueous chemistry have been limited to acid. Here, we report synthesis, crystal growth, and structural characterization of the first polynuclear hydroxo hafnium cluster isolated from base, [TMA]6 [Hf6 (μ-O2 )6 (μ-OH)6 (OH)12 ]⋅38 H2 O. The solution behavior of the cluster, including supramolecular assembly via hydrogen bonding is detailed via small-angle X-ray scattering (SAXS) and electrospray ionization mass spectrometry (ESI-MS). The study opens a new chapter in the aqueous chemistry of hafnium, exemplifying the concept of amphoteric clusters and informing a critical process in single-digit-nm lithography. PMID:27094575

  3. GLIAL ANKYRINS FACILITATE PARANODAL AXOGLIAL JUNCTION ASSEMBLY

    PubMed Central

    Chang, Kae-Jiun; Zollinger, Daniel R.; Susuki, Keiichiro; Sherman, Diane L.; Makara, Michael A.; Brophy, Peter J.; Cooper, Edward C.; Bennett, Vann; Mohler, Peter J.; Rasband, Matthew N.

    2014-01-01

    Neuron-glia interactions establish functional membrane domains along myelinated axons. These include nodes of Ranvier, paranodal axoglial junctions, and juxtaparanodes. Paranodal junctions are the largest vertebrate junctional adhesion complex, are essential for rapid saltatory conduction, and contribute to assembly and maintenance of nodes. However, the molecular mechanisms underlying paranodal junction assembly are poorly understood. Ankyrins are cytoskeletal scaffolds traditionally associated with Na+ channel clustering in neurons and important for membrane domain establishment and maintenance in many cell types. Here, we show that ankyrinB, expressed by Schwann cells, and ankyrinG, expressed by oligodendrocytes, are highly enriched at the glial side of paranodal junctions where they interact with the essential glial junctional component neurofascin 155. Conditional knockout of ankyrins in oligodendrocytes disrupts paranodal junction assembly and delays nerve conduction during early development in mice. Thus, glial ankyrins function as major scaffolds that facilitate early and efficient paranodal junction assembly in the developing central nervous system. PMID:25362471

  4. Glial ankyrins facilitate paranodal axoglial junction assembly.

    PubMed

    Chang, Kae-Jiun; Zollinger, Daniel R; Susuki, Keiichiro; Sherman, Diane L; Makara, Michael A; Brophy, Peter J; Cooper, Edward C; Bennett, Vann; Mohler, Peter J; Rasband, Matthew N

    2014-12-01

    Neuron-glia interactions establish functional membrane domains along myelinated axons. These include nodes of Ranvier, paranodal axoglial junctions and juxtaparanodes. Paranodal junctions are the largest vertebrate junctional adhesion complex, and they are essential for rapid saltatory conduction and contribute to assembly and maintenance of nodes. However, the molecular mechanisms underlying paranodal junction assembly are poorly understood. Ankyrins are cytoskeletal scaffolds traditionally associated with Na(+) channel clustering in neurons and are important for membrane domain establishment and maintenance in many cell types. Here we show that ankyrin-B, expressed by Schwann cells, and ankyrin-G, expressed by oligodendrocytes, are highly enriched at the glial side of paranodal junctions where they interact with the essential glial junctional component neurofascin 155. Conditional knockout of ankyrins in oligodendrocytes disrupts paranodal junction assembly and delays nerve conduction during early development in mice. Thus, glial ankyrins function as major scaffolds that facilitate early and efficient paranodal junction assembly in the developing CNS. PMID:25362471

  5. Latching relay switch assembly

    DOEpatents

    Duimstra, Frederick A.

    1991-01-01

    A latching relay switch assembly which includes a coil section and a switch or contact section. The coil section includes at least one permanent magnet and at least one electromagnet. The respective sections are, generally, arranged in separate locations or cavities in the assembly. The switch is latched by a permanent magnet assembly and selectively switched by an overriding electromagnetic assembly.

  6. SVM clustering

    PubMed Central

    Winters-Hilt, Stephen; Merat, Sam

    2007-01-01

    Background Support Vector Machines (SVMs) provide a powerful method for classification (supervised learning). Use of SVMs for clustering (unsupervised learning) is now being considered in a number of different ways. Results An SVM-based clustering algorithm is introduced that clusters data with no a priori knowledge of input classes. The algorithm initializes by first running a binary SVM classifier against a data set with each vector in the set randomly labelled, this is repeated until an initial convergence occurs. Once this initialization step is complete, the SVM confidence parameters for classification on each of the training instances can be accessed. The lowest confidence data (e.g., the worst of the mislabelled data) then has its' labels switched to the other class label. The SVM is then re-run on the data set (with partly re-labelled data) and is guaranteed to converge in this situation since it converged previously, and now it has fewer data points to carry with mislabelling penalties. This approach appears to limit exposure to the local minima traps that can occur with other approaches. Thus, the algorithm then improves on its weakly convergent result by SVM re-training after each re-labeling on the worst of the misclassified vectors – i.e., those feature vectors with confidence factor values beyond some threshold. The repetition of the above process improves the accuracy, here a measure of separability, until there are no misclassifications. Variations on this type of clustering approach are shown. Conclusion Non-parametric SVM-based clustering methods may allow for much improved performance over parametric approaches, particularly if they can be designed to inherit the strengths of their supervised SVM counterparts. PMID:18047717

  7. Inlet nozzle assembly

    DOEpatents

    Christiansen, David W.; Karnesky, Richard A.; Precechtel, Donald R.; Smith, Bob G.; Knight, Ronald C.

    1987-01-01

    An inlet nozzle assembly for directing coolant into the duct tube of a fuel assembly attached thereto. The nozzle assembly includes a shell for housing separable components including an orifice plate assembly, a neutron shield block, a neutron shield plug, and a diffuser block. The orifice plate assembly includes a plurality of stacked plates of differently configurated and sized openings for directing coolant therethrough in a predesigned flow pattern.

  8. Inlet nozzle assembly

    DOEpatents

    Christiansen, D.W.; Karnesky, R.A.; Knight, R.C.; Precechtel, D.R.; Smith, B.G.

    1985-09-09

    An inlet nozzle assembly for directing coolant into the duct tube of a fuel assembly attached thereto. The nozzle assembly includes a shell for housing separable components including an orifice plate assembly, a neutron shield block, a neutron shield plug, and a diffuser block. The orifice plate assembly includes a plurality of stacked plates of differently configurated and sized openings for directing coolant therethrough in a predesigned flow pattern.

  9. Structural assembly in space

    NASA Technical Reports Server (NTRS)

    Stokes, J. W.; Pruett, E. C.

    1980-01-01

    A cost algorithm for predicting assembly costs for large space structures is given. Assembly scenarios are summarized which describe the erection, deployment, and fabrication tasks for five large space structures. The major activities that impact total costs for structure assembly from launch through deployment and assembly to scientific instrument installation and checkout are described. Individual cost elements such as assembly fixtures, handrails, or remote minipulators are also presented.

  10. Tilt assembly for tracking solar collector assembly

    DOEpatents

    Almy, Charles; Peurach, John; Sandler, Reuben

    2012-01-24

    A tilt assembly is used with a solar collector assembly of the type comprising a frame, supporting a solar collector, for movement about a tilt axis by pivoting a drive element between first and second orientations. The tilt assembly comprises a drive element coupler connected to the drive element and a driver, the driver comprising a drive frame, a drive arm and a drive arm driver. The drive arm is mounted to the drive frame for pivotal movement about a drive arm axis. Movement on the drive arm mimics movement of the drive element. Drive element couplers can extend in opposite directions from the outer portion of the drive arm, whereby the assembly can be used between adjacent solar collector assemblies in a row of solar collector assemblies.

  11. Transmetalation of self-assembled, supramolecular complexes.

    PubMed

    Carnes, Matthew E; Collins, Mary S; Johnson, Darren W

    2014-03-21

    Substituting one metal for another in inorganic and organometallic systems is a proven strategy for synthesizing complex molecules, and in some cases, provides the only route to a particular system. The multivalent nature of the coordination in metal-ligand assemblies lends itself more readily to some types of transmetalation. For instance, a binding site can open up for exchange without greatly effecting the many other interactions holding the structure together. In addition to exchanging the metal and altering the local binding environment, transmetalation in supramolecular systems can also lead to substantial changes in the nature of the secondary and tertiary structure of a larger assembly. In this tutorial review we will cover discrete supramolecular assemblies in which metals are exchanged. First we will address fully formed structures where direct substitution replaces one type of metal for another without changing the overall supramolecular assembly. We will then address systems where the disruptive exchange of one metal for another leads to a larger change in the supramolecular assembly. When possible we have tried to highlight systems that use supramolecular self-assembly in tandem with transmetalation to synthesize new structures not accessible through a more direct approach. At the end of this review, we highlight the use of transmetalation in self-assembled aqueous inorganic clusters and discuss the consequences for material science applications. PMID:24346298

  12. Universal behavior of dense clusters of magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Usov, N. A.; Serebryakova, O. N.

    2016-07-01

    A detailed numerical simulation of quasistatic hysteresis loops of dense clusters of interacting magnetic nanoparticles is carried out. Both clusters of magnetically soft and magnetically hard nanoparticles are considered. The clusters are characterized by an average particle diameter D, the cluster radius Rc, the particle saturation magnetization Ms, and the uniaxial anisotropy constant K. The number of particles in the cluster varies between Np = 30 - 120. The particle centers are randomly distributed within the cluster, their easy anisotropy axes being randomly oriented. It is shown that a dilute assembly of identical random clusters of magnetic nanoparticles can be characterized by two dimensionless parameters: 1) the relative strength of magneto-dipole interaction, K/Ms2, and the average particle concentration within the cluster, η = V Np/Vc. Here V is the nanoparticle volume, and Vc is the volume of the cluster, respectively. In the strong interaction limit, Msη/Ha > > 1, where Ha = 2K/Ms is the anisotropy field, the ultimate hysteresis loops of dilute assemblies of clusters have been constructed. In the variables (M/Ms, H/Ms) these hysteresis loops depend only on the particle volume fraction η. In the weak interaction limit, Msη/Ha < < 1, the assembly hysteresis loops in the variables (M/Ms, H/Ha) are close to the standard Stoner-Wohlfarth hysteresis loop.

  13. Structural assembly demonstration experiment

    NASA Technical Reports Server (NTRS)

    Stokes, J. W.

    1982-01-01

    The experiment is of an operational variety, designed to assess crew capability in Large Space System (LSS) assembly. The six Structural Assembly Demonstration Experiment objectives include: (1) the establishment of a quantitative correlation between LSS neutral buoyancy simulation and on-orbit assembly operations in order to enhance the validity of those assembly simulations; (2) the quantitative study of the capabilities and mechanics of human assembly in an Extravehicular Activity environment; (3) the further corroboration of the LSS Assembly Analysis cost algorithm through the obtainment of hard data base information; (4) the verification of LSS assembly techniques and timeless, as well as the identification of crew imposed loads and assembly aid requirements and concepts; (5) verification of a Launch/Assembly Platform structure concept for other LSS missions; and (6) lastly, to advance thermal control concepts through a flexible heat pipe.

  14. Chicken rRNA Gene Cluster Structure

    PubMed Central

    Dyomin, Alexander G.; Koshel, Elena I.; Kiselev, Artem M.; Saifitdinova, Alsu F.; Galkina, Svetlana A.; Fukagawa, Tatsuo; Kostareva, Anna A.

    2016-01-01

    Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5’ETS (1836 bp), 18S rRNA gene (1823 bp), ITS1 (2530 bp), 5.8S rRNA gene (157 bp), ITS2 (733 bp), 28S rRNA gene (4441 bp) and 3’ETS (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity. PMID:27299357

  15. Clustering effects in ionic polymers: Molecular dynamics simulations

    DOE PAGESBeta

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less

  16. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

  17. Supramolecular assembled of hexameric water clusters into a 1D chain containing (H2O)6 and [(H2O)4O2] stabilized by hydrogen bonding in a copper complex

    PubMed Central

    2012-01-01

    Background Various water clusters including hexamers, heptamers, octamers, decamers and 1D or 2D infinite water chains in a number of organic and inorganic-organic hybrid hosts, have been reported. Results {[Cu(pydc)(amp)].3H2O}n has been hydrothermally synthesized and characterized by elemental analysis and by IR spectroscopy. A wide range of hydrogen bonds (of the O-H...O, N-H...O and N-H...N type) are present in the crystal structure. Hydrogen bond interactions between the co-crystallized water molecules led to formation of six-membered rings with chair conformation. Conclusion In {[Cu(pydc)(amp)].3H2O}n, there are three uncoordinated water molecules. Thermal methods confirm number of co-crystallized water molecules in polymer. Hydrogen bond interactions between the co-crystallized water molecules led to the formation of a six-membered ring with the chair conformation. These rings are part of a 1D chain containing six-membered O6 rings, which are alternately made from (H2O)6 and [(H2O)4O2] rings. [(H2O)4O2] rings are also in chair conformation. PMID:22264401

  18. Autonomous electrochromic assembly

    DOEpatents

    Berland, Brian Spencer; Lanning, Bruce Roy; Stowell, Jr., Michael Wayne

    2015-03-10

    This disclosure describes system and methods for creating an autonomous electrochromic assembly, and systems and methods for use of the autonomous electrochromic assembly in combination with a window. Embodiments described herein include an electrochromic assembly that has an electrochromic device, an energy storage device, an energy collection device, and an electrochromic controller device. These devices may be combined into a unitary electrochromic insert assembly. The electrochromic assembly may have the capability of generating power sufficient to operate and control an electrochromic device. This control may occur through the application of a voltage to an electrochromic device to change its opacity state. The electrochromic assembly may be used in combination with a window.

  19. Firearm trigger assembly

    DOEpatents

    Crandall, David L.; Watson, Richard W.

    2010-02-16

    A firearm trigger assembly for use with a firearm includes a trigger mounted to a forestock of the firearm so that the trigger is movable between a rest position and a triggering position by a forwardly placed support hand of a user. An elongated trigger member operatively associated with the trigger operates a sear assembly of the firearm when the trigger is moved to the triggering position. An action release assembly operatively associated with the firearm trigger assembly and a movable assembly of the firearm prevents the trigger from being moved to the triggering position when the movable assembly is not in the locked position.

  20. Self-assembly of mixed-valence Co(II/III) and Ni(II) clusters: azide-bridged 1D single chain coordination polymers comprised of tetranuclear units, tetranuclear Co(II/III) complexes, ferromagnetically coupled azide-bridged tetranuclear, and hexanuclear Ni(II) complexes: synthesis, structural, and magnetic properties.

