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

PubMed Central

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

2016-01-01

Cells contain hundreds of proteins that require iron cofactors for activity. Iron cofactors are synthesized in the cell, but the pathways involved in distributing heme, iron-sulfur clusters, and ferrous/ferric ions to apoproteins remain incompletely defined. In particular, cytosolic monothiol glutaredoxins and BolA-like proteins have been identified as [2Fe-2S]-coordinating complexes in vitro and iron-regulatory proteins in fungi, but it is not clear how these proteins function in mammalian systems or how this complex might affect Fe-S proteins or the cytosolic Fe-S assembly machinery. To explore these questions, we use quantitative immunoprecipitation and live cell proximity-dependent biotinylation to monitor interactions between Glrx3, BolA2, and components of the cytosolic iron-sulfur cluster assembly system. We characterize cytosolic Glrx3·BolA2 as a [2Fe-2S] chaperone complex in human cells. Unlike complexes formed by fungal orthologs, human Glrx3-BolA2 interaction required the coordination of Fe-S clusters, whereas Glrx3 homodimer formation did not. Cellular Glrx3·BolA2 complexes increased 6–8-fold in response to increasing iron, forming a rapidly expandable pool of Fe-S clusters. Fe-S coordination by Glrx3·BolA2 did not depend on Ciapin1 or Ciao1, proteins that bind Glrx3 and are involved in cytosolic Fe-S cluster assembly and distribution. Instead, Glrx3 and BolA2 bound and facilitated Fe-S incorporation into Ciapin1, a [2Fe-2S] protein functioning early in the cytosolic Fe-S assembly pathway. Thus, Glrx3·BolA is a [2Fe-2S] chaperone complex capable of transferring [2Fe-2S] clusters to apoproteins in human cells. PMID:27519415

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

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

PubMed

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

2015-06-30

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.

Structural and Functional Analyses of the Proteins Involved in the Iron-Sulfur Cluster Biosynthesis

NASA Astrophysics Data System (ADS)

Wada, Kei

The iron-sulfur (Fe-S) clusters are ubiquitous prosthetic groups that are required to maintain such fundamental life processes as respiratory chain, photosynthesis and the regulation of gene expression. Assembly of intracellular Fe-S cluster requires the sophisticated biosynthetic systems called ISC and SUF machineries. To shed light on the molecular mechanism of Fe-S cluster assembly mediated by SUF machinery, several structures of the SUF components and their sub-complex were determined. The structural findings together with biochemical characterization of the core-complex (SufB-SufC-SufD complex) have led me to propose a working model for the cluster biosynthesis in the SUF machinery.

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

Fe-S cluster biogenesis in Gram-positive bacteria: SufU is a zinc-dependent sulfur transfer protein.

PubMed

Selbach, Bruna P; Chung, Alexander H; Scott, Aubrey D; George, Simon J; Cramer, Stephen P; Dos Santos, Patricia C

2014-01-14

The biosynthesis of Fe-S clusters in Bacillus subtilis and other Gram-positive bacteria is catalyzed by the SufCDSUB system. The first step in this pathway involves the sulfur mobilization from the free amino acid cysteine to a sulfur acceptor protein SufU via a PLP-dependent cysteine desulfurase SufS. In this reaction scheme, the formation of an enzyme S-covalent intermediate is followed by the binding of SufU. This event leads to the second half of the reaction where a deprotonated thiol of SufU promotes the nucleophilic attack onto the persulfide intermediate of SufS. Kinetic analysis combined with spectroscopic methods identified that the presence of a zinc atom tightly bound to SufU (Ka = 10(17) M(-1)) is crucial for its structural and catalytic competency. Fe-S cluster assembly experiments showed that despite the high degree of sequence and structural similarity to the ortholog enzyme IscU, the B. subtilis SufU does not act as a standard Fe-S cluster scaffold protein. The involvement of SufU as a dedicated agent of sulfur transfer, rather than as an assembly scaffold, in the biogenesis of Fe-S clusters in Gram-positive microbes indicates distinct strategies used by bacterial systems to assemble Fe-S clusters.

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

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

PubMed

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.

Nanoscale alloys and core-shell materials: Model predictions of the nanostructure and mechanical properties

NASA Astrophysics Data System (ADS)

Zhurkin, E. E.; van Hoof, T.; Hou, M.

2007-06-01

Atomic scale modeling methods are used to investigate the relationship between the properties of clusters of nanometer size and the materials that can be synthesized by assembling them. The examples of very different bimetallic systems are used. The first one is the Ni3Al ordered alloy and the second is the AgCo core-shell system. While the Ni3Al cluster assembled materials modeling is already reported in our previous work, here we focus on the prediction of new materials synthesized by low energy deposition and accumulation of AgCo clusters. It is found that the core-shell structure is preserved by deposition with energies typical of low energy cluster beam deposition, although deposition may induce substantial cluster deformation. In contrast with Ni3Al deposited cluster assemblies, no grain boundary between clusters survives deposition and the silver shells merge into a noncrystalline system with a layered structure, in which the fcc Co grains are embedded. To our knowledge, such a material has not yet been synthesized experimentally. Mechanical properties are discussed by confronting the behaviors of Ni3Al and AgCo under the effect of a uniaxial load. To this end, a molecular dynamics scheme is established in view of circumventing rate effects inherent to short term modeling and thereby allowing to examine large plastic deformation mechanisms. Although the mechanisms are different, large plastic deformations are found to improve the elastic properties of both the Ni3Al and AgCo systems by stabilizing their nanostructure. Beyond this improvement, when the load is further increased, the Ni3Al system displays reduced ductility while the AgCo system is superplastic. The superplasticity is explained by the fact that the layered structure of the Ag system is not modified by the deformation. Some coalescence of the Co grains is identified as a geometrical effect and is suggested to be a limiting factor to superplasticity.

Self-assembly and speed distributions of active granular particles

NASA Astrophysics Data System (ADS)

Sánchez, R.; Díaz-Leyva, P.

2018-06-01

The relationship between the dynamics of self-propelled systems and the self-assembly of structured clusters are studied via the experimental speed distributions of submonolayers of self-propelled granular particles. A distribution developed for non-self-propelled granular particles describes the speed distributions remarkably well, despite some of the assumptions behind its original derivation not being applicable. This is explained in terms of clustering and dissipation being the key phenomena governing this regime.

The Newly-Discovered Outer Halo Globular Cluster System of M31

NASA Astrophysics Data System (ADS)

Mackey, D.; Huxor, A.; Ferguson, A.

2012-08-01

In this contribution we describe the discovery of a large number of globular clusters in the outer halo of M31 from the Pan-Andromeda Archaeological Survey (PAndAS). New globular clusters have also been found in the outskirts of M33, and NGC 147 and 185. Many of the remote M31 clusters are observed to preferentially project onto tidal debris streams in the stellar halo, suggesting that much of the outer M31 globular cluster system has been assembled via the accretion of satellite galaxies. We briefly discuss the global properties of the M31 halo globular cluster system.

The Dependence of Galaxy Clustering on Stellar-mass Assembly History for LRGs

NASA Astrophysics Data System (ADS)

Montero-Dorta, Antonio D.; Pérez, Enrique; Prada, Francisco; Rodríguez-Torres, Sergio; Favole, Ginevra; Klypin, Anatoly; Cid Fernandes, Roberto; González Delgado, Rosa M.; Domínguez, Alberto; Bolton, Adam S.; García-Benito, Rubén; Jullo, Eric; Niemiec, Anna

2017-10-01

We analyze the spectra of 300,000 luminous red galaxies (LRGs) with stellar masses {M}* ≳ {10}11 {M}⊙ from the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS). By studying their star formation histories, we find two main evolutionary paths converging into the same quiescent galaxy population at z˜ 0.55. Fast-growing LRGs assemble 80% of their stellar mass very early on (z˜ 5), whereas slow-growing LRGs reach the same evolutionary state at z˜ 1.5. Further investigation reveals that their clustering properties on scales of ˜1-30 Mpc are, at a high level of significance, also different. Fast-growing LRGs are found to be more strongly clustered and reside in overall denser large-scale structure environments than slow-growing systems, for a given stellar-mass threshold. Our results show a dependence of clustering on a property that is directly related to the evolution of galaxies, I.e., the stellar-mass assembly history, for a homogeneous population of similar mass and color. In a forthcoming work, we will address the halo connection in the context of galaxy assembly bias.

Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis

PubMed Central

Tsaousis, Anastasios D.; Ollagnier de Choudens, Sandrine; Gentekaki, Eleni; Long, Shaojun; Gaston, Daniel; Stechmann, Alexandra; Vinella, Daniel; Py, Béatrice; Fontecave, Marc; Barras, Frédéric; Lukeš, Julius; Roger, Andrew J.

2012-01-01

Iron/sulfur cluster (ISC)-containing proteins are essential components of cells. In most eukaryotes, Fe/S clusters are synthesized by the mitochondrial ISC machinery, the cytosolic iron/sulfur assembly system, and, in photosynthetic species, a plastid sulfur-mobilization (SUF) system. Here we show that the anaerobic human protozoan parasite Blastocystis, in addition to possessing ISC and iron/sulfur assembly systems, expresses a fused version of the SufC and SufB proteins of prokaryotes that it has acquired by lateral transfer from an archaeon related to the Methanomicrobiales, an important lineage represented in the human gastrointestinal tract microbiome. Although components of the Blastocystis ISC system function within its anaerobic mitochondrion-related organelles and can functionally replace homologues in Trypanosoma brucei, its SufCB protein has similar biochemical properties to its prokaryotic homologues, functions within the parasite’s cytosol, and is up-regulated under oxygen stress. Blastocystis is unique among eukaryotic pathogens in having adapted to its parasitic lifestyle by acquiring a SUF system from nonpathogenic Archaea to synthesize Fe/S clusters under oxygen stress. PMID:22699510

A Complex Between Biotin Synthase and The Iron-Sulfur Cluster Assembly Chaperone HscA That Enhances In Vivo Cluster Assembly†

PubMed Central

Reyda, Michael R.; Fugate, Corey J.; Jarrett, Joseph T.

2009-01-01

Biotin synthase (BioB) is an iron-sulfur enzyme that catalyzes the last step in biotin biosynthesis, the insertion of sulfur between the C6 and C9 carbons of dethiobiotin to complete the thiophane ring of biotin. Recent in vitro experiments suggest that the sulfur is derived from a [2Fe-2S]2+ cluster within BioB, and that the remnants of this cluster dissociate from the enzyme following each turnover. In order for BioB to catalyze multiple rounds of biotin synthesis, the [2Fe-2S]2+ cluster in BioB must be reassembled, a process that could be carried out in vivo by the ISC or SUF iron-sulfur cluster assembly systems. The bacterial ISC system includes HscA, an Hsp70-class molecular chaperone, whose yeast homolog has been shown to play an important but nonessential role in assembly of mitochondrial FeS clusters in S. cerevesiae. In the present work we show that in E. coli, HscA significantly improves the efficiency of the in vivo assembly of the [2Fe-2S]2+ cluster on BioB under conditions of low to moderate iron. In vitro, we show that HscA binds with increased affinity to BioB missing one or both FeS clusters, with a maximum of two HscA molecules per BioB dimer. BioB binds to HscA in an ATP/ADP-independent manner and a high affinity complex is also formed with a truncated form of HscA that lacks the nucleotide binding domain. Further, the BioB:HscA complex binds the FeS cluster scaffold protein IscU in a noncompetitive manner, generating a complex that contains all three proteins. We propose that HscA plays a role in facilitating the transfer of FeS clusters from IscU into the appropriate target apoproteins such as biotin synthase, perhaps by enhancing or prolonging the requisite protein:protein interaction. PMID:19821612

Proteomic analysis of protein-protein interactions within the Cysteine Sulfinate Desulfinase Fe-S cluster biogenesis system.

PubMed

Bolstad, Heather M; Botelho, Danielle J; Wood, Matthew J

2010-10-01

Fe-S cluster biogenesis is of interest to many fields, including bioenergetics and gene regulation. The CSD system is one of three Fe-S cluster biogenesis systems in E. coli and is comprised of the cysteine desulfurase CsdA, the sulfur acceptor protein CsdE, and the E1-like protein CsdL. The biological role, biochemical mechanism, and protein targets of the system remain uncharacterized. Here we present that the active site CsdE C61 has a lowered pK(a) value of 6.5, which is nearly identical to that of C51 in the homologous SufE protein and which is likely critical for its function. We observed that CsdE forms disulfide bonds with multiple proteins and identified the proteins that copurify with CsdE. The identification of Fe-S proteins and both putative and established Fe-S cluster assembly (ErpA, glutaredoxin-3, glutaredoxin-4) and sulfur trafficking (CsdL, YchN) proteins supports the two-pathway model, in which the CSD system is hypothesized to synthesize both Fe-S clusters and other sulfur-containing cofactors. We suggest that the identified Fe-S cluster assembly proteins may be the scaffold and/or shuttle proteins for the CSD system. By comparison with previous analysis of SufE, we demonstrate that there is some overlap in the CsdE and SufE interactomes.

Interaction of the iron–sulfur cluster assembly protein IscU with the Hsc66/Hsc20 molecular chaperone system of Escherichia coli

PubMed Central

Hoff, Kevin G.; Silberg, Jonathan J.; Vickery, Larry E.

2000-01-01

The iscU gene in bacteria is located in a gene cluster encoding proteins implicated in iron–sulfur cluster assembly and an hsc70-type (heat shock cognate) molecular chaperone system, iscSUA-hscBA. To investigate possible interactions between these systems, we have overproduced and purified the IscU protein from Escherichia coli and have studied its interactions with the hscA and hscB gene products Hsc66 and Hsc20. IscU and its iron–sulfur complex (IscU–Fe/S) stimulated the basal steady-state ATPase activity of Hsc66 weakly in the absence of Hsc20 but, in the presence of Hsc20, increased the ATPase activity up to 480-fold. Hsc20 also decreased the apparent Km for IscU stimulation of Hsc66 ATPase activity, and surface plasmon resonance studies revealed that Hsc20 enhances binding of IscU to Hsc66. Surface plasmon resonance and isothermal titration calorimetry further showed that IscU and Hsc20 form a complex, and Hsc20 may thereby aid in the targeting of IscU to Hsc66. These results establish a direct and specific role for the Hsc66/Hsc20 chaperone system in functioning with isc gene components for the assembly of iron–sulfur cluster proteins. PMID:10869428

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

PubMed Central

Cook, Jeremy D.; Kondapalli, Kalyan C.; Rawat, Swati; Childs, William C.; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L.

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 n the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to better understand 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 (ITC). 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 a 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. PMID:20815377

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, J.; Kondapalli, K; Rawat, S

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 modulemore » 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.« less

Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly.

PubMed

Cook, Jeremy D; Kondapalli, Kalyan C; Rawat, Swati; Childs, William C; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L

2010-10-12

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.

NIF-type iron-sulfur cluster assembly system is duplicated and distributed in the mitochondria and cytosol of Mastigamoeba balamuthi.

PubMed

Nývltová, Eva; Šuták, Robert; Harant, Karel; Šedinová, Miroslava; Hrdy, Ivan; Paces, Jan; Vlček, Čestmír; Tachezy, Jan

2013-04-30

In most eukaryotes, the mitochondrion is the main organelle for the formation of iron-sulfur (FeS) clusters. This function is mediated through the iron-sulfur cluster assembly machinery, which was inherited from the α-proteobacterial ancestor of mitochondria. In Archamoebae, including pathogenic Entamoeba histolytica and free-living Mastigamoeba balamuthi, the complex iron-sulfur cluster machinery has been replaced by an ε-proteobacterial nitrogen fixation (NIF) system consisting of two components: NifS (cysteine desulfurase) and NifU (scaffold protein). However, the cellular localization of the NIF system and the involvement of mitochondria in archamoebal FeS assembly are controversial. Here, we show that the genes for both NIF components are duplicated within the M. balamuthi genome. One paralog of each protein contains an amino-terminal extension that targets proteins to mitochondria (NifS-M and NifU-M), and the second paralog lacks a targeting signal, thereby reflecting the cytosolic form of the NIF machinery (NifS-C and NifU-C). The dual localization of the NIF system corresponds to the presence of FeS proteins in both cellular compartments, including detectable hydrogenase activity in Mastigamoeba cytosol and mitochondria. In contrast, E. histolytica possesses only single genes encoding NifS and NifU, respectively, and there is no evidence for the presence of the NIF machinery in its reduced mitochondria. Thus, M. balamuthi is unique among eukaryotes in that its FeS cluster formation is mediated through two most likely independent NIF machineries present in two cellular compartments.

NIF-type iron-sulfur cluster assembly system is duplicated and distributed in the mitochondria and cytosol of Mastigamoeba balamuthi

PubMed Central

Nývltová, Eva; Šuták, Robert; Harant, Karel; Šedinová, Miroslava; Hrdý, Ivan; Pačes, Jan; Vlček, Čestmír; Tachezy, Jan

2013-01-01

In most eukaryotes, the mitochondrion is the main organelle for the formation of iron-sulfur (FeS) clusters. This function is mediated through the iron-sulfur cluster assembly machinery, which was inherited from the α-proteobacterial ancestor of mitochondria. In Archamoebae, including pathogenic Entamoeba histolytica and free-living Mastigamoeba balamuthi, the complex iron-sulfur cluster machinery has been replaced by an ε-proteobacterial nitrogen fixation (NIF) system consisting of two components: NifS (cysteine desulfurase) and NifU (scaffold protein). However, the cellular localization of the NIF system and the involvement of mitochondria in archamoebal FeS assembly are controversial. Here, we show that the genes for both NIF components are duplicated within the M. balamuthi genome. One paralog of each protein contains an amino-terminal extension that targets proteins to mitochondria (NifS-M and NifU-M), and the second paralog lacks a targeting signal, thereby reflecting the cytosolic form of the NIF machinery (NifS-C and NifU-C). The dual localization of the NIF system corresponds to the presence of FeS proteins in both cellular compartments, including detectable hydrogenase activity in Mastigamoeba cytosol and mitochondria. In contrast, E. histolytica possesses only single genes encoding NifS and NifU, respectively, and there is no evidence for the presence of the NIF machinery in its reduced mitochondria. Thus, M. balamuthi is unique among eukaryotes in that its FeS cluster formation is mediated through two most likely independent NIF machineries present in two cellular compartments. PMID:23589868

Self-assembly of bimodal particles inside emulsion droplets

NASA Astrophysics Data System (ADS)

Cho, Young-Sang; Yi, Gi-Ra; Yang, Seung-Man; Kim, Young-Kuk; Choi, Chul-Jin

2010-08-01

Colloidal dispersion of bimodal particles were self-organized inside water-in-oil emulsion droplets by evaporationdriven self-assembly method. After droplet shrinkage by heating the complex fluid system, small numbers of microspheres were packed into minimal second moment clusters, which are partially coated with silica nanospheres, resulting in the generation of patchy particles. The patchy particles in this study possess potential applications for selfassembly of non-isotropic particles such as dimmers or tetramers for colloidal photonic crystals with diamond lattice structures. The composite micro-clusters of amidine polystyrene microspheres and titania nanoparticles were also generated by evaporation-driven self-assembly to fabricate nonspherical hollow micro-particles made of titania shell.

Combinatoric analysis of heterogeneous stochastic self-assembly.

PubMed

D'Orsogna, Maria R; Zhao, Bingyu; Berenji, Bijan; Chou, Tom

2013-09-28

We analyze a fully stochastic model of heterogeneous nucleation and self-assembly in a closed system with a fixed total particle number M, and a fixed number of seeds Ns. Each seed can bind a maximum of N particles. A discrete master equation for the probability distribution of the cluster sizes is derived and the corresponding cluster concentrations are found using kinetic Monte-Carlo simulations in terms of the density of seeds, the total mass, and the maximum cluster size. In the limit of slow detachment, we also find new analytic expressions and recursion relations for the cluster densities at intermediate times and at equilibrium. Our analytic and numerical findings are compared with those obtained from classical mass-action equations and the discrepancies between the two approaches analyzed.

Towards Cluster-Assembled Materials of True Monodispersity in Size and Chemical Environment: Synthesis, Dynamics and Activity

DTIC Science & Technology

2016-10-27

AFRL-AFOSR-UK-TR-2016-0037 Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and...Towards cluster-assembled materials of true monodispersity in size and chemical environment: synthesis, dynamics and activity 5a.  CONTRACT NUMBER 5b...report Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and Activity Ulrich Heiz

Extension of lattice cluster theory to strongly interacting, self-assembling polymeric systems.

PubMed

Freed, Karl F

2009-02-14

A new extension of the lattice cluster theory is developed to describe the influence of monomer structure and local correlations on the free energy of strongly interacting and self-assembling polymer systems. This extension combines a systematic high dimension (1/d) and high temperature expansion (that is appropriate for weakly interacting systems) with a direct treatment of strong interactions. The general theory is illustrated for a binary polymer blend whose two components contain "sticky" donor and acceptor groups, respectively. The free energy is determined as an explicit function of the donor-acceptor contact probabilities that depend, in turn, on the local structure and both the strong and weak interactions.

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

PubMed

Reddy, Rachamalla Maheedhar; Mohammed, Monzoorul Haque; Mande, Sharmila S

2014-01-01

A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient assembly of metagenomic sequence datasets. In this study, we present MetaCAA - a clustering-aided methodology which helps in improving the quality of metagenomic sequence assembly. MetaCAA initially groups sequences constituting a given metagenome into smaller clusters. Subsequently, sequences in each cluster are independently assembled using CAP3, an existing single genome assembly program. Contigs formed in each of the clusters along with the unassembled reads are then subjected to another round of assembly for generating the final set of contigs. Validation using simulated and real-world metagenomic datasets indicates that MetaCAA aids in improving the overall quality of assembly. A software implementation of MetaCAA is available at https://metagenomics.atc.tcs.com/MetaCAA. Copyright © 2014 Elsevier Inc. All rights reserved.

Creating Quasi Two-Dimensional Cluster-Assembled Materials through Self-Assembly of a Janus Polyoxometalate-Silsesquioxane Co-Cluster.

PubMed

Wu, Han; Zhang, Yu-Qi; Hu, Min-Biao; Ren, Li-Jun; Lin, Yue; Wang, Wei

2017-05-30

Clusters are an important class of nanoscale molecules or superatoms that exhibit an amazing diversity in structure, chemical composition, shape, and functionality. Assembling two types of clusters is creating emerging cluster-assembled materials (CAMs). In this paper, we report an effective approach to produce quasi two-dimensional (2D) CAMs of two types of spherelike clusters, polyhedral oligomeric silsesquioxanes (POSS), and polyoxometalates (POM). To avoid macrophase separation between the two clusters, they are covalently linked to form a POM-POSS cocluster with Janus characteristics and a dumbbell shape. This Janus characteristics enables the cocluster to self-assemble into diverse nanoaggregates, as conventional amphiphilic molecules and macromolecules do, in selective solvents. In our study, we obtained micelles, vesicles, nanosheets, and nanoribbons by tuning the n-hexane content in mixed solvents of acetone and n-hexane. Ordered packing of clusters in the nanosheets and nanoribbons were directly visualized using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) technique. We infer that the increase of packing order results in the vesicle-to-sheet transition and the change in packing mode causes the sheet-to-ribbon transitions. Our findings have verified the effectivity of creating quasi 2D cluster-assembled materials though the cocluster self-assembly as a new approach to produce novel CAMs.

Distinct functional domains within the acidic cluster of tegument protein pp28 required for trafficking and cytoplasmic envelopment of human cytomegalovirus.

PubMed

Seo, Jun-Young; Jeon, Hyejin; Hong, Sookyung; Britt, William J

2016-10-01

Human cytomegalovirus UL99-encoded tegument protein pp28 contains a 16 aa acidic cluster that is required for pp28 trafficking to the assembly compartment (AC) and the virus assembly. However, functional signals within the acidic cluster of pp28 remain undefined. Here, we demonstrated that an acidic cluster rather than specific sorting signals was required for trafficking to the AC. Recombinant viruses with chimeric pp28 proteins expressing non-native acidic clusters exhibited delayed viral growth kinetics and decreased production of infectious virus, indicating that the native acidic cluster of pp28 was essential for wild-type virus assembly. These results suggested that the acidic cluster of pp28 has distinct functional domains required for trafficking and for efficient virus assembly. The first half (aa 44-50) of the acidic cluster was sufficient for pp28 trafficking, whereas the native acidic cluster consisting of aa 51-59 was required for the assembly of wild-type levels of infectious virus.

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

MedlinePlus

... Myopathy with deficiency of iron-sulfur cluster assembly enzyme Printable PDF Open All Close All Enable Javascript ... Myopathy with deficiency of iron-sulfur cluster assembly enzyme is an inherited disorder that primarily affects muscles ...

Self-Assembly of Trimer Colloids: Effect of Shape and Interaction Range†

PubMed Central

Hatch, Harold W.; Yang, Seung-Yeob; Mittal, Jeetain; Shen, Vincent K.

2016-01-01

Trimers with one attractive bead and two repulsive beads, similar to recently synthesized trimer patchy colloids, were simulated with flat-histogram Monte Carlo methods to obtain the stable self-assembled structures for different shapes and interaction potentials. Extended corresponding states principle was successfully applied to self-assembling systems in order to approximately collapse the results for models with the same shape, but different interaction range. This helps us directly compare simulation results with previous experiment, and good agreement was found between the two. In addition, a variety of self-assembled structures were observed by varying the trimer geometry, including spherical clusters, elongated clusters, monolayers, and spherical shells. In conclusion, our results help to compare simulations and experiments, via extended corresponding states, and we predict the formation of self-assembled structures for trimer shapes that have not been experimentally synthesized. PMID:27087490

Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers.

PubMed

Galeano, B K; Ranatunga, W; Gakh, O; Smith, D Y; Thompson, J R; Isaya, G

2017-06-21

Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrison, Craig D.; Miller, Christopher J.; Richards, Joseph W.

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 brightestmore » 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.« less

Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes.

PubMed

Zhong, Xingyu; Tian, Yuqing; Niu, Guoqing; Tan, Huarong

2013-07-01

A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using 454 sequencing technology. In combination with local BLAST searches and gap filling techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. A total of at least 35 putative gene clusters were identified and assembled. Transcriptional analysis showed that 20 of the 35 gene clusters were expressed in either or all of the three different media tested, whereas the other 15 gene clusters were silent in all three different media. This study provides a comprehensive method to identify and assemble secondary metabolite biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote functional studies of these secondary metabolite biosynthetic gene clusters.

Bottom-up strategies for the assembling of magnetic systems using nanoclusters

NASA Astrophysics Data System (ADS)

Dupuis, V.; Hillion, A.; Robert, A.; Loiselet, O.; Khadra, G.; Capiod, P.; Albin, C.; Boisron, O.; Le Roy, D.; Bardotti, L.; Tournus, F.; Tamion, A.

2018-05-01

In the frame of the 20th Anniversary of the Journal of Nanoparticle Research (JNR), our aim is to start from the historical context 20 years ago and to give some recent results and perspectives concerning nanomagnets prepared from clusters preformed in the gas phase using the low-energy cluster beam deposition (LECBD) technique. In this paper, we focus our attention on the typical case of Co clusters embedded in various matrices to study interface magnetic anisotropy and magnetic interactions as a function of volume concentrations, and on still current and perspectives through two examples of binary metallic 3d-5d TM (namely CoPt and FeAu) cluster assemblies to illustrate size-related and nanoalloy phenomena on magnetic properties in well-defined mass-selected clusters. The structural and magnetic properties of these cluster assemblies were investigated using various experimental techniques that include high-resolution transmission electron microscopy (HRTEM), superconducting quantum interference device (SQUID) magnetometry, and synchrotron techniques such as extended X-ray absorption fine structure (EXAFS) and X-ray magnetic circular dichroism (XMCD). Depending on the chemical nature of both NPs and matrix, we observe different magnetic responses compared to their bulk counterparts. In particular, we show how finite size effects (size reduction) enhance their magnetic moment and how specific relaxation in nanoalloys can impact their magnetic anisotropy.

Density Functional Investigation of the Inclusion of Gold Clusters on a CH 3 S Self-Assembled Lattice on Au(111)

DOE PAGES

Allen, Darnel J.; Archibald, Wayne E.; Harper, John A.; ...

2016-01-01

We employ first-principles density functional theoretical calculations to address the inclusion of gold (Au) clusters in a well-packed CH 3 S self-assembled lattice. We compute CH 3 S adsorption energies to quantify the energetic stability of the self-assembly and gold adsorption and dissolution energies to characterize the structural stability of a series of Au clusters adsorbed at the SAM-Au interface. Our results indicate that the inclusion of Au clusters with less than four Au atoms in the SAM-Au interface enhances the binding of CH 3 S species. In contrast, larger Au clusters destabilize the self-assembly. We attribute this effect tomore » the low-coordinated gold atoms in the cluster. For small clusters, these low-coordinated sites have significantly different electronic properties compared to larger islands, which makes the binding with the self-assembly energetically more favorable. Our results further indicate that Au clusters in the SAM-Au interface are thermodynamically unstable and they will tend to dissolve, producing Au adatoms incorporated in the self-assembly in the form of CH 3 S-Au-SCH 3 species. This is due to the strong S-Au bond which stabilizes single Au adatoms in the self-assembly. Our results provide solid insight into the impact of adatom islands at the CH 3 S-Au interface.« less

The Nature of LSB galaxies revealed by their Globular Clusters

NASA Astrophysics Data System (ADS)

Kissler-Patig, Markus

2005-07-01

Low Surface Brightness {LSB} galaxies encompass many of the extremes in galaxy properties. Their understanding is essential to complete our picture of galaxy formation and evolution. Due to their historical under-representation on galaxy surveys, their importance to many areas of astronomy has only recently began to be realized. Globular clusters are superb tracers of the formation histories of galaxies and have been extensively used as such in high surface brightness galaxies. We propose to investigate the nature of massive LSB galaxies by studying their globular cluster systems. No globular cluster study has been reported for LSB galaxies to date. Yet, both the presence or absence of globular clusters set very strong constraints on the conditions prevailing during LSB galaxy formation and evolution. Both in dwarf and giant high surface brightness {HSB} galaxies, globular clusters are known to form as a constant fraction of baryonic mass. Their presence/absence immediately indicates similarities or discrepancies in the formation and evolution conditions of LSB and HSB galaxies. In particular, the presence/absence of metal-poor halo globular clusters infers similarities/differences in the halo formation and assembly processes of LSB vs. HSB galaxies, while the presence/absence of metal-rich globular clusters can be used to derive the occurrence and frequency of violent events {such as mergers} in the LSB galaxy assembly history. Two band imaging with ACS will allow us to identify the globular clusters {just resolved at the selected distance} and to determine their metallicity {potentially their rough age}. The composition of the systems will be compared to the extensive census built up on HSB galaxies. Our representative sample of six LSB galaxies {cz < 2700 km/s} are selected such, that a large system of globular clusters is expected. Globular clusters will constrain phases of LSB galaxy formation and evolution that can currently not be probed by other means. HST/ACS imaging is the only facility capable of studying the globular cluster systems of LSB galaxies given their distance and relative scarcity.

Tracing the `ninth sulfur' of the nitrogenase cofactor via a semi-synthetic approach

NASA Astrophysics Data System (ADS)

Tanifuji, Kazuki; Lee, Chi Chung; Sickerman, Nathaniel S.; Tatsumi, Kazuyuki; Ohki, Yasuhiro; Hu, Yilin; Ribbe, Markus W.

2018-05-01

The M-cluster is the [(homocitrate)MoFe7S9C] active site of nitrogenase that is derived from an 8Fe core assembled viacoupling and rearrangement of two [Fe4S4] clusters concomitant with the insertion of an interstitial carbon and a `ninth sulfur'. Combining synthetic [Fe4S4] clusters with an assembly protein template, here we show that sulfite can give rise to the ninth sulfur that is incorporated in the catalytically important belt region of the cofactor after the radical S-adenosyl-l-methionine-dependent carbide insertion and the concurrent 8Fe-core rearrangement have already taken place. Based on the differential reactivity of the formed cluster species, we also propose a new [Fe8S8C] cluster intermediate, the L*-cluster, which is similar to the [Fe8S9C] L-cluster, but lacks the ninth sulfur from sulfite. This work provides a semi-synthetic tool for protein reconstitution that could be widely applicable for the functional analysis of other FeS systems.

Tracing the 'ninth sulfur' of the nitrogenase cofactor via a semi-synthetic approach.

PubMed

Tanifuji, Kazuki; Lee, Chi Chung; Sickerman, Nathaniel S; Tatsumi, Kazuyuki; Ohki, Yasuhiro; Hu, Yilin; Ribbe, Markus W

2018-05-01

The M-cluster is the [(homocitrate)MoFe 7 S 9 C] active site of nitrogenase that is derived from an 8Fe core assembled viacoupling and rearrangement of two [Fe 4 S 4 ] clusters concomitant with the insertion of an interstitial carbon and a 'ninth sulfur'. Combining synthetic [Fe 4 S 4 ] clusters with an assembly protein template, here we show that sulfite can give rise to the ninth sulfur that is incorporated in the catalytically important belt region of the cofactor after the radical S-adenosyl-L-methionine-dependent carbide insertion and the concurrent 8Fe-core rearrangement have already taken place. Based on the differential reactivity of the formed cluster species, we also propose a new [Fe 8 S 8 C] cluster intermediate, the L*-cluster, which is similar to the [Fe 8 S 9 C] L-cluster, but lacks the ninth sulfur from sulfite. This work provides a semi-synthetic tool for protein reconstitution that could be widely applicable for the functional analysis of other FeS systems.

Concept design and cluster control of advanced space connectable intelligent microsatellite

NASA Astrophysics Data System (ADS)

Wang, Xiaohui; Li, Shuang; She, Yuchen

2017-12-01

In this note, a new type of advanced space connectable intelligent microsatellite is presented to extend the range of potential application of microsatellite and improve the efficiency of cooperation. First, the overall concept of the micro satellite cluster is described, which is characterized by autonomously connecting with each other and being able to realize relative rotation through the external interfaces. Second, the multi-satellite autonomous assembly algorithm and control algorithm of the cluster motion are developed to make the cluster system combine into a variety of configurations in order to achieve different types of functionality. Finally, the design of the satellite cluster system is proposed, and the possible applications are discussed.

Self-assembled clusters of spheres related to spherical codes.

PubMed

Phillips, Carolyn L; Jankowski, Eric; Marval, Michelle; Glotzer, Sharon C

2012-10-01

We consider the thermodynamically driven self-assembly of spheres onto the surface of a central sphere. This assembly process forms self-limiting, or terminal, anisotropic clusters (N-clusters) with well-defined structures. We use Brownian dynamics to model the assembly of N-clusters varying in size from two to twelve outer spheres and free energy calculations to predict the expected cluster sizes and shapes as a function of temperature and inner particle diameter. We show that the arrangements of outer spheres at finite temperatures are related to spherical codes, an ideal mathematical sequence of points corresponding to the densest possible sphere packings. We demonstrate that temperature and the ratio of the diameters of the inner and outer spheres dictate cluster morphology. We present a surprising result for the equilibrium structure of a 5-cluster, for which the square pyramid arrangement is preferred over a more symmetric structure. We show this result using Brownian dynamics, a Monte Carlo simulation, and a free energy approximation. Our results suggest a promising way to assemble anisotropic building blocks from constituent colloidal spheres.

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn 4CaO 5-cluster in photosystem II

DOE PAGES

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; ...

2017-07-18

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4CaO 5-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4CaO 5-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water moleculesmore » largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4CaO 5-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn4CaO5-cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.« less

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II.

PubMed

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; Hussein, Rana; Yano, Junko; Dau, Holger; Kern, Jan; Dobbek, Holger; Zouni, Athina

2017-07-18

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4 CaO 5 -cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4 CaO 5 -cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4 CaO 5 -cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn 4 CaO 5 -cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.

Maturation of nitrogenase cofactor—the role of a class E radical SAM methyltransferase NifB

PubMed Central

Hu, Yilin; Ribbe, Markus W.

2016-01-01

Nitrogenase catalyzes the important reactions of N2-, CO- and CO2-reduction at its active cofactor site. Designated the M-cluster, this complex metallocofactor is assembled through the generation of a characteristic 8Fe-core prior to the insertion of Mo and homocitrate that completes the stoichiometry of the M-cluster. NifB catalyzes the critical step of radical SAM-dependent carbide insertion that occurs concomitant with the insertion a “9th” sulfur and the rearrangement/coupling of two 4Fe-clusters into a complete 8Fe-core of the M-cluster. Further categorization of a family of NifB proteins as a new class of radical SAM methyltransferases suggests a general function of these proteins in complex metallocofactor assembly and provides a new platform for unveiling unprecedented chemical reactions catalyzed by biological systems. PMID:26969410

Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20.

PubMed

Maio, N; Rouault, T A

2016-10-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery.

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

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.

Nitrogenase assembly

PubMed Central

Hu, Yilin; Ribbe, Markus W.

2013-01-01

Nitrogenase contains two unique metalloclusters: the P-cluster and the M-cluster. The assembly processes of P- and M-clusters are arguably the most complicated processes in bioinorganic chemistry. There is considerable interest in decoding the biosynthetic mechanisms of the P- and M-clusters, because these clusters are not only biologically important, but also chemically unprecedented. Understanding the assembly mechanisms of these unique metalloclusters is crucial for understanding the structure-function relationship of nitrogenase. Here, we review the recent advances in this research area, with an emphasis on our work that provide important insights into the biosynthetic pathways of these high-nuclearity metal centers. PMID:23232096

Physical controls on directed virus assembly at nanoscale chemical templates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheung, C L; Chung, S; Chatterji, A

2006-05-10

Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In-situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, andmore » drove 1D and 2D condensation at subcritical volume fractions. The growth kinetics followed a t{sup 1/2} law controlled by the slow diffusion of viruses. The lateral expansion of virus clusters that initially form on the 1D templates following introduction of polyethylene glycol (PEG) into the solution suggests a significant role for weak interaction.« less

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II

PubMed Central

Zhang, Miao; Bommer, Martin; Chatterjee, Ruchira; Hussein, Rana; Yano, Junko; Dau, Holger; Kern, Jan; Dobbek, Holger; Zouni, Athina

2017-01-01

In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn4CaO5-cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn4CaO5-cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn4CaO5-cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn4CaO5-cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate. DOI: http://dx.doi.org/10.7554/eLife.26933.001 PMID:28718766

Theory and modeling of particles with DNA-mediated interactions

NASA Astrophysics Data System (ADS)

Licata, Nicholas A.

In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. A quantitative comparison between the theory and experiments is made by calculating the experimentally observed melting profile. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. The model predicts a crossover from localized to diffusive behavior. The random walk statistics for the particles' in plane diffusion is discussed. The lateral motion is analogous to dispersive transport in disordered semiconductors, ranging from standard diffusion with a renormalized diffusion coefficient to anomalous, subdiffusive behavior. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. An optimal concentration ratio is determined for the experimental implementation of our self-assembly proposal. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. We determine the probability that the system self-assembles the desired cluster geometry, and discuss the connections to jamming in granular and colloidal systems. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. A key-lock model is proposed to describe the results of in-vitro experiments, and the situation in-vivo is discussed. The cooperative binding, and hence the specificity to cancerous cells, is kinetically limited. The implications for optimizing the design of nanoparticle based drug delivery platforms is discussed. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

Magnetic assembly of 3D cell clusters: visualizing the formation of an engineered tissue.

PubMed

Ghosh, S; Kumar, S R P; Puri, I K; Elankumaran, S

2016-02-01

Contactless magnetic assembly of cells into 3D clusters has been proposed as a novel means for 3D tissue culture that eliminates the need for artificial scaffolds. However, thus far its efficacy has only been studied by comparing expression levels of generic proteins. Here, it has been evaluated by visualizing the evolution of cell clusters assembled by magnetic forces, to examine their resemblance to in vivo tissues. Cells were labeled with magnetic nanoparticles, then assembled into 3D clusters using magnetic force. Scanning electron microscopy was used to image intercellular interactions and morphological features of the clusters. When cells were held together by magnetic forces for a single day, they formed intercellular contacts through extracellular fibers. These kept the clusters intact once the magnetic forces were removed, thus serving the primary function of scaffolds. The cells self-organized into constructs consistent with the corresponding tissues in vivo. Epithelial cells formed sheets while fibroblasts formed spheroids and exhibited position-dependent morphological heterogeneity. Cells on the periphery of a cluster were flattened while those within were spheroidal, a well-known characteristic of connective tissues in vivo. Cells assembled by magnetic forces presented visual features representative of their in vivo states but largely absent in monolayers. This established the efficacy of contactless assembly as a means to fabricate in vitro tissue models. © 2016 John Wiley & Sons Ltd.

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.

Spectroscopic and Functional Characterization of Iron-Sulfur Cluster-Bound Forms of Azotobacter vinelandii NifIscA†

PubMed Central

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

2012-01-01

The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of NifIscA 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 NifIscA, and the ability of NifIscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that NifIscA 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 O2-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+-NifIscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-NifIscA 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

The immitigable nature of assembly bias: the impact of halo definition on assembly bias

NASA Astrophysics Data System (ADS)

Villarreal, Antonio S.; Zentner, Andrew R.; Mao, Yao-Yuan; Purcell, Chris W.; van den Bosch, Frank C.; Diemer, Benedikt; Lange, Johannes U.; Wang, Kuan; Campbell, Duncan

2017-11-01

Dark matter halo clustering depends not only on halo mass, but also on other properties such as concentration and shape. This phenomenon is known broadly as assembly bias. We explore the dependence of assembly bias on halo definition, parametrized by spherical overdensity parameter, Δ. We summarize the strength of concentration-, shape-, and spin-dependent halo clustering as a function of halo mass and halo definition. Concentration-dependent clustering depends strongly on mass at all Δ. For conventional halo definitions (Δ ∼ 200 - 600 m), concentration-dependent clustering at low mass is driven by a population of haloes that is altered through interactions with neighbouring haloes. Concentration-dependent clustering can be greatly reduced through a mass-dependent halo definition with Δ ∼ 20 - 40 m for haloes with M200 m ≲ 1012 h-1M⊙. Smaller Δ implies larger radii and mitigates assembly bias at low mass by subsuming altered, so-called backsplash haloes into now larger host haloes. At higher masses (M200 m ≳ 1013 h-1M⊙) larger overdensities, Δ ≳ 600 m, are necessary. Shape- and spin-dependent clustering are significant for all halo definitions that we explore and exhibit a relatively weaker mass dependence. Generally, both the strength and the sense of assembly bias depend on halo definition, varying significantly even among common definitions. We identify no halo definition that mitigates all manifestations of assembly bias. A halo definition that mitigates assembly bias based on one halo property (e.g. concentration) must be mass dependent. The halo definitions that best mitigate concentration-dependent halo clustering do not coincide with the expected average splashback radii at fixed halo mass.

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 apparent assistance of mitosomes. PMID:25271645

Interaction between Nbp35 and Cfd1 proteins of cytosolic Fe-S cluster assembly reveals a stable complex formation in Entamoeba histolytica.

PubMed

Anwar, Shadab; Dikhit, Manas Ranjan; Singh, Krishn Pratap; Kar, Rajiv Kumar; Zaidi, Amir; Sahoo, Ganesh Chandra; Roy, Awadh Kishore; Nozaki, Tomoyoshi; Das, Pradeep; Ali, Vahab

2014-01-01

Iron-Sulfur (Fe-S) proteins are involved in many biological functions such as electron transport, photosynthesis, regulation of gene expression and enzymatic activities. Biosynthesis and transfer of Fe-S clusters depend on Fe-S clusters assembly processes such as ISC, SUF, NIF, and CIA systems. Unlike other eukaryotes which possess ISC and CIA systems, amitochondriate Entamoeba histolytica has retained NIF & CIA systems for Fe-S cluster assembly in the cytosol. In the present study, we have elucidated interaction between two proteins of E. histolytica CIA system, Cytosolic Fe-S cluster deficient 1 (Cfd1) protein and Nucleotide binding protein 35 (Nbp35). In-silico analysis showed that structural regions ranging from amino acid residues (P33-K35, G131-V135 and I147-E151) of Nbp35 and (G5-V6, M34-D39 and G46-A52) of Cfd1 are involved in the formation of protein-protein complex. Furthermore, Molecular dynamic (MD) simulations study suggested that hydrophobic forces surpass over hydrophilic forces between Nbp35 and Cfd1 and Van-der-Waal interaction plays crucial role in the formation of stable complex. Both proteins were separately cloned, expressed as recombinant fusion proteins in E. coli and purified to homogeneity by affinity column chromatography. Physical interaction between Nbp35 and Cfd1 proteins was confirmed in vitro by co-purification of recombinant Nbp35 with thrombin digested Cfd1 and in vivo by pull down assay and immunoprecipitation. The insilico, in vitro as well as in vivo results prove a stable interaction between these two proteins, supporting the possibility of its involvement in Fe-S cluster transfer to target apo-proteins through CIA machinery in E. histolytica. Our study indicates that initial synthesis of a Fe-S precursor in mitochondria is not necessary for the formation of Cfd1-Nbp35 complex. Thus, Cfd1 and Nbp35 with the help of cytosolic NifS and NifU proteins can participate in the maturation of non-mitosomal Fe-S proteins without any apparent assistance of mitosomes.

Systems and methods for creation of conducting networks of magnetic particles through dynamic self-assembly process

DOEpatents

Snezhko, Oleksiy [Woodridge, IL; Aronson, Igor [Darien, IL; Kwok, Wai-Kwong [Downers Grove, IL

2011-01-25

Self-assembly of magnetic microparticles in AC magnetic fields. Excitation of the system by an AC magnetic field provides a variety of patterns that can be controlled by adjusting the frequency and the amplitude of the field. At low particle densities the low-frequency magnetic excitation favors cluster phase formation, while high frequency excitation favors chains and netlike structures. For denser configurations, an abrupt transition to the network phase was obtained.

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.

Global Identification of Genes Affecting Iron-Sulfur Cluster Biogenesis and Iron Homeostasis

PubMed Central

Hidese, Ryota; Kurihara, Tatsuo; Esaki, Nobuyoshi

2014-01-01

Iron-sulfur (Fe-S) clusters are ubiquitous cofactors that are crucial for many physiological processes in all organisms. In Escherichia coli, assembly of Fe-S clusters depends on the activity of the iron-sulfur cluster (ISC) assembly and sulfur mobilization (SUF) apparatus. However, the underlying molecular mechanisms and the mechanisms that control Fe-S cluster biogenesis and iron homeostasis are still poorly defined. In this study, we performed a global screen to identify the factors affecting Fe-S cluster biogenesis and iron homeostasis using the Keio collection, which is a library of 3,815 single-gene E. coli knockout mutants. The approach was based on radiolabeling of the cells with [2-14C]dihydrouracil, which entirely depends on the activity of an Fe-S enzyme, dihydropyrimidine dehydrogenase. We identified 49 genes affecting Fe-S cluster biogenesis and/or iron homeostasis, including 23 genes important only under microaerobic/anaerobic conditions. This study defines key proteins associated with Fe-S cluster biogenesis and iron homeostasis, which will aid further understanding of the cellular mechanisms that coordinate the processes. In addition, we applied the [2-14C]dihydrouracil-labeling method to analyze the role of amino acid residues of an Fe-S cluster assembly scaffold (IscU) as a model of the Fe-S cluster assembly apparatus. The analysis showed that Cys37, Cys63, His105, and Cys106 are essential for the function of IscU in vivo, demonstrating the potential of the method to investigate in vivo function of proteins involved in Fe-S cluster assembly. PMID:24415728

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.

Nano Cu interaction with single amino acid tyrosine derived self-assemblies; study through XRD, AFM, confocal Raman microscopy, SERS and DFT methods

NASA Astrophysics Data System (ADS)

Govindhan, Raman; Karthikeyan, Balakrishnan

2017-12-01

3,5-Bis(trifluoromethyl)benzylamine derivatives of single amino acid tyrosine produced self-assembled nanotubes (BTTNTs) as simple Phe-Phe. It has been observed that tyrosine derivative gives exclusively micro and nano tubes irrespective of the concentration of the precursor monomer. However, the introduced xenobiotic trifluoromethyl group (TFM) present in key backbone positionsof the self assembly gives the specific therapeutic function has been highlighted. Herein this work study of such self assembled nanotubes were studied through experimental and theoretical methods. The interaction of nanocopper cluster with the nanotubes (Cu@BTTNTs) were extensively studied by various methods like XRD, AFM, confocal Raman microscopy, SERS and theoretical methods like Mulliken's atomic charge analysis. SERS reveals that the interactions of Cu cluster with NH2, OH, NH and phenyl ring π-electrons system of BTTNTs. DFT studies gave the total dipole moment values of Cu@BTTNTs and explained the nature of interaction.

Iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis

PubMed Central

Landry, Aaron P.; Cheng, Zishuo; Ding, Huangen

2013-01-01

Iron-sulphur cluster biogenesis requires coordinated delivery of iron and sulphur to scaffold proteins, followed by transfer of the assembled clusters from scaffold proteins to target proteins. This complex process is accomplished by a group of dedicated iron-sulphur cluster assembly proteins that are conserved from bacteria to humans. While sulphur in iron-sulphur clusters is provided by L-cysteine via cysteine desulfurase, the iron donor(s) for iron-sulphur cluster assembly remains largely elusive. Here we report that among the primary iron-sulphur cluster assembly proteins, IscA has a unique and strong binding activity for mononuclear iron in vitro and in vivo. Furthermore, the ferric iron centre tightly bound in IscA can be readily extruded by L-cysteine, followed by reduction to ferrous iron for iron-sulphur cluster biogenesis. Substitution of the highly conserved residue tyrosine 40 with phenylalanine (Y40F) in IscA results in a mutant protein that has a diminished iron binding affinity but retains the iron-sulphur cluster binding activity. Genetic complementation studies show that the IscA Y40F mutant is inactive in vivo, suggesting that the iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis. PMID:23258274

Iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis.

PubMed

Landry, Aaron P; Cheng, Zishuo; Ding, Huangen

2013-03-07

Iron-sulphur cluster biogenesis requires coordinated delivery of iron and sulphur to scaffold proteins, followed by transfer of the assembled clusters from scaffold proteins to target proteins. This complex process is accomplished by a group of dedicated iron-sulphur cluster assembly proteins that are conserved from bacteria to humans. While sulphur in iron-sulphur clusters is provided by L-cysteine via cysteine desulfurase, the iron donor(s) for iron-sulphur cluster assembly remains largely elusive. Here we report that among the primary iron-sulphur cluster assembly proteins, IscA has a unique and strong binding activity for mononuclear iron in vitro and in vivo. Furthermore, the ferric iron centre tightly bound in IscA can be readily extruded by l-cysteine, followed by reduction to ferrous iron for iron-sulphur cluster biogenesis. Substitution of the highly conserved residue tyrosine 40 with phenylalanine (Y40F) in IscA results in a mutant protein that has a diminished iron binding affinity but retains the iron-sulphur cluster binding activity. Genetic complementation studies show that the IscA Y40F mutant is inactive in vivo, suggesting that the iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis.

Development of a 12-Thrust Chamber Kerosene /Oxygen Primary Rocket Sub-System for an Early (1964) Air-Augmented Rocket Ground-Test System

NASA Technical Reports Server (NTRS)

Pryor, D.; Hyde, E. H.; Escher, W. J. D.

1999-01-01

Airbreathing/Rocket combined-cycle, and specifically rocket-based combined- cycle (RBCC), propulsion systems, typically employ an internal engine flow-path installed primary rocket subsystem. To achieve acceptably short mixing lengths in effecting the "air augmentation" process, a large rocket-exhaust/air interfacial mixing surface is needed. This leads, in some engine design concepts, to a "cluster" of small rocket units, suitably arrayed in the flowpath. To support an early (1964) subscale ground-test of a specific RBCC concept, such a 12-rocket cluster was developed by NASA's Marshall Space Flight Center (MSFC). The small primary rockets used in the cluster assembly were modified versions of an existing small kerosene/oxygen water-cooled rocket engine unit routinely tested at MSFC. Following individual thrust-chamber tests and overall subsystem qualification testing, the cluster assembly was installed at the U. S. Air Force's Arnold Engineering Development Center (AEDC) for RBCC systems testing. (The results of the special air-augmented rocket testing are not covered here.) While this project was eventually successfully completed, a number of hardware integration problems were met, leading to catastrophic thrust chamber failures. The principal "lessons learned" in conducting this early primary rocket subsystem experimental effort are documented here as a basic knowledge-base contribution for the benefit of today's RBCC research and development community.

Final Scientific Report - Electromagnetic Interactions in Self-Assembled Metallo-Dielectric Biomaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dragnea, Bogdan G.

Achievements which resulted from previous DOE funding include: templated virus-like particle assembly thermodynamics, development of single particle photothermal absorption spectroscopy and dark- field spectroscopy instrumentation for the measurement of optical properties of virus-like nanoparticles, electromagnetic simulations of coupled nanoparticle cluster systems, virus contact mechanics, energy transfer and fluorescence quenching in multichromophore systems supported on biomolecular templates, and photo physical work on virus-aptamer systems. A current total of eight published research articles and a book chapter are acknowledging DOE support for the period 2013-2016.

Assembling the Tat protein translocase

PubMed Central

Alcock, Felicity; Stansfeld, Phillip J; Basit, Hajra; Habersetzer, Johann; Baker, Matthew AB; Palmer, Tracy; Wallace, Mark I; Berks, Ben C

2016-01-01

The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues. Unexpectedly, we find that TatA also associates with TatC at the polar cluster site. Our data provide a structural model for assembly of the active Tat translocase in which substrate binding triggers replacement of TatB by TatA at the polar cluster site. Our work demonstrates the power of co-evolution analysis to predict protein interfaces in multi-subunit complexes. DOI: http://dx.doi.org/10.7554/eLife.20718.001 PMID:27914200

Stepwise assembly of a semiconducting coordination polymer [Cd8S(SPh)14(DMF)(bpy)]n and its photodegradation of organic dyes.

PubMed

Xu, Chao; Hedin, Niklas; Shi, Hua-Tian; Xin, ZhiFeng; Zhang, Qian-Feng

2015-04-14

Chalcogenolate clusters can be interlinked with organic linkers into semiconducting coordination polymers with photocatalytic properties. Here, discrete clusters of Cd8S(SPh)14(DMF)3 were interlinked with 4,4'-bipyridine into a one dimensional coordination polymer of [Cd8S(SPh)14(DMF)(bpy)]n with helical chains. A stepwise mechanism for the assembly of the coordination polymer in DMF was revealed by an ex situ dynamic light scattering study. The cluster was electrostatically neutral and showed a penta-supertetrahedral structure. During the assembly each cluster was interlinked with two 4,4'-bipyridine molecules, which replaced the two terminal DMF molecules of the clusters. In their solid-state forms, the cluster and the coordination polymer were semiconductors with wide band gaps of 3.08 and 2.80 ev. They photocatalytically degraded rhodamine B and methylene blue in aqueous solutions. The moderate conditions used for the synthesis could allow for further in situ studies of the reaction-assembly of related clusters and coordination polymers.

Theory and modeling of particles with DNA-mediated interactions

NASA Astrophysics Data System (ADS)

Licata, Nicholas A.

2008-05-01

In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

Cluster-assembled metallic glasses

PubMed Central

2013-01-01

A bottom-up approach to nanofabricate metallic glasses from metal clusters as building blocks is presented. Considering metallic glasses as a subclass of cluster-assembled materials, the relation between the two lively fields of metal clusters and metallic glasses is pointed out. Deposition of selected clusters or collections of them, generated by state-of-the-art cluster beam sources, could lead to the production of a well-defined amorphous material. In contrast to rapidly quenched glasses where only the composition of the glass can be controlled, in cluster-assembled glasses, one can precisely control the structural building blocks. Comparing properties of glasses with similar compositions but differing in building blocks and therefore different in structure will facilitate the study of structure–property correlation in metallic glasses. This bottom-up method provides a novel alternative path to the synthesis of glassy alloys and will contribute to improving fundamental understanding in the field of metallic glasses. It may even permit the production of glassy materials for alloys that cannot be quenched rapidly enough to circumvent crystallization. Additionally, gaining deeper insight into the parameters governing the structure–property relation in metallic glasses can have a great impact on understanding and design of other cluster-assembled materials. PMID:23899019

Mammalian Fe-S proteins: definition of a consensus motif recognized by the co-chaperone HSC20

PubMed Central

Maio, N.; Rouault, T. A.

2017-01-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are fundamental to several biological processes in all three kingdoms of life. In most organisms, Fe-S clusters are initially assembled on a scaffold protein, ISCU, and subsequently transferred to target proteins or to intermediate carriers by a dedicated chaperone/co-chaperone system. The delivery of assembled Fe-S clusters to recipient proteins is a crucial step in the biogenesis of Fe-S proteins, and, in mammals, it relies on the activity of a multiprotein transfer complex that contains the chaperone HSPA9, the co-chaperone HSC20 and the scaffold ISCU. How the transfer complex efficiently engages recipient Fe-S target proteins involves specific protein interactions that are not fully understood. This mini review focuses on recent insights into the molecular mechanism of amino acid motif recognition and discrimination by the co-chaperone HSC20, which guides Fe-S cluster delivery. PMID:27714045

Properties of the gold-sulphur interface: from self-assembled monolayers to clusters

NASA Astrophysics Data System (ADS)

Bürgi, Thomas

2015-09-01

The gold-sulphur interface of self-assembled monolayers (SAMs) was extensively studied some time ago. More recently tremendous progress has been made in the preparation and characterization of thiolate-protected gold clusters. In this feature article we address different properties of the two systems such as their structure, the mobility of the thiolates on the surface and other dynamical aspects, the chirality of the structures and characteristics related to it and their vibrational properties. SAMs and clusters are in the focus of different communities that typically use different experimental approaches to study the respective systems. However, it seems that the nature of the Au-S interfaces in the two cases is quite similar. Recent single crystal X-ray structures of thiolate-protected gold clusters reveal staple motifs characterized by gold ad-atoms sandwiched between two sulphur atoms. This finding contradicts older work on SAMs. However, newer studies on SAMs also reveal ad-atoms. Whether this finding can be generalized remains to be shown. In any case, more and more studies highlight the dynamic nature of the Au-S interface, both on flat surfaces and in clusters. At temperatures slightly above ambient thiolates migrate on the gold surface and on clusters. Evidence for desorption of thiolates at room temperature, at least under certain conditions, has been demonstrated for both systems. The adsorbed thiolate can lead to chirality at different lengths scales, which has been shown both on surfaces and for clusters. Chirality emerges from the organization of the thiolates as well as locally at the molecular level. Chirality can also be transferred from a chiral surface to an adsorbate, as evidenced by vibrational spectroscopy.

