Science.gov

Sample records for re4q4x124 cluster complexes

  1. DNA clustering and genome complexity.

    PubMed

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Ichihashi, Masahiko; Odaka, Hideho

    2015-03-01

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

  3. Atomic clusters with addressable complexity

    NASA Astrophysics Data System (ADS)

    Wales, David J.

    2017-02-01

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

  4. Competitive cluster growth in complex networks

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  6. Motion of clusters on complex surfaces

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

  7. Pinning control of clustered complex networks with different size

    NASA Astrophysics Data System (ADS)

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

    2017-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Bekki, Kenji

    2017-01-01

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

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

    PubMed

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Pecora, Louis

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Bekki, Kenji

    2017-05-01

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

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

    PubMed

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

    2008-11-01

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

  13. Cluster type EAS array of the NEVOD experimental complex

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

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

    PubMed

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

    2009-09-01

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

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

    PubMed

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

    2012-02-01

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

  16. Ionization reactions of ion complexes in mesoscopic water clusters

    NASA Astrophysics Data System (ADS)

    Consta, Styliani; Kapral, Raymond

    1999-12-01

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

  17. Mathematical modelling of complex contagion on clustered networks

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    DTIC Science & Technology

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Zhuang, Yong; Arenas, Alex; Yaǧan, Osman

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  1. Structural and functional clusters of complex brain networks

    NASA Astrophysics Data System (ADS)

    Zemanová, Lucia; Zhou, Changsong; Kurths, Jürgen

    2006-12-01

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

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

    PubMed

    Maeda, Robert K; Karch, François

    2009-01-01

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

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

    PubMed

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

    2009-09-17

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  6. Knockout driven reactions in complex molecules and their clusters

    NASA Astrophysics Data System (ADS)

    Gatchell, Michael; Zettergren, Henning

    2016-08-01

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

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

    PubMed

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

    2016-10-01

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

  8. Thiol surface complexation on growing CdS clusters

    SciTech Connect

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

    1990-05-09

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2014-09-07

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

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

    PubMed

    Lindner, Robert

    2017-02-10

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

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

    PubMed Central

    Lindner, Robert

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Seddon, Elisa Joy

    2000-12-01

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

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

    PubMed

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

    2007-05-09

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

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

    NASA Astrophysics Data System (ADS)

    Robbins, David Lee

    1995-01-01

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

  16. Analysis of cluster explosive synchronization in complex networks.

    PubMed

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

    2014-12-01

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

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

    PubMed

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

    2017-03-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

    Xiaobing, Xie

    1997-10-17

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

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

    SciTech Connect

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

    2011-06-03

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

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

  3. Reconstructing Histories of Complex Gene Clusters on a Phylogeny

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

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

    PubMed

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

    2014-02-01

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

  6. 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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2016-08-01

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

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

    PubMed

    Burgess, Matthew; Adar, Eytan; Cafarella, Michael

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-10-01

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

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

    PubMed

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

    2016-10-01

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

  14. Clustering of ventricular arrhythmic complexes in heart rhythm

    NASA Astrophysics Data System (ADS)

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

    2011-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

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

    PubMed

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

    2008-04-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-11-15

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

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

    PubMed

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

    2015-03-01

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

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

    PubMed

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

    2009-02-28

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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

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

    PubMed

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

    2006-08-11

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

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

    NASA Astrophysics Data System (ADS)

    Luijten, Erik

    2005-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

    Kass, Steven R

    2005-09-28

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2017-06-20

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

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

    PubMed

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

    2016-08-15

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

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    SciTech Connect

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

    2011-06-20

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

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    PubMed Central

    2014-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2013-10-01

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

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

    PubMed

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

    2015-04-02

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

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

    PubMed

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

    2006-04-01

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

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

    PubMed

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

    2016-04-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    PubMed

    Saha, Sumit; Zhu, Lei; Captain, Burjor

    2013-03-04

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

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

    NASA Astrophysics Data System (ADS)

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

    1991-04-01

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

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

    SciTech Connect

    Imoto, Hideo; Saito, Taro; Adachi, Hirohiko

    1995-04-26

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    DOE PAGES

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

    2016-02-01

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

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

    SciTech Connect

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

    2016-02-01

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

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

    SciTech Connect

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

    2009-01-01

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

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

    PubMed

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

    2013-02-07

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

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

    PubMed

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

    2016-01-01

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

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

    SciTech Connect

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

    2014-11-15

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

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

    PubMed

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

    2016-11-01

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

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

    PubMed

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

    2006-10-14

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

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2016-10-21

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

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

    PubMed

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

    2017-06-01

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

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

    SciTech Connect

    Felker, P.M.

    1991-12-31

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

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

    SciTech Connect

    Felker, P.M.

    1991-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

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

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

    SciTech Connect

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

    2010-10-22

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    PubMed

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

    2010-12-21

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

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

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

    PubMed

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

    2004-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Benda, Zsuzsanna; Jagau, Thomas-C.

    2017-01-01

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

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

    PubMed

    Adams, Richard D; Captain, Burjor

    2008-01-01

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

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

    SciTech Connect

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

    2015-05-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

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

    PubMed

    Rozan; Lassman; Ridge; Luther

    2000-08-24

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

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

    SciTech Connect

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

    2011-11-15

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

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

    SciTech Connect

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

    2006-08-15

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2017-04-04

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    SciTech Connect

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

    2012-07-01

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

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

    PubMed

    Marshall, Bennett D

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Jagau, Thomas-C.

    2016-11-01

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

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

    PubMed

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

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

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

    SciTech Connect

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

    2011-05-20

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

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

    PubMed

    Kryachko, E S; Remacle, F

    2005-12-08

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

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

    SciTech Connect

    Liang, Wenchuan

    1994-11-01

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

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

    PubMed

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

    2016-08-22

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

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

    PubMed

    Saha, Sumit; Captain, Burjor

    2014-01-21

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

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

    NASA Astrophysics Data System (ADS)

    Franke, R.

    2016-11-01

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

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

    PubMed

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

    2001-03-26

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

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

    SciTech Connect

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

    1992-11-25

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Remacle, F.; Kryachko, E. S.

    2004-12-01

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

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

    PubMed

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

    2013-07-23

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

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

    PubMed

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

    2013-09-28

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

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

    SciTech Connect

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

    1992-11-01

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

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

    SciTech Connect

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

    1992-07-01

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

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

    PubMed

    Serna, Pedro; Gates, B C

    2011-04-06

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

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

    SciTech Connect

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

    2008-11-03

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

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

    SciTech Connect

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

    2001-07-25

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

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

    PubMed

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

    2015-03-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    SciTech Connect

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

    2014-07-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    2013-01-01

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

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

    SciTech Connect

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

    2016-03-10

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

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

    NASA Astrophysics Data System (ADS)

    Thompson, Richard A.; Helz, George R.

    1994-07-01

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

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

    SciTech Connect

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

    1992-10-01

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

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

    PubMed

    Adams, Richard D; Captain, Burjor

    2009-03-17

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

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

    USDA-ARS?s Scientific Manuscript database

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

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

    SciTech Connect

    Krishnan Balasubramanian

    2009-07-18

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

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

    PubMed

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

    2014-05-05

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

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

    PubMed

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

    2015-12-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

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

    2014-01-21

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

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

    NASA Astrophysics Data System (ADS)

    Luther, George W.; Rickard, David T.

    2005-10-01

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

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

    PubMed

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

    2014-12-28

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

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

    NASA Astrophysics Data System (ADS)

    Xue, Xiao; Zhang, Jibiao; Wang, Yang

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2016-04-21

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

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

    PubMed

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

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2012-01-10

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

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

    PubMed Central

    2011-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2011-01-17

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

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

    PubMed Central

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Teller, Sara; Soriano, Jordi

    2016-06-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2012-07-16

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

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

    SciTech Connect

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

    2015-05-15

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed

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

    2002-10-29

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

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

    PubMed

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

    2010-07-01

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

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

    SciTech Connect

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

    2002-08-02

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed

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

    2005-12-19

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

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

    SciTech Connect

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

    2013-09-01

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

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

    PubMed

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

    2014-11-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed

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

    2012-12-14

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

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

    PubMed

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

    2017-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-06-01

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

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

    PubMed

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

    2017-02-14

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

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

    SciTech Connect

    Balasubramanian, K

    2008-10-06

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

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

    DTIC Science & Technology

    1987-04-30

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

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

    SciTech Connect

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

    1980-09-01

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

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

    PubMed

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

    2011-04-29

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

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

    PubMed Central

    Weaver, Michael N.; Yang, Yue

    2010-01-01

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

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

    PubMed

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

    2011-11-11

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

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

    SciTech Connect

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

    2005-06-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

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

    SciTech Connect

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

    2014-07-28

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

  15. 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.

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

    SciTech Connect

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

    2007-01-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    SciTech Connect

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

    2014-07-08

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

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

    PubMed

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

    2014-10-13

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

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

    PubMed Central

    Liu, Siqi; Xu, Yi-Jun

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    DTIC Science & Technology

    1988-07-01

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

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

    PubMed

    Saha, Sumit; Zhu, Lei; Captain, Burjor

    2010-04-05

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

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

    PubMed

    Xie, Jianhui

    2012-08-01

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

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

    PubMed

    Xia, Yong; Han, Junze; Wang, Kuanquan

    2015-01-01

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

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

    SciTech Connect

    Fenwick, Michael K.; Ealick, Steven E.

    2016-07-12

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Li, Guangzhe; Salim, Chris; Hinode, Hirofumi

    2008-02-01

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

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

    PubMed

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

    2012-01-01

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

  14. Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa).

    PubMed

    Christopoulou, Marilena; McHale, Leah K; Kozik, Alex; Reyes-Chin Wo, Sebastian; Wroblewski, Tadeusz; Michelmore, Richard W

    2015-07-01

    Of the over 50 phenotypic resistance genes mapped in lettuce, 25 colocalize to three major resistance clusters (MRC) on chromosomes 1, 2, and 4. Similarly, the majority of candidate resistance genes encoding nucleotide binding-leucine rich repeat (NLR) proteins genetically colocalize with phenotypic resistance loci. MRC1 and MRC4 span over 66 and 63 Mb containing 84 and 21 NLR-encoding genes, respectively, as well as 765 and 627 genes that are not related to NLR genes. Forward and reverse genetic approaches were applied to dissect MRC1 and MRC4. Transgenic lines exhibiting silencing were selected using silencing of β-glucuronidase as a reporter. Silencing of two of five NLR-encoding gene families resulted in abrogation of nine of 14 tested resistance phenotypes mapping to these two regions. At MRC1, members of the coiled coil-NLR-encoding RGC1 gene family were implicated in host and nonhost resistance through requirement for Dm5/8- and Dm45-mediated resistance to downy mildew caused by Bremia lactucae as well as the hypersensitive response to effectors AvrB, AvrRpm1, and AvrRpt2 of the nonpathogen Pseudomonas syringae. At MRC4, RGC12 family members, which encode toll interleukin receptor-NLR proteins, were implicated in Dm4-, Dm7-, Dm11-, and Dm44-mediated resistance to B. lactucae. Lesions were identified in the sequence of a candidate gene within dm7 loss-of-resistance mutant lines, confirming that RGC12G confers Dm7.

  15. The connection between prestellar cores and filaments in cluster-forming clumps of the Aquila Rift complex

    NASA Astrophysics Data System (ADS)

    Könyves, Vera; André, Philippe; Maury, Anaëlle

    2015-08-01

    One of the main goals of the Herschel Gould Belt survey (André et al. 2010) is to elucidate the physicalmechanisms responsible for the formation and evolution of prestellar cores in molecular clouds. In theAquila cloud complex imaged with Herschel/SPIRE-PACS between 70-500 μm, we have recently identifieda complete sample of 651 starless cores, 446 of them are gravitationally-bound prestellar cores, likelyforming stars in the future. We also detected 58 protostellar cores (Könyves et al. 2010 and 2015, subm.- see http://gouldbelt-herschel.cea.fr/archives). This region is dominated by two (proto)clusters which arecurrently active sites of clustered star formation (SF): the filamentary Serpens South cloud and the W40HII region. The latter is powered by massive young stars, and a 2nd-generation SF can be witnessed inthe surroundings (Maury et al. 2011).Our Herschel observations also provide an unprecedented census of filaments in Aquila and suggest aclose connection between them and the formation process of prestellar cores, where both structures arehighly concentrated around the protoclusters. About 10-20% of the gas mass is in the form of filamentsbelow Av~7, while ~50-75% of the dense gas mass above Av~7-10 is in filamentary structures.Furthermore, ~90% of our prestellar cores are located above a background column density correspondingto Av~7, and ~75% of them lie within the densest filamentary structures with supercritical masses per unitlength >16 M⊙/pc. Indeed, a strong correlation is found between the spatial distribution of prestellar coresand the densest filaments.Comparing the statistics of cores and filaments with the number of young stellar objects found by Spitzerin the same complex, we also infer a typical timescale ~1 Myr for the formation and evolution of bothprestellar cores and filaments.In summary, our Herschel findings in Aquila support a filamentary paradigm for the early stages of SF,where the cores result from the gravitational fragmentation

  16. Lessons learnt during a complex, multicentre cluster randomised controlled trial: the ProAct65+ trial

    PubMed Central

    2013-01-01

    Background Failure to recruit to target or schedule is common in randomized controlled trials (RCTs). Innovative interventions are not always fully developed before being tested, and maintenance of fidelity to the intervention during trials can be problematic. Missing data can compromise analyses, and inaccurate capture of risks to participants can influence reporting of intervention harms and benefits. In this paper we describe how challenges of recruitment and retention of participants, standardisation and quality control of interventions and capture of adverse events were overcome in the ProAct65+ cluster RCT. This trial compared class-based and home-based exercise with usual care in people aged 65 years and over, recruited through general practice. The home-based exercise participants were supported by Peer Mentors. Results (1) Organisational factors, including room availability in general practices, slowed participant recruitment so the recruitment period was extended and the number invited to participate increased. (2) Telephone pre-screening was introduced to exclude potential participants who were already very active and those who were frequent fallers. (3) Recruitment of volunteer peer mentors was difficult and time consuming and their acceptable case load less than expected. Lowering the age limit for peer mentors and reducing their contact schedule with participants did not improve recruitment. (4) Fidelity to the group intervention was optimised by introducing quality assurance observation of classes by experienced exercise instructors. (5) Diaries were used to capture data on falls, service use and other exercise-related costs, but completion was variable so their frequency was reduced. (6) Classification of adverse events differed between research sites so all events were assessed by both sites and discrepancies discussed. Conclusions Recruitment rates for trials in general practice may be limited by organisational factors and longer recruitment

  17. Synaptonemal complex extension from clustered telomeres mediates full-length chromosome pairing in Schmidtea mediterranea

    PubMed Central

    Xiang, Youbin; Miller, Danny E.; Ross, Eric J.; Sánchez Alvarado, Alejandro; Hawley, R. Scott

    2014-01-01

    In the 1920s, József Gelei proposed that chromosome pairing in flatworms resulted from the formation of a telomere bouquet followed by the extension of synapsis from telomeres at the base of the bouquet, thus facilitating homolog pairing in a processive manner. A modern interpretation of Gelei’s model postulates that the synaptonemal complex (SC) is nucleated close to the telomeres and then extends progressively along the full length of chromosome arms. We used the easily visible meiotic chromosomes, a well-characterized genome, and RNAi in the sexual biotype of the planarian Schmidtea mediterranea to test that hypothesis. By identifying and characterizing S. mediterranea homologs of genes encoding synaptonemal complex protein 1 (SYCP1), the topoisomerase-like protein SPO11, and RAD51, a key player in homologous recombination, we confirmed that SC formation begins near the telomeres and progresses along chromosome arms during zygotene. Although distal regions pair at the time of bouquet formation, pairing of a unique interstitial locus is not observed until the formation of full-length SC at pachytene. Moreover, neither full extension of the SC nor homologous pairing is dependent on the formation of double-strand breaks. These findings validate Gelei’s speculation that full-length pairing of homologous chromosomes is mediated by the extension of the SC formed near the telomeres. S. mediterranea thus becomes the first organism described (to our knowledge) that forms a canonical telomere bouquet but does not require double-strand breaks for synapsis between homologous chromosomes. However, the initiation of SC formation at the base of the telomere bouquet, which then is followed by full-length homologous pairing in planarian spermatocytes, is not observed in other species and may not be conserved. PMID:25404302

  18. The formation of complex acetylcholine receptor clusters requires MuSK kinase activity and structural information from the MuSK extracellular domain

    PubMed Central

    Mazhar, Sania; Herbst, Ruth

    2012-01-01

    Efficient synaptic transmission at the neuromuscular junction (NMJ) requires the topological maturation of the postsynaptic apparatus from an oval acetylcholine receptor (AChR)-rich plaque into a complex pretzel-shaped array of branches. However, compared to NMJ formation very little is known about the mechanisms that regulate NMJ maturation. Recently the process of in vivo transformation from plaque into pretzel has been reproduced in vitro by culturing myotubes aneurally on laminin-coated substrate. It was proposed that the formation of complex AChR clusters is regulated by a MuSK-dependent muscle intrinsic program. To elucidate the structure–function role of MuSK in the aneural maturation of AChR pretzels, we used muscle cell lines expressing MuSK mutant and chimeric proteins. Here we report, that besides its role during agrin-induced AChR clustering, MuSK kinase activity is also necessary for substrate-dependent cluster formation. Constitutive-active MuSK induces larger AChR clusters, a faster cluster maturation on laminin and increases the anchorage of AChRs to the cytoskeleton compared to MuSK wild-type. In addition, we find that the juxtamembrane region of MuSK, which has previously been shown to regulate agrin-induced AChR clustering, is unable to induce complex AChR clusters on laminin substrate. Most interestingly, MuSK kinase activity is not sufficient for laminin-dependent AChR cluster formation since the MuSK ectodomain is also required suggesting a so far undiscovered instructive role for the extracellular domain of MuSK. PMID:22210232

  19. The formation of complex acetylcholine receptor clusters requires MuSK kinase activity and structural information from the MuSK extracellular domain.