    PubMed

    Tandon, Santokh S; Bunge, Scott D; Rakosi, Robert; Xu, Zhiqiang; Thompson, Laurence K

    2009-09-01

    One-pot reactions between 2,6-diformyl-4-methylphenol (DFMP) and 2-aminoethanol (AE) in the presence of cobalt(II) salts [Co(ClO4)2, CoCl2, Co(CH3CO2)2, Co(NO3)2] and sodium azide result in the self-assembly of novel one-dimensional single chain mixed-valence cobalt coordination polymers {[Co2(II)Co2(III) (HL)2(OCH3)2(N3)3]ClO(4).5H2O.CH3OH}n (1), {[Co2(II)Co2(III) (HL)2(OCH3)2(N3)3]Cl.H2O}n (2) in which tetra-cobalt cationic units are bridged by symmetrical 1,3-azides, forming single chains; mixed valence neutral tetranuclear clusters [Co2(II)Co2(III) (HL)2(OCH3)2(N3)4]CH3OH.2H2O (3), [Co2(II)Co2(III)(HL)2(OCH3)2(N3)2(CH3CO2)2].2CH3OH.2H2O (4), and the cationic cluster [Co2(II) Co2(III) (HL)2(OCH3)2(CH3OH)2(N3)2](NO3)2 (5). In all these reactions, H3L, the potentially pentadentate (N2O3), trianionic double Schiff base ligand 2,6-bis[(2-hydroxy-ethylimino)-methyl]-4-methylphenol is formed. The reaction between DFMP and AE in the presence of nickel(ii) salts and sodium azide in methanol-water mixture results in the self-assembly of ferromagnetically coupled hexanuclear complexes [Ni6(H2L)2(HL-1)2(H2O)2(N3)6](ClO4)(2).2CH3OH (6), and [Ni6(H2L)2(HL-1)2(CH3OH)2(N3)6](BF4)2 (7), involving double (H3L) and single (H2L-1) Schiff base ligands, and a neutral tetranuclear complex [Ni4(H2L)2(OCH3)2(CH3CO2)2(N3)2] (8) with only double Schiff-base (H3L). In these complexes, the nature of the anion and the reaction conditions seem to play an important role in directing the formation of tetranuclear, hexanuclear or polymeric clusters. All complexes involve divacant double cubane-type cores containing three to four different types of bridging ligands (phenoxy, azido, methoxy/alkoxy, and acetate). Variable temperature magnetic properties of these spin coupled clusters have been investigated and magneto-structural correlations have been established. PMID:19672499

  1. Dynamics of nanoparticle assembly from disjointed images of nanoparticle-polymer composites

    NASA Astrophysics Data System (ADS)

    Murthy, Chaitanya R.; Gao, Bo; Tao, Andrea R.; Arya, Gaurav

    2016-02-01

    Understanding how nanoparticles (NPs) diffuse, stick, and assemble into larger structures within polymers is key to the design and fabrication of NP-polymer composites. Here we describe an approach for inferring the dynamic parameters of NP assembly from spatially and temporally disjointed images of composites. The approach involves iterative adjustment of the parameters of a kinetic model of assembly until the computed size statistics of NP clusters match those obtained from high-throughput analysis of the experimental images. Application of this approach to the assembly of shaped, metal NPs in polymer films suggests that NP structures grow via a cluster-cluster aggregation mechanism, where NPs and their clusters diffuse with approximately Stokes-Einstein diffusivity and stick to other NPs or clusters with a probability that depends strongly on the size and shape of the NPs and the molecular weight of the polymer.

  2. Toward the Development of Cluster-Based Materials

    SciTech Connect

    Bowen, Kit H.

    1995-06-01

    Our research program provided experimental results that made fundamental, underpinning contributions to the development of cluster-based materials. Specific topics we have studied include the non-metal-to-metallic transition in divalent metal clusters, the search for (and discovery of) theoretically-predicted, ionically-bonded cluster-assembled “molecules” and other Magic Clusters, the interaction of transition metal atoms and clusters with organic molecular templates, the synthesis and characterization of Zintl phase clusters, the magnetic properties of semiconductor clusters, the molecular properties of electronic materials, the magnetic properties of silicon-encapsulated rare earth metal atom cages, and the magnetic and electronic properties of gold/silica and gold/iron clusters.

  3. The evolution of galaxy groups and clusters

    NASA Astrophysics Data System (ADS)

    Mazzotta, Pasquale

    2016-07-01

    The Athena mission will implement the Hot and Energetic Universe science theme which poses the question of How does ordinary matter assemble into the large-scale structures we see today?. Groups and Galaxy clusters are key laboratories to understand the role of the various physical processes governing the baryonic matter from the kilo-parsec scale of super-massive black holes to the mega-parsec one of the clusters outskirts on assembling and evolving large scale structures. We will focus on the study of the galaxy groups and clusters evolution with the Athen a mission. We will review the status of current constraints in light of the newest results obtained from state of the art cosmological simulations and will discuss the perspectives out to the mission launch time in 2028.

  4. Modeling the Kinetics of Open Self-Assembly.

    PubMed

    Verdier, Timothée; Foret, Lionel; Castelnovo, Martin

    2016-07-01

    In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly. PMID:27295398

  5. Space assembly methodology

    NASA Astrophysics Data System (ADS)

    Stokes, J. W.; Watters, H. H.

    1981-02-01

    Large space structure assembly analysis techniques are defined and simulation activities are described. The simulations included are: an extravehicular activity assembly simulation; a fabricated beam assembly series using a beam generating machine end caps, and cross beam brackets; deployment of a deployable truss, using the neutral buoyancy remote manipulator system with crewman assistance; and a series aboard the KC-135 zero g aircraft.

  6. Membrane module assembly

    DOEpatents

    Kaschemekat, Jurgen

    1994-01-01

    A membrane module assembly adapted to provide a flow path for the incoming feed stream that forces it into prolonged heat-exchanging contact with a heating or cooling mechanism. Membrane separation processes employing the module assembly are also disclosed. The assembly is particularly useful for gas separation or pervaporation.

  7. Membrane module assembly

    DOEpatents

    Kaschemekat, J.

    1994-03-15

    A membrane module assembly is described which is adapted to provide a flow path for the incoming feed stream that forces it into prolonged heat-exchanging contact with a heating or cooling mechanism. Membrane separation processes employing the module assembly are also disclosed. The assembly is particularly useful for gas separation or pervaporation. 2 figures.

  8. The Oncogenic Small Tumor Antigen of Merkel Cell Polyomavirus Is an Iron-Sulfur Cluster Protein That Enhances Viral DNA Replication

    PubMed Central

    Tsang, Sabrina H.; Wang, Ranran; Nakamaru-Ogiso, Eiko; Knight, Simon A. B.; Buck, Christopher B.

    2015-01-01

    ABSTRACT Merkel cell polyomavirus (MCPyV) plays an important role in Merkel cell carcinoma (MCC). MCPyV small T (sT) antigen has emerged as the key oncogenic driver in MCC carcinogenesis. It has also been shown to promote MCPyV LT-mediated replication by stabilizing LT. The importance of MCPyV sT led us to investigate sT functions and to identify potential ways to target this protein. We discovered that MCPyV sT purified from bacteria contains iron-sulfur (Fe/S) clusters. Electron paramagnetic resonance analysis showed that MCPyV sT coordinates a [2Fe-2S] and a [4Fe-4S] cluster. We also observed phenotypic conservation of Fe/S coordination in the sTs of other polyomaviruses. Since Fe/S clusters are critical cofactors in many nucleic acid processing enzymes involved in DNA unwinding and polymerization, our results suggested the hypothesis that MCPyV sT might be directly involved in viral replication. Indeed, we demonstrated that MCPyV sT enhances LT-mediated replication in a manner that is independent of its previously reported ability to stabilize LT. MCPyV sT translocates to nuclear foci containing actively replicating viral DNA, supporting a direct role for sT in promoting viral replication. Mutations of Fe/S cluster-coordinating cysteines in MCPyV sT abolish its ability to stimulate viral replication. Moreover, treatment with cidofovir, a potent antiviral agent, robustly inhibits the sT-mediated enhancement of MCPyV replication but has little effect on the basal viral replication driven by LT alone. This finding further indicates that MCPyV sT plays a direct role in stimulating viral DNA replication and introduces cidofovir as a possible drug for controlling MCPyV infection. IMPORTANCE MCPyV is associated with a highly aggressive form of skin cancer in humans. Epidemiological surveys for MCPyV seropositivity and sequencing analyses of healthy human skin suggest that MCPyV may represent a common component of the human skin microbial flora. However, much of the

  9. A global assembly line to cyanobactins

    PubMed Central

    Donia, Mohamed S.; Ravel, Jacques; Schmidt, Eric W.

    2009-01-01

    More than 100 cyclic peptides harboring heterocyclized residues are known from marine ascidians, sponges and different genera of cyanobacteria. Here, we report an assembly line responsible for the biosynthesis of these diverse peptides, now called cyanobactins, both in symbiotic and free-living cyanobacteria. By comparing five new cyanobactin biosynthetic clusters, we could produce the prenylated antitumor preclinical candidate, trunkamide, in E. coli culture using genetic engineering. PMID:18425112

  10. Sensor mount assemblies and sensor assemblies

    DOEpatents

    Miller, David H.

    2012-04-10

    Sensor mount assemblies and sensor assemblies are provided. In an embodiment, by way of example only, a sensor mount assembly includes a busbar, a main body, a backing surface, and a first finger. The busbar has a first end and a second end. The main body is overmolded onto the busbar. The backing surface extends radially outwardly relative to the main body. The first finger extends axially from the backing surface, and the first finger has a first end, a second end, and a tooth. The first end of the first finger is disposed on the backing surface, and the tooth is formed on the second end of the first finger.

  11. CARTILAGE CELL CLUSTERS

    PubMed Central

    Lotz, Martin K.; Otsuki, Shuhei; Grogan, Shawn P.; Sah, Robert; Terkeltaub, Robert; D’Lima, Darryl

    2010-01-01

    The formation of new cell clusters is a histological hallmark of arthritic cartilage but the biology of clusters and their role in disease are poorly understood. This is the first comprehensive review of clinical and experimental conditions associated with cluster formation. Genes and proteins that are expressed in cluster cells, the cellular origin of the clusters, mechanisms that lead to cluster formation and the role of cluster cells in pathogenesis are discussed. PMID:20506158

  12. Constraining the Mass-Richness Relationship of redMaPPer Clusters with Angular Clustering

    NASA Astrophysics Data System (ADS)

    Baxter, Eric J.; Rozo, Eduardo; Jain, Bhuvnesh; Rykoff, Eli; Wechsler, Risa H.

    2016-08-01

    The potential of using cluster clustering for calibrating the mass-richness relation of galaxy clusters has been recognized theoretically for over a decade. Here, we demonstrate the feasibility of this technique to achieve high precision mass calibration using redMaPPer clusters in the Sloan Digital Sky Survey North Galactic Cap. By including cross-correlations between several richness bins in our analysis we significantly improve the statistical precision of our mass constraints. The amplitude of the mass-richness relation is constrained to 7% statistical precision by our analysis. However, the error budget is systematics dominated, reaching a 19% total error that is dominated by theoretical uncertainty in the bias-mass relation for dark matter halos. We confirm the result from Miyatake et al. (2015) that the clustering amplitude of redMaPPer clusters depends on galaxy concentration as defined therein, and we provide additional evidence that this dependence cannot be sourced by mass dependencies: some other effect must account for the observed variation in clustering amplitude with galaxy concentration. Assuming that the observed dependence of redMaPPer clustering on galaxy concentration is a form of assembly bias, we find that such effects introduce a systematic error on the amplitude of the mass-richness relation that is comparable to the errorbar from statistical noise. The results presented here demonstrate the power of cluster clustering for mass calibration and cosmology provided the current theoretical systematics can be ameliorated.

  13. Interconnect assembly for an electronic assembly and assembly method therefor

    DOEpatents

    Gerbsch, Erich William

    2003-06-10

    An interconnect assembly and method for a semiconductor device, in which the interconnect assembly can be used in lieu of wirebond connections to form an electronic assembly. The interconnect assembly includes first and second interconnect members. The first interconnect member has a first surface with a first contact and a second surface with a second contact electrically connected to the first contact, while the second interconnect member has a flexible finger contacting the second contact of the first interconnect member. The first interconnect member is adapted to be aligned and registered with a semiconductor device having a contact on a first surface thereof, so that the first contact of the first interconnect member electrically contacts the contact of the semiconductor device. Consequently, the assembly method does not require any wirebonds, but instead merely entails aligning and registering the first interconnect member with the semiconductor device so that the contacts of the first interconnect member and the semiconductor device make electrically contact, and then contacting the second contact of the first interconnect member with the flexible finger of the second interconnect member.

  14. Superlattices assembled through shape-induced directional binding

    NASA Astrophysics Data System (ADS)

    Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg

    2015-04-01

    Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.

  15. Superlattices assembled through shape-induced directional binding

    PubMed Central

    Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg

    2015-01-01

    Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks—cubes and octahedrons—when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices. PMID:25903309

  16. Superlattices assembled through shape-induced directional binding.

    PubMed

    Lu, Fang; Yager, Kevin G; Zhang, Yugang; Xin, Huolin; Gang, Oleg

    2015-01-01

    Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices. PMID:25903309

  17. Superlattices assembled through shape-induced directional binding

    SciTech Connect

    Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg

    2015-04-23

    Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks—cubes and octahedrons—when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block’s facets, while structural order depends on DNA-tuned interactions and particle size ratio. Lastly, the presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.

  18. Telerobotic truss assembly

    NASA Technical Reports Server (NTRS)

    Sheridan, Philip L.

    1987-01-01

    The ACCESS truss was telerobotically assembled in order to gain experience with robotic assembly of hardware designed for astronaut extravehicular (EVA) assembly. Tight alignment constraints of the ACCESS hardware made telerobotic assembly difficult. A wider alignment envelope and a compliant end effector would have reduced the problem. The manipulator had no linear motion capability, but many of the assembly operations required straight line motion. The manipulator was attached to a motion table in order to provide the X, Y, and Z translations needed. A programmable robot with linear translation capability would have eliminated the need for the motion table and streamlined the assembly. Poor depth perception was a major problem. Shaded paint schemes and alignment lines were helpful in reducing this problem. The four cameras used worked well for only some operations. It was not possible to identify camera locations that worked well for all assembly steps. More cameras or movable cameras would have simplified some operations. The audio feedback system was useful.

  19. Assembly of Nanoions via Electrostatic Interactions: Ion-Like Behavior of Charged Noble Metal Nanoclusters

    PubMed Central

    Yao, Qiaofeng; Luo, Zhentao; Yuan, Xun; Yu, Yue; Zhang, Chao; Xie, Jianping; Lee, Jim Yang

    2014-01-01

    The assembly of ultrasmall metal nanoclusters (NCs) is of interest to both basic and applied research as it facilitates the determination of cluster structures and the customization of cluster physicochemical properties. Here we present a facile and general approach to assemble noble metal NCs by selectively inducing electrostatic interactions between negatively-charged metal NCs and divalent cations. The charged metal NCs, which have well-defined sizes, charges and structures; and behave similarly to multivalent anions, can be considered as nanoions. These nanoions exhibit step-like assembly behavior when interacting with the counter cations – assembly only occurs when the solubility product (Ksp) between the carboxylate ions on the NC surface and the divalent cations is exceeded. The assembly here is distinctively different from the random aggregation of colloidal particles by counter ions. The nanoions would assemble into fractal-like monodisperse spherical particles with a high order of regularity that mimic the assembly of ionic crystals. PMID:24457992

  20. An exactly solvable model of hierarchical self-assembly

    NASA Astrophysics Data System (ADS)

    Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.

    2009-06-01

    Many living and nonliving structures in the natural world form by hierarchical organization, but physical theories that describe this type of organization are scarce. To address this problem, a model of equilibrium self-assembly is formulated in which dynamically associating species organize into hierarchical structures that preserve their shape at each stage of assembly. In particular, we consider symmetric m-gons that associate at their vertices into Sierpinski gasket structures involving the hierarchical association of triangles, squares, hexagons, etc., at their corner vertices, thereby leading to fractal structures after many generations of assembly. This rather idealized model of hierarchical assembly yields an infinite sequence of self-assembly transitions as the morphology progressively organizes to higher levels of the hierarchy, and these structures coexists at dynamic equilibrium, as found in real hierarchically self-assembling systems such as amyloid fiber forming proteins. Moreover, the transition sharpness progressively grows with increasing m, corresponding to larger and larger loops in the assembled structures. Calculations are provided for several basic thermodynamic properties (including the order parameters for assembly for each stage of the hierarchy, average mass of clusters, specific heat, transition sharpness, etc.) that are required for characterizing the interaction parameters governing this type of self-assembly and for elucidating other basic qualitative aspects of these systems. Our idealized model of hierarchical assembly gives many insights into this ubiquitous type of self-organization process.