Properties of the gold-sulphur interface: from self-assembled monolayers to clusters.

PubMed

Bürgi, Thomas

2015-10-14

The gold-sulphur interface of self-assembled monolayers (SAMs) was extensively studied some time ago. More recently tremendous progress has been made in the preparation and characterization of thiolate-protected gold clusters. In this feature article we address different properties of the two systems such as their structure, the mobility of the thiolates on the surface and other dynamical aspects, the chirality of the structures and characteristics related to it and their vibrational properties. SAMs and clusters are in the focus of different communities that typically use different experimental approaches to study the respective systems. However, it seems that the nature of the Au-S interfaces in the two cases is quite similar. Recent single crystal X-ray structures of thiolate-protected gold clusters reveal staple motifs characterized by gold ad-atoms sandwiched between two sulphur atoms. This finding contradicts older work on SAMs. However, newer studies on SAMs also reveal ad-atoms. Whether this finding can be generalized remains to be shown. In any case, more and more studies highlight the dynamic nature of the Au-S interface, both on flat surfaces and in clusters. At temperatures slightly above ambient thiolates migrate on the gold surface and on clusters. Evidence for desorption of thiolates at room temperature, at least under certain conditions, has been demonstrated for both systems. The adsorbed thiolate can lead to chirality at different lengths scales, which has been shown both on surfaces and for clusters. Chirality emerges from the organization of the thiolates as well as locally at the molecular level. Chirality can also be transferred from a chiral surface to an adsorbate, as evidenced by vibrational spectroscopy.

Structure and Symmetry of Ground States of Colloidal Clusters

NASA Astrophysics Data System (ADS)

Klein, Ellen D.; Rogers, W. Benjamin; Manoharan, Vinothan N.

We experimentally study colloidal clusters consisting of 6 to 100 spherical particles bound together with short range, DNA-mediated attractions. These clusters are a model system for understanding colloidal self-assembly and dynamics, since the positions and motion of all particles can be observed in real space. For 10 particles and fewer, the ground states are degenerate, and, as shown in previous work, the probabilities of observing specific clusters depend primarily on their rotational entropy, which is determined by symmetry. Thus less symmetric structures are more frequently observed. However, for larger numbers of particles the ground states appear to be subsets of close-packed lattices, which tend to have higher symmetry. To understand how this transition occurs as a function of the number of particles, we coat colloidal particles with complementary DNA strands that induce a short-range, temperature-dependent interparticle attraction. We then assemble and anneal an ensemble of clusters with 10 or more particles. We characterize the number of apparent ground states, their symmetries, and their probabilities as a function of the size of the cluster using confocal microscopy. This work is supported by NSF DMR-1306410. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program.

High-throughput shadow mask printing of passive electrical components on paper by supersonic cluster beam deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caruso, Francesco; Bellacicca, Andrea; Milani, Paolo, E-mail: pmilani@mi.infn.it

We report the rapid prototyping of passive electrical components (resistors and capacitors) on plain paper by an additive and parallel technology consisting of supersonic cluster beam deposition (SCBD) coupled with shadow mask printing. Cluster-assembled films have a growth mechanism substantially different from that of atom-assembled ones providing the possibility of a fine tuning of their electrical conduction properties around the percolative conduction threshold. Exploiting the precise control on cluster beam intensity and shape typical of SCBD, we produced, in a one-step process, batches of resistors with resistance values spanning a range of two orders of magnitude. Parallel plate capacitors withmore » paper as the dielectric medium were also produced with capacitance in the range of tens of picofarads. Compared to standard deposition technologies, SCBD allows for a very efficient use of raw materials and the rapid production of components with different shape and dimensions while controlling independently the electrical characteristics. Discrete electrical components produced by SCBD are very robust against deformation and bending, and they can be easily assembled to build circuits with desired characteristics. The availability of large batches of these components enables the rapid and cheap prototyping and integration of electrical components on paper as building blocks of more complex systems.« less

Self-Assembly of Octopus Nanoparticles into Pre-Programmed Finite Clusters

NASA Astrophysics Data System (ADS)

Halverson, Jonathan; Tkachenko, Alexei

2012-02-01

The precise control of the spatial arrangement of nanoparticles (NP) is often required to take full advantage of their novel optical and electronic properties. NPs have been shown to self-assemble into crystalline structures using either patchy surface regions or complementary DNA strands to direct the assembly. Due to a lack of specificity of the interactions these methods lead to only a limited number of structures. An emerging approach is to bind ssDNA at specific sites on the particle surface making so-called octopus NPs. Using octopus NPs we investigate the inverse problem of the self-assembly of finite clusters. That is, for a given target cluster (e.g., arranging the NPs on the vertices of a dodecahedron) what are the minimum number of complementary DNA strands needed for the robust self-assembly of the cluster from an initially homogeneous NP solution? Based on the results of Brownian dynamics simulations we have compiled a set of design rules for various target clusters including cubes, pyramids, dodecahedrons and truncated icosahedrons. Our approach leads to control over the kinetic pathway and has demonstrated nearly perfect yield of the target.

Beyond assembly bias: exploring secondary halo biases for cluster-size haloes

NASA Astrophysics Data System (ADS)

Mao, Yao-Yuan; Zentner, Andrew R.; Wechsler, Risa H.

2018-03-01

Secondary halo bias, commonly known as `assembly bias', is the dependence of halo clustering on a halo property other than mass. This prediction of the Λ Cold Dark Matter cosmology is essential to modelling the galaxy distribution to high precision and interpreting clustering measurements. As the name suggests, different manifestations of secondary halo bias have been thought to originate from halo assembly histories. We show conclusively that this is incorrect for cluster-size haloes. We present an up-to-date summary of secondary halo biases of high-mass haloes due to various halo properties including concentration, spin, several proxies of assembly history, and subhalo properties. While concentration, spin, and the abundance and radial distribution of subhaloes exhibit significant secondary biases, properties that directly quantify halo assembly history do not. In fact, the entire assembly histories of haloes in pairs are nearly identical to those of isolated haloes. In general, a global correlation between two halo properties does not predict whether or not these two properties exhibit similar secondary biases. For example, assembly history and concentration (or subhalo abundance) are correlated for both paired and isolated haloes, but follow slightly different conditional distributions in these two cases. This results in a secondary halo bias due to concentration (or subhalo abundance), despite the lack of assembly bias in the strict sense for cluster-size haloes. Due to this complexity, caution must be exercised in using any one halo property as a proxy to study the secondary bias due to another property.

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

DOE PAGES

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad; ...

2017-10-06

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

A Protein Interaction Map of the Kalimantacin Biosynthesis Assembly Line

PubMed Central

Uytterhoeven, Birgit; Lathouwers, Thomas; Voet, Marleen; Michiels, Chris W.; Lavigne, Rob

2016-01-01

The antimicrobial secondary metabolite kalimantacin (also called batumin) is produced by a hybrid polyketide/non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein–protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites. This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters. PMID:27853452

Elimination-Fusion Self-Assembly of a Nanometer-Scale 72-Nucleus Silver Cluster Caging a Pair of [EuW10 O36 ]9- Polyoxometalates.

PubMed

Zhang, Shan-Shan; Su, Hai-Feng; Wang, Zhi; Wang, Xing-Po; Chen, Wen-Xian; Zhao, Quan-Qin; Tung, Chen-Ho; Sun, Di; Zheng, Lan-Sun

2018-02-06

The largest known polyoxometalate (POM)-templated silver-alkynyl cluster, [(EuW 10 O 36 ) 2 @Ag 72 (tBuC≡C) 48 Cl 2 ⋅4 BF 4 ] (SD/Ag20), was isolated under solvothermal conditions and structurally characterized. It was confirmed by single-crystal X-ray diffraction (SCXRD) as a {EuW 10 } 2 -in-{Ag 72 } clusters-in-cluster rod-like compound. The high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) shows that such a double anion-templated cluster is assembled from a crucial single anion-templated Ag 42 intermediate in the solution. The crystallization of Ag 42 species (SD/Ag21), followed by SCXRD, gave an important clue about the assembly route of SD/Ag20 in solution: the Ag 42 cluster eliminates six silver atoms laterally, then fuses together at the vacant face to form the final Ag 72 cluster (elimination-fusion mechanism). The characteristic emission of [EuW 10 O 36 ] 9- is well maintained in SD/Ag20. This work not only provides a new method for the synthesis of larger silver clusters as well as the functional integration of the silver cluster and POMs, but also gives deep insights about the high-nuclear silver cluster assembly mechanism. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

PubMed

Condon, Joshua E; Jayaraman, Arthi

2017-10-04

Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

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

Regulated Assembly of Vacuolar ATPase Is Increased during Cluster Disruption-induced Maturation of Dendritic Cells through a Phosphatidylinositol 3-Kinase/mTOR-dependent Pathway*

PubMed Central

Liberman, Rachel; Bond, Sarah; Shainheit, Mara G.; Stadecker, Miguel J.; Forgac, Michael

2014-01-01

The vacuolar (H+)-ATPases (V-ATPases) are ATP-driven proton pumps composed of a peripheral V1 domain and a membrane-embedded V0 domain. Regulated assembly of V1 and V0 represents an important regulatory mechanism for controlling V-ATPase activity in vivo. Previous work has shown that V-ATPase assembly increases during maturation of bone marrow-derived dendritic cells induced by activation of Toll-like receptors. This increased assembly is essential for antigen processing, which is dependent upon an acidic lysosomal pH. Cluster disruption of dendritic cells induces a semi-mature phenotype associated with immune tolerance. Thus, semi-mature dendritic cells are able to process and present self-peptides to suppress autoimmune responses. We have investigated V-ATPase assembly in bone marrow-derived, murine dendritic cells and observed an increase in assembly following cluster disruption. This increased assembly is not dependent upon new protein synthesis and is associated with an increase in concanamycin A-sensitive proton transport in FITC-loaded lysosomes. Inhibition of phosphatidylinositol 3-kinase with wortmannin or mTORC1 with rapamycin effectively inhibits the increased assembly observed upon cluster disruption. These results suggest that the phosphatidylinositol 3-kinase/mTOR pathway is involved in controlling V-ATPase assembly during dendritic cell maturation. PMID:24273170

Optical and Photothermal Behaviors of Colloidal and Self-Assembled Magnetic-Plasmonic Nanostructures

NASA Astrophysics Data System (ADS)

Liu, Kai

This dissertation is based on numerous efforts in exploring the capabilties of numerical simulation for investigating novel optical phenomena in different colloidal plasmonic systems. The dissertation includes five chapters. Chapter 1 contains a general introduction to the fundamentals of plasmonic behaviors in colloidal clusters and bottom-up self-assembly methods for manufacturing colloidal clusters which include magnetic based and DNA-assisted pathways. Chapter 2 presents a systematic comparison of optical and thermodynamic properties of near-infrared colloidal nanoparticles, including SiO2 Au core-shell, Au nanocage and Au nanorod, and an example of the nanobubble-based photothermal therapy application. In Chapter 3, a optical phenomenon named Fano resonance is demonstrated in a colloidal heptamer design which consists of seven Fe 3O4 Au core-shell nanoparticles. The incorporation of the magnetic core enables a magnetic-assisted self-assembly process which will be discussed after the photonic analysis. In Chapter 4, the optical behaviors in a 1D magnetic-plasmonic chain are explored. A demonstration of the magnetic-based self-assembly of this 1D chain is given. Chapter 5 is focused on the study of the chiral optical responses in a helical nanoscale system which follows a 3D helical arrangement of Fe3O4 Au core-shell nanoparticles.

Bi cluster-assembled interconnects produced using SU8 templates

NASA Astrophysics Data System (ADS)

Partridge, J. G.; Matthewson, T.; Brown, S. A.

2007-04-01

Bi clusters with an average diameter of 25 nm have been deposited from an inert gas aggregation source and assembled into thin-film interconnects which are formed between planar electrical contacts and supported on Si substrates passivated with Si3N4 or thermally grown oxide. A layer of SU8 (a negative photoresist based on EPON SU-8 epoxy resin) is patterned using optical or electron-beam lithography, and it defines the position and dimensions of the cluster film. The conduction between the contacts is monitored throughout the deposition/assembly process, and subsequent I(V) characterization is performed in situ. Bi cluster-assembled interconnects have been fabricated with nanoscale widths and with up to 1:1 thickness:width aspect ratios. The conductivity of these interconnects has been increased, post-deposition, using a simple thermal annealing process.

Beyond assembly bias: exploring secondary halo biases for cluster-size haloes

DOE PAGES

Mao, Yao-Yuan; Zentner, Andrew R.; Wechsler, Risa H.

2017-12-01

Secondary halo bias, commonly known as ‘assembly bias’, is the dependence of halo clustering on a halo property other than mass. This prediction of the Λ Cold Dark Matter cosmology is essential to modelling the galaxy distribution to high precision and interpreting clustering measurements. As the name suggests, different manifestations of secondary halo bias have been thought to originate from halo assembly histories. We show conclusively that this is incorrect for cluster-size haloes. We present an up-to-date summary of secondary halo biases of high-mass haloes due to various halo properties including concentration, spin, several proxies of assembly history, and subhalomore » properties. While concentration, spin, and the abundance and radial distribution of subhaloes exhibit significant secondary biases, properties that directly quantify halo assembly history do not. In fact, the entire assembly histories of haloes in pairs are nearly identical to those of isolated haloes. In general, a global correlation between two halo properties does not predict whether or not these two properties exhibit similar secondary biases. For example, assembly history and concentration (or subhalo abundance) are correlated for both paired and isolated haloes, but follow slightly different conditional distributions in these two cases. Lastly, this results in a secondary halo bias due to concentration (or subhalo abundance), despite the lack of assembly bias in the strict sense for cluster-size haloes. Due to this complexity, caution must be exercised in using any one halo property as a proxy to study the secondary bias due to another property.« less

Beyond assembly bias: exploring secondary halo biases for cluster-size haloes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Yao-Yuan; Zentner, Andrew R.; Wechsler, Risa H.

Secondary halo bias, commonly known as ‘assembly bias’, is the dependence of halo clustering on a halo property other than mass. This prediction of the Λ Cold Dark Matter cosmology is essential to modelling the galaxy distribution to high precision and interpreting clustering measurements. As the name suggests, different manifestations of secondary halo bias have been thought to originate from halo assembly histories. We show conclusively that this is incorrect for cluster-size haloes. We present an up-to-date summary of secondary halo biases of high-mass haloes due to various halo properties including concentration, spin, several proxies of assembly history, and subhalomore » properties. While concentration, spin, and the abundance and radial distribution of subhaloes exhibit significant secondary biases, properties that directly quantify halo assembly history do not. In fact, the entire assembly histories of haloes in pairs are nearly identical to those of isolated haloes. In general, a global correlation between two halo properties does not predict whether or not these two properties exhibit similar secondary biases. For example, assembly history and concentration (or subhalo abundance) are correlated for both paired and isolated haloes, but follow slightly different conditional distributions in these two cases. Lastly, this results in a secondary halo bias due to concentration (or subhalo abundance), despite the lack of assembly bias in the strict sense for cluster-size haloes. Due to this complexity, caution must be exercised in using any one halo property as a proxy to study the secondary bias due to another property.« less

Role of the HSPA9/HSC20 chaperone pair in promoting directional human iron-sulfur cluster exchange involving monothiol glutaredoxin 5.

PubMed

Olive, Joshua A; Cowan, J A

2018-07-01

Iron‑sulfur clusters are essential cofactors found across all domains of life. Their assembly and transfer are accomplished by highly conserved protein complexes and partners. In eukaryotes a [2Fe-2S] cluster is first assembled in the mitochondria on the iron‑sulfur cluster scaffold protein ISCU in tandem with iron, sulfide, and electron donors. Current models suggest that a chaperone pair interacts with a cluster-bound ISCU to facilitate cluster transfer to a monothiol glutaredoxin. In humans this protein is glutaredoxin 5 (GLRX5) and the cluster can then be exchanged with a variety of target apo proteins. By use of circular dichroism spectroscopy, the kinetics of cluster exchange reactivity has been evaluated for human GLRX5 with a variety of cluster donor and acceptor partners, and the role of chaperones determined for several of these. In contrast to the prokaryotic model, where heat-shock type chaperone proteins HscA and HscB are required for successful and efficient transfer of a [2Fe-2S] cluster from the ISCU scaffold to a monothiol glutaredoxin. However, in the human system the chaperone homologs, HSPA9 and HSC20, are not necessary for human ISCU to promote cluster transfer to GLRX5, and appear to promote the reverse transfer. Cluster exchange with the human iron‑sulfur cluster carrier protein NFU1 and ferredoxins (FDX's), and the role of chaperones, has also been evaluated, demonstrating in certain cases control over the directionality of cluster transfer. In contrast to other prokaryotic and eukaryotic organisms, NFU1 is identified as a more likely physiological donor of [2Fe-2S] cluster to human GLRX5 than ISCU. Copyright © 2018 Elsevier Inc. All rights reserved.

Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

DOEpatents

Alivisatos, A. Paul; Colvin, Vicki L.

1998-01-01

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed.

Daclatasvir Prevents Hepatitis C Virus Infectivity by Blocking Transfer of the Viral Genome to Assembly Sites.

PubMed

Boson, Bertrand; Denolly, Solène; Turlure, Fanny; Chamot, Christophe; Dreux, Marlène; Cosset, François-Loïc

2017-03-01

Daclatasvir is a direct-acting antiviral agent and potent inhibitor of NS5A, which is involved in replication of the hepatitis C virus (HCV) genome, presumably via membranous web shaping, and assembly of new virions, likely via transfer of the HCV RNA genome to viral particle assembly sites. Daclatasvir inhibits the formation of new membranous web structures and, ultimately, of replication complex vesicles, but also inhibits an early assembly step. We investigated the relationship between daclatasvir-induced clustering of HCV proteins, intracellular localization of viral RNAs, and inhibition of viral particle assembly. Cell-culture-derived HCV particles were produced from Huh7.5 hepatocarcinoma cells in presence of daclatasvir for short time periods. Infectivity and production of physical particles were quantified and producer cells were subjected to subcellular fractionation. Intracellular colocalization between core, E2, NS5A, NS4B proteins, and viral RNAs was quantitatively analyzed by confocal microscopy and by structured illumination microscopy. Short exposure of HCV-infected cells to daclatasvir reduced viral assembly and induced clustering of structural proteins with non-structural HCV proteins, including core, E2, NS4B, and NS5A. These clustered structures appeared to be inactive assembly platforms, likely owing to loss of functional connection with replication complexes. Daclatasvir greatly reduced delivery of viral genomes to these core clusters without altering HCV RNA colocalization with NS5A. In contrast, daclatasvir neither induced clustered structures nor inhibited HCV assembly in cells infected with a daclatasvir-resistant mutant (NS5A-Y93H), indicating that daclatasvir targets a mutual, specific function of NS5A inhibiting both processes. In addition to inhibiting replication complex biogenesis, daclatasvir prevents viral assembly by blocking transfer of the viral genome to assembly sites. This leads to clustering of HCV proteins because viral particles and replication complex vesicles cannot form or egress. This dual mode of action of daclatasvir could explain its efficacy in blocking HCV replication in cultured cells and in treatment of patients with HCV infection. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Effector role reversal during evolution: the case of frataxin in Fe-S cluster biosynthesis†

PubMed Central

Bridwell-Rabb, Jennifer; Iannuzzi, Clara; Pastore, Annalisa; Barondeau, David P.

2012-01-01

Human frataxin (FXN) has been intensively studied since the discovery that the FXN gene is associated with the neurodegenerative disease Friedreich’s ataxia. Human FXN is a component of the NFS1-ISD11-ISCU2-FXN (SDUF) core Fe-S assembly complex and activates the cysteine desulfurase and Fe-S cluster biosynthesis reactions. In contrast, the Escherichia coli FXN homolog CyaY inhibits Fe-S cluster biosynthesis. To resolve this discrepancy, enzyme kinetic experiments were performed for the human and E. coli systems in which analogous cysteine desulfurase, Fe-S assembly scaffold, and frataxin components were interchanged. Surprisingly, our results reveal that activation or inhibition by the frataxin homolog is determined by which cysteine desulfurase is present and not by the identity of the frataxin homolog. These data are consistent with a model in which the frataxin-less Fe-S assembly complex exists as a mixture of functional and nonfunctional states, which are stabilized by binding of frataxin homologs. Intriguingly, this appears to be an unusual example in which modifications to an enzyme during evolution inverts or reverses the mode of control imparted by a regulatory molecule. PMID:22352884

Effector role reversal during evolution: the case of frataxin in Fe-S cluster biosynthesis.

PubMed

Bridwell-Rabb, Jennifer; Iannuzzi, Clara; Pastore, Annalisa; Barondeau, David P

2012-03-27

Human frataxin (FXN) has been intensively studied since the discovery that the FXN gene is associated with the neurodegenerative disease Friedreich's ataxia. Human FXN is a component of the NFS1-ISD11-ISCU2-FXN (SDUF) core Fe-S assembly complex and activates the cysteine desulfurase and Fe-S cluster biosynthesis reactions. In contrast, the Escherichia coli FXN homologue CyaY inhibits Fe-S cluster biosynthesis. To resolve this discrepancy, enzyme kinetic experiments were performed for the human and E. coli systems in which analogous cysteine desulfurase, Fe-S assembly scaffold, and frataxin components were interchanged. Surprisingly, our results reveal that activation or inhibition by the frataxin homologue is determined by which cysteine desulfurase is present and not by the identity of the frataxin homologue. These data are consistent with a model in which the frataxin-less Fe-S assembly complex exists as a mixture of functional and nonfunctional states, which are stabilized by binding of frataxin homologues. Intriguingly, this appears to be an unusual example in which modifications to an enzyme during evolution inverts or reverses the mode of control imparted by a regulatory molecule.

Yeast Mitoribosome Large Subunit Assembly Proceeds by Hierarchical Incorporation of Protein Clusters and Modules on the Inner Membrane.

PubMed

Zeng, Rui; Smith, Erin; Barrientos, Antoni

2018-03-06

Mitoribosomes are specialized for the synthesis of hydrophobic membrane proteins encoded by mtDNA, all essential for oxidative phosphorylation. Despite their linkage to human mitochondrial diseases and the recent cryoelectron microscopy reconstruction of yeast and mammalian mitoribosomes, how they are assembled remains obscure. Here, we dissected the yeast mitoribosome large subunit (mtLSU) assembly process by systematic genomic deletion of 44 mtLSU proteins (MRPs). Analysis of the strain collection unveiled 37 proteins essential for functional mtLSU assembly, three of which are critical for mtLSU 21S rRNA stability. Hierarchical cluster analysis of mtLSU subassemblies accumulated in mutant strains revealed co-operative assembly of protein sets forming structural clusters and preassembled modules. It also indicated crucial roles for mitochondrion-specific membrane-binding MRPs in anchoring newly transcribed 21S rRNA to the inner membrane, where assembly proceeds. Our results define the yeast mtLSU assembly landscape in vivo and provide a foundation for studies of mitoribosome assembly across evolution. Copyright © 2018 Elsevier Inc. All rights reserved.

The nanocoherer: an electrically and mechanically resettable resistive switching device based on gold clusters assembled on paper

NASA Astrophysics Data System (ADS)

Minnai, Chloé; Mirigliano, Matteo; Brown, Simon A.; Milani, Paolo

2018-03-01

We report the realization of a resettable resistive switching device based on a nanostructured film fabricated by supersonic cluster beam deposition of gold clusters on plain paper substrates. Through the application of suitable voltage ramps, we obtain, in the same device, either a complex pattern of resistive switchings, or reproducible and stable switchings between low resistance and high resistance states, with an amplitude up to five orders of magnitude. Our device retains a state of internal resistance following the history of the applied voltage similar to that reported for memristors. The two different switching regimes in the same device are both stable, the transition between them is reversible, and it can be controlled by applying voltage ramps or by mechanical deformation of the substrate. The device behavior can be related to the formation, growth and breaking of junctions between the loosely aggregated gold clusters forming the nanostructured films. The fact that our cluster-assembled device is mechanically resettable suggests that it can be considered as the analog of the coherer: a switching device based on metallic powders used for the first radio communication system.

Correction to: Fe-S cluster assembly in the supergroup Excavata.

PubMed

Peña-Diaz, Priscila; Lukeš, Julius

2018-05-29

The article "Fe-S cluster assembly in the supergroup Excavata", written by Priscila Peña‑Diaz, Julius Lukeš was originally published electronically on the publisher's internet portal (currently SpringerLink) without open access.

Linker-mediated assembly of gold nanoparticles into multimeric motifs

NASA Astrophysics Data System (ADS)

Sikora, Mateusz; Szymczak, Piotr; Thompson, Damien; Cieplak, Marek

2011-11-01

We present a theoretical description of linker-mediated self-assembly of gold nanoparticles (Au-NP). Using mesoscale simulations with a coarse-grained model for the Au NPs and dirhenium-based linker molecules, we investigate the conditions under which large clusters can grow and construct a phase diagram that identifies favorable growth conditions in terms of floating and bound linker concentrations. The findings can be considered as generic, as we expect other NP-linker systems to behave in a qualitatively similar way. In particular, we also discuss the case of antibody-functionalised Au NPs connected by the C-reactive proteins (CRPs). We extract some general rules for NP linking that may aid the production of size- and shape-specific NP clusters for technology applications.

Recent advances in the Suf Fe-S cluster biogenesis pathway: Beyond the Proteobacteria

PubMed Central

Outten, F. Wayne

2014-01-01

Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. PMID:25447545

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

2009-04-02

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.

Growth-dissolution-regrowth transitions of Fe3O4 nanoparticles as building blocks for 3D magnetic nanoparticle clusters under hydrothermal conditions.

PubMed

Lin, Mouhong; Huang, Haoliang; Liu, Zuotao; Liu, Yingju; Ge, Junbin; Fang, Yueping

2013-12-10

Magnetic nanoparticle clusters (MNCs) are a class of secondary structural materials that comprise chemically defined nanoparticles assembled into clusters of defined size. Herein, MNCs are fabricated through a one-pot solvothermal reaction featuring self-limiting assembly of building blocks and the controlled reorganization process. Such growth-dissolution-regrowth fabrication mechanism overcomes some limitations of conventional solvothermal fabrication methods with regard to restricted available feature size and structural complexity, which can be extended to other oxides (as long as one can be chelated by EDTA-2Na). Based on this method, the nanoparticle size of MNCs is tuned between 6.8 and 31.2 nm at a fixed cluster diameter of 120 nm, wherein the critical size for superparamagnetic-ferromagnetic transition is estimated from 13.5 to 15.7 nm. Control over the nature and secondary structure of MNCs gives an excellent model system to understand the nanoparticle size-dependent magnetic properties of MNCs. MNCs have potential applications in many different areas, while this work evaluates their cytotoxicity and Pb(2+) adsorption capacity as initial application study.

Structure and dynamics of optically directed self-assembly of nanoparticles

PubMed Central

Roy, Debjit; Mondal, Dipankar; Goswami, Debabrata

2016-01-01

Self-assembly of nanoparticles leading to the formation of colloidal clusters often serves as the representative analogue for understanding molecular assembly. Unravelling the in situ structure and dynamics of such clusters in liquid suspensions is highly challenging. Presently colloidal clusters are first isolated from their generating environment and then their structures are probed by light scattering methods. In order to measure the in situ structure and dynamics of colloidal clusters, we have generated them using the high-repetition-rate femtosecond laser pulse optical tweezer. Since the constituent of our dimer, trimer or tetramer clusters are 250 nm radius two-photon resonant fluorophore coated nanospheres under the optical trap, they inherently produce Two-Photon Fluorescence, which undergo intra-nanosphere Fluorescence Energy Transfer. This unique energy transfer signature, in turn, enables us to visualize structures and orientations of these colloidal clusters during the process of their formation and subsequent dynamics in a liquid suspension. We also show that due to shape-birefringence, orientation and structural control of these colloidal clusters are possible as the polarization of the trapping laser is changed from linear to circular. We thus report important progress in sampling the smallest possible aggregates of nanoparticles, dimers, trimers or tetramers, formed early in the self-assembly process. PMID:27006305

Does aspartate 170 of the D1 polypeptide ligate the manganese cluster in photosystem II? An EPR and ESEEM Study.

PubMed

Debus, Richard J; Aznar, Constantino; Campbell, Kristy A; Gregor, Wolfgang; Diner, Bruce A; Britt, R David

2003-09-16

Aspartate 170 of the D1 polypeptide provides part of the high-affinity binding site for the first Mn(II) ion that is photooxidized during the light-driven assembly of the (Mn)(4) cluster in photosystem II [Campbell, K. A., Force, D. A., Nixon, P. J., Dole, F., Diner, B. A., and Britt, R. D. (2000) J. Am. Chem. Soc. 122, 3754-3761]. However, despite a wealth of data on D1-Asp170 mutants accumulated over the past decade, there is no consensus about whether this residue ligates the assembled (Mn)(4) cluster. To address this issue, we have conducted an EPR and ESEEM (electron spin-echo envelope modulation) study of D1-D170H PSII particles purified from the cyanobacterium Synechocystis sp. PCC 6803. The line shapes of the S(1) and S(2) state multiline EPR signals of D1-D170H PSII particles are unchanged from those of wild-type PSII particles, and the signal amplitudes correlate approximately with the lower O(2) evolving activity of the mutant PSII particles (40-60% compared to that of the wild type). These data provide further evidence that the assembled (Mn)(4) clusters in D1-D170H cells function normally, even though the assembly of the (Mn)(4) cluster is inefficient in this mutant. In the two-pulse frequency domain ESEEM spectrum of the 9.2 GHz S(2) state multiline EPR signal of D1-D170H PSII particles, the histidyl nitrogen modulation observed at 4-5 MHz is unchanged from that of wild-type PSII particles and no significant new modulation is observed. Three scenarios are presented to explain this result. (1) D1-Asp170 ligates the assembled (Mn)(4) cluster, but the hyperfine couplings to the ligating histidyl nitrogen of D1-His170 are too large or anisotropic to be detected by ESEEM analyses conducted at 9.2 GHz. (2) D1-Asp170 ligates the assembled (Mn)(4) cluster, but D1-His170 does not. (3) D1-Asp170 does not ligate the assembled (Mn)(4) cluster.

Cluster-assembled materials based on M12N12 (M = Al, Ga) fullerene-like clusters.

PubMed

Yong, Yongliang; Song, Bin; He, Pimo

2011-09-28

We report the results of density functional theory calculations on cluster-assembled materials based on M(12)N(12) (M = Al, Ga) fullerene-like clusters. Our results show that the M(12)N(12) fullerene-like structure with six isolated four-membered rings (4NRs) and eight six-membered rings (6NRs) has a T(h) symmetry and a large HOMO-LUMO gap, indicating that the M(12)N(12) cluster would be ideal building blocks for the synthesis of cluster-assembled materials. Via the coalescence of M(12)N(12) building blocks, we find that the M(12)N(12) clusters can bind into stable assemblies by either 6NR or 4NR face coalescence, which enables the construction of rhombohedral or cubic nanoporous framework of varying porosity. The rhombohedral-MN phase is energetically more favorable than the cubic-MN phase. The M(12)N(12) fullerene-like structures in both phases are maintained and the M-N bond lengths between M(12)N(12) monomers are slightly larger than that in isolated M(12)N(12) clusters and the bulk wurtzite phases. The band analysis of both phases reveals that they are all wide-gap semiconductors. Because of the nanoporous character of these phases, they could be used for gas storage, heterogeneous catalysis, filtration and so on.

Particle-based simulations of bilayer membranes: self-assembly, structural analysis, and shock-wave damage

NASA Astrophysics Data System (ADS)

Steinhauser, Martin O.; Schindler, Tanja

2017-01-01

We report on the results of particle-based, coarse-grained molecular dynamics simulations of amphiphilic lipid molecules in aqueous environment where the membrane structures at equilibrium are subsequently exposed to strong shock waves, and their damage is analyzed. The lipid molecules self-assemble from unbiased random initial configurations to form stable bilayer membranes, including closed vesicles. During self-assembly of lipid molecules, we observe several stages of clustering, starting with many small clusters of lipids, gradually merging together to finally form one single bilayer membrane. We find that the clustering of lipids sensitively depends on the hydrophobic interaction h_c of the lipid tails in our model and on temperature T of the system. The self-assembled bilayer membranes are quantitatively analyzed at equilibrium with respect to their degree of order and their local structure. We also show that—by analyzing the membrane fluctuations and using a linearized theory— we obtain area compression moduli K_A and bending stiffnesses κ _B for our bilayer membranes which are within the experimental range of in vivo and in vitro measurements of biological membranes. We also discuss the density profile and the pair correlation function of our model membranes at equilibrium which has not been done in previous studies of particle-based membrane models. Furthermore, we present a detailed phase diagram of our lipid model that exhibits a sol-gel transition between quasi-solid and fluid domains, and domains where no self-assembly of lipids occurs. In addition, we present in the phase diagram the conditions for temperature T and hydrophobicity h_c of the lipid tails of our model to form closed vesicles. The stable bilayer membranes obtained at equilibrium are then subjected to strong shock waves in a shock tube setup, and we investigate the damage in the membranes due to their interaction with shock waves. Here, we find a transition from self-repairing membranes (reducing their damage after impact) and permanent (irreversible) damage, depending on the shock front speed. The here presented idea of using coarse-grained (CG) particle models for soft matter systems in combination with the investigation of shock-wave effects in these systems is a quite new approach.

Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

DOEpatents

Alivisatos, A.P.; Colvin, V.L.

1998-05-12

Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed. 10 figs.

Supra-Nanoparticle Functional Assemblies through Programmable Stacking

DOE PAGES

Tian, Cheng; Cordeiro, Marco Aurelio L.; Lhermitte, Julien; ...

2017-05-25

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. We report a general method of assembling nanoparticles in a linear “pillar” morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization.more » Furthermore, by controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.« less

Supra-Nanoparticle Functional Assemblies through Programmable Stacking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Cheng; Cordeiro, Marco Aurelio L.; Lhermitte, Julien

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. We report a general method of assembling nanoparticles in a linear “pillar” morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization.more » Furthermore, by controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.« less

Supra-Nanoparticle Functional Assemblies through Programmable Stacking.

PubMed

Tian, Cheng; Cordeiro, Marco Aurelio L; Lhermitte, Julien; Xin, Huolin L; Shani, Lior; Liu, Mingzhao; Ma, Chunli; Yeshurun, Yosef; DiMarzio, Donald; Gang, Oleg

2017-07-25

The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. Here, we report a general method of assembling nanoparticles in a linear "pillar" morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization. By controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.

Effect of Self-Assembly of Fullerene Nano-Particles on Lipid Membrane

PubMed Central

Zhang, Saiqun; Mu, Yuguang; Zhang, John Z. H.; Xu, Weixin

2013-01-01

Carbon nanoparticles can penetrate the cell membrane and cause cytotoxicity. The diffusion feature and translocation free energy of fullerene through lipid membranes is well reported. However, the knowledge on self-assembly of fullerenes and resulting effects on lipid membrane is poorly addressed. In this work, the self-assembly of fullerene nanoparticles and the resulting influence on the dioleoylphosphtidylcholine (DOPC) model membrane were studied by using all-atom molecular dynamics simulations with explicit solvents. Our simulation results confirm that gathered small fullerene cluster can invade lipid membrane. Simulations show two pathways: 1) assembly process is completely finished before penetration; 2) assembly process coincides with penetration. Simulation results also demonstrate that in the membrane interior, fullerene clusters tend to stay at the position which is 1.0 nm away from the membrane center. In addition, the diverse microscopic stacking mode (i.e., equilateral triangle, tetrahedral pentahedral, trigonal bipyramid and octahedron) of these small fullerene clusters are well characterized. Thus our simulations provide a detailed high-resolution characterization of the microscopic structures of the small fullerene clusters. Further, we found the gathered small fullerene clusters have significant adverse disturbances to the local structure of the membrane, but no great influence on the global integrity of the lipid membrane, which suggests the prerequisite of high-content fullerene for cytotoxicity. PMID:24204827

Wide-field Precision Kinematics of the M87 Globular Cluster System

NASA Astrophysics Data System (ADS)

Strader, Jay; Romanowsky, Aaron J.; Brodie, Jean P.; Spitler, Lee R.; Beasley, Michael A.; Arnold, Jacob A.; Tamura, Naoyuki; Sharples, Ray M.; Arimoto, Nobuo

2011-12-01

We present the most extensive combined photometric and spectroscopic study to date of the enormous globular cluster (GC) system around M87, the central giant elliptical galaxy in the nearby Virgo Cluster. Using observations from DEIMOS and the Low Resolution Imaging Spectrometer at Keck, and Hectospec on the Multiple Mirror Telescope, we derive new, precise radial velocities for 451 GCs around M87, with projected radii from ~5 to 185 kpc. We combine these measurements with literature data for a total sample of 737 objects, which we use for a re-examination of the kinematics of the GC system of M87. The velocities are analyzed in the context of archival wide-field photometry and a novel Hubble Space Telescope catalog of half-light radii, which includes sizes for 344 spectroscopically confirmed clusters. We use this unique catalog to identify 18 new candidate ultracompact dwarfs and to help clarify the relationship between these objects and true GCs. We find much lower values for the outer velocity dispersion and rotation of the GC system than in earlier papers and also differ from previous work in seeing no evidence for a transition in the inner halo to a potential dominated by the Virgo Cluster, nor for a truncation of the stellar halo. We find little kinematical evidence for an intergalactic GC population. Aided by the precision of the new velocity measurements, we see significant evidence for kinematical substructure over a wide range of radii, indicating that M87 is in active assembly. A simple, scale-free analysis finds less dark matter within ~85 kpc than in other recent work, reducing the tension between X-ray and optical results. In general, out to a projected radius of ~150 kpc, our data are consistent with the notion that M87 is not dynamically coupled to the Virgo Cluster; the core of Virgo may be in the earliest stages of assembly.

Atomic scale simulations of vapor cooled carbon clusters

NASA Astrophysics Data System (ADS)

Bogana, M. P.; Colombo, L.

2007-03-01

By means of atomistic simulations we observed the formation of many topologically non-equivalent carbon clusters formed by the condensation of liquid droplets, including: (i) standard fullerenes and onion-like structures, (ii) clusters showing extremely complex surfaces with both positive and negative curvatures and (iii) complex endohedral structures. In this work we offer a thorough structural characterization of the above systems, as well as an attempt to correlate the resulting structure to the actual protocol of growth. The IR and Raman responses of some exotic linear carbon structures have been further investigated, finding good agreement with experimental evidence of carbinoid structures in cluster-assembled films. Towards the aim of fully understanding the process of cluster-to-cluster coalescence dynamics, we further simulated an aerosol of amorphous carbon clusters at controlled temperatures. Various annealing temperatures and times have been observed, identifying different pathways for cluster ripening, ranging from simple coalescence to extensive reconstruction.

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.

Haspin kinase regulates microtubule-organizing center clustering and stability through Aurora kinase C in mouse oocytes.

PubMed

Balboula, Ahmed Z; Nguyen, Alexandra L; Gentilello, Amanda S; Quartuccio, Suzanne M; Drutovic, David; Solc, Petr; Schindler, Karen

2016-10-01

Meiotic oocytes lack classic centrosomes and, therefore, bipolar spindle assembly depends on clustering of acentriolar microtubule-organizing centers (MTOCs) into two poles. However, the molecular mechanism regulating MTOC assembly into two poles is not fully understood. The kinase haspin (also known as GSG2) is required to regulate Aurora kinase C (AURKC) localization at chromosomes during meiosis I. Here, we show that inhibition of haspin perturbed MTOC clustering into two poles and the stability of the clustered MTOCs. Furthermore, we show that AURKC localizes to MTOCs in mouse oocytes. Inhibition of haspin perturbed the localization of AURKC at MTOCs, and overexpression of AURKC rescued the MTOC-clustering defects in haspin-inhibited oocytes. Taken together, our data uncover a role for haspin as a regulator of bipolar spindle assembly by regulating AURKC function at acentriolar MTOCs in oocytes. © 2016. Published by The Company of Biologists Ltd.

A novel cluster-tube self-adaptive robot hand.

PubMed

Fu, Hong; Yang, Haokun; Song, Weishu; Zhang, Wenzeng

2017-01-01

This paper proposes a novel cluster-tube self-adaptive robot hand (CTSA Hand). The CTSA Hand consists of a base, a motor, a transmission mechanism, multiple elastic tendons, and a group of sliding-tube assemblies. Each sliding-tube assembly is composed of a sliding tube, a guide rod, two springs and a hinge. When the hand grasping an object, the object pushes some sliding tubes to different positions according to the surface shape of the object, the motor pulls the tendons tight to cluster tubes. The CTSA Hand can realize self-adaptive grasping of objects of different sizes and shapes. The CTSA Hand can grasp multiple objects simultaneously because the grasping of the hand acts as many grippers in different directions and heights. The grasping forces of the hand are adjusted by a closed-loop control system with potentiometer. Experimental results show that the CTSA Hand has the features of highly self-adaption and large grasping forces when grasping various objects.

Posttranslational stability of the heme biosynthetic enzyme ferrochelatase is dependent on iron availability and intact iron-sulfur cluster assembly machinery

PubMed Central

Crooks, Daniel R.; Ghosh, Manik C.; Haller, Ronald G.; Tong, Wing-Hang

2010-01-01

Mammalian ferrochelatase, the terminal enzyme in the heme biosynthetic pathway, possesses an iron-sulfur [2Fe-2S] cluster that does not participate in catalysis. We investigated ferrochelatase expression in iron-deficient erythropoietic tissues of mice lacking iron regulatory protein 2, in iron-deficient murine erythroleukemia cells, and in human patients with ISCU myopathy. Ferrochelatase activity and protein levels were dramatically decreased in Irp2−/− spleens, whereas ferrochelatase mRNA levels were increased, demonstrating posttranscriptional regulation of ferrochelatase in vivo. Translation of ferrochelatase mRNA was unchanged in iron-depleted murine erythroleukemia cells, and the stability of mature ferrochelatase protein was also unaffected. However, the stability of newly formed ferrochelatase protein was dramatically decreased during iron deficiency. Ferrochelatase was also severely depleted in muscle biopsies and cultured myoblasts from patients with ISCU myopathy, a disease caused by deficiency of a scaffold protein required for Fe-S cluster assembly. Together, these data suggest that decreased Fe-S cluster availability because of cellular iron depletion or impaired Fe-S cluster assembly causes reduced maturation and stabilization of apo-ferrochelatase, providing a direct link between Fe-S biogenesis and completion of heme biosynthesis. We propose that decreased heme biosynthesis resulting from impaired Fe-S cluster assembly can contribute to the pathogenesis of diseases caused by defective Fe-S cluster biogenesis. PMID:19965627

Testing the Large-scale Environments of Cool-core and Non-cool-core Clusters with Clustering Bias

NASA Astrophysics Data System (ADS)

Medezinski, Elinor; Battaglia, Nicholas; Coupon, Jean; Cen, Renyue; Gaspari, Massimo; Strauss, Michael A.; Spergel, David N.

2017-02-01

There are well-observed differences between cool-core (CC) and non-cool-core (NCC) clusters, but the origin of this distinction is still largely unknown. Competing theories can be divided into internal (inside-out), in which internal physical processes transform or maintain the NCC phase, and external (outside-in), in which the cluster type is determined by its initial conditions, which in turn leads to different formation histories (I.e., assembly bias). We propose a new method that uses the relative assembly bias of CC to NCC clusters, as determined via the two-point cluster-galaxy cross-correlation function (CCF), to test whether formation history plays a role in determining their nature. We apply our method to 48 ACCEPT clusters, which have well resolved central entropies, and cross-correlate with the SDSS-III/BOSS LOWZ galaxy catalog. We find that the relative bias of NCC over CC clusters is b = 1.42 ± 0.35 (1.6σ different from unity). Our measurement is limited by the small number of clusters with core entropy information within the BOSS footprint, 14 CC and 34 NCC clusters. Future compilations of X-ray cluster samples, combined with deep all-sky redshift surveys, will be able to better constrain the relative assembly bias of CC and NCC clusters and determine the origin of the bimodality.

Testing the Large-scale Environments of Cool-core and Non-cool-core Clusters with Clustering Bias

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medezinski, Elinor; Battaglia, Nicholas; Cen, Renyue

2017-02-10

There are well-observed differences between cool-core (CC) and non-cool-core (NCC) clusters, but the origin of this distinction is still largely unknown. Competing theories can be divided into internal (inside-out), in which internal physical processes transform or maintain the NCC phase, and external (outside-in), in which the cluster type is determined by its initial conditions, which in turn leads to different formation histories (i.e., assembly bias). We propose a new method that uses the relative assembly bias of CC to NCC clusters, as determined via the two-point cluster-galaxy cross-correlation function (CCF), to test whether formation history plays a role in determiningmore » their nature. We apply our method to 48 ACCEPT clusters, which have well resolved central entropies, and cross-correlate with the SDSS-III/BOSS LOWZ galaxy catalog. We find that the relative bias of NCC over CC clusters is b = 1.42 ± 0.35 (1.6 σ different from unity). Our measurement is limited by the small number of clusters with core entropy information within the BOSS footprint, 14 CC and 34 NCC clusters. Future compilations of X-ray cluster samples, combined with deep all-sky redshift surveys, will be able to better constrain the relative assembly bias of CC and NCC clusters and determine the origin of the bimodality.« less

Study of cluster formation in a quasi-square well model of Janus ellipsoids

NASA Astrophysics Data System (ADS)

Ruth, Donovan; Rickman, Jeffrey; Gunton, James; Li, Wei

2014-03-01

We investigate the effect of geometry and range of attractive interaction on the self-assembly of Janus particles. In particular, we consider Janus spheroids with an aspect ratio of 0.6 and a quasi-square well model with a short range attractive interaction of 0.2 sigma where sigma is the characteristic length of the spheroid. We find that below a certain transition temperature the system forms orientationally ordered micelles and vesicles, with a cluster distribution qualitatively similar to that found in an earlier study of Janus spheres. (Phys. Chem. Chem. Phys. (2010) vol 12, 11869-11877, F. Sciortino, A. Giacometti and G. Pastore) Finally we discuss the implications of our work for encapsulation by self-assembly. Acknowledgement: This work was supported by a grant from the Mathers Foundation.

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.

Clustering effects in ionic polymers: Molecular dynamics simulations.

PubMed

Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S

2015-08-01

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. 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. Decrease in electrostatic interaction significantly enhances the mobility of the polymer.

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

Design of hydrophobic polyoxometalate hybrid assemblies beyond surfactant encapsulation.

PubMed

Song, Yu-Fei; McMillan, Nicola; Long, De-Liang; Thiel, Johannes; Ding, Yulong; Chen, Haisheng; Gadegaard, Nikolaj; Cronin, Leroy

2008-01-01

Grafting of C-6, C-16 and C-18 alkyl chains onto the hydrophilic Mn-Anderson clusters (compounds 2-4) has been achieved. Exchange of the tetrabutyl ammonium (TBA) with dimethyldioctadecyl ammonium (DMDOA) results in the formation of new polyoxometalate (POM) assemblies (compounds 5-6), in which the POM cores are covalently functionalized by hydrophilic alkyl-chains and enclosed by surfactant of DMDOABr. As a result, we have been able to design and synthesize POM-containing hydrophobic materials beyond surfactant encapsulation. In solid state, scanning electron and transmission electron microscopy (SEM and TEM) studies of the TBA salts of compounds 3 and 4 show highly ordered, uniform, reproducible assemblies with unique segmented rodlike morphology. SEM and TEM studies of the DMDOA salts of compounds 5 and 6 show that they form spherical and sea urchin 3D objects in different solvent systems. In solution, the physical properties of compound 5 and 6 (combination of surfactant-encapsulated cluster (SEC) and surface-grafted cluster (SGC)) show a liquid-to-gel phase transition in pure chloroform below 0 degrees C, which are much lower than other reported SECs. By utilizing light scattering measurements, the nanoparticle size for compounds 5 and 6 were measured at 5 degrees C and 30 degrees C, respectively. Other physical properties including differential scanning calorimetry have been reported.

EVIDENCE FOR AN ACCRETION ORIGIN FOR THE OUTER HALO GLOBULAR CLUSTER SYSTEM OF M31

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mackey, A. D.; Huxor, A. P.; Ferguson, A. M. N.

2010-07-01

We use a sample of newly discovered globular clusters from the Pan-Andromeda Archaeological Survey (PAndAS) in combination with previously cataloged objects to map the spatial distribution of globular clusters in the M31 halo. At projected radii beyond {approx}30 kpc, where large coherent stellar streams are readily distinguished in the field, there is a striking correlation between these features and the positions of the globular clusters. Adopting a simple Monte Carlo approach, we test the significance of this association by computing the probability that it could be due to the chance alignment of globular clusters smoothly distributed in the M31 halo.more » We find that the likelihood of this possibility is low, below 1%, and conclude that the observed spatial coincidence between globular clusters and multiple tidal debris streams in the outer halo of M31 reflects a genuine physical association. Our results imply that the majority of the remote globular cluster system of M31 has been assembled as a consequence of the accretion of cluster-bearing satellite galaxies. This constitutes the most direct evidence to date that the outer halo globular cluster populations in some galaxies are largely accreted.« less

Recent advances in the Suf Fe-S cluster biogenesis pathway: Beyond the Proteobacteria.

PubMed

Outten, F Wayne

2015-06-01

Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases. Copyright © 2014 Elsevier B.V. All rights reserved.

Cluster analysis in systems of magnetic spheres and cubes

NASA Astrophysics Data System (ADS)

Pyanzina, E. S.; Gudkova, A. V.; Donaldson, J. G.; Kantorovich, S. S.

2017-06-01

In the present work we use molecular dynamics simulations and graph-theory based cluster analysis to compare self-assembly in systems of magnetic spheres, and cubes where the dipole moment is oriented along the side of the cube in the [001] crystallographic direction. We show that under the same conditions cubes aggregate far less than their spherical counterparts. This difference can be explained in terms of the volume of phase space in which the formation of the bond is thermodynamically advantageous. It follows that this volume is much larger for a dipolar sphere than for a dipolar cube.

Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

PubMed

Cory, Seth A; Van Vranken, Jonathan G; Brignole, Edward J; Patra, Shachin; Winge, Dennis R; Drennan, Catherine L; Rutter, Jared; Barondeau, David P

2017-07-03

In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.

CYP76M7 Is an ent-Cassadiene C11α-Hydroxylase Defining a Second Multifunctional Diterpenoid Biosynthetic Gene Cluster in Rice[W][OA

PubMed Central

Swaminathan, Sivakumar; Morrone, Dana; Wang, Qiang; Fulton, D. Bruce; Peters, Reuben J.

2009-01-01

Biosynthetic gene clusters are common in microbial organisms, but rare in plants, raising questions regarding the evolutionary forces that drive their assembly in multicellular eukaryotes. Here, we characterize the biochemical function of a rice (Oryza sativa) cytochrome P450 monooxygenase, CYP76M7, which seems to act in the production of antifungal phytocassanes and defines a second diterpenoid biosynthetic gene cluster in rice. This cluster is uniquely multifunctional, containing enzymatic genes involved in the production of two distinct sets of phytoalexins, the antifungal phytocassanes and antibacterial oryzalides/oryzadiones, with the corresponding genes being subject to distinct transcriptional regulation. The lack of uniform coregulation of the genes within this multifunctional cluster suggests that this was not a primary driving force in its assembly. However, the cluster is dedicated to specialized metabolism, as all genes in the cluster are involved in phytoalexin metabolism. We hypothesize that this dedication to specialized metabolism led to the assembly of the corresponding biosynthetic gene cluster. Consistent with this hypothesis, molecular phylogenetic comparison demonstrates that the two rice diterpenoid biosynthetic gene clusters have undergone independent elaboration to their present-day forms, indicating continued evolutionary pressure for coclustering of enzymatic genes encoding components of related biosynthetic pathways. PMID:19825834

Separate Fe-S Scaffold And Carrier Functions For SufB2C2 And SufA During In Vitro Maturation Of [2Fe-2S] Fdx

PubMed Central

Chahal, Harsimranjit K.; Outten, F. Wayne

2012-01-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors required for a variety of biological processes. In vivo biogenesis of Fe-S clusters proceeds via complex pathways involving multiple protein complexes. In the Suf Fe-S cluster biogenesis system, SufB may be a scaffold for nascent Fe-S cluster assembly whereas SufA is proposed to act as either a scaffold or an Fe-S cluster carrier from the scaffold to target apo-proteins. However, SufB can form multiple stable complexes with other Suf proteins, such as SufB2C2 and SufBC2D and the specific functions of these complexes in Fe-S cluster assembly are not clear. Here we compare the ability of the SufB2C2 and SufBC2D complexes as well as SufA to promote in vitro maturation of the [2Fe-2S] ferredoxin (Fdx). We found that SufB2C2 was most proficient as a scaffold for de novo assembly of holo-Fdx using sulfide and iron as freely available building blocks while SufA was best at direct transfer of a pre-formed Fe-S cluster to Fdx. Furthermore, cluster transfer from [4Fe-4S] SufB2C2 or SufBC2D to Fdx will proceed through a SufA intermediate to Fdx is SufA is present. Finally, addition of ATP repressed cluster transfer from [4Fe-4S] SufB2C2 to Fdx and from SufBC2D to [2Fe-2S] SufA or Fdx. These studies indicate that SufB2C2 can serve as a terminal scaffold to load the SufA Fe-S cluster carrier for in vitro maturation of [2Fe-2S] enzymes like Fdx. This work is the first to systematically compare the cluster transfer rates of a scaffold (SufB) to the transfer rates of a carrier (SufA) under the same conditions to the same target enzyme and is also the first to reconstitute the full transfer pathway (from scaffold to carrier to target enzyme) in a single reaction. PMID:23018275

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.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Self-catalyzed growth of S layers via an amorphous-to-crystalline transition limited by folding kinetics.

PubMed

Chung, Sungwook; Shin, Seong-Ho; Bertozzi, Carolyn R; De Yoreo, James J

2010-09-21

The importance of nonclassical, multistage crystallization pathways is increasingly evident from theoretical studies on colloidal systems and experimental investigations of proteins and biomineral phases. Although theoretical predictions suggest that proteins follow these pathways as a result of fluctuations that create unstable dense-liquid states, microscopic studies indicate these states are long-lived. Using in situ atomic force microscopy to follow 2D assembly of S-layer proteins on supported lipid bilayers, we have obtained a molecular-scale picture of multistage protein crystallization that reveals the importance of conformational transformations in directing the pathway of assembly. We find that monomers with an extended conformation first form a mobile adsorbed phase, from which they condense into amorphous clusters. These clusters undergo a phase transition through S-layer folding into crystalline clusters composed of compact tetramers. Growth then proceeds by formation of new tetramers exclusively at cluster edges, implying tetramer formation is autocatalytic. Analysis of the growth kinetics leads to a quantitative model in which tetramer creation is rate limiting. However, the estimated barrier is much smaller than expected for folding of isolated S-layer proteins, suggesting an energetic rationale for this multistage pathway.

DuOCam: A Two-Channel Camera for Simultaneous Photometric Observations of Stellar Clusters

NASA Astrophysics Data System (ADS)

Maier, Erin R.; Witt, Emily; Depoy, Darren L.; Schmidt, Luke M.

2017-01-01

We have designed the Dual Observation Camera (DuOCam), which uses commercial, off-the-shelf optics to perform simultaneous photometric observations of astronomical objects at red and blue wavelengths. Collected light enters DuOCam’s optical assembly, where it is collimated by a negative doublet lens. It is then separated by a 45 degree blue dichroic filter (transmission bandpass: 530 - 800 nm, reflection bandpass: 400 - 475 nm). Finally, the separated light is focused by two identical positive doublet lenses onto two independent charge-coupled devices (CCDs), the SBIG ST-8300M and the SBIG STF-8300M. This optical assembly converts the observing telescope to an f/11 system, which balances maximum field of view with optimum focus. DuOCam was commissioned on the McDonald Observatory 0.9m, f/13.5 telescope from July 21st - 24th, 2016. Observations of three globular and three open stellar clusters were carried out. The resulting data were used to construct R vs. B-R color magnitude diagrams for a selection of the observed clusters. The diagrams display the characteristic evolutionary track for a stellar cluster, including the main sequence and main sequence turn-off.

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. This journal is © The Royal Society of Chemistry 2011

Human frataxin activates Fe-S cluster biosynthesis by facilitating sulfur transfer chemistry.

PubMed

Bridwell-Rabb, Jennifer; Fox, Nicholas G; Tsai, Chi-Lin; Winn, Andrew M; Barondeau, David P

2014-08-05

Iron-sulfur clusters are ubiquitous protein cofactors with critical cellular functions. The mitochondrial Fe-S assembly complex, which consists of the cysteine desulfurase NFS1 and its accessory protein (ISD11), the Fe-S assembly protein (ISCU2), and frataxin (FXN), converts substrates l-cysteine, ferrous iron, and electrons into Fe-S clusters. The physiological function of FXN has received a tremendous amount of attention since the discovery that its loss is directly linked to the neurodegenerative disease Friedreich's ataxia. Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe-S cluster biosynthesis activities of the Fe-S assembly complex. Here we present radiolabeling experiments that indicate FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe-S clusters. Additional mutagenesis, enzyme kinetic, UV-visible, and circular dichroism spectroscopic studies suggest conserved ISCU2 residue C104 is critical for FXN activation, whereas C35, C61, and C104 are all essential for Fe-S cluster formation on the assembly complex. These results cannot be fully explained by the hypothesis that FXN functions as an iron donor for Fe-S cluster biosynthesis, and further support an allosteric regulator role for FXN. Together, these results lead to an activation model in which FXN accelerates persulfide formation on NFS1 and favors a helix-to-coil interconversion on ISCU2 that facilitates the transfer of sulfur from NFS1 to ISCU2 as an initial step in Fe-S cluster biosynthesis.