    PubMed

    Mazhar, Sania; Herbst, Ruth

    2012-04-01

    Efficient synaptic transmission at the neuromuscular junction (NMJ) requires the topological maturation of the postsynaptic apparatus from an oval acetylcholine receptor (AChR)-rich plaque into a complex pretzel-shaped array of branches. However, compared to NMJ formation very little is known about the mechanisms that regulate NMJ maturation. Recently the process of in vivo transformation from plaque into pretzel has been reproduced in vitro by culturing myotubes aneurally on laminin-coated substrate. It was proposed that the formation of complex AChR clusters is regulated by a MuSK-dependent muscle intrinsic program. To elucidate the structure-function role of MuSK in the aneural maturation of AChR pretzels, we used muscle cell lines expressing MuSK mutant and chimeric proteins. Here we report, that besides its role during agrin-induced AChR clustering, MuSK kinase activity is also necessary for substrate-dependent cluster formation. Constitutive-active MuSK induces larger AChR clusters, a faster cluster maturation on laminin and increases the anchorage of AChRs to the cytoskeleton compared to MuSK wild-type. In addition, we find that the juxtamembrane region of MuSK, which has previously been shown to regulate agrin-induced AChR clustering, is unable to induce complex AChR clusters on laminin substrate. Most interestingly, MuSK kinase activity is not sufficient for laminin-dependent AChR cluster formation since the MuSK ectodomain is also required suggesting a so far undiscovered instructive role for the extracellular domain of MuSK. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. A CEP215–HSET complex links centrosomes with spindle poles and drives centrosome clustering in cancer

    PubMed Central

    Chavali, Pavithra L.; Chandrasekaran, Gayathri; Barr, Alexis R.; Tátrai, Péter; Taylor, Chris; Papachristou, Evaggelia K.; Woods, C. Geoffrey; Chavali, Sreenivas; Gergely, Fanni

    2016-01-01

    Numerical centrosome aberrations underlie certain developmental abnormalities and may promote cancer. A cell maintains normal centrosome numbers by coupling centrosome duplication with segregation, which is achieved through sustained association of each centrosome with a mitotic spindle pole. Although the microcephaly- and primordial dwarfism-linked centrosomal protein CEP215 has been implicated in this process, the molecular mechanism responsible remains unclear. Here, using proteomic profiling, we identify the minus end-directed microtubule motor protein HSET as a direct binding partner of CEP215. Targeted deletion of the HSET-binding domain of CEP215 in vertebrate cells causes centrosome detachment and results in HSET depletion at centrosomes, a phenotype also observed in CEP215-deficient patient-derived cells. Moreover, in cancer cells with centrosome amplification, the CEP215–HSET complex promotes the clustering of extra centrosomes into pseudo-bipolar spindles, thereby ensuring viable cell division. Therefore, stabilization of the centrosome–spindle pole interface by the CEP215–HSET complex could promote survival of cancer cells containing supernumerary centrosomes. PMID:26987684

  1. Small-volume potentiometric titrations: EPR investigations of Fe-S cluster N2 in mitochondrial complex I.

    PubMed

    Wright, John J; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

    2016-09-01

    EPR-based potentiometric titrations are a well-established method for determining the reduction potentials of cofactors in large and complex proteins with at least one EPR-active state. However, such titrations require large amounts of protein. Here, we report a new method that requires an order of magnitude less protein than previously described methods, and that provides EPR samples suitable for measurements at both X- and Q-band microwave frequencies. We demonstrate our method by determining the reduction potential of the terminal [4Fe-4S] cluster (N2) in the intramolecular electron-transfer relay in mammalian respiratory complex I. The value determined by our method, Em7=-158mV, is precise, reproducible, and consistent with previously reported values. Our small-volume potentiometric titration method will facilitate detailed investigations of EPR-active centres in non-abundant and refractory proteins that can only be prepared in small quantities. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  2. Synthesis and Characterization of Bioinspired [Mo2 Fe2 ]-Hydride Cluster Complexes and Their Application in the Catalytic Silylation of N2.

    PubMed

    Ohki, Yasuhiro; Araki, Yuna; Tada, Mizuki; Sakai, Yoichi

    2017-09-21

    The hydride-supported [Mo2 Fe2 ] cluster complex {Cp*Mo(PMe3 )}2 {FeN(SiMe3 )2 }2 (H)8 (2 a; Cp*=η(5) -C5 Me5 ) and its [Mo2 Mn2 ] congener 2 b were synthesized from the reactions of Cp*Mo(PMe3 )(H)5 (1) with M{N(SiMe3 )2 }2 (M=Fe, Mn). The amide-to-thiolate ligand-exchange reactions of complex 2 a with bulky thiol reagents (HSR; R=2,4,6-iPr3 C6 H2 (Tip), 2,6-(SiMe3 )2 C6 H3 (Btp)) furnished the corresponding hydride-supported [Mo2 Fe2 ](SR)2 cluster complexes. The [Mo2 Fe2 ] clusters served as catalyst precursors for the reductive silylation of N2 and yielded ≈65-69 equivalents of N(SiMe3 )3 relative to the [Mo2 Fe2 ] clusters. Treatment of complexes 2 a and b with an excess of CNtBu resulted in the formation of dinuclear Mo-Fe and Mo-Mn complexes, which indicated that the [Mo2 M2 ] cores (M=Fe, Mn) split into two dinuclear species upon accommodation of substrates. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Clustering dynamics of the metal-benzene sandwich complex: the role of microscopic structure of the solute in the bis(eta6-benzene)chromium .Arn Clusters (n = 1-15).

    PubMed

    Choi, Kyo-Won; Choi, Sunyoung; Ahn, Doo-Sik; Han, Songhee; Kang, Tae Yeon; Baek, Sun Jong; Kim, Sang Kyu

    2008-08-07

    Ar clustering dynamics around the metal-benzene sandwich complex, bis(eta (6)-benzene)chromium: Cr(Bz) 2, is found to occur in two distinct regimes. The shift of the ionization potential (IP) upon the addition of Ar is measured to be 151 cm (-1), and it is constant until the number of Ar solvents ( n) becomes 6. The IP shift per Ar is found to be suddenly decreased to 82 cm (-1) for the clusters of n = 7-12. The cluster distribution indicates that the n = 6 cluster is most populated in the molecular beam. These experimental findings with the aid of ab initio calculation indicate that the first six Ar solvent molecules are attached to top and bottom of Cr(Bz) 2 to give the robust structure for the Cr(Bz) 2-Ar 6 cluster whereas the next six Ar molecules are gathered on the side of the solute core to give the highly symmetric structure of the Cr(Bz) 2-Ar 12 cluster.

  4. Complex magnetic structure of clusters and chains of Ni and Fe on Pt(111)

    PubMed Central

    Bezerra-Neto, Manoel M.; Ribeiro, Marcelo S.; Sanyal, Biplab; Bergman, Anders; Muniz, Roberto B.; Eriksson, Olle; Klautau, Angela B.

    2013-01-01

    We present an approach to control the magnetic structure of adatoms adsorbed on a substrate having a high magnetic susceptibility. Using finite Ni-Pt and Fe-Pt nanowires and nanostructures on Pt(111) surfaces, our ab initio results show that it is possible to tune the exchange interaction and magnetic configuration of magnetic adatoms (Fe or Ni) by introducing different numbers of Pt atoms to link them, or by including edge effects. The exchange interaction between Ni (or Fe) adatoms on Pt(111) can be considerably increased by introducing Pt chains to link them. The magnetic ordering can be regulated allowing for ferromagnetic or antiferromagnetic configurations. Noncollinear magnetic alignments can also be stabilized by changing the number of Pt-mediated atoms. An Fe-Pt triangularly-shaped nanostructure adsorbed on Pt(111) shows the most complex magnetic structure of the systems considered here: a spin-spiral type of magnetic order that changes its propagation direction at the triangle vertices. PMID:24165828

  5. Metal-sulfide species in oxic waters: Complexes, clusters, or colloids?

    NASA Astrophysics Data System (ADS)

    Wang, F.; Sukola, K.; Tessier, A.

    2003-12-01

    A weight-of-evidence approach is employed to characterize metal-sulfide species that have recently been suggested to be present in oxic waters. Sulfide in synthetic Cd-, Zn-, Pb-, Cu-sulfide solutions persists in oxic waters for a prolonged period of time (2 to more than 10 weeks) whereas it is oxidized rapidly in Fe-, Mn- and Ni-sulfide solutions. Direct mass spectrometric (MS) analysis and transmission electron microscopic (TEM) analysis revealed that the metal-sulfide species resistant to oxidation in oxic waters are not soluble molecular nanoclusters as suggested previously; instead, they are a mixture of truly dissolved metal-sulfide complexes and dynamic metal-sulfide colloids. The morphology and size of the colloids change significantly with time. Nanomolar to sub-micromolar levels of acid-volatile sulfide (AVS) and chromous-volatile sulfide (CVS) were measured in oxic surface waters of 6 lakes located on the Canadian Shield and nearby areas. Thermodynamic calculations indicated that at the AVS levels measured, the dissolved metal-sulfide species play a minor role in the speciation of Class B metal ions such as Pb, Cd, Cu, Hg.

  6. Evolution of a Complex Disease Resistance Gene Cluster in Diploid Phaseolus and Tetraploid Glycine1[W][OA

    PubMed Central

    Ashfield, Tom; Egan, Ashley N.; Pfeil, Bernard E.; Chen, Nicolas W.G.; Podicheti, Ram; Ratnaparkhe, Milind B.; Ameline-Torregrosa, Carine; Denny, Roxanne; Cannon, Steven; Doyle, Jeff J.; Geffroy, Valérie; Roe, Bruce A.; Saghai Maroof, M.A.; Young, Nevin D.; Innes, Roger W.

    2012-01-01

    We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay. PMID:22457424

  7. The Resistance of Electron Transport Chain Fe-S Clusters to Oxidative Damage during the Reaction of Peroxynitrite with Mitochondrial Complex II and Rat Heart Pericardium

    PubMed Central

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

    2009-01-01

    The effects of peroxynitrite and nitric oxide on the iron-sulfur clusters in complex II (succinate dehydrogenase) isolated from bovine heart have been studied primarily by EPR spectroscopy and no measurable damage to the constitutive 2Fe-2S, 3Fe-4S, or 4Fe-4S clusters was observed. The enzyme can be repeatedly oxidized with a slight excess of peroxynitrite and then quantitatively re-reduced with succinate. When added in large excess, peroxynitrite reacted with at least one tyrosine in each subunit of complex II to form 3-nitrotyrosines, but activity was barely compromised. Examination of rat-heart pericardium subjected to conditions leading to peroxynitrite production showed a small inhibition of complex II (16%) and a greater inhibition of aconitase (77%). In addition, experiments performed with excesses of sodium citrate and sodium succinate on rat-heart pericardium indicated that the “g ~2.01” EPR signal observed immediately following the beginning of conditions modeling oxidative/nitrosative stress, could be a consequence of both reversible oxidation of the constitutive 3Fe-4S cluster in complex II and degradation of the 4Fe-4S cluster in aconitase. However, the net signal envelope, which becomes apparent in less than one minute following the start of oxidative/nitrosative conditions, is dominated by the component arising from complex II. Taking into account the findings of a previous study concerning complexes I and III [L.L. Pearce, A.J. Kanai, M.W. Epperly, J. Peterson (2005) Nitric Oxide 13, 254-63] it is now apparent that, with the exception of the cofactor in aconitase, mammalian (mitochondrial) iron-sulfur clusters are surprisingly resistant to degradation stemming from oxidative/nitrosative stress. PMID:19118636

  8. Three tetranuclear copper(II) cluster-based complexes constructed from 4-amino-1,2,4-triazole and different aromatic carboxylates: Assembly, structures, electrochemical and magnetic properties

    SciTech Connect

    Wang, Xiu-Li; Zhao, Wei; Zhang, Ju-Wen; Lu, Qi-Lin

    2013-02-15

    Three new tetranuclear copper(II) cluster-based complexes constructed from 4-amino-1,2,4-triazole (atrz) and three types of aromatic carboxylates, [Cu{sub 4}({mu}{sub 3}-OH){sub 2}(atrz){sub 2}(DNBA){sub 6}] (1), [Cu{sub 4}({mu}{sub 3}-OH){sub 2}(atrz){sub 2}(1,3-BDC){sub 3}]{center_dot}2H{sub 2}O (2) and [Cu{sub 4}({mu}{sub 3}-OH){sub 2}(atrz){sub 2}(SIP){sub 2}]{center_dot}4H{sub 2}O (3) (HDNBA=3,5-dinitrobenzoic acid, 1,3-H{sub 2}BDC=1,3-benzenedicarboxylic acid and NaH{sub 2}SIP=sodium 5-sulfoisophthalate), have been hydrothermally synthesized and structurally characterized. Complex 1 displays a single-molecular Cu{sup II}{sub 4} cluster structure, which is further connected by the intermolecular hydrogen-bonding interactions to form a 2D supramolecular layer. In 2, there also exist tetranuclear Cu{sup II}{sub 4} clusters, which are linked by the 1,3-BDC anions to give a 3D NaCl-type framework. In 3, the Cu{sup II}{sub 4} clusters are connected by the carboxyl and sulfo groups of SIP anions to generate 3D (4,8)-connected framework with a (4{sup 10}{center_dot}6{sup 14}{center_dot}8{sup 4})(4{sup 5}{center_dot}6){sub 2} topology. The atrz ligand conduces to the construction of tetranuclear copper(II) clusters and the carboxylates with different non-carboxyl substituent show important effects on the final structures of the title complexes. The electrochemical and magnetic properties of 1-3 have been investigated. - Graphical abstract: Three tetranuclear copper(II) cluster-based complexes based on different carboxylates have been synthesized under hydrothermal conditions. The carboxylate anions play a key role in the formation of three different structures. Highlights: Black-Right-Pointing-Pointer Three new tetranuclear copper(II) cluster-based complexes have been obtained. Black-Right-Pointing-Pointer The atrz conduces to the construction of tetranuclear copper(II) clusters. Black-Right-Pointing-Pointer Carboxylates show important effect on the structures of

  9. Packing of Russian doll clusters to form a nanometer-scale CsCl-type compound in a Cr–Zn–Sn complex metallic alloy

    DOE PAGES

    Xie, Weiwei; Cava, Robert J.; Miller, Gordon J.

    2017-07-03

    A new cubic complex metallic alloy phase, Cr22Zn72Sn24, with a lattice parameter near 2.5 nm was discovered in crystals grown using a Zn/Sn flux. The structure consists of Russian doll clusters or a 3-d network of Cr-centered icosahedra (shown) with bcc-metal fragments in void spaces.

  10. Synthesis, structural and magnetic characterisation of iron(II/III), cobalt(II) and copper(II) cluster complexes of the polytopic ligand: N-(2-pyridyl)-3-carboxypropanamide.

    PubMed

    Russell, Mark E; Hawes, Chris S; Ferguson, Alan; Polson, Matthew I J; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S; Kruger, Paul E

    2013-10-07

    Herein we describe the synthesis, structural and magnetic characterisation of three transition metal cluster complexes that feature the polytopic ligand N-(2-pyridyl)-3-carboxypropanamide (H2L): [Fe3(III)Fe2(II)(HL)6(O)(H2O)3][ClO4]5·3MeCN·4H2O, 1, [Co8(HL)8(O)(OH)4(MeOH)3(H2O)]-[ClO4]3·5MeOH·2H2O, 2, and [Cu6(L(ox))4(MeOH)(H2O)3]·MeOH, 3. Complex 1 is a mixed valence penta-nuclear iron cluster containing the archetypal {Fe3(III)O} triangular basic carboxylate cluster at its core, with two Fe(II) ions above and below the core coordinated to three bidentate pyridyl-amide groups. The structure of the octanuclear Co(II) complex, 2, is based upon a central Co4 square with the remaining four Co(II) centres at the 'wing-tips' of the complex. The cluster core is replete with bridging oxide, hydroxide and carboxylate groups. Cluster 3 contains an oxidised derivative of the ligand, L(ox), generated in situ through hydroxylation of an α-carbon atom. This hexanuclear cluster has a 'barrel-like' core and contains Cu(II) ions in both square planar and square-based pyramidal geometries. Bridging between Cu(II) centres is furnished by alkoxide and carboxylate groups. Magnetic studies on 1-3 reveals dominant antiferro-magnetic interactions for 1 and 2, leading to small non-zero spin ground states, while 3 shows ferro-magnetic exchange between the Cu(II) centres to give an S = 3 spin ground state.

  11. Detecting hidden spatial and spatio-temporal structures in glasses and complex physical systems by multiresolution network clustering.

    PubMed

    Ronhovde, P; Chakrabarty, S; Hu, D; Sahu, M; Sahu, K K; Kelton, K F; Mauro, N A; Nussinov, Z

    2011-09-01

    We elaborate on a general method that we recently introduced for characterizing the "natural" structures in complex physical systems via multi-scale network analysis. The method is based on "community detection" wherein interacting particles are partitioned into an "ideal gas" of optimally decoupled groups of particles. Specifically, we construct a set of network representations ("replicas") of the physical system based on interatomic potentials and apply a multiscale clustering ("multiresolution community detection") analysis using information-based correlations among the replicas. Replicas may i) be different representations of an identical static system, ii) embody dynamics by considering replicas to be time separated snapshots of the system (with a tunable time separation), or iii) encode general correlations when different replicas correspond to different representations of the entire history of the system as it evolves in space-time. Inputs for our method are the inter-particle potentials or experimentally measured two (or higher order) particle correlations. We apply our method to computer simulations of a binary Kob-Andersen Lennard-Jones system in a mixture ratio of A(80)B(20) , a ternary model system with components "A", "B", and "C" in ratios of A(88)B(7)C(5) (as in Al(88)Y(7)Fe(5) , and to atomic coordinates in a Zr(80)Pt(20) system as gleaned by reverse Monte Carlo analysis of experimentally determined structure factors. We identify the dominant structures (disjoint or overlapping) and general length scales by analyzing extrema of the information theory measures. We speculate on possible links between i) physical transitions or crossovers and ii) changes in structures found by this method as well as phase transitions associated with the computational complexity of the community detection problem. We also briefly consider continuum approaches and discuss rigidity and the shear penetration depth in amorphous systems; this latter length scale increases as

  12. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB

    PubMed Central

    Khara, Pratick; Roy, Madhumita; Chakraborty, Joydeep; Ghosal, Debajyoti; Dutta, Tapan K.

    2014-01-01

    Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO) genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET) proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads. PMID:24918041

  13. Deficiency of the iron-sulfur clusters of mitochondrial reduced nicotinamide-adenine dinucleotide-ubiquinone oxidoreductase (complex I) in an infant with congenital lactic acidosis.