  1. Informed kmer selection for de novo transcriptome assembly

    PubMed Central

    Durai, Dilip A.; Schulz, Marcel H.

    2016-01-01

    Motivation: De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice. Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies. Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use. Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: mschulz@mmci.uni-saarland.de PMID:27153653

  2. MODELING THE METALLICITY DISTRIBUTION OF GLOBULAR CLUSTERS

    SciTech Connect

    Muratov, Alexander L.; Gnedin, Oleg Y. E-mail: ognedin@umich.ed

    2010-08-01

    Observed metallicities of globular clusters reflect physical conditions in the interstellar medium of their high-redshift host galaxies. Globular cluster systems in most large galaxies display bimodal color and metallicity distributions, which are often interpreted as indicating two distinct modes of cluster formation. The metal-rich and metal-poor clusters have systematically different locations and kinematics in their host galaxies. However, the red and blue clusters have similar internal properties, such as their masses, sizes, and ages. It is therefore interesting to explore whether both metal-rich and metal-poor clusters could form by a common mechanism and still be consistent with the bimodal distribution. We present such a model, which prescribes the formation of globular clusters semi-analytically using galaxy assembly history from cosmological simulations coupled with observed scaling relations for the amount and metallicity of cold gas available for star formation. We assume that massive star clusters form only during mergers of massive gas-rich galaxies and tune the model parameters to reproduce the observed distribution in the Galaxy. A wide, but not the entire, range of model realizations produces metallicity distributions consistent with the data. We find that early mergers of smaller hosts create exclusively blue clusters, whereas subsequent mergers of more massive galaxies create both red and blue clusters. Thus, bimodality arises naturally as the result of a small number of late massive merger events. This conclusion is not significantly affected by the large uncertainties in our knowledge of the stellar mass and cold gas mass in high-redshift galaxies. The fraction of galactic stellar mass locked in globular clusters declines from over 10% at z > 3 to 0.1% at present.

  3. Extreme Mergers from the Massive Cluster Survey

    NASA Astrophysics Data System (ADS)

    Morris, Roger

    2010-09-01

    We propose to observe two extraordinary, high-redshift galaxy clusters from the Massive Cluster Survey. Both targets are very rare, triple merger systems (one a nearly co-linear merger), and likely lie at the deepest nodes of the cosmic web. Both targets show multiple strong gravitational lensing arcs in the cluster cores. These targets only possess very short (10ks) Chandra observations, and are unobserved by XMM-Newton. The X-ray data will be used to probe the mass distribution of hot, baryonic gas, and to reveal the details of the merger physics and the process of cluster assembly. We will also search for hints of X-ray emission from filaments between the merging clumps. Subaru and Hubble Space Telescope imaging data are in hand; we request additional HST coverage for one object.

  4. Extreme Mergers from the Massive Cluster Survey

    NASA Astrophysics Data System (ADS)

    Morris, R.

    2010-09-01

    We will observe an extraordinary, high-redshift galaxy cluster from the Massive Cluster Survey. The target is a very rare, triple merger system, and likely lies at the one of deepest nodes of the cosmic web. The target shows multiple strong gravitational lensing arcs in the cluster core. This target only possesses a very short {10ks} Chandra observations, and is unobserved by XMM-Newton. The X-ray data from this joint Chandra/HST proposal will be used to probe the mass distribution of hot, baryonic gas, and to reveal the details of the merger physics and the process of cluster assembly. We will also search for hints of X-ray emission from filaments between the merging clumps. Subaru and some Hubble Space Telescope imaging data are in hand; we will gather additional HST coverage for a lensing analysis.

  5. Internal Dynamics of Equilibrium Colloidal Clusters

    NASA Astrophysics Data System (ADS)

    Perry, Rebecca Wood

    Colloidal clusters, aggregates of a few micrometer-sized spherical particles, are a model experimental system for understanding the physics of self-assembly and processes such as nucleation. Colloidal clusters are well suited for studies on these topics because they are the simplest colloidal system with internal degrees of freedom. Clusters made from particles that weakly attract one another continually rearrange between different structures. By characterizing these internal dynamics and the structures connected by the rearrangement pathways, we seek to understand the statistical physics underlying self-assembly and equilibration. In this thesis, we examine the rearrangement dynamics of colloidal clusters and analyze the equilibrium distributions of ground and excited states. We prepare clusters of up to ten microspheres bound by short-range depletion interactions that are tuned to allow equilibration between multiple isostatic arrangements. To study these clusters, we use bright-field and digital holographic microscopy paired with computational post-processing to amass ensemble-averaged and time-averaged probabilities. We study both two-dimensional (2D) and three-dimensional (3D) clusters composed of either one or two species of particles. To learn about geometrical nucleation barriers, we track rearrangements of particles within freely rotating and translating 3D clusters. We show that rearrangements occur on a timescale of seconds, consistent with diffusion-dominated internal dynamics. To better understand excited states and transition pathways, we track hundreds of rearrangements between degenerate ground states in 2D clusters. We show that the rearrangement rates can be understood using a model with two parameters, which account for the diffusion coefficient along the excited-state rearrangement pathways and the interaction potential. To explore new methods to control self-assembly, we analyze clusters of two species with different masses and different

  6. Wind turbine rotor assembly

    SciTech Connect

    Kaiser, H. W.

    1984-11-20

    A vertical axis wind turbine having a horizontal arm member which supports an upright blade assembly. Bearing structure coupling the blade assembly to the turbine arm permits blade movement about its longitudinal axis as well as flexing motion of the blade assembly about axes perpendicular to the longitudinal axis. A latching mechanism automatically locks the blade assembly to its supporting arm during normal turbine operation and automatically unlocks same when the turbine is at rest. For overspeed prevention, a centrifugally actuated arm functions to unlatch the blade assembly permitting same to slipstream or feather into the wind. Manually actuated means are also provided for unlatching the moving blade assembly. The turbine arm additionally carries a switching mechanism in circuit with a turbine generator with said mechanism functioning to open and hence protect the generator circuit in the event of an overspeed condition of the turbine.

  7. THE STELLAR MASS GROWTH OF BRIGHTEST CLUSTER GALAXIES IN THE IRAC SHALLOW CLUSTER SURVEY

    SciTech Connect

    Lin, Yen-Ting; Brodwin, Mark; Gonzalez, Anthony H.; Bode, Paul; Eisenhardt, Peter R. M.; Stanford, S. A.; Vikhlinin, Alexey

    2013-07-01

    The details of the stellar mass assembly of brightest cluster galaxies (BCGs) remain an unresolved problem in galaxy formation. We have developed a novel approach that allows us to construct a sample of clusters that form an evolutionary sequence, and have applied it to the Spitzer IRAC Shallow Cluster Survey (ISCS) to examine the evolution of BCGs in progenitors of present-day clusters with mass of (2.5-4.5) Multiplication-Sign 10{sup 14} M{sub Sun }. We follow the cluster mass growth history extracted from a high resolution cosmological simulation, and then use an empirical method that infers the cluster mass based on the ranking of cluster luminosity to select high-z clusters of appropriate mass from ISCS to be progenitors of the given set of z = 0 clusters. We find that, between z = 1.5 and 0.5, the BCGs have grown in stellar mass by a factor of 2.3, which is well-matched by the predictions from a state-of-the-art semi-analytic model. Below z = 0.5 we see hints of differences in behavior between the model and observation.

  8. Clustering and Pattern Formation in Chemorepulsive Active Colloids.

    PubMed

    Liebchen, Benno; Marenduzzo, Davide; Pagonabarraga, Ignacio; Cates, Michael E

    2015-12-18

    We demonstrate that migration away from self-produced chemicals (chemorepulsion) generates a generic route to clustering and pattern formation among self-propelled colloids. The clustering instability can be caused either by anisotropic chemical production, or by a delayed orientational response to changes of the chemical environment. In each case, chemorepulsion creates clusters of a self-limiting area which grows linearly with self-propulsion speed. This agrees with recent observations of dynamic clusters in Janus colloids (albeit not yet known to be chemorepulsive). More generally, our results could inform design principles for the self-assembly of chemorepulsive synthetic swimmers and/or bacteria into nonequilibrium patterns. PMID:26722949

  9. Clustering and Pattern Formation in Chemorepulsive Active Colloids

    NASA Astrophysics Data System (ADS)

    Liebchen, Benno; Marenduzzo, Davide; Pagonabarraga, Ignacio; Cates, Michael E.

    2015-12-01

    We demonstrate that migration away from self-produced chemicals (chemorepulsion) generates a generic route to clustering and pattern formation among self-propelled colloids. The clustering instability can be caused either by anisotropic chemical production, or by a delayed orientational response to changes of the chemical environment. In each case, chemorepulsion creates clusters of a self-limiting area which grows linearly with self-propulsion speed. This agrees with recent observations of dynamic clusters in Janus colloids (albeit not yet known to be chemorepulsive). More generally, our results could inform design principles for the self-assembly of chemorepulsive synthetic swimmers and/or bacteria into nonequilibrium patterns.

  10. Star Formation in Galaxy Clusters Over the Past 10 Billion Years

    NASA Astrophysics Data System (ADS)

    Tran, Kim-Vy

    2012-01-01

    Galaxy clusters are the largest gravitationally bound systems in the universe and include the most massive galaxies in the universe; this makes galaxy clusters ideal laboratories for disentangling the nature versus nurture aspect of how galaxies evolve. Understanding how galaxies form and evolve in clusters continues to be a fundamental question in astronomy. The ages and assembly histories of galaxies in rich clusters test both stellar population models and hierarchical formation scenarios. Is star formation in cluster galaxies simply accelerated relative to their counterparts in the lower density field, or do cluster galaxies assemble their stars in a fundamentally different manner? To answer this question, I review multi-wavelength results on star formation in galaxy clusters from Coma to the most distant clusters yet discovered at look-back times of 10 billion years (z 2).

  11. Force-Based Reasoning for Assembly Planning and Subassembly Stability Analysis

    NASA Technical Reports Server (NTRS)

    Lee, S.; Yi, C.; Wang, F-C.

    1993-01-01

    In this paper, we show that force-based reasoning, for identifying a cluster of parts that can be decomposed naturally by the applied force, plays an important role in selecting feasible subassemblies and analyzing subassembly stability in assembly planning.

  12. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme.

    PubMed

    Dong, Min; Horitani, Masaki; Dzikovski, Boris; Pandelia, Maria-Eirini; Krebs, Carsten; Freed, Jack H; Hoffman, Brian M; Lin, Hening

    2016-08-10

    Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes. PMID:27465315

  13. Radiological characterization of spent control rod assemblies

    SciTech Connect

    Lepel, E.A.; Robertson, D.E.; Thomas, C.W.; Pratt, S.L.; Haggard, D.L.

    1995-10-01

    This document represents the final report of an ongoing study to provide radiological characterizations, classifications, and assessments in support of the decommissioning of nuclear power stations. This report describes the results of non-destructive and laboratory radionuclide measurements, as well as waste classification assessments, of BWR and PWR spent control rod assemblies. The radionuclide inventories of these spent control rods were determined by three separate methodologies, including (1) direct assay techniques, (2) calculational techniques, and (3) by sampling and laboratory radiochemical analyses. For the BWR control rod blade (CRB) and PWR burnable poison rod assembly (BPRA), {sup 60}Co and {sup 63}Ni, present in the stainless steel cladding, were the most abundant neutron activation products. The most abundant radionuclide in the PWR rod cluster control assembly (RCCA) was {sup 108m}Ag (130 yr halflife) produced in the Ag-In-Cd alloy used as the neutron poison. This radionuclide will be the dominant contributor to the gamma dose rate for many hundreds of years. The results of the direct assay methods agree very well ({+-}10%) with the sampling/radiochemical measurements. The results of the calculational methods agreed fairly well with the empirical measurements for the BPRA, but often varied by a factor of 5 to 10 for the CRB and the RCCA assemblies. If concentration averaging and encapsulation, as allowed by 10CFR61.55, is performed, then each of the entire control assemblies would be classified as Class C low-level radioactive waste.

  14. Composite turbine bucket assembly

    DOEpatents

    Liotta, Gary Charles; Garcia-Crespo, Andres

    2014-05-20

    A composite turbine blade assembly includes a ceramic blade including an airfoil portion, a shank portion and an attachment portion; and a transition assembly adapted to attach the ceramic blade to a turbine disk or rotor, the transition assembly including first and second transition components clamped together, trapping said ceramic airfoil therebetween. Interior surfaces of the first and second transition portions are formed to mate with the shank portion and the attachment portion of the ceramic blade, and exterior surfaces of said first and second transition components are formed to include an attachment feature enabling the transition assembly to be attached to the turbine rotor or disk.

  15. Hybrid Lanthanide-Actinide Peroxide Cage Clusters.

    PubMed

    Sigmon, Ginger E; Szymanowski, Jennifer E S; Carter, Korey P; Cahill, Christopher L; Burns, Peter C

    2016-03-21

    A cage cluster consisting of 31 uranyl and 9 Sm(3+) polyhedra self-assembles in an alkaline aqueous peroxide solution and crystallizes (U31Sm9). Trimers of Sm(3+) polyhedra are templated by μ3-η(2):η(2):η(2)-peroxide groups and link to oxo atoms of uranyl ions. Three such trimers link into a ring through uranyl hexagonal bipyramids, and these are attached through six polyhedra to a unit consisting of 21 uranyl hexagonal bipyramids to complete the cage. Luminescence spectra collected with an excitation wavelength of 420 nm reveal fine structure, which is not observed for a cluster containing only uranyl polyhedra. PMID:26923457

  16. Hydrothermal crystallization of Na{sub 2}Ti{sub 6}O{sub 13}, Na{sub 2}Ti{sub 3}O{sub 7}, and Na{sub 16}Ti{sub 10}O{sub 28} in the NaOH-TiO{sub 2}-H{sub 2}O system at a temperature of 500 deg. C and a pressure of 0.1 GPa: The structural mechanism of self-assembly of titanates from suprapolyhedral clusters

    SciTech Connect

    Hyushin, G. D.

    2006-07-15

    An increase in the NaOH concentration in the NaOH-TiO{sub 2} (rutile)-H{sub 2}O system at a temperature of 500 deg. C and a pressure of 0.1 GPa leads to the crystallization R-TiO{sub 2} + Na{sub 2}Ti{sub 6}O{sub 13} {sup {yields}} Na{sub 2}Ti{sub 3}O{sub 7} {sup {yields}} Na{sub 16}Ti{sub 10}O{sub 28}. Crystals of the Na{sub 2}Ti{sub 6}O{sub 13} titanate (space group C2/m) have the three-dimensional framework structure Ti{sub 6}O{sub 13}. The structure of the Na{sub 2}Ti{sub 3}O{sub 7} titanate (space group P2{sub 1}/m) contains the two-dimensional layers Ti{sub 3}O{sub 7}. The structure of the Na{sub 16}Ti{sub 10}O{sub 28} titanate (space group P-1) is composed of the isolated ten-polyhedron cluster precursors Ti{sub 10}O{sub 28}. In all the structures, the titanium atoms have an octahedral coordination (MTiO{sub 6}). The matrix self-assembly of the Na{sub 2}Ti{sub 6}O{sub 13} and Na{sub 2}Ti{sub 3}O{sub 7} (Na{sub 4}Ti{sub 6}O{sub 14}) crystal structures from Na{sub 4}M{sub 12} invariant precursors is modeled. These precursors are clusters consisting of twelve M polyhedra linked through the edges. It is demonstrated that the structurally rigid precursors Na{sub 4}M{sub 12} control all processes of the subsequent evolution of the crystal-forming titanate clusters. The specific features of the self-assembly of the Na{sub 2}Ti{sub 3}O{sub 7} structure that result from the additional incorporation of twice the number of sodium atoms into the composition of the high-level clusters are considered.