Human Frataxin Activates Fe–S Cluster Biosynthesis by Facilitating Sulfur Transfer Chemistry

PubMed Central

2015-01-01

Iron–sulfur clusters are ubiquitous protein cofactors with critical cellular functions. The mitochondrial Fe–S assembly complex, which consists of the cysteine desulfurase NFS1 and its accessory protein (ISD11), the Fe–S assembly protein (ISCU2), and frataxin (FXN), converts substrates l-cysteine, ferrous iron, and electrons into Fe–S clusters. The physiological function of FXN has received a tremendous amount of attention since the discovery that its loss is directly linked to the neurodegenerative disease Friedreich’s ataxia. Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe–S cluster biosynthesis activities of the Fe–S assembly complex. Here we present radiolabeling experiments that indicate FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe–S clusters. Additional mutagenesis, enzyme kinetic, UV–visible, and circular dichroism spectroscopic studies suggest conserved ISCU2 residue C104 is critical for FXN activation, whereas C35, C61, and C104 are all essential for Fe–S cluster formation on the assembly complex. These results cannot be fully explained by the hypothesis that FXN functions as an iron donor for Fe–S cluster biosynthesis, and further support an allosteric regulator role for FXN. Together, these results lead to an activation model in which FXN accelerates persulfide formation on NFS1 and favors a helix-to-coil interconversion on ISCU2 that facilitates the transfer of sulfur from NFS1 to ISCU2 as an initial step in Fe–S cluster biosynthesis. PMID:24971490

Clustering effects in ionic polymers: Molecular dynamics simulations

DOE PAGES

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

Synthesis, Delivery and Regulation of Eukaryotic Heme and Fe-S Cluster Cofactors

PubMed Central

Barupala, Dulmini P.; Dzul, Stephen P.; Riggs-Gelasco, Pamela Jo; Stemmler, Timothy L.

2016-01-01

In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways. PMID:26785297

Tools and Functions of Reconfigurable Colloidal Assembly.

PubMed

Solomon, Michael J

2018-02-19

We review work in reconfigurable colloidal assembly, a field in which rapid, back-and-forth transitions between the equilibrium states of colloidal self-assembly are accomplished by dynamic manipulation of the size, shape, and interaction potential of colloids, as well as the magnitude and direction of the fields applied to them. It is distinguished from the study of colloidal phase transitions by the centrality of thermodynamic variables and colloidal properties that are time switchable; by the applicability of these changes to generate transitions in assembled colloids that may be spatially localized; and by its incorporation of the effects of generalized potentials due to, for example, applied electric and magnetic fields. By drawing upon current progress in the field, we propose a matrix classification of reconfigurable colloidal systems based on the tool used and function performed by reconfiguration. The classification distinguishes between the multiple means by which reconfigurable assembly can be accomplished (i.e., the tools of reconfiguration) and the different kinds of structural transitions that can be achieved by it (i.e., the functions of reconfiguration). In the first case, the tools of reconfiguration can be broadly classed as (i) those that control the colloidal contribution to the system entropy-as through volumetric and/or shape changes of the particles; (ii) those that control the internal energy of the colloids-as through manipulation of colloidal interaction potentials; and (iii) those that control the spatially resolved potential energy that is imposed on the colloids-as through the introduction of field-induced phoretic mechanisms that yield colloidal displacement and accumulation. In the second case, the functions of reconfiguration include reversible: (i) transformation between different phases-including fluid, cluster, gel, and crystal structures; (ii) manipulation of the spacing between colloids in crystals and clusters; and (iii) translation, rotation, or shape-change of finite-size objects self-assembled from colloids. With this classification in hand, we correlate the current limits on the spatiotemporal scales for reconfigurable colloidal assembly and identify a set of future research challenges.

The correlation between the sizes of globular cluster systems and their host dark matter haloes

NASA Astrophysics Data System (ADS)

Hudson, Michael J.; Robison, Bailey

2018-07-01

The sizes of entire systems of globular clusters (GCs) depend not only on the formation and destruction histories of the GCs themselves but also on the assembly, merger, and accretion history of the dark matter (DM) haloes that they inhabit. Recent work has shown a linear relation between total mass of GCs in the GC system and the mass of its host DM halo, calibrated from weak lensing. Here, we extend this to GC system sizes, by studying the radial density profiles of GCs around galaxies in nearby galaxy groups. We find that radial density profiles of the GC systems are well fit with a de Vaucouleurs profile. Combining our results with those from the literature, we find tight relationship (˜0.2 dex scatter) between the effective radius of the GC system and the virial radius (or mass) of its host DM halo, for haloes with masses greater than ˜1012 M⊙. The steep non-linear dependence of this relationship (R_{ {e, GCS}} ∝ R_{200}^{2.5 - 3} ∝ M_{200}^{0.8 - 1}) is currently not well understood, but is an important clue regarding the assembly history of DM haloes and of the GC systems that they host.

Electrical transport properties in Fe-Cr nanocluster-assembled granular films

NASA Astrophysics Data System (ADS)

Wang, Xiong-Zhi; Wang, Lai-Sen; Zhang, Qin-Fu; Liu, Xiang; Xie, Jia; Su, A.-Mei; Zheng, Hong-Fei; Peng, Dong-Liang

2017-09-01

The Fe100-xCrx nanocluster-assembled granular films with Cr atomic fraction (x) ranging from 0 to 100 were fabricated by using a plasma-gas-condensation cluster deposition system. The TEM characterization revealed that the uniform Fe clusters were coated with a Cr layer to form a Fe-Cr core-shell structure. Then, the as-prepared Fe100-xCrx nanoclusters were randomly assembled into a granular film in vacuum environments with increasing the deposition time. Because of the competition between interfacial resistance and shunting effect of Cr layer, the room temperature resistivity of the Fe100-xCrx nanocluster-assembled granular films first increased and then decreased with increasing the Cr atomic fraction (x), and revealed a maximum of 2 × 104 μΩ cm at x = 26 at.%. The temperature-dependent longitudinal resistivity (ρxx), magnetoresistance (MR) effect and anomalous Hall effect (AHE) of these Fe100-xCrx nanocluster-assembled granular films were also studied systematically. As the x increased from 0 to 100, the ρxx of all samples firstly decreased and then increased with increasing the measuring temperature. The dependence of ρxx on temperature could be well addressed by a mechanism incorporated for the fluctuation-induced-tunneling (FIT) conduction process and temperature-dependent scattering effect. It was found that the anomalous Hall effect (AHE) had no legible scaling relation in Fe100-xCrx nanocluster-assembled granular films. However, after deducting the contribution of tunneling effect, the scaling relation was unambiguous. Additionally, the Fe100-xCrx nanocluster-assembled granular films revealed a small negative magnetoresistance (MR), which decreased with the increase of x. The detailed physical mechanism of the electrical transport properties in these Fe100-xCrx nanocluster-assembled granular films was also studied.

Controlling transformations in the assembly of polyoxometalate clusters: {Mo11V7}, {Mo17V8} and {Mo72V30}.

PubMed

Miras, Haralampos N; Ochoa, M Nieves Corella; Long, De-Liang; Cronin, Leroy

2010-11-21

The reaction of molybdate with vanadium(V) in the presence of sulfite anions is explored showing how, via cation control, stepwise assembly through the {Mo(11)V(7)} cluster yields a {M(25)} cluster-based compound, [Mo(VI)(11)V(V)(5)V(IV)(2)O(52)(μ(9)-SO(3))(Mo(VI)(6)V(V)O(22))](10-) (1a), which was first discovered using cryospray mass spectrometry, whereas switching the cation away from ammonium allows the direct formation of the spherical 'Keplerate' {Mo(72)V(30)} cluster.

Carbon dot-Au(i)Ag(0) assembly for the construction of an artificial light harvesting system.

PubMed

Jana, Jayasmita; Aditya, Teresa; Pal, Tarasankar

2018-03-06

Artificial light harvesting systems (LHS) with inorganic counterparts are considered to be robust as well as mechanistically simple, where the system follows the donor-acceptor principle with an unchanged structural pattern. Plasmonic gold or silver nanoparticles are mostly chosen as inorganic counterparts to design artificial LHS. To capitalize on its electron accepting capability, Au(i) has been considered in this work for the synergistic stabilization of a system with intriguingly fluorescing silver(0) clusters produced in situ. Thus a stable fluorescent Au(i)Ag(0) assembly is generated with electron accepting capabilities. On the other hand, carbon dots have evolved as new fluorescent probes due to their unique physicochemical properties. Utilizing the simple electronic behavior of carbon dots, an electronic interaction between the fluorescent Au(i)Ag(0) and a carbon dot has been investigated for the construction of a new artificial light harvesting system. This coinage metal assembly allows surface energy transfer where it acts as an acceptor, while the carbon dot behaves as a good donor. The energy transfer efficiency has been calculated experimentally to be significant (81.3%) and the Au(i)Ag(0)-carbon dot assembly paves the way for efficient artificial LHS.

Free energy of singular sticky-sphere clusters.

PubMed

Kallus, Yoav; Holmes-Cerfon, Miranda

2017-02-01

Networks of particles connected by springs model many condensed-matter systems, from colloids interacting with a short-range potential and complex fluids near jamming, to self-assembled lattices and various metamaterials. Under small thermal fluctuations the vibrational entropy of a ground state is given by the harmonic approximation if it has no zero-frequency vibrational modes, yet such singular modes are at the epicenter of many interesting behaviors in the systems above. We consider a system of N spherical particles, and directly account for the singularities that arise in the sticky limit where the pairwise interaction is strong and short ranged. Although the contribution to the partition function from singular clusters diverges in the limit, its asymptotic value can be calculated and depends on only two parameters, characterizing the depth and range of the potential. The result holds for systems that are second-order rigid, a geometric characterization that describes all known ground-state (rigid) sticky clusters. To illustrate the applications of our theory we address the question of emergence: how does crystalline order arise in large systems when it is strongly disfavored in small ones? We calculate the partition functions of all known rigid clusters up to N≤21 and show the cluster landscape is dominated by hyperstatic clusters (those with more than 3N-6 contacts); singular and isostatic clusters are far less frequent, despite their extra vibrational and configurational entropies. Since the most hyperstatic clusters are close to fragments of a close-packed lattice, this underlies the emergence of order in sticky-sphere systems, even those as small as N=10.

Free energy of singular sticky-sphere clusters

NASA Astrophysics Data System (ADS)

Kallus, Yoav; Holmes-Cerfon, Miranda

2017-02-01

Networks of particles connected by springs model many condensed-matter systems, from colloids interacting with a short-range potential and complex fluids near jamming, to self-assembled lattices and various metamaterials. Under small thermal fluctuations the vibrational entropy of a ground state is given by the harmonic approximation if it has no zero-frequency vibrational modes, yet such singular modes are at the epicenter of many interesting behaviors in the systems above. We consider a system of N spherical particles, and directly account for the singularities that arise in the sticky limit where the pairwise interaction is strong and short ranged. Although the contribution to the partition function from singular clusters diverges in the limit, its asymptotic value can be calculated and depends on only two parameters, characterizing the depth and range of the potential. The result holds for systems that are second-order rigid, a geometric characterization that describes all known ground-state (rigid) sticky clusters. To illustrate the applications of our theory we address the question of emergence: how does crystalline order arise in large systems when it is strongly disfavored in small ones? We calculate the partition functions of all known rigid clusters up to N ≤21 and show the cluster landscape is dominated by hyperstatic clusters (those with more than 3 N -6 contacts); singular and isostatic clusters are far less frequent, despite their extra vibrational and configurational entropies. Since the most hyperstatic clusters are close to fragments of a close-packed lattice, this underlies the emergence of order in sticky-sphere systems, even those as small as N =10 .

Linked supramolecular building blocks for enhanced cluster formation

DOE PAGES

McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; ...

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.

A Commodity Computing Cluster

NASA Astrophysics Data System (ADS)

Teuben, P. J.; Wolfire, M. G.; Pound, M. W.; Mundy, L. G.

We have assembled a cluster of Intel-Pentium based PCs running Linux to compute a large set of Photodissociation Region (PDR) and Dust Continuum models. For various reasons the cluster is heterogeneous, currently ranging from a single Pentium-II 333 MHz to dual Pentium-III 450 MHz CPU machines. Although this will be sufficient for our ``embarrassingly parallelizable problem'' it may present some challenges for as yet unplanned future use. In addition the cluster was used to construct a MIRIAD benchmark, and compared to equivalent Ultra-Sparc based workstations. Currently the cluster consists of 8 machines, 14 CPUs, 50GB of disk-space, and a total peak speed of 5.83 GHz, or about 1.5 Gflops. The total cost of this cluster has been about $12,000, including all cabling, networking equipment, rack, and a CD-R backup system. The URL for this project is http://dustem.astro.umd.edu.

The Role of Large-Scale Structure and Assembly in the Quenching of Star Formation in Cluster Galaxies at z 0.2

NASA Astrophysics Data System (ADS)

Moran, Sean; Smith, G.; Haines, C.; Egami, E.; Hardegree-Ullman, E.; Heckman, T.

2010-01-01

We present results from LoCuSS, the Local Cluster Substructure Survey, on the distribution and abundance of cluster galaxies showing signatures of recently quenched star formation, within a sample of 15 z 0.2 clusters. Combining LoCuSS' wide-field UV through NIR photometry with weak-lensing derived mass maps for these clusters, we identify passive galaxies that have undergone recent quenching via both rapid (100Myr) and slow (1Gyr) mechanisms. By studying their abundance in a statistically significant sample of z 0.2 clusters, we explore how the effectiveness of environmental quenching of star formation varies as a function of the level of cluster substructure, in addition to global cluster characteristics such as mass or X-ray luminosity and temperature, with the aim of understanding the role that pre-processing of galaxies within groups and filaments plays in the overall buildup of the morphology-density and SFR-density relations. We find that clusters with large levels of substructure indicative of recent assembly or cluster-cluster mergers host a higher fraction of galaxies with signs of recent ram-pressure stripping by the hot intra-cluster gas. In addition, we find that the fraction of post-starburst galaxies increases with cluster mass (M500), but fractions of optically-selected AGN and GALEX-defined "Green Valley" galaxies show the opposite trend, being most abundant in rather low-mass clusters. These trends suggest a picture where quenching of star formation occurs most vigorously in actively assembling structures, with comparatively little activity in the most massive structures where most of the nearby large-scale structure has already been accreted and Virialized into the main cluster body.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Panchao; Wu, Bin; Li, Tao

A 2.9 nm molybdenum oxide cluster {Mo 132} (Formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH 3COOH/CH 3COO- 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 {Mo 132} 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 coordinationmore » effect of the acetate groups. Once the concentration of {Mo V 2(acetate)} reaches a critical value, it triggers the assembly of Mo V and Mo VI species into {Mo 132} 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, {Mo 132} (formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 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 {Mo V 2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the co-assembly of Mo V and Mo VI species into the giant clusters.« less

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

DOE PAGES

Yin, Panchao; Wu, Bin; Li, Tao; ...

2016-07-26

A 2.9 nm molybdenum oxide cluster {Mo 132} (Formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 72] 42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH 3COOH/CH 3COO- 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 {Mo 132} 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 coordinationmore » effect of the acetate groups. Once the concentration of {Mo V 2(acetate)} reaches a critical value, it triggers the assembly of Mo V and Mo VI species into {Mo 132} 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, {Mo 132} (formula: [Mo VI 72Mo V 60O 372(CH 3COO) 30(H 2O) 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 {Mo V 2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the co-assembly of Mo V and Mo VI species into the giant clusters.« less

Diverse assembly behavior in colloidal Platonic polyhedral sphere clusters

NASA Astrophysics Data System (ADS)

Marson, Ryan; Teich, Erin; Dshemuchadse, Julia; Glotzer, Sharon; Larson, Ronald

We simulate the self-assembly of colloidal ``polyhedral sphere clusters (PSCs)'', which consist of equal-sized spheres placed at the vertices of a polyhedron such that they just touch along each edge. These colloidal building blocks have recently been experimentally fabricated; here we predict crystal structures that would appear in the phase diagram of resulting particle assemblies. We use Brownian dynamics (BD) simulations of rigid body clusters performed in the open-source GPU-based HOOMD-Blue particle simulation package to show the assembly behavior of the 5 Platonic PSCs. The simulations contain as many as 4096 individual polyhedra, across over 30 different densities per cluster geometry, with some ordered phases possessing unit cells with 20 or more particles. We observe the formation of not only traditional cubic structures such as BCC and FCC, but also more complex phases having structure symmetries with Pearson symbols - hP7, cP20, cI2, mP6, and hR3. The observations reported here will serve as a guide for future colloidal assembly experiments using an expanded library of PSCs, consisting of other regular and irregular polyhedra, allowing researchers to target specific arrangements of ``halo'' and ``core'' particles for technologically relevant applications including photonics and structural color.

[Nitrogen oxide is involved in the regulation of the Fe-S cluster assembly in proteins and the formation of biofilms by Escherichia coli cells].

PubMed

Vasil'eva, S V; Streltsova, D A; Starostina, I A; Sanina, N A

2013-01-01

The functions of nitrogen oxide (NO) in the regulation of the reversible processes of Fe-S cluster assembly in proteins and the formation of Escherichia coli biofilms have been investigated. S-nitrosoglutathione (GSNO) and crystalline nitrosyl complexes of iron with sulfur-containing aliphatic ligands cisaconite (CisA) and penaconite have been used as NO donors for the first time. Wild-type E. coli cells of the strain MC4100, mutants deltaiscA and deltasufA, and the double paralog mutant deltaiscA/sufA with deletions in the alternative pathways of Fe2+ supply for cluster assembly (all derived from the above-named strain) were used in this study. Plankton growth of bacterial cultures, the mass of mature biofilms, and the expression of the SoxRS[2Fe-2S] regulon have been investigated and shown to depend on strain genotype, the process of Fe-S cluster assembly in iron-sulfur proteins, NO donor structure, and the presence of Fe2+ chelator ferene in the incubation medium. The antibiotic ciprofloxacine (CF) was used as an inhibitor of E. coli biofilm formation in the positive control. NO donors regulating Fe-S cluster assembly in E. coli have been shown to control plankton growth of the cultures and the process of mature biofilm formation; toxic doses of NO caused a dramatic (3- to 4-fold) stimulation of cell entry into biofilms as a response to nitrosative stress; NO donors CisA and GSNO in physiological concentrations suppressed the formation of mature biofilms, and the activity of these compounds was comparable to that of CE Regulation of both Fe-S cluster assembly in iron-sulfur proteins and biofilm formation by NO is indicative of the connection between these processes in E. coli.

Synthesis, delivery and regulation of eukaryotic heme and Fe-S cluster cofactors.

PubMed

Barupala, Dulmini P; Dzul, Stephen P; Riggs-Gelasco, Pamela Jo; Stemmler, Timothy L

2016-02-15

In humans, the bulk of iron in the body (over 75%) is directed towards heme- or Fe-S cluster cofactor synthesis, and the complex, highly regulated pathways in place to accomplish biosynthesis have evolved to safely assemble and load these cofactors into apoprotein partners. In eukaryotes, heme biosynthesis is both initiated and finalized within the mitochondria, while cellular Fe-S cluster assembly is controlled by correlated pathways both within the mitochondria and within the cytosol. Iron plays a vital role in a wide array of metabolic processes and defects in iron cofactor assembly leads to human diseases. This review describes progress towards our molecular-level understanding of cellular heme and Fe-S cluster biosynthesis, focusing on the regulation and mechanistic details that are essential for understanding human disorders related to the breakdown in these essential pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

Tailoring magnetic properties of Co nanocluster assembled films using hydrogen

NASA Astrophysics Data System (ADS)

Romero, C. P.; Volodin, A.; Paddubrouskaya, H.; Van Bael, M. J.; Van Haesendonck, C.; Lievens, P.

2018-07-01

Tailoring magnetic properties in nanocluster assembled cobalt (Co) thin films was achieved by admitting a small percentage of H2 gas (∼2%) into the Co gas phase cluster formation chamber prior to deposition. The oxygen content in the films is considerably reduced by the presence of hydrogen during the cluster formation, leading to enhanced magnetic interactions between clusters. Two sets of Co samples were fabricated, one without hydrogen gas and one with hydrogen gas. Magnetic properties of the non-hydrogenated and the hydrogen-treated Co nanocluster assembled films are comparatively studied using magnetic force microscopy and vibrating sample magnetometry. When comparing the two sets of samples the considerably larger coercive field of the H2-treated Co nanocluster film and the extended micrometer-sized magnetic domain structure confirm the enhancement of magnetic interactions between clusters. The thickness of the antiferromagnetic CoO layer is controlled with this procedure and modifies the exchange bias effect in these films. The exchange bias shift is lower for the H2-treated Co nanocluster film, which indicates that a thinner antiferromagnetic CoO reduces the coupling with the ferromagnetic Co. The hydrogen-treatment method can be used to tailor the oxidation levels thus controlling the magnetic properties of ferromagnetic cluster-assembled films.

Molybdenum-oxide based unique polyprotic nanoacids showing different deprotonations and related assembly processes in solution.

PubMed

Kistler, Melissa L; Liu, Tianbo; Gouzerh, Pierre; Todea, Ana Maria; Müller, Achim

2009-07-14

We report the self-assembly processes in solution of three Keplerate-type molybdenum-oxide based clusters {Mo72V30}, {Mo72Cr30} and {Mo72Fe30} (all with diameters of approximately 2.5 nm). These clusters behave as unique weak polyprotic acids owing to the external water ligands attached to the non-Mo metal centers. Whereas the Cr and Fe clusters have 30 water ligands attached at the 30 M3+ centers pointing outside, {Mo72V30} has 20 water ligands coordinated to vanadium atoms, of which only 10 are pointing outside. The self-assembly processes of the Keplerates leading to supramolecular blackberry-type structures are influenced by the effective charge densities on the cluster surfaces, which can be tuned by the pH values and solvent properties. As expected, {Mo72Cr30} and {Mo72Fe30} behave similarly in aqueous solution due to their analogous structures and in both cases the self-assembly follows the partial deprotonation of the external water ligands attached to the non-Mo metal centers. However, the M-OH2 functionalities differ not only in acidity but also lability, i.e. in different residence times of the H2O ligands. In contrast to {Mo72Cr30} and {Mo72Fe30}, the {Mo72V30} clusters carry a rather large number of negative charges so that their solution properties are different. They exist as discrete macroions in dilute aqueous solution, and form only in mixed water/organic solvent (like acetone) blackberry-type structures whose size increases with acetone content. The comparison of the properties of the clusters allows more general information about the interesting self-assembly phenomenon to be unveiled.

RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi

PubMed Central

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I–II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I–II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions. PMID:24691066

RNA-Seq analysis using de novo transcriptome assembly as a reference for the salmon louse Caligus rogercresseyi.

PubMed

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I-II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I-II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions.

Lattice cluster theory of associating polymers. I. Solutions of linear telechelic polymer chains.

PubMed

Dudowicz, Jacek; Freed, Karl F

2012-02-14

The lattice cluster theory (LCT) for the thermodynamics of a wide array of polymer systems has been developed by using an analogy to Mayer's virial expansions for non-ideal gases. However, the high-temperature expansion inherent to the LCT has heretofore precluded its application to systems exhibiting strong, specific "sticky" interactions. The present paper describes a reformulation of the LCT necessary to treat systems with both weak and strong, "sticky" interactions. This initial study concerns solutions of linear telechelic chains (with stickers at the chain ends) as the self-assembling system. The main idea behind this extension of the LCT lies in the extraction of terms associated with the strong interactions from the cluster expansion. The generalized LCT for sticky systems reduces to the quasi-chemical theory of hydrogen bonding of Panyioutou and Sanchez when correlation corrections are neglected in the LCT. A diagrammatic representation is employed to facilitate the evaluation of the corrections to the zeroth-order approximation from short range correlations. © 2012 American Institute of Physics

The impact of anisotropy and interaction range on the self-assembly of Janus ellipsoids

NASA Astrophysics Data System (ADS)

Ruth, D. P.; Gunton, J. D.; Rickman, J. M.; Li, Wei

2014-12-01

We assess the roles of anisotropy and interaction range on the self-assembly of Janus colloidal particles. In particular, Monte Carlo simulation is employed to investigate the propensity for the formation of aggregates in a spheroidal model of a colloid having a relatively short-ranged interaction that is consistent with experimentally realizable systems. By monitoring the equilibrium distribution of aggregates as a function of temperature and density, we identify a "micelle" transition temperature and discuss its dependence on particle shape. We find that, unlike systems with longer ranged interactions, this system does not form micelles below a transition temperature at low density. Rather, larger clusters comprising 20-40 particles characterize the transition. We then examine the dependence of the second virial coefficient on particle shape and well width to determine how these important system parameters affect aggregation. Finally, we discuss possible strategies suggested by this work to promote self-assembly for the encapsulation of particles.

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.

Molecular codes for neuronal individuality and cell assembly in the brain

PubMed Central

Yagi, Takeshi

2012-01-01

The brain contains an enormous, but finite, number of neurons. The ability of this limited number of neurons to produce nearly limitless neural information over a lifetime is typically explained by combinatorial explosion; that is, by the exponential amplification of each neuron's contribution through its incorporation into “cell assemblies” and neural networks. In development, each neuron expresses diverse cellular recognition molecules that permit the formation of the appropriate neural cell assemblies to elicit various brain functions. The mechanism for generating neuronal assemblies and networks must involve molecular codes that give neurons individuality and allow them to recognize one another and join appropriate networks. The extensive molecular diversity of cell-surface proteins on neurons is likely to contribute to their individual identities. The clustered protocadherins (Pcdh) is a large subfamily within the diverse cadherin superfamily. The clustered Pcdh genes are encoded in tandem by three gene clusters, and are present in all known vertebrate genomes. The set of clustered Pcdh genes is expressed in a random and combinatorial manner in each neuron. In addition, cis-tetramers composed of heteromultimeric clustered Pcdh isoforms represent selective binding units for cell-cell interactions. Here I present the mathematical probabilities for neuronal individuality based on the random and combinatorial expression of clustered Pcdh isoforms and their formation of cis-tetramers in each neuron. Notably, clustered Pcdh gene products are known to play crucial roles in correct axonal projections, synaptic formation, and neuronal survival. Their molecular and biological features induce a hypothesis that the diverse clustered Pcdh molecules provide the molecular code by which neuronal individuality and cell assembly permit the combinatorial explosion of networks that supports enormous processing capability and plasticity of the brain. PMID:22518100

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.

Star-like supramolecular polymers fabricated by a Keplerate cluster with cationic terminated polymers and their self-assembly into vesicles.

PubMed

Zhang, Qian; He, Lipeng; Wang, Hui; Zhang, Cheng; Liu, Weisheng; Bu, Weifeng

2012-07-18

The electrostatic combination of a Keplerate cluster, [Mo(132)O(372)(CH(3)COO)(30)(H(2)O)(72)](42-) with cationic terminated poly(styrene) yields polyoxometalate-based supramolecular star polymers, which can further self-assemble into vesicular aggregates in CHCl(3)-MeOH mixed solvent.

Structure formation of lipid membranes: Membrane self-assembly and vesicle opening-up to octopus-like micelles

NASA Astrophysics Data System (ADS)

Noguchi, Hiroshi

2013-02-01

We briefly review our recent studies on self-assembly and vesicle rupture of lipid membranes using coarse-grained molecular simulations. For single component membranes, lipid molecules self-assemble from random gas states to vesicles via disk-shaped clusters. Clusters aggregate into larger clusters, and subsequently the large disks close into vesicles. The size of vesicles are determined by kinetics than by thermodynamics. When a vesicle composed of lipid and detergent types of molecules is ruptured, a disk-shaped micelle called bicelle can be formed. When both surfactants have negligibly low critical micelle concentration, it is found that bicelles connected with worm-like micelles are also formed depending on the surfactant ratio and spontaneous curvature of the membrane monolayer.

Morphology manipulation of M13 bacteriophage template for nanostructure assembly

NASA Astrophysics Data System (ADS)

Ngo-Duc, Tam-Triet; Zaman, Mohammed S.; Moon, Chung-Hee; Haberer, Elaine D.

2014-08-01

A gold-binding M13 bacteriophage was used as a model system to explore templating of inorganic material on geometrically transformed viruses . Gold-binding filamentous phage were converted to spheroid form with a short chloroform treatment, and the resulting morphology was investigated with electron microscopy. Binding studies revealed that spheroid-shaped gold-binding phage preserved its affinity for gold. Spheroids adhered to a planar substrate assembled clusters or rings of gold nanoparticles. This gold-binding phage served as a demonstration of a highly shape-modifiable viral-template for inorganic materials.

Chirally directed formation of nanometer-scale proline clusters.

PubMed

Myung, Sunnie; Fioroni, Marco; Julian, Ryan R; Koeniger, Stormy L; Baik, Mu-Hyun; Clemmer, David E

2006-08-23

Ion mobility measurements, combined with molecular mechanics simulations, are used to study enantiopure and racemic proline clusters formed by electrospray ionization. Broad distributions of cluster sizes and charge states are observed, ranging from clusters containing only a few proline units to clusters that contain more than 100 proline units (i.e., protonated clusters of the form [xPro + nH](n+) with x = 1 to >100 and n = 1-7). As the sizes of clusters increase, there is direct evidence for nanometer scale, chirally induced organization into specific structures. For n = 4 and 5, enantiopure clusters of approximately 50 to 100 prolines assemble into structures that are more elongated than the most compact structure that is observed from the racemic proline clusters. A molecular analogue, cis-4-hydroxy-proline, displays significantly different behavior, indicating that in addition to the rigidity of the side chain ring, intermolecular interactions are important in the formation of chirally directed clusters. This is the first case in which assemblies of chirally selective elongated structures are observed in this size range of amino acid clusters. Relationships between enantiopurity, cluster shape, and overall energetics are discussed.

Star clusters in evolving galaxies

NASA Astrophysics Data System (ADS)

Renaud, Florent

2018-04-01

Their ubiquity and extreme densities make star clusters probes of prime importance of galaxy evolution. Old globular clusters keep imprints of the physical conditions of their assembly in the early Universe, and younger stellar objects, observationally resolved, tell us about the mechanisms at stake in their formation. Yet, we still do not understand the diversity involved: why is star cluster formation limited to 105M⊙ objects in the Milky Way, while some dwarf galaxies like NGC 1705 are able to produce clusters 10 times more massive? Why do dwarfs generally host a higher specific frequency of clusters than larger galaxies? How to connect the present-day, often resolved, stellar systems to the formation of globular clusters at high redshift? And how do these links depend on the galactic and cosmological environments of these clusters? In this review, I present recent advances on star cluster formation and evolution, in galactic and cosmological context. The emphasis is put on the theory, formation scenarios and the effects of the environment on the evolution of the global properties of clusters. A few open questions are identified.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ilyushin, G. D., E-mail: ilyushin@nc.cryst.ras.ru; 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-polyhedralmore » 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.« less

Effects of climate legacies on above- and belowground community assembly.

PubMed

Delgado-Baquerizo, Manuel; Eldridge, David J; Travers, Samantha K; Val, James; Oliver, Ian; Bissett, Andrew

2018-05-11

The role of climatic legacies in regulating community assembly of above- and belowground species in terrestrial ecosystems remains largely unexplored and poorly understood. Here, we report on two separate regional and continental empirical studies, including >500 locations, aiming to identify the relative importance of climatic legacies (climatic anomaly over the last 20,000 years) compared to current climates in predicting the relative abundance of ecological clusters formed by species strongly co-occurring within two independent above- and belowground networks. Climatic legacies explained a significant portion of the variation in the current community assembly of terrestrial ecosystems (up to 15.4%) that could not be accounted for by current climate, soil properties, and management. Changes in the relative abundance of ecological clusters linked to climatic legacies (e.g., past temperature) showed the potential to indirectly alter other clusters, suggesting cascading effects. Our work illustrates the role of climatic legacies in regulating ecosystem community assembly and provides further insights into possible winner and loser community assemblies under global change scenarios. © 2018 John Wiley & Sons Ltd.

Self-assembled monolayer and multilayer films of the nanocluster [HxPMo12O40 subsetH4Mo72Fe30(O2CMe)15O254(H2O)68] on gold.

PubMed

Colorado, Ramon; Crouse, Christopher A; Zeigler, Christopher N; Barron, Andrew R

2008-08-19

Films of the molybdenum-iron nanocluster [H x PMo 12O 40 subsetH 4Mo 72Fe 30(O 2CMe) 15O 254(H2O) 68] (FeMoC) were generated on gold via the self-assembly technique using two divergent routes. The first route entails the self-assembly of unfunctionalized FeMoC onto a preprepared carboxyl-terminated SAM on gold. The second route involves the preparation of thiol-terminated functionalized FeMoC clusters, which are then allowed to self-assemble onto bare gold surfaces. Monolayer films of FeMoC clusters are attained via both routes, with the second route requiring shorter immersion times (2 days) than the first route (6 days). Multilayer films of FeMoC are formed via the second route for immersion times longer than 2 days. Characterization of these films using optical ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy confirm the self-assembly of the clusters on the surfaces.

Microcapsule Structure with a Tunable Textured Surface via the Assembly of Polyoxomolybdate Clusters: A Bioinspired Strategy and Enhanced Activities in Alkene Oxidation.

PubMed

Chilivery, Rakesh; Rana, Rohit Kumar

2017-01-25

A polyamine-mediated bioinspired strategy to assemble Keggin-type phosphomolybdic acid (PMA) clusters is demonstrated for the fabrication of microcapsule (MC) structures with unique surface textures. It involves supramolecular aggregation of polyamines with multivalent anions, which then allows the assembly of negatively charged PMA into MCs in an aqueous medium under ambient conditions. Resembling the role of polyamines in biosilicification of diatoms, the polyamine-anion interaction is shown to be the key for the assembly process. It not only provides structural stability but also facilitates an interesting transition from a smooth to a wrinkled surface alongside a change in the Keggin form to its lacunary form depending on the pH of the medium. Moreover, the presence of isolated PMA units in the hybrid structure enables them to be active in catalyzing the aerobic oxidation of alkenes under solvent-free conditions with better selectivity and reusability. Hence, the assembly approach represents an effective way for heterogenization of PMA-based materials and is expected to find considerable application in the wider hybrid-cluster field.

Hybrid Assembly of Different-Sized Supertetrahedral Clusters into a Unique Non-Interpenetrated Mn-In-S Open Framework with Large Cavity.

PubMed

Wang, Hongxiang; Wang, Wei; Hu, Dandan; Luo, Min; Xue, Chaozhuang; Li, Dongsheng; Wu, Tao

2018-06-04

Reported here is a unique crystalline semiconductor open-framework material built from the large-sized supertetrahedral T4 and T5 clusters with the Mn-In-S compositions. The hybrid assembly between T4 and T5 clusters by sharing terminal μ 2 -S 2- is for the first time observed among the cluster-based chalcogenide open frameworks. Such three-dimensional structure displays non-interpenetrated diamond-type topology with extra-large nonframework volume of 82%. Moreover, ion exchange, CO 2 adsorption, as well as photoluminescence properties of the title compound are also investigated.

Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe-S Cluster Biosynthetic Pathways.

PubMed

Vranish, James N; Das, Deepika; Barondeau, David P

2016-11-18

Iron-sulfur (Fe-S) clusters are protein cofactors that are required for many essential cellular functions. Fe-S clusters are synthesized and inserted into target proteins by an elaborate biosynthetic process. The insensitivity of most Fe-S assembly and transfer assays requires high concentrations for components and places major limits on reaction complexity. Recently, fluorophore labels were shown to be effective at reporting cluster content for Fe-S proteins. Here, the incorporation of this labeling approach allowed the design and interrogation of complex Fe-S cluster biosynthetic reactions that mimic in vivo conditions. A bacterial Fe-S assembly complex, composed of the cysteine desulfurase IscS and scaffold protein IscU, was used to generate [2Fe-2S] clusters for transfer to mixtures of putative intermediate carrier and acceptor proteins. The focus of this study was to test whether the monothiol glutaredoxin, Grx4, functions as an obligate [2Fe-2S] carrier protein in the Fe-S cluster distribution network. Interestingly, [2Fe-2S] clusters generated by the IscS-IscU complex transferred to Grx4 at rates comparable to previous assays using uncomplexed IscU as a cluster source in chaperone-assisted transfer reactions. Further, we provide evidence that [2Fe-2S]-Grx4 delivers clusters to multiple classes of Fe-S targets via direct ligand exchange in a process that is both dynamic and reversible. Global fits of cluster transfer kinetics support a model in which Grx4 outcompetes terminal target proteins for IscU-bound [2Fe-2S] clusters and functions as an intermediate cluster carrier. Overall, these studies demonstrate the power of chemically conjugated fluorophore reporters for unraveling mechanistic details of biological metal cofactor assembly and distribution networks.

Steps Toward Understanding Mitochondrial Fe/S Cluster Biogenesis.

PubMed

Melber, Andrew; Winge, Dennis R

2018-01-01

Iron-sulfur clusters (Fe/S clusters) are essential cofactors required throughout the clades of biology for performing a myriad of unique functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. Although Fe/S clusters can be synthesized in vitro and transferred to a client protein without enzymatic assistance, biology has evolved intricate mechanisms to assemble and transfer Fe/S clusters within the cellular environment. In eukaryotes, the foundation of all cellular clusters starts within the mitochondria. The focus of this review is to detail the mitochondrial Fe/S biogenesis (ISC) pathway along with the Fe/S cluster transfer steps necessary to mature Fe/S proteins. New advances in our understanding of the mitochondrial Fe/S biogenesis machinery will be highlighted. Additionally, we will address various experimental approaches that have been successful in the identification and characterization of components of the ISC pathway. © 2018 Elsevier Inc. All rights reserved.

Passive colloids work together to become Active

NASA Astrophysics Data System (ADS)

Kandula, Hima Nagamanasa; Wang, Wei; Zhang, Jie; Wu, Huanxin; Han, Ming; Luijten, Erik; Granick, Steve

In recent years there is growing body of research to design self-propelled colloids to gain insights into non-equilibrium systems including living matter. While most active colloids developed hitherto entail prefabrication of Janus colloids and possess single fixed active site, we present one simple system where active colloids are formed in-situ naturally with multiple active sites and are reversible as well as reconfigurable. A binary mixture of Brownian colloids which have opposite polarizations when subjected to an AC electric field spontaneously assemble into clusters which are propelled by asymmetric induced charge electro osmosis. We find that tuning the relative sizes of the two species allows for the control over the number of active sites. More interestingly, the patches are dynamic enabling reconfiguration of the active cluster. Consequently, the clusters are active not only in motion but also in their structure.

Self-assembled three-dimensional chiral colloidal architecture

NASA Astrophysics Data System (ADS)

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C.; Sha, Ruojie; Seeman, Nadrian C.; Chaikin, Paul M.

2017-11-01

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.

Equilibrium Phase Behavior of a Continuous-Space Microphase Former.

PubMed

Zhuang, Yuan; Zhang, Kai; Charbonneau, Patrick

2016-03-04

Periodic microphases universally emerge in systems for which short-range interparticle attraction is frustrated by long-range repulsion. The morphological richness of these phases makes them desirable material targets, but our relatively coarse understanding of even simple models hinders controlling their assembly. We report here the solution of the equilibrium phase behavior of a microscopic microphase former through specialized Monte Carlo simulations. The results for cluster crystal, cylindrical, double gyroid, and lamellar ordering qualitatively agree with a Landau-type free energy description and reveal the nontrivial interplay between cluster, gel, and microphase formation.

Community trait overdispersion due to trophic interactions: concerns for assembly process inference

PubMed Central

Petchey, Owen L.

2016-01-01

The expected link between competitive exclusion and community trait overdispersion has been used to infer competition in local communities, and trait clustering has been interpreted as habitat filtering. Such community assembly process inference has received criticism for ignoring trophic interactions, as competition and trophic interactions might create similar trait patterns. While other theoretical studies have generally demonstrated the importance of predation for coexistence, ours provides the first quantitative demonstration of such effects on assembly process inference, using a trait-based ecological model to simulate the assembly of a competitive primary consumer community with and without the influence of trophic interactions. We quantified and contrasted trait dispersion/clustering of the competitive communities with the absence and presence of secondary consumers. Trophic interactions most often decreased trait clustering (i.e. increased dispersion) in the competitive communities due to evenly distributed invasions of secondary consumers and subsequent competitor extinctions over trait space. Furthermore, effects of trophic interactions were somewhat dependent on model parameters and clustering metric. These effects create considerable problems for process inference from trait distributions; one potential solution is to use more process-based and inclusive models in inference. PMID:27733548

Polycation-induced assembly of purified tubulin.

PubMed Central

Erickson, H P; Voter, W A

1976-01-01

Several different polycations have been found that can substitute for the microtubule-associated proteins, or tau factor, in facilitating assembly of tubulin that has been purified by ion exchange chromatography. In low concentrations of the polycation diethylaminoethyl-dextran, 7 mg of tubulin is pelleted per 1 mg of polycation added. Under conditions favorable to microtubule assembly the entire pellet is seen by electron microscopy to consist of "double wall microtubules", which are essentially identical to normal microtubules in subunit structure and arrangement. When assembly is inhibited approximately the same amount of tubulin is pelleted, but it is in the form of clusters of curved sheets or filaments apparently related to tubulin rings. When conditions are changed to favor assembly, the tubulin within these clusters appears to reassemble to form the double wall microtubules. Images PMID:1066692

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

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

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

2015-03-06

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. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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

Ferromagnetic ordering in superatomic solids.

PubMed

Lee, Chul-Ho; Liu, Lian; Bejger, Christopher; Turkiewicz, Ari; Goko, Tatsuo; Arguello, Carlos J; Frandsen, Benjamin A; Cheung, Sky C; Medina, Teresa; Munsie, Timothy J S; D'Ortenzio, Robert; Luke, Graeme M; Besara, Tiglet; Lalancette, Roger A; Siegrist, Theo; Stephens, Peter W; Crowther, Andrew C; Brus, Louis E; Matsuo, Yutaka; Nakamura, Eiichi; Uemura, Yasutomo J; Kim, Philip; Nuckolls, Colin; Steigerwald, Michael L; Roy, Xavier

2014-12-03

In order to realize significant benefits from the assembly of solid-state materials from molecular cluster superatomic building blocks, several criteria must be met. Reproducible syntheses must reliably produce macroscopic amounts of pure material; the cluster-assembled solids must show properties that are more than simply averages of those of the constituent subunits; and rational changes to the chemical structures of the subunits must result in predictable changes in the collective properties of the solid. In this report we show that we can meet these requirements. Using a combination of magnetometry and muon spin relaxation measurements, we demonstrate that crystallographically defined superatomic solids assembled from molecular nickel telluride clusters and fullerenes undergo a ferromagnetic phase transition at low temperatures. Moreover, we show that when we modify the constituent superatoms, the cooperative magnetic properties change in predictable ways.

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

PubMed

Dhaka, Kapil; Bandyopadhyay, Debashis

2016-08-02

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.

Molecular cloning and analysis of the ergopeptine assembly system in the ergot fungus Claviceps purpurea.

PubMed

Correia, Telmo; Grammel, Nicolas; Ortel, Ingo; Keller, Ullrich; Tudzynski, Paul

2003-12-01

Claviceps purpurea produces the pharmacological important ergopeptines, a class of cyclol-structured alkaloid peptides containing D-lysergic acid. These compounds are assembled from D-lysergic acid and three different amino acids by the nonribosomal peptide synthetase enzymes LPS1 and LPS2. Cloning of alkaloid biosynthesis genes from C. purpurea has revealed a gene cluster including two NRPS genes, cpps 1 and cpps 2. Protein sequence data had assigned earlier cpps1 to encode the trimodular LPS1 assembling the tripeptide portion of ergopeptines. Here, we show by transcriptional analysis, targeted inactivation, analysis of disruption mutants, and heterologous expression that cpps 2 encodes the monomodular LPS2 responsible for D-lysergic acid activation and incorporation into the ergopeptine backbone. The presence of two distinct NRPS subunits catalyzing formation of ergot peptides is the first example of a fungal NRPS system consisting of different NRPS subunits.

Spitzer Imaging of Planck-Herschel Dusty Proto-Clusters at z=2-3

NASA Astrophysics Data System (ADS)

Cooray, Asantha; Ma, Jingzhe; Greenslade, Joshua; Kubo, Mariko; Nayyeri, Hooshang; Clements, David; Cheng, Tai-An

2018-05-01

We have recently introduced a new proto-cluster selection technique by combing Herschel/SPIRE imaging data and Planck/HFIk all-sky survey point source catalog. These sources are identified as Planck point sources with clumps of Herschel source over-densities with far-IR colors comparable to z=0 ULIRGS redshifted to z=2 to 3. The selection is sensitive to dusty starbursts and obscured QSOs and we have recovered couple of the known proto-clusters and close to 30 new proto-clusters. The candidate proto-clusters selected from this technique have far-IR flux densities several times higher than those that are optically selected, such as using LBG selection, implying that the member galaxies are in a special phase of heightened dusty starburst and dusty QSO activity. This far-IR luminous phase may be short but likely to be necessary piece to understand the whole stellar mass assembly history of clusters. Moreover, our photo-clusters are missed in optical selections, suggesting that optically selected proto-clusters alone do not provide adequate statistics and a comparison of the far-IR and optical selected clusters may reveal the importance of the dusty stellar mass assembly. Here, we propose IRAC observations of six of the highest priority new proto-clusters, to establish the validity of the technique and to determine the total stellar mass through SED models. For a modest observing time the science program will have a substantial impact on an upcoming science topic in cosmology with implications for observations with JWST and WFIRST to understand the mass assembly in the universe.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Yudie; Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei 230031; Liu, Honglin, E-mail: hlliu@iim.ac.cn

Graphical abstract: - Highlights: • Mercapto groups were grafted to chitosan molecule by a reactive amine reduction. • Functional polymer with well-defined monomer units controls AuNPs assembly. • Assembled morphologies depend on the ratio of AuNPs to thiolate groups. • Microcubes with side length of ∼20 μm was synthesized through a dialysis step. • A edge-to-middle growth mechanism of gold microcubes was observed. - Abstract: The L-cysteine molecules were successfully grafted to the 2-amino group of chitosan by a reactive amine reduction, and the as-synthesized thiolated chitosan (TC) molecules were used as the templates to direct the self-assembly of goldmore » nanoparticles and induce the transformation of these assemblies to gold microcubes through a deep-going dialysis. We found that the ratio of gold nanoparticles to TC molecules could greatly affect the shape of the assembled clusters. Different stages of these clusters and microstructures during the dialysis process were characterized by scanning electron microscope (SEM), and the microcubes with average side length of about 20 μm were successfully synthesized. According to the morphology evolution of the assembly, it could be concluded that the microcubes were formed from external to internal. The SERS area mapping images of microcubes and some clusters were also collected to study the formation mechanism of gold microcubes. Our work demonstrates a simple and highly effective way to assemble gold nanoparticles into microcubes with unique properties.« less

Nanoparticle Clusters: Assembly and Control Over Internal Order, Current Capabilities, and Future Potential.

PubMed

Stolarczyk, Jacek K; Deak, Andras; Brougham, Dermot F

2016-07-01

The current state of the art in the use of colloidal methods to form nanoparticle assemblies, or clusters (NPCs) is reviewed. The focus is on the two-step approach, which exploits the advantages of bottom-up wet chemical NP synthesis procedures, with subsequent colloidal destabilization to trigger assembly in a controlled manner. Recent successes in the application of functional NPCs with enhanced emergent collective properties for a wide range of applications, including in biomedical detection, surface enhanced Raman scattering (SERS) enhancement, photocatalysis, and light harvesting, are highlighted. The role of the NP-NP interactions in the formation of monodisperse ordered clusters is described and the different assembly processes from a wide range of literature sources are classified according to the nature of the perturbation from the initial equilibrium state (dispersed NPs). Finally, the future for the field and the anticipated role of computational approaches in developing next-generation functional NPCs are briefly discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cluster-mediated assembly enables step-growth copolymerization from binary nanoparticle mixtures with rationally designed architectures† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc00220g

PubMed Central

Zhang, Xianfeng; Lv, Longfei; Wu, Guanhong; Yang, Dong

2018-01-01

Directed co-assembly of binary nanoparticles (NPs) into one-dimensional copolymer-like chains is fascinating but challenging in the realm of material science. While many strategies have been developed to induce the polymerization of NPs, it remains a grand challenge to produce colloidal copolymers with widely tailored compositions and precisely controlled architectures. Herein we report a robust colloidal polymerization strategy, which enables the growth of sophisticated NP chains with elaborately designed structures. By quantifying NP assembly statistics and kinetics, we establish that the linear assembly of colloidal NPs, with the assistance of PbSO4 clusters, follows a step-growth polymerization mechanism, and on the basis of this, we design and fabricate NP chains structurally analogous to random, block, and alternating copolymers, respectively. Our studies offer mechanistic insights into cluster-mediated colloidal polymerization, paving the way toward the rational synthesis of colloidal copolymers with quantitatively predicted architectures and functionalities. PMID:29862003

Phases and Dynamics of Self-Assembled DNA Programmed Nanocubes

NASA Astrophysics Data System (ADS)

Knorowski, Christopher; Travesset, Alex

2013-03-01

Systems of Nanoparticles grafted with complementary DNA strands have been shown to self-assemble into an array of superlattices. In this talk, we extend our previous model, which successfully predicted equilibrium phases and dynamics of assembly for spherical Nanoparticles without fitting parameters, to the case of nanocubes. We show that the phase diagram consists of bcc and sc lattices, depending on DNA length. The bcc lattices are either rotator and orientational glass or cubatic. For temperatures above the DNA melting temperature, the system is equivalent to f-star polymer systems, and consist of bcc, also with rotator, orientational glass or cubatic orientational order as well as sc. We also provide a characterization of the dynamics, including the role of topological defects in crystal nucleation and growth. This work is funded by DOE through the Ames Lab under Contract DE-AC02-07CH11358. Most simulations are performed on the Exalted GPU cluster, which is funded by a grant from Iowa State University and Nvidia Corp.

Multiple filters affect tree species assembly in mid-latitude forest communities.

PubMed

Kubota, Y; Kusumoto, B; Shiono, T; Ulrich, W

2018-05-01

Species assembly patterns of local communities are shaped by the balance between multiple abiotic/biotic filters and dispersal that both select individuals from species pools at the regional scale. Knowledge regarding functional assembly can provide insight into the relative importance of the deterministic and stochastic processes that shape species assembly. We evaluated the hierarchical roles of the α niche and β niches by analyzing the influence of environmental filtering relative to functional traits on geographical patterns of tree species assembly in mid-latitude forests. Using forest plot datasets, we examined the α niche traits (leaf and wood traits) and β niche properties (cold/drought tolerance) of tree species, and tested non-randomness (clustering/over-dispersion) of trait assembly based on null models that assumed two types of species pools related to biogeographical regions. For most plots, species assembly patterns fell within the range of random expectation. However, particularly for cold/drought tolerance-related β niche properties, deviation from randomness was frequently found; non-random clustering was predominant in higher latitudes with harsh climates. Our findings demonstrate that both randomness and non-randomness in trait assembly emerged as a result of the α and β niches, although we suggest the potential role of dispersal processes and/or species equalization through trait similarities in generating the prevalence of randomness. Clustering of β niche traits along latitudinal climatic gradients provides clear evidence of species sorting by filtering particular traits. Our results reveal that multiple filters through functional niches and stochastic processes jointly shape geographical patterns of species assembly across mid-latitude forests.

PAVE: program for assembling and viewing ESTs.

PubMed

Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

2009-08-26

New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

Superstructure based on β-CD self-assembly induced by a small guest molecule†

PubMed Central

De Sousa, Frederico B.; Lima, Ana C.; Denadai, Ângelo M. L.; Anconi, Cleber P. A.; De Almeida, Wagner B.; Novato, Willian T. G.; Dos Santos, Hélio F.; Drum, Chester L.; Langer, Robert

2014-01-01

The size, shape and surface chemistry of nanoparticles play an important role in cellular interaction. Thus, the main objective of the present study was the determination of the β-cyclodextrin (β-CD) self-assembly thermodynamic parameters and its structure, aiming to use these assemblies as a possible controlled drug release system. Light scattering measurements led us to obtain the β-CD’s critical aggregation concentration (cac) values, and consequently the thermodynamic parameters of the β-CD spontaneous self-assembly in aqueous solution: ΔaggGo = − 16.31 kJ mol−1, ΔaggHo = − 26.48 kJ mol−1 and TΔaggSo = − 10.53 kJ mol−1 at 298.15 K. Size distribution of the self-assembled nanoparticles below and above cac was 1.5 nm and 60–120 nm, respectively. The number of β-CD molecules per cluster and the second virial coefficient were identified through Debye’s plot and molecular dynamic simulations proposed the three-fold assembly for this system below cac. Ampicillin (AMP) was used as a drug model in order to investigate the key role of the guest molecule in the self-assembly process and the β-CD:AMP supramolecular system was studied in solution, aiming to determine the structure of the supramolecular aggregate. Results obtained in solution indicated that the β-CD’s cac was not affected by adding AMP. Moreover, different complex stoichiometries were identified by nuclear magnetic resonance and isothermal titration calorimetry experiments. PMID:22234498

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 bidispersity in DNA strand lengths on the thermodynamics and structure of assembly of functionalized nanoparticles. We find that higher G/C content increases cluster dissociation temperature for smaller particles. Placement of G/C block inward along the strand decreases number of neighbors within the assembled cluster. Finally, increased bidispersity in DNA strand lengths leads a distribution of inter-particle distances in the assembled cluster.

Intra-spindle Microtubule Assembly Regulates Clustering of Microtubule-Organizing Centers during Early Mouse Development.

PubMed

Watanabe, Sadanori; Shioi, Go; Furuta, Yasuhide; Goshima, Gohta

2016-04-05

Errors during cell division in oocytes and early embryos are linked to birth defects in mammals. Bipolar spindle assembly in early mouse embryos is unique in that three or more acentriolar microtubule-organizing centers (MTOCs) are initially formed and are then clustered into two spindle poles. Using a knockout mouse and live imaging of spindles in embryos, we demonstrate that MTOC clustering during the blastocyst stage requires augmin, a critical complex for MT-dependent MT nucleation within the spindle. Functional analyses in cultured cells with artificially increased numbers of centrosomes indicate that the lack of intra-spindle MT nucleation, but not loss of augmin per se or overall reduction of spindle MTs, is the cause of clustering failure. These data suggest that onset of mitosis with three or more MTOCs is turned into a typical bipolar division through augmin-dependent intra-spindle MT assembly. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Fe-S cluster assembly in the supergroup Excavata.

PubMed

Peña-Diaz, Priscila; Lukeš, Julius

2018-04-05

The majority of established model organisms belong to the supergroup Opisthokonta, which includes yeasts and animals. While enlightening, this focus has neglected protists,  organisms that represent the bulk of eukaryotic diversity and are often regarded as primitive eukaryotes. One of these is the "supergroup" Excavata, which comprises unicellular flagellates of diverse lifestyles and contains species of medical importance, such as Trichomonas, Giardia, Naegleria, Trypanosoma and Leishmania. Excavata exhibits a continuum in mitochondrial forms, ranging from classical aerobic, cristae-bearing mitochondria to mitochondria-related organelles, such as hydrogenosomes and mitosomes, to the extreme case of a complete absence of the organelle. All forms of mitochondria house a machinery for the assembly of Fe-S clusters, ancient cofactors required in various biochemical activities needed to sustain every extant cell. In this review, we survey what is known about the Fe-S cluster assembly in the supergroup Excavata. We aim to bring attention to the diversity found in this group, reflected in gene losses and gains that have shaped the Fe-S cluster biogenesis pathways.

Clustering of cycloidal wave energy converters

DOEpatents

Siegel, Stefan G.

2016-03-29

A wave energy conversion system uses a pair of wave energy converters (WECs) on respective active mountings on a floating platform, so that the separation of the WECs from each other or from a central WEC can be actively adjusted according to the wavelength of incident waves. The adjustable separation facilitates operation of the system to cancel reactive forces, which may be generated during wave energy conversion. Modules on which such pairs of WECs are mounted can be assembled with one or more central WECs to form large clusters in which reactive forces and torques can be made to cancel. WECs of different sizes can be employed to facilitate cancelation of reactive forces and torques.

Investigating the Co-Adsorption Behavior of Nucleic-Acid Base (Thymine and Cytosine) and Melamine at Liquid/Solid Interface

NASA Astrophysics Data System (ADS)

Zhao, Huiling; Li, Yinli; Chen, Dong; Liu, Bo

2016-12-01

The co-adsorption behavior of nucleic-acid base (thymine; cytosine) and melamine was investigated by scanning tunneling microscopy (STM) technique at liquid/solid (1-octanol/graphite) interface. STM characterization results indicate that phase separation happened after dropping the mixed solution of thymine-melamine onto highly oriented pyrolytic graphite (HOPG) surface, while the hetero-component cluster-like structure was observed when cytosine-melamine binary assembly system is used. From the viewpoints of non-covalent interactions calculated by using density functional theory (DFT) method, the formation mechanisms of these assembled structures were explored in detail. This work will supply a methodology to design the supramolecular assembled structures and the hetero-component materials composed by biological and chemical compound.

Galaxy And Mass Assembly (GAMA): the signatures of galaxy interactions as viewed from small scale galaxy clustering

NASA Astrophysics Data System (ADS)

Gunawardhana, M. L. P.; Norberg, P.; Zehavi, I.; Farrow, D. J.; Loveday, J.; Hopkins, A. M.; Davies, L. J. M.; Wang, L.; Alpaslan, M.; Bland-Hawthorn, J.; Brough, S.; Holwerda, B. W.; Owers, M. S.; Wright, A. H.

2018-06-01

Statistical studies of galaxy-galaxy interactions often utilise net change in physical properties of progenitors as a function of the separation between their nuclei to trace both the strength and the observable timescale of their interaction. In this study, we use two-point auto, cross and mark correlation functions to investigate the extent to which small-scale clustering properties of star forming galaxies can be used to gain physical insight into galaxy-galaxy interactions between galaxies of similar optical brightness and stellar mass. The Hα star formers, drawn from the highly spatially complete Galaxy And Mass Assembly (GAMA) survey, show an increase in clustering on small separations. Moreover, the clustering strength shows a strong dependence on optical brightness and stellar mass, where (1) the clustering amplitude of optically brighter galaxies at a given separation is larger than that of optically fainter systems, (2) the small scale clustering properties (e.g. the strength, the scale at which the signal relative to the fiducial power law plateaus) of star forming galaxies appear to differ as a function of increasing optical brightness of galaxies. According to cross and mark correlation analyses, the former result is largely driven by the increased dust content in optically bright star forming galaxies. The latter could be interpreted as evidence of a correlation between interaction-scale and optical brightness of galaxies, where physical evidence of interactions between optically bright star formers, likely hosted within relatively massive halos, persist over larger separations than those between optically faint star formers.