    PubMed Central

    Moreadith, R W; Batshaw, M L; Ohnishi, T; Kerr, D; Knox, B; Jackson, D; Hruban, R; Olson, J; Reynafarje, B; Lehninger, A L

    1984-01-01

    We report the case of an infant with hypoglycemia, progressive lactic acidosis, an increased serum lactate/pyruvate ratio, and elevated plasma alanine, who had a moderate to profound decrease in the ability of mitochondria from four organs to oxidize pyruvate, malate plus glutamate, citrate, and other NAD+-linked respiratory substrates. The capacity to oxidize the flavin adenine dinucleotide-linked substrate, succinate, was normal. The most pronounced deficiency was in skeletal muscle, the least in kidney mitochondria. Enzymatic assays on isolated mitochondria ruled out defects in complexes II, III, and IV of the respiratory chain. Further studies showed that the defect was localized in the inner membrane mitochondrial NADH-ubiquinone oxidoreductase (complex I). When ferricyanide was used as an artificial electron acceptor, complex I activity was normal, indicating that electrons from NADH could reduce the flavin mononucleotide cofactor. However, electron paramagnetic resonance spectroscopy performed on liver submitochondrial particles showed an almost total loss of the iron-sulfur clusters characteristic of complex I, whereas normal signals were noted for other mitochondrial iron-sulfur clusters. This infant is presented as the first reported case of congenital lactic acidosis caused by a deficiency of the iron-sulfur clusters of complex I of the mitochondrial electron transport chain. Images PMID:6432847

  14. Deficiency of the iron-sulfur clusters of mitochondrial reduced nicotinamide-adenine dinucleotide-ubiquinone oxidoreductase (complex I) in an infant with congenital lactic acidosis.

    PubMed

    Moreadith, R W; Batshaw, M L; Ohnishi, T; Kerr, D; Knox, B; Jackson, D; Hruban, R; Olson, J; Reynafarje, B; Lehninger, A L

    1984-09-01

    We report the case of an infant with hypoglycemia, progressive lactic acidosis, an increased serum lactate/pyruvate ratio, and elevated plasma alanine, who had a moderate to profound decrease in the ability of mitochondria from four organs to oxidize pyruvate, malate plus glutamate, citrate, and other NAD+-linked respiratory substrates. The capacity to oxidize the flavin adenine dinucleotide-linked substrate, succinate, was normal. The most pronounced deficiency was in skeletal muscle, the least in kidney mitochondria. Enzymatic assays on isolated mitochondria ruled out defects in complexes II, III, and IV of the respiratory chain. Further studies showed that the defect was localized in the inner membrane mitochondrial NADH-ubiquinone oxidoreductase (complex I). When ferricyanide was used as an artificial electron acceptor, complex I activity was normal, indicating that electrons from NADH could reduce the flavin mononucleotide cofactor. However, electron paramagnetic resonance spectroscopy performed on liver submitochondrial particles showed an almost total loss of the iron-sulfur clusters characteristic of complex I, whereas normal signals were noted for other mitochondrial iron-sulfur clusters. This infant is presented as the first reported case of congenital lactic acidosis caused by a deficiency of the iron-sulfur clusters of complex I of the mitochondrial electron transport chain.

  15. Perturbation of the Quinone-binding Site of Complex II Alters the Electronic Properties of the Proximal [3Fe-4S] Iron-Sulfur Cluster*

    PubMed Central

    Ruprecht, Jonathan; Iwata, So; Rothery, Richard A.; Weiner, Joel H.; Maklashina, Elena; Cecchini, Gary

    2011-01-01

    Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis. PMID:21310949

  16. Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.

    PubMed

    Ruprecht, Jonathan; Iwata, So; Rothery, Richard A; Weiner, Joel H; Maklashina, Elena; Cecchini, Gary

    2011-04-08

    Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis.

  17. Hausdorff clustering

    NASA Astrophysics Data System (ADS)

    Basalto, Nicolas; Bellotti, Roberto; de Carlo, Francesco; Facchi, Paolo; Pantaleo, Ester; Pascazio, Saverio

    2008-10-01

    A clustering algorithm based on the Hausdorff distance is analyzed and compared to the single, complete, and average linkage algorithms. The four clustering procedures are applied to a toy example and to the time series of financial data. The dendrograms are scrutinized and their features compared. The Hausdorff linkage relies on firm mathematical grounds and turns out to be very effective when one has to discriminate among complex structures.

  18. The Yeast Iron Regulatory Proteins Grx3/4 and Fra2 Form Heterodimeric Complexes Containing a [2Fe-2S] Cluster with Cysteinyl and Histidyl Ligation†

    PubMed Central

    Li, Haoran; Mapolelo, Daphne T.; Dingra, Nin N.; Naik, Sunil G.; Lees, Nicolas S.; Hoffman, Brian M.; Riggs-Gelasco, Pamela J.; Huynh, Boi Hanh; Johnson, Michael K.; Outten, Caryn E.

    2009-01-01

    The transcription of iron uptake and storage genes in S. cerevisiae is primarily regulated by the transcription factor Aft1. Nucleocytoplasmic shuttling of Aft1 is dependent upon mitochondrial Fe-S cluster biosynthesis via a signaling pathway that includes the cytosolic monothiol glutaredoxins (Grx3 and Grx4) and the BolA homologue Fra2. However the interactions between these proteins and the iron-dependent mechanism by which they control Aft1 localization are unclear. To reconstitute and characterize components of this signaling pathway in vitro, we have overexpressed yeast Fra2 and Grx3/4 in E. coli. We have shown that co-expression of recombinant Fra2 with Grx3 or Grx4 allows purification of a stable [2Fe-2S]2+ cluster-containing Fra2-Grx3 or Fra2-Grx4 heterodimeric complex. Reconstitution of a [2Fe-2S] cluster on Grx3 or Grx4 without Fra2 produces a [2Fe-2S]-bridged homodimer. UV-visible absorption and CD, resonance Raman, EPR, ENDOR, Mössbauer, and EXAFS studies of [2Fe-2S] Grx3/4 homodimers and the [2Fe-2S] Fra2-Grx3/4 heterodimers indicate that inclusion of Fra2 in the Grx3/4 Fe-S complex causes a change in the cluster stability and coordination environment. Taken together, our analytical, spectroscopic, and mutagenesis data indicate that Grx3/4 and Fra2 form a Fe-S-bridged heterodimeric complex with Fe ligands provided by the active site cysteine of Grx3/4, glutathione, and a histidine residue. Overall, these results suggest that the ability of the Fra2-Grx3/4 complex to assemble a [2Fe-2S] cluster may act as a signal to control the iron regulon in response to cellular iron status in yeast. PMID:19715344

  19. Structural diversity of copper-CO2 complexes: infrared spectra and structures of [Cu(CO2)n]- clusters.

    PubMed

    Knurr, Benjamin J; Weber, J Mathias

    2014-11-06

    We  present infrared spectra of  [Cu(CO2)n](-) (n = 2-9) clusters in the wavenumber range 1600-2400 cm(-1). The CO stretching modes in this region encode the structural nature of the cluster core and are interpreted with the aid of density functional theory. We find a variety of core species in [Cu(CO2)n](-) clusters, but the dominant core structure is a [Cu(CO2)2](-) core where the two CO2 ligands are bound to the Cu atom in a bidentate fashion. We compare the results of [Cu(CO2)n](-) clusters to those of other [M(CO2)n](-) clusters (M = Au, Ag, Co, Ni) to establish trends of how the metal-CO2 interaction depends on the metal partner.

  20. Infrared and electronic spectroscopy of benzene-ammonia cluster radical cations [C(6)H(6)(NH(3))(1,2)](+): observation of isolated and microsolvated σ-complexes.

    PubMed

    Mizuse, Kenta; Hasegawa, Hayato; Mikami, Naohiko; Fujii, Asuka

    2010-10-28

    We report infrared (IR) and electronic spectra of benzene-ammonia cluster radical cations [C(6)H(6)(NH(3))(n)](+) (n = 1 and 2) in the gas phase to explore cluster structures and chemical reactivity of the simplest aromatic radical cation with base (nucleophile) molecules. The electronic spectra in the visible region indicate that these cluster cations no longer have the benzene cation chromophore as a result of an intracluster reaction. Analyses of the IR spectra, on the basis quantum chemical calculations and the vibration-internal rotation analysis, reveal that both [C(6)H(6)(NH(3))(1,2)](+) form σ-complex structures, in which the ammonia moiety is covalently bonded to the benzene moiety due to the intracluster nucleophilic addition. For [C(6)H(6)(NH(3))(2)](+), it is also shown that the second ammonia molecule solvates the σ-complex core via a N-H···N hydrogen bond. Such σ-complex structures are generally supposed to be a key intermediate of aromatic substitution reactions. The observed mass spectra and energetics calculations, however, show that [C(6)H(6)(NH(3))(n)](+) systems are inert for aromatic substitutions. The present experimental observations indicate the inherent stability of these σ-complex structures, even though they do not show the aromatic substitution reactivity.

  1. A structure-based analysis of the vibrational spectra of nitrosyl ligands in transition-metal coordination complexes and clusters.

    PubMed

    De La Cruz, Carlos; Sheppard, Norman

    2011-01-01

    The vibrational spectra of nitrogen monoxide or nitric oxide (NO) bonded to one or to several transition-metal (M) atom(s) in coordination and cluster compounds are analyzed in relation to the various types of such structures identified by diffraction methods. These structures are classified in: (a) terminal (linear and bent) nitrosyls, [M(σ-NO)] or [M(NO)]; (b) twofold nitrosyl bridges, [M2(μ2-NO)]; (c) threefold nitrosyl bridges, [M3(μ3-NO)]; (d) σ/π-dihaptonitrosyls or "side-on" nitrosyls; and (e) isonitrosyls (oxygen-bonded nitrosyls). Typical ranges for the values of internuclear N-O and M-N bond-distances and M-N-O bond-angles for linear nitrosyls are: 1.14-1.20 Å/1.60-1.90 Å/180-160° and for bent nitrosyls are 1.16-1.22 Å/1.80-2.00 Å/140-110°. The [M2(μ2-NO)] bridges have been divided into those that contain one or several metal-metal bonds and those without a formal metal/metal bond (M⋯M). Typical ranges for the M-M, N-O, M-N bond distances and M-N-M bond angles for the normal twofold NO bridges are: 2.30-3.00 Å/1.18-1.22 Å/1.80-2.00 Å/90-70°, whereas for the analogous ranges of the long twofold NO bridges these are 3.10-3.40 Å/1.20-1.24 Å/1.90-2.10 Å/130-110°. In both situations the N-O vector is approximately at right angle to the M-M (or M⋯M) vector within the experimental error; i.e. the NO group is symmetrical bonded to the two metal atoms. In contrast the threefold NO bridges can be symmetrically or unsymmetrically bonded to an M3-plane of a cluster compound. Characteristic values for the N-O and M-N bond-distances of these NO bridges are: 1.24-1.28 Å/1.80-1.90 Å, respectively. As few dihaptonitrosyl and isonitrosyl complexes are known, the structural features of these are discussed on an individual basis. The very extensive vibrational spectroscopy literature considered gives emphasis to the data from linearly bonded NO ligands in stable closed-shell metal complexes; i.e. those which are consistent with the

  2. A structure-based analysis of the vibrational spectra of nitrosyl ligands in transition-metal coordination complexes and clusters

    NASA Astrophysics Data System (ADS)

    De La Cruz, Carlos; Sheppard, Norman

    2011-01-01

    The vibrational spectra of nitrogen monoxide or nitric oxide (NO) bonded to one or to several transition-metal (M) atom(s) in coordination and cluster compounds are analyzed in relation to the various types of such structures identified by diffraction methods. These structures are classified in: (a) terminal (linear and bent) nitrosyls, [M(σ-NO)] or [M(NO)]; (b) twofold nitrosyl bridges, [M 2(μ 2-NO)]; (c) threefold nitrosyl bridges, [M 3(μ 3-NO)]; (d) σ/π-dihaptonitrosyls or " side-on" nitrosyls; and (e) isonitrosyls (oxygen-bonded nitrosyls). Typical ranges for the values of internuclear N-O and M-N bond-distances and M-N-O bond-angles for linear nitrosyls are: 1.14-1.20 Å/1.60-1.90 Å/180-160° and for bent nitrosyls are 1.16-1.22 Å/1.80-2.00 Å/140-110°. The [M 2(μ 2-NO)] bridges have been divided into those that contain one or several metal-metal bonds and those without a formal metal/metal bond (M⋯M). Typical ranges for the M-M, N-O, M-N bond distances and M-N-M bond angles for the normal twofold NO bridges are: 2.30-3.00 Å/1.18-1.22 Å/1.80-2.00 Å/90-70°, whereas for the analogous ranges of the long twofold NO bridges these are 3.10-3.40 Å/1.20-1.24 Å/1.90-2.10 Å/130-110°. In both situations the N-O vector is approximately at right angle to the M-M (or M⋯M) vector within the experimental error; i.e. the NO group is symmetrical bonded to the two metal atoms. In contrast the threefold NO bridges can be symmetrically or unsymmetrically bonded to an M 3-plane of a cluster compound. Characteristic values for the N-O and M-N bond-distances of these NO bridges are: 1.24-1.28 Å/1.80-1.90 Å, respectively. As few dihaptonitrosyl and isonitrosyl complexes are known, the structural features of these are discussed on an individual basis. The very extensive vibrational spectroscopy literature considered gives emphasis to the data from linearly bonded NO ligands in stable closed-shell metal complexes; i.e. those which are consistent with the

  3. Complexes of DNA Bases and Watson-Crick Base Pairs Interaction with Neutral Silver Agn (n = 8, 10, 12) Clusters: A DFT and TDDFT Study.

    PubMed

    Srivastava, Ruby

    2017-03-21

    We study the binding of the neutral Agn (n = 8, 10, 12) to the DNA base- adenine (A), guanine (G) and Watson-Crick -adenine-thymine (AT), guanine-cytosine (GC) pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential (ECP) was used for silver and 6-31+G(**) was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Agn-A,G/WC complexes were also studied using time-dependent density functional theory (TDDFT). The absorption spectra for these complexes show wavelength in the visible region. It was revealed that silver clusters interact more strongly with WC pairs than with isolated DNA complexes. Furthermore, it was found that the electronic charge transferred from silver to isolated DNA clusters are less than the electronic charge transferred from silver to the Agn-WC complexes. The vertical ionization potential, vertical electron affinity, hardness and electrophilicity index of Agn-DNA/WC complexes have also been discussed.

  4. Hydrothermal syntheses, crystal structures of three new organic-inorganic hybrids constructed from Keggin-type [BW 12O 40] 5- clusters and transition metal complexes

    NASA Astrophysics Data System (ADS)

    Wang, Jing-Ping; Guo, Gui-Ling; Niu, Jing-Yang

    2008-08-01

    Three new organic-inorganic hybrid compounds constructed from Keggin-type polyanions and transition metal complexes, [Mn(2,2'-bipy) 3] 1.5[BW 12O 40Mn(2,2'-bipy) 2(H 2O)]·0.25H 2O ( 1), [Fe(2,2'-bipy) 3] 1.5[BW 12O 40Fe(2,2'-bipy) 2(H 2O)]·0.5H 2O ( 2) and [Cu 2(phen) 2(OH) 2] 2H[Cu(H 2O) 2{BW 12O 40Cu 0.75(phen)(H 2O)} 2]·1.5H 2O ( 3), have been hydrothermally synthesized and characterized by elemental analyses, IR, TGA and single-crystal X-ray diffraction. Compounds 1 and 2 are isostructural and both exhibit monosupporting polyoxometalate cluster structure, each of which contains a [BW 12O 40] 5- cluster decorated by one transition metal complex. Compound 3 contains a bisupporting polyoxometalate cluster anion where two {Cu 0.75(phen)(H 2O)} 0.75+ fragments are supported on the polyoxometalate dimer {Cu(H 2O) 2(BW 12O 40) 2} 8-, this represents the first bisupporting polyoxometalate cluster based on a Keggin-type polyoxometalate dimer, which are further packed together via π-π stacking contacts into an extended 1-D chain.

  5. Differentiation of the gene clusters encoding botulinum neurotoxin type A complexes in Clostridium botulinum type A, Ab, and A(B) strains.

    PubMed

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-12-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained.

  6. Differentiation of the Gene Clusters Encoding Botulinum Neurotoxin Type A Complexes in Clostridium botulinum Type A, Ab, and A(B) Strains

    PubMed Central

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-01-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained. PMID:15574917

  7. Path-integral molecular dynamics simulations of BeO embedded in helium clusters: Formation of the stable HeBeO complex

    NASA Astrophysics Data System (ADS)

    Motegi, Haruki; Kakizaki, Akira; Takayanagi, Toshiyuki; Taketsugu, Yuriko; Taketsugu, Tetsuya; Shiga, Motoyuki

    2008-12-01

    Path-integral molecular dynamics simulations have been performed to understand the quantum helium solvation structures in the He nBeO cluster up to n = 100. Our simulations show that one helium atom is strongly bound to BeO to form HeBeO and that the first solvation shell around the HeBeO complex includes roughly 12-14 helium atoms. The second solvation structure was also observed for n > 20. Both the first and second solvation shells show an anisotropic behavior but the anisotropy for the second solvation shell was found to be much weaker than that for the first solvation shell, as expected. The present simulations suggest that the HeBeO complex may be formed in large helium clusters.

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

    SciTech Connect

    Tsai, Chi-Lin; Bridwell-Rabb, Jennifer; Barondeau, David P

    2011-11-07

    Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease that has been linked to defects in the protein frataxin (Fxn). Most FRDA patients have a GAA expansion in the first intron of their Fxn gene that decreases protein expression. Some FRDA patients have a GAA expansion on one allele and a missense mutation on the other allele. Few functional details are known for the ~15 different missense mutations identified in FRDA patients. Here in vitro evidence is presented that indicates the FRDA I154F and W155R variants bind more weakly to the complex of Nfs1, Isd11, and Isu2 and thereby are defective in forming the four-component SDUF complex that constitutes the core of the Fe-S cluster assembly machine. The binding affinities follow the trend Fxn ~ I154F > W155F > W155A ~ W155R. The Fxn variants also have diminished ability to function as part of the SDUF complex to stimulate the cysteine desulfurase reaction and facilitate Fe-S cluster assembly. Four crystal structures, including the first for a FRDA variant, reveal specific rearrangements associated with the loss of function and lead to a model for Fxn-based activation of the Fe-S cluster assembly complex. Importantly, the weaker binding and lower activity for FRDA variants correlate with the severity of disease progression. Together, these results suggest that Fxn facilitates sulfur transfer from Nfs1 to Isu2 and that these in vitro assays are sensitive and appropriate for deciphering functional defects and mechanistic details for human Fe-S cluster biosynthesis.