  17. Laser bottom hole assembly

    DOEpatents

    Underwood, Lance D; Norton, Ryan J; McKay, Ryan P; Mesnard, David R; Fraze, Jason D; Zediker, Mark S; Faircloth, Brian O

    2014-01-14

    There is provided for laser bottom hole assembly for providing a high power laser beam having greater than 5 kW of power for a laser mechanical drilling process to advance a borehole. This assembly utilizes a reverse Moineau motor type power section and provides a self-regulating system that addresses fluid flows relating to motive force, cooling and removal of cuttings.

  18. Liquid rocket valve assemblies

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The design and operating characteristics of valve assemblies used in liquid propellant rocket engines are discussed. The subjects considered are as follows: (1) valve selection parameters, (2) major design aspects, (3) design integration of valve subassemblies, and (4) assembly of components and functional tests. Information is provided on engine, stage, and spacecraft checkout procedures.

  19. Turbine disc sealing assembly

    DOEpatents

    Diakunchak, Ihor S.

    2013-03-05

    A disc seal assembly for use in a turbine engine. The disc seal assembly includes a plurality of outwardly extending sealing flange members that define a plurality of fluid pockets. The sealing flange members define a labyrinth flow path therebetween to limit leakage between a hot gas path and a disc cavity in the turbine engine.

  20. High speed door assembly

    DOEpatents

    Shapiro, Carolyn

    1993-01-01

    A high speed door assembly, comprising an actuator cylinder and piston rods, a pressure supply cylinder and fittings, an electrically detonated explosive bolt, a honeycomb structured door, a honeycomb structured decelerator, and a structural steel frame encasing the assembly to close over a 3 foot diameter opening within 50 milliseconds of actuation, to contain hazardous materials and vapors within a test fixture.

  1. High speed door assembly

    DOEpatents

    Shapiro, C.

    1993-04-27

    A high speed door assembly is described, comprising an actuator cylinder and piston rods, a pressure supply cylinder and fittings, an electrically detonated explosive bolt, a honeycomb structured door, a honeycomb structured decelerator, and a structural steel frame encasing the assembly to close over a 3 foot diameter opening within 50 milliseconds of actuation, to contain hazardous materials and vapors within a test fixture.

  2. Permanent magnet assembly

    DOEpatents

    Chell, Jeremy; Zimm, Carl B.

    2006-12-12

    A permanent magnet assembly is disclosed that is adapted to provide a magnetic field across an arc-shaped gap. Such a permanent magnet assembly can be used, for example, to provide a time-varying magnetic field to an annular region for use in a magnetic refrigerator.

  3. Assembly: a resource for assembled genomes at NCBI.

    PubMed

    Kitts, Paul A; Church, Deanna M; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D; Pruitt, Kim D; Kimchi, Avi

    2016-01-01

    The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

  4. Assembly: a resource for assembled genomes at NCBI

    PubMed Central

    Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

    2016-01-01

    The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

  5. Foodservice Occupations Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    Intended to assist vocational teachers in developing and implementing a cluster program in food service occupations, this guide contains sections on cluster organization and implementation and instructional emphasis areas. The cluster organization and implementation section covers goal-based planning and includes a proposed cluster curriculum, a…

  6. Cluster-impact fusion

    SciTech Connect

    Echenique, P.M.; Manson, J.R.; Ritchie, R.H. )

    1990-03-19

    We present a model for the cluster-impact-fusion experiments of Buehler, Friedlander, and Friedman, Calculated fusion rates as a function of bombarding energy for constant cluster size agree well with experiment. The dependence of the fusion rate on cluster size at fixed bombarding energy is explained qualitatively. The role of correlated, coherent collisions in enhanced energy loss by clusters is emphasized.

  7. Mechanisms of Virus Assembly

    PubMed Central

    Perlmutter, Jason D.; Hagan, Michael F.

    2015-01-01

    Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assembles within their host cells and in vitro. We describe the thermodynamics and kinetics for assembly of protein subunits into icosahedral capsid shells, and how these are modified in cases where the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques that have been used to characterize capsid assembly, and we highlight aspects of virus assembly which are likely to receive significant attention in the near future. PMID:25532951

  8. Modeling Viral Capsid Assembly

    PubMed Central

    2014-01-01

    I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened. PMID:25663722

  9. Constrained space camera assembly

    DOEpatents

    Heckendorn, Frank M.; Anderson, Erin K.; Robinson, Casandra W.; Haynes, Harriet B.

    1999-01-01

    A constrained space camera assembly which is intended to be lowered through a hole into a tank, a borehole or another cavity. The assembly includes a generally cylindrical chamber comprising a head and a body and a wiring-carrying conduit extending from the chamber. Means are included in the chamber for rotating the body about the head without breaking an airtight seal formed therebetween. The assembly may be pressurized and accompanied with a pressure sensing means for sensing if a breach has occurred in the assembly. In one embodiment, two cameras, separated from their respective lenses, are installed on a mounting apparatus disposed in the chamber. The mounting apparatus includes means allowing both longitudinal and lateral movement of the cameras. Moving the cameras longitudinally focuses the cameras, and moving the cameras laterally away from one another effectively converges the cameras so that close objects can be viewed. The assembly further includes means for moving lenses of different magnification forward of the cameras.

  10. Automated assembly in space

    NASA Technical Reports Server (NTRS)

    Srivastava, Sandanand; Dwivedi, Suren N.; Soon, Toh Teck; Bandi, Reddy; Banerjee, Soumen; Hughes, Cecilia

    1989-01-01

    The installation of robots and their use of assembly in space will create an exciting and promising future for the U.S. Space Program. The concept of assembly in space is very complicated and error prone and it is not possible unless the various parts and modules are suitably designed for automation. Certain guidelines are developed for part designing and for an easy precision assembly. Major design problems associated with automated assembly are considered and solutions to resolve these problems are evaluated in the guidelines format. Methods for gripping and methods for part feeding are developed with regard to the absence of gravity in space. The guidelines for part orientation, adjustments, compliances and various assembly construction are discussed. Design modifications of various fasteners and fastening methods are also investigated.

  11. Superconducting radiofrequency window assembly

    DOEpatents

    Phillips, H.L.; Elliott, T.S.

    1997-03-11

    The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly has a superconducting metal-ceramic design. The srf window assembly comprises a superconducting frame, a ceramic plate having a superconducting metallized area, and a superconducting eyelet for sealing plate into frame. The plate is brazed to eyelet which is then electron beam welded to frame. A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator. 11 figs.

  12. Superconductive radiofrequency window assembly

    DOEpatents

    Phillips, H.L.; Elliott, T.S.

    1998-05-19

    The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The SRF window assembly has a superconducting metal-ceramic design. The SRF window assembly comprises a superconducting frame, a ceramic plate having a superconducting metallized area, and a superconducting eyelet for sealing plate into frame. The plate is brazed to eyelet which is then electron beam welded to frame. A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the SRF window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator. 11 figs.

  13. Protein-coat dynamics and cluster phases in intracellular trafficking

    NASA Astrophysics Data System (ADS)

    Huber, Greg; Wang, Hui; Mukhopadhyay, Ranjan

    2011-09-01

    Clustering of membrane proteins is a hallmark of biological membranes' lateral organization and crucial to their function. However, the physical properties of these protein aggregates remain poorly understood. Ensembles of coat proteins, the example considered here, are necessary for intracellular transport in eukaryotic cells. Assembly and disassembly rates for coat proteins involved in intracellular vesicular trafficking must be carefully controlled: their assembly deforms the membrane patch and drives vesicle formation, yet the protein coat must rapidly disassemble after vesiculation. Motivated by recent experimental findings for protein-coat dynamics, we study a dynamical Ising-type model for coat assembly and disassembly, and demonstrate how simple dynamical rules generate a robust, steady-state distribution of protein clusters (corresponding to intermediate budded shapes) and how cluster sizes are controlled by the kinetics. We interpret the results in terms of both vesiculation and the coupling to cargo proteins.

  14. Occupational Education for Students with Special Needs: Mechanical Assembly.

    ERIC Educational Resources Information Center

    Nassau County Board of Cooperative Educational Services, Westbury, NY.

    This curriculum resource guide on mechanical assembly is one of a series of seventeen specialized curriculum guides for occupational education for the marginal, handicapped, or special needs occupational education student. The guide begins with six behavior clusters that contain a series of forty-two instructional topics designed to teach…

  15. Occupational Education for Students with Special Needs: Electronic Assembly.

    ERIC Educational Resources Information Center

    Nassau County Board of Cooperative Educational Services, Westbury, NY.

    This curriculum resource guide on electronic assembly is one of a series of seventeen specialized curriculum guides for occupational education of the marginal, handicapped, or special needs occupational education student. The guide begins with six behavior clusters that contain a series of forty-two instructional topics designed to teach…

  16. Occupational Education for Students with Special Needs: Wood Products Assembly.

    ERIC Educational Resources Information Center

    Nassau County Board of Cooperative Educational Services, Westbury, NY.

    This curriculum resource guide on wood products assembly is one of a series of seventeen specialized curriculum guides for occupational education of the marginal, handicapped, or special needs occupational education student. The guide begins with six behavior clusters that contain a series of forty-two instructional topics designed to teach…

  17. Cooperative Self-Assembly of Peptide Gelators and Proteins

    PubMed Central

    2014-01-01

    Molecular self-assembly provides a versatile route for the production of nanoscale materials for medical and technological applications. Herein, we demonstrate that the cooperative self-assembly of amphiphilic small molecules and proteins can have drastic effects on supramolecular nanostructuring of resulting materials. We report that mesoscale, fractal-like clusters of proteins form at concentrations that are orders of magnitude lower compared to those usually associated with molecular crowding at room temperature. These protein clusters have pronounced effects on the molecular self-assembly of aromatic peptide amphiphiles (fluorenylmethoxycarbonyl- dipeptides), resulting in a reversal of chiral organization and enhanced order through templating and binding. Moreover, the morphological and mechanical properties of the resultant nanostructured gels can be controlled by the cooperative self-assembly of peptides and protein fractal clusters, having implications for biomedical applications where proteins and peptides are both present. In addition, fundamental insights into cooperative interplay of molecular interactions and confinement by clusters of chiral macromolecules is relevant to gaining understanding of the molecular mechanisms of relevance to the origin of life and development of synthetic mimics of living systems. PMID:24256076

  18. Assembly and clustering of natural antibiotics guides target identification.

    PubMed

    Johnston, Chad W; Skinnider, Michael A; Dejong, Chris A; Rees, Philip N; Chen, Gregory M; Walker, Chelsea G; French, Shawn; Brown, Eric D; Bérdy, János; Liu, Dennis Y; Magarvey, Nathan A

    2016-04-01

    Antibiotics are essential for numerous medical procedures, including the treatment of bacterial infections, but their widespread use has led to the accumulation of resistance, prompting calls for the discovery of antibacterial agents with new targets. A majority of clinically approved antibacterial scaffolds are derived from microbial natural products, but these valuable molecules are not well annotated or organized, limiting the efficacy of modern informatic analyses. Here, we provide a comprehensive resource defining the targets, chemical origins and families of the natural antibacterial collective through a retrobiosynthetic algorithm. From this we also detail the directed mining of biosynthetic scaffolds and resistance determinants to reveal structures with a high likelihood of having previously unknown modes of action. Implementing this pipeline led to investigations of the telomycin family of natural products from Streptomyces canus, revealing that these bactericidal molecules possess a new antibacterial mode of action dependent on the bacterial phospholipid cardiolipin. PMID:26829473

  19. Self-assembly of PEGylated gold nanoparticles with satellite structures as seeds.

    PubMed

    Bachelet, Marie; Chen, Rongjun

    2016-07-21

    We report a very simple method for the self-assembly of spherical gold nanoparticles (AuNPs), coated with poly(ethylene glycol) (PEG), through a slow evaporation process at room temperature. Clusters of particles forming satellite structures may act as seeds for the self-assembly in a crystallization-like process. Based on the transmission electron microscopy (TEM) images obtained a mechanism for the self-assembly was suggested. PMID:27384086

  20. Cysteine Methylation Controls Radical Generation in the Cfr Radical AdoMet rRNA Methyltransferase

    PubMed Central

    Challand, Martin R.; Salvadori, Enrico; Driesener, Rebecca C.; Kay, Christopher W. M.; Roach, Peter L.; Spencer, James

    2013-01-01

    The ‘radical S-adenosyl-L-methionine (AdoMet)’ enzyme Cfr methylates adenosine 2503 of the 23S rRNA in the peptidyltransferase centre (P-site) of the bacterial ribosome. This modification protects host bacteria, notably methicillin-resistant Staphylococcus aureus (MRSA), from numerous antibiotics, including agents (e.g. linezolid, retapamulin) that were developed to treat such organisms. Cfr contains a single [4Fe-4S] cluster that binds two separate molecules of AdoMet during the reaction cycle. These are used sequentially to first methylate a cysteine residue, Cys338; and subsequently generate an oxidative radical intermediate that facilitates methyl transfer to the unreactive C8 (and/or C2) carbon centres of adenosine 2503. How the Cfr active site, with its single [4Fe-4S] cluster, catalyses these two distinct activities that each utilise AdoMet as a substrate remains to be established. Here, we use absorbance and electron paramagnetic resonance (EPR) spectroscopy to investigate the interactions of AdoMet with the [4Fe-4S] clusters of wild-type Cfr and a Cys338 Ala mutant, which is unable to accept a methyl group. Cfr binds AdoMet with high (∼ 10 µM) affinity notwithstanding the absence of the RNA cosubstrate. In wild-type Cfr, where Cys338 is methylated, AdoMet binding leads to rapid oxidation of the [4Fe-4S] cluster and production of 5'-deoxyadenosine (DOA). In contrast, while Cys338 Ala Cfr binds AdoMet with equivalent affinity, oxidation of the [4Fe-4S] cluster is not observed. Our results indicate that the presence of a methyl group on Cfr Cys338 is a key determinant of the activity of the enzyme towards AdoMet, thus enabling a single active site to support two distinct modes of AdoMet cleavage. PMID:23861844

  1. The rise of operon-like gene clusters in plants.

    PubMed

    Boycheva, Svetlana; Daviet, Laurent; Wolfender, Jean-Luc; Fitzpatrick, Teresa B

    2014-07-01

    Gene clusters are common features of prokaryotic genomes also present in eukaryotes. Most clustered genes known are involved in the biosynthesis of secondary metabolites. Although horizontal gene transfer is a primary source of prokaryotic gene cluster (operon) formation and has been reported to occur in eukaryotes, the predominant source of cluster formation in eukaryotes appears to arise de novo or through gene duplication followed by neo- and sub-functionalization or translocation. Here we aim to provide an overview of the current knowledge and open questions related to plant gene cluster functioning, assembly, and regulation. We also present potential research approaches and point out the benefits of a better understanding of gene clusters in plants for both fundamental and applied plant science. PMID:24582794

  2. Dynamic Nanoparticles Assemblies

    PubMed Central

    WANG, LIBING; XU, LIGUANG; KUANG, HUA; XU, CHUANLAI; KOTOV, NICHOLAS A.