Soybean Fe-S cluster biosynthesis regulated by external iron or phosphate fluctuation.

PubMed

Qin, Lu; Wang, Meihuan; Chen, Liyu; Liang, Xuejiao; Wu, Zhigeng; Lin, Zhihao; Zuo, Jia; Feng, Xiangyang; Zhao, Jing; Liao, Hong; Ye, Hong

2015-03-01

Iron and phosphorus are essential for soybean nodulation. Our results suggested that the deficiency of Fe or P impairs nodulation by affecting the assembly of functional iron-sulfur cluster via different mechanisms. Iron (Fe) and phosphorus (P) are important mineral nutrients for soybean and are indispensable for nodulation. However, it remains elusive how the pathways of Fe metabolism respond to the fluctuation of external Fe or P. Iron is required for the iron-sulfur (Fe-S) cluster assembly in higher plant. Here, we investigated the expression pattern of Fe-S cluster biosynthesis genes in the nodulated soybean. Soybean genome encodes 42 putative Fe-S cluster biosynthesis genes, which were expressed differently in shoots and roots, suggesting of physiological relevance. Nodules initiated from roots of soybean after rhizobia inoculation. In comparison with that in shoots, iron concentration was three times higher in nodules. The Fe-S cluster biosynthesis genes were activated and several Fe-S protein activities were increased in nodules, indicating that a more effective Fe-S cluster biosynthesis is accompanied by nodulation. Fe-S cluster biosynthesis genes were massively repressed and some Fe-S protein activities were decreased in nodules by Fe deficiency, leading to tiny nodules. Notably, P deficiency induced a similar Fe-deficiency response in nodules, i.e, certain Fe-S enzyme activity loss and tiny nodules. However, distinct from Fe-deficient nodules, higher iron concentration was accumulated and the Fe-S cluster biosynthesis genes were not suppressed in the P-deficiency-treated nodules. Taken together, our results showed that both Fe deficiency and P deficiency impair nodulation, but they affect the assembly of Fe-S cluster maybe via different mechanisms. The data also suggested that Fe-S cluster biosynthesis likely links Fe metabolism and P metabolism in root and nodule cells of soybean.

An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

NASA Astrophysics Data System (ADS)

Poursina, Mohammad; Anderson, Kurt S.

2014-08-01

This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

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

PubMed

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

2014-03-03

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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

PubMed Central

Heidelberg, John F.; Tully, Benjamin J.

2017-01-01

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes. PMID:28289564

Engineering emergent multicellular behavior through synthetic adhesion

NASA Astrophysics Data System (ADS)

Glass, David; Riedel-Kruse, Ingmar

In over a decade, synthetic biology has developed increasingly robust gene networks within single cells, but constructed very few systems that demonstrate multicellular spatio-temporal dynamics. We are filling this gap in synthetic biology's toolbox by developing an E. coli self-assembly platform based on modular cell-cell adhesion. We developed a system in which adhesive selectivity is provided by a library of outer membrane-displayed peptides with intra-library specificities, while affinity is provided by consistent expression across the entire library. We further provide a biophysical model to help understand the parameter regimes in which this tool can be used to self-assemble into cellular clusters, filaments, or meshes. The combined platform will enable future development of synthetic multicellular systems for use in consortia-based metabolic engineering, in living materials, and in controlled study of minimal multicellular systems. Stanford Bio-X Bowes Fellowship.

A Bridging [4Fe-4S] Cluster and Nucleotide Binding Are Essential for Function of the Cfd1-Nbp35 Complex as a Scaffold in Iron-Sulfur Protein Maturation*

PubMed Central

Netz, Daili J. A.; Pierik, Antonio J.; Stümpfig, Martin; Bill, Eckhard; Sharma, Anil K.; Pallesen, Leif J.; Walden, William E.; Lill, Roland

2012-01-01

The essential P-loop NTPases Cfd1 and Nbp35 of the cytosolic iron-sulfur (Fe-S) protein assembly machinery perform a scaffold function for Fe-S cluster synthesis. Both proteins contain a nucleotide binding motif of unknown function and a C-terminal motif with four conserved cysteine residues. The latter motif defines the Mrp/Nbp35 subclass of P-loop NTPases and is suspected to be involved in transient Fe-S cluster binding. To elucidate the function of these two motifs, we first created cysteine mutant proteins of Cfd1 and Nbp35 and investigated the consequences of these mutations by genetic, cell biological, biochemical, and spectroscopic approaches. The two central cysteine residues (CPXC) of the C-terminal motif were found to be crucial for cell viability, protein function, coordination of a labile [4Fe-4S] cluster, and Cfd1-Nbp35 hetero-tetramer formation. Surprisingly, the two proximal cysteine residues were dispensable for all these functions, despite their strict evolutionary conservation. Several lines of evidence suggest that the C-terminal CPXC motifs of Cfd1-Nbp35 coordinate a bridging [4Fe-4S] cluster. Upon mutation of the nucleotide binding motifs Fe-S clusters could no longer be assembled on these proteins unless wild-type copies of Cfd1 and Nbp35 were present in trans. This result indicated that Fe-S cluster loading on these scaffold proteins is a nucleotide-dependent step. We propose that the bridging coordination of the C-terminal Fe-S cluster may be ideal for its facile assembly, labile binding, and efficient transfer to target Fe-S apoproteins, a step facilitated by the cytosolic iron-sulfur (Fe-S) protein assembly proteins Nar1 and Cia1 in vivo. PMID:22362766

Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting.

PubMed

Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying

2015-06-01

In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. Copyright © 2015 Elsevier Inc. All rights reserved.

Atomically precise arrays of fluorescent silver clusters: a modular approach for metal cluster photonics on DNA nanostructures.

PubMed

Copp, Stacy M; Schultz, Danielle E; Swasey, Steven; Gwinn, Elisabeth G

2015-03-24

The remarkable precision that DNA scaffolds provide for arraying nanoscale optical elements enables optical phenomena that arise from interactions of metal nanoparticles, dye molecules, and quantum dots placed at nanoscale separations. However, control of ensemble optical properties has been limited by the difficulty of achieving uniform particle sizes and shapes. Ligand-stabilized metal clusters offer a route to atomically precise arrays that combine desirable attributes of both metals and molecules. Exploiting the unique advantages of the cluster regime requires techniques to realize controlled nanoscale placement of select cluster structures. Here we show that atomically monodisperse arrays of fluorescent, DNA-stabilized silver clusters can be realized on a prototypical scaffold, a DNA nanotube, with attachment sites separated by <10 nm. Cluster attachment is mediated by designed DNA linkers that enable isolation of specific clusters prior to assembly on nanotubes and preserve cluster structure and spectral purity after assembly. The modularity of this approach generalizes to silver clusters of diverse sizes and DNA scaffolds of many types. Thus, these silver cluster nano-optical elements, which themselves have colors selected by their particular DNA templating oligomer, bring unique dimensions of control and flexibility to the rapidly expanding field of nano-optics.

Change the Collective Behaviors of Colloidal Motors by Tuning Electrohydrodynamic Flow at the Subparticle Level.

PubMed

Yang, Xingfu; Wu, Ning

2018-01-23

As demonstrated in biological systems, breaking the symmetry of surrounding hydrodynamic flow is the key to achieve autonomous locomotion of microscopic objects. In recent years, a variety of synthetic motors have been developed based on different propulsion mechanisms. Most work, however, focuses on the propulsion of individual motors. Here, we study the collective behaviors of colloidal dimers actuated by a perpendicularly applied AC electric field, which controls the electrohydrodynamic flow at subparticle levels. Although these motors experience strong dipolar repulsion from each other and are highly active, surprisingly, they assemble into a family of stable planar clusters with handedness. We show that this type of unusual structure arises from the contractile hydrodynamic flow around small lobes but extensile flow around the large lobes. We further reveal that the collective behavior, assembled structure, and assembly dynamics of these motors all depend on the specific directions of electrohydrodynamic flow surrounding each lobe of the dimers. By fine-tuning the surface charge asymmetry on particles and salt concentration in solution, we demonstrate the ability to control their collective behaviors on demand. This novel type of active assembly via hydrodynamic interactions has the potential to grow monodisperse clusters in a self-limiting fashion. The underlying concept revealed in this work should also apply to other types of active and asymmetric particles.

Lipid self-assembly and lectin-induced reorganization of the plasma membrane.

PubMed

Sych, Taras; Mély, Yves; Römer, Winfried

2018-05-26

The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Self-assembled inorganic clusters of semiconducting quantum dots for effective solar hydrogen evolution.

PubMed

Gao, Yu-Ji; Yang, Yichen; Li, Xu-Bing; Wu, Hao-Lin; Meng, Shu-Lin; Wang, Yang; Guo, Qing; Huang, Mao-Yong; Tung, Chen-Ho; Wu, Li-Zhu

2018-05-08

Owing to promoted electron-hole separation, the catalytic activity of semiconducting quantum dots (QDs) towards solar hydrogen (H2) production has been significantly enhanced by forming self-assembled clusters with ZnSe QDs made ex situ. Taking advantage of the favored interparticle hole transfer to ZnSe QDs, the rate of solar H2 evolution of CdSe QDs can be increased to ∼30 000 μmol h-1 g-1 with ascorbic acid as the sacrificial reagent, ∼150-fold higher than that of bare CdSe QDs clusters under the same conditions.

Rotation in young massive star clusters

NASA Astrophysics Data System (ADS)

Mapelli, Michela

2017-05-01

Hydrodynamical simulations of turbulent molecular clouds show that star clusters form from the hierarchical merger of several sub-clumps. We run smoothed-particle hydrodynamics simulations of turbulence-supported molecular clouds with mass ranging from 1700 to 43 000 M⊙. We study the kinematic evolution of the main cluster that forms in each cloud. We find that the parent gas acquires significant rotation, because of large-scale torques during the process of hierarchical assembly. The stellar component of the embedded star cluster inherits the rotation signature from the parent gas. Only star clusters with final mass < few × 100 M⊙ do not show any clear indication of rotation. Our simulated star clusters have high ellipticity (˜0.4-0.5 at t = 4 Myr) and are subvirial (Qvir ≲ 0.4). The signature of rotation is stronger than radial motions due to subvirial collapse. Our results suggest that rotation is common in embedded massive (≳1000 M⊙) star clusters. This might provide a key observational test for the hierarchical assembly scenario.

A Modified Gibson Assembly Method for Cloning Large DNA Fragments with High GC Contents.

PubMed

Li, Lei; Jiang, Weihong; Lu, Yinhua

2018-01-01

Gibson one-step, isothermal assembly method (Gibson assembly) can be used to efficiently assemble large DNA molecules by in vitro recombination involving a 5'-exonuclease, a DNA polymerase and a DNA ligase. In the past few years, this robust DNA assembly method has been widely applied to seamlessly construct genes, genetic pathways and even entire genomes. Here, we expand this method to clone large DNA fragments with high GC contents, such as antibiotic biosynthetic gene clusters from Streptomyces . Due to the low isothermal condition (50 °C) in the Gibson reaction system, the complementary overlaps with high GC contents are proposed to easily form mismatched linker pairings, which leads to low assembly efficiencies mainly due to vector self-ligation. So, we modified this classic method by the following two steps. First, a pair of universal terminal single-stranded DNA overhangs with high AT contents are added to the ends of the BAC vector. Second, two restriction enzyme sites are introduced into the respective sides of the designed overlaps to achieve the hierarchical assembly of large DNA molecules. The optimized Gibson assembly method facilitates fast acquisition of large DNA fragments with high GC contents from Streptomyces.

A PEG/copper(i) halide cluster as an eco-friendly catalytic system for C-N bond formation.

PubMed

Li, Cheng-An; Ji, Wei; Qu, Jian; Jing, Su; Gao, Fei; Zhu, Dun-Ru

2018-05-22

The catalytic activities of eight copper(i) halide clusters assembled from copper(i) halide and ferrocenyltelluroethers, 1-8, were investigated in C-N formation under various conditions. A catalytic procedure using poly(ethylene glycol) (PEG-400) as a greener alternative organic solvent has been developed. The PEG-400/5 system can achieve 99% targeted yield with a mild reaction temperature and short reaction time. After the isolation of the products by extraction with diethyl ether, this PEG-400/cluster system could be easily recycled. Spectroscopic studies elucidate a stepwise mechanism: firstly, proton-coupled electron transfer (PCET) involving the transfer of an electron from Cu+ and a proton from imidazole results in the formation of a labile penta-coordinated Cu2+ and aryl radical; the following effective electron transfer from the ferrocene unit reduces Cu2+ and forms the target product; finally, the ferrocenium unit is reduced by the I- anion. The merits of this eco-friendly synthesis are the efficient utilization of reagents and easy recyclability.

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.

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

Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals

PubMed Central

2013-01-01

Background Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea. Results We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs longer than 100 bp, with N50 values of 1,665 bp and 1,439 bp, respectively. Using the proteome of the sea anemone Nematostella vectensis as a reference, we were able to annotate almost 20% of each dataset using reciprocal homology searches. Homologous clustering of these annotated transcripts allowed us to divide them into 7,186 (Fav1) and 6,862 (Fav2) homologous transcript clusters (E-value ≤ 2e-30). Functional annotation categories were assigned to homologous clusters using the functional annotation of Nematostella vectensis. General annotation of the assembled transcripts was improved 1-3% using the Acropora digitifera proteome. In addition, we screened these transcript isoform clusters for fluorescent proteins (FPs) homologs and identified seven potential FP homologs in Fav1, and four in Fav2. These transcripts were validated as bona fide FP transcripts via robust fluorescence heterologous expression. Annotation of the assembled contigs revealed that 1.34% and 1.61% (in Fav1 and Fav2, respectively) of the total assembled contigs likely originated from the corals’ algal symbiont, Symbiodinium spp. Conclusions Here we present a study to identify the homologous transcript isoform clusters from the transcriptome of Favia corals using a far-related reference proteome. Furthermore, the symbiont-derived transcripts were isolated from the datasets and their contribution quantified. This is the first annotated transcriptome of the genus Favia, a major increase in genomics resources available in this important family of corals. PMID:23937070

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design

NASA Astrophysics Data System (ADS)

Indelicato, G.; Burkhard, P.; Twarock, R.

2017-04-01

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.

Environmental filtering of eudicot lineages underlies phylogenetic clustering in tropical South American flooded forests.

PubMed

Aldana, Ana M; Carlucci, Marcos B; Fine, Paul V A; Stevenson, Pablo R

2017-02-01

The phylogenetic community assembly approach has been used to elucidate the role of ecological and historical processes in shaping tropical tree communities. Recent studies have shown that stressful environments, such as seasonally dry, white-sand and flooded forests tend to be phylogenetically clustered, arguing for niche conservatism as the main driver for this pattern. Very few studies have attempted to identify the lineages that contribute to such assembly patterns. We aimed to improve our understanding of the assembly of flooded forest tree communities in Northern South America by asking the following questions: are seasonally flooded forests phylogenetically clustered? If so, which angiosperm lineages are over-represented in seasonally flooded forests? To assess our hypotheses, we investigated seasonally flooded and terra firme forests from the Magdalena, Orinoco and Amazon Basins, in Colombia. Our results show that, regardless of the river basin in which they are located, seasonally flooded forests of Northern South America tend to be phylogenetically clustered, which means that the more abundant taxa in these forests are more closely related to each other than expected by chance. Based on our alpha and beta phylodiversity analyses we interpret that eudicots are more likely to adapt to extreme environments such as seasonally flooded forests, which indicates the importance of environmental filtering in the assembly of the Neotropical flora.

Kinetic Assembly of Near-IR Active Gold Nanoclusters using Weakly Adsorbing Polymers to Control Size

PubMed Central

Tam, Jasmine M.; Murthy, Avinash K.; Ingram, Davis R.; Nguyen, Robin; Sokolov, Konstantin V.; Johnston, Keith P.

2013-01-01

Clusters of metal nanoparticles with an overall size less than 100 nm and high metal loadings for strong optical functionality, are of interest in various fields including microelectronics, sensors, optoelectronics and biomedical imaging and therapeutics. Herein we assemble ~5 nm gold particles into clusters with controlled size, as small as 30 nm and up to 100 nm, which contain only small amounts of polymeric stabilizers. The assembly is kinetically controlled with weakly adsorbing polymers, PLA(2K)-b-PEG(10K)-b-PLA(2K) or PEG (MW = 3350), by manipulating electrostatic, van der Waals (VDW), steric, and depletion forces. The cluster size and optical properties are tuned as a function of particle volume fractions and polymer/gold ratios to modulate the interparticle interactions. The close spacing between the constituent gold nanoparticles and high gold loadings (80–85% w/w gold) produce a strong absorbance cross section of ~9×10−15 m2 in the NIR at 700 nm. This morphology results from VDW and depletion attractive interactions that exclude the weakly adsorbed polymeric stabilizer from the cluster interior. The generality of this kinetic assembly platform is demonstrated for gold nanoparticles with a range of surface charges from highly negative to neutral, with the two different polymers. PMID:20361735

Type III Pilus of Corynebacteria: Pilus Length Is Determined by the Level of Its Major Pilin Subunit

PubMed Central

Swierczynski, Arlene; Ton-That, Hung

2006-01-01

Multiple pilus gene clusters have been identified in several gram-positive bacterial genomes sequenced to date, including the Actinomycetales, clostridia, streptococci, and corynebacteria. The genome of Corynebacterium diphtheriae contains three pilus gene clusters, two of which have been previously characterized. Here, we report the characterization of the third pilus encoded by the spaHIG cluster. By using electron microscopy and biochemical analysis, we demonstrate that SpaH forms the pilus shaft, while SpaI decorates the structure and SpaG is largely located at the pilus tip. The assembly of the SpaHIG pilus requires a specific sortase located within the spaHIG pilus gene cluster. Deletion of genes specific for the synthesis and polymerization of the other two pilus types does not affect the SpaHIG pilus. Moreover, SpaH but not SpaI or SpaG is essential for the formation of the filament. When expressed under the control of an inducible promoter, the amount of the SpaH pilin regulates pilus length; no pili are assembled from an SpaH precursor that has an alanine in place of the conserved lysine of the SpaH pilin motif. Thus, the spaHIG pilus gene cluster encodes a pilus structure that is independently assembled and antigenically distinct from other pili of C. diphtheriae. We incorporate these findings in a model of sortase-mediated pilus assembly that may be applicable to many gram-positive pathogens. PMID:16923899

Type III pilus of corynebacteria: Pilus length is determined by the level of its major pilin subunit.

PubMed

Swierczynski, Arlene; Ton-That, Hung

2006-09-01

Multiple pilus gene clusters have been identified in several gram-positive bacterial genomes sequenced to date, including the Actinomycetales, clostridia, streptococci, and corynebacteria. The genome of Corynebacterium diphtheriae contains three pilus gene clusters, two of which have been previously characterized. Here, we report the characterization of the third pilus encoded by the spaHIG cluster. By using electron microscopy and biochemical analysis, we demonstrate that SpaH forms the pilus shaft, while SpaI decorates the structure and SpaG is largely located at the pilus tip. The assembly of the SpaHIG pilus requires a specific sortase located within the spaHIG pilus gene cluster. Deletion of genes specific for the synthesis and polymerization of the other two pilus types does not affect the SpaHIG pilus. Moreover, SpaH but not SpaI or SpaG is essential for the formation of the filament. When expressed under the control of an inducible promoter, the amount of the SpaH pilin regulates pilus length; no pili are assembled from an SpaH precursor that has an alanine in place of the conserved lysine of the SpaH pilin motif. Thus, the spaHIG pilus gene cluster encodes a pilus structure that is independently assembled and antigenically distinct from other pili of C. diphtheriae. We incorporate these findings in a model of sortase-mediated pilus assembly that may be applicable to many gram-positive pathogens.

Architecture of Eph receptor clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Himanen, Juha P.; Yermekbayeva, Laila; Janes, Peter W.

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 mechanismmore » 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.« less

The Balloon Experimental Twin Telescope for Infrared Interferometry (BETTII): Towards the First Flight

NASA Technical Reports Server (NTRS)

Rizzo, Maxime J.; Rinehart, S. A.; Dhabal, A.; Ade, P.; Benford, D. J.; Fixsen, D. J.; Griffin, M.; Juanola Parramon, R.; Leisawitz, D. T.; Maher, S. F.;

Robust X-ray angular correlations for the study of meso-structures

DOE PAGES

Lhermitte, Julien R.; Tian, Cheng; Stein, Aaron; ...

2017-05-08

As self-assembling nanomaterials become more sophisticated, it is becoming increasingly important to measure the structural order of finite-sized assemblies of nano-objects. These mesoscale clusters represent an acute challenge to conventional structural probes, owing to the range of implicated size scales (10 nm to several micrometres), the weak scattering signal and the dynamic nature of meso-clusters in native solution environments. The high X-ray flux and coherence of modern synchrotrons present an opportunity to extract structural information from these challenging systems, but conventional ensemble X-ray scattering averages out crucial information about local particle configurations. Conversely, a single meso-cluster scatters too weakly tomore » recover the full diffraction pattern. Using X-ray angular cross-correlation analysis, it is possible to combine multiple noisy measurements to obtain robust structural information. This paper explores the key theoretical limits and experimental challenges that constrain the application of these methods to probing structural order in real nanomaterials. A metric is presented to quantify the signal-to-noise ratio of angular correlations, and it is used to identify several experimental artifacts that arise. In particular, it is found that background scattering, data masking and inter-cluster interference profoundly affect the quality of correlation analyses. A robust workflow is demonstrated for mitigating these effects and extracting reliable angular correlations from realistic experimental data.« less

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.

Superlattices assembled through shape-induced directional binding

DOE PAGES

Lu, Fang; Yager, Kevin G.; Zhang, Yugang; ...

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 bymore » 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.« less

Room-temperature isolation of V(benzene)2 sandwich clusters via soft-landing into n-alkanethiol self-assembled monolayers.

PubMed

Nagaoka, Shuhei; Matsumoto, Takeshi; Okada, Eiji; Mitsui, Masaaki; Nakajima, Atsushi

2006-08-17

The adsorption state and thermal stability of V(benzene)2 sandwich clusters soft-landed onto a self-assembled monolayer of different chain-length n-alkanethiols (Cn-SAM, n = 8, 12, 16, 18, and 22) were studied by means of infrared reflection absorption spectroscopy (IRAS) and temperature-programmed desorption (TPD). The IRAS measurement confirmed that V(benzene)2 clusters are molecularly adsorbed and maintain a sandwich structure on all of the SAM substrates. In addition, the clusters supported on the SAM substrates are oriented with their molecular axes tilted 70-80 degrees off the surface normal. An Arrhenius analysis of the TPD spectra reveals that the activation energy for the desorption of the supported clusters increases linearly with the chain length of the SAMs. For the longest chain C22-SAM, the activation energy reaches approximately 150 kJ/mol, and the thermal desorption of the supported clusters can be considerably suppressed near room temperature. The clear chain-length-dependent thermal stability of the supported clusters observed here can be explained well in terms of the cluster penetration into the SAM matrixes.

Cysteine 295 indirectly affects Ni coordination of carbon monoxide dehydrogenase-II C-cluster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inoue, Takahiro; Takao, Kyosuke; Yoshida, Takashi

2013-11-08

Highlights: •CODH-II harbors a unique [Ni-Fe-S] cluster. •We substituted the ligand residues of Cys{sup 295} and His{sup 261}. •Dramatic decreases in Ni content upon substitutions were observed. •All substitutions did not affect Fe-S clusters assembly. •CO oxidation activity was decreased by the substitutions. -- Abstract: A unique [Ni–Fe–S] cluster (C-cluster) constitutes the active center of Ni-containing carbon monoxide dehydrogenases (CODHs). His{sup 261}, which coordinates one of the Fe atoms with Cys{sup 295}, is suggested to be the only residue required for Ni coordination in the C-cluster. To evaluate the role of Cys{sup 295}, we constructed CODH-II variants. Ala substitution formore » the Cys{sup 295} substitution resulted in the decrease of Ni content and didn’t result in major change of Fe content. In addition, the substitution had no effect on the ability to assemble a full complement of [Fe–S] clusters. This strongly suggests Cys{sup 295} indirectly and His{sup 261} together affect Ni-coordination in the C-cluster.« less

QCS : a system for querying, clustering, and summarizing documents.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunlavy, Daniel M.

2006-08-01

Information retrieval systems consist of many complicated components. Research and development of such systems is often hampered by the difficulty in evaluating how each particular component would behave across multiple systems. We present a novel hybrid information retrieval system--the Query, Cluster, Summarize (QCS) system--which is portable, modular, and permits experimentation with different instantiations of each of the constituent text analysis components. Most importantly, the combination of the three types of components in the QCS design improves retrievals by providing users more focused information organized by topic. We demonstrate the improved performance by a series of experiments using standard test setsmore » from the Document Understanding Conferences (DUC) along with the best known automatic metric for summarization system evaluation, ROUGE. Although the DUC data and evaluations were originally designed to test multidocument summarization, we developed a framework to extend it to the task of evaluation for each of the three components: query, clustering, and summarization. Under this framework, we then demonstrate that the QCS system (end-to-end) achieves performance as good as or better than the best summarization engines. Given a query, QCS retrieves relevant documents, separates the retrieved documents into topic clusters, and creates a single summary for each cluster. In the current implementation, Latent Semantic Indexing is used for retrieval, generalized spherical k-means is used for the document clustering, and a method coupling sentence ''trimming'', and a hidden Markov model, followed by a pivoted QR decomposition, is used to create a single extract summary for each cluster. The user interface is designed to provide access to detailed information in a compact and useful format. Our system demonstrates the feasibility of assembling an effective IR system from existing software libraries, the usefulness of the modularity of the design, and the value of this particular combination of modules.« less

QCS: a system for querying, clustering and summarizing documents.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunlavy, Daniel M.; Schlesinger, Judith D.; O'Leary, Dianne P.

2006-10-01

Information retrieval systems consist of many complicated components. Research and development of such systems is often hampered by the difficulty in evaluating how each particular component would behave across multiple systems. We present a novel hybrid information retrieval system--the Query, Cluster, Summarize (QCS) system--which is portable, modular, and permits experimentation with different instantiations of each of the constituent text analysis components. Most importantly, the combination of the three types of components in the QCS design improves retrievals by providing users more focused information organized by topic. We demonstrate the improved performance by a series of experiments using standard test setsmore » from the Document Understanding Conferences (DUC) along with the best known automatic metric for summarization system evaluation, ROUGE. Although the DUC data and evaluations were originally designed to test multidocument summarization, we developed a framework to extend it to the task of evaluation for each of the three components: query, clustering, and summarization. Under this framework, we then demonstrate that the QCS system (end-to-end) achieves performance as good as or better than the best summarization engines. Given a query, QCS retrieves relevant documents, separates the retrieved documents into topic clusters, and creates a single summary for each cluster. In the current implementation, Latent Semantic Indexing is used for retrieval, generalized spherical k-means is used for the document clustering, and a method coupling sentence 'trimming', and a hidden Markov model, followed by a pivoted QR decomposition, is used to create a single extract summary for each cluster. The user interface is designed to provide access to detailed information in a compact and useful format. Our system demonstrates the feasibility of assembling an effective IR system from existing software libraries, the usefulness of the modularity of the design, and the value of this particular combination of modules.« less

Novel Soluble Dietary Fiber-Tannin Self-Assembled Film: A Promising Protein Protective Material.

PubMed

Song, Guo-Bin; Xu, Juan; Zheng, Hua; Feng, Ying; Zhang, Wen-Wen; Li, Kun; Ge, Shuang-shuang; Li, Kai; Zhang, Hong

2015-06-24

In this experiment, a natural promising protein protective film was fabricated through soluble dietary fiber (SDF)-tannin nanocluster self-assembly. FT-IR, XRD, and DSC tests were employed to investigate the interaction between the SDF and tannins before and after cross-linking induced by calcium ion. On the other hand, referring to the SEM and TEM results, the self-assembly process of the protein protective film could be indicated as follows: first, calcium ion, with its cross-ability, served as the "nucleus"; SDF and tannins were combined to prepare the nanoscale SDF-tannin clusters; then, the clusters were homogeneously deposited on the surface of protein to form a protective film by self-assembling hydrogen bond between tannin component of clusters as "adhesive" and protein in aqueous solutions under very mild conditions. Film thickness could also be controlled by tannin of different concentrations ranging from 114 to 1384 μm. Antibacterial test and in vitro cytotoxicity test proved that the film had a broad spectrum of antimicrobial properties and excellent cell biocompatibility, respectively, which might open up new applications in the food preservation and biomedical fields.

Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations

PubMed Central

Miller, Ian J.; Chevrette, Marc G.; Kwan, Jason C.

2017-01-01

Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction. Finally, to explore sequencing parameters that affect the recovery and contiguity of large and repetitive BGCs assembled de novo, we simulate Illumina and PacBio sequencing of the Salinispora tropica genome focusing on assembly of the salinilactam (slm) BGC. PMID:28587290

Atomically precise organomimetic cluster nanomolecules assembled via perfluoroaryl-thiol SNAr chemistry

NASA Astrophysics Data System (ADS)

Qian, Elaine A.; Wixtrom, Alex I.; Axtell, Jonathan C.; Saebi, Azin; Jung, Dahee; Rehak, Pavel; Han, Yanxiao; Moully, Elamar Hakim; Mosallaei, Daniel; Chow, Sylvia; Messina, Marco S.; Wang, Jing Yang; Royappa, A. Timothy; Rheingold, Arnold L.; Maynard, Heather D.; Král, Petr; Spokoyny, Alexander M.

2017-04-01

The majority of biomolecules are intrinsically atomically precise, an important characteristic that enables rational engineering of their recognition and binding properties. However, imparting a similar precision to hybrid nanoparticles has been challenging because of the inherent limitations of existing chemical methods and building blocks. Here we report a new approach to form atomically precise and highly tunable hybrid nanomolecules with well-defined three-dimensionality. Perfunctionalization of atomically precise clusters with pentafluoroaryl-terminated linkers produces size-tunable rigid cluster nanomolecules. These species are amenable to facile modification with a variety of thiol-containing molecules and macromolecules. Assembly proceeds at room temperature within hours under mild conditions, and the resulting nanomolecules exhibit high stabilities because of their full covalency. We further demonstrate how these nanomolecules grafted with saccharides can exhibit dramatically improved binding affinity towards a protein. Ultimately, the developed strategy allows the rapid generation of precise molecular assemblies to investigate multivalent interactions.

Controlled expression of nif and isc iron-sulfur protein maturation components reveals target specificity and limited functional replacement between the two systems.

PubMed

Dos Santos, Patricia C; Johnson, Deborah C; Ragle, Brook E; Unciuleac, Mihaela-Carmen; Dean, Dennis R

2007-04-01

The nitrogen-fixing organism Azotobacter vinelandii contains at least two systems that catalyze formation of [Fe-S] clusters. One of these systems is encoded by nif genes, whose products supply [Fe-S] clusters required for maturation of nitrogenase. The other system is encoded by isc genes, whose products are required for maturation of [Fe-S] proteins that participate in general metabolic processes. The two systems are similar in that they include an enzyme for the mobilization of sulfur (NifS or IscS) and an assembly scaffold (NifU or IscU) upon which [Fe-S] clusters are formed. Normal cellular levels of the Nif system, which supplies [Fe-S] clusters for the maturation of nitrogenase, cannot also supply [Fe-S] clusters for the maturation of other cellular [Fe-S] proteins. Conversely, when produced at the normal physiological levels, the Isc system cannot supply [Fe-S] clusters for the maturation of nitrogenase. In the present work we found that such target specificity for IscU can be overcome by elevated production of NifU. We also found that NifU, when expressed at normal levels, is able to partially replace the function of IscU if cells are cultured under low-oxygen-availability conditions. In contrast to the situation with IscU, we could not establish conditions in which the function of IscS could be replaced by NifS. We also found that elevated expression of the Isc components, as a result of deletion of the regulatory iscR gene, improved the capacity for nitrogen-fixing growth of strains deficient in either NifU or NifS.

Polyion-induced aggregation of oppositely charged liposomes and charged colloidal particles: the many facets of complex formation in low-density colloidal systems.

PubMed

Cametti, C

2008-10-01

This review focusses on recent developments in the experimental study of polyion-induced charged colloidal particle aggregation, with particular emphasis on the formation of cationic liposome clusters induced by the addition of anionic adsorbing polyions. These structures can be considered, under certain points of view, a new class of colloidal systems, with intriguing properties that opens interesting and promising new opportunities in various biotechnological applications. Lipidic structures of different morphologies and different structural complexities interacting with oppositely charged polyions give rise to a rich variety of self-assembled structures that present various orders of hierarchy in the sense that, starting from a basic level, for example a lipid bilayer, they arrange themselves into superstructures as, for example, multilamellar stacks or liquid-crystalline structures. These structures can be roughly divided into two classes according to the fact that the elementary structure, involved in building a more complex one, keeps or does not keeps its basic arrangement. To the first one, belong those aggregates composed by single structures that maintain their integrity, for example, lipidic vesicles assembled together by an appropriate external agent. The second one encompasses structures that do not resemble the ones of the original objects which form them, but, conversely, derive from a deep restructuring and rearrangement process, where the original morphology of the initial constitutive elements is completely lost. In this review, I will only briefly touch on higher level hierarchy structures and I will focus on the assembling processes involving preformed lipid bilayer vesicles that organize themselves into clusters, the process being induced by the adsorption of oppositely charged polyions. The scientific interest in polyion-induced liposome aggregates is two-fold. On the one hand, in soft-matter physics, they represent an interesting colloidal system, governed by a balance between long-range electrostatic repulsion and short-range attraction, resulting in relatively large, equilibrium clusters, whose size and overall charge can be continuously tunable by simple environmental parameters. These structures present a variety of behaviors with a not yet completely understood phenomenology. On the other hand, the resulting structures possess some peculiar properties that justify their employment as drug delivery systems. Bio-compatibility, stability and ability to deliver various bio-active molecules and, moreover, their environmental responsiveness make liposome-based clusters a versatile carrier, with possibility of efficient targeting to different organs and tissues. Among the different structures made possible by the aggregating mechanism (cationic particles stuck together by anionic polyions or conversely anionic particles stuck together by cationic polyions), I will review the main experimental evidences for the existence of cationic liposome clusters. Especial attention is paid to our own work, mainly aimed at the characterization of these novel structures from a physical point of view.

Bacterial motility complexes require the actin-like protein, MreB and the Ras homologue, MglA.

PubMed

Mauriello, Emilia M F; Mouhamar, Fabrice; Nan, Beiyan; Ducret, Adrien; Dai, David; Zusman, David R; Mignot, Tâm

2010-01-20

Gliding motility in the bacterium Myxococcus xanthus uses two motility engines: S-motility powered by type-IV pili and A-motility powered by uncharacterized motor proteins and focal adhesion complexes. In this paper, we identified MreB, an actin-like protein, and MglA, a small GTPase of the Ras superfamily, as essential for both motility systems. A22, an inhibitor of MreB cytoskeleton assembly, reversibly inhibited S- and A-motility, causing rapid dispersal of S- and A-motility protein clusters, FrzS and AglZ. This suggests that the MreB cytoskeleton is involved in directing the positioning of these proteins. We also found that a DeltamglA motility mutant showed defective localization of AglZ and FrzS clusters. Interestingly, MglA-YFP localization mimicked both FrzS and AglZ patterns and was perturbed by A22 treatment, consistent with results indicating that both MglA and MreB bind to motility complexes. We propose that MglA and the MreB cytoskeleton act together in a pathway to localize motility proteins such as AglZ and FrzS to assemble the A-motility machineries. Interestingly, M. xanthus motility systems, like eukaryotic systems, use an actin-like protein and a small GTPase spatial regulator.

Bacterial motility complexes require the actin-like protein, MreB and the Ras homologue, MglA

PubMed Central

Mauriello, Emilia M F; Mouhamar, Fabrice; Nan, Beiyan; Ducret, Adrien; Dai, David; Zusman, David R; Mignot, Tâm

2010-01-01

Gliding motility in the bacterium Myxococcus xanthus uses two motility engines: S-motility powered by type-IV pili and A-motility powered by uncharacterized motor proteins and focal adhesion complexes. In this paper, we identified MreB, an actin-like protein, and MglA, a small GTPase of the Ras superfamily, as essential for both motility systems. A22, an inhibitor of MreB cytoskeleton assembly, reversibly inhibited S- and A-motility, causing rapid dispersal of S- and A-motility protein clusters, FrzS and AglZ. This suggests that the MreB cytoskeleton is involved in directing the positioning of these proteins. We also found that a ΔmglA motility mutant showed defective localization of AglZ and FrzS clusters. Interestingly, MglA–YFP localization mimicked both FrzS and AglZ patterns and was perturbed by A22 treatment, consistent with results indicating that both MglA and MreB bind to motility complexes. We propose that MglA and the MreB cytoskeleton act together in a pathway to localize motility proteins such as AglZ and FrzS to assemble the A-motility machineries. Interestingly, M. xanthus motility systems, like eukaryotic systems, use an actin-like protein and a small GTPase spatial regulator. PMID:19959988

CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.

PubMed

Chou, A; Burke, J

1999-05-01

DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets. We present CRAWview, a Java based visualization extension to CRAW. Features that vary between gene forms are displayed using an automatically generated color coded index. The reporting format of CRAWview gives a brief, high level summary report to display overlap and divergence within clusters of sequences as well as the ability to 'drill down' and see detailed information concerning regions of interest. Additionally, the alignment viewing and editing capabilities of CRAWview make it possible to interactively correct frame-shifts and otherwise edit cluster assemblies. We have implemented CRAWview as a Java application across windows NT/95 and UNIX platforms. A beta version of CRAWview will be freely available to academic users from Pangea Systems (http://www.pangeasystems.com). Contact :

Mechanical gate control for atom-by-atom cluster assembly with scanning probe microscopy.

PubMed

Sugimoto, Yoshiaki; Yurtsever, Ayhan; Hirayama, Naoki; Abe, Masayuki; Morita, Seizo

2014-07-11

Nanoclusters supported on substrates are of great importance in physics and chemistry as well as in technical applications, such as single-electron transistors and nanocatalysts. The properties of nanoclusters differ significantly from those of either the constituent atoms or the bulk solid, and are highly sensitive to size and chemical composition. Here we propose a novel atom gating technique to assemble various atom clusters composed of a defined number of atoms at room temperature. The present gating operation is based on the transfer of single diffusing atoms among nanospaces governed by gates, which can be opened in response to the chemical interaction force with a scanning probe microscope tip. This method provides an alternative way to create pre-designed atom clusters with different chemical compositions and to evaluate their chemical stabilities, thus enabling investigation into the influence that a single dopant atom incorporated into the host clusters has on a given cluster stability.

The BUFFALO HST Survey

NASA Astrophysics Data System (ADS)

Steinhardt, Charles; Jauzac, Mathilde; Capak, Peter; Koekemoer, Anton; Oesch, Pascal; Richard, Johan; Sharon, Keren q.; BUFFALO

2018-01-01

Beyond Ultra-deep Frontier Fields And Legacy Observations (BUFFALO) is an astronomical survey built around the six Hubble Space Telescope (HST) Frontier Fields clusters designed to learn about early galactic assembly and clustering and prepare targets for observations with the James Webb Space Telescope. BUFFALO will place significant new constraints on how and when the most massive and luminous galaxies in the universe formed and how early galaxy formation is linked to dark matter assembly. The same data will also probe the temperature and cross section of dark matter in the massive Frontier Fields galaxy clusters, and tell us how the dark matter, cluster gas, and dynamics of the clusters influence the galaxies in and around them. These studies are possible because the Spitzer Space Telescope, Chandra X-ray Observatory, XMM-Newton, and ground based telescopes have already invested heavily in deep observations around the Frontier Fields, so that the addition of HST observations can yield significant new results.

Binding branched and linear DNA structures: From isolated clusters to fully bonded gels

NASA Astrophysics Data System (ADS)

Fernandez-Castanon, J.; Bomboi, F.; Sciortino, F.

2018-01-01

The proper design of DNA sequences allows for the formation of well-defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well-defined valence, namely, tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10 °C to 55 °C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel, and as a cluster fluid depending on the selected r.

Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics.

PubMed

Zou, Xuan; Wang, Lianrong; Li, Zhiqiang; Luo, Jie; Wang, Yunfu; Deng, Zixin; Du, Shiming; Chen, Shi

2018-01-01

Antibiotic production is often governed by large gene clusters composed of genes related to antibiotic scaffold synthesis, tailoring, regulation, and resistance. With the expansion of genome sequencing, a considerable number of antibiotic gene clusters has been isolated and characterized. The emerging genome engineering techniques make it possible towards more efficient engineering of antibiotics. In addition to genomic editing, multiple synthetic biology approaches have been developed for the exploration and improvement of antibiotic natural products. Here, we review the progress in the development of these genome editing techniques used to engineer new antibiotics, focusing on three aspects of genome engineering: direct cloning of large genomic fragments, genome engineering of gene clusters, and regulation of gene cluster expression. This review will not only summarize the current uses of genomic engineering techniques for cloning and assembly of antibiotic gene clusters or for altering antibiotic synthetic pathways but will also provide perspectives on the future directions of rebuilding biological systems for the design of novel antibiotics. © 2017 Wiley Periodicals, Inc.

Living Clusters and Crystals from Low-Density Suspensions of Active Colloids

NASA Astrophysics Data System (ADS)

Mognetti, B. M.; Šarić, A.; Angioletti-Uberti, S.; Cacciuto, A.; Valeriani, C.; Frenkel, D.

2013-12-01

Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.

Clustering and assembly dynamics of a one-dimensional microphase former.

PubMed

Hu, Yi; Charbonneau, Patrick

2018-05-23

Both ordered and disordered microphases ubiquitously form in suspensions of particles that interact through competing short-range attraction and long-range repulsion (SALR). While ordered microphases are more appealing materials targets, understanding the rich structural and dynamical properties of their disordered counterparts is essential to controlling their mesoscale assembly. Here, we study the disordered regime of a one-dimensional (1D) SALR model, whose simplicity enables detailed analysis by transfer matrices and Monte Carlo simulations. We first characterize the signature of the clustering process on macroscopic observables, and then assess the equilibration dynamics of various simulation algorithms. We notably find that cluster moves markedly accelerate the mixing time, but that event chains are of limited help in the clustering regime. These insights will inspire further study of three-dimensional microphase formers.

Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches (474th Brookhaven Lecture)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gang, Oleg

2012-01-18

In the field of nanoscience, if you can control how nanoparticles self-assemble in particular structures — joining each other, for example, as molecules can form, atom-by-atom — you can design new materials that have unique properties that industry needs. Nature already uses the DNA genetic code to instruct the building of specific proteins and whole organisms in both plants and people. Taking a cue from nature, scientists at BNL devised a way of using strands of synthetic DNA attached to the surface of nanoparticles to instruct them to self-assemble into specific nanoscale structures, clusters, and three-dimensional organizations. Novel materials designedmore » and fabricated this way promise use in photovoltaics, energy storage, catalysis, cell-targeted systems for more effective medical treatments, and biomolecular sensing for environmental monitoring and medical applications. To find out more about the rapid evolution of this nanoassembly method and its applications, join Physicist Oleg Gang of the Center for Functional Nanomaterials (CFN) as he gives the 474th Brookhaven Lecture, titled “Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches." Gang, who has led this work at the CFN, will explain the rapid evolution of this nanoassembly method, and discuss its present and future applications in highly specific biosensors, optically active nano-materials, and new ways to fabricate complex architectures in a rational manner via self-assembly. Gang and his colleagues used the CFN and the National Synchrotron Light Source (NSLS) facilities to perform their groundbreaking research. At the CFN, the scientists used electron microscopes and optical methods to visualize the clusters that they fabricated. At the NSLS, they applied x-rays to study a particles-assembly process in solution, DNA’s natural environment. Gang earned a Ph.D. in soft matter physics from Bar-Ilan University in 2000, and he was a Rothschild Fellow at Harvard University from 1999 to 2002. After joining BNL as a Goldhaber Fellow in 2002, he became an assistant scientist at the CFN in 2004. He became the CFN’s leader for Soft and Biological Nanomaterials Theme Group in 2006, and earned the title of scientist in 2009. Gang has received numerous honors and recognitions, including the 2010 Gordon Battelle Prize for Scientific Discovery.« less

Self-assembly of colloids with magnetic caps

NASA Astrophysics Data System (ADS)

Novak, E. V.; Kantorovich, S. S.

2017-06-01

In our earlier work (Steinbach et al., 2016 [1]) we investigated a homogeneous system of magnetically capped colloidal particles that self-assembled via two structural patterns of different symmetry. The particles could form a compact, equilateral triangle with a three-fold rotational symmetry and zero dipole moment and a staggered chain with mirror symmetry with a net magnetisation perpendicular to the chain. The system exhibited a bistability already in clusters of three particles. Based on observations of a real magnetic particles system, analytical calculations and molecular dynamics simulations, it has been shown that the bistability is a result of an anisotropic magnetisation distribution with rotational symmetry inside the particles. The present study is a logical extension of the above research and forms a preparatory stage for the study of a self-assembly of such magnetic particles under the influence of an external magnetic field. Since the magnetic field is only an additive contribution to the total ground state energy, we can study the interparticle interaction energies of candidate ground state structures based on the field-free terms.

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. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A VTVH MCD and EPR Spectroscopic Study of the Maturation of the "Second" Nitrogenase P-Cluster.

PubMed

Rupnik, Kresimir; Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W; Hales, Brian J

2018-04-16

The P-cluster of the nitrogenase MoFe protein is a [ Fe 8 S 7 ] cluster that mediates efficient transfer of electrons to the active site for substrate reduction. Arguably the most complex homometallic FeS cluster found in nature, the biosynthetic mechanism of the P-cluster is of considerable theoretical and synthetic interest to chemists and biochemists alike. Previous studies have revealed a biphasic assembly mechanism of the two P-clusters in the MoFe protein upon incubation with Fe protein and ATP, in which the first P-cluster is formed through fast fusion of a pair of [ Fe 4 S 4 ] + clusters within 5 min and the second P-cluster is formed through slow fusion of the second pair of [ Fe 4 S 4 ] + clusters in a period of 2 h. Here we report a VTVH MCD and EPR spectroscopic study of the biosynthesis of the slow-forming, second P-cluster within the MoFe protein. Our results show that the first major step in the formation of the second P-cluster is the conversion of one of the precursor [ Fe 4 S 4 ] + clusters into the integer spin cluster [ Fe 4 S 3-4 ] α , a process aided by the assembly protein NifZ, whereas the second major biosynthetic step appears to be the formation of a diamagnetic cluster with a possible structure of [ Fe 8 S 7-8 ] β , which is eventually converted into the P-cluster.

Aqueous Isolation of 17-Nuclear Zr-/Hf- Oxide Clusters during the Hydrothermal Synthesis of ZrO2/HfO2.

PubMed

Sung, Qing; Liu, Caiyun; Zhang, Guanyun; Zhang, Jian; Tung, Chen-Ho; Wang, Yifeng

2018-06-21

Novel 17-nuclear Zr-/Hf- oxide clusters ({Zr17} and {Hf17}) are isolated from aqueous systems. In the clusters, Zr/Hf ions are connected via μ3-O, μ3-OH and μ2-OH linkages into a pinwheel core which is wrapped with SO42-, HCOO- and aqua ligands. Octahedral hexanuclear Zr-/Hf- oxide clusters ({Zr6}oct and {Hf6}oct) are also isolated from the same hydrothermal system by decreasing the synthesis temperature. Structural analysis, synthetic conditions, vibrational spectra and ionic conductivity of the clusters are studied. Structural studies and synthesis inspection suggest that formation of {Zr6}oct and {Zr17} involves assembly of the same transferable building blocks, but the condensation degree and thermodynamic stability of the products increase with hydrothermal temperature. The role of {Zr6}oct and {Zr17} in the formation of ZrO2 nanocrystals are then discussed in the scenario of nonclassical nucleation theory. Besides, the Zr-oxide clusters exhibit ionic conductivity due to the mobility of protons. This study not only adds new members to the Zr-/Hf- oxide cluster family, but also establishes a connection from Zr4+ ions to ZrO2 in the hydrothermal preparation of zirconium oxide nanomaterials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Globular clusters and environmental effects in galaxy clusters

NASA Astrophysics Data System (ADS)

Sales, Laura

2016-10-01

Globular clusters are old compact stellar systems orbiting around galaxies of all types. Tens of thousands of them can also be found populating the intra-cluster regions of nearby galaxy clusters like Virgo and Coma. Thanks to the HST Frontier Fields program, GCs are starting now to be detected also in intermediate redshift clusters. Yet, despite their ubiquity, a theoretical model for the formation and evolution of GCs is still missing, especially within the cosmological context.Here we propose to use cosmological hydrodynamical simulations of 18 galaxy clusters coupled to a post-processing GC formation model to explore the assembly of galaxies in clusters together with their expected GC population. The method, which has already been implemented and tested, will allow us to characterize for the first time the number, radial distribution and kinematics of GCs in clusters, with products directly comparable to observational maps. We will explore cluster-to-cluster variations and also characterize the build up of the intra-cluster component of GCs with time.As the method relies on a detailed study of the star-formation history of galaxies, we will jointly constrain the predicted quenching time-scales for satellites and the occurrence of starburst events associated to infall and orbital pericenters of galaxies in massive clusters. This will inform further studies on the distribution, velocity and properties of post-starburst galaxies in past, ongoing and future HST programs.

Electrodynamic tailoring of self-assembled three-dimensional electrospun constructs

NASA Astrophysics Data System (ADS)

Reis, Tiago C.; Correia, Ilídio J.; Aguiar-Ricardo, Ana

2013-07-01

The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive electrostatic forces between the positively charged aerial fibers and the already collected ones, which tend to acquire a negatively charged network oriented towards the nozzle. The in situ polarization degree is strengthened by higher amounts of clustered fibers, and therefore the initial high density fibrous regions are the preliminary motifs for the self-assembly mechanism. As such regions increase their in situ polarization electrostatic repulsive forces will appear, favoring a competitive growth of these self-assembled fibrous clusters. Highly polarized regions will evidence higher distances between consecutive micro-assembled fibers (MAFs). Different processing parameters - deposition time, electric field intensity, concentration of polymer solution, environmental temperature and relative humidity - were evaluated in an attempt to control material's design.The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive electrostatic forces between the positively charged aerial fibers and the already collected ones, which tend to acquire a negatively charged network oriented towards the nozzle. The in situ polarization degree is strengthened by higher amounts of clustered fibers, and therefore the initial high density fibrous regions are the preliminary motifs for the self-assembly mechanism. As such regions increase their in situ polarization electrostatic repulsive forces will appear, favoring a competitive growth of these self-assembled fibrous clusters. Highly polarized regions will evidence higher distances between consecutive micro-assembled fibers (MAFs). Different processing parameters - deposition time, electric field intensity, concentration of polymer solution, environmental temperature and relative humidity - were evaluated in an attempt to control material's design. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr01668d

Clustering biomolecular complexes by residue contacts similarity.

PubMed

Rodrigues, João P G L M; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J

2012-07-01

Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions. Albeit widely used, these measures suffer from several theoretical and technical limitations (e.g., choice of regions for fitting) that impair their application in multicomponent systems (N > 2), large-scale studies (e.g., interactomes), and other time-critical scenarios. We present here a simple similarity measure for structural clustering based on atomic contacts--the fraction of common contacts--and compare it with the most used similarity measure of the protein docking community--interface backbone RMSD. We show that this method produces very compact clusters in remarkably short time when applied to a collection of binary and multicomponent protein-protein and protein-DNA complexes. Furthermore, it allows easy clustering of similar conformations of multicomponent symmetrical assemblies in which chain permutations can occur. Simple contact-based metrics should be applicable to other structural biology clustering problems, in particular for time-critical or large-scale endeavors. Copyright © 2012 Wiley Periodicals, Inc.

Iron loading site on the Fe-S cluster assembly scaffold protein is distinct from the active site.

PubMed

Rodrigues, Andria V; Kandegedara, Ashoka; Rotondo, John A; Dancis, Andrew; Stemmler, Timothy L

2015-06-01

Iron-sulfur (Fe-S) cluster containing proteins are utilized in almost every biochemical pathway. The unique redox and coordination chemistry associated with the cofactor allows these proteins to participate in a diverse set of reactions, including electron transfer, enzyme catalysis, DNA synthesis and signaling within several pathways. Due to the high reactivity of the metal, it is not surprising that biological Fe-S cluster assembly is tightly regulated within cells. In yeast, the major assembly pathway for Fe-S clusters is the mitochondrial ISC pathway. Yeast Fe-S cluster assembly is accomplished using the scaffold protein (Isu1) as the molecular foundation, with assistance from the cysteine desulfurase (Nfs1) to provide sulfur, the accessory protein (Isd11) to regulate Nfs1 activity, the yeast frataxin homologue (Yfh1) to regulate Nfs1 activity and participate in Isu1 Fe loading possibly as a chaperone, and the ferredoxin (Yah1) to provide reducing equivalents for assembly. In this report, we utilize calorimetric and spectroscopic methods to provide molecular insight into how wt-Isu1 from S. cerevisiae becomes loaded with iron. Isothermal titration calorimetry and an iron competition binding assay were developed to characterize the energetics of protein Fe(II) binding. Differential scanning calorimetry was used to identify thermodynamic characteristics of the protein in the apo state or under iron loaded conditions. Finally, X-ray absorption spectroscopy was used to characterize the electronic and structural properties of Fe(II) bound to Isu1. Current data are compared to our previous characterization of the D37A Isu1 mutant, and these suggest that when Isu1 binds Fe(II) in a manner not perturbed by the D37A substitution, and that metal binding occurs at a site distinct from the cysteine rich active site in the protein.

Self-assembled three-dimensional chiral colloidal architecture.

PubMed

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C; Sha, Ruojie; Seeman, Nadrian C; Chaikin, Paul M

2017-11-03

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Central tracker for BM@N experiment based on double side Si-microstrip detectors

NASA Astrophysics Data System (ADS)

Kovalev, Yu.; Kapishin, M.; Khabarov, S.; Shafronovskaia, A.; Tarasov, O.; Makankin, A.; Zamiatin, N.; Zubarev, E.

2017-07-01

Design of central tracker system based on Double-Sided Silicon Detectors (DSSD) for BM@N experiment is described. A coordinate plane with 10240 measuring channels, pitch adapter, reading electronics was developed. Each element was tested and assembled into a coordinate plane. The first tests of the plane with 106Ru source were carried out before installation for the BM@N experiment. The results of the study indicate that noisy channels and inefficient channels are less than 3%. In general, single clusters 87% (one group per module of consecutive strips) and 75% of clusters with a width equal to one strip.

Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules.

PubMed

Morphew, Daniel; Shaw, James; Avins, Christopher; Chakrabarti, Dwaipayan

2018-03-27

Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals. We obtain cubic diamond and body-centered cubic crystals via distinct clusters of uniform size and shape, namely, tetrahedra and octahedra, respectively. Such a conceptual design framework has the potential to reliably encode hierarchical self-assembly of colloidal particles into a high level of sophistication. Moreover, the design framework underpins a bottom-up route to cubic diamond colloidal crystals, which have remained elusive despite being much sought after for their attractive photonic applications.

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems.

PubMed

Lee, Eun Cheol; Kim, Dongwook; Jurecka, Petr; Tarakeshwar, P; Hobza, Pavel; Kim, Kwang S

2007-05-10

Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.

Roles of Fe-S proteins: from cofactor synthesis to iron homeostasis to protein synthesis.

PubMed

Pain, Debkumar; Dancis, Andrew

2016-06-01

Fe-S cluster assembly is an essential process for all cells. Impairment of Fe-S cluster assembly creates diseases in diverse and surprising ways. In one scenario, the loss of function of lipoic acid synthase, an enzyme with Fe-S cluster cofactor in mitochondria, impairs activity of various lipoamide-dependent enzymes with drastic consequences for metabolism. In a second scenario, the heme biosynthetic pathway in red cell precursors is specifically targeted, and iron homeostasis is perturbed, but lipoic acid synthesis is unaffected. In a third scenario, tRNA modifications arising from action of the cysteine desulfurase and/or Fe-S cluster proteins are lost, which may lead to impaired protein synthesis. These defects can then result in cancer, neurologic dysfunction or type 2 diabetes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Light Irradiation as Key to Shape and Function of Nano-Assemblies in Solution

NASA Astrophysics Data System (ADS)

Groehn, Franziska

Developing strategies to exploit solar energy become more and more important. Inspired by natural systems it is highly promising to self-assemble functional species into effective tailored supramolecular units. Here we report self-assembled polymer structures in solution, taking advantage of optical properties of hybrid structures and light responsiveness. A new type of photocatalytically active self-assembled polymer structure in aqueous solution consists of supramolecular nano-objects obtained from macroions and multivalent inorganic ``counterions'' such as nanoparticles or clusters. These can exhibit expressed selectivity or even allow catalytic reactions in solution that are not possible with the building blocks only. Further, polyelectrolyte-porphyrin nanoscale assemblies exhibit tunable optical properties including strong fluorescence and an up to 20-fold higher photocatalytic activity than without polymeric template. A different approach is to transfer light energy into mechanical energy. Here, light energy is converted into nanoscale shape changes. This route for the conversion of light is highly promising for applications in drug delivery, nanosensors and solar energy conversion. Membership of DPG, Germany ID 153159-.

Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery

PubMed Central

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

2016-01-01

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

Symmetry and topology code of the cluster self-assembly of framework MT structures of alumophosphates AlPO4(H2O)2 (metavariscite and variscite) and Al2(PO4)2(H2O)3 (APC)

NASA Astrophysics Data System (ADS)

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

2017-03-01

The supramolecular chemistry of alumophosphates, which form framework 3D MT structures from polyhedral AlO4(H2O)2 clusters with octahedral O coordination (of M polyhedra) and PO4 and AlO4 with tetrahedral O coordination (of T polyhedra), is considered. A combinatorial-topological modeling of the formation of possible types of linear (six types) and ring (two types) tetrapolyhedral cluster precursors M2T2 from MT monomers is carried out. Different versions of chain formation from linked (MT)2 rings (six types) are considered. The model, which has a universal character, has been used to simulate the cluster selfassembly of the crystal structure of AlPO4(H2O)2 minerals (metavariscite, m-VAR, and variscite, VAR) and zeolite [Al2(PO4)2(H2O)2] · H2O (APC). A tetrapolyhedral linear precursor is established for m-VAR and a ring precursor (MT)2 is established for VAR and APC. The symmetry and topology code of the processes of crystal structure self-assembly from cluster precursors is completely reconstructed. The functional role of the O-H···O hydrogen bonds is considered for the first time. The cluster self-assembly model explains the specific features of the morphogenesis of single crystals: m-VAR prisms, flattened VAR octahedra, and needleshaped APC square-base prisms.

Collective transport for active matter run-and-tumble disk systems on a traveling-wave substrate

DOE PAGES

Sándor, Csand; Libál, Andras; Reichhardt, Charles; ...

2017-01-17

Here, we examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of themore » substrate speed, maximum substrate force, disk run time, and disk density. Since variation of the disk activity parameters produces different disk drift rates for a fixed traveling-wave speed on the substrate, the system we consider could be used as an efficient method for active matter species separation. Within the cluster phase, we find that in some regimes the motion of the cluster center of mass is in the opposite direction to that of the traveling wave, while when the maximum substrate force is increased, the cluster drifts in the direction of the traveling wave. This suggests that swarming or clustering motion can serve as a method by which an active system can collectively move against an external drift.« less

Collective transport for active matter run-and-tumble disk systems on a traveling-wave substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sándor, Csand; Libál, Andras; Reichhardt, Charles

Here, we examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of themore » substrate speed, maximum substrate force, disk run time, and disk density. Since variation of the disk activity parameters produces different disk drift rates for a fixed traveling-wave speed on the substrate, the system we consider could be used as an efficient method for active matter species separation. Within the cluster phase, we find that in some regimes the motion of the cluster center of mass is in the opposite direction to that of the traveling wave, while when the maximum substrate force is increased, the cluster drifts in the direction of the traveling wave. This suggests that swarming or clustering motion can serve as a method by which an active system can collectively move against an external drift.« less

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

DTIC Science & Technology

2009-07-01

Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102...dimensional (3-D) protein structures are critical for the understanding of molecular mechanisms of living systems. Traditionally, X-ray crystallography...disordered proteins are often responsible for molecular recognition, molecular assembly, protein modifica- tion, and entropic chain activities in organisms [26

Association and dissociation of an aqueous amphiphile at elevated temperatures.

PubMed

Bowron, D T; Finney, J L

2007-08-23

The hydrophobic interaction is often thought to increase with increasing temperature. Although there is good experimental evidence for decreased aqueous solubility and increased clustering of both nonpolar and amphiphilic molecules as temperature is increased, the detailed nature of the changes in intermolecular interactions with temperature remain unknown. By use of isotope substitution neutron scattering difference measurements on a 0.04 mole fraction solution of tert-butanol in water as the solute clustering passes through a temperature maximum, the changes in local intermolecular structures are examined. Although, as expected, the solute molecules cluster through increased contact between their nonpolar head groups with the exclusion of water, the detailed geometry of the mutual interactions changes as temperature increases. As the clustering breaks up with further temperature increase, the local structures formed do not mirror those that were found in the low-temperature dispersed system: the disassembly process is not the reverse of assembly. The clusters formed by the solute head groups are reminiscent of structures that are found in systems of spherical molecules, modulated by the additional constraint of near-maximal hydrogen bonding between the polar tails of the alcohol and the solvent water. Although the overall temperature behavior is qualitatively what would be expected of a hydrophobically driven system, the way the system resolves the competing interactions and their different temperature dependencies is complex, suggesting it could be misleading to think of the aggregation of aqueous amphiphiles solely in terms of a hydrophobic driving force.

Cluster assembly in nitrogenase.

PubMed

Sickerman, Nathaniel S; Rettberg, Lee A; Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W

2017-05-09

The versatile enzyme system nitrogenase accomplishes the challenging reduction of N 2 and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe 8 S 7 ]-core P-cluster and a [MoFe 7 S 9 C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N 2 , and both originate from [Fe 4 S 4 ] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe 4 S 4 ] clusters on NifDK called the P*-cluster. An accessory protein NifZ aids in P-cluster fusion, and reductive coupling is facilitated by NifH in a stepwise manner to form P-cluster on each half of NifDK. For M-cluster biosynthesis, two [Fe 4 S 4 ] clusters on NifB are coupled with a carbon atom in a radical-SAM dependent process, and concomitant addition of a 'ninth' sulfur atom generates the [Fe 8 S 9 C]-core L-cluster. On the scaffold protein NifEN, L-cluster is matured to M-cluster by the addition of Mo and homocitrate provided by NifH. Finally, matured M-cluster in NifEN is directly transferred to NifDK, where a conformational change locks the cofactor in place. Mechanistic insights into these fascinating biosynthetic processes are detailed in this chapter. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Temperature-dependent self-assembly and rheological behavior of a thermoreversible pmma-P n BA-PMMA triblock copolymer gel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zabet, Mahla; Mishra, Satish; Boy, Ramiz

Self-assembly and mechanical properties of triblock copolymers in a mid-block selective solvent are of interest in many applications. Herein, we report physical assembly of an ABA triblock copolymer, [PMMA–PnBA–PMMA] in two different mid-block selective solvents, n-butanol and 2-ethyl-1-hexanol. Gel formation resulting from end-block associations and the corresponding changes in mechanical properties have been investigated over a temperature range of -80 °C to 60 °C, from near the solvent melting points to above the gelation temperature. Shear-rheometry, thermal analysis, and small-angle neutron scattering data reveal formation and transition of structure in these systems from a liquid state to a gel statemore » to a percolated cluster network with decrease in temperature. The aggregated PMMA end-blocks display a glass transition temperature. Our results provide new understanding into the structural changes of a self-assembled triblock copolymer gel over a large length scale and wide temperature range.« less

SufD and SufC ATPase activity are required for iron acquisition during in vivo Fe-S cluster formation on SufB.

PubMed

Saini, Avneesh; Mapolelo, Daphne T; Chahal, Harsimranjit K; Johnson, Michael K; Outten, F Wayne

2010-11-02

In vivo biogenesis of Fe-S cluster cofactors requires complex biosynthetic machinery to limit release of iron and sulfide, to protect the Fe-S cluster from oxidation, and to target the Fe-S cluster to the correct apoenzyme. The SufABCDSE pathway for Fe-S cluster assembly in Escherichia coli accomplishes these tasks under iron starvation and oxidative stress conditions that disrupt Fe-S cluster metabolism. Although SufB, SufC, and SufD are all required for in vivo Suf function, their exact roles are unclear. Here we show that SufB, SufC, and SufD, coexpressed with the SufS-SufE sulfur transfer pair, purify as two distinct complexes (SufBC(2)D and SufB(2)C(2)) that contain Fe-S clusters and FADH(2). These studies also show that SufC and SufD are required for in vivo Fe-S cluster formation on SufB. Furthermore, while SufD is dispensable for in vivo sulfur transfer, it is absolutely required for in vivo iron acquisition. Finally, we demonstrate for the first time that the ATPase activity of SufC is necessary for in vivo iron acquisition during Fe-S cluster assembly.

Evidence for an Accretion Origin for the Outer Halo Globular Cluster System of M31

NASA Astrophysics Data System (ADS)

Mackey, A. D.; Huxor, A. P.; Ferguson, A. M. N.; Irwin, M. J.; Tanvir, N. R.; McConnachie, A. W.; Ibata, R. A.; Chapman, S. C.; Lewis, G. F.

2010-07-01

We use a sample of newly discovered globular clusters from the Pan-Andromeda Archaeological Survey (PAndAS) in combination with previously cataloged objects to map the spatial distribution of globular clusters in the M31 halo. At projected radii beyond ≈30 kpc, where large coherent stellar streams are readily distinguished in the field, there is a striking correlation between these features and the positions of the globular clusters. Adopting a simple Monte Carlo approach, we test the significance of this association by computing the probability that it could be due to the chance alignment of globular clusters smoothly distributed in the M31 halo. We find that the likelihood of this possibility is low, below 1%, and conclude that the observed spatial coincidence between globular clusters and multiple tidal debris streams in the outer halo of M31 reflects a genuine physical association. Our results imply that the majority of the remote globular cluster system of M31 has been assembled as a consequence of the accretion of cluster-bearing satellite galaxies. This constitutes the most direct evidence to date that the outer halo globular cluster populations in some galaxies are largely accreted. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii.

Boundaries Control Collective Dynamics of Inertial Self-Propelled Robots.

PubMed

Deblais, A; Barois, T; Guerin, T; Delville, P H; Vaudaine, R; Lintuvuori, J S; Boudet, J F; Baret, J C; Kellay, H

2018-05-04

Simple ingredients, such as well-defined interactions and couplings for the velocity and orientation of self-propelled objects, are sufficient to produce complex collective behavior in assemblies of such entities. Here, we use assemblies of rodlike robots made motile through self-vibration. When confined in circular arenas, dilute assemblies of these rods act as a gas. Increasing the surface fraction leads to a collective behavior near the boundaries: polar clusters emerge while, in the bulk, gaslike behavior is retained. The coexistence between a gas and surface clusters is a direct consequence of inertial effects as shown by our simulations. A theoretical model, based on surface mediated transport accounts for this coexistence and illustrates the exact role of the boundaries. Our study paves the way towards the control of collective behavior: By using deformable but free to move arenas, we demonstrate that the surface induced clusters can lead to directed motion, while the topology of the surface states can be controlled by biasing the motility of the particles.

Preparation and high-resolution microscopy of gold cluster labeled nucleic acid conjugates and nanodevices

PubMed Central

Powell, Richard D.; Hainfeld, James F.

2013-01-01

Nanogold and undecagold are covalently linked gold cluster labels which enable the identification and localization of biological components with molecular precision and resolution. They can be prepared with different reactivities, which means they can be conjugated to a wide variety of molecules, including nucleic acids, at specific, unique sites. The location of these sites can be synthetically programmed in order to preserve the binding affinity of the conjugate and impart novel characteristics and useful functionality. Methods for the conjugation of undecagold and Nanogold to DNA and RNA are discussed, and applications of labeled conjugates to the high-resolution microscopic identification of binding sites and characterization of biological macromolecular assemblies are described. In addition to providing insights into their molecular structure and function, high-resolution microscopic methods also show how Nanogold and undecagold conjugates can be synthetically assembled, or self-assemble, into supramolecular materials to which the gold cluster labels impart useful functionality. PMID:20869258

Boundaries Control Collective Dynamics of Inertial Self-Propelled Robots

NASA Astrophysics Data System (ADS)

Deblais, A.; Barois, T.; Guerin, T.; Delville, P. H.; Vaudaine, R.; Lintuvuori, J. S.; Boudet, J. F.; Baret, J. C.; Kellay, H.

2018-05-01

Simple ingredients, such as well-defined interactions and couplings for the velocity and orientation of self-propelled objects, are sufficient to produce complex collective behavior in assemblies of such entities. Here, we use assemblies of rodlike robots made motile through self-vibration. When confined in circular arenas, dilute assemblies of these rods act as a gas. Increasing the surface fraction leads to a collective behavior near the boundaries: polar clusters emerge while, in the bulk, gaslike behavior is retained. The coexistence between a gas and surface clusters is a direct consequence of inertial effects as shown by our simulations. A theoretical model, based on surface mediated transport accounts for this coexistence and illustrates the exact role of the boundaries. Our study paves the way towards the control of collective behavior: By using deformable but free to move arenas, we demonstrate that the surface induced clusters can lead to directed motion, while the topology of the surface states can be controlled by biasing the motility of the particles.

Friedreich's Ataxia Variants I154F and W155R Diminish Frataxin-Based Activation of the Iron-Sulfur Cluster Assembly Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 defectivemore » 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.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Fang; Yager, Kevin G.; Zhang, Yugang

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 bymore » 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.« less

Structure and formation of highly luminescent protein-stabilized gold clusters† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc05086k

PubMed Central

Chevrier, D. M.; Thanthirige, V. D.; Luo, Z.; Driscoll, S.; Cho, P.; MacDonald, M. A.; Yao, Q.; Guda, R.; Xie, J.; Johnson, E. R.; Chatt, A.; Zheng, N.

2018-01-01

Highly luminescent gold clusters simultaneously synthesized and stabilized by protein molecules represent a remarkable category of nanoscale materials with promising applications in bionanotechnology as sensors. Nevertheless, the atomic structure and luminescence mechanism of these gold clusters are still unknown after several years of developments. Herein, we report findings on the structure, luminescence and biomolecular self-assembly of gold clusters stabilized by the large globular protein, bovine serum albumin. We highlight the surprising identification of interlocked gold-thiolate rings as the main gold structural unit. Importantly, such gold clusters are in a rigidified state within the protein scaffold, offering an explanation for their highly luminescent character. Combined free-standing cluster synthesis (without protecting protein scaffold) with rigidifying and un-rigidifying experiments, were designed to further verify the luminescence mechanism and gold atomic structure within the protein. Finally, the biomolecular self-assembly process of the protein-stabilized gold clusters was elucidated by time-dependent X-ray absorption spectroscopy measurements and density functional theory calculations. PMID:29732064

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

DOE PAGES

Tian, Ye; Wang, Tong; Liu, Wenyan; ...

2015-05-25

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling 3D nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA framemore » and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled that have designed particle arrangements.« less

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

NASA Astrophysics Data System (ADS)

Tian, Ye; Wang, Tong; Liu, Wenyan; Xin, Huolin L.; Li, Huilin; Ke, Yonggang; Shih, William M.; Gang, Oleg

2015-07-01

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling three-dimensional nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA frame and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled with designed particle arrangements.

Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

NASA Astrophysics Data System (ADS)

Podestà, Alessandro; Borghi, Francesca; Indrieri, Marco; Bovio, Simone; Piazzoni, Claudio; Milani, Paolo

2015-12-01

Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO2) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevant interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.

Nanomanufacturing of titania interfaces with controlled structural and functional properties by supersonic cluster beam deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podestà, Alessandro, E-mail: alessandro.podesta@mi.infn.it, E-mail: pmilani@mi.infn.it; Borghi, Francesca; Indrieri, Marco

Great emphasis is placed on the development of integrated approaches for the synthesis and the characterization of ad hoc nanostructured platforms, to be used as templates with controlled morphology and chemical properties for the investigation of specific phenomena of great relevance in interdisciplinary fields such as biotechnology, medicine, and advanced materials. Here, we discuss the crucial role and the advantages of thin film deposition strategies based on cluster-assembling from supersonic cluster beams. We select cluster-assembled nanostructured titania (ns-TiO{sub 2}) as a case study to demonstrate that accurate control over morphological parameters can be routinely achieved, and consequently, over several relevantmore » interfacial properties and phenomena, like surface charging in a liquid electrolyte, and proteins and nanoparticles adsorption. In particular, we show that the very good control of nanoscale morphology is obtained by taking advantage of simple scaling laws governing the ballistic deposition regime of low-energy, mass-dispersed clusters with reduced surface mobility.« less

Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly.

PubMed

Cai, Kai; Frederick, Ronnie O; Tonelli, Marco; Markley, John L

2018-06-01

Frataxin (FXN) is involved in mitochondrial iron‑sulfur (Fe-S) cluster biogenesis and serves to accelerate Fe-S cluster formation. FXN deficiency is associated with Friedreich ataxia, a neurodegenerative disease. We have used a combination of isothermal titration calorimetry and multinuclear NMR spectroscopy to investigate interactions among the components of the biological machine that carries out the assembly of iron‑sulfur clusters in human mitochondria. Our results show that FXN tightly binds a single Fe 2+ but not Fe 3+ . While FXN (with or without bound Fe 2+ ) does not bind the scaffold protein ISCU directly, the two proteins interact mutually when each is bound to the cysteine desulfurase complex ([NFS1] 2 :[ISD11] 2 :[Acp] 2 ), abbreviated as (NIA) 2 , where "N" represents the cysteine desulfurase (NFS1), "I" represents the accessory protein (ISD11), and "A" represents acyl carrier protein (Acp). FXN binds (NIA) 2 weakly in the absence of ISCU but more strongly in its presence. Fe 2+ -FXN binds to the (NIA) 2 -ISCU 2 complex without release of iron. However, upon the addition of both l-cysteine and a reductant (either reduced FDX2 or DTT), Fe 2+ is released from FXN as consistent with Fe 2+ -FXN being the proximal source of iron for Fe-S cluster assembly. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiang; Zhang, Shuai; Jiao, Fang

Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct vs two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent. When a short hydrophobic region is added to a sequence that directly forms crystalline particles, crystallization instead follows a two-stepmore » pathway that begins with creation of disordered clusters of 10-20 molecules and is characterized by highly non-linear crystallization kinetics in which clusters transform into ordered structures that then enter the growth phase. The results shed new light on non-classical crystallization mechanisms and have implications for design of self-assembling polymer systems.« less

Possible nucleus of the Bergman cluster in the Zn-Mg-Y alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Nakagawa, Masaya; Koyama, Yasumasa

2018-01-01

To understand the formation of the Bergman cluster in the F-type icosahedral quasicrystal (IQ), crystallographic relations between the quasicrystal and the intermetallic-compound H and Zn23Y6 phases in the Zn-Mg-Y alloy system were investigated mainly by transmission electron microscopy. It was found that, although sample rotations of about 1° were required to obtain simple crystallographic relations, the orientation relationship was established among the cubic-Fm?m Zn23Y6 structure, the hexagonal-P63/mmc H structure and the F-type IQ; that is, [? 1 3]c // the five-fold axis in the IQ // N(2 ? 0)H, and [1 1 0]c // the two-fold axis in the IQ // N(0 5 ? 3)H, where N(h k m l)H means the normal direction of the (h k m l)H plane in the H structure. The correspondences between atomic positions in the Bergman cluster and in the Zn23Y6 structure and between those in the cluster and in the H structure were investigated on the basis of the established relationship. As a result, an assembly of six short-penetrated-decagonal columns was identified as an appropriate nucleus in the formation of the Bergman cluster from these two structures.

The Role of SufS Is Restricted to Fe-S Cluster Biosynthesis in Escherichia coli.

PubMed

Bühning, Martin; Valleriani, Angelo; Leimkühler, Silke

2017-04-11

In Escherichia coli, two different systems that are important for the coordinate formation of Fe-S clusters have been identified, namely, the ISC and SUF systems. The ISC system is the housekeeping Fe-S machinery, which provides Fe-S clusters for numerous cellular proteins. The IscS protein of this system was additionally revealed to be the primary sulfur donor for several sulfur-containing molecules with important biological functions, among which are the molybdenum cofactor (Moco) and thiolated nucleosides in tRNA. Here, we show that deletion of central components of the ISC system in addition to IscS leads to an overall decrease in Fe-S cluster enzyme and molybdoenzyme activity in addition to a decrease in the number of Fe-S-dependent thiomodifications of tRNA, based on the fact that some proteins involved in Moco biosynthesis and tRNA thiolation are Fe-S-dependent. Complementation of the ISC deficient strains with the suf operon restored the activity of Fe-S-containing proteins, including the MoaA protein, which is involved in the conversion of 5'GTP to cyclic pyranopterin monophosphate in the fist step of Moco biosynthesis. While both systems share a high degree of similarity, we show that the function of their respective l-cysteine desulfurase IscS or SufS is specific for each cellular pathway. It is revealed that SufS cannot play the role of IscS in sulfur transfer for the formation of 2-thiouridine, 4-thiouridine, or the dithiolene group of molybdopterin, being unable to interact with TusA or ThiI. The results demonstrate that the role of the SUF system is exclusively restricted to Fe-S cluster assembly in the cell.

[Ti8Zr2O12(COO)16] Cluster: An Ideal Inorganic Building Unit for Photoactive Metal–Organic Frameworks

PubMed Central

2017-01-01

Metal–organic frameworks (MOFs) based on Ti-oxo clusters (Ti-MOFs) represent a naturally self-assembled superlattice of TiO2 nanoparticles separated by designable organic linkers as antenna chromophores, epitomizing a promising platform for solar energy conversion. However, despite the vast, diverse, and well-developed Ti-cluster chemistry, only a scarce number of Ti-MOFs have been documented. The synthetic conditions of most Ti-based clusters are incompatible with those required for MOF crystallization, which has severely limited the development of Ti-MOFs. This challenge has been met herein by the discovery of the [Ti8Zr2O12(COO)16] cluster as a nearly ideal building unit for photoactive MOFs. A family of isoreticular photoactive MOFs were assembled, and their orbital alignments were fine-tuned by rational functionalization of organic linkers under computational guidance. These MOFs demonstrate high porosity, excellent chemical stability, tunable photoresponse, and good activity toward photocatalytic hydrogen evolution reactions. The discovery of the [Ti8Zr2O12(COO)16] cluster and the facile construction of photoactive MOFs from this cluster shall pave the way for the development of future Ti-MOF-based photocatalysts. PMID:29392182

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

PubMed Central

Gregg, Christina M.; Goetzl, Sebastian; Jeoung, Jae-Hun

2016-01-01

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

Exploring the galaxy cluster-group transition regime at high redshifts. Physical properties of two newly detected z > 1 systems

NASA Astrophysics Data System (ADS)

Šuhada, R.; Fassbender, R.; Nastasi, A.; Böhringer, H.; de Hoon, A.; Pierini, D.; Santos, J. S.; Rosati, P.; Mühlegger, M.; Quintana, H.; Schwope, A. D.; Lamer, G.; Kohnert, J.; Pratt, G. W.

2011-06-01

Context. Multi-wavelength surveys for clusters of galaxies are opening a window on the elusive high-redshift (z > 1) cluster population. Well controlled statistical samples of distant clusters will enable us to answer questions about their cosmological context, early assembly phases and the thermodynamical evolution of the intracluster medium. Aims: We report on the detection of two z > 1 systems, XMMU J0302.2-0001 and XMMU J1532.2-0836, as part of the XMM-Newton Distant Cluster Project (XDCP) sample. We investigate the nature of the sources, measure their spectroscopic redshift and determine their basic physical parameters. Methods: The results of the present paper are based on the analysis of XMM-Newton archival data, optical/near-infrared imaging and deep optical follow-up spectroscopy of the clusters. Results: We confirm the X-ray source XMMU J0302.2-0001 as a gravitationally bound, bona fide cluster of galaxies at spectroscopic redshift z = 1.185. We estimate its M500 mass to (1.6 ± 0.3) × 1014 M⊙ from its measured X-ray luminosity. This ranks the cluster among intermediate mass system. In the case of XMMU J1532.2-0836 we find the X-ray detection to be coincident with a dynamically bound system of galaxies at z = 1.358. Optical spectroscopy reveals the presence of a central active galactic nucleus, which can be a dominant source of the detected X-ray emission from this system. We provide upper limits of X-ray parameters for the system and discuss cluster identification challenges in the high-redshift low-mass cluster regime. A third, intermediate redshift (z = 0.647) cluster, XMMU J0302.1-0000, is serendipitously detected in the same field as XMMU J0302.2-0001. We provide its analysis as well. Based on observations obtained with ESO Telescopes at the Paranal Observatory under program ID 080.A-0659 and 081.A-0312, observations collected at the Centro Astrnómico Hispano Alemán (CAHA) at Calar Alto, Spain operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC). X-ray observations were obtained by XMM-Newton.

Modular assembly of optical nanocircuits.

PubMed

Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

2014-05-29

A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic 'lumped' circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

Modular assembly of optical nanocircuits

NASA Astrophysics Data System (ADS)

Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

2014-05-01

A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic ‘lumped’ circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

Mapping the formation areas of giant molybdenum blue clusters: a spectroscopic study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Botar, Bogdan; Ellern, Arkady; Kogerler, Paul

2012-05-18

The self-assembly of soluble molybdenum blue species from simple molybdate solutions has primarily been associated with giant mixed-valent wheel-shaped cluster anions, derived from the {MoV/VI154/176} archetypes, and a {MoV/VI368} lemon-shaped cluster. The combined use of Raman spectroscopy and kinetic precipitation as self-assembly monitoring techniques and single-crystal X-ray diffraction is key to mapping the realm of molybdenum blue species by establishing spherical {MoV/VI102}-type Keplerates as an important giant molybdenum blue-type species. We additionally rationalize the empirical effect of reducing agent concentration on the formation of all three relevant skeletal types: wheel, lemon and spheres. Whereas both wheels and the lemon-shaped {MoV/VI368}more » cluster are obtained from weakly reduced molybdenum blue solutions, considerably higher reduced solutions lead to {MoV/VI102}-type Keplerates.« less

Graph-theoretic quantum system modelling for neuronal microtubules as hierarchical clustered quantum Hopfield networks

NASA Astrophysics Data System (ADS)

Srivastava, D. P.; Sahni, V.; Satsangi, P. S.

2014-08-01

Graph-theoretic quantum system modelling (GTQSM) is facilitated by considering the fundamental unit of quantum computation and information, viz. a quantum bit or qubit as a basic building block. Unit directional vectors "ket 0" and "ket 1" constitute two distinct fundamental quantum across variable orthonormal basis vectors, for the Hilbert space, specifying the direction of propagation of information, or computation data, while complementary fundamental quantum through, or flow rate, variables specify probability parameters, or amplitudes, as surrogates for scalar quantum information measure (von Neumann entropy). This paper applies GTQSM in continuum of protein heterodimer tubulin molecules of self-assembling polymers, viz. microtubules in the brain as a holistic system of interacting components representing hierarchical clustered quantum Hopfield network, hQHN, of networks. The quantum input/output ports of the constituent elemental interaction components, or processes, of tunnelling interactions and Coulombic bidirectional interactions are in cascade and parallel interconnections with each other, while the classical output ports of all elemental components are interconnected in parallel to accumulate micro-energy functions generated in the system as Hamiltonian, or Lyapunov, energy function. The paper presents an insight, otherwise difficult to gain, for the complex system of systems represented by clustered quantum Hopfield network, hQHN, through the application of GTQSM construct.

Correlating the magic numbers of inorganic nanomolecular assemblies with a {Pd84} molecular-ring Rosetta Stone

PubMed Central

Xu, Feng; Miras, Haralampos N.; Scullion, Rachel A.; Long, De-Liang; Thiel, Johannes; Cronin, Leroy

2012-01-01

Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate {Pd84}-ring cluster 3.3 nm in diameter; [Pd84O42(OAc)28(PO4)42]70- ({Pd84} ≡ {Pd12}7) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the {Pd84}-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the {Pd84} we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a “Rosetta Stone” to rationalize the “magic numbers” defining a number of other systems. This is because the discovery of {Pd84} allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families. PMID:22753516

Scholarly Research Program in Fuel Analysis and Combustion Research

DTIC Science & Technology

1993-02-01

Public reporting burden for this collection of information is es•tmated to average I hour per response, ilnduding the time fo," reviwing ...Thermal Oxidative Flask Test 45 9. Advanced Fuel System Configuration Descent Condition 57 10. TGPGC for n-Alkane Mixture 63 11. Hierarchical Cluster ...will include all analytical data, data analysis conclusions, recommendations and rationale. 16 a& k : 05 Titl: Development of Test Cell Assemblies for

Chevrons, filaments, spinning clusters and phase coexistence: emergent dynamics of 2- and 3-d particle suspensions driven by multiaxial magnetic fields

DOE PAGES

Solis, Kyle J.; Martin, James E.

2017-07-06

In recent years a rich variety of emergent phenomena have been observed when suspensions of magnetic particles are subjected to alternating magnetic fields. These particle assemblies often exhibit vigorous dynamics due to the injection of energy from the field. These include surface and interface phenomena, such as highly organized, segmented “snakes” that can be induced to swim by structural symmetry breaking, and “asters” and “anti-asters,” particle assemblies that can be manipulated to capture and transport cargo. In bulk suspensions of magnetic platelets subjected to multiaxial alternating fields, advection lattices and even vortex lattices have been created, and a variety ofmore » biomimetic dynamics – serpents, bees and amoebas – have been discovered in magnetic fluids suspended in an immiscible liquid. In this paper several new driven phases are presented, including flying chevrons, dense spinning clusters, filaments, and examples of phase coexistence in driven phases. These observations broaden the growing field of driven magnetic suspensions and present new challenges to those interested in simulating the dynamics of these complex systems.« less

A new method to prepare colloids of size-controlled clusters from a matrix assembly cluster source

NASA Astrophysics Data System (ADS)

Cai, Rongsheng; Jian, Nan; Murphy, Shane; Bauer, Karl; Palmer, Richard E.

2017-05-01

A new method for the production of colloidal suspensions of physically deposited clusters is demonstrated. A cluster source has been used to deposit size-controlled clusters onto water-soluble polymer films, which are then dissolved to produce colloidal suspensions of clusters encapsulated with polymer molecules. This process has been demonstrated using different cluster materials (Au and Ag) and polymers (polyvinylpyrrolidone, polyvinyl alcohol, and polyethylene glycol). Scanning transmission electron microscopy of the clusters before and after colloidal dispersion confirms that the polymers act as stabilizing agents. We propose that this method is suitable for the production of biocompatible colloids of ultraprecise clusters.

Potential of mean force of DNA guided assemblies past Debye-Hückel regime

NASA Astrophysics Data System (ADS)

Girard, Martin; Seo, Soyoung; Li, Yaohua; Mirkin, Chad; Olvera de La Cruz, Monica

Many of the bioinspired systems make use of biopolymers such as polypeptides or DNA. The latter is widely used in self-assembled systems, from colloidal crystals to origami construction. In these systems, salt is commonly required to screen the electrostatic repulsion between the strands. In the classical Debye-Hückel picture, salt ions are point particles and the screening distance is a decreasing monotonic function of salt concentration. This picture breaks down at moderate salt concentrations, where the behavior becomes non-monotonic. In this talk, we will show results for potential of mean force of DNA grafted colloids obtained through multiscale molecular dynamics. In this picture, the highly charged DNA causes non-trivial behavior at moderate salt concentrations (c 0 . 3 - 0 . 7 M), namely increase of repulsion for non-complementary DNA strands while repulsion decreases for complementary strands. We will show spatial cluster distribution as function of size and charge as well as implications for experimental systems.

Rheological transition in simple shear of moderately dense assemblies of dry cohesive granules

NASA Astrophysics Data System (ADS)

Murphy, Eric; Sundararajan, Sriram; Subramaniam, Shankar

2018-06-01

The rheology of homogeneous cohesive granular assemblies under shear at moderate volume fractions is investigated using the discrete element method for both frictionless and frictional granules. A transition in rheology from inertial to quasistatic scaling is observed at volume fractions below the jamming point of noncohesive systems, which is a function of the granular temperature, energy dissipation, and cohesive potential. The transition is found to be the result of growing clusters, which eventually percolate the domain, and change the mode of momentum transport in the system. Differences in the behavior of the shear stress normalized by the pressure are observed when frictionless and frictional cases are compared. These differences are explained through contact anisotropy after percolation occurs. Both frictionless and frictional systems are found to be vulnerable to instabilities after full system percolation has occurred, where the former becomes thermodynamically unstable and the latter may form shear bands. Finally, implications for constitutive modeling are discussed.

A 32 vertex polyhedron via supramolecular assembly of silanedithiolate silanolate units.

PubMed

Spirk, Stefan; Belaj, Ferdinand; Hurkes, Natascha; Pietschnig, Rudolf

2012-08-28

A high yield synthesis of the first silanedithiolate silanolate is reported which spontaneously assembles forming an inorganic rugby ball shaped 32 vertex polyhedral cluster stabilized by sterically demanding 2,6-dimesitylphenyl substituents and two LiCl units.

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.

Cluster synthesis and direct ordering of rare-earth transition-metal nanomagnets.

PubMed

Balasubramanian, Balamurugan; Skomski, Ralph; Li, Xingzhong; Valloppilly, Shah R; Shield, Jeffrey E; Hadjipanayis, George C; Sellmyer, David J

2011-04-13

Rare-earth transition-metal (R-TM) alloys show superior permanent magnetic properties in the bulk, but the synthesis and application of R-TM nanoparticles remains a challenge due to the requirement of high-temperature annealing above about 800 °C for alloy formation and subsequent crystalline ordering. Here we report a single-step method to produce highly ordered R-TM nanoparticles such as YCo(5) and Y(2)Co(17), without high-temperature thermal annealing by employing a cluster-deposition system and investigate their structural and magnetic properties. The direct ordering is highly desirable to create and assemble R-TM nanoparticle building blocks for future permanent-magnet and other significant applications.

Copper Efflux Is Induced during Anaerobic Amino Acid Limitation in Escherichia coli To Protect Iron-Sulfur Cluster Enzymes and Biogenesis

PubMed Central

Fung, Danny Ka Chun; Lau, Wai Yin; Chan, Wing Tat

2013-01-01

Adaptation to changing environments is essential to bacterial physiology. Here we report a unique role of the copper homeostasis system in adapting Escherichia coli to its host-relevant environment of anaerobiosis coupled with amino acid limitation. We found that expression of the copper/silver efflux pump CusCFBA was significantly upregulated during anaerobic amino acid limitation in E. coli without the supplement of exogenous copper. Inductively coupled plasma mass spectrometry analysis of the total intracellular copper content combined with transcriptional assay of the PcusC-lacZ reporter in the presence of specific Cu(I) chelators indicated that anaerobic amino acid limitation led to the accumulation of free Cu(I) in the periplasmic space of E. coli, resulting in Cu(I) toxicity. Cells lacking cusCFBA and another copper transporter, copA, under this condition displayed growth defects and reduced ATP production during fumarate respiration. Ectopic expression of the Fe-S cluster enzyme fumarate reductase (Frd), or supplementation with amino acids whose biosynthesis involves Fe-S cluster enzymes, rescued the poor growth of ΔcusC cells. Yet, Cu(I) treatment did not impair the Frd activity in vitro. Further studies revealed that the alternative Fe-S cluster biogenesis system Suf was induced during the anaerobic amino acid limitation, and ΔcusC enhanced this upregulation, indicating the impairment of the Fe-S cluster assembly machinery and the increased Fe-S cluster demands under this condition. Taken together, we conclude that the copper efflux system CusCFBA is induced during anaerobic amino acid limitation to protect Fe-S cluster enzymes and biogenesis from the endogenously originated Cu(I) toxicity, thus facilitating the physiological adaptation of E. coli. PMID:23893112

Large-scale parallel genome assembler over cloud computing environment.

PubMed

Das, Arghya Kusum; Koppa, Praveen Kumar; Goswami, Sayan; Platania, Richard; Park, Seung-Jong

2017-06-01

The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

Receptor clustering drives polarized assembly of ankyrin.

PubMed

Jefford, G; Dubreuil, R R

2000-09-08

Expression of the L1 family cell adhesion molecule neuroglian in Drosophila S2 cells leads to cell aggregation and polarized ankyrin accumulation at sites of cell-cell contact. Thus neuroglian adhesion generates a spatial cue for polarized assembly of ankyrin and the spectrin cytoskeleton. Here we characterized a chimera of the extracellular and transmembrane domains of rat CD2 fused to the cytoplasmic domain of neuroglian. The chimera was used to test the hypothesis that clustering of neuroglian at sites of adhesion generates the signal that activates ankyrin binding. Abundant expression of the chimera at the plasma membrane was not a sufficient cue to drive ankyrin assembly, since ankyrin remained diffusely distributed throughout the cytoplasm of CD2-neuroglian-expressing cells. However, ankyrin became highly enriched at sites of antibody-induced capping of CD2-neuroglian. Spectrin codistributed with ankyrin at capped sites. A green fluorescent protein-tagged ankyrin was used to monitor ankyrin distribution in living cells. Enhanced green fluorescent protein-ankyrin behaved identically to antibody-stained endogenous ankyrin, proving that the polarized accumulation of ankyrin was not an artifact of fixing and staining cells. We propose a model in which clustering of neuroglian induces a conformational change in the cytoplasmic domain that drives polarized assembly of the spectrin cytoskeleton.

Directed self-assembly of virus particles at nanoscale chemical templates

NASA Astrophysics Data System (ADS)

Chung, Sung-Wook; Cheung, Chin Li; Chatterji, Anju; Lin, Tianwei; Johnson, Jack; de Yoreo, Jim

2006-03-01

Because viruses can be site-specifically engineered to present catalytic, electronic, and optical moieties, they are attractive as building blocks for hierarchical nanostructures. We report results using scanned probe nanolithography to direct virus organization into 1D and 2D patterns and in situ AFM investigations of organization dynamics as pattern geometry, inter-viral potential, virus flux, and virus-pattern interaction are varied. Cowpea Mosaic Virus was modified to present surface sites with histidine (His) or cysteine (Cys) groups. Flat gold substrates were patterned with 10-100nm features of alkyl thiols terminated by Ni-NTA or meleimide groups to reversibly and irreversibly bind to the Hys and Cys groups, respectively. We show how assembly kinetics, degree of ordering and cluster-size distribution at these templates depend on the control parameters and present a physical picture of virus assembly at templates that incorporates growth dynamics of small-molecule epitaxial systems and condensation dynamics of colloidal systems. This work was performed under the auspices of the U. S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.

Functional reconstitution of mitochondrial Fe/S cluster synthesis on Isu1 reveals the involvement of ferredoxin.

PubMed

Webert, Holger; Freibert, Sven-Andreas; Gallo, Angelo; Heidenreich, Torsten; Linne, Uwe; Amlacher, Stefan; Hurt, Ed; Mühlenhoff, Ulrich; Banci, Lucia; Lill, Roland

2014-10-31

Maturation of iron-sulphur (Fe/S) proteins involves complex biosynthetic machinery. In vivo synthesis of [2Fe-2S] clusters on the mitochondrial scaffold protein Isu1 requires the cysteine desulphurase complex Nfs1-Isd11, frataxin, ferredoxin Yah1 and its reductase Arh1. The roles of Yah1-Arh1 have remained enigmatic, because they are not required for in vitro Fe/S cluster assembly. Here, we reconstitute [2Fe-2S] cluster synthesis on Isu1 in a reaction depending on Nfs1-Isd11, frataxin, Yah1, Arh1 and NADPH. Unlike in the bacterial system, frataxin is an essential part of Fe/S cluster biosynthesis and is required simultaneously and stoichiometrically to Yah1. Reduced but not oxidized Yah1 tightly interacts with apo-Isu1 indicating a dynamic interaction between Yah1-apo-Isu1. Nuclear magnetic resonance structural studies identify the Yah1-apo-Isu1 interaction surface and suggest a pathway for electron flow from reduced ferredoxin to Isu1. Together, our study defines the molecular function of the ferredoxin Yah1 and its human orthologue FDX2 in mitochondrial Fe/S cluster synthesis.

α-synuclein assemblies sequester neuronal α3-Na+/K+-ATPase and impair Na+ gradient

PubMed Central

Shrivastava, Amulya Nidhi; Redeker, Virginie; Fritz, Nicolas; Pieri, Laura; Almeida, Leandro G; Spolidoro, Maria; Liebmann, Thomas; Bousset, Luc; Renner, Marianne; Léna, Clément; Aperia, Anita; Melki, Ronald; Triller, Antoine

2015-01-01

Extracellular α-synuclein (α-syn) assemblies can be up-taken by neurons; however, their interaction with the plasma membrane and proteins has not been studied specifically. Here we demonstrate that α-syn assemblies form clusters within the plasma membrane of neurons. Using a proteomic-based approach, we identify the α3-subunit of Na+/K+-ATPase (NKA) as a cell surface partner of α-syn assemblies. The interaction strength depended on the state of α-syn, fibrils being the strongest, oligomers weak, and monomers none. Mutations within the neuron-specific α3-subunit are linked to rapid-onset dystonia Parkinsonism (RDP) and alternating hemiplegia of childhood (AHC). We show that freely diffusing α3-NKA are trapped within α-syn clusters resulting in α3-NKA redistribution and formation of larger nanoclusters. This creates regions within the plasma membrane with reduced local densities of α3-NKA, thereby decreasing the efficiency of Na+ extrusion following stimulus. Thus, interactions of α3-NKA with extracellular α-syn assemblies reduce its pumping activity as its mutations in RDP/AHC. PMID:26323479

Integrating Xgrid into the HENP distributed computing model

NASA Astrophysics Data System (ADS)

Hajdu, L.; Kocoloski, A.; Lauret, J.; Miller, M.

2008-07-01

Modern Macintosh computers feature Xgrid, a distributed computing architecture built directly into Apple's OS X operating system. While the approach is radically different from those generally expected by the Unix based Grid infrastructures (Open Science Grid, TeraGrid, EGEE), opportunistic computing on Xgrid is nonetheless a tempting and novel way to assemble a computing cluster with a minimum of additional configuration. In fact, it requires only the default operating system and authentication to a central controller from each node. OS X also implements arbitrarily extensible metadata, allowing an instantly updated file catalog to be stored as part of the filesystem itself. The low barrier to entry allows an Xgrid cluster to grow quickly and organically. This paper and presentation will detail the steps that can be taken to make such a cluster a viable resource for HENP research computing. We will further show how to provide to users a unified job submission framework by integrating Xgrid through the STAR Unified Meta-Scheduler (SUMS), making tasks and jobs submission effortlessly at reach for those users already using the tool for traditional Grid or local cluster job submission. We will discuss additional steps that can be taken to make an Xgrid cluster a full partner in grid computing initiatives, focusing on Open Science Grid integration. MIT's Xgrid system currently supports the work of multiple research groups in the Laboratory for Nuclear Science, and has become an important tool for generating simulations and conducting data analyses at the Massachusetts Institute of Technology.

The Zn12O12 cluster-assembled nanowires as a highly sensitive and selective gas sensor for NO and NO2.

PubMed

Yong, Yongliang; Su, Xiangying; Zhou, Qingxiao; Kuang, Yanmin; Li, Xiaohong

2017-12-13

Motivated by the recent realization of cluster-assembled nanomaterials as gas sensors, first-principles calculations are carried out to explore the stability and electronic properties of Zn 12 O 12 cluster-assembled nanowires and the adsorption behaviors of environmental gases on the Zn 12 O 12 -based nanowires, including CO, NO, NO 2 , SO 2 , NH 3 , CH 4 , CO 2 , O 2 and H 2 . Our results indicate that the ultrathin Zn 12 O 12 cluster-assembled nanowires are particularly thermodynamic stable at room temperature. The CO, NO, NO 2 , SO 2 , and NH 3 molecules are all chemisorbed on the Zn 12 O 12 -based nanowires with reasonable adsorption energies, but CH 4 , CO 2 , O 2 and H 2 molecules are only physically adsorbed on the nanowire. The electronic properties of the Zn 12 O 12 -based nanowire present dramatic changes after the adsorption of the NO and NO 2 molecules, especially their electric conductivity and magnetic properties, however, the other molecules adsorption hardly change the electric conductivity of the nanowire. Meanwhile, the recovery time of the nanowire sensor at T = 300 K is estimated at 1.5 μs and 16.7 μs for NO and NO 2 molecules, respectively. Furthermore, the sensitivities of NO and NO 2 are much larger than that of the other molecules. Our results thus conclude that the Zn 12 O 12 -based nanowire is a potential candidate for gas sensors with highly sensitivity for NO and NO 2 .

Testing and evaluation of sign support with cluster attachments.

DOT National Transportation Integrated Search

1990-04-01

Two full-scale crash tests were conducted on the Louisiana two-post, inclined, slip-base sign assembly with cluster sign attachment. These two tests were performed and evaluated in accordance with guidelines under NCHRP Report 230 and standards estab...

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

NASA Astrophysics Data System (ADS)

Gao, Lin

Clusters, defined as "a number of similar things that occur together" in Webster's dictionary, has different meanings depending on the given subject. To physicists and chemists, the word cluster means "a group of atoms or molecules formed by interactions ranging from very weak van der Waals interactions to strong ionic bonds." Unlike molecules, which are made by nature and are stable under ambient conditions, clusters discovered in a laboratory are often metastable. Molecules have specific stoichiometry, whereas the cluster's composition can usually be altered atom by atom. Thus, clusters can be taken as intrinsically "artificial molecules" with considerably more tunabilities in their properties. Research into the relative stability and instability of clusters has in recent years become a very active research area, especially following the study by Khanna and Castleman that first suggested that by varying size and composition, clusters can expand the periodic table to the 3 rd-dimension; that is, clusters can mimic the chemistry of atoms and may, therefore, be used as the building blocks of new materials. The discovery of Met-Cars has drawn worldwide interests and has been actively investigated by researchers from a variety of fields, including physics, chemistry and material science. However, the unsuccessful search for a solvent capable of isolating Met-Cars has impeded progress in characterizing the material in the condensed state and, hence, limited its potential applications as a novel nanoscale material. An alternative method involving the deposition of mass-gated species and the subsequent structural investigation via Transmission Electron Microscopy (TEM) has been employed. With particularly interesting results, soft-landed deposits of zirconium Met-Cars were found to form a face-centered-cubic (FCC) structure with a lattice parameter ˜ 15A. The production of Met-Cars is conducted with the direct laser vaporization (DLV) of metal/graphite composite pellets. 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 (ESI-MS), Ultraviolet-Visible Spectroscopy (Uv-Vis), Nuclear Magnetic Resonance (NMR) for solution phase and Transmission Electron Microscopy (TEM) for the condensed phase. In particular, undeca-, dodeca- and trideca-gold clusters protected by depp and halogen ligands, i.e. [Au11-13(depp) 4Cl2-4]+, are found to be all predominant and persist in solution for months, while they gradually and spontaneously grow into a monomial trideca-gold clusters series. The unique preferred ligand combination, depp along with Cl, is discussed in terms of the ligand-core interaction and the closed-shell electronic configurations of the Au n (n = 11-13) cores, which enables them to serve as building units for larger cluster-assembled nanoparticles and form Self-Assembled Arrays (SAAs), as discovered by TEM measurements. Such spontaneous-growth behavior and the resultant SAAs observations are correlated by icosahedra-close-packing modes of clusters, following "magic numbers" rules. ˜7 shells of such cluster packing are proposed to be in the SAAs.

Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy.

PubMed

Yang, Yantao; Qu, Na; Tan, Jie; Rushdi, Muaz N; Krueger, Christopher J; Chen, Antony K

2018-06-11

During HIV-1 assembly, the retroviral structural protein Gag forms an immature capsid, containing thousands of Gag molecules, at the plasma membrane (PM). Interactions between Gag nucleocapsid (NC) and viral RNA (vRNA) are thought to drive assembly, but the exact roles of these interactions have remained poorly understood. Since previous studies have shown that Gag dimer- or trimer-forming mutants (Gag ZiL ) lacking an NC domain can form immature capsids independent of RNA binding, it is often hypothesized that vRNA drives Gag assembly by inducing Gag to form low-ordered multimers, but is dispensable for subsequent assembly. In this study, we examined the role of vRNA in HIV-1 assembly by characterizing the distribution and mobility of Gag and Gag NC mutants at the PM using photoactivated localization microscopy (PALM) and single-particle tracking PALM (spt-PALM). We showed that both Gag and Gag ZiL assembly involve a similar basic assembly unit, as expected. Unexpectedly, the two proteins underwent different subsequent assembly pathways, with Gag cluster density increasing asymptotically, while Gag ZiL cluster density increased linearly. Additionally, the directed movement of Gag, but not Gag ZiL , was maintained at a constant speed, suggesting that the two proteins experience different external driving forces. Assembly was abolished when Gag was rendered monomeric by NC deletion. Collectively, these results suggest that, beyond inducing Gag to form low-ordered multimer basic assembly units, vRNA is essential in scaffolding and maintaining the stability of the subsequent assembly process. This finding should advance the current understanding of HIV-1 and, potentially, other retroviruses. Copyright © 2018 the Author(s). Published by PNAS.

Impaired mitochondrial Fe-S cluster biogenesis activates the DNA damage response through different signaling mediators.

PubMed

Pijuan, Jordi; María, Carlos; Herrero, Enrique; Bellí, Gemma

2015-12-15

Fe-S cluster biogenesis machinery is required for multiple DNA metabolism processes. In this work, we show that, in Saccharomyces cerevisiae, defects at different stages of the mitochondrial Fe-S cluster assembly machinery (ISC) result in increased spontaneous mutation rate and hyper-recombination, accompanied by an increment in Rad52-associated DNA repair foci and a higher phosphorylated state of γH2A histone, altogether supporting the presence of constitutive DNA lesions. Furthermore, ISC assembly machinery deficiency elicits a DNA damage response that upregulates ribonucleotide reductase activity by promoting the reduction of Sml1 levels and the cytosolic redistribution of Rnr2 and Rnr4 enzyme subunits. Depending on the impaired stage of the ISC machinery, different signaling pathway mediators contribute to such a response, converging on Dun1. Thus, cells lacking the glutaredoxin Grx5, which are compromised at the core ISC system, show Mec1- and Rad53-independent Dun1 activation, whereas both Mec1 and Chk1 are required when the non-core ISC member Iba57 is absent. Grx5-null cells exhibit a strong dependence on the error-free post-replication repair and the homologous recombination pathways, demonstrating that a DNA damage response needs to be activated upon ISC impairment to preserve cell viability. © 2015. Published by The Company of Biologists Ltd.

Altered Actin Centripetal Retrograde Flow in Physically Restricted Immunological Synapses

PubMed Central

Yu, Cheng-han; Wu, Hung-Jen; Kaizuka, Yoshihisa; Vale, Ronald D.; Groves, Jay T.

2010-01-01

Antigen recognition by T cells involves large scale spatial reorganization of numerous receptor, adhesion, and costimulatory proteins within the T cell-antigen presenting cell (APC) junction. The resulting patterns can be distinctive, and are collectively known as the immunological synapse. Dynamical assembly of cytoskeletal network is believed to play an important role in driving these assembly processes. In one experimental strategy, the APC is replaced with a synthetic supported membrane. An advantage of this configuration is that solid structures patterned onto the underlying substrate can guide immunological synapse assembly into altered patterns. Here, we use mobile anti-CD3ε on the spatial-partitioned supported bilayer to ligate and trigger T cell receptor (TCR) in live Jurkat T cells. Simultaneous tracking of both TCR clusters and GFP-actin speckles reveals their dynamic association and individual flow patterns. Actin retrograde flow directs the inward transport of TCR clusters. Flow-based particle tracking algorithms allow us to investigate the velocity distribution of actin flow field across the whole synapse, and centripetal velocity of actin flow decreases as it moves toward the center of synapse. Localized actin flow analysis reveals that, while there is no influence on actin motion from substrate patterns directly, velocity differences of actin are observed over physically trapped TCR clusters. Actin flow regains its velocity immediately after passing through confined TCR clusters. These observations are consistent with a dynamic and dissipative coupling between TCR clusters and viscoelastic actin network. PMID:20686692

Reefing Line Tension in CPAS Main Parachute Clusters

NASA Technical Reports Server (NTRS)

Ray, Eric S.

2013-01-01

Reefing lines are an essential feature to manage inflation loads. During each Engineering Development Unit (EDU) test of the Capsule Parachute Assembly System (CPAS), a chase aircraft is staged to be level with the cluster of Main ringsail parachutes during the initial inflation and reefed stages. This allows for capturing high-quality still photographs of the reefed skirt, suspension line, and canopy geometry. The over-inflation angles are synchronized with measured loads data in order to compute the tension force in the reefing line. The traditional reefing tension equation assumes radial symmetry, but cluster effects cause the reefed skirt of each parachute to elongate to a more elliptical shape. This effect was considered in evaluating multiple parachutes to estimate the semi-major and semi-minor axes. Three flight tests are assessed, including one with a skipped first stage, which had peak reefing line tension over three times higher than the nominal parachute disreef sequence.

Respiratory chain supercomplexes associate with the cysteine desulfurase complex of the iron–sulfur cluster assembly machinery

PubMed Central

Böttinger, Lena; Mårtensson, Christoph U.; Song, Jiyao; Zufall, Nicole; Wiedemann, Nils; Becker, Thomas

2018-01-01

Mitochondria are the powerhouses of eukaryotic cells. The activity of the respiratory chain complexes generates a proton gradient across the inner membrane, which is used by the F1FO-ATP synthase to produce ATP for cellular metabolism. In baker’s yeast, Saccharomyces cerevisiae, the cytochrome bc1 complex (complex III) and cytochrome c oxidase (complex IV) associate in respiratory chain supercomplexes. Iron–sulfur clusters (ISC) form reactive centers of respiratory chain complexes. The assembly of ISC occurs in the mitochondrial matrix and is essential for cell viability. The cysteine desulfurase Nfs1 provides sulfur for ISC assembly and forms with partner proteins the ISC-biogenesis desulfurase complex (ISD complex). Here, we report an unexpected interaction of the active ISD complex with the cytochrome bc1 complex and cytochrome c oxidase. The individual deletion of complex III or complex IV blocks the association of the ISD complex with respiratory chain components. We conclude that the ISD complex binds selectively to respiratory chain supercomplexes. We propose that this molecular link contributes to coordination of iron–sulfur cluster formation with respiratory activity. PMID:29386296

Self-assembly of [Pt(3n)(CO)(6n)]2- (n = 4-8) carbonyl clusters: from molecules to conducting molecular metal wires.

PubMed

Femoni, Cristina; Iapalucci, Maria Carmela; Longoni, Giuliano; Lovato, Tatiana; Stagni, Stefano; Zacchini, Stefano

2010-07-05

A comprehensive study discussing the different parameters that influence the self-assembly of [Pt(3n)(CO)(6n)](2-) (n = 4-8) clusters with miscellaneous mono- and dications into 0-D, 1-D, 2-D, and 3-D materials is herein reported. As an unexpected bonus, the use of Ru(II) dications allowed the first structural characterization of the previously unknown [Pt(21)(CO)(42)](2-) dianion. 0-D structures, which contain isolated ions, are electrical insulators in solid form. Conversely, as soon as infinite chains of clusters are formed, the electrical resistivity, measured in pressed pellets, decreases to 10(5)-10(6), 10(4), and 10(2) ohms cm for discontinuous, semicontinuous, and continuous chains, respectively. Therefore, the resemblance of these materials to molecular metal wires is not only morphological but also functional. Preliminary results of possible self-assembly phenomena in a solution of [Pt(15)(CO)(30)](2-) and [Pt(18)(CO)(36)](2-) according to dynamic light scattering experiments are also reported.

Pattern formation and collective effects in populations of magnetic microswimmers

NASA Astrophysics Data System (ADS)

Vach, Peter J.; Walker, Debora; Fischer, Peer; Fratzl, Peter; Faivre, Damien

2017-03-01

Self-propelled particles are one prototype of synthetic active matter used to understand complex biological processes, such as the coordination of movement in bacterial colonies or schools of fishes. Collective patterns such as clusters were observed for such systems, reproducing features of biological organization. However, one limitation of this model is that the synthetic assemblies are made of identical individuals. Here we introduce an active system based on magnetic particles at colloidal scales. We use identical but also randomly-shaped magnetic micropropellers and show that they exhibit dynamic and reversible pattern formation.

Colloidal assembly directed by virtual magnetic moulds

NASA Astrophysics Data System (ADS)

Demirörs, Ahmet F.; Pillai, Pramod P.; Kowalczyk, Bartlomiej; Grzybowski, Bartosz A.

2013-11-01

Interest in assemblies of colloidal particles has long been motivated by their applications in photonics, electronics, sensors and microlenses. Existing assembly schemes can position colloids of one type relatively flexibly into a range of desired structures, but it remains challenging to produce multicomponent lattices, clusters with precisely controlled symmetries and three-dimensional assemblies. A few schemes can efficiently produce complex colloidal structures, but they require system-specific procedures. Here we show that magnetic field microgradients established in a paramagnetic fluid can serve as `virtual moulds' to act as templates for the assembly of large numbers (~108) of both non-magnetic and magnetic colloidal particles with micrometre precision and typical yields of 80 to 90 per cent. We illustrate the versatility of this approach by producing single-component and multicomponent colloidal arrays, complex three-dimensional structures and a variety of colloidal molecules from polymeric particles, silica particles and live bacteria and by showing that all of these structures can be made permanent. In addition, although our magnetic moulds currently resemble optical traps in that they are limited to the manipulation of micrometre-sized objects, they are massively parallel and can manipulate non-magnetic and magnetic objects simultaneously in two and three dimensions.

Modeling the self-assembly of functionalized fullerenes on solid surfaces using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Bubnis, Gregory J.

Since their discovery 25 years ago, carbon fullerenes have been widely studied for their unique physicochemical properties and for applications including organic electronics and photovoltaics. For these applications it is highly desirable for crystalline fullerene thin films to spontaneously self-assemble on surfaces. Accordingly, many studies have functionalized fullerenes with the aim of tailoring their intermolecular interactions and controlling interactions with the solid substrate. The success of these rational design approaches hinges on the subtle interplay of intermolecular forces and molecule-substrate interactions. Molecular modeling is well-suited to studying these interactions by directly simulating self-assembly. In this work, we consider three different fullerene functionalization approaches and for each approach we carry out Monte Carlo simulations of the self-assembly process. In all cases, we use a "coarse-grained" molecular representation that preserves the dominant physical interactions between molecules and maximizes computational efficiency. The first approach we consider is the traditional gold-thiolate SAM (self-assembled monolayer) strategy which tethers molecules to a gold substrate via covalent sulfur-gold bonds. For this we study an asymmetric fullerene thiolate bridged by a phenyl group. Clusters of 40 molecules are simulated on the Au(111) substrate at different temperatures and surface coverage densities. Fullerenes and S atoms are found to compete for Au(111) surface sites, and this competition prevents self-assembly of highly ordered monolayers. Next, we investigate self-assembled monolayers formed by fullerenes with hydrogen-bonding carboxylic acid substituents. We consider five molecules with different dimensions and symmetries. Monte Carlo cooling simulations are used to find the most stable solid structures of clusters adsorbed to Au(111). The results show cases where fullerene-Au(111) attraction, fullerene close-packing, and hydrogen-bonding interactions can cooperate to guide self-assembly or compete to hinder it. Finally, we consider three bis-fullerene molecules, each with a different "bridging group" covalently joining two fullerenes. To effectively study the competing "standing-up" and "lying-down" morphologies, we use Monte Carlo simulations in conjunction with replica exchange and force field biasing methods. For clusters adsorbed to smooth model surfaces, we determine free energy landscapes and demonstrate their utility for rationalizing and predicting self-assembly.