  9. Semiquinone and Cluster N6 Signals in His-tagged Proton-translocating NADH:Ubiquinone Oxidoreductase (Complex I) from Escherichia coli*

    PubMed Central

    Narayanan, Madhavan; Gabrieli, David J.; Leung, Steven A.; Elguindy, Mahmoud M.; Glaser, Carl A.; Saju, Nitha; Sinha, Subhash C.; Nakamaru-Ogiso, Eiko

    2013-01-01

    NADH:ubiquinone oxidoreductase (complex I) pumps protons across the membrane using downhill redox energy. The Escherichia coli complex I consists of 13 different subunits named NuoA-N coded by the nuo operon. Due to the low abundance of the protein and some difficulty with the genetic manipulation of its large ∼15-kb operon, purification of E. coli complex I has been technically challenging. Here, we generated a new strain in which a polyhistidine sequence was inserted upstream of nuoE in the operon. This allowed us to prepare large amounts of highly pure and active complex I by efficient affinity purification. The purified complex I contained 0.94 ± 0.1 mol of FMN, 29.0 ± 0.37 mol of iron, and 1.99 ± 0.07 mol of ubiquinone/1 mol of complex I. The extinction coefficient of isolated complex I was 495 mm−1 cm−1 at 274 nm and 50.3 mm−1 cm−1 at 410 nm. NADH:ferricyanide activity was 219 ± 9.7 μmol/min/mg by using HEPES-Bis-Tris propane, pH 7.5. Detailed EPR analyses revealed two additional iron-sulfur cluster signals, N6a and N6b, in addition to previously assigned signals. Furthermore, we found small but significant semiquinone signal(s), which have been reported only for bovine complex I. The line width was ∼12 G, indicating its neutral semiquinone form. More than 90% of the semiquinone signal originated from the single entity with P½ (half-saturation power level) = 1.85 milliwatts. The semiquinone signal(s) decreased by 60% when with asimicin, a potent complex I inhibitor. The functional role of semiquinone and the EPR assignment of clusters N6a/N6b are discussed. PMID:23543743

  10. Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe–2S] cluster

    PubMed Central

    Abdalla, Mohnad; Dai, Ya-Nan; Chi, Chang-Biao; Cheng, Wang; Cao, Dong-Dong; Zhou, Kang; Ali, Wafa; Chen, Yuxing; Zhou, Cong-Zhao

    2016-01-01

    Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe–2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe–2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe–2S] cluster-incorporated dithiol Grxs, which share a highly conserved [2Fe–2S] cluster-binding pattern and dimeric conformation that is distinct from the previously identified [2Fe–2S] cluster-ligated monothiol Grxs. PMID:27710937

  11. Histidine 129 in the 75-kDa subunit of mitochondrial complex I from Yarrowia lipolytica is not a ligand for [Fe4S4] cluster N5 but is required for catalytic activity.

    PubMed

    Waletko, Antje; Zwicker, Klaus; Abdrakhmanova, Albina; Zickermann, Volker; Brandt, Ulrich; Kerscher, Stefan

    2005-02-18

    Respiratory chain complex I contains 8-9 iron-sulfur clusters. In several cases, the assignment of these clusters to subunits and binding motifs is still ambiguous. To test the proposed ligation of the tetranuclear iron-sulfur cluster N5 of respiratory chain complex I, we replaced the conserved histidine 129 in the 75-kDa subunit from Yarrowia lipolytica with alanine. In the mutant strain, reduced amounts of fully assembled but destabilized complex I could be detected. Deamino-NADH: ubiquinone oxidoreductase activity was abolished completely by the mutation. However, EPR spectroscopic analysis of mutant complex I exhibited an unchanged cluster N5 signal, excluding histidine 129 as a cluster N5 ligand.

  12. Properties of clusters in the gas phase. IV. Complexes of H/sub 2/O and HNO/sub x/ clustering on NO/sub x//sup -/

    SciTech Connect

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

    1980-01-15

    Thermodynamic quantities for the gas-phase clustering equilibria of NO/sub 2//sup -/ and NO/sub 3//sup -/ were determined with high-pressure mass spectrometry. Comparison of ..delta..G/sup 0//sub n/,n+1 values derived from our data shows good agreement with formerly reported values at 296 /sup 0/K. New data for larger NO/sub 2//sup -/ and NO/sub 3//sup -/ hydrates as well as NO/sub 2//sup -/(HNO/sub 2/) were obtained in this study. To aid in understanding the bonding and stability of the hydrates of nitrite and nitrate ions, CNDO/2 calculations were performed, and the results are discussed herein. A correlation between the aqueous phase total hydration enthalpy of a single ion and its gas-phase hydration enthalpy was obtained. Atmoshperic implications of the data are also briefly discussed.

  13. Lifetime of Major Histocompatibility Complex Class-I Membrane Clusters Is Controlled by the Actin Cytoskeleton

    PubMed Central

    Lavi, Yael; Gov, Nir; Edidin, Michael; Gheber, Levi A.

    2012-01-01

    Lateral heterogeneity of cell membranes has been demonstrated in numerous studies showing anomalous diffusion of membrane proteins; it has been explained by models and experiments suggesting dynamic barriers to free diffusion, that temporarily confine membrane proteins into microscopic patches. This picture, however, comes short of explaining a steady-state patchy distribution of proteins, in face of the transient opening of the barriers. In our previous work we directly imaged persistent clusters of MHC-I, a type I transmembrane protein, and proposed a model of a dynamic equilibrium between proteins newly delivered to the cell surface by vesicle traffic, temporary confinement by dynamic barriers to lateral diffusion, and dispersion of the clusters by diffusion over the dynamic barriers. Our model predicted that the clusters are dynamic, appearing when an exocytic vesicle fuses with the plasma membrane and dispersing with a typical lifetime that depends on lateral diffusion and the dynamics of barriers. In a subsequent work, we showed this to be the case. Here we test another prediction of the model, and show that changing the stability of actin barriers to lateral diffusion changes cluster lifetimes. We also develop a model for the distribution of cluster lifetimes, consistent with the function of barriers to lateral diffusion in maintaining MHC-I clusters. PMID:22500754

  14. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

    PubMed Central

    2012-01-01

    Background Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection of arCOGs is expected to

  15. Density-based clustering: A ‘landscape view’ of multi-channel neural data for inference and dynamic complexity analysis

    PubMed Central

    Gigante, Guido; Del Giudice, Paolo

    2017-01-01

    Two, partially interwoven, hot topics in the analysis and statistical modeling of neural data, are the development of efficient and informative representations of the time series derived from multiple neural recordings, and the extraction of information about the connectivity structure of the underlying neural network from the recorded neural activities. In the present paper we show that state-space clustering can provide an easy and effective option for reducing the dimensionality of multiple neural time series, that it can improve inference of synaptic couplings from neural activities, and that it can also allow the construction of a compact representation of the multi-dimensional dynamics, that easily lends itself to complexity measures. We apply a variant of the ‘mean-shift’ algorithm to perform state-space clustering, and validate it on an Hopfield network in the glassy phase, in which metastable states are largely uncorrelated from memories embedded in the synaptic matrix. In this context, we show that the neural states identified as clusters’ centroids offer a parsimonious parametrization of the synaptic matrix, which allows a significant improvement in inferring the synaptic couplings from the neural activities. Moving to the more realistic case of a multi-modular spiking network, with spike-frequency adaptation inducing history-dependent effects, we propose a procedure inspired by Boltzmann learning, but extending its domain of application, to learn inter-module synaptic couplings so that the spiking network reproduces a prescribed pattern of spatial correlations; we then illustrate, in the spiking network, how clustering is effective in extracting relevant features of the network’s state-space landscape. Finally, we show that the knowledge of the cluster structure allows casting the multi-dimensional neural dynamics in the form of a symbolic dynamics of transitions between clusters; as an illustration of the potential of such reduction, we define

  16. Altered Structure of the Mn4Ca Cluster in the Oxygen-evolving Complex of Photosystem II by a Histidine Ligand Mutation*

    PubMed Central

    Yano, Junko; Walker, Lee M.; Strickler, Melodie A.; Service, Rachel J.; Yachandra, Vittal K.; Debus, Richard J.

    2011-01-01

    The effect of replacing a histidine ligand on the properties of the oxygen-evolving complex (OEC) and the structure of the Mn4Ca cluster in Photosystem II (PSII) is studied by x-ray absorption spectroscopy using PSII core complexes from the Synechocystis sp. PCC 6803 D1 polypeptide mutant H332E. In the x-ray crystallographic structures of PSII, D1-His332 has been assigned as a direct ligand of a manganese ion, and the mutation of this histidine ligand to glutamate has been reported to prevent the advancement of the OEC beyond the S2Yz• intermediate state. The manganese K-edge (1s core electron to 4p) absorption spectrum of D1-H332E shifts to a lower energy compared with that of the native WT samples, suggesting that the electronic structure of the manganese cluster is affected by the presence of the additional negative charge on the OEC of the mutant. The extended x-ray absorption spectrum shows that the geometric structure of the cluster is altered substantially from that of the native WT state, resulting in an elongation of manganese-ligand and manganese-manganese interactions in the mutant. The strontium-H332E mutant, in which calcium is substituted by strontium, confirms that strontium (calcium) is a part of the altered cluster. The structural perturbations caused by the D1-H332E mutation are much larger than those produced by any biochemical treatment or mutation examined previously with x-ray absorption spectroscopy. The substantial structural changes provide an explanation not only for the altered properties of the D1-H332E mutant but also the importance of the histidine ligand for proper assembly of the Mn4Ca cluster. PMID:21233216

  17. Altered structure of the Mn4Ca cluster in the oxygen-evolving complex of photosystem II by a histidine ligand mutation.

    PubMed

    Yano, Junko; Walker, Lee M; Strickler, Melodie A; Service, Rachel J; Yachandra, Vittal K; Debus, Richard J

    2011-03-18

    The effect of replacing a histidine ligand on the properties of the oxygen-evolving complex (OEC) and the structure of the Mn(4)Ca cluster in Photosystem II (PSII) is studied by x-ray absorption spectroscopy using PSII core complexes from the Synechocystis sp. PCC 6803 D1 polypeptide mutant H332E. In the x-ray crystallographic structures of PSII, D1-His(332) has been assigned as a direct ligand of a manganese ion, and the mutation of this histidine ligand to glutamate has been reported to prevent the advancement of the OEC beyond the S(2)Yz(•) intermediate state. The manganese K-edge (1s core electron to 4p) absorption spectrum of D1-H332E shifts to a lower energy compared with that of the native WT samples, suggesting that the electronic structure of the manganese cluster is affected by the presence of the additional negative charge on the OEC of the mutant. The extended x-ray absorption spectrum shows that the geometric structure of the cluster is altered substantially from that of the native WT state, resulting in an elongation of manganese-ligand and manganese-manganese interactions in the mutant. The strontium-H332E mutant, in which calcium is substituted by strontium, confirms that strontium (calcium) is a part of the altered cluster. The structural perturbations caused by the D1-H332E mutation are much larger than those produced by any biochemical treatment or mutation examined previously with x-ray absorption spectroscopy. The substantial structural changes provide an explanation not only for the altered properties of the D1-H332E mutant but also the importance of the histidine ligand for proper assembly of the Mn(4)Ca cluster.

  18. The neuronal protein Neurexin directly interacts with the Scribble-Pix complex to stimulate F-actin assembly for synaptic vesicle clustering.

    PubMed

    Rui, Menglong; Qian, Jinjun; Liu, Lijuan; Cai, Yihan; Lv, Huihui; Han, Junhai; Jia, Zhengping; Xie, Wei

    2017-09-01

    Synaptic vesicles (SVs) form distinct pools at synaptic terminals, and this well-regulated separation is necessary for normal neurotransmission. However, how the SV cluster, in particular synaptic compartments, maintains normal neurotransmitter release remains a mystery. The presynaptic protein Neurexin (NRX) plays a significant role in synaptic architecture and function, and some evidence suggests that NRX is associated with neurological disorders, including autism spectrum disorders. However, the role of NRX in SV clustering is unclear. Here, using the neuromuscular junction at the 2-3 instar stages of Drosophila larvae as a model and biochemical imaging and electrophysiology techniques, we demonstrate that Drosophila NRX (DNRX) plays critical roles in regulating synaptic terminal clustering and release of SVs. We found that DNRX controls the terminal clustering and release of SVs by stimulating presynaptic F-actin. Furthermore, our results indicate that DNRX functions through the scaffold protein Scribble and the GEF protein DPix to activate the small GTPase Ras-related C3 Botulinum toxin substrate 1 (Rac1). We observed a direct interaction between the C-terminal PDZ-binding motif of DNRX and the PDZ domains of Scribble and that Scribble bridges DNRX to DPix, forming a DNRX-Scribble-DPix complex that activates Rac1 and subsequently stimulates presynaptic F-actin assembly and SV clustering. Taken together, our work provides important insights into the function of DNRX in regulating SV clustering, which could help inform further research into pathological neurexin-mediated mechanisms in neurological disorders such as autism. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. A new quantum chemical approach to the magnetic properties of oligonuclear transition-metal complexes: application to a model for the tetranuclear manganese cluster of photosystem II.

    PubMed

    Pantazis, Dimitrios A; Orio, Maylis; Petrenko, Taras; Zein, Samir; Bill, Eckhard; Lubitz, Wolfgang; Messinger, Johannes; Neese, Frank

    2009-01-01

    The reliable correlation of structural features and magnetic or spectroscopic properties of oligonuclear transition-metal complexes is a critical requirement both for research into innovative magnetic materials and for elucidating the structure and function of many metalloenzymes. We have developed a novel method that for the first time enables the extraction of hyperfine coupling constants (HFCs) from broken-symmetry density functional theory (BS-DFT) calculations on clusters. Using the geometry-optimized tetranuclear manganese complex [Mn(4)O(6)(bpy)(6)](4+/3+) as a model, we first examine in detail the calculation of exchange coupling constants J through the BS-DFT approach. Complications arising from the indeterminacy of experimentally fitted J constants are identified and analyzed. It is found that only the energy levels derived from Hamiltonian diagonalization are a physically meaningful basis for comparing theory and experiment. Subsequently, the proposed theoretical scheme is applied to the calculation of (55)Mn HFCs of the Mn(III,IV,IV,IV) state of the complex, which is similar to the S(2) state of the oxygen-evolving complex (OEC) in photosystem II of oxygenic photosynthesis. The new approach performs reliably and accurately, and yields calculated HFCs that can be directly compared with experimental data. Finally, we carefully examine the dependence of HFC on the J value and draw attention to the sensitivity of the calculated values to the exchange coupling parameters. The proposed strategy extends naturally to hetero-oligonuclear clusters of arbitrary shape and nuclearity, and hence is of general validity and usefulness in the study of magnetic metal clusters. The successful application of the new approach presented here is a first step in the effort to establish correlations between the available spectroscopic information and the structural features of complex metalloenzymes like OEC.

  20. HIGH-RESOLUTION STUDY OF THE CLUSTER COMPLEXES IN A LENSED SPIRAL AT REDSHIFT 1.5: CONSTRAINTS ON THE BULGE FORMATION AND DISK EVOLUTION

    SciTech Connect

    Adamo, Angela; Oestlin, G.; Zackrisson, E.; Guaita, L.; Bastian, N.; Livermore, R. C.

    2013-04-01

    We analyze the clump population of the spiral galaxy Sp 1149 at redshift 1.5. Located behind the galaxy cluster MACS J1149.5+2223, Sp 1149 has been significantly magnified allowing us to study the galaxy on physical scales down to {approx}100 pc. The galaxy cluster frame is among the targets of the Cluster Lensing And Supernova survey with Hubble (CLASH), an ongoing Hubble Space Telescope (HST) Multi-Cycle Treasury program. We have used the publicly available multi-band imaging data set to reconstruct the spectral energy distributions of the clumps in Sp 1149, and derive, by means of stellar evolutionary models, their physical properties. We found that 40% of the clumps observed in Sp 1149 are older than 30 Myr and can be as old as 300 Myr. These are also the more massive (luminous) clumps in the galaxy. Among the complexes in the local reference sample, the star-forming knots in luminous blue compact galaxies could be considered progenitor analogs of these long-lived clumps. The remaining 60% of clumps have colors comparable to local cluster complexes, suggesting a similar young age. We observe that the Sp 1149 clumps follow the M{proportional_to}R {sup 2} relation similar to local cluster complexes, suggesting similar formation mechanisms although they may have different initial conditions (e.g., higher gas surface densities). We suggest that the galaxy is experiencing a slow decline in star formation rate and a likely transitional phase toward a more quiescent star formation mode. The older clumps have survived between 6 and 20 dynamical times and are all located at projected distances smaller than 4 kpc from the center. Their current location suggests migration toward the center and the possibility of being the building blocks of the bulge. On the other hand, the dynamical timescale of the younger clumps is significantly shorter, meaning that they are quite close to their birthplace. We show that the clumps of Sp 1149 may account for the expected metal

  1. High-resolution Study of the Cluster Complexes in a Lensed Spiral at Redshift 1.5: Constraints on the Bulge Formation and Disk Evolution

    NASA Astrophysics Data System (ADS)

    Adamo, Angela; Östlin, G.; Bastian, N.; Zackrisson, E.; Livermore, R. C.; Guaita, L.

    2013-04-01

    We analyze the clump population of the spiral galaxy Sp 1149 at redshift 1.5. Located behind the galaxy cluster MACS J1149.5+2223, Sp 1149 has been significantly magnified allowing us to study the galaxy on physical scales down to ~100 pc. The galaxy cluster frame is among the targets of the Cluster Lensing And Supernova survey with Hubble (CLASH), an ongoing Hubble Space Telescope (HST) Multi-Cycle Treasury program. We have used the publicly available multi-band imaging data set to reconstruct the spectral energy distributions of the clumps in Sp 1149, and derive, by means of stellar evolutionary models, their physical properties. We found that 40% of the clumps observed in Sp 1149 are older than 30 Myr and can be as old as 300 Myr. These are also the more massive (luminous) clumps in the galaxy. Among the complexes in the local reference sample, the star-forming knots in luminous blue compact galaxies could be considered progenitor analogs of these long-lived clumps. The remaining 60% of clumps have colors comparable to local cluster complexes, suggesting a similar young age. We observe that the Sp 1149 clumps follow the MvpropR 2 relation similar to local cluster complexes, suggesting similar formation mechanisms although they may have different initial conditions (e.g., higher gas surface densities). We suggest that the galaxy is experiencing a slow decline in star formation rate and a likely transitional phase toward a more quiescent star formation mode. The older clumps have survived between 6 and 20 dynamical times and are all located at projected distances smaller than 4 kpc from the center. Their current location suggests migration toward the center and the possibility of being the building blocks of the bulge. On the other hand, the dynamical timescale of the younger clumps is significantly shorter, meaning that they are quite close to their birthplace. We show that the clumps of Sp 1149 may account for the expected metal-rich globular cluster population

  2. Effect of the Keggin anions on assembly of CuI-bis(tetrazole) thioether complexes containing multinuclear CuI-cluster

    NASA Astrophysics Data System (ADS)

    Wang, Xiu-Li; Gao, Qiang; Tian, Ai-Xiang; Hu, Hai-Liang; Liu, Guo-Cheng

    2012-03-01

    In order to investigate the effect of polyoxometalate (POM) on the assembly of transition metal-bis(tetrazole) thioether complexes, three new complexes based on different Keggin anions and multinuclear CuI-cluster [CuI12(bmtr)9(HSiMo12O40)4] (1), [CuI3(bmtr)3(PM12O40)] (M=W for 2; Mo for 3) (bmtr=1,3-bis(1-methyl-5-mercapto-1,2,3,4-tetrazole)propane), have been hydrothermally synthesized and characterized by routine physical methods and single crystal X-ray diffraction. In compound 1, two kinds of nanometer-scale tetranuclear subunits linked by [SiMo12O40]4- polyanions assemble a (3, 4)-connected three-dimensional (3D) self-penetrating framework. Compounds 2 and 3 are isostructural, exhibiting a 1D chain with [PW12O40]3-/[PMo12O40]3- polyanions and trinuclear clusters arranging alternately. The distinct structural differences between these POM-based CuI-bmtr complexes of 1 and 2/3 maybe rest on the contrast of Keggin-type polyoxometalate with different central heteroatoms, which have been discussed in detail. In addition, the electrochemical properties of the title complexes have been investigated.