    2012-01-01

    CONSPECTUS Importance Although nanoparticle (NP) assemblies are at the beginning of their development, their unique geometrical shapes and media-responsive optical, electronic and magnetic properties have attracted significant interest. Nanoscale assembly bridges multiple sizes of materials: individual nanoparticles, discrete molecule-like or virus-like nanoscale agglomerates, microscale devices, and macroscale materials. The capacity to self-assemble can greatly facilitate the integration of nanotechnology with other technologies and, in particular, with microscale fabrication. In this Account, we describe developments in the emerging field of dynamic NP assemblies, which are spontaneously formed superstructures containing more than two inorganic nanoscale particles that display ability to change their geometrical, physical, chemical, and other attributes. In many ways, dynamic assemblies can represent a bottleneck in the ‘bottom-up’ fabrication of NP-based devices because they can produce a much greater variety of assemblies, but they also provide a convenient tool for variation of geometries and dimensions of nanoparticle assemblies. Classification Superstructures of NPs (and those held together by similar intrinsic forces) are classified into two groups: Class 1 where media and external fields can alter shape, conformation, and order of stable superstructures with a nearly constant number same. The future development of successful dynamic assemblies requires understanding the equilibrium in dynamic NP systems. The dynamic nature of Class 1 assemblies is associated with the equilibrium between different conformations of a superstructure and is comparable to the isomerization in classical chemistry. Class 2 assemblies involve the formation and/or breakage of linkages between the NPs, which is analogous to the classical chemical equilibrium for the formation of a molecule from atoms. Finer classification of NP assemblies in accord with established conventions

  3. Linked supramolecular building blocks for enhanced cluster formation

    DOE PAGESBeta

    McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; Teat, Simon J.; Piligkos, Stergios; Brechin, Euan K.; Dalgarno, Scott J.

    2015-01-09

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

  4. Linked supramolecular building blocks for enhanced cluster formation

    SciTech Connect

    McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; Teat, Simon J.; Piligkos, Stergios; Brechin, Euan K.; Dalgarno, Scott J.

    2015-01-09

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

  5. Linked Supramolecular Building Blocks for Enhanced Cluster Formation

    PubMed Central

    McLellan, Ross; Palacios, Maria A; Beavers, Christine M; Teat, Simon J; Piligkos, Stergios; Brechin, Euan K; Dalgarno, Scott J

    2015-01-01

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures. PMID:25641542

  6. HUBBLE SPIES GLOBULAR CLUSTER IN NEIGHBORING GALAXY

    NASA Technical Reports Server (NTRS)

    2002-01-01

    Hubble Space Telescope has captured a view of a globular cluster called G1, a large, bright ball of light in the center of the photograph consisting of at least 300,000 old stars. G1, also known as Mayall II, orbits the Andromeda galaxy (M31), the nearest major spiral galaxy to our Milky Way. Located 130,000 light-years from Andromeda's nucleus, G1 is the brightest globular cluster in the Local Group of galaxies. The Local Group consists of about 20 nearby galaxies, including the Milky Way. The crisp image is comparable to ground-based telescope views of similar clusters orbiting the Milky Way. The Andromeda cluster, however, is nearly 100 times farther away. A glimpse into the cluster's finer details allow astronomers to see its fainter helium-burning stars whose temperatures and brightnesses show that this cluster in Andromeda and the oldest Milky Way clusters have approximately the same age. These clusters probably were formed shortly after the beginning of the universe, providing astronomers with a record of the earliest era of galaxy formation. During the next two years, astronomers will use Hubble to study about 20 more globular clusters in Andromeda. The color picture was assembled from separate images taken in visible and near-infrared wavelengths taken in July of 1994. CREDIT: Michael Rich, Kenneth Mighell, and James D. Neill (Columbia University), and Wendy Freedman (Carnegie Observatories), and NASA Image files in GIF and JPEG format and captions may be accessed on Internet via anonymous ftp from oposite.stsci.edu in /pubinfo.

  7. Note: Proof of principle of a new type of cluster beam source with potential for scale-up.

    PubMed

    Palmer, R E; Cao, L; Yin, F

    2016-04-01

    We introduce a new type of cluster beam source based on the assembly of (metal) clusters within a condensed (rare gas) matrix. The "Matrix Assembly Cluster Source" employs an ion beam to enhance collisions between metal atoms in the matrix and to sputter out clusters to form a beam. We demonstrate the formation and deposition of gold and silver nanoclusters with mean size tunable from a few atoms to a few thousand atoms. The cluster flux is equivalent to a current nanoAmp regime but potentially scalable to milliAmps, which would open up a number of interesting experiments and applications. PMID:27131719

  8. Note: Proof of principle of a new type of cluster beam source with potential for scale-up

    NASA Astrophysics Data System (ADS)

    Palmer, R. E.; Cao, L.; Yin, F.

    2016-04-01

    We introduce a new type of cluster beam source based on the assembly of (metal) clusters within a condensed (rare gas) matrix. The "Matrix Assembly Cluster Source" employs an ion beam to enhance collisions between metal atoms in the matrix and to sputter out clusters to form a beam. We demonstrate the formation and deposition of gold and silver nanoclusters with mean size tunable from a few atoms to a few thousand atoms. The cluster flux is equivalent to a current nanoAmp regime but potentially scalable to milliAmps, which would open up a number of interesting experiments and applications.

  9. Arrangement of discs in 2d binary assemblies

    NASA Astrophysics Data System (ADS)

    Gervois, A.; Annic, C.; Lemaitre, J.; Ammi, M.; Oger, L.; Troadec, J.-P.

    1995-02-01

    We study arrangements of the two species of discs in binary assemblies at an intermediate scale. Small discs rearrange along large ones in clusters whose mass and compactness are analyzed with the tools of percolation. The assemblies are generated analogically on an air table or numerically from RSA or Powell algorithms. At a given packing fraction, an infinite cluster of small discs exists above a critical composition; a phenomenological expression for this threshold is proposed. Like in usual percolation problems, the number of inner links in a cluster is a linear function of its mass, with a slope depending both on the packing fraction, the composition of the mixture and the building procedure. An approximate expression is derived for it.

  10. Protective helmet assembly

    NASA Technical Reports Server (NTRS)

    Dawn, Frederic S. (Inventor); Weiss, Fred R. (Inventor); Eck, John D. (Inventor)

    1992-01-01

    The invention is a protective helmet assembly with improved safety and impact resistance, high resistance to ignition and combustion, and reduced offgassing. The assembly comprises a hard rigid ballistic outer shell with one or more impact absorbing pads fitted to the interior surface. The pads are made of open cell flexible polyimide foam material, each of which is attached to the inner surface of the ballistic outer shell by cooperative VELCRO fastener strips of hook-and-loop material affixed respectively to the rigid outer shell and the impact absorbing pads. The helmet assembly with shell and pads is sized to fit relatively close over a wearer's head.

  11. DC source assemblies

    DOEpatents

    Campbell, Jeremy B; Newson, Steve

    2013-02-26

    Embodiments of DC source assemblies of power inverter systems of the type suitable for deployment in a vehicle having an electrically grounded chassis are provided. An embodiment of a DC source assembly comprises a housing, a DC source disposed within the housing, a first terminal, and a second terminal. The DC source also comprises a first capacitor having a first electrode electrically coupled to the housing, and a second electrode electrically coupled to the first terminal. The DC source assembly further comprises a second capacitor having a first electrode electrically coupled to the housing, and a second electrode electrically coupled to the second terminal.

  12. Survey on granularity clustering.

    PubMed

    Ding, Shifei; Du, Mingjing; Zhu, Hong

    2015-12-01

    With the rapid development of uncertain artificial intelligent and the arrival of big data era, conventional clustering analysis and granular computing fail to satisfy the requirements of intelligent information processing in this new case. There is the essential relationship between granular computing and clustering analysis, so some researchers try to combine granular computing with clustering analysis. In the idea of granularity, the researchers expand the researches in clustering analysis and look for the best clustering results with the help of the basic theories and methods of granular computing. Granularity clustering method which is proposed and studied has attracted more and more attention. This paper firstly summarizes the background of granularity clustering and the intrinsic connection between granular computing and clustering analysis, and then mainly reviews the research status and various methods of granularity clustering. Finally, we analyze existing problem and propose further research. PMID:26557926

  13. Harnessing Surface Dislocation Networks for Molecular Self-Assembly

    NASA Astrophysics Data System (ADS)

    Pohl, Karsten

    2009-03-01

    The controlled fabrication of functional wafer-based nano-arrays is one of the ultimate quests in current nanotechnologies. Well-ordered misfit dislocation networks of ultrathin metal films are viable candidates for the growth of two- dimensional ordered cluster arrays in the nanometer regime. Such bottom-up processes can be very complex, involving collective effects from a large number of atoms. Unraveling the fundamental forces that drive these self-assembly processes requires detailed experimental information at the atomic level of large ensembles of hundreds to thousands of atoms. The combination of variable temperature measurements from our home-built STM correlated with 2D Frenkel-Kontorova models based on first-principle interaction parameters is used to explain how uniform arrays can form with the strain in the thin film as the driving force responsible for the surface self-assembly process. This process is generally applicable to assemble many molecular species thus opening avenues towards complex self-assembled structures based on a lock-and-key type approach. Moreover, when increasing the molecular coverage and/or decreasing the strain in the thin film the intermolecular interactions will eventually dominate the elastic effects and dictate the self-assembly process via molecular structure and functionality. We will show that controlling this delicate balance leads to a richness of structures, ranging from disperse ordered arrays of molecular clusters to patterned self-assembled monolayers (SAMs) of functionalized fullerenes and methanethiol.

  14. Optimal Feedback Controlled Assembly of Perfect Crystals.

    PubMed

    Tang, Xun; Rupp, Bradley; Yang, Yuguang; Edwards, Tara D; Grover, Martha A; Bevan, Michael A

    2016-07-26

    Perfectly ordered states are targets in diverse molecular to microscale systems involving, for example, atomic clusters, protein folding, protein crystallization, nanoparticle superlattices, and colloidal crystals. However, there is no obvious approach to control the assembly of perfectly ordered global free energy minimum structures; near-equilibrium assembly is impractically slow, and faster out-of-equilibrium processes generally terminate in defective states. Here, we demonstrate the rapid and robust assembly of perfect crystals by navigating kinetic bottlenecks using closed-loop control of electric field mediated crystallization of colloidal particles. An optimal policy is computed with dynamic programming using a reaction coordinate based dynamic model. By tracking real-time stochastic particle configurations and adjusting applied fields via feedback, the evolution of unassembled particles is guided through polycrystalline states into single domain crystals. This approach to controlling the assembly of a target structure is based on general principles that make it applicable to a broad range of processes from nano- to microscales (where tuning a global thermodynamic variable yields temporal control over thermal sampling of different states via their relative free energies). PMID:27387146

  15. Design strategies for self-assembly of discrete targets

    SciTech Connect

    Madge, Jim; Miller, Mark A.

    2015-07-28

    Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks to hierarchical sequences of intermediates, all the way to the fully addressable limit in which each component is unique. In this paper, we introduce an idealized model of cubic particles with patterned faces that allows self-assembly strategies to be compared and tested. We consider a simple octameric target, starting with the minimal requirements for successful self-assembly and comparing the benefits and limitations of more sophisticated hierarchical and addressable schemes. Simulations are performed using a hybrid dynamical Monte Carlo protocol that allows self-assembling clusters to rearrange internally while still providing Stokes-Einstein-like diffusion of aggregates of different sizes. Our simulations explicitly capture the thermodynamic, dynamic, and steric challenges typically faced by self-assembly processes, including competition between multiple partially completed structures. Self-assembly pathways are extracted from the simulation trajectories by a fully extendable scheme for identifying structural fragments, which are then assembled into history diagrams for successfully completed target structures. For the simple target, a one-component assembly scheme is most efficient and robust overall, but hierarchical and addressable strategies can have an advantage under some conditions if high yield is a priority.

  16. Design strategies for self-assembly of discrete targets

    NASA Astrophysics Data System (ADS)

    Madge, Jim; Miller, Mark A.

    2015-07-01

    Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks to hierarchical sequences of intermediates, all the way to the fully addressable limit in which each component is unique. In this paper, we introduce an idealized model of cubic particles with patterned faces that allows self-assembly strategies to be compared and tested. We consider a simple octameric target, starting with the minimal requirements for successful self-assembly and comparing the benefits and limitations of more sophisticated hierarchical and addressable schemes. Simulations are performed using a hybrid dynamical Monte Carlo protocol that allows self-assembling clusters to rearrange internally while still providing Stokes-Einstein-like diffusion of aggregates of different sizes. Our simulations explicitly capture the thermodynamic, dynamic, and steric challenges typically faced by self-assembly processes, including competition between multiple partially completed structures. Self-assembly pathways are extracted from the simulation trajectories by a fully extendable scheme for identifying structural fragments, which are then assembled into history diagrams for successfully completed target structures. For the simple target, a one-component assembly scheme is most efficient and robust overall, but hierarchical and addressable strategies can have an advantage under some conditions if high yield is a priority.

  17. Climate Modeling with a Linux Cluster

    NASA Astrophysics Data System (ADS)

    Renold, M.; Beyerle, U.; Raible, C. C.; Knutti, R.; Stocker, T. F.; Craig, T.

    2004-08-01

    Until recently, computationally intensive calculations in many scientific disciplines have been limited to institutions which have access to supercomputing centers. Today, the computing power of PC processors permits the assembly of inexpensive PC clusters that nearly approach the power of supercomputers. Moreover, the combination of inexpensive network cards and Open Source software provides an easy linking of standard computer equipment to enlarge such clusters. Universities and other institutions have taken this opportunity and built their own mini-supercomputers on site. Computing power is a particular issue for the climate modeling and impacts community. The purpose of this article is to make available a Linux cluster version of the Community Climate System Model developed by the National Center for Atmospheric Research (NCAR; http://www.cgd.ucar.edu/csm).

  18. Station Assembly Animation

    NASA Video Gallery

    This animation depicts the assembly of the International Space Station since Nov. 20, 1998, with the delivery of the Zarya module, through May 16, 2011, with the delivery of the EXPRESS Logistics C...

  19. Hypergolic Ignitor Assembly

    NASA Technical Reports Server (NTRS)

    Taylor, Eric S. (Inventor); Myers, W. Neill (Inventor); Martin, Michael A. (Inventor)

    2002-01-01

    An ignitor for use with the MC-I rocket engine has a cartridge bounded by two end caps with rupture disc assemblies connected thereto. A piston assembly within the cartridge moves from one end of the cartridge during the ignition process. The inlet of the ignitor communicates with a supply taken from the discharge of the fuel pump. When the pump is initially started, the pressure differential bursts the first rupture disc to begin the movement of the piston assembly toward the discharge end. The pressurization of the cartridge causes the second rupture to rupture and hypergolic fluid contained within the cartridge is discharged out the outlet. Once the piston assembly reaches the discharge end of the cartridge, purge grooves allow for fuel and remaining hypergolic fluid, to be discharged out the ignitor outlet into the combustion chamber to purge the ignitor of any remaining hypergolic fluid.

  20. Swipe transfer assembly

    DOEpatents

    Christiansen, Robert M.; Mills, William C.

    1992-01-01

    The swipe transfer assembly is a mechanical assembly which is used in conjunction with glove boxes and other sealed containments. It is used to pass small samples into or out of glove boxes without an open breach of the containment, and includes a rotational cylinder inside a fixed cylinder, the inside cylinder being rotatable through an arc of approximately 240.degree. relative to the outer cylinder. An offset of 120.degree. from end to end allows only one port to be opened at a time. The assembly is made of stainless steel or aluminum and clear acrylic plastic to enable visual observation. The assembly allows transfer of swipes and smears from radiological and other specially controlled environments.

  1. Automated Assembly Center (AAC)

    NASA Technical Reports Server (NTRS)

    Stauffer, Robert J.

    1993-01-01

    The objectives of this project are as follows: to integrate advanced assembly and assembly support technology under a comprehensive architecture; to implement automated assembly technologies in the production of high-visibility DOD weapon systems; and to document the improved cost, quality, and lead time. This will enhance the production of DOD weapon systems by utilizing the latest commercially available technologies combined into a flexible system that will be able to readily incorporate new technologies as they emerge. Automated assembly encompasses the following areas: product data, process planning, information management policies and framework, three schema architecture, open systems communications, intelligent robots, flexible multi-ability end effectors, knowledge-based/expert systems, intelligent workstations, intelligent sensor systems, and PDES/PDDI data standards.