Human mitochondrial MIA40 (CHCHD4) is a component of the Fe-S cluster export machinery.

PubMed

Murari, Anjaneyulu; Thiriveedi, Venkata Ramana; Mohammad, Fareed; Vengaldas, Viswamithra; Gorla, Madhavi; Tammineni, Prasad; Krishnamoorthy, Thanuja; Sepuri, Naresh Babu V

2015-10-15

Mitochondria play an essential role in synthesis and export of iron-sulfur (Fe-S) clusters to other sections of a cell. Although the mechanism of Fe-S cluster synthesis is well elucidated, information on the identity of the proteins involved in the export pathway is limited. The present study identifies hMIA40 (human mitochondrial intermembrane space import and assembly protein 40), also known as CHCHD4 (coiled-coil-helix-coiled-coil-helix domain-containing 4), as a component of the mitochondrial Fe-S cluster export machinery. hMIA40 is an iron-binding protein with the ability to bind iron in vivo and in vitro. hMIA40 harbours CPC (Cys-Pro-Cys) motif-dependent Fe-S clusters that are sensitive to oxidation. Depletion of hMIA40 results in accumulation of iron in mitochondria concomitant with decreases in the activity and stability of Fe-S-containing cytosolic enzymes. Intriguingly, overexpression of either the mitochondrial export component or cytosolic the Fe-S cluster assembly component does not have any effect on the phenotype of hMIA40-depleted cells. Taken together, our results demonstrate an indispensable role for hMIA40 for the export of Fe-S clusters from mitochondria. © 2015 Authors; published by Portland Press Limited.

Exome sequencing identifies NFS1 deficiency in a novel Fe-S cluster disease, infantile mitochondrial complex II/III deficiency.

PubMed

Farhan, Sali M K; Wang, Jian; Robinson, John F; Lahiry, Piya; Siu, Victoria M; Prasad, Chitra; Kronick, Jonathan B; Ramsay, David A; Rupar, C Anthony; Hegele, Robert A

2014-01-01

Iron-sulfur (Fe-S) clusters are a class of highly conserved and ubiquitous prosthetic groups with unique chemical properties that allow the proteins that contain them, Fe-S proteins, to assist in various key biochemical pathways. Mutations in Fe-S proteins often disrupt Fe-S cluster assembly leading to a spectrum of severe disorders such as Friedreich's ataxia or iron-sulfur cluster assembly enzyme (ISCU) myopathy. Herein, we describe infantile mitochondrial complex II/III deficiency, a novel autosomal recessive mitochondrial disease characterized by lactic acidemia, hypotonia, respiratory chain complex II and III deficiency, multisystem organ failure and abnormal mitochondria. Through autozygosity mapping, exome sequencing, in silico analyses, population studies and functional tests, we identified c.215G>A, p.Arg72Gln in NFS1 as the likely causative mutation. We describe the first disease in man likely caused by deficiency in NFS1, a cysteine desulfurase that is implicated in respiratory chain function and iron maintenance by initiating Fe-S cluster biosynthesis. Our results further demonstrate the importance of sufficient NFS1 expression in human physiology.

LoCuSS: The infall of X-ray groups onto massive clusters

NASA Astrophysics Data System (ADS)

Haines, C. P.; Finoguenov, A.; Smith, G. P.; Babul, A.; Egami, E.; Mazzotta, P.; Okabe, N.; Pereira, M. J.; Bianconi, M.; McGee, S. L.; Ziparo, F.; Campusano, L. E.; Loyola, C.

2018-03-01

Galaxy clusters are expected to form hierarchically in a ΛCDM universe, growing primarily through mergers with lower mass clusters and the continual accretion of group-mass halos. Galaxy clusters assemble late, doubling their masses since z ˜ 0.5, and so the outer regions of clusters should be replete with accreting group-mass systems. We present an XMM-Newton survey to search for X-ray groups in the infall regions of 23 massive galaxy clusters ( ˜ 1015 M⊙) at z ˜ 0.2, identifying 39 X-ray groups that have been spectroscopically confirmed to lie at the cluster redshift. These groups have mass estimates in the range 2 × 1013 - 7 × 1014 M⊙, and group-to-cluster mass ratios as low as 0.02. The comoving number density of X-ray groups in the infall regions is ˜25 × higher than that seen for isolated X-ray groups from the XXL survey. The average mass per cluster contained within these X-ray groups is 2.2 × 1014 M⊙, or 19 ± 5% of the mass within the primary cluster itself. We estimate that ˜1015 M⊙ clusters increase their masses by 16 ± 4% between z = 0.223 and the present day due to the accretion of groups with M200 ≥ 1013.2 M⊙. This represents about half of the expected mass growth rate of clusters at these late epochs. The other half is likely to come from smooth accretion of matter not bound within halos. The mass function of the infalling X-ray groups appears significantly top heavy with respect to that of "field" X-ray systems, consistent with expectations from numerical simulations, and the basic consequences of collapsed massive dark matter halos being biased tracers of the underlying large-scale density distribution.

LoCuSS: The infall of X-ray groups on to massive clusters

NASA Astrophysics Data System (ADS)

Haines, C. P.; Finoguenov, A.; Smith, G. P.; Babul, A.; Egami, E.; Mazzotta, P.; Okabe, N.; Pereira, M. J.; Bianconi, M.; McGee, S. L.; Ziparo, F.; Campusano, L. E.; Loyola, C.

2018-07-01

Galaxy clusters are expected to form hierarchically in a Λ cold dark matter (ΛCDM) universe, growing primarily through mergers with lower mass clusters and the continual accretion of group-mass haloes. Galaxy clusters assemble late, doubling their masses since z ˜ 0.5, and so the outer regions of clusters should be replete with accreting group-mass systems. We present an XMM-Newton survey to search for X-ray groups in the infall regions of 23 massive galaxy clusters ( ˜ 1015 M⊙) at z ˜ 0.2, identifying 39 X-ray groups that have been spectroscopically confirmed to lie at the cluster redshift. These groups have mass estimates in the range 2 × 1013-7 × 1014 M⊙, and group-to-cluster mass ratios as low as 0.02. The comoving number density of X-ray groups in the infall regions is ˜25× higher than that seen for isolated X-ray groups from the XXL survey. The average mass per cluster contained within these X-ray groups is 2.2 × 1014 M⊙, or 19 ± 5 per cent of the mass within the primary cluster itself. We estimate that ˜1015 M⊙ clusters increase their masses by 16 ± 4 per cent between z = 0.223 and the present day due to the accretion of groups with M200 ≥ 1013.2 M⊙. This represents about half of the expected mass growth rate of clusters at these late epochs. The other half is likely to come from smooth accretion of matter not bound within haloes. The mass function of the infalling X-ray groups appears significantly top heavy with respect to that of `field' X-ray systems, consistent with expectations from numerical simulations, and the basic consequences of collapsed massive dark matter haloes being biased tracers of the underlying large-scale density distribution.

Detecting pin diversion from pressurized water reactors spent fuel assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ham, Young S.; Sitaraman, Shivakumar

Detecting diversion of spent fuel from Pressurized Water Reactors (PWR) by determining possible diversion including the steps of providing a detector cluster containing gamma ray and neutron detectors, inserting the detector cluster containing the gamma ray and neutron detectors into the spent fuel assembly through the guide tube holes in the spent fuel assembly, measuring gamma ray and neutron radiation responses of the gamma ray and neutron detectors in the guide tube holes, processing the gamma ray and neutron radiation responses at the guide tube locations by normalizing them to the maximum value among each set of responses and takingmore » the ratio of the gamma ray and neutron responses at the guide tube locations and normalizing the ratios to the maximum value among them and producing three signatures, gamma, neutron, and gamma-neutron ratio, based on these normalized values, and producing an output that consists of these signatures that can indicate possible diversion of the pins from the spent fuel assembly.« less

The use of a versatile o-vanilloyl hydrazone ligand to prepare SMM-like Dy3 molecular cluster pair.

PubMed

Xue, Shufang; Zhao, Lang; Guo, Yun-Nan; Zhang, Peng; Tang, Jinkui

2012-09-14

A novel lanthanide molecular cluster pair (MCP), displaying single molecule magnet behaviour, was assembled using the novel o-vanilloyl hydrazone ligand, versatile in terms of denticity, tautomerism and the rotatable C-C bond.

Substituent-Modulated Assembly Formation: An Approach to Enhancing the Photostability of Photoelectric-Sensitive Chalcogenide-Based Ion-Pair Hybrids.

PubMed

Lin, Jian; Fu, Zhixing; Zhang, Jiaxu; Zhu, Yujia; Hu, Dandan; Li, Dongsheng; Wu, Tao

2017-03-20

A series of electronically active viologen dications (RV) with tunable substituent groups were utilized to hybridize with [Ge 4 S 10 ] 4- (T2 cluster) to form the hybrids of T2@RV. These hybrids exhibited variable supermolecular assembly formation, tunable optical absorption properties, and different photoelectric response under the influence of different RV dications. Raman testing and time-dependent photocurrent response indicated that the photosensitivity and photostability of T2@RV could be integrated while choosing suitable RV dications. Current research provides a general method to build a tunable hybrid system based on crystalline metal chalcogenide compounds through the replacement of photoinactive cationic organic templates with photoactive ones with different substituent groups.

Analysis on the hot spot and trend of the foreign assembly building research

NASA Astrophysics Data System (ADS)

Bi, Xiaoqing; Luo, Yanbing

2017-03-01

First of all, the paper analyzes the research on the front of the assembly building in the past 15 years. This article mainly adopts the method of CO word analysis, construct the co word matrix, correlation matrix, and then into a dissimilarity matrix, and on this basis, using factor analysis, cluster analysis and multi scale analysis method to study the structure of prefabricated construction field display. Finally, the results of the analysis are discussed, and summarized the current research focus of foreign prefabricated construction mainly concentrated in 7 aspects: embankment construction, wood construction, bridge construction, crane layout, PCM wall and glass system, based on neural network test, energy saving and recycling, and forecast the future trend of development study.

Application of Geostatistical Methods and Machine Learning for spatio-temporal Earthquake Cluster Analysis

NASA Astrophysics Data System (ADS)

Schaefer, A. M.; Daniell, J. E.; Wenzel, F.

2014-12-01

Earthquake clustering tends to be an increasingly important part of general earthquake research especially in terms of seismic hazard assessment and earthquake forecasting and prediction approaches. The distinct identification and definition of foreshocks, aftershocks, mainshocks and secondary mainshocks is taken into account using a point based spatio-temporal clustering algorithm originating from the field of classic machine learning. This can be further applied for declustering purposes to separate background seismicity from triggered seismicity. The results are interpreted and processed to assemble 3D-(x,y,t) earthquake clustering maps which are based on smoothed seismicity records in space and time. In addition, multi-dimensional Gaussian functions are used to capture clustering parameters for spatial distribution and dominant orientations. Clusters are further processed using methodologies originating from geostatistics, which have been mostly applied and developed in mining projects during the last decades. A 2.5D variogram analysis is applied to identify spatio-temporal homogeneity in terms of earthquake density and energy output. The results are mitigated using Kriging to provide an accurate mapping solution for clustering features. As a case study, seismic data of New Zealand and the United States is used, covering events since the 1950s, from which an earthquake cluster catalogue is assembled for most of the major events, including a detailed analysis of the Landers and Christchurch sequences.

Temperature-dependent self-assembly and rheological behavior of a thermoreversible pmma-P n BA-PMMA triblock copolymer gel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zabet, Mahla; Mishra, Satish; Boy, Ramiz

We present that self-assembly and mechanical properties of triblock copolymers in a mid-block selective solvent are of interest in many applications. Herein, we report physical assembly of an ABA triblock copolymer, [PMMA–PnBA–PMMA] in two different mid-block selective solvents, n-butanol and 2-ethyl-1-hexanol. Gel formation resulting from end-block associations and the corresponding changes in mechanical properties have been investigated over a temperature range of -80 °C to 60 °C, from near the solvent melting points to above the gelation temperature. Shear-rheometry, thermal analysis, and small-angle neutron scattering data reveal formation and transition of structure in these systems from a liquid state tomore » a gel state to a percolated cluster network with decrease in temperature. The aggregated PMMA end-blocks display a glass transition temperature. Finally, our results provide new understanding into the structural changes of a self-assembled triblock copolymer gel over a large length scale and wide temperature range.« less

Temperature-dependent self-assembly and rheological behavior of a thermoreversible pmma-P n BA-PMMA triblock copolymer gel

DOE PAGES

Zabet, Mahla; Mishra, Satish; Boy, Ramiz; ...

2017-03-25

We present that self-assembly and mechanical properties of triblock copolymers in a mid-block selective solvent are of interest in many applications. Herein, we report physical assembly of an ABA triblock copolymer, [PMMA–PnBA–PMMA] in two different mid-block selective solvents, n-butanol and 2-ethyl-1-hexanol. Gel formation resulting from end-block associations and the corresponding changes in mechanical properties have been investigated over a temperature range of -80 °C to 60 °C, from near the solvent melting points to above the gelation temperature. Shear-rheometry, thermal analysis, and small-angle neutron scattering data reveal formation and transition of structure in these systems from a liquid state tomore » a gel state to a percolated cluster network with decrease in temperature. The aggregated PMMA end-blocks display a glass transition temperature. Finally, our results provide new understanding into the structural changes of a self-assembled triblock copolymer gel over a large length scale and wide temperature range.« less

Self-Assembly of Parallel Atomic Wires and Periodic Clusters of Silicon on a Vicinal Si(111) Surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sekiguchi, Takeharu; Yoshida, Shunji; Itoh, Kohei M.

2005-09-02

Silicon self-assembly at step edges in the initial stage of homoepitaxial growth on a vicinal Si(111) surface is studied by scanning tunneling microscopy. The resulting atomic structures change dramatically from a parallel array of 0.7 nm wide wires to one-dimensionally aligned periodic clusters of diameter {approx}2 nm and periodicity 2.7 nm in the very narrow range of growth temperatures between 400 and 300 deg. C. These nanostructures are expected to play important roles in future developments of silicon quantum computers. Mechanisms leading to such distinct structures are discussed.

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

2016-05-06

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. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Protection of scaffold protein Isu from degradation by the Lon protease Pim1 as a component of Fe-S cluster biogenesis regulation.

PubMed

Ciesielski, Szymon J; Schilke, Brenda; Marszalek, Jaroslaw; Craig, Elizabeth A

2016-04-01

Iron-sulfur (Fe-S) clusters, essential protein cofactors, are assembled on the mitochondrial scaffold protein Isu and then transferred to recipient proteins via a multistep process in which Isu interacts sequentially with multiple protein factors. This pathway is in part regulated posttranslationally by modulation of the degradation of Isu, whose abundance increases >10-fold upon perturbation of the biogenesis process. We tested a model in which direct interaction with protein partners protects Isu from degradation by the mitochondrial Lon-type protease. Using purified components, we demonstrated that Isu is indeed a substrate of the Lon-type protease and that it is protected from degradation by Nfs1, the sulfur donor for Fe-S cluster assembly, as well as by Jac1, the J-protein Hsp70 cochaperone that functions in cluster transfer from Isu. Nfs1 and Jac1 variants known to be defective in interaction with Isu were also defective in protecting Isu from degradation. Furthermore, overproduction of Jac1 protected Isu from degradation in vivo, as did Nfs1. Taken together, our results lead to a model of dynamic interplay between a protease and protein factors throughout the Fe-S cluster assembly and transfer process, leading to up-regulation of Isu levels under conditions when Fe-S cluster biogenesis does not meet cellular demands. © 2016 Ciesielski et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

SEEDisCs: How Clusters Form and Galaxies Transform in the Cosmic Web

NASA Astrophysics Data System (ADS)

Jablonka, P.

2017-08-01

This presentation introduces a new survey, the Spatial Extended EDisCS Survey (SEEDisCS), which aims at understanding how clusters assemble and the level at which galaxies are preprocessed before falling on the cluster cores. I focus on the changes in galaxy properties in the cluster large scale environments, and how we can get constraints on the timescale of star formation quenching. I also discuss new ALMA CO observations, which trace the fate of the galaxy cold gas content along the infalling paths towards the cluster cores.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.

PubMed

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

2016-09-30

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN 42-210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN 42-210 ] 24 ·[NFS1] 24 ·[ISD11] 24 ·[ISCU] 24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN 42-210 ] 24 ·[ISCU] 24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN 42-210 trimer at each of its eight vertices. Binding of 12 [NFS1] 2 ·[ISD11] 2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN 42-210 to ISCU. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery*

PubMed Central

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y.; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

2016-01-01

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42–210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42–210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42–210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42–210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42–210 to ISCU. PMID:27519411

Environment-based pin-power reconstruction method for homogeneous core calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leroyer, H.; Brosselard, C.; Girardi, E.

2012-07-01

Core calculation schemes are usually based on a classical two-step approach associated with assembly and core calculations. During the first step, infinite lattice assemblies calculations relying on a fundamental mode approach are used to generate cross-sections libraries for PWRs core calculations. This fundamental mode hypothesis may be questioned when dealing with loading patterns involving several types of assemblies (UOX, MOX), burnable poisons, control rods and burn-up gradients. This paper proposes a calculation method able to take into account the heterogeneous environment of the assemblies when using homogeneous core calculations and an appropriate pin-power reconstruction. This methodology is applied to MOXmore » assemblies, computed within an environment of UOX assemblies. The new environment-based pin-power reconstruction is then used on various clusters of 3x3 assemblies showing burn-up gradients and UOX/MOX interfaces, and compared to reference calculations performed with APOLLO-2. The results show that UOX/MOX interfaces are much better calculated with the environment-based calculation scheme when compared to the usual pin-power reconstruction method. The power peak is always better located and calculated with the environment-based pin-power reconstruction method on every cluster configuration studied. This study shows that taking into account the environment in transport calculations can significantly improve the pin-power reconstruction so far as it is consistent with the core loading pattern. (authors)« less

A stellar tracking reference system

NASA Technical Reports Server (NTRS)

Klestadt, B.

1971-01-01

A stellar attitude reference system concept for satellites was studied which promises to permit continuous precision pointing of payloads with accuracies of 0.001 degree without the use of gyroscopes. It is accomplished with the use of a single, clustered star tracker assembly mounted on a non-orthogonal, two gimbal mechanism, driven so as to unwind satellite orbital and orbit precession rates. A set of eight stars was found which assures the presence of an adequate inertial reference on a continuous basis in an arbitrary orbit. Acquisition and operational considerations were investigated and inherent reference redundancy/reliability was established. Preliminary designs for the gimbal mechanism, its servo drive, and the star tracker cluster with its associated signal processing were developed for a baseline sun-synchronous, noon-midnight orbit. The functions required of the onboard computer were determined and the equations to be solved were found. In addition detailed error analyses were carried out, based on structural, thermal and other operational considerations.

Load Asymmetry Observed During Orion Main Parachute Inflation

NASA Technical Reports Server (NTRS)

Morris, Aaron L.; Taylor, Thomas; Olson, Leah

2011-01-01

The Crew Exploration Vehicle Parachute Assembly System (CPAS) has flight tested the first two generations of the Orion parachute program. Three of the second generation tests instrumented the dispersion bridles of the Main parachute with a Tension Measuring System. The goal of this load measurement was to better understand load asymmetry during the inflation process of a cluster of Main parachutes. The CPAS Main parachutes exhibit inflations that are much less symmetric than current parachute literature and design guides would indicate. This paper will examine loads data gathered on three cluster tests, quantify the degree of asymmetry observed, and contrast the results with published design guides. Additionally, the measured loads data will be correlated with videos of the parachute inflation to make inferences about the shape of the parachute and the relative load asymmetry. The goal of this inquiry and test program is to open a dialogue regarding asymmetrical parachute inflation load factors.

Selective Metal-Ion-Mediated Vesicle Adhesion Based on Dynamic Self-Organization of a Pyrene-Appended Glutamic Acid.

PubMed

Xing, Pengyao; Wang, Yajie; Yang, Minmin; Zhang, Yimeng; Wang, Bo; Hao, Aiyou

2016-07-13

Vesicles with dynamic membranes provide an ideal model system for investigating biological membrane activities, whereby vesicle aggregation behaviors including adhesion, fusion, fission, and membrane contraction/extension have attracted much attention. In this work we utilize an aromatic amino acid (pyrene-appended glutamic acid, PGlu) to prepare nanovesicles that aggregate to form vesicle clusters selectively induced by Fe(3+) or Cu(2+), and the vesicles transform into irregular nano-objects when interacting with Al(3+). Vesicle clusters have better stability than pristine vesicles, which hinders the spontaneous morphological transformation from vesicles into lamellar nanosheets with long incubation period. The difference between complexation of Fe(3+) and Al(3+) with vesicles was studied by various techniques. On the basis of metal ion-vesicle interactions, this self-assembled nanovesicle system also behaves as an effective fluorescent sensor for Fe(3+) and Al(3+), which cause fluorescence quenching and enhanced excimer emission, respectively.

Structural properties of medium-range order in CuNiZr alloy

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Hu, Xuechen; Xie, Quan; Li, Yidan; Ren, Lei

2017-10-01

The evolution characteristics of icosahedral clusters during the rapid solidification of Cu50Ni10Zr40 alloy at cooling rate of 1011 K s-1 are investigated based on molecular dynamics simulations. The structural properties of the short-range order and medium-range order of Cu50Ni10Zr40 alloy are analyzed by several structural characterization methods. The results reveal that the icosahedral clusters are the dominant short-range order structure, and that they assemble themselves into medium-range order by interpenetrating connections. The different morphologies of medium-range order are found in the system and include chain, triangle, tetrahedral, and their combination structures. The tetrahedral morphologies of medium-range order have excellent structural stability with decreasing temperature. The Zr atoms are favorable to form longer chains, while the Cu atoms are favorable to form shorter chains in the system. Those chains interlocked with each other to improve the structural stability.

Magnetic field induced quantum dot brightening in liquid crystal synergized magnetic and semiconducting nanoparticle composite assemblies

DOE PAGES

Amaral, Jose Jussi; Wan, Jacky; Rodarte, Andrea L.; ...

2014-10-22

The design and development of multifunctional composite materials from artificial nano-constituents is one of the most compelling current research areas. This drive to improve over nature and produce ‘meta-materials’ has met with some success, but results have proven limited with regards to both the demonstration of synergistic functionalities and in the ability to manipulate the material properties post-fabrication and in situ. Here, magnetic nanoparticles (MNPs) and semiconducting quantum dots (QDs) are co-assembled in a nematic liquid crystalline (LC) matrix, forming composite structures in which the emission intensity of the quantum dots is systematically and reversibly controlled with a small appliedmore » magnetic field (<100 mT). This magnetic field-driven brightening, ranging between a two- to three-fold peak intensity increase, is a truly cooperative effect: the LC phase transition creates the co-assemblies, the clustering of the MNPs produces LC re-orientation at atypical low external field, and this re-arrangement produces compaction of the clusters, resulting in the detection of increased QD emission. These results demonstrate a synergistic, reversible, and an all-optical process to detect magnetic fields and additionally, as the clusters are self-assembled in a fluid medium, they offer the possibility for these sensors to be used in broad ranging fluid-based applications.« less

Discovery of the X-ray selected galaxy cluster XMMU J0338.8+0021 at z = 1.49. Indications of a young system with a brightest galaxy in formation

NASA Astrophysics Data System (ADS)

Nastasi, A.; Fassbender, R.; Böhringer, H.; Šuhada, R.; Rosati, P.; Pierini, D.; Verdugo, M.; Santos, J. S.; Schwope, A. D.; de Hoon, A.; Kohnert, J.; Lamer, G.; Mühlegger, M.; Quintana, H.

2011-08-01

We report the discovery of a galaxy cluster at z = 1.490 originally selected as an extended X-ray source in the XMM-Newton Distant Cluster Project. Further observations carried out with the VLT-FORS2 spectrograph allowed the spectroscopic confirmation of seven secure cluster members, providing a median system redshift of z = 1.490 ± 0.009. The color-magnitude diagram of XMMU J0338.8+0021 reveals the presence of a well-populated red sequence with z - H ≈ 3, albeit with an apparent significant scatter in color. Since we do not detect indications of any strong star formation activity in these objects, the color spread could represent the different stellar ages of the member galaxies. In addition, we found the brightest cluster galaxy in a very active dynamical state, with an interacting, merging companion located at a physical projected distance of d ≈ 20 kpc. From the X-ray luminosity, we estimate a cluster mass of M200 ~ 1.2 × 1014 M⊙. The data appear to be consistent with a scenario in which XMMU J0338.8+0021 is a young system, possibly caught in a moment of active ongoing mass assembly. Based on observations under programme ID 084.A-0844 collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, and observations collected at the Centro Astronómico Hispano Alemán at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).Tables 1, 2 and Figs. 3-6 are available in electronic form at http://www.aanda.org

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Broad spectrum antibiotic compounds and use thereof

DOEpatents

Koglin, Alexander; Strieker, Matthias

2016-07-05

The discovery of a non-ribosomal peptide synthetase (NRPS) gene cluster in the genome of Clostridium thermocellum that produces a secondary metabolite that is assembled outside of the host membrane is described. Also described is the identification of homologous NRPS gene clusters from several additional microorganisms. The secondary metabolites produced by the NRPS gene clusters exhibit broad spectrum antibiotic activity. Thus, antibiotic compounds produced by the NRPS gene clusters, and analogs thereof, their use for inhibiting bacterial growth, and methods of making the antibiotic compounds are described.

Cluster optical coding: from biochips to counterfeit security

NASA Astrophysics Data System (ADS)

Haglmueller, Jakob; Alguel, Yilmaz; Mayer, Christian; Matyushin, Viacheslav; Bauer, Georg; Pittner, Fritz; Leitner, Alfred; Aussenegg, Franz R.; Schalkhammer, Thomas G.

2004-07-01

Spatially tuned resonant nano-clusters allow high local field enhancement when exited by electromagnetic radiation. A number of phenomena had been described and subsequently applied to novel nano- and bionano-devices. Decisive for these types of devices and sensors is the precise nanometric assembly, coupling the local field surrounding a cluster to allow resonance with other elements interacting with this field. In particular, the distance cluster-mirror or cluster-fluorophore gives rise to a variety of enhancement phenomena. High throughput transducers using metal cluster resonance technology are based on surface-enhancement of metal cluster light absorption (SEA). The optical property for the analytical application of metal cluster films is the so-called anomalous absorption. At a well defined nanometric distance of a cluster to a mirror the reflected electromagnetic field has the same phase at the position of the absorbing cluster as the incident fields. This feedback mechanism strongly enhances the effective cluster absorption coefficient. The system is characterised by a narrow reflection minimum. Based on this SEA-phenomenon (licensed to and further developed and optimized by NovemberAG, Germany Erlangen) a number of commercial products have been constructed. Brandsealing(R) uses the patented SEA cluster technology to produce optical codings. Cluster SEA thin film systems show a characteristic color-flip effect and are extremely mechanically and thermally robust. This is the basis for its application as an unique security feature. The specific spectroscopic properties as e.g. narrow band multi-resonance of the cluster layers allow the authentication of the optical code which can be easily achieved with a mobile hand-held reader developed by november AG and Siemens AG. Thus, these features are machine-readable which makes them superior to comparable technologies. Cluster labels are available in two formats: as a label for tamper-proof product packaging, and as a direct label, where label and logo are permanently applied directly and unremovable to the product surface. Together with Infineon Technologies and HUECK FOLIEN, the SEA technology is currently developed as a direct label for e.g. SmartCards.

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.

PubMed

Eaton, Deren A R

2014-07-01

Restriction-site-associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations to restriction recognition sites that disrupt data generation, an additional source of data loss comes from the failure to identify homology during bioinformatic analyses. Clustering methods that allow for lower similarity thresholds and the inclusion of indel variation will perform better at assembling RADseq loci at the phylogenetic scale. PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets. It uses a wrapper around an alignment-clustering algorithm, which allows for indel variation within and between samples, as well as for incomplete overlap among reads (e.g. paired-end). Here I compare PyRAD with the program Stacks in their performance analyzing a simulated RADseq dataset that includes indel variation. Indels disrupt clustering of homologous loci in Stacks but not in PyRAD, such that the latter recovers more shared loci across disparate taxa. I show through reanalysis of an empirical RADseq dataset that indels are a common feature of such data, even at shallow phylogenetic scales. PyRAD uses parallel processing as well as an optional hierarchical clustering method, which allows it to rapidly assemble phylogenetic datasets with hundreds of sampled individuals. Software is written in Python and freely available at http://www.dereneaton.com/software/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads

PubMed Central

2013-01-01

Background Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly. Results Previously, we presented an overlap graph coarsening scheme for modeling read overlap relationships on multiple levels. Most current read assembly and analysis approaches use a single graph or set of clusters to represent the relationships among a read dataset. Instead, we use a series of graphs to represent the reads and their overlap relationships across a spectrum of information granularity. At each information level our algorithm is capable of generating clusters of reads from the reduced graph, forming an integrated graph modeling and clustering approach for read analysis and assembly. Previously we applied our algorithm to simulated and real 454 datasets to assess its ability to efficiently model and cluster next generation sequencing data. In this paper we extend our algorithm to large simulated and real Illumina datasets to demonstrate that our algorithm is practical for both sequencing technologies. Conclusions Our overlap graph theoretic algorithm is able to model next generation sequencing reads at various levels of granularity through the process of graph coarsening. Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies. PMID:24564333

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters.

PubMed

Dallery, Jean-Félix; Lapalu, Nicolas; Zampounis, Antonios; Pigné, Sandrine; Luyten, Isabelle; Amselem, Joëlle; Wittenberg, Alexander H J; Zhou, Shiguo; de Queiroz, Marisa V; Robin, Guillaume P; Auger, Annie; Hainaut, Matthieu; Henrissat, Bernard; Kim, Ki-Tae; Lee, Yong-Hwan; Lespinet, Olivier; Schwartz, David C; Thon, Michael R; O'Connell, Richard J

2017-08-29

The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.

Clustering and heterogeneous dynamics in a kinetic Monte Carlo model of self-propelled hard disks

NASA Astrophysics Data System (ADS)

Levis, Demian; Berthier, Ludovic

2014-06-01

We introduce a kinetic Monte Carlo model for self-propelled hard disks to capture with minimal ingredients the interplay between thermal fluctuations, excluded volume, and self-propulsion in large assemblies of active particles. We analyze in detail the resulting (density, self-propulsion) nonequilibrium phase diagram over a broad range of parameters. We find that purely repulsive hard disks spontaneously aggregate into fractal clusters as self-propulsion is increased and rationalize the evolution of the average cluster size by developing a kinetic model of reversible aggregation. As density is increased, the nonequilibrium clusters percolate to form a ramified structure reminiscent of a physical gel. We show that the addition of a finite amount of noise is needed to trigger a nonequilibrium phase separation, showing that demixing in active Brownian particles results from a delicate balance between noise, interparticle interactions, and self-propulsion. We show that self-propulsion has a profound influence on the dynamics of the active fluid. We find that the diffusion constant has a nonmonotonic behavior as self-propulsion is increased at finite density and that activity produces strong deviations from Fickian diffusion that persist over large time scales and length scales, suggesting that systems of active particles generically behave as dynamically heterogeneous systems.

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…

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…

Molecular Clusters: Nanoscale Building Blocks for Solid-State Materials.

PubMed

Pinkard, Andrew; Champsaur, Anouck M; Roy, Xavier

2018-04-17

The programmed assembly of nanoscale building blocks into multicomponent hierarchical structures is a powerful strategy for the bottom-up construction of functional materials. To develop this concept, our team has explored the use of molecular clusters as superatomic building blocks to fabricate new classes of materials. The library of molecular clusters is rich with exciting properties, including diverse functionalization, redox activity, and magnetic ordering, so the resulting cluster-assembled solids, which we term superatomic crystals (SACs), hold the promise of high tunability, atomic precision, and robust architectures among a diverse range of other material properties. Molecular clusters have only seldom been used as precursors for functional materials. Our team has been at the forefront of new developments in this exciting research area, and this Account focuses on our progress toward designing materials from cluster-based precursors. In particular, this Account discusses (1) the design and synthesis of molecular cluster superatomic building blocks, (2) their self-assembly into SACs, and (3) their resulting collective properties. The set of molecular clusters discussed herein is diverse, with different cluster cores and ligand arrangements to create an impressive array of solids. The cluster cores include octahedral M 6 E 8 and cubane M 4 E 4 (M = metal; E = chalcogen), which are typically passivated by a shell of supporting ligands, a feature upon which we have expanded upon by designing and synthesizing more exotic ligands that can be used to direct solid-state assembly. Building from this library, we have designed whole families of binary SACs where the building blocks are held together through electrostatic, covalent, or van der Waals interactions. Using single-crystal X-ray diffraction (SCXRD) to determine the atomic structure, a remarkable range of compositional variability is accessible. We can also use this technique, in tandem with vibrational spectroscopy, to ascertain features about the constituent superatomic building blocks, such as the charge of the cluster cores, by analysis of bond distances from the SCXRD data. The combination of atomic precision and intercluster interactions in these SACs produces novel collective properties, including tunable electrical transport, crystalline thermal conductivity, and ferromagnetism. In addition, we have developed a synthetic strategy to insert redox-active guests into the superstructure of SACs via single-crystal-to-single-crystal intercalation. This intercalation process allows us to tune the optical and electrical transport properties of the superatomic crystal host. These properties are explored using a host of techniques, including Raman spectroscopy, SQUID magnetometry, electrical transport measurements, electronic absorption spectroscopy, differential scanning calorimetry, and frequency-domain thermoreflectance. Superatomic crystals have proven to be both robust and tunable, representing a new method of materials design and architecture. This Account demonstrates how precisely controlling the structure and properties of nanoscale building blocks is key in developing the next generation of functional materials; several examples are discussed and detailed herein.

Pendulum Motion in Main Parachute Clusters

NASA Technical Reports Server (NTRS)

Ray, Eric S.; Machin, Ricardo A.

2015-01-01

The coupled dynamics of a cluster of parachutes to a payload are notoriously difficult to predict. Often the payload is designed to be insensitive to the range of attitude and rates that might occur, but spacecraft generally do not have the mass and volume budgeted for this robust of a design. The National Aeronautics and Space Administration (NASA) Orion Capsule Parachute Assembly System (CPAS) implements a cluster of three mains for landing. During testing of the Engineering Development Unit (EDU) design, it was discovered that with a cluster of two mains (a fault tolerance required for human rating) the capsule coupled to the parachute cluster could get into a limit cycle pendulum motion which would exceed the spacecraft landing capability. This pendulum phenomenon could not be predicted with the existing models and simulations. A three phased effort has been undertaken to understand the consequence of the pendulum motion observed, and explore potential design changes that would mitigate this phenomenon. This paper will review the early analysis that was performed of the pendulum motion observed during EDU testing, summarize the analysis ongoing to understand the root cause of the pendulum phenomenon, and discuss the modeling and testing that is being pursued to identify design changes that would mitigate the risk.

Saturn Apollo Program

NASA Image and Video Library

1969-01-01

In the clustering procedure, an initial assembly step for the Saturn IB launch vehicle's S-IB (first) stage, workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, position the central liquid-oxygen tank. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.

The mitochondrial Hsp70 chaperone Ssq1 facilitates Fe/S cluster transfer from Isu1 to Grx5 by complex formation.

PubMed

Uzarska, Marta A; Dutkiewicz, Rafal; Freibert, Sven-Andreas; Lill, Roland; Mühlenhoff, Ulrich

2013-06-01

The mitochondrial Hsp70 chaperone Ssq1 plays a dedicated role in the maturation of iron-sulfur (Fe/S) proteins, an essential process of mitochondria. Similar to its bacterial orthologue HscA, Ssq1 binds to the scaffold protein Isu1, thereby facilitating dissociation of the newly synthesized Fe/S cluster on Isu1 and its transfer to target apoproteins. Here we use in vivo and in vitro approaches to show that Ssq1 also interacts with the monothiol glutaredoxin 5 (Grx5) at a binding site different from that of Isu1. Grx5 binding does not stimulate the ATPase activity of Ssq1 and is most pronounced for the ADP-bound form of Ssq1, which interacts with Isu1 most tightly. The vicinity of Isu1 and Grx5 on the Hsp70 chaperone facilitates rapid Fe/S cluster transfer from Isu1 to Grx5. Grx5 and its bound Fe/S cluster are required for maturation of all cellular Fe/S proteins, regardless of the type of bound Fe/S cofactor and subcellular localization. Hence Grx5 functions as a late-acting component of the core Fe/S cluster (ISC) assembly machinery linking the Fe/S cluster synthesis reaction on Isu1 with late assembly steps involving Fe/S cluster targeting to dedicated apoproteins.

Collagen peptide-based biomaterials for protein delivery and peptide-promoted self-assembly of gold nanoparticles

NASA Astrophysics Data System (ADS)

Ernenwein, Dawn M.

2011-12-01

Bottom-up self-assembly of peptides has driven the research progress for the following two projects: protein delivery vehicles of collagen microflorettes and the assembly of gold nanoparticles with coiled-coil peptides. Collagen is the most abundant protein in the mammals yet due to immunogenic responses, batch-to-batch variability and lack of sequence modifications, synthetic collagen has been designed to self-assemble into native collagen-like structures. In particular with this research, metal binding ligands were incorporated on the termini of collagen-like peptides to generate micron-sized particles, microflorettes. The over-arching goal of the first research project is to engineer MRI-active microflorettes, loaded with His-tagged growth factors with differential release rates while bound to stem cells that can be implemented toward regenerative cell-based therapies. His-tagged proteins, such as green fluorescent protein, have successfully been incorporated on the surface and throughout the microflorettes. Protein release was monitored under physiological conditions and was related to particle degradation. In human plasma full release was obtained within six days. Stability of the microflorettes under physiological conditions was also examined for the development of a therapeutically relevant delivery agent. Additionally, MRI active microflorettes have been generated through the incorporation of a gadolinium binding ligand, DOTA within the collagen-based peptide sequence. To probe peptide-promoted self-assemblies of gold nanoparticles (GNPs) by non-covalent, charge complementary interactions, a highly anionic coiled-coil peptide was designed and synthesized. Upon formation of peptide-GNP interactions, the hydrophobic domain of the coiled-coil were shown to promote the self-assembly of peptide-GNPs clustering. Hydrophobic forces were found to play an important role in the assembly process, as a peptide with an equally overall negative charge, but lacking an ordered hydrophobic face had no effect on GNP assembly. The self-assembly system herein is advantageous due to its reversible nature upon addition of high salt concentrations which masks the surface charge. There is great potential for using this uniquely designed self-assembled peptide-gold nanoparticle system for exploring the interplay between peptide ligation and GNP self-assembly.

FAST TRACK COMMUNICATION: Poly(methyl methacrylate)-palladium clusters nanocomposite formation by supersonic cluster beam deposition: a method for microstructured metallization of polymer surfaces

NASA Astrophysics Data System (ADS)

Ravagnan, Luca; Divitini, Giorgio; Rebasti, Sara; Marelli, Mattia; Piseri, Paolo; Milani, Paolo

2009-04-01

Nanocomposite films were fabricated by supersonic cluster beam deposition (SCBD) of palladium clusters on poly(methyl methacrylate) (PMMA) surfaces. The evolution of the electrical conductance with cluster coverage and microscopy analysis show that Pd clusters are implanted in the polymer and form a continuous layer extending for several tens of nanometres beneath the polymer surface. This allows the deposition, using stencil masks, of cluster-assembled Pd microstructures on PMMA showing a remarkably high adhesion compared with metallic films obtained by thermal evaporation. These results suggest that SCBD is a promising tool for the fabrication of metallic microstructures on flexible polymeric substrates.

Lipid Rafts Assemble Dynein Ensembles.

PubMed

Nirschl, Jeffrey J; Ghiretti, Amy E; Holzbaur, Erika L F

2016-05-01

New work by Rai et al. identifies a novel mechanism regulating phagosome transport in cells: the clustering of dynein motors into lipid microdomains, leading to enhanced unidirectional motility. Clustering may be especially important for dynein, a motor that works most efficiently in teams. Copyright © 2016 Elsevier Ltd. All rights reserved.

DNA-Mediated Patterning of Single Quantum Dot Nanoarrays: A Reusable Platform for Single-Molecule Control

NASA Astrophysics Data System (ADS)

Huang, Da; Freeley, Mark; Palma, Matteo

2017-03-01

We present a facile strategy of general applicability for the assembly of individual nanoscale moieties in array configurations with single-molecule control. Combining the programming ability of DNA as a scaffolding material with a one-step lithographic process, we demonstrate the patterning of single quantum dots (QDs) at predefined locations on silicon and transparent glass surfaces: as proof of concept, clusters of either one, two, or three QDs were assembled in highly uniform arrays with a 60 nm interdot spacing within each cluster. Notably, the platform developed is reusable after a simple cleaning process and can be designed to exhibit different geometrical arrangements.

Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fasolato, C.; Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, Rome; Domenici, F., E-mail: fabiodomenici@gmail.com

2015-06-23

The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we reportmore » on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 10{sup 9}) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM measurements confirmed the regularity in spacing and size (i.e. area and layer number) of the aggregates. Preliminary SERS measurements confirm the high signal enhancement and demonstrate a quite good reproducibility over large number of aggregates within 100×100 μm{sup 2} 2D super-structure. The availability of such a multisensor could allow a careful statistical analysis of the SERS response, thus leading to a reliable quantitative estimate of the presence of relevant molecular species even at ultra-low concentration.« less

Mechanisms of kinetic trapping in self-assembly and phase transformation

PubMed Central

Hagan, Michael F.; Elrad, Oren M.; Jack, Robert L.

2011-01-01

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. PMID:21932884

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

Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ3-oxo)Tris[(μ2-peroxo)] triiron(III) cluster

PubMed Central

Pozzi, Cecilia; Di Pisa, Flavio; Mangani, Stefano; Turano, Paola

2017-01-01

X-ray structures of homopolymeric L-ferritin obtained by freezing protein crystals at increasing exposure times to a ferrous solution showed the progressive formation of a triiron cluster on the inner cage surface of each subunit. After 60 min exposure, a fully assembled (μ3-oxo)Tris[(μ2-peroxo)(μ2-glutamato-κO:κO′)](glutamato-κO)(diaquo)triiron(III) anionic cluster appears in human L-ferritin. Glu60, Glu61, and Glu64 provide the anchoring of the cluster to the protein cage. Glu57 shuttles incoming iron ions toward the cluster. We observed a similar metallocluster in horse spleen L-ferritin, indicating that it represents a common feature of mammalian L-ferritins. The structures suggest a mechanism for iron mineral formation at the protein interface. The functional significance of the observed patch of carboxylate side chains and resulting metallocluster for biomineralization emerges from the lower iron oxidation rate measured in the E60AE61AE64A variant of human L-ferritin, leading to the proposal that the observed metallocluster corresponds to the suggested, but yet unobserved, nucleation site of L-ferritin. PMID:28202724

Chemistry at the protein-mineral interface in L-ferritin assists the assembly of a functional (μ3-oxo)Tris[(μ2-peroxo)] triiron(III) cluster.

PubMed

Pozzi, Cecilia; Ciambellotti, Silvia; Bernacchioni, Caterina; Di Pisa, Flavio; Mangani, Stefano; Turano, Paola

2017-03-07

X-ray structures of homopolymeric L-ferritin obtained by freezing protein crystals at increasing exposure times to a ferrous solution showed the progressive formation of a triiron cluster on the inner cage surface of each subunit. After 60 min exposure, a fully assembled (μ 3 -oxo)Tris[(μ 2 -peroxo)(μ 2 -glutamato-κ O :κ O ')](glutamato-κ O )(diaquo)triiron(III) anionic cluster appears in human L-ferritin. Glu60, Glu61, and Glu64 provide the anchoring of the cluster to the protein cage. Glu57 shuttles incoming iron ions toward the cluster. We observed a similar metallocluster in horse spleen L-ferritin, indicating that it represents a common feature of mammalian L-ferritins. The structures suggest a mechanism for iron mineral formation at the protein interface. The functional significance of the observed patch of carboxylate side chains and resulting metallocluster for biomineralization emerges from the lower iron oxidation rate measured in the E60AE61AE64A variant of human L-ferritin, leading to the proposal that the observed metallocluster corresponds to the suggested, but yet unobserved, nucleation site of L-ferritin.

Anthranilate-Activating Modules from Fungal Nonribosomal Peptide Assembly Lines†

PubMed Central

Ames, Brian D.; Walsh, Christopher T.

2010-01-01

Fungal natural products containing benzodiazepinone- and quinazolinone-fused ring systems can be assembled by nonribosomal peptide synthetases (NRPS) using the conformationally restricted β-amino acid anthranilate as one of the key building blocks. We validated that the first module of the acetylaszonalenin synthetase of Neosartorya fischeri NRRL 181 activates anthranilate to anthranilyl-AMP. With this as starting point, we then used bioinformatic predictions about fungal adenylation domain selectivities to identify and confirm an anthranilate-activating module in the fumiquinazoline A producer Aspergillus fumigatus Af293 as well as a second anthranilate-activating NRPS in N. fischeri. This establishes an anthranilate adenylation domain code for fungal NRPS and should facilitate detection and cloning of gene clusters for benzodiazepine- and quinazoline-containing polycyclic alkaloids with a wide range of biological activities. PMID:20225828

The Azotobacter vinelandii NifEN complex contains two identical [4Fe-4S] clusters.

PubMed

Goodwin, P J; Agar, J N; Roll, J T; Roberts, G P; Johnson, M K; Dean, D R

1998-07-21

The nifE and nifN gene products from Azotobacter vinelandii form an alpha2beta2 tetramer (NifEN complex) that is required for the biosynthesis of the nitrogenase FeMo cofactor. In the current model for NifEN complex organization and function, the complex is structurally analogous to the nitrogenase MoFe protein and provides an assembly site for a portion of FeMo cofactor biosynthesis. In this work, gene fusion and immobilized metal-affinity chromatography strategies were used to elevate the in vivo production of the NifEN complex and to facilitate its rapid and efficient purification. The NifEN complex produced and purified in this way exhibits an FeMo cofactor biosynthetic activity similar to that previously described for the NifEN complex purified by traditional chromatography methods. UV-visible, EPR, variable-temperature magnetic circular dichroism, and resonance Raman spectroscopies were used to show that the NifEN complex contains two identical [4Fe-4S]2+ clusters. These clusters have a predominantly S = 1/2 ground state in the reduced form, exhibit a reduction potential of -350 mV, and are likely to be coordinated entirely by cysteinyl residues on the basis of spectroscopic properties and sequence comparisons. A model is proposed where each NifEN complex [4Fe-4S] cluster is bridged between a NifE-NifN subunit interface at a position analogous to that occupied by the P clusters in the nitrogenase MoFe protein. In contrast to the MoFe protein P clusters, the NifEN complex [4Fe-4S] clusters are proposed to be asymmetrically coordinated to the NifEN complex where NifE cysteines-37, -62, and -124 and NifN cysteine-44 are the coordinating ligands. On the basis of a homology model of the three-dimensional structure of the NifEN complex, the [4Fe-4S] cluster sites are likely to be remote from the proposed FeMo cofactor assembly site and are unlikely to become incorporated into the FeMo cofactor during its assembly.

Monodisperse hexagonal silver nanoprisms: synthesis via thiolate-protected cluster precursors and chiral, ligand-imprinted self-assembly.

PubMed

Cathcart, Nicole; Kitaev, Vladimir

2011-09-27

Silver nanoprisms of a predominantly hexagonal shape have been prepared using a ligand combination of a strongly binding thiol, captopril, and charge-stabilizing citrate together with hydrogen peroxide as an oxidative etching agent and a strong base that triggered nanoprism formation. The role of the reagents and their interplay in the nanoprism synthesis is discussed in detail. The beneficial role of chloride ions to attain a high degree of reproducibility and monodispersity of the nanoprisms is elucidated. Control over the nanoprism width, thickness, and, consequently, plasmon resonance in the system has been demonstrated. One of the crucial factors in the nanoprism synthesis was the slow, controlled aggregation of thiolate-stabilized silver nanoclusters as the intermediates. The resulting superior monodispersity (better than ca. 10% standard deviation in lateral size and ca. 15% standard deviation in thickness (<1 nm variation)) and charge stabilization of the produced silver nanoprisms enabled the exploration of the rich diversity of the self-assembled morphologies in the system. Regular columnar assemblies of the self-assembled nanoprisms spanning 2-3 μm in length have been observed. Notably, the helicity of the columnar phases was evident, which can be attributed to the chirality of the strongly binding thiol ligand. Finally, the enhancement of Raman scattering has been observed after oxidative removal of thiolate ligands from the AgNPR surface. © 2011 American Chemical Society

NRVS and EPR Spectroscopy of 57Fe-enriched [FeFe] Hydrogenase Indicate Stepwise Assembly of the H-cluster†

PubMed Central

Kuchenreuther, Jon M.; Guo, Yisong; Wang, Hongxin; Myers, William K.; George, Simon J.; Boyke, Christine A.; Yoda, Yoshitaka; Alp, E. Ercan; Zhao, Jiyong; Britt, R. David; Swartz, James R.; Cramer, Stephen P.

2013-01-01

The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe–S clusters that facilitate electron transfer to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H2. Here, we have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe–4S] ferredoxin as well as a model complex resembling the [2Fe]H catalytic domain of the H-cluster. In order to enrich the hydrogenase with 57Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with 56Fe-labeled Fe–S clusters was activated in vitro using 57Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe]H subcluster with 57Fe, which NRVS confirms by detecting 57Fe–CO and 57Fe–CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second 57Fe–S cluster. EPR spectroscopy indicates that this 57Fe-enriched metal center is not the [4Fe– 4S]H subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an 56Fe-enriched [4Fe–4S]H cluster during in vitro maturation, providing unambiguous evidence for stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases. PMID:23249091

Occupational Education for Students with Special Needs: Plastics Manufacturing and Assembling.

ERIC Educational Resources Information Center

Nassau County Board of Cooperative Educational Services, Westbury, NY.

This curriculum resource guide on plastics manufacturing and assembling 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…

Encapsulation of [F4(H2O)10](4-) in a dimeric assembly of an unidirectional arene based hexapodal amide receptor.

PubMed

Arunachalam, M; Ghosh, Pradyut

2011-06-14

An unidirectional orientation of all six arms of an arene based hexapodal amide receptor shows dimeric capsular assembly templated by a [F(4)(H(2)O)(10)](4-) cluster. This journal is © The Royal Society of Chemistry 2011

Polyalanine expansions drive a shift into α-helical clusters without amyloid-fibril formation.

PubMed

Polling, Saskia; Ormsby, Angelique R; Wood, Rebecca J; Lee, Kristie; Shoubridge, Cheryl; Hughes, James N; Thomas, Paul Q; Griffin, Michael D W; Hill, Andrew F; Bowden, Quill; Böcking, Till; Hatters, Danny M

2015-12-01

Polyglutamine (polyGln) expansions in nine human proteins result in neurological diseases and induce the proteins' tendency to form β-rich amyloid fibrils and intracellular deposits. Less well known are at least nine other human diseases caused by polyalanine (polyAla)-expansion mutations in different proteins. The mechanisms of how polyAla aggregates under physiological conditions remain unclear and controversial. We show here that aggregation of polyAla is mechanistically dissimilar to that of polyGln and hence does not exhibit amyloid kinetics. PolyAla assembled spontaneously into α-helical clusters with diverse oligomeric states. Such clustering was pervasive in cells irrespective of visible aggregate formation, and it disrupted the normal physiological oligomeric state of two human proteins natively containing polyAla: ARX and SOX3. This self-assembly pattern indicates that polyAla expansions chronically disrupt protein behavior by imposing a deranged oligomeric status.

Disruption of Chemoreceptor Signaling Arrays by High Levels of CheW, the Receptor-Kinase Coupling Protein

PubMed Central

Cardozo, Marcos J.; Massazza, Diego A.; Parkinson, John S.; Studdert, Claudia A.

2017-01-01

Summary During chemotactic signaling by Escherichia coli, the small cytoplasmic CheW protein couples the histidine kinase CheA to chemoreceptor control. Although essential for assembly and operation of receptor signaling complexes, CheW in stoichiometric excess disrupts chemotactic behavior. To explore the mechanism of the CheW excess effect, we measured the physiological consequences of high cellular levels of wild-type CheW and of several CheW variants with reduced or enhanced binding affinities for receptor molecules. We found that high levels of CheW interfered with trimer assembly, prevented CheA activation, blocked cluster formation, disrupted chemotactic ability, and elevated receptor methylation levels. The severity of these effects paralleled the receptor binding affinities of the CheW variants. Because trimer formation may be an obligate step in the assembly of ternary signaling complexes and higher-order receptor arrays, we suggest that all CheW excess effects stem from disruption of trimer assembly. We propose that the CheW-binding sites in receptor dimers overlap their trimer contact sites and that high levels of CheW saturate the receptor binding sites, preventing trimer assembly. The CheW-trapped receptor dimers seem to be improved substrates for methyltransferase reactions, but cannot activate CheA or assemble into clusters, processes that are essential for chemotactic signaling. PMID:20487303

Nature's polyoxometalate chemistry: X-ray structure of the Mo storage protein loaded with discrete polynuclear Mo-O clusters.

PubMed

Kowalewski, Björn; Poppe, Juliane; Demmer, Ulrike; Warkentin, Eberhard; Dierks, Thomas; Ermler, Ulrich; Schneider, Klaus

2012-06-13

Some N(2)-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo(8), three Mo(5-7), and one Mo(3) clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)(3) protein complex. The structurally identical Mo(8) clusters (three layers of two, four, and two MoO(n) octahedra) are distinguishable from the [Mo(8)O(26)](4-) cluster formed in acidic solutions by two displaced MoO(n) octahedra implicating three kinetically labile terminal ligands. Stabilization in the covalent Mo(8) cluster is achieved by Mo bonding to Hisα156-N(ε2) and Gluα129-O(ε1). The absence of covalent protein interactions in the noncovalent Mo(8) cluster is compensated by a more extended hydrogen-bond network involving three pronounced histidines. One displaced MoO(n) octahedron might serve as nucleation site for an inhomogeneous Mo(5-7) cluster largely surrounded by bulk solvent. In the Mo(3) cluster located on the 3-fold axis, the three accurately positioned His140-N(ε2) atoms of the α subunits coordinate to the Mo atoms. The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host-guest system. Template, nucleation/protection, and catalyst functions of the polypeptide as well as perspectives for designing new clusters are discussed.

Isolated ellipticals and their globular cluster systems. III. NGC 2271, NGC 2865, NGC 3962, NGC 4240, and IC 4889

NASA Astrophysics Data System (ADS)

Salinas, R.; Alabi, A.; Richtler, T.; Lane, R. R.

2015-05-01

As tracers of star formation, galaxy assembly, and mass distribution, globular clusters have provided important clues to our understanding of early-type galaxies. But their study has been mostly constrained to galaxy groups and clusters where early-type galaxies dominate, leaving the properties of the globular cluster systems (GCSs) of isolated ellipticals as a mostly uncharted territory. We present Gemini-South/GMOS g'i' observations of five isolated elliptical galaxies: NGC 3962, NGC 2865, IC 4889, NGC 2271, and NGC 4240. Photometry of their GCSs reveals clear color bimodality in three of them, but remains inconclusive for the other two. All the studied GCSs are rather poor with a mean specific frequency SN ~ 1.5, independently of the parent galaxy luminosity. Considering information from previous work as well, it is clear that bimodality and especially the presence of a significant, even dominant, population of blue clusters occurs at even the most isolated systems, which casts doubts on a possible accreted origin of metal-poor clusters, as suggested by some models. Additionally, we discuss the possible existence of ultra-compact dwarfs around the isolated elliptical NGC 3962. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the Science and Technology Facilities Council (United Kingdom), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), Ministério da Ciência, Tecnologia e Inovação (Brazil) and Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina).Globular cluster photometry is available in electronic form at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/577/A59Appendices are available in electronic form at http://www.aanda.org

Smallest fullerene-like silicon cage stabilized by a V(2) unit.

PubMed

Xu, Hong-Guang; Kong, Xiang-Yu; Deng, Xiao-Jiao; Zhang, Zeng-Guang; Zheng, Wei-Jun

2014-01-14

We conducted a combined anion photoelectron spectroscopy and density functional theory study on V2Si20 cluster. Our results show that the V2Si20 cluster has an elongated dodecahedron cage structure with a V2 unit encapsulated inside the cage. It is the smallest fullerene-like silicon cage and can be used as building block to make cluster-assembled materials, such as pearl-chain style nanowires.

Smallest fullerene-like silicon cage stabilized by a V2 unit

NASA Astrophysics Data System (ADS)

Xu, Hong-Guang; Kong, Xiang-Yu; Deng, Xiao-Jiao; Zhang, Zeng-Guang; Zheng, Wei-Jun

2014-01-01

We conducted a combined anion photoelectron spectroscopy and density functional theory study on V2Si20 cluster. Our results show that the V2Si20 cluster has an elongated dodecahedron cage structure with a V2 unit encapsulated inside the cage. It is the smallest fullerene-like silicon cage and can be used as building block to make cluster-assembled materials, such as pearl-chain style nanowires.

Use of ion-mobility mass spectrometry (IMS-MS) to map polyoxometalate Keplerate clusters and their supramolecular assemblies.

PubMed

Robbins, Philip J; Surman, Andrew J; Thiel, Johannes; Long, De-Liang; Cronin, Leroy

2013-03-07

We present the high-resolution (HRES-MS) and ion-mobility (IMS-MS) mass spectrometry studies of icosahedral nanoscale polyoxometalate-based {L(30)}{(Mo)Mo(5)} Keplerate clusters, and demonstrate the use of IMS-MS to resolve and map intact nanoclusters, and its potential for the discovery of new structures, in this case the first gas phase observation of 'proto-clustering' of higher order Keplerate supramolecular aggregates.