  3. Protons bound to the Mn cluster in photosystem II oxygen evolving complex detected by proton matrix ENDOR.

    PubMed

    Yamada, Hiroiku; Mino, Hiroyuki; Itoh, Shigeru

    2007-03-01

    Protons in the vicinity of the oxygen-evolving manganese cluster in photosystem II were studied by proton matrix ENDOR. Six pairs of proton ENDOR signals were detected in both the S(0) and S(2) states of the Mn-cluster. Two pairs of signals that show hyperfine constants of 2.3/2.2 and 4.0 MHz, respectively, disappeared after D(2)O incubation in both states. The signals with 2.3/2.2 MHz hyperfine constants in S(0) and S(2) state multiline disappeared after 3 h of D(2)O incubation in the S(0) and S(1) states, respectively. The signal with 4.0 MHz hyperfine constants in S(0) state multiline disappeared after 3 h of D(2)O incubation in the S(0) state, while the similar signal in S(2) state multiline disappeared only after 24 h of D(2)O incubation in the S(1) state. The different proton exchange rates seem to be ascribable to the change in affinities of water molecules to the variation in oxidation state of the Mn cluster during the water oxidation cycle. Based on the point dipole approximation, the distances between the center of electronic spin of the Mn cluster and the exchangeable protons were estimated to be 3.3/3.2 and 2.7 A, respectively. These short distances suggest the protons belong to the water molecules ligated to the manganese cluster. We propose a model for the binding of water to the manganese cluster based on these results.

  4. Electron Transfer and Proton-Coupled Electron Transfer Reactivity and Self-Exchange of Synthetic [2Fe–2S] Complexes: Models for Rieske and mitoNEET Clusters

    PubMed Central

    2015-01-01

    This report describes the thermochemistry, proton-coupled electron transfer (PCET) reactions and self-exchange rate constants for a set of bis-benzimidazolate-ligated [2Fe–2S] clusters. These clusters serve as a model for the chemistry of biological Rieske and mitoNEET clusters. PCET from [Fe2S2(Prbbim)(PrbbimH)]2– (4) and [Fe2S2(Prbbim)(PrbbimH2)]1– (5) to TEMPO occurs via concerted proton–electron transfer (CPET) mechanisms (PrbbimH2 = 4,4-bis-(benzimidazol-2-yl)heptane). Intermolecular electron transfer (ET) self-exchange between [Fe2S2(Prbbim)2]2– (1) and [Fe2S2(Prbbim)2]3– (2) occurs with a rate constant of (1.20 ± 0.06) × 105 M–1 s–1 at 26 °C. A similar self-exchange rate constant is found for the related [2Fe–2S] cluster [Fe2S2(SArO)2]2–/3–, SArO2– = thiosalicylate. These are roughly an order of magnitude slower than that reported for larger [4Fe–4S] clusters and 1 order of magnitude faster than that reported for N-ligated high-spin iron complexes. These results suggest that the rate of intermolecular ET to/from [Fe–S] clusters is modulated by cluster size. The measured PCET self-exchange rate constant for 1 and 4 at −30 °C is (3.8 ± 0.7) × 104 M–1 s–1. Analysis of rate constants using the Marcus cross-relation suggests that this process likely occurs via a concerted proton–electron transfer (CPET) mechanism. The implications of these findings to biological systems are also discussed, including the conclusion that histidine-ligated [2Fe–2S] clusters should not have a strong bias to undergo concerted e–/H+ transfers. PMID:24592857

  5. A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex from natural MnO2 precipitates in the early ocean

    SciTech Connect

    Sauer, Kenneth; Yachandra, Vittal K.

    2002-04-30

    The photosynthetic water oxidation complex consists of a cluster of 4 Mn atoms bridged by O atoms, associated with Ca2+ and Cl- and incorporated into protein. The structure is similar in higher plants and algae, as well as in cyanobacteria of more ancient lineage, dating back more than 2.5 Ga on Earth. It has been proposed that the proto-enzyme derived from a component of a natural early marine manganese precipitate that contained a CaMn4O9 cluster. A variety of MnO2 minerals is found in nature. Three major classes are spinels, sheet-like layered structures and 3-dimensional networks that contain parallel tunnels. These relatively open structures readily incorporate cations (Na+, Li+, Mg2+, Ca2+, Ba2+, H+ and even Mn2+) and water. The minerals have different ratios of Mn(III) and Mn(IV) octahedrally coordinated to oxygens. Using X-ray spectroscopy we compare the chemical structures of Mn in the minerals with what is known about the arrangement in the water-oxidation complex to define the parameters of a structural model for the photosynthetic catalytic site. This comparison provides for the structural model a set of candidate Mn4 clusters -- some previously proposed and considered and others entirely novel.

  6. A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex from natural MnO2 precipitates in the early ocean.

    PubMed

    Sauer, Kenneth; Yachandra, Vittal K

    2002-06-25

    The photosynthetic water oxidation complex consists of a cluster of four Mn atoms bridged by O atoms, associated with Ca2+ and Cl-, and incorporated into protein. The structure is similar in higher plants and algae, as well as in cyanobacteria of more ancient lineage, dating back more than 2.5 billion years ago on Earth. It has been proposed that the proto-enzyme derived from a component of a natural early marine manganese precipitate that contained a CaMn4O9 cluster. A variety of MnO2 minerals are found in nature. Three major classes are spinels, sheet-like layered structures, and three-dimensional networks that contain parallel tunnels. These relatively open structures readily incorporate cations (Na+, Li+, Mg2+, Ca2+, Ba2+, H+, and even Mn2+) and water. The minerals have different ratios of Mn(III) and Mn(IV) octahedrally coordinated to oxygens. Using x-ray spectroscopy we compare the chemical structures of Mn in the minerals with what is known about the arrangement in the water oxidation complex to define the parameters of a structural model for the photosynthetic catalytic site. This comparison provides for the structural model a set of candidate Mn(4) clusters-some previously proposed and considered and others entirely novel.

  7. Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

    DOE PAGES

    White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; ...

    2017-06-21

    The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies. Furthermore, themore » ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

  8. Mixed-metal chloro sulfido cluster complex of molybdenum and platinum, (Mo sub 3 Pt sub 2 S sub 4 Cl sub 4 (PEt sub 3 ) sub 6 )

    SciTech Connect

    Saito, Taro; Tsuboi, Toshio; Kajitani, Yoshimichi; Yamagata, Tsuneaki; Imoto, Hideo )

    1991-09-04

    In the authors recent publication, syntheses of mixed-metal chloro sulfido and chloro selenido complexes of molybdenum and nickel were reported. They were prepared by the reaction of (Mo{sub 3}X{sub 4}Cl{sub 4}(PEt{sub 3}){sub 3}(MeOH){sub 2}) (X = S, Se){sup 2} with Ni(cod){sub 2} (cod = 1,5-cyclooctadiene). In the present study, another excellent building block compound, Pt(cot){sub 2}, was reacted with the same trinuclear molybdenum complex, and the mixed-metal cluster complex (Mo{sub 3}Pt{sub 2}S{sub 4}Cl{sub 4}(PEt{sub 3}){sub 6}) (1) with an unexpected structure was obtained.

  9. Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

    NASA Astrophysics Data System (ADS)

    White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; Head-Gordon, Martin

    2017-06-01

    The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N2-, CO-, CO2-, and CH2O-. Analytic continuation of complex 𝜃 -trajectories is used to compute Siegert energies, and the 𝜃 -trajectories of energy differences are found to yield more consistent results than those of total energies. The ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.

  10. Extensive Variation in the O-Antigen Gene Cluster within One Salmonella enterica Serogroup Reveals an Unexpected Complex History

    PubMed Central

    Wang, Lei; Andrianopoulos, Kanella; Liu, Dan; Popoff, Michel Y.; Reeves, Peter R.

    2002-01-01

    The 46 serogroups of Salmonella enterica have different O-antigens, and each is thought to have a specific form of the O-antigen cluster. Comparison of the 145 serovars of serogroup B revealed much more intraserogroup genetic diversity than expected. The O27 factor, due to an α 1-6 linkage between O units in place of the more common α 1-2 linkage and previously thought to be due to a converting bacteriophage, is now shown to be due to a wzyα(1-6) gene located within the major gene cluster. Surprisingly a remnant of this gene in all O27− serovars shows that the ancestor was O27+. There are six distinct gene cluster forms, five apparently derived by a series of deletions and one by an insertion from an ancestral O27+ form present in 57 serovars. The history of the gene cluster and movement between subspecies I and II can be traced. Two of the derivative forms still have a functional wzyα(1-6) gene, while in three it has been inactivated by deletion or insertion. Two of the forms lacking a functional wzyα(1-6) gene have the wzyα(1-2) gene first described for strain LT2 as rfc, whereas for the third the wzy gene has not been located. PMID:11872718

  11. Complex-to-Predict Generational Shift between Nested and Clustered Organization of Individual Prey Networks in Digger Wasps

    PubMed Central

    Ballesteros, Yolanda; Polidori, Carlo; Tormos, José; Baños-Picón, Laura; Asís, Josep Daniel

    2014-01-01

    Although diet has traditionally been considered to be a property of the species or populations as a whole, there is nowadays extensive knowledge that individual specialization is widespread among animal populations. Nevertheless, the factors determining the shape of interactions within food webs remain largely undiscovered, especially in predatory insects. We used an aggregation of the digger wasp Bembix merceti to 1) analyse patterns of individual prey use across three flying seasons in a network–based context; and 2) test the effect of four potential factors that might explain network topologies (wasp mass, nest spatial distribution, simultaneous nest-provisioning, prey availability). Inter-individual diet variation was found in all three years, under different predator-prey network topologies: Individuals arranged in dietary clusters and displayed a checkerboard pattern in 2009, but showed nestedness in 2008 and 2010. Network topologies were not fully explained by the tested factors. Larger females consumed a higher proportion of the total number of prey species captured by the population as a whole, in such a way that nested patterns may arise from mass-dependent prey spectrum width. Conversely, individuals with similar body mass didn’t form clusters. Nested patterns seemed to be associated with a greater availability of the main prey species (a proxy for reduced intra-specific competition). Thus, according with theory, clusters seemed to appear when competition increased. On the other hand, the nests of the individuals belonging to a given cluster were not more closely located, and neither did individuals within a cluster provision their nests simultaneously. Thus, a female-female copying behaviour during foraging was unlikely. In conclusion, wasp populations can maintain a considerable individual variation across years under different food web organizations. The tested factors only partially accounted for the shift in network properties, and new analyses

  12. Bacillus cereus Fnr binds a [4Fe-4S] cluster and forms a ternary complex with ResD and PlcR

    PubMed Central

    2012-01-01

    Background Bacillus cereus is a facultative anaerobe that causes diarrheal disease in humans. Diarrheal syndrome may result from the secretion of various virulence factors including hemolysin BL and nonhemolytic enterotoxin Nhe. Expression of genes encoding Hbl and Nhe is regulated by the two redox systems, ResDE and Fnr, and the virulence regulator PlcR. B. cereus Fnr is a member of the Crp/Fnr family of iron-sulfur (Fe-S) proteins. Only its apo-form has so far been studied. A major goal in deciphering the Fnr-dependent regulation of enterotoxin genes is thus to obtain and characterize holoFnr. Results Fnr has been subjected to in vitro Fe-S cluster reconstitution under anoxic conditions. UV-visible and EPR spectroscopic analyses together with the chemical estimation of the iron content indicated that Fnr binds one [4Fe-4S]2+ cluster per monomer. Atmospheric O2 causes disassembly of the Fe-S cluster, which exhibited a half-life of 15 min in air. Holo- and apoFnr have similar affinities for the nhe and hbl promoter regions, while holoFnr has a higher affinity for fnr promoter region than apoFnr. Both the apo- and holo-form of Fnr interact with ResD and PlcR to form a ternary complex. Conclusions Overall, this work shows that incorporation of the [4Fe-4S]2+ cluster is not required for DNA binding of Fnr to promoter regions of hbl and nhe enterotoxin genes or for the formation of a ternary complex with ResD and PlcR. This points to some new unusual properties of Fnr that may have physiological relevance in the redox regulation of enterotoxin gene regulation. PMID:22731107

  13. Malfunctioning of the Iron–Sulfur Cluster Assembly Machinery in Saccharomyces cerevisiae Produces Oxidative Stress via an Iron-Dependent Mechanism, Causing Dysfunction in Respiratory Complexes

    PubMed Central

    Gomez, Mauricio; Pérez-Gallardo, Rocío V.; Sánchez, Luis A.; Díaz-Pérez, Alma L.; Cortés-Rojo, Christian; Meza Carmen, Victor; Saavedra-Molina, Alfredo; Lara-Romero, Javier; Jiménez-Sandoval, Sergio; Rodríguez, Francisco; Rodríguez-Zavala, José S.; Campos-García, Jesús

    2014-01-01

    Biogenesis and recycling of iron–sulfur (Fe–S) clusters play important roles in the iron homeostasis mechanisms involved in mitochondrial function. In Saccharomyces cerevisiae, the Fe–S clusters are assembled into apoproteins by the iron–sulfur cluster machinery (ISC). The aim of the present study was to determine the effects of ISC gene deletion and consequent iron release under oxidative stress conditions on mitochondrial functionality in S. cerevisiae. Reactive oxygen species (ROS) generation, caused by H2O2, menadione, or ethanol, was associated with a loss of iron homeostasis and exacerbated by ISC system dysfunction. ISC mutants showed increased free Fe2+ content, exacerbated by ROS-inducers, causing an increase in ROS, which was decreased by the addition of an iron chelator. Our study suggests that the increment in free Fe2+ associated with ROS generation may have originated from mitochondria, probably Fe–S cluster proteins, under both normal and oxidative stress conditions, suggesting that Fe–S cluster anabolism is affected. Raman spectroscopy analysis and immunoblotting indicated that in mitochondria from SSQ1 and ISA1 mutants, the content of [Fe–S] centers was decreased, as was formation of Rieske protein-dependent supercomplex III2IV2, but this was not observed in the iron-deficient ATX1 and MRS4 mutants. In addition, the activity of complexes II and IV from the electron transport chain (ETC) was impaired or totally abolished in SSQ1 and ISA1 mutants. These results confirm that the ISC system plays important roles in iron homeostasis, ROS stress, and in assembly of supercomplexes III2IV2 and III2IV1, thus affecting the functionality of the respiratory chain. PMID:25356756

  14. Size evolution relativistic DFT-QTAIM study on the gold cluster complexes Au4-S-CnH2n-S‧-Au4‧ (n = 2-5)

    NASA Astrophysics Data System (ADS)

    Rodríguez, Juan I.; Uribe, Emilbus A.; Baltazar-Méndez, María I.; Autschbach, Jochen; Castillo-Alvarado, F. L.; Gutiérrez-González, Israel

    2016-09-01

    We introduce relativistic density functional theory (DFT) calculations on the gold cluster complexes (cluster-molecule-cluster) Au4-S-CnH2n-S‧-Au4‧ (n = 2-5). The structural, electronic and relativistic (ZORA) Bader's quantum theory of atoms in molecules (QTAIM) properties of the two lowest-energy complex isomers were computed as a function of the alkanedithiol size (n). The lowest-energy isomer is a triplet spin state independently of the complex size. According to QTAIM, the Au-Au and S-Au bonds are classified as closed shell (non-covalent) type. The HOMO-LUMO gap of the cluster complexes shows a zigzag behavior typical of gold nanoclusters with respect to the size of the alkanedithiol chain (n).

  15. 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

  16. 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

  17. Comprehensive study of hexarhenium cluster complex Na4[{Re6Te8}(CN)6] - In terms of a new promising luminescent and X-ray contrast agent.

    PubMed

    Krasilnikova, Anna A; Solovieva, Anastasiya O; Ivanov, Anton A; Trifonova, Kristina E; Pozmogova, Tatiana N; Tsygankova, Alphiya R; Smolentsev, Anton I; Kretov, Evgeniy I; Sergeevichev, David S; Shestopalov, Michael A; Mironov, Yuri V; Shestopalov, Alexander M; Poveshchenko, Alexander F; Shestopalova, Lidiya V

    2017-02-01

    Octahedral rhenium cluster complexes may have considerable potential as therapeutic and diagnostic drugs due to their luminescent and X-ray contrast properties, as well as their ability to generate singlet oxygen upon photoirradiation. However, their potential biological effects and toxicity in vitro and in vivo are rather far from being understood. Thus, the aim of our research was to study cytotoxicity, intracellular localization and cellular uptake/elimination kinetics in vitro, biodistribution and acute intravenous toxicity in vivo of a complex Na4[{Re6Te8}(CN)6] as the promising compound for biomedical application. The results have demonstrated that the complex penetrates through cell membranes with the maximum accumulation in cells in 24h of incubation and have low toxic effects in vitro and in vivo. The median lethal dose (LD50) of intravenously administrated Na4[{Re6Te8}(CN)6] is equal to 1082±83mg/kg. These findings will be useful for future development of cluster-based agents for different biomedical applications. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Cu(II)-azide polynuclear complexes of Cu4 building clusters with Schiff-base co-ligands: synthesis, structures, magnetic behavior and DFT studies.