  2. Magnetostrictive valve assembly

    NASA Technical Reports Server (NTRS)

    Richard, James A. (Inventor)

    2008-01-01

    A magnetostrictive valve assembly includes a housing that defines a passage with a seat being formed therein. A magnetically-biased and axially-compressed magnetostrictive assembly slidingly fitted in the passage is configured as a hollow and open-ended conduit adapted to support a flow of a fluid therethrough. Current-carrying coil(s) disposed about the passage in the region of the magnetostrictive assembly generate a magnetic field in the passage when current flows through the coil(s). A hollow valve body with side ports is coupled on one end thereof to an axial end of the magnetostrictive assembly. The other end of the valve body is designed to seal with the seat formed in the housing's passage when brought into contact therewith.

  3. IAHS General Assembly

    NASA Astrophysics Data System (ADS)

    Peters, Helen J.

    The International Association of Hydrological Sciences (IAHS) General Assembly, held as part of the International Union of Geodesy and Geophysics (IUGG) Assembly, August 9-22, 1987, in Vancouver, Canada, had an estimated 500 attendees. At least 20 countries were represented by official delegates. Attendance from the United States is estimated at 120, with Helen J. Peters (California Department of Water Resources, Sacramento) as chief delegate and Marshall E. Moss (U.S. Geological Survey (USGS), Reston, Va.) as alternate delegate and future chief delegate for the 1991 General Assembly.The Canadian Organizing Committee had done a masterful job of organizing the assembly, with excellent housing and meeting facilities on the University of British Columbia campus. In addition to five symposia and nine workshops, the IAHS Bureau and all commissions and the committees held several meetings. Some excellent social events and tours were included.

  4. Core assembly storage structure

    DOEpatents

    Jones, Jr., Charles E.; Brunings, Jay E.

    1988-01-01

    A structure for the storage of core assemblies from a liquid metal-cooled nuclear reactor. The structure comprises an enclosed housing having a substantially flat horizontal top plate, a bottom plate and substantially vertical wall members extending therebetween. A plurality of thimble members extend downwardly through the top plate. Each thimble member is closed at its bottom end and has an open end adjacent said top plate. Each thimble member has a length and diameter greater than that of the core assembly to be stored therein. The housing is provided with an inlet duct for the admission of cooling air and an exhaust duct for the discharge of air therefrom, such that when hot core assemblies are placed in the thimbles, the heat generated will by convection cause air to flow from the inlet duct around the thimbles and out the exhaust duct maintaining the core assemblies at a safe temperature without the necessity of auxiliary powered cooling equipment.

  5. Rnnotator Assembly Pipeline

    SciTech Connect

    Martin, Jeff

    2010-06-03

    Jeff Martin of the DOE Joint Genome Institute discusses a de novo transcriptome assembly pipeline from short RNA-Seq reads on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  6. Integrated thruster assembly program

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The program is reported which has provided technology for a long life, high performing, integrated ACPS thruster assembly suitable for use in 100 typical flights of a space shuttle vehicle over a ten year period. The four integrated thruster assemblies (ITA) fabricated consisted of: propellant injector; a capacitive discharge, air gap torch type igniter assembly; fast response igniter and main propellant valves; and a combined regen-dump film cooled chamber. These flightweight 6672 N (1500 lb) thruster assemblies employed GH2/GO2 as propellants at a chamber pressure of 207 N/sq cm (300 psia). Test data were obtained on thrusted performance, thermal and hydraulic characteristics, dynamic response in pulsing, and cycle life. One thruster was fired in excess of 42,000 times.

  7. Steam separator latch assembly

    DOEpatents

    Challberg, R.C.; Kobsa, I.R.

    1994-02-01

    A latch assembly removably joins a steam separator assembly to a support flange disposed at a top end of a tubular shroud in a nuclear reactor pressure vessel. The assembly includes an annular head having a central portion for supporting the steam separator assembly thereon, and an annular head flange extending around a perimeter thereof for supporting the head to the support flange. A plurality of latches are circumferentially spaced apart around the head flange with each latch having a top end, a latch hook at a bottom end thereof, and a pivot support disposed at an intermediate portion therebetween and pivotally joined to the head flange. The latches are pivoted about the pivot supports for selectively engaging and disengaging the latch hooks with the support flange for fixedly joining the head to the shroud or for allowing removal thereof. 12 figures.

  8. Steam separator latch assembly

    DOEpatents

    Challberg, Roy C.; Kobsa, Irvin R.

    1994-01-01

    A latch assembly removably joins a steam separator assembly to a support flange disposed at a top end of a tubular shroud in a nuclear reactor pressure vessel. The assembly includes an annular head having a central portion for supporting the steam separator assembly thereon, and an annular head flange extending around a perimeter thereof for supporting the head to the support flange. A plurality of latches are circumferentially spaced apart around the head flange with each latch having a top end, a latch hook at a bottom end thereof, and a pivot support disposed at an intermediate portion therebetween and pivotally joined to the head flange. The latches are pivoted about the pivot supports for selectively engaging and disengaging the latch hooks with the support flange for fixedly joining the head to the shroud or for allowing removal thereof.

  9. The proteasome assembly line

    PubMed Central

    Madura, Kiran

    2013-01-01

    The assembly of the proteasome — the cellular machine that eliminates unwanted proteins — is a carefully choreographed affair, involving a complex sequence of steps overseen by dedicated protein chaperones. PMID:19516331

  10. Cluster Morphology Analysis

    PubMed Central

    Jacquez, Geoffrey M.

    2009-01-01

    Most disease clustering methods assume specific shapes and do not evaluate statistical power using the applicable geography, at-risk population, and covariates. Cluster Morphology Analysis (CMA) conducts power analyses of alternative techniques assuming clusters of different relative risks and shapes. Results are ranked by statistical power and false positives, under the rationale that surveillance should (1) find true clusters while (2) avoiding false clusters. CMA then synthesizes results of the most powerful methods. CMA was evaluated in simulation studies and applied to pancreatic cancer mortality in Michigan, and finds clusters of flexible shape while routinely evaluating statistical power. PMID:20234799

  11. Functional connectivity in in vitro neuronal assemblies

    PubMed Central

    Poli, Daniele; Pastore, Vito P.; Massobrio, Paolo

    2015-01-01

    Complex network topologies represent the necessary substrate to support complex brain functions. In this work, we reviewed in vitro neuronal networks coupled to Micro-Electrode Arrays (MEAs) as biological substrate. Networks of dissociated neurons developing in vitro and coupled to MEAs, represent a valid experimental model for studying the mechanisms governing the formation, organization and conservation of neuronal cell assemblies. In this review, we present some examples of the use of statistical Cluster Coefficients and Small World indices to infer topological rules underlying the dynamics exhibited by homogeneous and engineered neuronal networks. PMID:26500505

  12. Record-breaking ancient galaxy clusters

    NASA Astrophysics Data System (ADS)

    2003-12-01

    A tale of two record-breaking clusters hi-res Size hi-res: 768 kb Credits: for RDCS1252: NASA, ESA, J.Blakeslee (Johns Hopkins Univ.), M.Postman (Space Telescope Science Inst.) and P.Rosati, Chris Lidman & Ricardo Demarco (European Southern Observ.) for TNJ1338: NASA, ESA, G.Miley (Leiden Observ.) and R.Overzier (Leiden Obs) A tale of two record-breaking clusters Looking back in time to when the universe was in its formative youth, the Advanced Camera for Surveys (ACS) aboard the NASA/ESA Hubble Space Telescope captured these revealing images of two galaxy clusters. The image at left, which is made with an additional infrared exposure taken with the European Southern Observatory’s Very Large Telescope, shows mature galaxies in a massive cluster that existed when the cosmos was 5000 million years old. The cluster, called RDCS1252.9-2927, is as massive as ‘300 trillion’ suns and is the most massive known cluster for its epoch. The image reveals the core of the cluster and is part of a much larger mosaic of the entire cluster. Dominating the core are a pair of large, reddish elliptical galaxies [near centre of image]. Their red colour indicates an older population of stars. Most of the stars are at least 1000 million years old. The two galaxies appear to be interacting and may eventually merge to form a larger galaxy that is comparable to the brightest galaxies seen in present-day clusters. The red galaxies surrounding the central pair are also cluster members. The cluster probably contains many thousands of galaxies, but only about 50 can be seen in this image. The full mosaic (heic0313d) reveals several hundred cluster members. Many of the other galaxies in the image, including several of the blue galaxies, are foreground or background galaxies. The colour-composite image was assembled from two observations (through i and z filters) taken between May and June 2002 by the ACS Wide Field Camera, and one image with the ISAAC instrument on the VLT taken in 2002

  13. Galaxy Cluster Smashes Distance Record

    NASA Astrophysics Data System (ADS)

    2009-10-01

    he most distant galaxy cluster yet has been discovered by combining data from NASA's Chandra X-ray Observatory and optical and infrared telescopes. The cluster is located about 10.2 billion light years away, and is observed as it was when the Universe was only about a quarter of its present age. The galaxy cluster, known as JKCS041, beats the previous record holder by about a billion light years. Galaxy clusters are the largest gravitationally bound objects in the Universe. Finding such a large structure at this very early epoch can reveal important information about how the Universe evolved at this crucial stage. JKCS041 is found at the cusp of when scientists think galaxy clusters can exist in the early Universe based on how long it should take for them to assemble. Therefore, studying its characteristics - such as composition, mass, and temperature - will reveal more about how the Universe took shape. "This object is close to the distance limit expected for a galaxy cluster," said Stefano Andreon of the National Institute for Astrophysics (INAF) in Milan, Italy. "We don't think gravity can work fast enough to make galaxy clusters much earlier." Distant galaxy clusters are often detected first with optical and infrared observations that reveal their component galaxies dominated by old, red stars. JKCS041 was originally detected in 2006 in a survey from the United Kingdom Infrared Telescope (UKIRT). The distance to the cluster was then determined from optical and infrared observations from UKIRT, the Canada-France-Hawaii telescope in Hawaii and NASA's Spitzer Space Telescope. Infrared observations are important because the optical light from the galaxies at large distances is shifted into infrared wavelengths because of the expansion of the universe. The Chandra data were the final - but crucial - piece of evidence as they showed that JKCS041 was, indeed, a genuine galaxy cluster. The extended X-ray emission seen by Chandra shows that hot gas has been detected

  14. Recuperator assembly and procedures

    DOEpatents

    Kang, Yungmo; McKeirnan, Jr., Robert D.

    2008-08-26

    A construction of recuperator core segments is provided which insures proper assembly of the components of the recuperator core segment, and of a plurality of recuperator core segments. Each recuperator core segment must be constructed so as to prevent nesting of fin folds of the adjacent heat exchanger foils of the recuperator core segment. A plurality of recuperator core segments must be assembled together so as to prevent nesting of adjacent fin folds of adjacent recuperator core segments.

  15. High speed door assembly

    SciTech Connect

    Shapiro, C.

    1991-12-31

    This invention is comprised of a high speed door assembly, comprising an actuator cylinder and piston rods, a pressure supply cylinder and fittings, an electrically detonated explosive bolt, a honeycomb structured door, a honeycomb structured decelerator, and a structural steel frame encasing the assembly to close over a 3 foot diameter opening within 50 milliseconds of actuation, to contain hazardous materials and vapors within a test fixture.

  16. ASSEMBLY OF PARALLEL PLATES

    DOEpatents

    Groh, E.F.; Lennox, D.H.

    1963-04-23

    This invention is concerned with a rigid assembly of parallel plates in which keyways are stamped out along the edges of the plates and a self-retaining key is inserted into aligned keyways. Spacers having similar keyways are included between adjacent plates. The entire assembly is locked into a rigid structure by fastening only the outermost plates to the ends of the keys. (AEC)

  17. Recuperator assembly and procedures

    DOEpatents

    Kang, Yungmo; McKeirnan, Jr., Robert D.

    2006-06-27

    A construction of recuperator core segments is provided which insures proper assembly of the components of the recuperator core segment, and of a plurality of recuperator core segments. Each recuperator core segment must be constructed so as to prevent nesting of fin folds of the adjacent heat exchanger foils of the recuperator core segment. A plurality of recuperator core segments must be assembled together so as to prevent nesting of adjacent fin folds of adjacent recuperator core segments.

  18. Computational study of trimer self-assembly and fluid phase behavior

    SciTech Connect

    Hatch, Harold W. Shen, Vincent K.; Mittal, Jeetain

    2015-04-28

    The fluid phase diagram of trimer particles composed of one central attractive bead and two repulsive beads was determined as a function of simple geometric parameters using flat-histogram Monte Carlo methods. A variety of self-assembled structures were obtained including spherical micelle-like clusters, elongated clusters, and densely packed cylinders, depending on both the state conditions and shape of the trimer. Advanced simulation techniques were employed to determine transitions between self-assembled structures and macroscopic phases using thermodynamic and structural definitions. Simple changes in particle geometry yield dramatic changes in phase behavior, ranging from macroscopic fluid phase separation to molecular-scale self-assembly. In special cases, both self-assembled, elongated clusters and bulk fluid phase separation occur simultaneously. Our work suggests that tuning particle shape and interactions can yield superstructures with controlled architecture.

  19. Human Assisted Assembly Processes

    SciTech Connect

    CALTON,TERRI L.; PETERS,RALPH R.

    2000-01-01

    Automatic assembly sequencing and visualization tools are valuable in determining the best assembly sequences, but without Human Factors and Figure Models (HFFMs) it is difficult to evaluate or visualize human interaction. In industry, accelerating technological advances and shorter market windows have forced companies to turn to an agile manufacturing paradigm. This trend has promoted computerized automation of product design and manufacturing processes, such as automated assembly planning. However, all automated assembly planning software tools assume that the individual components fly into their assembled configuration and generate what appear to be a perfectly valid operations, but in reality the operations cannot physically be carried out by a human. Similarly, human figure modeling algorithms may indicate that assembly operations are not feasible and consequently force design modifications; however, if they had the capability to quickly generate alternative assembly sequences, they might have identified a feasible solution. To solve this problem HFFMs must be integrated with automated assembly planning to allow engineers to verify that assembly operations are possible and to see ways to make the designs even better. Factories will very likely put humans and robots together in cooperative environments to meet the demands for customized products, for purposes including robotic and automated assembly. For robots to work harmoniously within an integrated environment with humans the robots must have cooperative operational skills. For example, in a human only environment, humans may tolerate collisions with one another if they did not cause much pain. This level of tolerance may or may not apply to robot-human environments. Humans expect that robots will be able to operate and navigate in their environments without collisions or interference. The ability to accomplish this is linked to the sensing capabilities available. Current work in the field of cooperative

  20. EINSTEIN Cluster Alignments Revisited

    NASA Astrophysics Data System (ADS)

    Chambers, S. W.; Melott, A. L.; Miller, C. J.

    2000-12-01

    We have examined whether the major axes of rich galaxy clusters tend to point (in projection) toward their nearest neighboring cluster. We used the data of Ulmer, McMillan and Kowalski, who used x-ray morphology to define position angles. Our cluster samples, with well measured redshifts and updated positions, were taken from the MX Northern Abell Cluster Survey. The usual Kolmogorov-Smirnov test shows no significant alignment signal for nonrandom angles for all separations less than 100 Mpc/h. Refining the null hypothesis, however, with the Wilcoxon rank-sum test, reveals a high confidence signal for alignment. This confidence is highest when we restrict our sample to small nearest neighbor separations. We conclude that we have identified a more powerful tool for testing cluster-cluster alignments. Moreover, there is a strong signal in the data for alignment, consistent with a picture of hierarchical cluster formation in which matter falls into clusters along large scale filamentary structures.

  1. Matlab Cluster Ensemble Toolbox

    SciTech Connect

    Sapio, Vincent De; Kegelmeyer, Philip

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  2. Assembly factors for the membrane arm of human complex I

    PubMed Central

    Andrews, Byron; Carroll, Joe; Ding, Shujing; Fearnley, Ian M.; Walker, John E.