Self Assembly Nonlinear Optical Effects with Novel Small Metal Cluster Systems

DTIC Science & Technology

2013-07-29

Regents of the University of Michigan 3003 S. State St Ann Arbor, MI 48109 -1274 REPORT DOCUMENTATION PAGE b . ABSTRACT UU c. THIS PAGE UU 2. REPORT TYPE...Journal of Physical Chemistry Letters, (09 2011): 0. doi: 10.1021/jz200738t 10/30/2011 4.00 Travis B . Clark, Meghan E. Orr, Daniel C. Flynn, Theodore...jp2005925 10/30/2011 5.00 Mary Sajini Devadas , Junhyung Kim, Ekkehard Sinn, Dongil Lee, Theodore Goodson, Guda Ramakrishna. Unique Ultrafast Visible

Characterization of a gene cluster responsible for the biosynthesis of anticancer agent FK228 in Chromobacterium violaceum No. 968.

PubMed

Cheng, Yi-Qiang; Yang, Min; Matter, Andrea M

2007-06-01

A gene cluster responsible for the biosynthesis of anticancer agent FK228 has been identified, cloned, and partially characterized in Chromobacterium violaceum no. 968. First, a genome-scanning approach was applied to identify three distinctive C. violaceum no. 968 genomic DNA clones that code for portions of nonribosomal peptide synthetase and polyketide synthase. Next, a gene replacement system developed originally for Pseudomonas aeruginosa was adapted to inactivate the genomic DNA-associated candidate natural product biosynthetic genes in vivo with high efficiency. Inactivation of a nonribosomal peptide synthetase-encoding gene completely abolished FK228 production in mutant strains. Subsequently, the entire FK228 biosynthetic gene cluster was cloned and sequenced. This gene cluster is predicted to encompass a 36.4-kb DNA region that includes 14 genes. The products of nine biosynthetic genes are proposed to constitute an unusual hybrid nonribosomal peptide synthetase-polyketide synthase-nonribosomal peptide synthetase assembly line including accessory activities for the biosynthesis of FK228. In particular, a putative flavin adenine dinucleotide-dependent pyridine nucleotide-disulfide oxidoreductase is proposed to catalyze disulfide bond formation between two sulfhydryl groups of cysteine residues as the final step in FK228 biosynthesis. Acquisition of the FK228 biosynthetic gene cluster and acclimation of an efficient genetic system should enable genetic engineering of the FK228 biosynthetic pathway in C. violaceum no. 968 for the generation of structural analogs as anticancer drug candidates.

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

Skipped Stage Modeling and Testing of the CPAS Main Parachutes

NASA Technical Reports Server (NTRS)

Varela, Jose G.; Ray, Eric S.

2013-01-01

The Capsule Parachute Assembly System (CPAS) has undergone the transition from modeling a skipped stage event using a simulation that treats a cluster of parachutes as a single composite canopy to the capability of simulating each parachute individually. This capability along with data obtained from skipped stage flight tests has been crucial in modeling the behavior of a skipping canopy as well as the crowding effect on non-skipping ("lagging") neighbors. For the finite mass inflation of CPAS Main parachutes, the cluster is assumed to inflate nominally through the nominal fill time, at which point the skipping parachute continues inflating. This sub-phase modeling method was used to reconstruct three flight tests involving skipped stages. Best fit inflation parameters were determined for both the skipping and lagging canopies.

Electrons on a spherical surface: Physical properties and hollow spherical clusters

NASA Astrophysics Data System (ADS)

Cricchio, Dario; Fiordilino, Emilio; Persico, Franco

2012-07-01

We discuss the physical properties of a noninteracting electron gas constrained to a spherical surface. In particular we consider its chemical potentials, its ionization potential, and its electric static polarizability. All these properties are discussed analytically as functions of the number N of electrons. The trends obtained with increasing N are compared with those of the corresponding properties experimentally measured or theoretically evaluated for quasispherical hollow atomic and molecular clusters. Most of the properties investigated display similar trends, characterized by a prominence of shell effects. This leads to the definition of a scale-invariant distribution of magic numbers which follows a power law with critical exponent -0.5. We conclude that our completely mechanistic and analytically tractable model can be useful for the analysis of self-assembling complex systems.

Exploring the Molecular Growth of Two Gigantic Half‐Closed Polyoxometalate Clusters {Mo180} and {Mo130Ce6}

PubMed Central

Xuan, Weimin; Pow, Robert; Long, De‐Liang

2017-01-01

Abstract Understanding the process of the self‐assembly of gigantic polyoxometalates and their subsequent molecular growth, by the addition of capping moieties onto the oxo‐frameworks, is critical for the development of the designed assembly of complex high‐nuclearity cluster species, yet such processes remain far from being understood. Herein we describe the molecular growth from {Mo150} and {Mo120Ce6} to afford two half‐closed gigantic molybdenum blue clusters {Mo180} (1) and {Mo130Ce6} (2), respectively. Compound 1 features a hat‐shaped structure with the parent wheel‐shaped {Mo150} being capped by a {Mo30} unit on one side. Similarly, 2 exhibits an elliptical lanthanide‐doped wheel {Mo120Ce6} that is sealed by a {Mo10} unit on one side. Moreover, the observation of the parent uncapped {Mo150} and {Mo120Ce6} clusters as minor products during the synthesis of 1 and 2 strongly suggests that the molecular growth process can be initialized from {Mo150} and {Mo120Ce6} in solution, respectively. PMID:28508585

The E-MOSAICS project: simulating the formation and co-evolution of galaxies and their star cluster populations

NASA Astrophysics Data System (ADS)

Pfeffer, Joel; Kruijssen, J. M. Diederik; Crain, Robert A.; Bastian, Nate

2018-04-01

We introduce the MOdelling Star cluster population Assembly In Cosmological Simulations within EAGLE (E-MOSAICS) project. E-MOSAICS incorporates models describing the formation, evolution, and disruption of star clusters into the EAGLE galaxy formation simulations, enabling the examination of the co-evolution of star clusters and their host galaxies in a fully cosmological context. A fraction of the star formation rate of dense gas is assumed to yield a cluster population; this fraction and the population's initial properties are governed by the physical properties of the natal gas. The subsequent evolution and disruption of the entire cluster population are followed accounting for two-body relaxation, stellar evolution, and gravitational shocks induced by the local tidal field. This introductory paper presents a detailed description of the model and initial results from a suite of 10 simulations of ˜L⋆ galaxies with disc-like morphologies at z = 0. The simulations broadly reproduce key observed characteristics of young star clusters and globular clusters (GCs), without invoking separate formation mechanisms for each population. The simulated GCs are the surviving population of massive clusters formed at early epochs (z ≳ 1-2), when the characteristic pressures and surface densities of star-forming gas were significantly higher than observed in local galaxies. We examine the influence of the star formation and assembly histories of galaxies on their cluster populations, finding that (at similar present-day mass) earlier-forming galaxies foster a more massive and disruption-resilient cluster population, while galaxies with late mergers are capable of forming massive clusters even at late cosmic epochs. We find that the phenomenological treatment of interstellar gas in EAGLE precludes the accurate modelling of cluster disruption in low-density environments, but infer that simulations incorporating an explicitly modelled cold interstellar gas phase will overcome this shortcoming.

Kentucky DOE EPSCoR Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grulke, Eric; Stencel, John

2011-09-13

The KY DOE EPSCoR Program supports two research clusters. The Materials Cluster uses unique equipment and computational methods that involve research expertise at the University of Kentucky and University of Louisville. This team determines the physical, chemical and mechanical properties of nanostructured materials and examines the dominant mechanisms involved in the formation of new self-assembled nanostructures. State-of-the-art parallel computational methods and algorithms are used to overcome current limitations of processing that otherwise are restricted to small system sizes and short times. The team also focuses on developing and applying advanced microtechnology fabrication techniques and the application of microelectrornechanical systems (MEMS)more » for creating new materials, novel microdevices, and integrated microsensors. The second research cluster concentrates on High Energy and Nuclear Physics. lt connects research and educational activities at the University of Kentucky, Eastern Kentucky University and national DOE research laboratories. Its vision is to establish world-class research status dedicated to experimental and theoretical investigations in strong interaction physics. The research provides a forum, facilities, and support for scientists to interact and collaborate in subatomic physics research. The program enables increased student involvement in fundamental physics research through the establishment of graduate fellowships and collaborative work.« less

The effects of assembly bias on the inference of matter clustering from galaxy-galaxy lensing and galaxy clustering

NASA Astrophysics Data System (ADS)

McEwen, Joseph E.; Weinberg, David H.

2018-07-01

The combination of galaxy-galaxy lensing and galaxy clustering is a promising route to measuring the amplitude of matter clustering and testing modified gravity theories of cosmic acceleration. Halo occupation distribution (HOD) modelling can extend the approach down to non-linear scales, but galaxy assembly bias could introduce systematic errors by causing the HOD to vary with the large-scale environment at fixed halo mass. We investigate this problem using the mock galaxy catalogs created by Hearin & Watson (2013, HW13), which exhibit significant assembly bias because galaxy luminosity is tied to halo peak circular velocity and galaxy colour is tied to halo formation time. The preferential placement of galaxies (especially red galaxies) in older haloes affects the cutoff of the mean occupation function ⟨Ncen(Mmin)⟩ for central galaxies, with haloes in overdense regions more likely to host galaxies. The effect of assembly bias on the satellite galaxy HOD is minimal. We introduce an extended, environment-dependent HOD (EDHOD) prescription to describe these results and fit galaxy correlation measurements. Crucially, we find that the galaxy-matter cross-correlation coefficient, rgm(r) ≡ ξgm(r) . [ξmm(r)ξgg(r)]-1/2, is insensitive to assembly bias on scales r ≳ 1 h-1 Mpc, even though ξgm(r) and ξgg(r) are both affected individually. We can therefore recover the correct ξmm(r) from the HW13 galaxy-galaxy and galaxy-matter correlations using either a standard HOD or EDHOD fitting method. For Mr ≤ -19 or Mr ≤ -20 samples the recovery of ξmm(r) is accurate to 2 per cent or better. For a sample of red Mr ≤ -20 galaxies, we achieve 2 per cent recovery at r ≳ 2 h-1 Mpc with EDHOD modelling but lower accuracy at smaller scales or with a standard HOD fit. Most of our mock galaxy samples are consistent with rgm = 1 down to r = 1 h-1 Mpc, to within the uncertainties set by our finite simulation volume.

The effects of assembly bias on the inference of matter clustering from galaxy-galaxy lensing and galaxy clustering

NASA Astrophysics Data System (ADS)

McEwen, Joseph E.; Weinberg, David H.

2018-04-01

The combination of galaxy-galaxy lensing (GGL) and galaxy clustering is a promising route to measuring the amplitude of matter clustering and testing modified gravity theories of cosmic acceleration. Halo occupation distribution (HOD) modeling can extend the approach down to nonlinear scales, but galaxy assembly bias could introduce systematic errors by causing the HOD to vary with large scale environment at fixed halo mass. We investigate this problem using the mock galaxy catalogs created by Hearin & Watson (2013, HW13), which exhibit significant assembly bias because galaxy luminosity is tied to halo peak circular velocity and galaxy colour is tied to halo formation time. The preferential placement of galaxies (especially red galaxies) in older halos affects the cutoff of the mean occupation function for central galaxies, with halos in overdense regions more likely to host galaxies. The effect of assembly bias on the satellite galaxy HOD is minimal. We introduce an extended, environment dependent HOD (EDHOD) prescription to describe these results and fit galaxy correlation measurements. Crucially, we find that the galaxy-matter cross-correlation coefficient, rgm(r) ≡ ξgm(r) . [ξmm(r)ξgg(r)]-1/2, is insensitive to assembly bias on scales r ≳ 1 h^{-1} Mpc, even though ξgm(r) and ξgg(r) are both affected individually. We can therefore recover the correct ξmm(r) from the HW13 galaxy-galaxy and galaxy-matter correlations using either a standard HOD or EDHOD fitting method. For Mr ≤ -19 or Mr ≤ -20 samples the recovery of ξmm(r) is accurate to 2% or better. For a sample of red Mr ≤ -20 galaxies we achieve 2% recovery at r ≳ 2 h^{-1} Mpc with EDHOD modeling but lower accuracy at smaller scales or with a standard HOD fit. Most of our mock galaxy samples are consistent with rgm = 1 down to r = 1h-1Mpc, to within the uncertainties set by our finite simulation volume.

Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins†

PubMed Central

Gao, Huanyao; Subramanian, Sowmya; Couturier, Jérémy; Naik, Sunil; Kim, Sung-Kun; Leustek, Thomas; Knaff, David B.; Wu, Hui-Chen; Vignols, Florence; Huynh, Boi Hanh; Rouhier, Nicolas; Johnson, Michael K.

2013-01-01

Nfu-type proteins are essential in the biogenesis of iron-sulfur (Fe-S) clusters in numerous organisms. A number of phenotypes including low levels of Fe-S cluster incorporation are associated with deletion of the gene encoding a chloroplast-specific Nfu-type protein, Nfu2 from Arabidopsis thaliana (AtNfu2). Here we report that recombinant AtNfu2 is able to assemble both [2Fe-2S] and [4Fe-4S] clusters. Analytical data and gel filtration studies support cluster/protein stoichiometries of one [2Fe-2S] cluster/homotetramer and one [4Fe-4S] cluster/homodimer. The combination of UV-visible absorption and circular dichroism, resonance Raman and Mössbauer spectroscopies has been employed to investigate the nature, properties and transfer of the clusters assembled on Nfu2. The results are consistent with subunit-bridging [2Fe-2S]2+ and [4Fe-4S]2+ clusters coordinated by the cysteines in the conserved CXXC motif. The results also provided insight into the specificity of Nfu2 for maturation of chloroplastic Fe-S proteins via intact, rapid and quantitative cluster transfer. [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S]2+ cluster donor for glutaredoxin S16, but not glutaredoxin S14. Moreover, [4Fe-4S] cluster-bound Nfu2 is shown to be a very rapid and efficient [4Fe-4S]2+ cluster donor for adenosine 5′-phosphosulfate reductase (APR1) and yeast two-hybrid studies indicate that APR1 forms a complex with Nfu2, but not with Nfu1 and Nfu3, the two other chloroplastic Nfu proteins. This cluster transfer is likely to be physiologically relevant and is particularly significant for plant metabolism as APR1 catalyzes the second step in reductive sulfur assimilation which ultimately results in the biosynthesis of cysteine, methionine, glutathione, and Fe-S clusters. PMID:24032747

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

PubMed

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

2013-06-01

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

Highlights of Commission 37 Science Results

NASA Astrophysics Data System (ADS)

Carraro, Giovanni; de Grijs, Richard; Elmegreen, Bruce; Stetson, Peter; Anthony-Twarog, Barbara; Goodwin, Simon; Geisler, Douglas; Minniti, Dante

2016-04-01

It is widely accepted that stars do not form in isolation but result from the fragmentation of molecular clouds, which in turn leads to star cluster formation. Over time, clusters dissolve or are destroyed by interactions with molecular clouds or tidal stripping, and their members become part of the general field population. Star clusters are thus among the basic building blocks of galaxies. In turn, star cluster populations, from young associations and open clusters to old globulars, are powerful tracers of the formation, assembly, and evolutionary history of their parent galaxies. Although their importance (e.g., in mapping out the Milky Way) had been recognised for decades, major progress in this area has only become possible in recent years, both for Galactic and extragalactic cluster populations. Star clusters are the observational foundation for stellar astrophysics and evolution, provide essential tracers of galactic structure, and are unique stellar dynamical environments. Star formation, stellar structure, stellar evolution, and stellar nucleosynthesis continue to benefit and improve tremendously from the study of these systems. Additionally, fundamental quantities such as the initial mass function can be successfully derived from modelling either the Hertzsprung-Russell diagrams or the integrated velocity structures of, respectively, resolved and unresolved clusters and cluster populations. Star cluster studies thus span the fields of Galactic and extragalactic astrophysics, while heavily affecting our detailed understanding of the process of star formation in dense environments. This report highlights science results of the last decade in the major fields covered by IAU Commission 37: Star clusters and associations. Instead of focusing on the business meeting - the out-going president presentation can be found here: http://www.sc.eso.org/gcarraro/splinter2015.pdf - this legacy report contains highlights of the most important scientific achievements in the Commission science area, compiled by 5 well expert members.

Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli.

PubMed

Cupp-Vickery, Jill R; Silberg, Jonathan J; Ta, Dennis T; Vickery, Larry E

2004-04-16

IscA, an 11 kDa member of the hesB family of proteins, binds iron and [2Fe-2S] clusters, and participates in the biosynthesis of iron-sulfur proteins. We report the crystal structure of the apo-protein form of IscA from Escherichia coli to a resolution of 2.3A. The crystals belong to the space group P3(2)21 and have unit cell dimensions a=b=66.104 A, c=150.167 A (alpha=beta=90 degrees, gamma=120 degrees ). The structure was solved using single-wavelength anomalous dispersion (SAD) phasing of a selenomethionyl derivative, and the IscA model was refined to R=21.4% (Rfree=25.4%). IscA exists as an (alpha1alpha2)2 homotetramer with the (alpha1alpha2) dimer comprising the asymmetric unit. Cys35, implicated in Fe-S cluster assembly, is located in a central cavity formed at the tetramer interface with the gamma-sulfur atoms of residues from the alpha1 and alpha2' monomers (and alpha1'alpha2) positioned close to one another (approximately equal 7 A). C-terminal residues 99-107 are disordered, and the exact positions of Cys99 and Cys101 could not be determined. However, computer modeling of C-terminal residues in the tetramer suggests that Cys99 and Cys101 in the alpha1 monomer and those of the alpha1' monomer (or alpha2 and alpha2') are positioned sufficiently close to coordinate [2Fe-2S] clusters between the two dimers, whereas this is not possible within the (alpha1alpha2) or (alpha1'alpha2') dimer. This symmetrical arrangement allows for binding of two [2Fe-2S] clusters on opposite sides of the tetramer. Modeling further reveals that Cys101 is positioned sufficiently close to Cys35 to allow Cys35 to participate in cluster assembly, formation, or transfer.

Synthesis and Molecular Structure of a Novel Compound Containing a Carbonate-Bridged Hexacalcium Cluster Cation Assembled on a Trimeric Trititanium(IV)-Substituted Wells-Dawson Polyoxometalate.

PubMed

Hoshino, Takahiro; Isobe, Rina; Kaneko, Takuya; Matsuki, Yusuke; Nomiya, Kenji

2017-08-21

A novel compound containing a hexacalcium cluster cation, one carbonate anion, and one calcium cation assembled on a trimeric trititanium(IV)-substituted Wells-Dawson polyoxometalate (POM), [{Ca 6 (CO 3 )(μ 3 -OH)(OH 2 ) 18 }(P 2 W 15 Ti 3 O 61 ) 3 Ca(OH 2 ) 3 ] 19- (Ca 7 Ti 9 Trimer), was obtained as the Na 7 Ca 6 salt (NaCa-Ca 7 Ti 9 Trimer) by the reaction of calcium chloride with the monomeric trititanium(IV)-substituted Wells-Dawson POM species "[P 2 W 15 Ti 3 O 59 (OH) 3 ] 9- " (Ti 3 Monomer). Ti 3 Monomer was generated in situ under basic conditions from the separately prepared tetrameric species with bridging Ti(OH 2 ) 3 groups and an encapsulated Cl - ion, [{P 2 W 15 Ti 3 O 59 (OH) 3 } 4 {μ 3 -Ti(H 2 O) 3 } 4 Cl] 21- (Ti 16 Tetramer). The Na 7 Ca 6 salt of Ca 7 Ti 9 Trimer was characterized by complete elemental analysis, thermogravimetric (TG) and differential thermal analyses (DTA), FTIR, single-crystal X-ray structure analysis, and solution 183 W and 31 P NMR spectroscopy. X-ray crystallography revealed that the [Ca 6 (CO 3 )(μ 3 -OH)(OH 2 ) 18 ] 9+ cluster cation was composed of six calcium cations linked by one μ 6 -carbonato anion and one μ 3 -OH - anion. The cluster cation was assembled, together with one calcium ion, on a trimeric species composed of three tri-Ti(IV)-substituted Wells-Dawson subunits linked by Ti-O-Ti bonds. Ca 7 Ti 9 Trimer is an unprecedented POM species containing an alkaline-earth-metal cluster cation and is the first example of alkaline-earth-metal ions clustered around a titanium(IV)-substituted POM.

Saturn Apollo Program

NASA Image and Video Library

1969-01-01

In the clustering procedure, an initial assembly step for the Saturn IB launch vehicle's S-IB (first) stage, workers at the Michoud Assembly Facility (MAF) near New Orleans, Louisiana, place the first of eight outboard fuel tanks atop the central liquid-oxygen tank. Developed by the Marshall Space Flight Center and built by the Chrysler Corporation at Michoud Assembly Facility (MAF), the S-IB utilized eight H-1 engines and each produced 200,000 pounds of thrust, a combined thrust of 1,600,000 pounds.

Learning robot actions based on self-organising language memory.

PubMed

Wermter, Stefan; Elshaw, Mark

2003-01-01

In the MirrorBot project we examine perceptual processes using models of cortical assemblies and mirror neurons to explore the emergence of semantic representations of actions, percepts and concepts in a neural robot. The hypothesis under investigation is whether a neural model will produce a life-like perception system for actions. In this context we focus in this paper on how instructions for actions can be modeled in a self-organising memory. Current approaches for robot control often do not use language and ignore neural learning. However, our approach uses language instruction and draws from the concepts of regional distributed modularity, self-organisation and neural assemblies. We describe a self-organising model that clusters actions into different locations depending on the body part they are associated with. In particular, we use actual sensor readings from the MIRA robot to represent semantic features of the action verbs. Furthermore, we outline a hierarchical computational model for a self-organising robot action control system using language for instruction.

Changing the ligation of the distal [4Fe4S] cluster in NiFe hydrogenase impairs inter- and intramolecular electron transfers.

PubMed

Dementin, Sébastien; Belle, Valérie; Bertrand, Patrick; Guigliarelli, Bruno; Adryanczyk-Perrier, Géraldine; De Lacey, Antonio L; Fernandez, Victor M; Rousset, Marc; Léger, Christophe

2006-04-19

In NiFe hydrogenases, electrons are transferred from the active site to the redox partner via a chain of three Iron-Sulfur clusters, and the surface-exposed [4Fe4S] cluster has an unusual His(Cys)3 ligation. When this Histidine (H184 in Desulfovibrio fructosovorans) is changed into a cysteine or a glycine, a distal cubane is still assembled but the oxidative activity of the mutants is only 1.5 and 3% of that of the WT, respectively. We compared the activities of the WT and engineered enzymes for H2 oxidation, H+ reduction and H/D exchange, under various conditions: (i) either with the enzyme directly adsorbed onto an electrode or using soluble redox partners, and (ii) in the presence of exogenous ligands whose binding to the exposed Fe of H184G was expected to modulate the properties of the distal cluster. Protein film voltammetry proved particularly useful to unravel the effects of the mutations on inter and intramolecular electron transfer (ET). We demonstrate that changing the coordination of the distal cluster has no effect on cluster assembly, protein stability, active-site chemistry and proton transfer; however, it slows down the first-order rates of ET to and from the cluster. All-sulfur coordination is actually detrimental to ET, and intramolecular (uphill) ET is rate determining in the glycine variant. This demonstrates that although [4Fe4S] clusters are robust chemical constructs, the direct protein ligands play an essential role in imparting their ability to transfer electrons.

Smallest fullerene-like silicon cage stabilized by a V{sub 2} unit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Hong-Guang, E-mail: xuhong@iccas.ac.cn, E-mail: zhengwj@iccas.ac.cn; Kong, Xiang-Yu; Deng, Xiao-Jiao

We conducted a combined anion photoelectron spectroscopy and density functional theory study on V{sub 2}Si{sub 20} cluster. Our results show that the V{sub 2}Si{sub 20} cluster has an elongated dodecahedron cage structure with a V{sub 2} unit encapsulated inside the cage. It is the smallest fullerene-like silicon cage and can be used as building block to make cluster-assembled materials, such as pearl-chain style nanowires.

Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein

PubMed Central

Thompson, Michael C.; Wheatley, Nicole M.; Jorda, Julien; Sawaya, Michael R.; Gidaniyan, Soheil D.; Ahmed, Hoda; Yang, Zhongyu; McCarty, Krystal N.; Whitelegge, Julian P.; Yeates, Todd O.

2014-01-01

Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein, whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date. PMID:25102080

Photogrammetric Analysis of CPAS Main Parachutes

NASA Technical Reports Server (NTRS)

Ray, Eric; Bretz, David

2011-01-01

The Crew Exploration Vehicle Parachute Assembly System (CPAS) is being designed to land the Orion Crew Module (CM) at a safe rate of descent at splashdown with a cluster of two to three Main parachutes. The instantaneous rate of descent varies based on parachute fly-out angles and geometric inlet area. Parachutes in a cluster oscillate between significant fly-out angles and colliding into each other. The former presents a sub-optimal inlet area and the latter lowers the effective drag area as the parachutes interfere with each other. The fly-out angles are also important in meeting a twist torque requirement. Understanding cluster behavior necessitates measuring the Mains with photogrammetric analysis. Imagery from upward looking cameras is analyzed to determine parachute geometry. Fly-out angles are measured from each parachute vent to an axis determined from geometry. Determining the scale of the objects requires knowledge of camera and lens calibration as well as features of known size. Several points along the skirt are tracked to compute an effective circumference, diameter, and inlet area as a function of time. The effects of this geometry are clearly seen in the system drag coefficient time history. Photogrammetric analysis is key in evaluating the effects of design features such as an Over-Inflation Control Line (OICL), Main Line Length Ratio (MLLR), and geometric porosity, which are varied in an attempt to minimize cluster oscillations. The effects of these designs are evaluated through statistical analysis.

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tripathi, Binu M.; Stegen, James C.; Kim, Mincheol

Little is known about the factors affecting the relative influence of stochastic and deterministic processes that governs the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soils data sets, scattered across different regions, with different pH conditions in early and late successional soils. We found that soil pH was the best predictor of bacterial community assembly and the relative importance of stochastic and deterministic processes along successional soils. Extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditionsmore » close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally-distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.« less

Trait-based assembly and phylogenetic structure in northeast Pacific rockfish assemblages.

PubMed

Ingram, Travis; Shurin, Jonathan B

2009-09-01

If natural communities are assembled according to deterministic rules, coexisting species will represent a nonrandom subset of the potential species pool. We tested for signatures of assembly rules in the distribution of species' traits in Pacific rockfish (Sebastes spp.) assemblages. We used morphology, dietary niche (estimated with stable nitrogen isotopes), and distribution data to identify traits that relate to local-scale resource use (the alpha-niche) and to environmental gradients (the beta-niche). We showed that gill raker morphology was related to trophic position (an alpha-niche axis), while relative eye size was associated with depth habitat (a beta-niche axis). We therefore hypothesized that, within assemblages of coexisting rockfish species, the gill raker trait would be overdispersed (evenly spaced) due to limiting similarity, while relative eye size would be clustered due to environmental filtering. We examined the evolutionary relatedness of coexisting species to ask whether phylogenetic community structure and trait distributions gave similar indications about the roles of assembly processes. We tested the trait distributions and phylogenetic structure of 30 published rockfish assemblages against a null model of random community assembly. As predicted, the gill raker trait tended to be more evenly spaced than expected by chance, as did overall body size, while relative eye size was more clustered than expected. Phylogenetic community structure appeared to reflect historical dispersal and speciation and did not provide consistent support for assembly rules. Our results indicate that rockfish community assembly is nonrandom with regard to species' traits and show how distinguishing traits related to the alpha- and beta-niches and incorporating functional morphology can provide for powerful tests of assembly rules.

Climate Ocean Modeling on a Beowulf Class System

NASA Technical Reports Server (NTRS)

Cheng, B. N.; Chao, Y.; Wang, P.; Bondarenko, M.

2000-01-01

With the growing power and shrinking cost of personal computers. the availability of fast ethernet interconnections, and public domain software packages, it is now possible to combine them to build desktop parallel computers (named Beowulf or PC clusters) at a fraction of what it would cost to buy systems of comparable power front supercomputer companies. This led as to build and assemble our own sys tem. specifically for climate ocean modeling. In this article, we present our experience with such a system, discuss its network performance, and provide some performance comparison data with both HP SPP2000 and Cray T3E for an ocean Model used in present-day oceanographic research.

Cysteine desulfurase Nfs1 and Pim1 protease control levels of Isu, the Fe-S cluster biogenesis scaffold.

PubMed

Song, Ji-Yoon; Marszalek, Jaroslaw; Craig, Elizabeth Anne

2012-06-26

Fe-S clusters are critical prosthetic groups for proteins involved in various critical biological processes. Before being transferred to recipient apo-proteins, Fe-S clusters are assembled on the highly conserved scaffold protein Isu, the abundance of which is regulated posttranslationally on disruption of the cluster biogenesis system. Here we report that Isu is degraded by the Lon-type AAA+ ATPase protease of the mitochondrial matrix, Pim1. Nfs1, the cysteine desulfurase responsible for providing sulfur for cluster formation, is required for the increased Isu stability occurring after disruption of cluster formation on or transfer from Isu. Physical interaction between the Isu and Nfs1 proteins, not the enzymatic activity of Nfs1, is the important factor in increased stability. Analysis of several conditions revealed that high Isu levels can be advantageous or disadvantageous, depending on the physiological condition. During the stationary phase, elevated Isu levels were advantageous, resulting in prolonged chronological lifespan. On the other hand, under iron-limiting conditions, high Isu levels were deleterious. Compared with cells expressing normal levels of Isu, such cells grew poorly and exhibited reduced activity of the heme-containing enzyme ferric reductase. Our results suggest that modulation of the degradation of Isu by the Pim1 protease is a regulatory mechanism serving to rapidly help balance the cell's need for critical iron-requiring processes under changing environmental conditions.

Connecting massive galaxies to dark matter haloes in BOSS - I. Is galaxy colour a stochastic process in high-mass haloes?

NASA Astrophysics Data System (ADS)

Saito, Shun; Leauthaud, Alexie; Hearin, Andrew P.; Bundy, Kevin; Zentner, Andrew R.; Behroozi, Peter S.; Reid, Beth A.; Sinha, Manodeep; Coupon, Jean; Tinker, Jeremy L.; White, Martin; Schneider, Donald P.

2016-08-01

We use subhalo abundance matching (SHAM) to model the stellar mass function (SMF) and clustering of the Baryon Oscillation Spectroscopic Survey (BOSS) `CMASS' sample at z ˜ 0.5. We introduce a novel method which accounts for the stellar mass incompleteness of CMASS as a function of redshift, and produce CMASS mock catalogues which include selection effects, reproduce the overall SMF, the projected two-point correlation function wp, the CMASS dn/dz, and are made publicly available. We study the effects of assembly bias above collapse mass in the context of `age matching' and show that these effects are markedly different compared to the ones explored by Hearin et al. at lower stellar masses. We construct two models, one in which galaxy colour is stochastic (`AbM' model) as well as a model which contains assembly bias effects (`AgM' model). By confronting the redshift dependent clustering of CMASS with the predictions from our model, we argue that that galaxy colours are not a stochastic process in high-mass haloes. Our results suggest that the colours of galaxies in high-mass haloes are determined by other halo properties besides halo peak velocity and that assembly bias effects play an important role in determining the clustering properties of this sample.

The Diabetes Drug Target MitoNEET Governs a Novel Trafficking Pathway to Rebuild an Fe-S Cluster into Cytosolic Aconitase/Iron Regulatory Protein 1*

PubMed Central

Ferecatu, Ioana; Gonçalves, Sergio; Golinelli-Cohen, Marie-Pierre; Clémancey, Martin; Martelli, Alain; Riquier, Sylvie; Guittet, Eric; Latour, Jean-Marc; Puccio, Hélène; Drapier, Jean-Claude; Lescop, Ewen; Bouton, Cécile

2014-01-01

In eukaryotes, mitochondrial iron-sulfur cluster (ISC), export and cytosolic iron-sulfur cluster assembly (CIA) machineries carry out biogenesis of iron-sulfur (Fe-S) clusters, which are critical for multiple essential cellular pathways. However, little is known about their export out of mitochondria. Here we show that Fe-S assembly of mitoNEET, the first identified Fe-S protein anchored in the mitochondrial outer membrane, strictly depends on ISC machineries and not on the CIA or CIAPIN1. We identify a dedicated ISC/export pathway in which augmenter of liver regeneration, a mitochondrial Mia40-dependent protein, is specific to mitoNEET maturation. When inserted, the Fe-S cluster confers mitoNEET folding and stability in vitro and in vivo. The holo-form of mitoNEET is resistant to NO and H2O2 and is capable of repairing oxidatively damaged Fe-S of iron regulatory protein 1 (IRP1), a master regulator of cellular iron that has recently been involved in the mitochondrial iron supply. Therefore, our findings point to IRP1 as the missing link to explain the function of mitoNEET in the control of mitochondrial iron homeostasis. PMID:25012650

IoT Big-Data Centred Knowledge Granule Analytic and Cluster Framework for BI Applications: A Case Base Analysis.

PubMed

Chang, Hsien-Tsung; Mishra, Nilamadhab; Lin, Chung-Chih

2015-01-01

The current rapid growth of Internet of Things (IoT) in various commercial and non-commercial sectors has led to the deposition of large-scale IoT data, of which the time-critical analytic and clustering of knowledge granules represent highly thought-provoking application possibilities. The objective of the present work is to inspect the structural analysis and clustering of complex knowledge granules in an IoT big-data environment. In this work, we propose a knowledge granule analytic and clustering (KGAC) framework that explores and assembles knowledge granules from IoT big-data arrays for a business intelligence (BI) application. Our work implements neuro-fuzzy analytic architecture rather than a standard fuzzified approach to discover the complex knowledge granules. Furthermore, we implement an enhanced knowledge granule clustering (e-KGC) mechanism that is more elastic than previous techniques when assembling the tactical and explicit complex knowledge granules from IoT big-data arrays. The analysis and discussion presented here show that the proposed framework and mechanism can be implemented to extract knowledge granules from an IoT big-data array in such a way as to present knowledge of strategic value to executives and enable knowledge users to perform further BI actions.

Analytical halo model of galactic conformity

NASA Astrophysics Data System (ADS)

Pahwa, Isha; Paranjape, Aseem

2017-09-01

We present a fully analytical halo model of colour-dependent clustering that incorporates the effects of galactic conformity in a halo occupation distribution framework. The model, based on our previous numerical work, describes conformity through a correlation between the colour of a galaxy and the concentration of its parent halo, leading to a correlation between central and satellite galaxy colours at fixed halo mass. The strength of the correlation is set by a tunable 'group quenching efficiency', and the model can separately describe group-level correlations between galaxy colour (1-halo conformity) and large-scale correlations induced by assembly bias (2-halo conformity). We validate our analytical results using clustering measurements in mock galaxy catalogues, finding that the model is accurate at the 10-20 per cent level for a wide range of luminosities and length-scales. We apply the formalism to interpret the colour-dependent clustering of galaxies in the Sloan Digital Sky Survey (SDSS). We find good overall agreement between the data and a model that has 1-halo conformity at a level consistent with previous results based on an SDSS group catalogue, although the clustering data require satellites to be redder than suggested by the group catalogue. Within our modelling uncertainties, however, we do not find strong evidence of 2-halo conformity driven by assembly bias in SDSS clustering.

IoT Big-Data Centred Knowledge Granule Analytic and Cluster Framework for BI Applications: A Case Base Analysis

PubMed Central

Chang, Hsien-Tsung; Mishra, Nilamadhab; Lin, Chung-Chih

2015-01-01

The current rapid growth of Internet of Things (IoT) in various commercial and non-commercial sectors has led to the deposition of large-scale IoT data, of which the time-critical analytic and clustering of knowledge granules represent highly thought-provoking application possibilities. The objective of the present work is to inspect the structural analysis and clustering of complex knowledge granules in an IoT big-data environment. In this work, we propose a knowledge granule analytic and clustering (KGAC) framework that explores and assembles knowledge granules from IoT big-data arrays for a business intelligence (BI) application. Our work implements neuro-fuzzy analytic architecture rather than a standard fuzzified approach to discover the complex knowledge granules. Furthermore, we implement an enhanced knowledge granule clustering (e-KGC) mechanism that is more elastic than previous techniques when assembling the tactical and explicit complex knowledge granules from IoT big-data arrays. The analysis and discussion presented here show that the proposed framework and mechanism can be implemented to extract knowledge granules from an IoT big-data array in such a way as to present knowledge of strategic value to executives and enable knowledge users to perform further BI actions. PMID:26600156

The diabetes drug target MitoNEET governs a novel trafficking pathway to rebuild an Fe-S cluster into cytosolic aconitase/iron regulatory protein 1.

PubMed

Ferecatu, Ioana; Gonçalves, Sergio; Golinelli-Cohen, Marie-Pierre; Clémancey, Martin; Martelli, Alain; Riquier, Sylvie; Guittet, Eric; Latour, Jean-Marc; Puccio, Hélène; Drapier, Jean-Claude; Lescop, Ewen; Bouton, Cécile

2014-10-10

In eukaryotes, mitochondrial iron-sulfur cluster (ISC), export and cytosolic iron-sulfur cluster assembly (CIA) machineries carry out biogenesis of iron-sulfur (Fe-S) clusters, which are critical for multiple essential cellular pathways. However, little is known about their export out of mitochondria. Here we show that Fe-S assembly of mitoNEET, the first identified Fe-S protein anchored in the mitochondrial outer membrane, strictly depends on ISC machineries and not on the CIA or CIAPIN1. We identify a dedicated ISC/export pathway in which augmenter of liver regeneration, a mitochondrial Mia40-dependent protein, is specific to mitoNEET maturation. When inserted, the Fe-S cluster confers mitoNEET folding and stability in vitro and in vivo. The holo-form of mitoNEET is resistant to NO and H2O2 and is capable of repairing oxidatively damaged Fe-S of iron regulatory protein 1 (IRP1), a master regulator of cellular iron that has recently been involved in the mitochondrial iron supply. Therefore, our findings point to IRP1 as the missing link to explain the function of mitoNEET in the control of mitochondrial iron homeostasis. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manz, Boryana N.; Jackson, Bryan L.; Petit, Rebecca S.

2011-05-31

T cells react to extremely small numbers of activating agonist peptides. Spatial organization of T-cell receptors (TCR) and their peptide-major histocompatibility complex (pMHC) ligands into microclusters is correlated with T-cell activation. In this study, we have designed an experimental strategy that enables control over the number of agonist peptides per TCR cluster, without altering the total number engaged by the cell. Supported membranes, partitioned with grids of barriers to lateral mobility, provide an effective way of limiting the total number of pMHC ligands that may be assembled within a single TCR cluster. Observations directly reveal that restriction of pMHC contentmore » within individual TCR clusters can decrease T-cell sensitivity for triggering initial calcium flux at fixed total pMHC density. Further analysis suggests that triggering thresholds are determined by the number of activating ligands available to individual TCR clusters, not by the total number encountered by the cell. Results from a series of experiments in which the overall agonist density and the maximum number of agonist per TCR cluster are independently varied in primary T cells indicate that the most probable minimal triggering unit for calcium signaling is at least four pMHC in a single cluster for this system. In conclusion, this threshold is unchanged by inclusion of coagonist pMHC, but costimulation of CD28 by CD80 can modulate the threshold lower.« less

Illuminating the star clusters and satellite galaxies with multi-scale baryonic simulations

NASA Astrophysics Data System (ADS)

Maji, Moupiya; Zhu, Qirong; Li, Yuexing; Marinacci, Federico; Charlton, Jane; Hernquist, Lars; Knebe, Alexander

2018-01-01

Over the past decade, advances in computational architecture have made it possible for the first time to investigate some of the fundamental questions around the formation, evolution and assembly of the building blocks of the universe; star clusters and galaxies. In this talk, I will focus on two major questions: What is the origin of the observed universal lognormal mass function in globular clusters? What is the statistical distribution of the properties of satellite planes in a large sample of satellite systems?Observations of globular clusters show that they have universal lognormal mass functions with a characteristic peak at 2X105 MSun, although the origin of this peaked distribution is unclear. We investigate the formation of star clusters in interacting galaxies using baryonic simulations and found that massive clusters preferentially form in extremely high pressure gas clouds which reside in highly shocked regions produced by galaxy interactions. These massive clusters have quasi-lognormal initial mass functions with a peak around ~106MSun which may survive dynamical evolution and slowly evolve into the universal lognormal profiles observed today.The classical Milky Way (MW) satellites are observed to be distributed in a highly-flattened plane, called Disk of Satellites (DoS). However the significance, coherence and origin of DoS is highly debated. To understand this, we first analyze all MW satellites and find that a small sample size can artificially produce a highly anisotropic spatial distribution and a strong clustering of their angular momentum. Comparing a baryonic simulation of a MW-sized galaxy with its N-body counterpart we find that an anisotropic DoS can originate from baryonic processes. Furthermore, we explore the statistical distribution of DoS properties by analyzing 2591 satellite systems in the cosmological hydrodynamic simulation Illustris. We find that the DoS becomes more isotropic with increasing sample sizes and most (~90%) satellite systems have no clear coherent rotation. Their overall evolution indicate that the DoS may be part of large scale filamentary structure. Our results show that baryonic processes may be the key to solve many long standing theoretical problems.

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

PubMed

Wang, Jiang; Gayatri, Mohit A; Ferguson, Andrew L

2017-05-11

Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood. We perform coarse-grained molecular dynamics simulations of a prototypical asphaltene molecule to establish a phase diagram mapping the self-assembled morphologies as a function of temperature, pressure, and n-heptane:toluene solvent ratio informing how to control asphaltene aggregation by regulating external processing conditions. We then combine our simulations with graph matching and nonlinear manifold learning to determine low-dimensional free energy surfaces governing asphaltene self-assembly. In doing so, we introduce a variant of diffusion maps designed to handle data sets with large local density variations, and report the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape. Increasing pressure only weakly affects the landscape, serving only to destabilize the largest aggregates. Increasing temperature and toluene solvent fraction stabilizes small cluster sizes and loose bonding arrangements. Although the underlying molecular mechanisms differ, the strikingly similar effect of these variables on the free energy landscape suggests that toluene acts upon asphaltene self-assembly as an effective temperature.

Formation and Assembly of Massive Star Clusters

NASA Astrophysics Data System (ADS)

McMillan, Stephen

The formation of stars and star clusters is a major unresolved problem in astrophysics. It is central to modeling stellar populations and understanding galaxy luminosity distributions in cosmological models. Young massive clusters are major components of starburst galaxies, while globular clusters are cornerstones of the cosmic distance scale and represent vital laboratories for studies of stellar dynamics and stellar evolution. Yet how these clusters form and how rapidly and efficiently they expel their natal gas remain unclear, as do the consequences of this gas expulsion for cluster structure and survival. Also unclear is how the properties of low-mass clusters, which form from small-scale instabilities in galactic disks and inform much of our understanding of cluster formation and star-formation efficiency, differ from those of more massive clusters, which probably formed in starburst events driven by fast accretion at high redshift, or colliding gas flows in merging galaxies. Modeling cluster formation requires simulating many simultaneous physical processes, placing stringent demands on both software and hardware. Simulations of galaxies evolving in cosmological contexts usually lack the numerical resolution to simulate star formation in detail. They do not include detailed treatments of important physical effects such as magnetic fields, radiation pressure, ionization, and supernova feedback. Simulations of smaller clusters include these effects, but fall far short of the mass of even single young globular clusters. With major advances in computing power and software, we can now directly address this problem. We propose to model the formation of massive star clusters by integrating the FLASH adaptive mesh refinement magnetohydrodynamics (MHD) code into the Astrophysical Multi-purpose Software Environment (AMUSE) framework, to work with existing stellar-dynamical and stellar evolution modules in AMUSE. All software will be freely distributed on-line, allowing 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.

Formation of Core-Shell Ethane-Silver Clusters in He Droplets.

PubMed

Loginov, Evgeny; Gomez, Luis F; Sartakov, Boris G; Vilesov, Andrey F

2017-08-17

Ethane core-silver shell clusters consisting of several thousand particles have been assembled in helium droplets upon capture of ethane molecules followed by Ag atoms. The composite clusters were studied via infrared laser spectroscopy in the range of the C-H stretching vibrations of ethane. The spectra reveal a splitting of the vibrational bands, which is ascribed to interaction with Ag. A rigorous analysis of band intensities for a varying number of trapped ethane molecules and Ag atoms indicates that the composite clusters consist of a core of ethane that is covered by relatively small Ag clusters. This metastable structure is stabilized due to fast dissipation in superfluid helium droplets of the cohesion energy of the clusters.

Orion Boiler Plate Airdrop Test System

NASA Technical Reports Server (NTRS)

Machin, Ricardo A.; Evans, Carol T.

2013-01-01

On the 29th of February 2012 the Orion Capsule Parachute Assembly System (CPAS) project attempted to perform an airdrop test of a boilerplate test article for the second time. The first attempt (Cluster Development Test 2, July 2008) to deliver a similar boilerplate from a C-17 using the Low Velocity Air Drop (LVAD) technique resulted in the programmer parachute failing to properly inflate, the test article failing to achieve the desired test initiation conditions, and the test article a total loss. This paper will pick up where the CDT-2 failure investigation left off, describing the test technique that was adopted, and outline the modeling that was performed to gain confidence that the second attempt would be successful. The second boiler plate test (Cluster Development Test 3-3) was indeed a complete success and has subsequently been repeated several times, allowing the CPAS project to proceed with the full scale system level development testing required to integrate the hardware to the first Entry Flight Test vehicle as well as go into the Critical Design Review with minimum risk and a mature design.

Cluster Development Test 2: An Assessment of a Failed Test

NASA Technical Reports Server (NTRS)

Machin, Ricardo A.; Evans, Carol T.

2009-01-01

On 31 July 2008 the National Aeronautics and Space Administration Crew Exploration Vehicle Parachute Assembly System team conducted the final planned cluster test of the first generation parachute recovery system design. The two primary test objectives were to demonstrate the operation of the complete parachute system deployed from a full scale capsule simulator and to demonstrate the test technique of separating the capsule simulator from the Low Velocity Air Drop pallet used to extract the test article from a United States Air Force C-17 aircraft. The capsule simulator was the Parachute Test Vehicle with an accurate heat shield outer mold line and forward bay compartment of the Crew Exploration Vehicle Command Module. The Parachute Test Vehicle separated cleanly from the pallet following extraction, but failed to reach test conditions resulting in the failure of the test and the loss of the test assets. No personnel were injured. This paper will discuss the design of the test and the findings of the team that investigated the test, including a discussion of what were determined to be the root causes of the failure.

Emergent structures and dynamics in suspensions of self-phoretic colloids

NASA Astrophysics Data System (ADS)

Scagliarini, Andrea; Pagonabarraga, Ignacio

2013-11-01

Active fluids, such as suspensions of self-propelled particles , are a fascinating example of Soft Matter displaying complex collective behaviours which provide challenges in non-equilibrium Statistical Physics. The recent development of techniques to assemble miniaturized devices has led to a growing interest for micro and nanoscale engines that can perform autonomous motion (``microrobots''), as, for instance, self-phoretic colloids, for which the propulsion is induced by the generation of a chemical species in a reaction catalyzed at the particle surface. We perform a mesoscopic numerical study of suspensions of self-phoretic colloids. We show that, at changing the sign of the phoretic mobility (which accounts for the colloid-solute interactions), the system switches from a cluster phase to a state with slowed dynamics. We find that the cluster size distribution follows an exponential behaviour, with a characteristic size growing linearly with the colloid activity, while the density fluctuations grow as a power-law with an exponent depending on the cluster fractal dimension.We single out hydrodynamic interactions, showing that their effect is to work against cluster formation. For positive μ, we observe that colloids tend to reach an ordered state on a triangular lattice.

Orientational ordering of lamellar structures on closed surfaces

NASA Astrophysics Data System (ADS)

PÈ©kalski, J.; Ciach, A.

2018-05-01

Self-assembly of particles with short-range attraction and long-range repulsion interactions on a flat and on a spherical surface is compared. Molecular dynamics simulations are performed for the two systems having the same area and the density optimal for formation of stripes of particles. Structural characteristics, e.g., a cluster size distribution, a number of defects, and an orientational order parameter (OP), as well as the specific heat, are obtained for a range of temperatures. In both cases, the cluster size distribution becomes bimodal and elongated clusters appear at the temperature corresponding to the maximum of the specific heat. When the temperature decreases, orientational ordering of the stripes takes place and the number of particles per cluster or stripe increases in both cases. However, only on the flat surface, the specific heat has another maximum at the temperature corresponding to a rapid change of the OP. On the sphere, the crossover between the isotropic and anisotropic structures occur in a much broader temperature interval; the orientational order is weaker and occurs at significantly lower temperature. At low temperature, the stripes on the sphere form spirals and the defects resemble defects in the nematic phase of rods adsorbed at a sphere.

Clustering of reads with alignment-free measures and quality values.

PubMed

Comin, Matteo; Leoni, Andrea; Schimd, Michele

2015-01-01

The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

Small Angle Neutron Scattering (SANS) Studies on the Structural Evolution of Pyromellitamide Self-assembled Gels

DOE PAGES

Scott, Jamieson; Tong, Katie; William, Hamilton; ...

2014-10-31

The kinetics of aggregation of two pyromellitamide gelators; tetrabutyl- (C4) and tetrahexylpyromellitamide (C6), in deuterated cyclohexane has been investigated by small angle neutron scattering (SANS) for up to six days. The purpose of this study was to improve our understanding of how self-assembled gels are formed. Short-term (< 3 hour) time scales revealed multiple phases with the data for the tetrabutylpyromellitamide C4 indicating one dimensional stacking and aggregation corresponding to a multi-fiber braided cluster arrangement that is about 35 Å in diameter. The corresponding tetrahexylpyromellitamide C6 data suggests that the C6 also forms one-dimensional stacks but that these aggregate tomore » a thicker multi-fiber braided cluster that have a diameter of 61.8 Å. Over a longer period of time, the radius, persistence length and contour length all continue to increase in 6 days after cooling. This data suggests that structural changes in self-assembled gels occur over a period exceeding several days and that fairly subtle changes in the structure (e.g. tail-length) can influence the packing of molecules in self-assembled gels on the single-to-few fiber bundle stage.« less

Small angle neutron scattering (SANS) studies on the structural evolution of pyromellitamide self-assembled gels.

PubMed

Jamieson, Scott A; Tong, Katie W K; Hamilton, William A; He, Lilin; James, Michael; Thordarson, Pall

2014-11-25

The kinetics of aggregation of two pyromellitamide gelators, tetrabutyl- (C4) and tetrahexyl-pyromellitamide (C6), in deuterated cyclohexane has been investigated by small angle neutron scattering (SANS) for up to 6 days. The purpose of this study was to improve our understanding of how self-assembled gels are formed. Short-term (< 3 h) time scales revealed multiple phases with the data for the tetrabutylpyromellitamide C4, indicating one-dimensional stacking and aggregation corresponding to a multifiber braided cluster arrangement that is about 35 Å in diameter. The corresponding tetrahexylpyromellitamide C6 data suggest that the C6 also forms one-dimensional stacks but that these aggregate to a thicker multifiber braided cluster that has a diameter of about 62 Å. Over a longer period of time, the radius, persistence length, and contour length all continue to increase in 6 days after cooling. These data suggest that structural changes in self-assembled gels occur over a period exceeding several days and that fairly subtle changes in the structure (e.g., tail-length) can influence the packing of molecules in self-assembled gels on the single-to-few fiber bundle stage.

Small Angle Neutron Scattering (SANS) Studies on the Structural Evolution of Pyromellitamide Self-assembled Gels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scott, Jamieson; Tong, Katie; William, Hamilton

The kinetics of aggregation of two pyromellitamide gelators; tetrabutyl- (C4) and tetrahexylpyromellitamide (C6), in deuterated cyclohexane has been investigated by small angle neutron scattering (SANS) for up to six days. The purpose of this study was to improve our understanding of how self-assembled gels are formed. Short-term (< 3 hour) time scales revealed multiple phases with the data for the tetrabutylpyromellitamide C4 indicating one dimensional stacking and aggregation corresponding to a multi-fiber braided cluster arrangement that is about 35 Å in diameter. The corresponding tetrahexylpyromellitamide C6 data suggests that the C6 also forms one-dimensional stacks but that these aggregate tomore » a thicker multi-fiber braided cluster that have a diameter of 61.8 Å. Over a longer period of time, the radius, persistence length and contour length all continue to increase in 6 days after cooling. This data suggests that structural changes in self-assembled gels occur over a period exceeding several days and that fairly subtle changes in the structure (e.g. tail-length) can influence the packing of molecules in self-assembled gels on the single-to-few fiber bundle stage.« less

Computational investigation on the structures and electronic properties of the nanosized rhenium clusters

DOE PAGES

Zhao, Run -Ning; Chen, Rui; Yuan, Yan -Hong; ...

2017-08-10

Here, the stable equilibrium geometries, relative stabilities, and electronic and magnetic characteristics of Re n (n = 2–16) clusters were investigated by density functional theory method. The calculated fragmentation energies and second-order differences of energies exhibited interestingly that the stabilities of Re n (n = 2–16) clusters show a dramatic odd-even alternative behavior of the cluster size n: with the even-numbered Ren clusters being obviously more stable than their neighboring odd-numbered Re n clusters (beside n = 11). Simultaneously, the calculated HOMO-LUMO gaps of Re n (n = 6–16) display an oscillatory feature at large-sized Ren clusters. From the calculatedmore » magnetic moments and growth behaviors of Rhenium clusters, the magnetic Re 6 unit can be seen as the building block for the novel magnetic cluster-assembled nanomaterial. Such calculated results are in good agreement with the available experimental measurements.« less

Computational investigation on the structures and electronic properties of the nanosized rhenium clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Run -Ning; Chen, Rui; Yuan, Yan -Hong

Here, the stable equilibrium geometries, relative stabilities, and electronic and magnetic characteristics of Re n (n = 2–16) clusters were investigated by density functional theory method. The calculated fragmentation energies and second-order differences of energies exhibited interestingly that the stabilities of Re n (n = 2–16) clusters show a dramatic odd-even alternative behavior of the cluster size n: with the even-numbered Ren clusters being obviously more stable than their neighboring odd-numbered Re n clusters (beside n = 11). Simultaneously, the calculated HOMO-LUMO gaps of Re n (n = 6–16) display an oscillatory feature at large-sized Ren clusters. From the calculatedmore » magnetic moments and growth behaviors of Rhenium clusters, the magnetic Re 6 unit can be seen as the building block for the novel magnetic cluster-assembled nanomaterial. Such calculated results are in good agreement with the available experimental measurements.« less

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.

2017-03-28

Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets.more » The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.« less

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

PubMed Central

Bian, Chao; Hu, Yinchang; Ravi, Vydianathan; Kuznetsova, Inna S.; Shen, Xueyan; Mu, Xidong; Sun, Ying; You, Xinxin; Li, Jia; Li, Xiaofeng; Qiu, Ying; Tay, Boon-Hui; Thevasagayam, Natascha May; Komissarov, Aleksey S.; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Luo, Jianren; Liu, Yi; Song, Hongmei; Liu, Chao; Wang, Xuejie; Gu, Dangen; Yang, Yexin; Li, Wujiao; Polgar, Gianluca; Fan, Guangyi; Zeng, Peng; Zhang, He; Xiong, Zijun; Tang, Zhujing; Peng, Chao; Ruan, Zhiqiang; Yu, Hui; Chen, Jieming; Fan, Mingjun; Huang, Yu; Wang, Min; Zhao, Xiaomeng; Hu, Guojun; Yang, Huanming; Wang, Jian; Wang, Jun; Xu, Xun; Song, Linsheng; Xu, Gangchun; Xu, Pao; Xu, Junmin; O’Brien, Stephen J.; Orbán, László; Venkatesh, Byrappa; Shi, Qiong

2016-01-01

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas. PMID:27089831

Protein dynamics during presynaptic complex assembly on individual ssDNA molecules

PubMed Central

Gibb, Bryan; Ye, Ling F.; Kwon, YoungHo; Niu, Hengyao; Sung, Patrick; Greene, Eric C.

2014-01-01

Homologous recombination is a conserved pathway for repairing double–stranded breaks, which are processed to yield single–stranded DNA overhangs that serve as platforms for presynaptic complex assembly. Here we use single–molecule imaging to reveal the interplay between Saccharomyce cerevisiae RPA, Rad52, and Rad51 during presynaptic complex assembly. We show that Rad52 binds RPA–ssDNA and suppresses RPA turnover, highlighting an unanticipated regulatory influence on protein dynamics. Rad51 binding extends the ssDNA, and Rad52–RPA clusters remain interspersed along the presynaptic complex. These clusters promote additional binding of RPA and Rad52. Together, our work illustrates the spatial and temporal progression of RPA and Rad52 association with the presynaptic complex, and reveals a novel RPA–Rad52–Rad51–ssDNA intermediate, which has implications for understanding how the activities of Rad52 and RPA are coordinated with Rad51 during the later stages recombination. PMID:25195049

Assembly of collagen matrices as a phase transition revealed by structural and rheologic studies.

PubMed

Forgacs, Gabor; Newman, Stuart A; Hinner, Bernhard; Maier, Christian W; Sackmann, Erich

2003-02-01

We have studied the structural and viscoelastic properties of assembling networks of the extracellular matrix protein type-I collagen by means of phase contrast microscopy and rotating disk rheometry. The initial stage of the assembly is a nucleation process of collagen monomers associating to randomly distributed branched clusters with extensions of several microns. Eventually a sol-gel transition takes place, which is due to the interconnection of these clusters. We analyzed this transition in terms of percolation theory. The viscoelastic parameters (storage modulus G' and loss modulus G") were measured as a function of time for five different frequencies ranging from omega = 0.2 rad/s to 6.9 rad/s. We found that at the gel point both G' and G" obey a scaling law, with the critical exponent Delta = 0.7 and a critical loss angle being independent of frequency as predicted by percolation theory. Gelation of collagen thus represents a second order phase transition.

Two-Dimensional Fullerene Assembly from an Exfoliated van der Waals Template.