    PubMed

    Mukherjee, Sandip; Mukherjee, Partha Sarathi

    2013-03-21

    Three new copper-azido complexes [Cu(4)(N(3))(8)(L(1))(2)](n) (1), [Cu(4)(N(3))(6)(L(2))(2)(H(2)O)(2)] (2), and [Cu(4)(N(3))(6)(L(3))(2)](n) (3) [L(1) is the imine resulting from the condensation of pyridine-2-carboxaldehyde with N-methylethylenediamine, HL(2) and HL(3) are the condensation products of 2-hydroxy-3-methoxybenzaldehyde with N,N-diethylethylenediamine and N-ethylethylenediamine respectively] have been synthesized by using 0.5 molar equivalents of the Schiff base ligands with Cu(NO(3))(2)·3H(2)O and an excess of NaN(3). Single crystal X-ray structures show that the basic unit of these complexes contains very similar Cu(II)(4) building blocks. While 1 and 3 have overall 1D structures, 2 forms discrete tetranuclear clusters due to blocking of two coordination sites on the tetranuclear cluster by water molecules. Magnetic susceptibility measurements over a wide range of temperatures exhibit the presence of both antiferromagnetic and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional and two different basis sets) have been performed on the complexes 1-3 to provide a qualitative theoretical interpretation of their overall magnetic behavior.

  19. Hydrido-ruthenium cluster complexes as models for reactive surface hydrogen species of ruthenium nanoparticles. Solid-state 2H NMR and quantum chemical calculations.

    PubMed

    Gutmann, Torsten; Walaszek, Bernadeta; Yeping, Xu; Wächtler, Maria; del Rosal, Iker; Grünberg, Anna; Poteau, Romuald; Axet, Rosa; Lavigne, Guy; Chaudret, Bruno; Limbach, Hans-Heinrich; Buntkowsky, Gerd

    2010-08-25

    The (2)H quadrupolar interaction is a sensitive tool for the characterization of deuterium-metal binding states. In the present study, experimental solid-state (2)H MAS NMR techniques are used in the investigations of two ruthenium clusters, D(4)Ru(4)(CO)(12) (1) and D(2)Ru(6)(CO)(18) (2), which serve as model compounds for typical two-fold, three-fold, and octahedral coordination sites on metal surfaces. By line-shape analysis of the (2)H MAS NMR measurements of sample 1, a quadrupolar coupling constant of 67 +/- 1 kHz, an asymmetry parameter of 0.67 +/- 0.1, and an isotropic chemical shift of -17.4 ppm are obtained. In addition to the neutral complex, sample 2 includes two ionic clusters, identified as anionic [DRu(6)(CO)(18)](-) (2(-)) and cationic [D(3)Ru(6)(CO)(18)](+) (2(+)). By virtue of the very weak quadrupolar interaction (<2 kHz) and the strong low-field shift (+16.8 ppm) of 2(-), it is shown that the deuteron is located in the symmetry center of the octahedron spanned by the six ruthenium atoms. For the cationic 2(+), the quadrupolar interaction is similar to that of the neutral 2. Quantum chemical DFT calculations at different model structures for these ruthenium clusters were arranged in order to help in the interpretation of the experimental results. It is shown that the (2)H nuclear quadrupolar interaction is a sensitive tool for distinguishing the binding state of the deuterons to the transition metal. Combining the data from the polynuclear complexes with the data from mononuclear complexes, a molecular ruler for quadrupolar interactions is created. This ruler now permits the solid-state NMR spectroscopic characterization of deuterium adsorbed on the surfaces of catalytically active metal nanoparticles.

  20. Ortho-para interconversion in cation-water complexes: The case of V+(H2O) and Nb+(H2O) clusters

    NASA Astrophysics Data System (ADS)

    Ward, T. B.; Miliordos, E.; Carnegie, P. D.; Xantheas, S. S.; Duncan, M. A.

    2017-06-01

    Vanadium and niobium cation-water complexes, V+(H2O) and Nb+(H2O), are produced by laser vaporization in a pulsed supersonic expansion, mass selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy using rare gas atom (Ar, Ne) complex predissociation. The vibrational bands measured in the O-H stretching region contain K-type rotational sub-band structure, which provides insight into the structures of these complexes. However, rotational sub-bands do not exhibit the simple patterns seen previously for other metal ion-water complexes. The A rotational constants are smaller than expected and the normal 3:1 intensity ratios for K = odd:even levels for independent ortho:para nuclear spin states are missing for some complexes. We relied on highly correlated internally contracted multi-reference configuration interaction and Coupled Cluster [CCSD(T)] electronic structure calculations of those complexes with and without the rare gas atoms to investigate these anomalies. Rare gas atoms were found to bind via asymmetric motifs to the hydrated complexes undergoing large amplitude motions that vibrationally average to the quasi-C2v symmetry with a significant probability off the C2 axis, thus explaining the reduced A values. Both vanadium and niobium cations exhibit unusually strong nuclear spin coupling to the hydrogen atoms of water, the values of which vary with their electronic state. This catalyzes ortho-para interconversion in some complexes and explains the rotational patterns. The rate of ortho-para relaxation in the equilibrated complexes must therefore be greater than the collisional cooling rate in the supersonic expansion (about 106 s-1).

  1. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  2. A Chandra Study of the Rosette Star-Forming Complex. II. Clusters in the Rosette Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Wang, Junfeng; Feigelson, Eric D.; Townsley, Leisa K.; Román-Zúñiga, Carlos G.; Lada, Elizabeth; Garmire, Gordon

    2009-05-01

    We explore here the young stellar populations in the Rosette Molecular Cloud (RMC) region with high spatial resolution X-ray images from the Chandra X-ray Observatory, which are effective in locating weak-lined T Tauri stars as well as disk-bearing young stars. A total of 395 X-ray point sources are detected, 299 of which (76%) have an optical or near-infrared (NIR) counterpart identified from deep FLAMINGOS images. From X-ray and mass sensitivity limits, we infer a total population of ~1700 young stars in the survey region. Based on smoothed stellar surface density maps, we investigate the spatial distribution of the X-ray sources and define three distinctive structures and substructures within them. Structures B and C are associated with previously known embedded IR clusters, while structure A is a new X-ray-identified unobscured cluster. A high-mass protostar RMCX #89 = IRAS 06306+0437 and its associated sparse cluster are studied. The different subregions are not coeval but do not show a simple spatial-age pattern. Disk fractions vary between subregions and are generally lsim20% of the total stellar population inferred from the X-ray survey. The data are consistent with speculations that triggered star formation around the H II region is present in the RMC, but do not support a simple sequential triggering process through the cloud interior. While a significant fraction of young stars are located in a distributed population throughout the RMC region, it is not clear if they originated in clustered environments.

  3. A CHANDRA STUDY OF THE ROSETTE STAR-FORMING COMPLEX. II. CLUSTERS IN THE ROSETTE MOLECULAR CLOUD

    SciTech Connect

    Wang Junfeng; Feigelson, Eric D.; Townsley, Leisa K.; Garmire, Gordon; Roman-Zuniga, Carlos G.; Lada, Elizabeth E-mail: edf@astro.psu.edu

    2009-05-01

    We explore here the young stellar populations in the Rosette Molecular Cloud (RMC) region with high spatial resolution X-ray images from the Chandra X-ray Observatory, which are effective in locating weak-lined T Tauri stars as well as disk-bearing young stars. A total of 395 X-ray point sources are detected, 299 of which (76%) have an optical or near-infrared (NIR) counterpart identified from deep FLAMINGOS images. From X-ray and mass sensitivity limits, we infer a total population of {approx}1700 young stars in the survey region. Based on smoothed stellar surface density maps, we investigate the spatial distribution of the X-ray sources and define three distinctive structures and substructures within them. Structures B and C are associated with previously known embedded IR clusters, while structure A is a new X-ray-identified unobscured cluster. A high-mass protostar RMCX no. 89 = IRAS 06306+0437 and its associated sparse cluster are studied. The different subregions are not coeval but do not show a simple spatial-age pattern. Disk fractions vary between subregions and are generally {approx}<20% of the total stellar population inferred from the X-ray survey. The data are consistent with speculations that triggered star formation around the H II region is present in the RMC, but do not support a simple sequential triggering process through the cloud interior. While a significant fraction of young stars are located in a distributed population throughout the RMC region, it is not clear if they originated in clustered environments.

  4. Crystal Structure of Human Arginase l Complexed with Thiosemicarbazide Reveals an Unusual Thiocarbonly u-Sulfide Ligand in the Binuclear Manganese Cluster

    SciTech Connect

    Di Costanzo,L.; Pique, M.; Christianson, D.

    2007-01-01

    The crystal structure of the human arginase I-thiosemicarbazide complex reveals an unusual thiocarbonyl {mu}-sulfide ligand in the binuclear manganese cluster. The CS moiety of thiosemicarbazide bridges Mn2+A and Mn2+B with coordination distances of 2.6 and 2.4 Angstroms, respectively. Otherwise, the binding of thiosemicarbazide to human arginase I does not cause any significant structural changes in the active site. The crystal structure of the unliganded enzyme reveals a hydrogen-bonded water molecule that could support proton transfer between a {mu}-water molecule and H141 to regenerate the nucleophilic {mu}-hydroxide ion in the final step of catalysis.

  5. Cellular internalization and morphological analysis after intravenous injection of a highly hydrophilic octahedral rhenium cluster complex - a new promising X-ray contrast agent.

    PubMed

    Krasilnikova, Anna A; Solovieva, Anastasiya O; Trifonova, Kristina E; Brylev, Konstantin A; Ivanov, Anton A; Kim, Sung-Jin; Shestopalov, Michael A; Fufaeva, Maria S; Shestopalov, Alexander M; Mironov, Yuri V; Poveshchenko, Alexander F; Shestopalova, Lidia V

    2016-11-01

    The octahedral cluster compound Na2 H8 [{Re6 Se8 }(P(C2 H4 CONH2 )(C2 H4 COO)2 )6 ] has been shown to be highly radio dense, thus becoming a promising X-ray contrast agent. It was also shown that this compound had low cytotoxic effect in vitro, low acute toxicity in vivo and was eliminated rapidly from the body through the urinary tract. The present contribution describes a more detailed cellular internalization assay and morphological analysis after intravenous injection of this hexarhenium cluster compound at different doses. The median lethal dose (LD50 ) of intravenously administrated compound was calculated (4.67 ± 0.69 g/kg). Results of the study clearly indicated that the cluster complex Hn [{Re6 Se8 }(P(C2 H4 CONH2 )(C2 H4 COO)2 )6 ](n-10) was not internalized into cells in vitro and induced only moderate morphological alterations of kidneys at high doses without any changes in morphology of liver, spleen, duodenum, or heart of mice. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Bismuth(III) complexes derived from α-amino acids: the impact of hydrolysis and oxido-cluster formation on their activity against Helicobacter pylori.

    PubMed

    Busse, Madleen; Border, Emily; Junk, Peter C; Ferrero, Richard L; Andrews, Philip C

    2014-12-28

    Eight bismuth(III) complexes derived from a variety of α-amino acids covering a range of physico-chemical properties (L-phenylalanine (Phe), L-proline (Pro), L-methionine (Met), L-cysteine (Cys), D,L-serine (Ser), L-tyrosine (Tyr), l-aspartic acid (Asp) and L-glutamic acid (Glu)) have been synthesised, characterised, and evaluated for their activity against Helicobacter pylori. The optimal synthetic procedure utilises [Bi(O(t)Bu)3], giving the complexes [BiL3] (L = Phe 1, Pro 2, Met 3, Ser 5, Tyr 6) and [Bi2L3] (L = Cys 4, Asp 7, Glu 8) cleanly and in good yield. However, the synthesis is sensitive to both temperature and moisture. The solubility and stability of the bismuth(III) complexes was investigated using ESI-MS. Almost all compounds (except for [Bi(Phe)3] and [Bi(Pro)3]) were found to be partially or completely soluble in aqueous solution giving a pH 2.5-5.0, indicating the presence of free α-amino acid and hydrolysis of the bismuth(III) complexes to polynuclear bismuth oxido-clusters. The results of the bactericidal studies against Helicobacter pylori demonstrate that this hydrolysis process impacts significantly on the observed Minimum Inhibitory Concentration (MICs) which are increased substantially, often by many orders of magnitude, when the complexes are initially prepared in water rather than DMSO.

  7. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states.

    PubMed

    Godtliebsen, Ian H; Christiansen, Ove

    2015-10-07

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  8. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states

    NASA Astrophysics Data System (ADS)

    Godtliebsen, Ian H.; Christiansen, Ove

    2015-10-01

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  9. Effect of the Keggin anions on assembly of Cu{sup I}-bis(tetrazole) thioether complexes containing multinuclear Cu{sup I}-cluster

    SciTech Connect

    Wang Xiuli; Gao Qiang; Tian Aixiang; Hu Hailiang; Liu Guocheng

    2012-03-15

    In order to investigate the effect of polyoxometalate (POM) on the assembly of transition metal-bis(tetrazole) thioether complexes, three new complexes based on different Keggin anions and multinuclear Cu{sup I}-cluster [Cu{sup I}{sub 12}(bmtr){sub 9}(HSiMo{sub 12}O{sub 40}){sub 4}] (1), [Cu{sup I}{sub 3}(bmtr){sub 3}(PM{sub 12}O{sub 40})] (M=W for 2; Mo for 3) (bmtr=1,3-bis(1-methyl-5-mercapto-1,2,3,4-tetrazole)propane), have been hydrothermally synthesized and characterized by routine physical methods and single crystal X-ray diffraction. In compound 1, two kinds of nanometer-scale tetranuclear subunits linked by [SiMo{sub 12}O{sub 40}]{sup 4-} polyanions assemble a (3, 4)-connected three-dimensional (3D) self-penetrating framework. Compounds 2 and 3 are isostructural, exhibiting a 1D chain with [PW{sub 12}O{sub 40}]{sup 3-}/[PMo{sub 12}O{sub 40}]{sup 3-} polyanions and trinuclear clusters arranging alternately. The distinct structural differences between these POM-based Cu{sup I}-bmtr complexes of 1 and 2/3 maybe rest on the contrast of Keggin-type polyoxometalate with different central heteroatoms, which have been discussed in detail. In addition, the electrochemical properties of the title complexes have been investigated. - Graphical abstract: Three new complexes based on different Keggin anions and multinuclear Cu{sup I}-cluster have been synthesized under hydrothermal conditions. The Keggin polyanions with different central heteroatoms play a key role. Highlights: Black-Right-Pointing-Pointer The flexible bis(tetrazole)-based thioether ligand with some advantages have been used. Black-Right-Pointing-Pointer The effect of Keggin anions with different central heteroatoms has been discussed in detail. Black-Right-Pointing-Pointer The electrochemical behaviors and electrocatalysis property have been investigated.

  10. Energy transfer efficiency based on one-and two-photon FRET microscopy differentiates between clustered and random distribution of membrane-bound receptor-ligand complexes

    NASA Astrophysics Data System (ADS)

    Wallrabe, Horst; Elangovan, Masilamani; Burchard, Almut; Barroso, Margarida

    2002-06-01

    We are investigating membrane-based sorting processes in polarized epithelial MDCK cells, which most likely involves membrane microdomains. We have postulated that proteins contained in these microdomains, cluster, and to prove this, we have internalized differently fluorophore labeled pIgA-R ligands in MDCK cells, stably transfected with polymeric IgA receptors (pIgA-R), from opposite plasma membranes. Our previous work showed that these receptor-ligand complexes colocalize in the apical recycling endosome (ARE), underneath the apical plasma membrane. Quantitative one-photon confocal and 2-photon (2-P) FRET microscopy allowed us to calculate energy transfer efficiency (E%). Unquenched donor levels where established based on a novel algorithm, which corrects the FRET contamination of acceptor bleed-through and donor crosstalk. Using different emission filters also confirmed the veracity of the algorithm. 2-P FRET allows the selection of a specific donor wavelength, which does not precipitate acceptor bleed-through, a clear advantage over 1-P confocal microscopy. Results show that E% is independent of acceptor levels, an indication of a clustered distribution, as in random distribution E% rises with increasing acceptor levels. However, E% decreases with increasing donor and donor:acceptor ratio levels, which we have termed 'donor geometric exclusion', where some donors in a cluster block others from interacting with an acceptor. We submit that this is a second indicator for a clustered pattern, because in a random, dispersed situation donors are not likely to be in close proximity to have such an effect. We have developed a model explaining this phenomenon.

  11. Calculation of Heats of Formation for Zn Complexes: Comparison of Density Functional Theory, Second Order Perturbation Theory, Coupled-Cluster and Complete Active Space Methods

    PubMed Central

    Weaver, Michael N.; Ma, Dongxia; Kim, Hyun Jung

    2013-01-01

    Heats of formation were predicted for nine ZnX complexes (X= Zn, H, O, F2, S, Cl, Cl2, CH3, (CH3)2) using fourteen density functionals, MP2 calculations and the CCSD and CCSD(T) coupled-cluster methods. Calculations utilized the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Heats of formation were most accurately predicted by the TPSSTPSS and TPSSKCIS density functionals, and the BLYP, B3LYP, MP2, CCSD and CCSD(T) levels were among the poorest performing methods based on accuracy. A wide range of Zn2 equilibrium bond distances were predicted, indicating that many of the studied levels of theory may be unable to adequately describe this transition metal dimer. To further benchmark the accuracy of the density functional methods, high-level CASSCF and CASPT2 calculations were performed to estimate bond dissociation energies, equilibrium bond lengths and heats of formation for the diatomic Zn complexes and the latter two quantities were compared with the results of DFT, MP2 and coupled-cluster calculations as well as experimental values. PMID:24409106

  12. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

    PubMed

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

    2011-06-17

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

  13. Complexation of the vulcanization accelerator tetramethylthiuram disulfide and related molecules with zinc compounds including zinc oxide clusters (Zn4O4).