    2013-01-01

    Mitochondrial respiratory complex I is a product of both the nuclear and mitochondrial genomes. The integration of seven subunits encoded in mitochondrial DNA into the inner membrane, their association with 14 nuclear-encoded membrane subunits, the construction of the extrinsic arm from 23 additional nuclear-encoded proteins, iron–sulfur clusters, and flavin mononucleotide cofactor require the participation of assembly factors. Some are intrinsic to the complex, whereas others participate transiently. The suppression of the expression of the NDUFA11 subunit of complex I disrupted the assembly of the complex, and subcomplexes with masses of 550 and 815 kDa accumulated. Eight of the known extrinsic assembly factors plus a hydrophobic protein, C3orf1, were associated with the subcomplexes. The characteristics of C3orf1, of another assembly factor, TMEM126B, and of NDUFA11 suggest that they all participate in constructing the membrane arm of complex I. PMID:24191001

  3. Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis.

    PubMed

    Lipper, Colin H; Paddock, Mark L; Onuchic, José N; Mittler, Ron; Nechushtai, Rachel; Jennings, Patricia A

    2015-01-01

    Iron-sulfur cluster biogenesis is executed by distinct protein assembly systems. Mammals have two systems, the mitochondrial Fe-S cluster assembly system (ISC) and the cytosolic assembly system (CIA), that are connected by an unknown mechanism. The human members of the NEET family of 2Fe-2S proteins, nutrient-deprivation autophagy factor-1 (NAF-1) and mitoNEET (mNT), are located at the interface between the mitochondria and the cytosol. These proteins have been implicated in cancer cell proliferation, and they can transfer their 2Fe-2S clusters to a standard apo-acceptor protein. Here we report the first physiological 2Fe-2S cluster acceptor for both NEET proteins as human Anamorsin (also known as cytokine induced apoptosis inhibitor-1; CIAPIN-1). Anamorsin is an electron transfer protein containing two iron-sulfur cluster-binding sites that is required for cytosolic Fe-S cluster assembly. We show, using UV-Vis spectroscopy, that both NAF-1 and mNT can transfer their 2Fe-2S clusters to apo-Anamorsin with second order rate constants similar to those of other known human 2Fe-2S transfer proteins. A direct protein-protein interaction of the NEET proteins with apo-Anamorsin was detected using biolayer interferometry. Furthermore, electrospray mass spectrometry of holo-Anamorsin prepared by cluster transfer shows that it receives both of its 2Fe-2S clusters from the NEETs. We propose that mNT and NAF-1 can provide parallel routes connecting the mitochondrial ISC system and the CIA. 2Fe-2S clusters assembled in the mitochondria are received by NEET proteins and when needed transferred to Anamorsin, activating the CIA. PMID:26448442

  4. Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis

    PubMed Central

    Lipper, Colin H.; Paddock, Mark L.; Onuchic, José N.; Mittler, Ron; Nechushtai, Rachel; Jennings, Patricia A.

    2015-01-01

    Iron-sulfur cluster biogenesis is executed by distinct protein assembly systems. Mammals have two systems, the mitochondrial Fe-S cluster assembly system (ISC) and the cytosolic assembly system (CIA), that are connected by an unknown mechanism. The human members of the NEET family of 2Fe-2S proteins, nutrient-deprivation autophagy factor-1 (NAF-1) and mitoNEET (mNT), are located at the interface between the mitochondria and the cytosol. These proteins have been implicated in cancer cell proliferation, and they can transfer their 2Fe-2S clusters to a standard apo-acceptor protein. Here we report the first physiological 2Fe-2S cluster acceptor for both NEET proteins as human Anamorsin (also known as cytokine induced apoptosis inhibitor-1; CIAPIN-1). Anamorsin is an electron transfer protein containing two iron-sulfur cluster-binding sites that is required for cytosolic Fe-S cluster assembly. We show, using UV-Vis spectroscopy, that both NAF-1 and mNT can transfer their 2Fe-2S clusters to apo-Anamorsin with second order rate constants similar to those of other known human 2Fe-2S transfer proteins. A direct protein-protein interaction of the NEET proteins with apo-Anamorsin was detected using biolayer interferometry. Furthermore, electrospray mass spectrometry of holo-Anamorsin prepared by cluster transfer shows that it receives both of its 2Fe-2S clusters from the NEETs. We propose that mNT and NAF-1 can provide parallel routes connecting the mitochondrial ISC system and the CIA. 2Fe-2S clusters assembled in the mitochondria are received by NEET proteins and when needed transferred to Anamorsin, activating the CIA. PMID:26448442

  5. [Pathophysiology of cluster headache].

    PubMed

    Donnet, Anne

    2015-11-01

    The aetiology of cluster headache is partially unknown. Three areas are involved in the pathogenesis of cluster headache: the trigeminal nociceptive pathways, the autonomic system and the hypothalamus. The cluster headache attack involves activation of the trigeminal autonomic reflex. A dysfunction located in posterior hypothalamic gray matter is probably pivotal in the process. There is a probable association between smoke exposure, a possible genetic predisposition and the development of cluster headache. PMID:26470883

  6. ASSEMBLY BIAS AND THE DYNAMICAL STRUCTURE OF DARK MATTER HALOS

    SciTech Connect

    Faltenbacher, Andreas; White, Simon D. M.

    2010-01-01

    Based on the Millennium Simulation we examine assembly bias for the halo properties: shape, triaxiality, concentration, spin, shape of the velocity ellipsoid, and velocity anisotropy. For consistency, we determine all these properties using the same set of particles, namely all gravitationally self-bound particles belonging to the most massive substructure of a given friends-of-friends halo. We confirm that near-spherical and high-spin halos show enhanced clustering. The opposite is true for strongly aspherical and low-spin halos. Further, below the typical collapse mass, M{sub *}, more concentrated halos show stronger clustering, whereas less concentrated halos are less clustered which is reversed for masses above M{sub *}. Going beyond earlier work we show that: (1) oblate halos are more strongly clustered than prolate ones; (2) the dependence of clustering on the shape of the velocity ellipsoid coincides with that of the real-space shape, although the signal is stronger; (3) halos with weak velocity anisotropy are more clustered, whereas radially anisotropic halos are more weakly clustered; (4) for all highly clustered subsets we find systematically less radially biased velocity anisotropy profiles. These findings indicate that the velocity structure of halos is tightly correlated with environment.

  7. Molecular simulations of assembly of functionalized spherical nanoparticles

    NASA Astrophysics Data System (ADS)

    Seifpour, Arezou

    Precise assembly of nanoparticles is crucial for creating spatially engineered materials that can be used for photonics, photovoltaic, and metamaterials applications. One way to control nanoparticle assembly is by functionalizing the nanoparticle with ligands, such as polymers, DNA, and proteins, that can manipulate the interactions between the nanoparticles in the medium the particles are placed in. This thesis research aims to design ligands to provide a new route to the programmable assembly of nanoparticles. We first investigate using Monte Carlo simulation the effect of copolymer ligands on nanoparticle assembly. We first study a single nanoparticle grafted with many copolymer chains to understand how monomer sequence (e.g. alternating ABAB, or diblock AxBx) and chemistry of the copolymers affect the grafted chain conformation at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We find that the size of the grafted chain varies non-monotonically with increasing blockiness of the monomer sequence for a small particle diameter. From this first study, we selected the two sequences with the most different chain conformations---alternating and diblock---and studied the effect of the sequence and a range of monomer chemistries of the copolymer on the characteristics of assembly of multiple copolymer-functionalized nanoparticles. We find that the alternating sequence produces nanoclusters that are relatively isotropic, whereas diblock sequence tends to form anisotropic structures that are smaller and more compact when the block closer to the surface is attractive and larger loosely held together clusters when the outer block is attractive. Next, we conduct molecular dynamics simulations to study the effect of DNA ligands on nanoparticle assembly. Specifically we investigate the effect of grafted DNA strand composition (e.g. G/C content, placement and sequence) and

  8. Assemblies of Conformal Tanks

    NASA Technical Reports Server (NTRS)

    DeLay, Tom

    2009-01-01

    Assemblies of tanks having shapes that conform to each other and/or conform to other proximate objects have been investigated for use in storing fuels and oxidizers in small available spaces in upper stages of spacecraft. Such assemblies might also prove useful in aircraft, automobiles, boats, and other terrestrial vehicles in which space available for tanks is limited. The basic concept of using conformal tanks to maximize the utilization of limited space is not new in itself: for example, conformal tanks are used in some automobiles to store windshield -washer liquid and coolant that overflows from radiators. The novelty of the present development lies in the concept of an assembly of smaller conformal tanks, as distinguished from a single larger conformal tank. In an assembly of smaller tanks, it would be possible to store different liquids in different tanks. Even if the same liquid were stored in all the tanks, the assembly would offer an advantage by reducing the mechanical disturbance caused by sloshing of fuel in a single larger tank: indeed, the requirement to reduce sloshing is critical in some applications. The figure shows a prototype assembly of conformal tanks. Each tank was fabricated by (1) copper plating a wax tank mandrel to form a liner and (2) wrapping and curing layers of graphite/epoxy composite to form a shell supporting the liner. In this case, the conformal tank surfaces are flat ones where they come in contact with the adjacent tanks. A band of fibers around the outside binds the tanks together tightly in the assembly, which has a quasi-toroidal shape. For proper functioning, it would be necessary to maintain equal pressure in all the tanks.

  9. WHO: World Health Assembly.

    PubMed

    McGregor, A

    1992-05-23

    1200 delegates from 175 member countries attended the 45th World Health Assembly in Geneva. Everyone at the Assembly ratified measures to prevent and control AIDS. 12 countries intended to do long term planning for community based care for AIDS patients. Further the Assembly denounced instances where countries and individuals denied the gravity of the AIDS pandemic. In fact, it expressed the importance for urgent and intensive action against HIV/AIDS. The assembly backed proposals to prevent and control sexually transmitted diseases that affect AIDS patients, especially hepatitis B. For example, in countries with hepatitis B prevalence 8% (many countries in Sub-Sahara Africa, Asia, the Pacific region, and South America), health officials should introduce hepatitis B vaccine into their existing immunization programs by 1995. By 1997, this vaccine should be part of all immunization programs. The Assembly was aware of the obstacles of establishing reliable cold chains for nationwide distribution, however. Delegates in Committee A objected to the fact that 50% of the populations of developing countries continued to have limited access to essential drugs. They also expressed disapproval in implementation of WHO's 1988 ethical criteria for promotion of drugs which WHO entrusted to the Council for International Organisations of Medical Sciences (CIOMS). CIOMS lacked WHO's status and thus could not effectively monitor drug advertising. In fact, the pharmaceutical industry as well as WHO provided the funds for a meeting of 25 experts to discuss principles included in the ethical criteria. At least 4 countries insisted that WHO have the ultimate authority in monitoring drug advertising. Delegates did adopt a compromise resolution on this topic which required that industry promotion methods be reported to the 1994 Assembly via the Executive Board. The Assembly requested WHO to establish an international advisory committee on nursing and midwifery and to improve the network of

  10. Participation of the iron-sulphur cluster and of the covalently bound coenzyme of trimethylamine dehydrogenase in catalysis.

    PubMed Central

    Steenkamp, D J; Singer, T P

    1978-01-01

    Bacterial trimethylamine dehydrogenase contains a novel type of covalently bound flavin mononucleotide and a tetrameric iron-sulphur centre. The dehydrogenase takes up 1.5mol of dithionite/mol of enzyme and is thereby converted into the flavin quinol-reduced (4Fe-4S) form, with the expected bleaching of the visible absorption band of the flavin and the emergence of signals of typical reduced ferredoxin in the electronparamagnetic-resonance spectrum. On reduction with a slight excess of substrate, however, unusual absorption and electron-paramagnetic-resonance spectra appear quite rapidly. The latter is attributed to extensive interaction between the reduced (4Fe-4S) centre and the flavin semiquinone. The species of enzyme arising during the catalytic cycle were studied by a combination of rapid-freeze e.p.r. and stopped-flow spectophotometry. The initial reduction of the flavin to the quinol form is far too rapid to be rate-limiting in catalysis, as is the reoxidation of the substrate-reduced enzyme by phenazine methosulphate. Formation of the spin-spin-interacting species from the dihydroflavin is considerably slower, however, and it may be the rate-limiting step in the catalytic cycle, since its rate of formation agrees reasonably well with the catalytic-centre activity determined in steady-state kinetic assays. In addition to the interacting form, a second form of the enzyme was noted during reduction by trimethylamine, differing in absorption spectrum, the structure of which remains to be determined. PMID:204297

  11. Participation of the iron-sulphur cluster and of the covalently bound coenzyme of trimethylamine dehydrogenase in catalysis.

    PubMed

    Steenkamp, D J; Singer, T P

    1978-02-01

    Bacterial trimethylamine dehydrogenase contains a novel type of covalently bound flavin mononucleotide and a tetrameric iron-sulphur centre. The dehydrogenase takes up 1.5mol of dithionite/mol of enzyme and is thereby converted into the flavin quinol-reduced (4Fe-4S) form, with the expected bleaching of the visible absorption band of the flavin and the emergence of signals of typical reduced ferredoxin in the electronparamagnetic-resonance spectrum. On reduction with a slight excess of substrate, however, unusual absorption and electron-paramagnetic-resonance spectra appear quite rapidly. The latter is attributed to extensive interaction between the reduced (4Fe-4S) centre and the flavin semiquinone. The species of enzyme arising during the catalytic cycle were studied by a combination of rapid-freeze e.p.r. and stopped-flow spectophotometry. The initial reduction of the flavin to the quinol form is far too rapid to be rate-limiting in catalysis, as is the reoxidation of the substrate-reduced enzyme by phenazine methosulphate. Formation of the spin-spin-interacting species from the dihydroflavin is considerably slower, however, and it may be the rate-limiting step in the catalytic cycle, since its rate of formation agrees reasonably well with the catalytic-centre activity determined in steady-state kinetic assays. In addition to the interacting form, a second form of the enzyme was noted during reduction by trimethylamine, differing in absorption spectrum, the structure of which remains to be determined. PMID:204297

  12. CLUSTERING OF RARE EVENTS

    EPA Science Inventory

    The clustering of cases of a rare disease is considered. The number of events observed for each unit is assumed to have a Poisson distribution, the mean of which depends upon the population size and the cluster membership of that unit. Here a cluster consists of those units that ...

  13. Photovoltaic self-assembly.

    SciTech Connect

    Lavin, Judith; Kemp, Richard Alan; Stewart, Constantine A.

    2010-10-01

    This late-start LDRD was focused on the application of chemical principles of self-assembly on the ordering and placement of photovoltaic cells in a module. The drive for this chemical-based self-assembly stems from the escalating prices in the 'pick-and-place' technology currently used in the MEMS industries as the size of chips decreases. The chemical self-assembly principles are well-known on a molecular scale in other material science systems but to date had not been applied to the assembly of cells in a photovoltaic array or module. We explored several types of chemical-based self-assembly techniques, including gold-thiol interactions, liquid polymer binding, and hydrophobic-hydrophilic interactions designed to array both Si and GaAs PV chips onto a substrate. Additional research was focused on the modification of PV cells in an effort to gain control over the facial directionality of the cells in a solvent-based environment. Despite being a small footprint research project worked on for only a short time, the technical results and scientific accomplishments were significant and could prove to be enabling technology in the disruptive advancement of the microelectronic photovoltaics industry.

  14. Linear hanger assembly

    SciTech Connect

    Baugh, J.L.