PubMed

Lee, Kihong; Choi, Bonnie; Plante, Ilan Jen-La; Paley, Maria V; Zhong, Xinjue; Crowther, Andrew C; Owen, Jonathan S; Zhu, Xiaoyang; Roy, Xavier

2018-05-22

Two-dimensional (2D) materials are commonly prepared by exfoliating bulk layered van der Waals crystals. The creation of synthetic 2D materials from bottom-up methods is an important challenge as their structural flexibility will enable chemists to tune the materials properties. A 2D material was assembled using C 60 as a polymerizable monomer. The C 60 building blocks are first assembled into a layered solid using a molecular cluster as structure director. The resulting hierarchical crystal is used as a template to polymerize its C 60 monolayers, which can be exfoliated down to 2D crystalline nanosheets. Derived from the parent template, the 2D structure is composed of a layer of inorganic cluster, sandwiched between two monolayers of polymerized C 60 . The nanosheets can be transferred onto solid substrates and depolymerized by heating. Electronic absorption spectroscopy reveals an optical gap of 0.25 eV, narrower than that of the bulk parent crystalline solid. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Partial bisulfite conversion for unique template sequencing

PubMed Central

Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua; Forcier, Talitha; Ronemus, Michael; Wigler, Michael

2018-01-01

Abstract We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone. PMID:29161423

Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

NASA Astrophysics Data System (ADS)

Lan, Yaqi

Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

Optical and Calorimetric Studies of Cholesterol-Rich Filamentous, Helical Ribbon and Crystal Microstructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miroshnikova, Y. A.; Elsenbeck, M.; Zastavker, Y. V.

2009-04-19

Formation of biological self-assemblies at all scales is a focus of studies in fields ranging from biology to physics to biomimetics. Understanding the physico-chemical properties of these self-assemblies may lead to the design of bio-inspired structures and technological applications. Here we examine self-assembled filamentous, helical ribbon, and crystal microstructures formed in chemically defined lipid concentrate (CDLC), a model system for cholesterol crystallization in gallbladder bile. CDLC consists of cholesterol, bilayer-forming amphiphiles, micelle-forming amphiphiles, and water. Phase contrast and differential interference contrast (DIC) microscopy indicate the presence of three microstructure types in all samples studied, and allow for an investigation ofmore » the structures' unique geometries. Additionally, confocal microscopy is used for qualitative assessment of surface and internal composition. To complement optical observations, calorimetric (differential-scanning and modulation) experiments, provide the basis for an in-depth understanding of collective and individual thermal behavior. Observed ''transition'' features indicate clustering and ''straightening'' of helical ribbons into short, increasingly thickening, filaments that dissolve with increasing temperature. These results suggest that all microstructures formed in CDLC may coexist in a metastable chemical equilibrium. Further investigation of the CDLC thermal profile should uncover the process of cholesterol crystallization as well as the unique design and function of microstructures formed in this system.« less

Fe-S Cluster Biogenesis in Isolated Mammalian Mitochondria

PubMed Central

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K.; Dancis, Andrew; Pain, Debkumar

2015-01-01

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [35S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-35S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the 35S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. PMID:25398879

Hierarchically assembled theranostic nanostructures for siRNA delivery and imaging applications.

PubMed

Shrestha, Ritu; Elsabahy, Mahmoud; Luehmann, Hannah; Samarajeewa, Sandani; Florez-Malaver, Stephanie; Lee, Nam S; Welch, Michael J; Liu, Yongjian; Wooley, Karen L

2012-10-24

Dual functional hierarchically assembled nanostructures, with two unique functions of carrying therapeutic cargo electrostatically and maintaining radiolabeled imaging agents covalently within separate component building blocks, have been developed via the supramolecular assembly of several spherical cationic shell cross-linked nanoparticles clustered around a central anionic shell cross-linked cylinder. The shells of the cationic nanoparticles and the hydrophobic core domain of the anionic central cylindrical nanostructure of the assemblies were utilized to complex negatively charged nucleic acids (siRNA) and to undergo radiolabeling, respectively, for potential theranostic applications. The assemblies exhibited exceptional cell transfection and radiolabeling efficiencies, providing an overall advantage over the individual components, which could each facilitate only one or the other of the functions.

Blood coagulation reactions on nanoscale membrane surfaces

NASA Astrophysics Data System (ADS)

Pureza, Vincent S.

Blood coagulation requires the assembly of several membrane-bound protein complexes composed of regulatory and catalytic subunits. The biomembranes involved in these reactions not only provide a platform for these procoagulant proteins, but can also affect their function. Increased exposure of acidic phospholipids on the outer leaflet of the plasma membrane can dramatically modulate the catalytic efficiencies of such membrane-bound enzymes. Under physiologic conditions, however, these phospholipids spontaneously cluster into a patchwork of membrane microdomains upon which membrane binding proteins may preferentially assemble. As a result, the membrane composition surrounding these proteins is largely unknown. Through the development and use of a nanometer-scale bilayer system that provides rigorous control of the phospholipid membrane environment, I investigated the role of phosphatidylserine, an acidic phospholipid, in the direct vicinity (within nanometers) of two critical membrane-bound procoagulant protein complexes and their respective natural substrates. Here, I present how the assembly and function of the tissue factor˙factor VIIa and factor Va˙factor Xa complexes, the first and final cofactor˙enzyme complexes of the blood clotting cascade, respectively, are mediated by changes in their immediate phospholipid environments.

Biocompatibility of cluster-assembled nanostructured TiO2 with primary and cancer cells.

PubMed

Carbone, Roberta; Marangi, Ida; Zanardi, Andrea; Giorgetti, Luca; Chierici, Elisabetta; Berlanda, Giuseppe; Podestà, Alessandro; Fiorentini, Francesca; Bongiorno, Gero; Piseri, Paolo; Pelicci, Pier Giuseppe; Milani, Paolo

2006-06-01

We have characterized the biocompatibility of nanostructured TiO2 films produced by the deposition of a supersonic beam of TiOx clusters. Physical analysis shows that these films possess, at the nanoscale, a granularity and porosity mimicking those of typical extracellular matrix structures and adsorption properties that could allow surface functionalization with different macromolecules such as DNA, proteins, and peptides. To explore the biocompatibility of this novel nanostructured surface, different cancer and primary cells were analyzed in terms of morphological appearance (by bright field microscopy and immunofluorescence) and growth properties, with the aim to evaluate cluster-assembled TiO2 films as substrates for cell-based and tissue-based applications. Our results strongly suggest that this new biomaterial supports normal growth and adhesion of primary and cancer cells with no need for coating with ECM proteins; we thus propose this new material as an optimal substrate for different applications in cell-based assays, biosensors or microfabricated medical devices.

Toward a modular multi-material nanoparticle synthesis and assembly strategy via bionanocombinatorics: bifunctional peptides for linking Au and Ag nanomaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Briggs, Beverly D.; Palafox-Hernandez, J. Pablo; Li, Yue

Materials-binding peptides represent a unique avenue towards controlling the shape and size of nanoparticles (NPs) grown under aqueous conditions. Here, employing a bionanocombinatorics approach, two such materials-binding peptides were linked at either end of a photoswitchable spacer, forming a multi-domain materials-binding molecule to control the in situ synthesis and organization of Ag and Au NPs under ambient conditions. These multi-domain molecules retained the peptides’ ability to nucleate, grow, and stabilize Ag and Au NPs in aqueous media. Disordered co-assemblies of the two nanomaterials were observed by TEM imaging of dried samples after sequential growth of the two metals, and showedmore » a clustering behavior that was not observed without both metals and the linker molecules. While TEM evidence indicated the formation of AuNP/AgNP assemblies upon drying, SAXS analysis indicated that no extended assemblies existed in solution, suggesting that sample drying plays an important role in facilitating NP clustering. Molecular simulations and experimental data revealed tunable materials-binding based upon the isomerization state of the photoswitchable unit and metal employed. This work is a first step in generating externally actuated biomolecules with specific material-binding properties that could be used as the building blocks to achieve multi-material switchable NP assemblies.« less

Split-GFP: SERS Enhancers in Plasmonic Nanocluster Probes.

PubMed

Chung, Taerin; Koker, Tugba; Pinaud, Fabien

2016-09-08

The assembly of plasmonic metal nanoparticles into hot spot surface-enhanced Raman scattering (SERS) nanocluster probes is a powerful, yet challenging approach for ultrasensitive biosensing. Scaffolding strategies based on self-complementary peptides and proteins are of increasing interest for these assemblies, but the electronic and the photonic properties of such hybrid nanoclusters remain difficult to predict and optimize. Here, split-green fluorescence protein (sGFP) fragments are used as molecular glue and the GFP chromophore is used as a Raman reporter to assemble a variety of gold nanoparticle (AuNP) clusters and explore their plasmonic properties by numerical modeling. It is shown that GFP seeding of plasmonic nanogaps in AuNP/GFP hybrid nanoclusters increases near-field dipolar couplings between AuNPs and provides SERS enhancement factors above 10 8 . Among the different nanoclusters studied, AuNP/GFP chains allow near-infrared SERS detection of the GFP chromophore imidazolinone/exocyclic CC vibrational mode with theoretical enhancement factors of 10 8 -10 9 . For larger AuNP/GFP assemblies, the presence of non-GFP seeded nanogaps between tightly packed nanoparticles reduces near-field enhancements at Raman active hot spots, indicating that excessive clustering can decrease SERS amplifications. This study provides rationales to optimize the controlled assembly of hot spot SERS nanoprobes for remote biosensing using Raman reporters that act as molecular glue between plasmonic nanoparticles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spin-canting magnetization in an unusual Co4 cluster-based layer compound from a 2,3-dihydroxyquinoxaline ligand.

PubMed

Yang, Chen-I; Chuang, Po-Hsiang; Lee, Gene-Hsiang; Peng, Shie-Ming; Lu, Kuang-Lieh

2012-01-16

The self-assembly of Co(O(2)CPh)(2) with a 2,3-dihydroxyquinoxaline (H(2)dhq) linker has revealed a new two-dimensional cluster-based compound, [Co(4)(OMe)(2)(O(2)CPh)(2)(dhq)(2)(MeOH)(2)](n), which shows spin-canted magnetization and a definite magnetic hysteresis loop.

Evaluation of diagnostic tools that tertiary teachers can apply to profile their students' conceptions

NASA Astrophysics Data System (ADS)

Schultz, Madeleine; Lawrie, Gwendolyn A.; Bailey, Chantal H.; Bedford, Simon B.; Dargaville, Tim R.; O'Brien, Glennys; Tasker, Roy; Thompson, Christopher D.; Williams, Mark; Wright, Anthony H.

2017-03-01

A multi-institution collaborative team of Australian chemistry education researchers, teaching a total of over 3000 first year chemistry students annually, has explored a tool for diagnosing students' prior conceptions as they enter tertiary chemistry courses. Five core topics were selected and clusters of diagnostic items were assembled linking related concepts in each topic together. An ordered multiple choice assessment strategy was adopted to enable provision of formative feedback to students through combination of the specific distractors that they chose. Concept items were either sourced from existing research instruments or developed by the project team. The outcome is a diagnostic tool consisting of five topic clusters of five concept items that has been delivered in large introductory chemistry classes at five Australian institutions. Statistical analysis of data has enabled exploration of the composition and validity of the instrument including a comparison between delivery of the complete 25 item instrument with subsets of five items, clustered by topic. This analysis revealed that most items retained their validity when delivered in small clusters. Tensions between the assembly, validation and delivery of diagnostic instruments for the purposes of acquiring robust psychometric research data versus their pragmatic use are considered in this study.

Glutaredoxin S15 Is Involved in Fe-S Cluster Transfer in Mitochondria Influencing Lipoic Acid-Dependent Enzymes, Plant Growth, and Arsenic Tolerance in Arabidopsis1[OPEN

PubMed Central

2016-01-01

Glutaredoxins (Grxs) are small proteins that function as oxidoreductases with roles in deglutathionylation of proteins, reduction of antioxidants, and assembly of iron-sulfur (Fe-S) cluster-containing enzymes. Which of the 33 Grxs in Arabidopsis (Arabidopsis thaliana) perform roles in Fe-S assembly in mitochondria is unknown. We have examined in detail the function of the monothiol GrxS15 in plants. Our results show its exclusive mitochondrial localization, and we are concluding it is the major or only Grx in this subcellular location. Recombinant GrxS15 has a very low deglutathionylation and dehydroascorbate reductase activity, but it binds a Fe-S cluster. Partially removing GrxS15 from mitochondria slowed whole plant growth and respiration. Native GrxS15 is shown to be especially important for lipoic acid-dependent enzymes in mitochondria, highlighting a putative role in the transfer of Fe-S clusters in this process. The enhanced effect of the toxin arsenic on the growth of GrxS15 knockdown plants compared to wild type highlights the role of mitochondrial glutaredoxin Fe-S-binding in whole plant growth and toxin tolerance. PMID:26672074

Self-assembly of a tetrahedral 58-nuclear barium vanadium oxide cluster.

PubMed

Kastner, Katharina; Puscher, Bianka; Streb, Carsten

2013-01-07

We report the synthesis and characterization of a molecular barium vanadium oxide cluster featuring high nuclearity and high symmetry. The tetrameric, 2.3 nm cluster H(5)[Ba(10)(NMP)(14)(H(2)O)(8)[V(12)O(33)](4)Br] is based on a bromide-centred, octahedral barium scaffold which is capped by four previously unknown [V(12)O(33)](6-) clusters in a tetrahedral fashion. The compound represents the largest polyoxovanadate-based heterometallic cluster known to date. The cluster is formed in organic solution and it is suggested that the bulky N-methyl-2-pyrrolidone (NMP) solvent ligands allow the isolation of this giant molecule and prevent further condensation to a solid-state metal oxide. The cluster is fully characterized using single-crystal XRD, elemental analysis, ESI mass spectrometry and other spectroscopic techniques.

Tidal Disruptions Due to Stellar Mass Black Hole Binaries: Modifying the Spin Magnitudes and Directions of LIGO Sources

NASA Astrophysics Data System (ADS)

Lopez, Martin; Batta, Aldo; Ramírez-Ruiz, Enrico

2018-01-01

Globular clusters have about a thousand times denser stellar environments than our Milky Way. This crowded setting leads to many interactions between inhabitants of the cluster and the formation of a whole myriad of exotic objects. One such object is a binary system that forms which is composed of two stellar mass black holes (BHs). Due to the recent detection of gravitational waves (GWs), we know that some of these BH binaries (BHBs) are able to merge. Upon coalescence, BHBs produce GW signals that can be measured by the Laser Interferometer Gravitational-Wave Observatory (LIGO) group on Earth. Spin is one such parameter that LIGO can estimate from the type of signals they observe and as such can be used to constrain their production site. After these BHBs are assembled in dense stellar systems they can continue to interact with other members, either through tidal interactions or physical collisions. When a BHB tidally disrupts a star, a significant fraction of the debris can be accreted by the binary, effectively altering the spin of the BH members. Therefore, although a dynamically formed BHB will initially have low randomly aligned spins, through these types of interactions their birth spins can be significantly altered both in direction and magnitude. We have used a Lagrangian 3D Smoothed Particle Hydrodynamics (SPH) code GADGET-3 to simulate these interactions. Our results allow us to understand whether accretion from a tidal disruption event can significantly alter the birth properties of dynamically assembled BHBs such as spin, mass, and orbital attributes. The implications of these results will help us constrain the properties of BHBs in dense stellar systems in anticipation of an exciting decade ahead of us.

Skylab

NASA Image and Video Library

1970-01-01

Assembling activities of the Skylab cluster are shown in this photograph. The Orbital Workshop (OWS) was lowered for joining to aft skirt and placed over the thrust structure inside the assembly tower. The OWS provided living and working quarters for the Skylab crew and the thruster provided short-term attitude control of the Skylab. The Marshall Space Flight Center had responsibilities for the design and development of the Skylab hardware, and management of experiments.

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

Development and Qualification of ATV Propulsion Assemblies

NASA Astrophysics Data System (ADS)

Riehle, M.; Jost, R.

2002-01-01

In the frame of the development and operation of the International Space Station ISS, the European Space Agency ESA is not only contributing experiments and a laboratory module but also logistics capacity. This purpose of supplying the ISS shall be covered by an unmanned, Automated Transfer Vehicle (ATV) that will be launched for the first time in 2004 by Ariane 5. The development of the ATV is in close conjunction to the future Ariane 5 launch capacity of about 20 tons injected into low earth orbit. Thus this unmanned transporter will be a quite large space craft that is subjected to fulfil several mission objectives apart of only delivering cargo such as multiple automatic docking/de-docking, re-boost services and re-fuelling. For those reasons and due to its dimensions the propulsion sub-system is one of the most sophisticated in the field of space propulsion. Even safety issues of manned space flight have to be applied since the pressurised cargo section is part of the ISS when docked to the manned modules. This leads to by far the largest but also the most sophisticated propulsion system ever built in Europe. Astrium as one of the major partners of this european project is responsible for this major system that will be described in the paper. Focusing on the major core assemblies such as multi thruster platforms, pressure control system incl. safety and redundancy mechanisms as well as tanks and other components that completes a propulsion system. System Design and Qualification Starting from the basic criteria the paper will present the major performance requirements such as pressures, thrust levels and other parameters that led to the selection of major components of the system such as thrusters, valves, tanks, etc. Some of the component could be selected from off the shelve, whereas other core components such as the 200N Attitude Control and Braking Thrusters or Propellant Tanks had to be newly developed. The stepwise approach of development and careful qualification will be presented starting from components and assemblies up to sub- system. Exemplarily, the path of the 200N shall be described in more detail since requirements of various kinds are to be applied here. This thruster is used in a total of 28 engines located on 4 thruster cluster assemblies on the bottom and 4 on the front of the space craft delivering steady state thrust as well as impulse bit to the ATV and can be used also as backup for the main thrusters. Safety and thus redundancy is one of the major driver for the design. As a first step i.e. the thrusters are equipped with measures to detect malfunctions and problems by continuous measuring chamber temperature and combustion pressure. The layout of the thruster clusters arrangement in combination with control electronics are such are such that multiple independent branches are controlling the system by which each of them could to fulfil the whole operational objectives. The thruster clusters are also affected by most of the environmental constraints that require careful thermal or mechanical design. For example severe shock loads induced by the stage separation nearby as well as meteorites and debris have to be taken into account for mechanical design. Or large transient pressure spikes and water hammer caused by simultaneous operation of thrusters have to be considered for hydraulic design. As well as extreme conditions for thermal design facing high thermal loads both radiation and conductive during thruster firing and sun exposure of the externally mounted assembly as well as low heater budget and I/F flux limitations when exposed to deep space during long phases. Intensive test programs have been carried out or are under preparation as well as complementary numerical analysis are completing and supporting each step of the development. The paper will describe those design and qualification activities as well as the results as far as available to that time in order to give an overview of the status of the development of the whole propulsion system.

Stress distribution and mechanical properties of free and assembled Ni3Al nanoclusters

NASA Astrophysics Data System (ADS)

Zhurkin, E. E.; Hautier, G.; Hou, M.

2006-03-01

Classical molecular dynamics with a semiempirical N -body potential is used to study the distribution of local stress in bimetallic Ni3Al nanoparticles and in cluster-assembled materials. The materials considered are synthesized with these particles by low-energy deposition at 0.5eV per atom and by compaction with an external pressure of 2GPa , thus featuring different nanostructures. Both are nanoporous, the lowest density being obtained by deposition. Their mechanical response to a uniaxial external load is then studied and deformation mechanisms are identified and are found to be similar in both nanostructures. In the core of isolated clusters, the partial pressures on the nickel and aluminium subsystems are found to differ by several GPa and, as a balance to surface tension, the hydrostatic core pressure is positive and depends on the cluster size. The surface stress is tensile and, because of structural disorder, the partial pressures distributions on Ni and Al at the surface are scattered. When nanostructured systems are formed, strong and highly inhomogeneous shear stress appears, the cluster cores may become tensile, and the interfacial areas remain mainly tensile as well. The partial pressure difference between Ni and Al is somewhat reduced. It is shown that the effect of temperature is to reduce this difference still further and to homogenize the spatial stress distribution. When subjected to a uniaxial stress, both materials display an elastic and a plastic regime. The elastic limit is the lowest for the most porous material and decreases with increasing temperature. Plastic deformation is dominated by both grain boundary sliding and by the enlargement of the open volumes, without evidence for the nucleation of cracks. These open volumes are found to facilitate dislocation activity which is evidenced in grains with sizes as small as two nanometers. This dislocation activity is found to result in the production of stacking faults as well as to the recovery of defects induced by the deposition or by the compaction.

Characterization of a Major Cluster of nif, fix, and Associated Genes in a Sugarcane Endophyte, Acetobacter diazotrophicus

PubMed Central

Lee, Sunhee; Reth, Alexander; Meletzus, Dietmar; Sevilla, Myrna; Kennedy, Christina

2000-01-01

A major 30.5-kb cluster of nif and associated genes of Acetobacter diazotrophicus (syn. Gluconacetobacter diazotrophicus), a nitrogen-fixing endophyte of sugarcane, was sequenced and analyzed. This cluster represents the largest assembly of contiguous nif-fix and associated genes so far characterized in any diazotrophic bacterial species. Northern blots and promoter sequence analysis indicated that the genes are organized into eight transcriptional units. The overall arrangement of genes is most like that of the nif-fix cluster in Azospirillum brasilense, while the individual gene products are more similar to those in species of Rhizobiaceae or in Rhodobacter capsulatus. PMID:11092875

Self-assembled magnetic theranostic nanoparticles for highly sensitive MRI of minicircle DNA delivery.

PubMed

Wan, Qian; Xie, Lisi; Gao, Lin; Wang, Zhiyong; Nan, Xiang; Lei, Hulong; Long, Xiaojing; Chen, Zhi-Ying; He, Cheng-Yi; Liu, Gang; Liu, Xin; Qiu, Bensheng

2013-01-21

As a versatile gene vector, minicircle DNA (mcDNA) has a great potential for gene therapy. However, some serious challenges remain, such as to effectively deliver mcDNA into targeted cells/tissues and to non-invasively monitor the delivery of the mcDNA. Superparamagnetic iron oxide (SPIO) nanoparticles have been extensively used for both drug/gene delivery and diagnosis. In this study, an MRI visible gene delivery system was developed with a core of SPIO nanocrystals and a shell of biodegradable stearic acid-modified low molecular weight polyethyleneimine (Stearic-LWPEI) via self-assembly. The Stearic-LWPEI-SPIO nanoparticles possess a controlled clustering structure, narrow size distribution and ultrasensitive imaging capacity. Furthermore, the nanoparticle can effectively bind with mcDNA and protect it from enzymatic degradation. In conclusion, the nanoparticle shows synergistic advantages in the effective transfection of mcDNA and non-invasive MRI of gene delivery.

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.

Turning Saccharomyces cerevisiae into a Frataxin-Independent Organism

PubMed Central

Yoon, Heeyong; Knight, Simon A. B.; Pandey, Alok; Pain, Jayashree; Turkarslan, Serdar; Pain, Debkumar; Dancis, Andrew

2015-01-01

Frataxin (Yfh1 in yeast) is a conserved protein and deficiency leads to the neurodegenerative disease Friedreich’s ataxia. Frataxin is a critical protein for Fe-S cluster assembly in mitochondria, interacting with other components of the Fe-S cluster machinery, including cysteine desulfurase Nfs1, Isd11 and the Isu1 scaffold protein. Yeast Isu1 with the methionine to isoleucine substitution (M141I), in which the E. coli amino acid is inserted at this position, corrected most of the phenotypes that result from lack of Yfh1 in yeast. This suppressor Isu1 behaved as a genetic dominant. Furthermore frataxin-bypass activity required a completely functional Nfs1 and correlated with the presence of efficient scaffold function. A screen of random Isu1 mutations for frataxin-bypass activity identified only M141 substitutions, including Ile, Cys, Leu, or Val. In each case, mitochondrial Nfs1 persulfide formation was enhanced, and mitochondrial Fe-S cluster assembly was improved in the absence of frataxin. Direct targeting of the entire E. coli IscU to ∆yfh1 mitochondria also ameliorated the mutant phenotypes. In contrast, expression of IscU with the reverse substitution i.e. IscU with Ile to Met change led to worsening of the ∆yfh1 phenotypes, including severely compromised growth, increased sensitivity to oxygen, deficiency in Fe-S clusters and heme, and impaired iron homeostasis. A bioinformatic survey of eukaryotic Isu1/prokaryotic IscU database entries sorted on the amino acid utilized at the M141 position identified unique groupings, with virtually all of the eukaryotic scaffolds using Met, and the preponderance of prokaryotic scaffolds using other amino acids. The frataxin-bypassing amino acids Cys, Ile, Leu, or Val, were found predominantly in prokaryotes. This amino acid position 141 is unique in Isu1, and the frataxin-bypass effect likely mimics a conserved and ancient feature of the prokaryotic Fe-S cluster assembly machinery. PMID:25996596

Hubble Sees 'Ghost Light' From Dead Galaxies

NASA Image and Video Library

2014-10-30

NASA’s Hubble Space Telescope has picked up the faint, ghostly glow of stars ejected from ancient galaxies that were gravitationally ripped apart several billion years ago. The mayhem happened 4 billion light-years away, inside an immense collection of nearly 500 galaxies nicknamed “Pandora’s Cluster,” also known as Abell 2744. The scattered stars are no longer bound to any one galaxy, and drift freely between galaxies in the cluster. By observing the light from the orphaned stars, Hubble astronomers have assembled forensic evidence that suggests as many as six galaxies were torn to pieces inside the cluster over a stretch of 6 billion years. Read more: 1.usa.gov/1yK2Ucp Credit: NASA/ESA/IAC/HFF Team, STScI NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Convective Self-Sustained Motion in Mixtures of Chemically Active and Passive Particles.

PubMed

Shklyaev, Oleg E; Shum, Henry; Yashin, Victor V; Balazs, Anna C

2017-08-15

We develop a model to describe the behavior of a system of active and passive particles in solution that can undergo spontaneous self-organization and self-sustained motion. The active particles are uniformly coated with a catalyst that decomposes the reagent in the surrounding fluid. The resulting variations in the fluid density give rise to a convective flow around the active particles. The generated fluid flow, in turn, drives the self-organization of both the active and passive particles into clusters that undergo self-sustained propulsion along the bottom wall of a microchamber. This propulsion continues until the reagents in the solution are consumed. Depending on the number of active and passive particles and the structure of the self-organized cluster, these assemblies can translate, spin, or remain stationary. We also illustrate a scenario in which the geometry of the container is harnessed to direct the motion of a self-organized, self-propelled cluster. The findings provide guidelines for creating autonomously moving active particles, or chemical "motors" that can transport passive cargo in microfluidic devices.

[Results of Simulation Studies

NASA Technical Reports Server (NTRS)

2003-01-01

Lattice Monte Carlo and off-lattice molecular dynamics simulations of h(sub 1)t(sub 4) and h(sub 4)t(sub l) (head/tail) amphiphile solutions have been performed as a function of surfactant concentration and temperature. The lattice and off-lattice systems exhibit quite different self-assembly behavior at equivalent thermodynamic conditions. We found that in the weakly aggregating regime (no preferred-size micelles), all models yield similar micelle size distributions at the same average aggregation number, albeit at different thermodynamic conditions (temperatures). In the strongly aggregating regime, this mapping between models (through temperature adjustment) fails, and the models exhibit qualitatively different micellization behavior. Incipient micellization in a model self-associating telechelic polymer solution results in a network with a transient elastic response that decays by a two-step relaxation: the first is due to a heterogeneous jump-diffusion process involving entrapment of end-groups within well-defined clusters and this is followed by rapid diffusion to neighboring clusters and a decay (terminal relaxation) due to cluster disintegration. The viscoelastic response of the solution manifests characteristics of a glass transition and entangled polymer network.

Mesoscale simulations of confined Nafion thin films.

PubMed

Vanya, P; Sharman, J; Elliott, J A

2017-12-07

The morphology and transport properties of thin films of the ionomer Nafion, with thicknesses on the order of the bulk cluster size, have been investigated as a model system to explain the anomalous behaviour of catalyst/electrode-polymer interfaces in membrane electrode assemblies. We have employed dissipative particle dynamics (DPD) to investigate the interaction of water and fluorocarbon chains, with carbon and quartz as confining materials, for a wide range of operational water contents and film thicknesses. We found confinement-induced clustering of water perpendicular to the thin film. Hydrophobic carbon forms a water depletion zone near the film interface, whereas hydrophilic quartz results in a zone with excess water. There are, on average, oscillating water-rich and fluorocarbon-rich regions, in agreement with experimental results from neutron reflectometry. Water diffusivity shows increasing directional anisotropy of up to 30% with decreasing film thickness, depending on the hydrophilicity of the confining material. A percolation analysis revealed significant differences in water clustering and connectivity with the confining material. These findings indicate the fundamentally different nature of ionomer thin films, compared to membranes, and suggest explanations for increased ionic resistances observed in the catalyst layer.

Discovery and introduction of a (3,18)-connected net as an ideal blueprint for the design of metal-organic frameworks.

PubMed

Guillerm, Vincent; Weseliński, Łukasz J; Belmabkhout, Youssef; Cairns, Amy J; D'Elia, Valerio; Wojtas, Łukasz; Adil, Karim; Eddaoudi, Mohamed

2014-08-01

Metal-organic frameworks (MOFs) are a promising class of porous materials because it is possible to mutually control their porous structure, composition and functionality. However, it is still a challenge to predict the network topology of such framework materials prior to their synthesis. Here we use a new rare earth (RE) nonanuclear carboxylate-based cluster as an 18-connected molecular building block to form a gea-MOF (gea-MOF-1) based on a (3,18)-connected net. We then utilized this gea net as a blueprint to design and assemble another MOF (gea-MOF-2). In gea-MOF-2, the 18-connected RE clusters are replaced by metal-organic polyhedra, peripherally functionalized so as to have the same connectivity as the RE clusters. These metal-organic polyhedra act as supermolecular building blocks when they form gea-MOF-2. The discovery of a (3,18)-connected MOF followed by deliberate transposition of its topology to a predesigned second MOF with a different chemical system validates the prospective rational design of MOFs.

Clustering and negative feedback by endocytosis in planar cell polarity signaling is modulated by ubiquitinylation of prickle.

PubMed

Cho, Bomsoo; Pierre-Louis, Gandhy; Sagner, Andreas; Eaton, Suzanne; Axelrod, Jeffrey D

2015-05-01

The core components of the planar cell polarity (PCP) signaling system, including both transmembrane and peripheral membrane associated proteins, form asymmetric complexes that bridge apical intercellular junctions. While these can assemble in either orientation, coordinated cell polarization requires the enrichment of complexes of a given orientation at specific junctions. This might occur by both positive and negative feedback between oppositely oriented complexes, and requires the peripheral membrane associated PCP components. However, the molecular mechanisms underlying feedback are not understood. We find that the E3 ubiquitin ligase complex Cullin1(Cul1)/SkpA/Supernumerary limbs(Slimb) regulates the stability of one of the peripheral membrane components, Prickle (Pk). Excess Pk disrupts PCP feedback and prevents asymmetry. We show that Pk participates in negative feedback by mediating internalization of PCP complexes containing the transmembrane components Van Gogh (Vang) and Flamingo (Fmi), and that internalization is activated by oppositely oriented complexes within clusters. Pk also participates in positive feedback through an unknown mechanism promoting clustering. Our results therefore identify a molecular mechanism underlying generation of asymmetry in PCP signaling.

Mesoscale simulations of confined Nafion thin films

NASA Astrophysics Data System (ADS)

Vanya, P.; Sharman, J.; Elliott, J. A.

2017-12-01

The morphology and transport properties of thin films of the ionomer Nafion, with thicknesses on the order of the bulk cluster size, have been investigated as a model system to explain the anomalous behaviour of catalyst/electrode-polymer interfaces in membrane electrode assemblies. We have employed dissipative particle dynamics (DPD) to investigate the interaction of water and fluorocarbon chains, with carbon and quartz as confining materials, for a wide range of operational water contents and film thicknesses. We found confinement-induced clustering of water perpendicular to the thin film. Hydrophobic carbon forms a water depletion zone near the film interface, whereas hydrophilic quartz results in a zone with excess water. There are, on average, oscillating water-rich and fluorocarbon-rich regions, in agreement with experimental results from neutron reflectometry. Water diffusivity shows increasing directional anisotropy of up to 30% with decreasing film thickness, depending on the hydrophilicity of the confining material. A percolation analysis revealed significant differences in water clustering and connectivity with the confining material. These findings indicate the fundamentally different nature of ionomer thin films, compared to membranes, and suggest explanations for increased ionic resistances observed in the catalyst layer.

Patterning C. elegans: homeotic cluster genes, cell fates and cell migrations.

PubMed

Salser, S J; Kenyon, C

1994-05-01

Despite its simple body form, the nematode C. elegans expresses homeotic cluster genes similar to those of insects and vertebrates in the patterning of many cell types and tissues along the anteroposterior axis. In the ventral nerve cord, these genes program spatial patterns of cell death, fusion, division and neurotransmitter production; in migrating cells they regulate the direction and extent of movement. Nematode development permits an analysis at the cellular level of how homeotic cluster genes interact to specify cell fates, and how cell behavior can be regulated to assemble an organism.

A strategy of gene overexpression based on tandem repetitive promoters in Escherichia coli.

PubMed

Li, Mingji; Wang, Junshu; Geng, Yanping; Li, Yikui; Wang, Qian; Liang, Quanfeng; Qi, Qingsheng

2012-02-06

For metabolic engineering, many rate-limiting steps may exist in the pathways of accumulating the target metabolites. Increasing copy number of the desired genes in these pathways is a general method to solve the problem, for example, the employment of the multi-copy plasmid-based expression system. However, this method may bring genetic instability, structural instability and metabolic burden to the host, while integrating of the desired gene into the chromosome may cause inadequate transcription or expression. In this study, we developed a strategy for obtaining gene overexpression by engineering promoter clusters consisted of multiple core-tac-promoters (MCPtacs) in tandem. Through a uniquely designed in vitro assembling process, a series of promoter clusters were constructed. The transcription strength of these promoter clusters showed a stepwise enhancement with the increase of tandem repeats number until it reached the critical value of five. Application of the MCPtacs promoter clusters in polyhydroxybutyrate (PHB) production proved that it was efficient. Integration of the phaCAB genes with the 5CPtacs promoter cluster resulted in an engineered E.coli that can accumulate 23.7% PHB of the cell dry weight in batch cultivation. The transcription strength of the MCPtacs promoter cluster can be greatly improved by increasing the tandem repeats number of the core-tac-promoter. By integrating the desired gene together with the MCPtacs promoter cluster into the chromosome of E. coli, we can achieve high and stale overexpression with only a small size. This strategy has an application potential in many fields and can be extended to other bacteria.

Different architectures in the assembly of infectious bursal disease virus capsid proteins expressed in insect cells.

PubMed

Martinez-Torrecuadrada, J L; Castón, J R; Castro, M; Carrascosa, J L; Rodriguez, J F; Casal, J I

2000-12-20

Infectious bursal disease virus (IBDV) capsid is formed by the processing of a large polyprotein and subsequent assembly of VPX/VP2 and VP3. To learn more about the processing of the polyprotein and factors affecting the correct assembly of the viral capsid in vitro, different constructs were made using two baculovirus transfer vectors, pFastBac and pAcYM1. Surprisingly, the expression of the capsid proteins gave rise to different types of particles in each system, as observed by electron microscopy and immunofluorescence. FastBac expression led to the production of only rigid tubular structures, similar to those described as type I in viral infection. Western blot analysis revealed that these rigid tubules are formed exclusively by VPX. These tubules revealed a hexagonal arrangement of units that are trimer clustered, similar to those observed in IBDV virions. In contrast, pAcYM1 expression led to the assembly of virus-like particles (VLPs), flexible tubules, and intermediate assembly products formed by icosahedral caps elongated in tubes, suggesting an aberrant morphogenesis. Processing of VPX to VP2 seems to be a crucial requirement for the proper morphogenesis and assembly of IBDV particles. After immunoelectron microscopy, VPX/VP2 was detected on the surface of tubules and VLPs. We also demonstrated that VP3 is found only on the inner surfaces of VLPs and caps of the tubular structures. In summary, assembly of VLPs requires the internal scaffolding of VP3, which seems to induce the closing of the tubular architecture into VLPs and, thereafter, the subsequent processing of VPX to VP2. Copyright 2000 Academic Press.

Kinetics of presynaptic filament assembly in the presence of single-stranded DNA binding protein and recombination mediator protein.

PubMed

Liu, Jie; Berger, Christopher L; Morrical, Scott W

2013-11-12

Enzymes of the RecA/Rad51 family catalyze DNA strand exchange reactions that are important for homologous recombination and for the accurate repair of DNA double-strand breaks. RecA/Rad51 recombinases are activated by their assembly into presynaptic filaments on single-stranded DNA (ssDNA), a process that is regulated by ssDNA binding protein (SSB) and mediator proteins. Mediator proteins stimulate strand exchange by accelerating the rate-limiting displacement of SSB from ssDNA by the incoming recombinase. The use of mediators is a highly conserved strategy in recombination, but the precise mechanism of mediator activity is unknown. In this study, the well-defined bacteriophage T4 recombination system (UvsX recombinase, Gp32 SSB, and UvsY mediator) is used to examine the kinetics of presynaptic filament assembly on native ssDNA in vitro. Results indicate that the ATP-dependent assembly of UvsX presynaptic filaments on Gp32-covered ssDNA is limited by a salt-sensitive nucleation step in the absence of mediator. Filament nucleation is selectively enhanced and rendered salt-resistant by mediator protein UvsY, which appears to stabilize a prenucleation complex. This mechanism potentially explains how UvsY promotes presynaptic filament assembly at physiologically relevant ionic strengths and Gp32 concentrations. Other data suggest that presynaptic filament assembly involves multiple nucleation events, resulting in many short UvsX-ssDNA filaments or clusters, which may be the relevant form for recombination in vivo. Together, these findings provide the first detailed kinetic model for presynaptic filament assembly involving all three major protein components (recombinase, mediator, and SSB) on native ssDNA.

Structure Formation in Salt-Free Solutions of Amphiphilic Sulfonated Polyelectrolytes

NASA Astrophysics Data System (ADS)

Bockstaller, Michael; Koehler, Werner

2000-03-01

Self-assembled systems have long attracted attention due to their practical importance in many technical and biological fields. Dodecyl-substituted poly(para-phenylen)sulfonates (abbreviated PPPS) are highly charged polyelectrolytes which in the uncharged state have been investigated extensively and an intrinsic persistence length of 15 nm has been reported. Due to their hydrophobic side chains, PPPS are compatible with water only as micellar aggregates and tend to form supramolecular structures even at concentrations as low as 10-5mol_mon.units/l. Because of the rodlike conformation of PPPS, this self-assembly leads to aggregates of anisotropic shape. Therefore, depolarized light scattering was employed to yield complementary information about structure and dynamics of these complex fluids. Aqueous solutions of PPPS at room temperature undergo a structural transition at a critical concentration of c_crit.=0.016 g/l. This transition is characterized by a strong increase of scattered intensity in forward direction and dynamic depolarized scattering. Above c_crit. the cylindrical micelles (L=310 nm, d=3.1 nm, N_radial=12) self assembly into large ellipsoidal clusters of size in the μ m range. Due to the strong increase of depolarized scattered intensity there has to be a preferential orientation of the micelles inside those clusters, which thus represent a lyotropic mesophase. By combining static and dynamic light scattering for the low q-range as well as small angle x-ray scattering for the higher q-range it is possible to determine size and shape of each aggregation step. Decreasing the molecular weight of the PPPS has profound influence on the micellar length and hence on c_crit. which is close to the overlap concentration (c ~ 1/L^3) allowing for the observation of the polyelectrolyte effect.

How Do Galaxies Grow?

NASA Astrophysics Data System (ADS)

2008-08-01

Astronomers have caught multiple massive galaxies in the act of merging about 4 billion years ago. This discovery, made possible by combining the power of the best ground- and space-based telescopes, uniquely supports the favoured theory of how galaxies form. ESO PR Photo 24/08 ESO PR Photo 24/08 Merging Galaxies in Groups How do galaxies form? The most widely accepted answer to this fundamental question is the model of 'hierarchical formation', a step-wise process in which small galaxies merge to build larger ones. One can think of the galaxies forming in a similar way to how streams merge to form rivers, and how these rivers, in turn, merge to form an even larger river. This theoretical model predicts that massive galaxies grow through many merging events in their lifetime. But when did their cosmological growth spurts finish? When did the most massive galaxies get most of their mass? To answer these questions, astronomers study massive galaxies in clusters, the cosmological equivalent of cities filled with galaxies. "Whether the brightest galaxies in clusters grew substantially in the last few billion years is intensely debated. Our observations show that in this time, these galaxies have increased their mass by 50%," says Kim-Vy Tran from the University of Zürich, Switzerland, who led the research. The astronomers made use of a large ensemble of telescopes and instruments, including ESO's Very Large Telescope (VLT) and the Hubble Space Telescope, to study in great detail galaxies located 4 billion light-years away. These galaxies lie in an extraordinary system made of four galaxy groups that will assemble into a cluster. In particular, the team took images with VIMOS and spectra with FORS2, both instruments on the VLT. From these and other observations, the astronomers could identify a total of 198 galaxies belonging to these four groups. The brightest galaxies in each group contain between 100 and 1000 billion of stars, a property that makes them comparable to the most massive galaxies belonging to clusters. "Most surprising is that in three of the four groups, the brightest galaxy also has a bright companion galaxy. These galaxy pairs are merging systems," says Tran. The brightest galaxy in each group can be ordered in a time sequence that shows how luminous galaxies continue to grow by merging until recently, that is, in the last 5 billion years. It appears that due to the most recent episode of this 'galactic cannibalism', the brightest galaxies became at least 50% more massive. This discovery provides unique and powerful validation of hierarchical formation as manifested in both galaxy and cluster assembly. "The stars in these galaxies are already old and so we must conclude that the recent merging did not produce a new generation of stars," concludes Tran. "Most of the stars in these galaxies were born at least 7 billion years ago." The team is composed of Kim-Vy H. Tran (Institute for Theoretical Physics, University of Zürich, Switzerland), John Moustakas (New York University, USA), Anthony H. Gonzalez and Stefan J. Kautsch (University of Florida, Gainesville, USA), and Lei Bai and Dennis Zaritsky (Steward Observatory, University of Arizona, USA). The results presented here are published in the Astrophysical Journal Letters: "The Late Stellar Assembly Of Massive Cluster Galaxies Via Major Merging", by Tran et al.

Lattice dynamics in Sn nanoislands and cluster-assembled films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Houben, Kelly; Couet, Sebastien; Trekels, Maarten

2017-04-01

To unravel the effects of phonon confinement, the influence of size and morphology on the atomic vibrations is investigated in Sn nanoislands and cluster-assembled films. Nuclear resonant inelastic x-ray scattering is used to probe the phonon densities of states of the Sn nanostructures which show significant broadening of the features compared to bulk phonon behavior. Supported by ab initio calculations, the broadening is attributed to phonon scattering and can be described within the damped harmonic oscillator model. Contrary to the expectations based on previous research, the appearance of high-energy modes above the cutoff energy is not observed. From the thermodynamicmore » properties extracted from the phonon densities of states, it was found that grain boundary Sn atoms are bound by weaker forces than bulk Sn atoms.« less

Benchmarking of calculation schemes in APOLLO2 and COBAYA3 for WER lattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheleva, N.; Ivanov, P.; Todorova, G.

This paper presents solutions of the NURISP WER lattice benchmark using APOLLO2, TRIPOLI4 and COBAYA3 pin-by-pin. The main objective is to validate MOC based calculation schemes for pin-by-pin cross-section generation with APOLLO2 against TRIPOLI4 reference results. A specific objective is to test the APOLLO2 generated cross-sections and interface discontinuity factors in COBAYA3 pin-by-pin calculations with unstructured mesh. The VVER-1000 core consists of large hexagonal assemblies with 2 mm inter-assembly water gaps which require the use of unstructured meshes in the pin-by-pin core simulators. The considered 2D benchmark problems include 19-pin clusters, fuel assemblies and 7-assembly clusters. APOLLO2 calculation schemes withmore » the step characteristic method (MOC) and the higher-order Linear Surface MOC have been tested. The comparison of APOLLO2 vs. TRIPOLI4 results shows a very close agreement. The 3D lattice solver in COBAYA3 uses transport corrected multi-group diffusion approximation with interface discontinuity factors of Generalized Equivalence Theory (GET) or Black Box Homogenization (BBH) type. The COBAYA3 pin-by-pin results in 2, 4 and 8 energy groups are close to the reference solutions when using side-dependent interface discontinuity factors. (authors)« less

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.

Monte Carlo simulation of Hamaker nanospheres coated with dipolar particles

NASA Astrophysics Data System (ADS)

Meyra, Ariel G.; Zarragoicoechea, Guillermo J.; Kuz, Victor A.

2012-01-01

Parallel tempering Monte Carlo simulation is carried out in systems of N attractive Hamaker spheres dressed with n dipolar particles, able to move on the surface of the spheres. Different cluster configurations emerge for given values of the control parameters. Energy per sphere, pair distribution functions of spheres and dipoles as function of temperature, density, external electric field, and/or the angular orientation of dipoles are used to analyse the state of aggregation of the system. As a consequence of the non-central interaction, the model predicts complex structures like self-assembly of spheres by a double crown of dipoles. This interesting result could be of help in understanding some recent experiments in colloidal science and biology.

UV-light-driven prebiotic synthesis of iron-sulfur clusters

NASA Astrophysics Data System (ADS)

Bonfio, Claudia; Valer, Luca; Scintilla, Simone; Shah, Sachin; Evans, David J.; Jin, Lin; Szostak, Jack W.; Sasselov, Dimitar D.; Sutherland, John D.; Mansy, Sheref S.

2017-12-01

Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols. Iron-sulfur clusters coordinate to and are stabilized by a wide range of cysteine-containing peptides and the assembly of iron-sulfur cluster-peptide complexes can take place within model protocells in a process that parallels extant pathways. Our experiments suggest that iron-sulfur clusters may have formed easily on early Earth, facilitating the emergence of an iron-sulfur-cluster-dependent metabolism.

Fe-S cluster biogenesis in isolated mammalian mitochondria: coordinated use of persulfide sulfur and iron and requirements for GTP, NADH, and ATP.

PubMed

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K; Dancis, Andrew; Pain, Debkumar

2015-01-02

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [(35)S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-(35)S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the (35)S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nam, Ki Hyun; Haitjema, Charles; Liu, Xueqi

Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3 single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing,more » Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.« less

Galaxy And Mass Assembly (GAMA): the effect of galaxy group environment on active galactic nuclei

NASA Astrophysics Data System (ADS)

Gordon, Yjan A.; Pimbblet, Kevin A.; Owers, Matt S.; Bland-Hawthorn, Joss; Brough, Sarah; Brown, Michael J. I.; Cluver, Michelle E.; Croom, Scott M.; Holwerda, Benne W.; Loveday, Jonathan; Mahajan, Smriti; Wang, Lingyu

2018-04-01

In galaxy clusters, efficiently accreting active galactic nuclei (AGNs) are preferentially located in the infall regions of the cluster projected phase-space, and are rarely found in the cluster core. This has been attributed to both an increase in triggering opportunities for infalling galaxies, and a reduction of those mechanisms in the hot, virialized, cluster core. Exploiting the depth and completeness (98 per cent at r < 19.8 mag) of the Galaxy And Mass Assembly survey (GAMA), we probe down the group halo mass function to assess whether AGNs are found in the same regions in groups as they are in clusters. We select 451 optical AGNs from 7498 galaxies with log10(M*/M⊙) > 9.9 in 695 groups with 11.53 ≤ log10(M200/M⊙) ≤ 14.56 at z < 0.15. By analysing the projected phase-space positions of these galaxies, we demonstrate that when split both radially, and into physically derived infalling and core populations, AGN position within group projected phase-space is dependent on halo mass. For groups with log10(M200/M⊙) > 13.5, AGNs are preferentially found in the infalling galaxy population with 3.6σ confidence. At lower halo masses, we observe no difference in AGN fraction between core and infalling galaxies. These observations support a model where a reduced number of low-speed interactions, ram pressure stripping and intra-group/cluster medium temperature, the dominance of which increase with halo mass, work to inhibit AGN in the cores of groups and clusters with log10(M200/M⊙) > 13.5, but do not significantly affect nuclear activity in cores of less massive structures.

Characterization of thermal-hydraulic and ignition phenomena in prototypic, full-length boiling water reactor spent fuel pool assemblies after a complete loss-of-coolant accident.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindgren, Eric Richard; Durbin, Samuel G

2007-04-01

The objective of this project was to provide basic thermal-hydraulic data associated with a SFP complete loss-of-coolant accident. The accident conditions of interest for the SFP were simulated in a full-scale prototypic fashion (electrically-heated, prototypic assemblies in a prototypic SFP rack) so that the experimental results closely represent actual fuel assembly responses. A major impetus for this work was to facilitate code validation (primarily MELCOR) and reduce questions associated with interpretation of the experimental results. It was necessary to simulate a cluster of assemblies to represent a higher decay (younger) assembly surrounded by older, lower-power assemblies. Specifically, this program providedmore » data and analysis confirming: (1) MELCOR modeling of inter-assembly radiant heat transfer, (2) flow resistance modeling and the natural convective flow induced in a fuel assembly as it heats up in air, (3) the potential for and nature of thermal transient (i.e., Zircaloy fire) propagation, and (4) mitigation strategies concerning fuel assembly management.« less

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

A peptide sequence N3-GVGV-OMe (G: glycine; V: valine) was attached to a benzene 1,3,5-tricarboxamide (BTA) derivative via ``click chemistry'' to afford a C3-symmetric artificial oligopeptide. The key feature of this oligopeptide is that the binding sites (triazole groups formed by click reaction) are located at the center, while the three oligopeptide arms with a strong tendency to assemble are located around it, which provides inner space to accommodate nanoparticles via self-assembly. The inclusion of Cu nanoclusters and the formation of one-dimensional (1D) arrays inside the nanofibers of the C3-symmetric artificial oligopeptide assembly were observed, which is quite different from the commonly observed nanoparticle growth on the surface of the pre-assembled oligopeptide nanofibers via the coordination sites located outside. Our finding provides an instructive concept for the design of other stable organic-inorganic hybrid 1D arrays with the inorganic nanoparticles inside.A peptide sequence N3-GVGV-OMe (G: glycine; V: valine) was attached to a benzene 1,3,5-tricarboxamide (BTA) derivative via ``click chemistry'' to afford a C3-symmetric artificial oligopeptide. The key feature of this oligopeptide is that the binding sites (triazole groups formed by click reaction) are located at the center, while the three oligopeptide arms with a strong tendency to assemble are located around it, which provides inner space to accommodate nanoparticles via self-assembly. The inclusion of Cu nanoclusters and the formation of one-dimensional (1D) arrays inside the nanofibers of the C3-symmetric artificial oligopeptide assembly were observed, which is quite different from the commonly observed nanoparticle growth on the surface of the pre-assembled oligopeptide nanofibers via the coordination sites located outside. Our finding provides an instructive concept for the design of other stable organic-inorganic hybrid 1D arrays with the inorganic nanoparticles inside. Electronic 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

The SUFBC2 D complex is required for the biogenesis of all major classes of plastid Fe-S proteins.

PubMed

Hu, Xueyun; Kato, Yukako; Sumida, Akihiro; Tanaka, Ayumi; Tanaka, Ryouichi

2017-04-01

Iron-sulfur (Fe-S) proteins play crucial roles in plastids, participating in photosynthesis and other metabolic pathways. Fe-S clusters are thought to be assembled on a scaffold complex composed of SUFB, SUFC and SUFD proteins. However, several additional proteins provide putative scaffold functions in plastids, and, therefore, the contribution of SUFB, C and D proteins to overall Fe-S assembly still remains unclear. In order to gain insights regarding Fe-S cluster biosynthesis in plastids, we analyzed the complex composed of SUFB, C and D in Arabidopsis by blue native-polyacrylamide gel electrophoresis. Using this approach, a major complex of 170 kDa containing all subunits was detected, indicating that these proteins constitute a SUFBC 2 D complex similar to their well characterized bacterial counterparts. The functional effects of SUFB, SUFC or SUFD depletion were analyzed using an inducible RNAi silencing system to specifically target the aforementioned components; resulting in a decrease of various plastidic Fe-S proteins including the PsaA/B and PsaC subunits of photosystem I, ferredoxin and glutamine oxoglutarate aminotransferase. In contrast, the knockout of potential Fe-S scaffold proteins, NFU2 and HCF101, resulted in a specific decrease in the PsaA/B and PsaC levels. These results indicate that the functions of SUFB, SUFC and SUFD for Fe-S cluster biosynthesis cannot be replaced by other scaffold proteins and that SUFBC 2 D, NFU2 and HCF101 are involved in the same pathway for the biogenesis of PSI. Taken together, our results provide in vivo evidence supporting the hypothesis that SUFBC 2 D is the major, and possibly sole scaffold in plastids. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Redox-Active Carbohydrate-Coated Nanoparticles: Self-Assembly of a Cyclodextrin-Polystyrene Glycopolymer with Tetrazine-Naphthalimide.

PubMed

Gross, Andrew J; Haddad, Raoudha; Travelet, Christophe; Reynaud, Eric; Audebert, Pierre; Borsali, Redouane; Cosnier, Serge

2016-11-15

The controlled self-assembly of precise and well-defined photochemically and electrochemically active carbohydrate-coated nanoparticles offers the exciting prospect of biocompatible catalysts for energy storage/conversion and biolabeling applications. Here an aqueous nanoparticle system has been developed with a versatile outer layer for host-guest molecule encapsulation via β-cyclodextrin inclusion complexes. A β-cyclodextrin-modified polystyrene polymer was first obtained by copper nanopowder click chemistry. The glycopolymer enables self-assembly and controlled encapsulation of tetrazine-naphthalimide, as a model redox-active agent, into nanoparticles via nanoprecipitation. Cyclodextrin host-guest interactions permit encapsulation and internanoparticle cross-linking for the formation of fluorescent compound and clustered self-assemblies with chemically reversible electroactivity in aqueous solution. Light scattering experiments revealed stable particles with hydrodynamic diameters of 138 and 654 nm for nanoparticles prepared with tetrazine, of which 95% of the nanoparticles represent the smaller objects by number. Dynamic light scattering revealed differences as a function of preparation method in terms of size, 3-month stability, polydispersity, radius of gyration, and shape factor. Individual self-assemblies were visualized by atomic force microscopy and fluorescence microscopy and monitored in real-time by nanoparticle tracking analysis. UV-vis and fluorescence spectra provided insight into the optical properties and critical evidence for host-guest encapsulation as evidenced by solvachromatism and enhanced tetrazine uptake. Cyclic voltammetry was used to investigate the electrochemical properties and provided further support for encapsulation and an estimate of the tetrazine loading capacity in tandem with light scattering data.

Strength of Neisseria meningitidis binding to endothelial cells requires highly-ordered CD147/β2-adrenoceptor clusters assembled by alpha-actinin-4

PubMed Central

Maïssa, Nawal; Covarelli, Valentina; Janel, Sébastien; Durel, Beatrice; Simpson, Nandi; Bernard, Sandra C.; Pardo-Lopez, Liliana; Bouzinba-Ségard, Haniaa; Faure, Camille; Scott, Mark G.H.; Coureuil, Mathieu; Morand, Philippe C.; Lafont, Frank; Nassif, Xavier; Marullo, Stefano; Bourdoulous, Sandrine

2017-01-01

Neisseria meningitidis (meningococcus) is an invasive bacterial pathogen that colonizes human vessels, causing thrombotic lesions and meningitis. Establishment of tight interactions with endothelial cells is crucial for meningococci to resist haemodynamic forces. Two endothelial receptors, CD147 and the β2-adrenergic receptor (β2AR), are sequentially engaged by meningococci to adhere and promote signalling events leading to vascular colonization, but their spatiotemporal coordination is unknown. Here we report that CD147 and β2AR form constitutive hetero-oligomeric complexes. The scaffolding protein α-actinin-4 directly binds to the cytosolic tail of CD147 and governs the assembly of CD147–β2AR complexes in highly ordered clusters at bacterial adhesion sites. This multimolecular assembly process increases the binding strength of meningococci to endothelial cells under shear stress, and creates molecular platforms for the elongation of membrane protrusions surrounding adherent bacteria. Thus, the specific organization of cellular receptors has major impacts on host–pathogen interaction. PMID:28569760

Patterns in the English language: phonological networks, percolation and assembly models

NASA Astrophysics Data System (ADS)

Stella, Massimo; Brede, Markus

2015-05-01

In this paper we provide a quantitative framework for the study of phonological networks (PNs) for the English language by carrying out principled comparisons to null models, either based on site percolation, randomization techniques, or network growth models. In contrast to previous work, we mainly focus on null models that reproduce lower order characteristics of the empirical data. We find that artificial networks matching connectivity properties of the English PN are exceedingly rare: this leads to the hypothesis that the word repertoire might have been assembled over time by preferentially introducing new words which are small modifications of old words. Our null models are able to explain the ‘power-law-like’ part of the degree distributions and generally retrieve qualitative features of the PN such as high clustering, high assortativity coefficient and small-world characteristics. However, the detailed comparison to expectations from null models also points out significant differences, suggesting the presence of additional constraints in word assembly. Key constraints we identify are the avoidance of large degrees, the avoidance of triadic closure and the avoidance of large non-percolating clusters.

Partial bisulfite conversion for unique template sequencing.

PubMed

Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua; Forcier, Talitha; Ronemus, Michael; Wigler, Michael; Levy, Dan

2018-01-25

We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Green fluorescent protein nanopolygons as monodisperse supramolecular assemblies of functional proteins with defined valency

PubMed Central

Kim, Young Eun; Kim, Yu-na; Kim, Jung A.; Kim, Ho Min; Jung, Yongwon

2015-01-01

Supramolecular protein assemblies offer novel nanoscale architectures with molecular precision and unparalleled functional diversity. A key challenge, however, is to create precise nano-assemblies of functional proteins with both defined structures and a controlled number of protein-building blocks. Here we report a series of supramolecular green fluorescent protein oligomers that are assembled in precise polygonal geometries and prepared in a monodisperse population. Green fluorescent protein is engineered to be self-assembled in cells into oligomeric assemblies that are natively separated in a single-protein resolution by surface charge manipulation, affording monodisperse protein (nano)polygons from dimer to decamer. Several functional proteins are multivalently displayed on the oligomers with controlled orientations. Spatial arrangements of protein oligomers and displayed functional proteins are directly visualized by a transmission electron microscope. By employing our functional protein assemblies, we provide experimental insight into multivalent protein–protein interactions and tools to manipulate receptor clustering on live cell surfaces. PMID:25972078