    PubMed

    Steudel, Ralf; Steudel, Yana; Wong, Ming Wah

    2008-01-01

    Zinc chemicals are used as activators in the vulcanization of organic polymers with sulfur to produce elastic rubbers. In this work, the reactions of Zn(2+), ZnMe(2), Zn(OMe)(2), Zn(OOCMe)(2), and the heterocubane cluster Zn(4)O(4) with the vulcanization accelerator tetramethylthiuram disulfide (TMTD) and with the related radicals and anions Me(2)NCS(2)(*), Me(2)NCS(3)(*), Me(2)NCS(2)(-), and Me(2)NCS(3)(-) have been studied by quantum chemical methods at the MP2/6-31+G(2df,p)//B3LYP/6-31+G* level of theory. More than 35 zinc complexes have been structurally characterized and the energies of formation from their components calculated for the first time. The binding energy of TMTD as a bidendate ligand increases in the order ZnMe(2)complexes with the radicals Me(2)NCS(2)(*) and Me(2)NCS(3)(*). Dissociation of the TMTD molecule at the S-S bond on reaction with the Zn(4)O(4) cluster is predicted to be strongly exothermic, in sharp contrast to the endothermic S-S bond dissociation of the free molecule. The same holds for tetramethylthiuram trisulfide (TMTT). Surprisingly, the resulting complexes contain Zn-S as well as S-O bonds. The Zn(4)O(4) nanocluster serves here as a model for bulk zinc oxide used as an activator in rubber vulcanization by sulfur. The further uptake of sulfur atoms by the various complexes from S(8) or TMTD with formation of species derived from the radical Me(2)NCS(3)(*) or the trithiocarbamate anion Me(2)NCS(3)(-) is endothermic for mono- and dinuclear zinc dithiocarbamate (dtc) complexes such as [Zn(dtc)(2)] and [Zn(2)(dtc)(4)], but exothermic in the case of polynuclear zinc oxide species containing bridging ligands as in [Zn(4)O(4)(mu-S(2)CNMe(2))] and [Zn(4)O(4)(mu-dtc)]. Therefore, zinc oxide as a polynuclear species is predicted to promote the formation of trisulfido complexes, which are generally assumed to serve as catalysts for the transfer of

  14. Edge-bridging and face-capping coordination of alkenyl ligands in triruthenium carbonyl cluster complexes derived from hydrazines: synthetic, structural, theoretical, and kinetic studies.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; Fernández-Colinas, José M; García-Granda, Santiago; Martínez-Méndez, Lorena; Pérez-Carreño, Enrique

    2004-12-03

    The reactions of the triruthenium cluster complex [Ru3(mu-H)(mu3-eta2-HNNMe2)(CO)9] (1; H2NNMe2=1,1-dimethylhydrazine) with alkynes (PhC triple bond CPh, HC triple bond CH, MeO2CC triple bond CCO2Me, PhC triple bond CH, MeO2CC triple bond CH, HOMe2CC triple bond CH, 2-pyC triple bond CH) give trinuclear complexes containing edge-bridging and/or face-capping alkenyl ligands. Whereas the edge-bridged products are closed triangular species (three Ru-Ru bonds), the face-capped products are open derivatives (two Ru-Ru bonds). For terminal alkynes, products containing gem (RCCH2) and/or trans (RHCCH) alkenyl ligands have been identified in both edge-bridging and face-capping positions, except for the complex [Ru3(mu3-eta2-HNNMe2)(mu3-eta3-HCCH-2-py)(mu-CO)(CO)7], which has the two alkenyl H atoms in a cis arrangement. Under comparable reaction conditions (1:1 molar ratio, THF at reflux, time required for the consumption of complex 1), some reactions give a single product, but most give mixtures of isomers (not all the possible ones), which were separated. To determine the effect of the hydrazido ligand, the reactions of [Ru3(mu-H)(mu3-eta2-MeNNHMe)(CO)9] (2; HMeNNHMe=1,2-dimethylhydrazine) with PhC triple bond CPh, PhC triple bond CH, and HC triple bond CH were also studied. For edge-bridged alkenyl complexes, the Ru--Ru edge that is spanned by the alkenyl ligand depends on the position of the methyl groups on the hydrazido ligand. For face-capped alkenyl complexes, the relative orientation of the hydrazido and alkenyl ligands also depends on the position of the methyl groups on the hydrazido ligand. A kinetic analysis of the reaction of 1 with PhC[triple chemical bond]CPh revealed that the reaction follows an associative mechanism, which implies that incorporation of the alkyne in the cluster is rate-limiting and precedes the release of a CO ligand. X-ray diffraction, IR and NMR spectroscopy, and calculations of minimum-energy structures by DFT methods were used to

  15. Raman study of in vivo synthesized Zn(II)-metallothionein complexes: structural insight into metal clusters and protein folding.

    PubMed

    Torreggiani, Armida; Domènech, Jordi; Atrian, Sílvia; Capdevila, Mercè; Tinti, Anna

    2008-12-01

    Metallothioneins (MTs) are metal-chelating peptides that play an active role in zinc homeostasis. The participation of metal ligands other than cysteines and the presence of secondary structure elements in metal-MT complexes are fairly unknown, especially in nonvertebrate MTs. Here, four Zn(II) complexes of invertebrate MTs (mollusc, insect, nematode, and echinoderm) and the Zn(II)-MT complex of the mammalian MT1 isoform, heterologously synthesized in E. coli, were studied by analytic and spectroscopic techniques. By Raman and circular dichroism spectroscopy, new structural informations were obtained. The five analyzed MT isoforms consist largely of beta-turns with the near exclusion of alpha-helical segments. Raman spectroscopy was revealed as an useful tool, providing information about the state of the cysteine sulfur atoms (metal coordinated and oxidized), the participation of histidine in metal coordination, and the molecular environment of tyrosine residues. In all the five Zn(II)-MT studied samples, acid-labile sulfide anions were found as nonproteic ligands, since sulfide-containing and sulfide-devoid species coexisted in the corresponding preparations. Significantly, Raman bands useful as markers of sulfide bridging ligands were identified. Overall, this work illustrates how the combination of analytical and spectroscopic techniques can be a very informative approach for the analysis of in vivo-synthesized metal-MT complexes, providing new data on the metal binding behavior of MTs from the most diverse organisms.

  16. Characterizing the intrinsic stability of gas-phase clusters of transition metal complex dianions with alkali metal counterions: counterion perturbation of multiply charged anions.

    PubMed

    Burke, Ruth M; Boxford, William E; Dessent, Caroline E H

    2007-02-14

    The authors report the gas-phase generation and characterization of a series of cation-dianion clusters, e.g., M(+).PtCl(6) (2-), M(+).PtCl(4) (2-), M(+).Pt(CN)(6) (2-), and M(+).Pd(CN)(4) (2-), where M(+)=Na(+),K(+),Rb(+), as model systems for investigating gas-phase contact ionpairs. Low-energy collisional excitation of these systems isolated within a quadrupole ion trap reveals that the fragmentation products are determined by the dianion and are independent of the counterion. This indicates that cation-dianion clusters represent gaseous ion-pair complexes, in line with recent findings for K(+).Pt(CN)(n) (2-), n=4,6 [Burke et al., J. Chem. Phys. 125, 021105 (2006)]. The relative fragmentation energies of several cation-dianion systems are obtained as a function of the counterion to explore the nature of ion-pair binding. For most of the systems studied, e.g., M(+).PtCl(6) (2-), the fragmentation energy increases as the cation size decreases, in line with a simple electrostatic description of the cation-dianion binding. However, the M(+).Pt(CN)(4) (2-) clusters displayed the reverse trend with the fragmentation energy increasing as the cation size increases. Density functional theory calculations of the cation-dianion fragmentation potential energy surfaces reveal the existence of a novel double-minima surface, separated by a repulsive Coulomb barrierlike feature at short range. The experimentally observed trends in the fragmentation energies can be fully understood with reference to the computed surfaces, hence providing strong support for the existence of the double-minima surface.

  17. σ-Aromatic cyclic M3(+) (M = Cu, Ag, Au) clusters and their complexation with dimethyl imidazol-2-ylidene, pyridine, isoxazole, furan, noble gases and carbon monoxide.

    PubMed

    Pan, Sudip; Saha, Ranajit; Mandal, Subhajit; Chattaraj, Pratim K

    2016-04-28

    The σ-aromaticity of M3(+) (M = Cu, Ag, Au) is analyzed and compared with that of Li3(+) and a prototype σ-aromatic system, H3(+). Ligands (L) like dimethyl imidazol-2-ylidene, pyridine, isoxazole and furan are employed to stabilize these monocationic M3(+) clusters. They all bind M3(+) with favorable interaction energy. Dimethyl imidazol-2-ylidene forms the strongest bond with M3(+) followed by pyridine, isoxazole and furan. Electrostatic contribution is considerably more than that of orbital contribution in these M-L bonds. The orbital interaction arises from both L → M σ donation and L ← M back donation. M3(+) clusters also bind noble gas atoms and carbon monoxide effectively. In general, among the studied systems Au3(+) binds a given L most strongly followed by Cu3(+) and Ag3(+). Computation of the nucleus-independent chemical shift (NICS) and its different extensions like the NICS-rate and NICS in-plane component vs. NICS out-of-plane component shows that the σ-aromaticity in L bound M3(+) increases compared to that of bare clusters. The aromaticity in pyridine, isoxazole and furan bound Au3(+) complexes is quite comparable with that in the recently synthesized Zn3(C5(CH3)5)3(+). The energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital also increases upon binding with L. The blue-shift and red-shift in the C-O stretching frequency of M3(CO)3(+) and M3(OC)3(+), respectively, are analyzed through reverse polarization of the σ- and π-orbitals of CO as well as the relative amount of OC → M σ donation and M → CO π back donation. The electron density analysis is also performed to gain further insight into the nature of interaction.

  18. Kinetics of excited states of pigment clusters in solubilized light-harvesting complex II: photon density-dependent fluorescence yield and transmittance.

    PubMed Central

    Schödel, R; Hillmann, F; Schrötter, T; Voigt, J; Irrgang, K D; Renger, G

    1996-01-01

    Relative fluorescence yield, phi F, and transmittance, T, were measured in solubilized light-harvesting complex II (LHCII) as a function of photon density, Ip, of monochromatic 645-nm laser pulses (duration: approximately 2.5 ns). Special efforts were made in constructing an optical set-up that allows the accurate determination of the fluorescence from an area of constant Ip, phi F(Ip) starts to decline at approximately 10(14) and drops to values below 0.01% at maximum Ip (approximately 10(19) photons cm-2 pulse-1). T(Ip) decreases only slightly at photon densities of approximately 10(15) but increases steeply at values of > 10(17) photons cm-2 pulse-1. The interpretation of the phi F(Ip) data using the saturation limit of Mauzerall's multiple hit model leads to a unit size of about 10-15 chlorophyll molecules. One interpretation is to attribute this result to a very fast exciton-exciton annihilation of multiple excited states generated within this small domain. Alternatively, based on the assumption that delocalized cluster states within the monomeric/trimeric subunit of LHCII exist, the results can be consistently described by a kinetic model comprising ground, monoexcitonic, and biexcitonic states of clusters and a triplet state that is quenched by carotenoids in LHCII. Within the framework of this model the annihilation of multiple excitations is explained as ultrafast radiationless relaxation of higher excited cluster states. Comparative measurements in diluted acetonic Chl a solution are consistently described by the depletion of the ground state, taking the absorption cross section at the used wavelength. Images FIGURE 1 PMID:8968606

  19. Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: theory, implementation, and examples.

    PubMed

    Bravaya, Ksenia B; Zuev, Dmitry; Epifanovsky, Evgeny; Krylov, Anna I

    2013-03-28

    Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e., excited states that are metastable with respect to electron ejection. The method is applied to Feshbach resonances in atomic systems (He, H(-), and Be). The dependence of the results on one-electron basis set is quantified and analyzed. Energy decomposition and wave function analysis reveal that the origin of the dependence is in electron correlation, which is essential for the lifetime of Feshbach resonances. It is found that one-electron basis should be sufficiently flexible to describe radial and angular electron correlation in a balanced fashion and at different values of the scaling parameter, θ. Standard basis sets that are optimized for not-complex-scaled calculations (θ = 0) are not sufficiently flexible to describe the θ-dependence of the wave functions even when heavily augmented by additional sets.

  20. Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: Theory, implementation, and examples

    SciTech Connect

    Bravaya, Ksenia B.; Zuev, Dmitry; Epifanovsky, Evgeny; Krylov, Anna I.

    2013-03-28

    Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e., excited states that are metastable with respect to electron ejection. The method is applied to Feshbach resonances in atomic systems (He, H{sup -}, and Be). The dependence of the results on one-electron basis set is quantified and analyzed. Energy decomposition and wave function analysis reveal that the origin of the dependence is in electron correlation, which is essential for the lifetime of Feshbach resonances. It is found that one-electron basis should be sufficiently flexible to describe radial and angular electron correlation in a balanced fashion and at different values of the scaling parameter, {theta}. Standard basis sets that are optimized for not-complex-scaled calculations ({theta} = 0) are not sufficiently flexible to describe the {theta}-dependence of the wave functions even when heavily augmented by additional sets.

  1. Genetic manipulation of the Fusarium fujikuroi fusarin gene cluster yields insight into the complex regulation and fusarin biosynthetic pathway.

    PubMed

    Niehaus, Eva-Maria; Kleigrewe, Karin; Wiemann, Philipp; Studt, Lena; Sieber, Christian M K; Connolly, Lanelle R; Freitag, Michael; Güldener, Ulrich; Tudzynski, Bettina; Humpf, Hans-Ulrich

    2013-08-22

    In this work, the biosynthesis and regulation of the polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS)-derived mutagenic mycotoxin fusarin C was studied in the fungus Fusarium fujikuroi. The fusarin gene cluster consists of nine genes (fus1-fus9) that are coexpressed under high-nitrogen and acidic pH conditions. Chromatin immunoprecipitation revealed a correlation between high expression and enrichment of activating H3K9-acetylation marks under inducing conditions. We provide evidence that only four genes are sufficient for the biosynthesis. The combination of genetic engineering with nuclear magnetic resonance and mass-spectrometry-based structure elucidation allowed the discovery of the putative fusarin biosynthetic pathway. Surprisingly, we indicate that PKS/NRPS releases its product with an open ring structure, probably as an alcohol. Our data indicate that 2-pyrrolidone ring closure, oxidation at C-20, and, finally, methylation at C-20 are catalyzed by Fus2, Fus8, and Fus9, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Accounting for interactions and complex inter-subject dependency in estimating treatment effect in cluster randomized trials with missing outcomes

    PubMed Central

    Prague, Melanie; Wang, Rui; Stephens, Alisa; Tchetgen Tchetgen, Eric; DeGruttola, Victor

    2016-01-01

    Summary Semi-parametric methods are often used for the estimation of intervention effects on correlated outcomes in cluster-randomized trials (CRTs). When outcomes are missing at random (MAR), Inverse Probability Weighted (IPW) methods incorporating baseline covariates can be used to deal with informative missingness. Also, augmented generalized estimating equations (AUG) correct for imbalance in baseline covariates but need to be extended for MAR outcomes. However, in the presence of interactions between treatment and baseline covariates, neither method alone produces consistent estimates for the marginal treatment effect if the model for interaction is not correctly specified. We propose an AUG-IPW estimator that weights by the inverse of the probability of being a complete case and allows different outcome models in each intervention arm. This estimator is doubly robust (DR), it gives correct estimates whether the missing data process or the outcome model is correctly specified. We consider the problem of covariate interference which arises when the outcome of an individual may depend on covariates of other individuals. When interfering covariates are not modeled, the DR property prevents bias as long as covariate interference is not present simultaneously for the outcome and the missingness. An R package is developed implementing the proposed method. An extensive simulation study and an application to a CRT of HIV risk reduction-intervention in South Africa illustrate the method. PMID:27060877

  3. Cancer Clusters

    MedlinePlus

    ... Genetics Services Directory Cancer Prevention Overview Research Cancer Clusters On This Page What is a cancer cluster? ... the number of cancer cases in the suspected cluster Many reported clusters include too few cancer cases ...

  4. Influence of Single Skimmer Versus Dual Funnel Transfer on the Appearance of ESI-Generated LiCl Cluster/ß-Cyclodextrin Inclusion Complexes

    NASA Astrophysics Data System (ADS)

    Kellner, Ina D.; Drewello, Thomas

    2015-08-01

    Singly and doubly charged adducts of LiCl with β-cyclodextrin (βCD) of the type (βCD)(LiCl)nLi+ and (βCD)2(LiCl)pLi2 2+ were studied using electrospray ionization mass spectrometry (ESI-MS). Insight into their structural composition was gained by analysis of their collision-induced dissociation (CID) mass spectra. The conditions the ions experience in the transfer region interfacing the ESI source and the mass analyzer were found to have a marked influence on the nature of the detected ions. In one instrument incorporating a single skimmer, individually attached LiCl ion pairs were observed, whereas the dual funnel ion guides of the second instrument allow the detection of previously unknown labile inclusion complexes of (LiCl)n clusters in βCD.

  5. High-nuclearity ruthenium carbonyl cluster complexes derived from 2-amino-6-methylpyridine: synthesis of nonanuclear derivatives containing mu4- and mu5-oxo ligands.

    PubMed

    Cabeza, Javier A; del Río, Ignacio; García-Alvarez, Pablo; Miguel, Daniel

    2006-07-24

    Nonanuclear cluster complexes [Ru9(mu3-H)2(mu-H)(mu5-O)(mu4-ampy)(mu3-Hampy)(CO)21] (4) (H2ampy = 2-amino-6-methylpyridine), [Ru9(mu5-O)2(mu4-ampy)(mu3-Hampy)2(mu-CO)(CO)20] (5), [Ru9(mu5-O)2(mu4-ampy)(mu3-Hampy)2(mu-CO)2(CO)19] (6), and [Ru9(mu4-O)(mu5-O)(mu4-ampy)(mu3-Hampy)(mu-Hampy)(mu-CO)(CO)19] (7), together with the known hexanuclear [Ru6(mu3-H)2(mu5-ampy)(mu-CO)2(CO)14] (2) and the novel pentanuclear [Ru5(mu4-ampy)(2)(mu-CO)(CO)12] (3) complexes, are products of the thermolysis of [Ru3(mu-H)(mu3-Hampy)(CO)9] (1) in decane at 150 degrees C. Two different and very unusual quadruply bridging coordination modes have been observed for the ampy ligand. Compounds 4-7 also feature one (4) or two (5-7) bridging oxo ligands. With the exception of one of the oxo ligands of 7, which is in a distorted tetrahedral environment, the remaining oxo ligands of 4-7 are surrounded by five metal atoms. In carbonyl metal clusters, quadruply bridging oxo ligands are very unusual, whereas quintuply bridging oxo ligands are unprecedented. By using 18O-labeled water, we have unambiguously established that these oxo ligands arise from water.

  6. In vitro reconstitution of the ordered assembly of the endosomal sorting complex required for transport at membrane-bound HIV-1 Gag clusters.