    1992-02-11

    This patent describes a hanger assembly securable to a workstring for carrying a liner conduit in a subterranean well and settable within a casing string. It comprises: an elongated tubular housing; a series of circumferentially extending slip elements carried exteriorly around and by the housing and axially movable relative to a slip seat from a radially retracted position to a radially spaded position for gripping engagement with the casing string; and each of the slip elements having circumferentially subscribed exteriorly protruding non-buttress teeth defined thereon, the teeth being symmetrical to both pus and pull forces applied through the assembly by either the work-string or the liner conduit subsequent to setting within the casing string; wherein the assembly is moved to a set position relative to the casing string by application of hydraulic pressure in a first predeterminable amount to transmit and apply a setting load to the slip elements; and further comprising compressive biasing means movable to a compressed biasing means movable to a compressed condition by mechanical manipulation of the workstring subsequent to movement of the assembly to the set position to transmit a second load to the slip elements in excess of the setting load; and locking means for locking the setting and second loads into the slip assembly.

  15. Constrained space camera assembly

    DOEpatents

    Heckendorn, F.M.; Anderson, E.K.; Robinson, C.W.; Haynes, H.B.

    1999-05-11

    A constrained space camera assembly which is intended to be lowered through a hole into a tank, a borehole or another cavity is disclosed. The assembly includes a generally cylindrical chamber comprising a head and a body and a wiring-carrying conduit extending from the chamber. Means are included in the chamber for rotating the body about the head without breaking an airtight seal formed therebetween. The assembly may be pressurized and accompanied with a pressure sensing means for sensing if a breach has occurred in the assembly. In one embodiment, two cameras, separated from their respective lenses, are installed on a mounting apparatus disposed in the chamber. The mounting apparatus includes means allowing both longitudinal and lateral movement of the cameras. Moving the cameras longitudinally focuses the cameras, and moving the cameras laterally away from one another effectively converges the cameras so that close objects can be viewed. The assembly further includes means for moving lenses of different magnification forward of the cameras. 17 figs.

  16. Assembly Test Article (ATA)

    NASA Technical Reports Server (NTRS)

    Ricks, Glen A.

    1988-01-01

    The assembly test article (ATA) consisted of two live loaded redesigned solid rocket motor (RSRM) segments which were assembled and disassembled to simulate the actual flight segment stacking process. The test assembly joint was flight RSRM design, which included the J-joint insulation design and metal capture feature. The ATA test was performed mid-November through 24 December 1987, at Kennedy Space Center (KSC), Florida. The purpose of the test was: certification that vertical RSRM segment mating and separation could be accomplished without any damage; verification and modification of the procedures in the segment stacking/destacking documents; and certification of various GSE to be used for flight assembly and inspection. The RSRM vertical segment assembly/disassembly is possible without any damage to the insulation, metal parts, or seals. The insulation J-joint contact area was very close to the predicted values. Numerous deviations and changes to the planning documents were made to ensure the flight segments are effectively and correctly stacked. Various GSE were also certified for use on flight segments, and are discussed in detail.

  17. Superconductive radiofrequency window assembly

    DOEpatents

    Phillips, Harry Lawrence; Elliott, Thomas S.

    1998-01-01

    The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly (20) has a superconducting metal-ceramic design. The srf window assembly (20) comprises a superconducting frame (30), a ceramic plate (40) having a superconducting metallized area, and a superconducting eyelet (50) for sealing plate (40) into frame (30). The plate (40) is brazed to eyelet (50) which is then electron beam welded to frame (30). A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator.

  18. Superconducting radiofrequency window assembly

    DOEpatents

    Phillips, Harry L.; Elliott, Thomas S.

    1997-01-01

    The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly (20) has a superconducting metal-ceramic design. The srf window assembly (20) comprises a superconducting frame (30), a ceramic plate (40) having a superconducting metallized area, and a superconducting eyelet (50) for sealing plate (40) into frame (30). The plate (40) is brazed to eyelet (50) which is then electron beam welded to frame (30). A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator.

  19. A new clustering strategy

    NASA Astrophysics Data System (ADS)

    Feng, Jian-xin; Tang, Jia-fu; Wang, Guang-xing

    2007-04-01

    On the basis of the analysis of clustering algorithm that had been proposed for MANET, a novel clustering strategy was proposed in this paper. With the trust defined by statistical hypothesis in probability theory and the cluster head selected by node trust and node mobility, this strategy can realize the function of the malicious nodes detection which was neglected by other clustering algorithms and overcome the deficiency of being incapable of implementing the relative mobility metric of corresponding nodes in the MOBIC algorithm caused by the fact that the receiving power of two consecutive HELLO packet cannot be measured. It's an effective solution to cluster MANET securely.

  20. Blade attachment assembly

    DOEpatents

    Garcia-Crespo, Andres Jose; Delvaux, John McConnell; Miller, Diane Patricia

    2016-05-03

    An assembly and method for affixing a turbomachine rotor blade to a rotor wheel are disclosed. In an embodiment, an adaptor member is provided disposed between the blade and the rotor wheel, the adaptor member including an adaptor attachment slot that is complementary to the blade attachment member, and an adaptor attachment member that is complementary to the rotor wheel attachment slot. A coverplate is provided, having a coverplate attachment member that is complementary to the rotor wheel attachment slot, and a hook for engaging the adaptor member. When assembled, the coverplate member matingly engages with the adaptor member, and retains the blade in the adaptor member, and the assembly in the rotor wheel.

  1. Liaison based assembly design

    SciTech Connect

    Ames, A.; Kholwadwala, D.; Wilson, R.H.

    1996-12-01

    Liaison Based Assembly Design extends the current information infrastructure to support design in terms of kinematic relationships between parts, or liaisons. These liaisons capture information regarding contact, degrees-of-freedom constraints and containment relationships between parts in an assembly. The project involved defining a useful collection of liaison representations, investigating their properties, and providing for maximum use of the data in downstream applications. We tested our ideas by implementing a prototype system involving extensions to Pro/Engineer and the Archimedes assembly planner. With an expanded product model, the design system is more able to capture design intent. When a product update is attempted, increased knowledge availability improves our ability to understand the effect of design changes. Manufacturing and analysis disciplines benefit from having liaison information available, so less time is wasted arguing over incomplete design specifications and our enterprise can be more completely integrated.

  2. Optical interconnect assembly

    SciTech Connect

    Laughlin, Daric; Abel, Philip

    2015-06-09

    An optical assembly includes a substrate with a first row of apertures and a second row of apertures. A first optical die includes a first plurality of optical transducer elements and is mounted on the substrate such that an optical signal interface of each transducer element is aligned with an aperture of the first row of optical apertures. A second optical die includes a second plurality of optical transducer elements and is mounted on the substrate such that an optical signal interface of each of the second plurality of optical transducer elements is aligned with an aperture of the second row of optical apertures. A connector configured to mate with the optical assembly supports a plurality of optical fibers. A terminal end of each optical fiber protrudes from the connector and extends into one of the apertures when the connector is coupled with the optical assembly.

  3. Supported PV module assembly

    SciTech Connect

    Mascolo, Gianluigi; Taggart, David F.; Botkin, Jonathan D.; Edgett, Christopher S.

    2013-10-15

    A supported PV assembly may include a PV module comprising a PV panel and PV module supports including module supports having a support surface supporting the module, a module registration member engaging the PV module to properly position the PV module on the module support, and a mounting element. In some embodiments the PV module registration members engage only the external surfaces of the PV modules at the corners. In some embodiments the assembly includes a wind deflector with ballast secured to a least one of the PV module supports and the wind deflector. An array of the assemblies can be secured to one another at their corners to prevent horizontal separation of the adjacent corners while permitting the PV modules to flex relative to one another so to permit the array of PV modules to follow a contour of the support surface.

  4. Power module assembly

    DOEpatents

    Campbell, Jeremy B.; Newson, Steve

    2011-11-15

    A power module assembly of the type suitable for deployment in a vehicular power inverter, wherein the power inverter has a grounded chassis, is provided. The power module assembly comprises a conductive base layer electrically coupled to the chassis, an insulating layer disposed on the conductive base layer, a first conductive node disposed on the insulating layer, a second conductive node disposed on the insulating layer, wherein the first and second conductive nodes are electrically isolated from each other. The power module assembly also comprises a first capacitor having a first electrode electrically connected to the conductive base layer, and a second electrode electrically connected to the first conductive node, and further comprises a second capacitor having a first electrode electrically connected to the conductive base layer, and a second electrode electrically connected to the second conductive node.

  5. Bulk synthesis of polymer-inorganic colloidal clusters.

    PubMed

    Perro, Adeline; Manoharan, Vinothan N

    2010-12-21

    We describe a procedure to synthesize colloidal clusters with polyhedral morphologies in high yield (liter quantities at up to 70% purity) using a combination of emulsion polymerization and inorganic surface chemistry. We show that the synthesis initially used for silica-polystyrene hybrid clusters can be generalized to create clusters from other inorganic and polymer particles. We also show that high yields of particular morphologies can be obtained by precise control of the inorganic seed particle size, a finding that can be explained using a hard-sphere packing model. These clusters can be further chemically modified for a variety of applications. Introducing a cross-linker leads to colloidal clusters that can be index matched in an appropriate solvent, allowing them to be used for particle tracking or optical studies of colloidal self-assembly. Also, depositing a thin silica layer on these colloids allows the surface properties to be controlled using silane chemistry. PMID:21080658

  6. Nanostar Clustering Improves the Sensitivity of Plasmonic Assays.

    PubMed

    Park, Yong Il; Im, Hyungsoon; Weissleder, Ralph; Lee, Hakho

    2015-08-19

    Star-shaped Au nanoparticles (Au nanostars, AuNS) have been developed to improve the plasmonic sensitivity, but their application has largely been limited to single-particle probes. We herein describe a AuNS clustering assay based on nanoscale self-assembly of multiple AuNS and which further increases detection sensitivity. We show that each cluster contains multiple nanogaps to concentrate electric fields, thereby amplifying the signal via plasmon coupling. Numerical simulation indicated that AuNS clusters assume up to 460-fold higher field density than Au nanosphere clusters of similar mass. The results were validated in model assays of protein biomarker detection. The AuNS clustering assay showed higher sensitivity than Au nanosphere. Minimizing the size of affinity ligand was found important to tightly confine electric fields and improve the sensitivity. The resulting assay is simple and fast and can be readily applied to point-of-care molecular detection schemes. PMID:26102604

  7. Mechanisms of kinetic trapping in self-assembly and phase transformation

    NASA Astrophysics Data System (ADS)

    Hagan, Michael F.; Elrad, Oren M.; Jack, Robert L.

    2011-09-01

    In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions.

  8. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  9. Self assembling proteins

    DOEpatents

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  10. Lightweight reflector assembly

    NASA Technical Reports Server (NTRS)

    Argoud, M. J.; Jolley, J.; Walker, W. L. (Inventor)

    1977-01-01

    An inexpensive, lightweight reflective assembly member having good optical quality and particularly adaptable to accommodating temperature variations without providing destructive thermal stresses and reflective slope errors is described. The reflective assembly consists of a thin sheet of glass with appropriate reflective coating and a cellular glass block substrate bonded together. The method of fabrication includes abrading the cellular substrate with an abrasive master die to form an appropriate concave surface. An adhesive is applied to the abraded surface and a lamina reflective surface is placed under a uniform pressure to conform the reflective surface onto the desired abraded surface of the substrate.

  11. Low inductance connector assembly

    DOEpatents

    Holbrook, Meghan Ann; Carlson, Douglas S

    2013-07-09

    A busbar connector assembly for coupling first and second terminals on a two-terminal device to first and second contacts on a power module is provided. The first terminal resides proximate the first contact and the second terminal resides proximate the second contact. The assembly comprises a first bridge having a first end configured to be electrically coupled to the first terminal, and a second end configured to be electrically coupled to the second contact, and a second bridge substantially overlapping the first bridge and having a first end electrically coupled to the first contact, and a second end electrically coupled to the second terminal.

  12. Hand Controller Assembly

    NASA Technical Reports Server (NTRS)

    Bandera, Pablo (Inventor); Buchele, Paul (Inventor)

    2015-01-01

    A user input device for a vehicular electrical system is provided. The user input device includes a handle sized and shaped to be gripped by a human hand and a gimbal assembly within the handle. The gimbal assembly includes a first gimbal component, a second gimbal component coupled to the first gimbal component such that the second gimbal component is rotatable relative to the first gimbal component about a first axis, and a third gimbal component coupled to the second gimbal component such that the third gimbal component is rotatable relative to the second gimbal component about a second axis.

  13. Assembling an aesthetic.

    PubMed

    Candela, Emily

    2012-12-01

    Recent research informing and related to the study of three-dimensional scientific models is assembled here in a way that explores an aesthetic, specifically, of touch. I concentrate on the materiality of models, drawing on insights from the history and philosophy of science, design and metaphysics. This article chronicles the ways in which touch, or material interactions, operate in the world of 3D models, and its role in what models mean and do. I end with a call for greater attention to scientific process, described as assembly of and within science, which is revealed by this focus on touch. PMID:23176974

  14. Phylogenetic Comparative Assembly

    NASA Astrophysics Data System (ADS)

    Husemann, Peter; Stoye, Jens

    Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a contig adjacency graph. From this a layout graph can be computed which indicates putative adjacencies of the contigs in order to aid biologists in finishing the complete genomic sequence.

  15. Modeling Clustered Data with Very Few Clusters.

    PubMed

    McNeish, Daniel; Stapleton, Laura M

    2016-01-01

    Small-sample inference with clustered data has received increased attention recently in the methodological literature, with several simulation studies being presented on the small-sample behavior of many methods. However, nearly all previous studies focus on a single class of methods (e.g., only multilevel models, only corrections to sandwich estimators), and the differential performance of various methods that can be implemented to accommodate clustered data with very few clusters is largely unknown, potentially due to the rigid disciplinary preferences. Furthermore, a majority of these studies focus on scenarios with 15 or more clusters and feature unrealistically simple data-generation models with very few predictors. This article, motivated by an applied educational psychology cluster randomized trial, presents a simulation study that simultaneously addresses the extreme small sample and differential performance (estimation bias, Type I error rates, and relative power) of 12 methods to account for clustered data with a model that features a more realistic number of predictors. The motivating data are then modeled with each method, and results are compared. Results show that generalized estimating equations perform poorly; the choice of Bayesian prior distributions affects performance; and fixed effect models perform quite well. Limitations and implications for applications are also discussed. PMID:27269278

  16. Fire resistant PV shingle assembly

    DOEpatents

    Lenox, Carl J.

    2012-10-02

    A fire resistant PV shingle assembly includes a PV assembly, including PV body, a fire shield and a connection member connecting the fire shield below the PV body, and a support and inter-engagement assembly. The support and inter-engagement assembly is mounted to the PV assembly and comprises a vertical support element, supporting the PV assembly above a support surface, an upper interlock element, positioned towards the upper PV edge, and a lower interlock element, positioned towards the lower PV edge. The upper interlock element of one PV shingle assembly is inter-engageable with the lower interlock element of an adjacent PV shingle assembly. In some embodiments the PV shingle assembly may comprise a ventilation path below the PV body. The PV body may be slidably mounted to the connection member to facilitate removal of the PV body.

  17. Subhalo abundance matching and assembly bias in the EAGLE simulation

    NASA Astrophysics Data System (ADS)

    Chaves-Montero, Jonás; Angulo, Raul E.; Schaye, Joop; Schaller, Matthieu; Crain, Robert A.; Furlong, Michelle; Theuns, Tom

    2016-08-01

    Subhalo abundance matching (SHAM) is a widely used method to connect galaxies with dark matter structures in numerical simulations. SHAM predictions agree remarkably well with observations, yet they still lack strong theoretical support. We examine the performance, implementation, and assumptions of SHAM using the `Evolution and Assembly of Galaxies and their Environment' (EAGLE) project simulations. We find that Vrelax, the highest value of the circular velocity attained by a subhalo while it sat