    PubMed

    Carlson, Lars-Anders; Hurley, James H

    2012-10-16

    Most membrane-enveloped viruses depend on host proteins of the endosomal sorting complex required for transport (ESCRT) machinery for their release. HIV-1 is the prototypic ESCRT-dependent virus. The direct interactions between HIV-1 and the early ESCRT factors TSG101 and ALIX have been mapped in detail. However, the full pathway of ESCRT recruitment to HIV-1 budding sites, which culminates with the assembly of the late-acting CHMP4, CHMP3, CHMP2, and CHMP1 subunits, is less completely understood. Here, we report the biochemical reconstitution of ESCRT recruitment to viral assembly sites, using purified proteins and giant unilamellar vesicles. The myristylated full-length Gag protein of HIV-1 was purified to monodispersity. Myr-Gag forms clusters on giant unilamellar vesicle membranes containing the plasma membrane lipid PI(4,5)P(2). These Gag clusters package a fluorescent oligonucleotide, and recruit early ESCRT complexes ESCRT-I or ALIX with the appropriate dependence on the Gag PTAP and LYP(X)(n)L motifs. ALIX directly recruits the key ESCRT-III subunit CHMP4. ESCRT-I can only recruit CHMP4 when ESCRT-II and CHMP6 are present as intermediary factors. Downstream of CHMP4, CHMP3 and CHMP2 assemble synergistically, with the presence of both subunits required for efficient recruitment. The very late-acting factor CHMP1 is not recruited unless the pathway is completed through CHMP3 and CHMP2. These findings define the minimal sets of components needed to complete ESCRT assembly at HIV-1 budding sites, and provide a starting point for in vitro structural and biophysical dissection of the system.

  7. In vitro reconstitution of the ordered assembly of the endosomal sorting complex required for transport at membrane-bound HIV-1 Gag clusters

    PubMed Central

    Carlson, Lars-Anders; Hurley, James H.

    2012-01-01

    Most membrane-enveloped viruses depend on host proteins of the endosomal sorting complex required for transport (ESCRT) machinery for their release. HIV-1 is the prototypic ESCRT-dependent virus. The direct interactions between HIV-1 and the early ESCRT factors TSG101 and ALIX have been mapped in detail. However, the full pathway of ESCRT recruitment to HIV-1 budding sites, which culminates with the assembly of the late-acting CHMP4, CHMP3, CHMP2, and CHMP1 subunits, is less completely understood. Here, we report the biochemical reconstitution of ESCRT recruitment to viral assembly sites, using purified proteins and giant unilamellar vesicles. The myristylated full-length Gag protein of HIV-1 was purified to monodispersity. Myr-Gag forms clusters on giant unilamellar vesicle membranes containing the plasma membrane lipid PI(4,5)P2. These Gag clusters package a fluorescent oligonucleotide, and recruit early ESCRT complexes ESCRT-I or ALIX with the appropriate dependence on the Gag PTAP and LYP(X)nL motifs. ALIX directly recruits the key ESCRT-III subunit CHMP4. ESCRT-I can only recruit CHMP4 when ESCRT-II and CHMP6 are present as intermediary factors. Downstream of CHMP4, CHMP3 and CHMP2 assemble synergistically, with the presence of both subunits required for efficient recruitment. The very late-acting factor CHMP1 is not recruited unless the pathway is completed through CHMP3 and CHMP2. These findings define the minimal sets of components needed to complete ESCRT assembly at HIV-1 budding sites, and provide a starting point for in vitro structural and biophysical dissection of the system. PMID:23027949

  8. The effect of complex workplace dietary interventions on employees' dietary intakes, nutrition knowledge and health status: a cluster controlled trial.

    PubMed

    Geaney, Fiona; Kelly, Clare; Di Marrazzo, Jessica Scotto; Harrington, Janas M; Fitzgerald, Anthony P; Greiner, Birgit A; Perry, Ivan J

    2016-08-01

    Evidence on effective workplace dietary interventions is limited. The comparative effectiveness of a workplace environmental dietary modification and an educational intervention both alone and in combination was assessed versus a control workplace on employees' dietary intakes, nutrition knowledge and health status. In the Food Choice at Work cluster controlled trial, four large, purposively selected manufacturing workplaces in Ireland were allocated to control (N=111), nutrition education (Education) (N=226), environmental dietary modification (Environment) (N=113) and nutrition education and environmental dietary modification (Combined) (N=400) in 2013. Nutrition education included group presentations, individual consultations and detailed nutrition information. Environmental dietary modification included menu modification, fruit price discounts, strategic positioning of healthier alternatives and portion size control. Data on dietary intakes, nutrition knowledge and health status were obtained at baseline and follow-up at 7-9months. Multivariate analysis of covariance compared changes across the four groups with adjustment for age, gender, educational status and other baseline characteristics. Follow-up data at 7-9months were obtained for 541 employees (64% of 850 recruited) aged 18-64years: control: 70 (63%), Education: 113 (50%), 74 (65%) and Combined: 284 (71%). There were significant positive changes in intakes of saturated fat (p=0.013), salt (p=0.010) and nutrition knowledge (p=0.034) between baseline and follow-up in the combined intervention versus the control. Small but significant changes in BMI (-1.2kg/m(2) (95% CI -2.385, -0.018, p=0.047) were observed in the combined intervention. Effects in the education and environment alone workplaces were smaller and generally non-significant. Combining nutrition education and environmental dietary modification may be an effective approach for promoting a healthy diet and weight loss at work. Copyright © 2016

  9. A multifrequency study of the active star-forming complex NGC 6357 - I. Interstellar structures linked to the open cluster Pis 24

    NASA Astrophysics Data System (ADS)

    Cappa, C. E.; Barbá, R.; Duronea, N. U.; Vasquez, J.; Arnal, E. M.; Goss, W. M.; Fernández Lajús, E.

    2011-08-01

    We investigate the distribution of gas (ionized, neutral atomic and molecular) and interstellar dust in the complex star-forming region NGC 6357 with the goal of studying the interplay between the massive stars in the open cluster Pis 24 and the surrounding interstellar matter. Our study of the distribution of the ionized gas is based on narrow-band Hα, [S II]and [O III] images obtained with the Curtis-Schmidt Camera at CTIO, Chile, and on radio continuum observations at 1465 MHz taken with the VLA with a synthesized beam of 40 arcsec. The distribution of the molecular gas is analysed using 12CO(1-0) data obtained with the NANTEN radiotelescope, Chile (angular resolution = 2.7 arcmin). The interstellar dust distribution was studied using mid-infrared data from the GLIMPSE survey and far-infrared observations from IRAS. NGC 6357 consists of a large ionized shell and a number of smaller optical nebulosities. The optical, radio continuum, and near- and mid-IR images delineate the distributions of the ionized gas and interstellar dust in the H II regions and in previously unknown wind-blown bubbles linked to the massive stars in Pis 24 revealing surrounding photodissociation regions. The CO line observations allowed us to identify the molecular counterparts of the ionized structures in the complex and to confirm the presence of photodissociation regions. The action of the WR star HD 157504 on the surrounding gas was also investigated. The molecular mass in the complex is estimated to be (4 ± 2) × 105 M⊙. The mean electron densities derived from the radio data suggest electron densities >200 cm-3, indicating that NGC 6357 is a complex formed in a region of high ambient density. The known massive stars in Pis 24 and a number of newly inferred massive stars are mainly responsible for the excitation and photodissociation of the parental molecular cloud.

  10. A rare tetranuclear thorium(IV) μ4 -oxo cluster and dinuclear thorium(IV) complex assembled by carbon-oxygen bond activation of 1,2-dimethoxyethane (DME).

    PubMed

    Travia, Nicholas E; Scott, Brian L; Kiplinger, Jaqueline L

    2014-12-15

    The synthesis and X-ray crystal structure of two new multinuclear thorium complexes are reported. The tetranuclear μ4 -oxo cluster complex Th4 (μ4 -O)(μ-Cl)2 I6 [κ(2) (O,O')-μ-O(CH2 )2 OCH3 ]6 and the dinuclear complex Th2 I5 [κ(2) (O,O')-μ-O(CH2 )2 OCH3 ]3 (DME) (DME=dimethoxyethane) are formed by CO bond activation of 1,2-dimethoxyethane (DME) mediated by thorium iodide complexes.

  11. Comparison of CBS-QB3, CBS-APNO, G2, and G3 thermochemical predictions with experiment for formation of ionic clusters of hydronium and hydroxide ions complexed with water.

    PubMed

    Pickard, Frank C; Pokon, Emma K; Liptak, Matthew D; Shields, George C

    2005-01-08

    The GAUSSIAN 2, GAUSSIAN 3, complete basis set-QB3, and complete basis set-APNO methods have been used to calculate DeltaH( composite function) and DeltaG( composite function) values for ionic clusters of hydronium and hydroxide ions complexed with water. Results for the clusters H3O+(H2O)n and OH-(H2O)n, where n=1-4 are reported in this paper, and compared against experimental values contained in the National Institutes of Standards and Technology (NIST) database. Agreement with experiment is excellent for the three ab initio methods for formation of these clusters. The high accuracy of these methods makes them reliable for calculating energetics for the formation of ionic clusters containing water. In addition this allows them to serve as a valuable check on the accuracy of experimental data reported in the NIST database, and makes them useful tools for addressing unresolved issues in atmospheric chemistry.

  12. Electronic Structure of the Mn(4)Ca Cluster in the Oxygen-Evolving Complex of Photosystem Ii Studied By Resonant Inelastic X-Ray Scattering

    SciTech Connect

    Yano, J.; Pushkar, Y.; Messinger, J.; Bergmann, U.; Glatzel, P.; Yachandra, V.K.

    2009-06-04

    Oxygen-evolving complex (Mn{sub 4}Ca cluster) of Photosystem II cycles through five intermediate states (S{sub i}-states, i=0--4) before a molecule of dioxygen is released. During the S-state transitions, electrons are extracted from the OEC, either from Mn or alternatively from a Mn ligand. The oxidation state of Mn is widely accepted as Mn{sub 4}(III{sub 2},IV{sub 2}) and Mn{sub 4}(III,IV{sub 3}) for S{sub 1} and S{sub 2} states, while it is still controversial for the S{sub 0} and S{sub 3} states. We used resonant inelastic X-ray scattering (RIXS) to study the electronic structure of Mn{sub 4}Ca complex in the OEC. The RIXS data yield two-dimensional plots that provide a significant advantage by obtaining both K-edge pre-edge and L-edge-like spectra simultaneously. The second energy dimension separates the pre-edge (1s to 3d) transitions from the main K-edge (1s to 4p), and thus more precise analysis is possible. The 1s2p RIXS final state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy and the RIXS spectra are therefore sensitive to the metal spin state. We have collected data from PS II samples in the each of the S-states and compared them with data from various inorganic Mn complexes. The spectral changes in the Mn 1s2p{sub 3/2} RIXS spectra between the S-states are small compared to those of the oxides of Mn and coordination complexes. The results indicate strong covalency for the electronic configuration in the OEC, and we conclude that the electron is transferred from a strongly delocalized orbital, compared to those in Mn oxides or coordination complexes. The magnitude for the S{sub 0} to S{sub 1}, and S{sub 1} to S{sub 2} transitions is twice as large as that during the S{sub 2} to S{sub 3} transition, indicating that the electron for this transition is extracted from a highly delocalized orbital with little change in charge density at the Mn atoms. The RIXS spectra of S{sub 0} and S{sub 3

  13. Electronic Structure of the Mn[subscript 4]Ca Cluster in the Oxygen-Evolving Complex of Photosystem II Studied by Resonant Inelastic X-Ray Scattering

    SciTech Connect

    Yano, Junko; Pushkar, Yulia; Messinger, Johannes; Bergmann, Uwe; Glatzel, Pieter; Yachandra, Vittal K.

    2007-11-12

    Oxygen-evolving complex (Mn{sub 4}Ca cluster) of Photosystem II cycles through five intermediate states (S{sub i}-states, i = 0-4) before a molecule of dioxygen is released. During the S-state transitions, electrons are extracted from the OEC, either from Mn or alternatively from a Mn ligand. The oxidation state of Mn is widely accepted as Mn{sub 4}(III{sub 2},IV{sub 2}) and Mn{sub 4}(III,IV{sub 3}) for S{sub 1} and S{sub 2} states, while it is still controversial for the S{sub 0} and S{sub 3} states. We used resonant inelastic X-ray scattering (RIXS) to study the electronic structure of Mn{sub 4}Ca complex in the OEC. The RIXS data yield two-dimensional plots that provide a significant advantage by obtaining both K-edge pre-edge and L-edge-like spectra simultaneously. The second energy dimension separates the pre-edge (1s to 3d) transitions from the main K-edge (1s to 4p), and thus more precise analysis is possible. The 1s2p RIXS final state electron configuration along the energy transfer axis is identical to conventional L-edge absorption spectroscopy and the RIXS spectra are therefore sensitive to the metal spin state. We have collected data from PS II samples in the each of the S-states and compared them with data from various inorganic Mn complexes. The spectral changes in the Mn 1s2p{sub 3/2} RIXS spectra between the S-states are small compared to those of the oxides of Mn and coordination complexes. The results indicate strong covalency for the electronic configuration in the OEC, and we conclude that the electron is transferred from a strongly delocalized orbital, compared to those in Mn oxides or coordination complexes. The magnitude for the S{sub 0} to S{sub 1}, and S{sub 1} to S{sub 2} transitions is twice as large as that during the S{sub 2} to S{sub 3} transition, indicating that the electron for this transition is extracted from a highly delocalized orbital with little change in charge density at the Mn atoms. The RIXS spectra of S{sub 0} and S{sub 3

  14. Barriers to and facilitators of implementing complex workplace dietary interventions: process evaluation results of a cluster controlled trial.

    PubMed

    Fitzgerald, Sarah; Geaney, Fiona; Kelly, Clare; McHugh, Sheena; Perry, Ivan J

    2016-04-21

    Ambiguity exists regarding the effectiveness of workplace dietary interventions. Rigorous process evaluation is vital to understand this uncertainty. This study was conducted as part of the Food Choice at Work trial which assessed the comparative effectiveness of a workplace environmental dietary modification intervention and an educational intervention both alone and in combination versus a control workplace. Effectiveness was assessed in terms of employees' dietary intakes, nutrition knowledge and health status in four large manufacturing workplaces. The study aimed to examine barriers to and facilitators of implementing complex workplace interventions, from the perspectives of key workplace stakeholders and researchers involved in implementation. A detailed process evaluation monitored and evaluated intervention implementation. Interviews were conducted at baseline (27 interviews) and at 7-9 month follow-up (27 interviews) with a purposive sample of workplace stakeholders (managers and participating employees). Topic guides explored factors which facilitated or impeded implementation. Researchers involved in recruitment and data collection participated in focus groups at baseline and at 7-9 month follow-up to explore their perceptions of intervention implementation. Data were imported into NVivo software and analysed using a thematic framework approach. Four major themes emerged; perceived benefits of participation, negotiation and flexibility of the implementation team, viability and intensity of interventions and workplace structures and cultures. The latter three themes either positively or negatively affected implementation, depending on context. The implementation team included managers involved in coordinating and delivering the interventions and the researchers who collected data and delivered intervention elements. Stakeholders' perceptions of the benefits of participating, which facilitated implementation, included managers' desire to improve company

  15. A density functional investigation of thiolate-protected bimetal PdAu(24)(SR)(18)(z) clusters: doping the superatom complex.

    PubMed

    Kacprzak, Katarzyna A; Lehtovaara, Lauri; Akola, Jaakko; Lopez-Acevedo, Olga; Häkkinen, Hannu

    2009-09-07

    Structure, electronic properties, optical absorption and charging properties of methylthiolate-protected bimetal PdAu(24)(SR)(18)(z) (R = Me) clusters with various charge states (-3 complex Au(25)(SR)(18)((-1)) [J. Akola, M. Walter, H. Häkkinen and H. Grönbeck, J. Am. Chem. Soc., 2008, 130, 3756]. The atomic structure of this all-gold complex can be written in a "divide-and-protect" way [H. Häkkinen, M. Walter and H. Grönbeck, J. Phys. Chem. B, 2006, 110, 9927] as Au(13)[Au(2)(SR)(3)](6)((-1)) where 6 v-shaped Au(2)(SR)(3) ligands protect the close-to-icosahedral Au(13) core and where eight delocalized metal electrons, derived from Au(6s) electrons, comprise a stable closed-shell 1S(2)1P(6)"superatom" configuration in the core. We show that the di-anion PdAu(24)(SR)(18)((-2)) is a corresponding eight-electron closed-shell species whereas the clusters PdAu(24)(SR)(18)(z), -1

  16. Cluster headache

    MedlinePlus

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... Doctors do not know exactly what causes cluster headaches. They ... (chemical in the body released during an allergic response) or ...

  17. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  18. Shaping a high-mass star-forming cluster through stellar feedback. The case of the NGC 7538 IRS 1-3 complex

    NASA Astrophysics Data System (ADS)

    Frau, P.; Girart, J. M.; Zhang, Q.; Rao, R.

    2014-07-01

    Context. NGC 7538 IRS 1-3 is a high-mass star-forming cluster with several detected dust cores, infrared sources, (ultra)compact H II regions, molecular outflows, and masers. In such a complex environment, interactions and feedback among the embedded objects are expected to play a major role in the evolution of the region. Aims: We study the dust, kinematic, and polarimetric properties of the NGC 7538 IRS 1-3 region to investigate the role of the different forces in the formation and evolution of high-mass star-forming clusters. Methods: We performed SMA high angular resolution observations at 880 μm with the compact configuration. We developed the RATPACKS code to generate synthetic velocity cubes from models of choice to be compared to the observational data. To quantify the stability against gravitational collapse we developed the "mass balance" analysis that accounts for all the energetics on core scales. Results: We detect 14 dust cores from 3.5 M⊙ to 37 M⊙ arranged in two larger scale structures: a central bar and a filamentary spiral arm. The spiral arm presents large-scale velocity gradients in H13CO+ 4-3 and C17O 3-2, and magnetic field segments aligned well to the dust main axis. The velocity gradient is reproduced well by a spiral arm expanding at 9 km s-1 with respect to the central core MM1, which is known to power a large precessing outflow. The energy of the outflow is comparable to the spiral-arm kinetic energy, which dominates gravitational and magnetic energies. In addition, the dynamical ages of the outflow and spiral arm are comparable. On core scales, those embedded in the central bar seem to be unstable against gravitational collapse and prone to forming high-mass stars, while those in the spiral arm have lower masses that seem to be supported by non-thermal motions and magnetic fields. Conclusions: The NGC 7538 IRS 1-3 cluster seems to be dominated by protostellar feedback. The dusty spiral arm appears to be formed in a snowplow fashion

  19. Effectiveness of a complex intervention in reducing the prevalence of smoking among adolescents: study design of a cluster-randomized controlled trial

    PubMed Central

    2014-01-01

    Background The likelihood of an adolescent taking up smoking may be influenced by his or her society, school and family. Thus, changes in the immediate environment may alter a young person’s perception of smoking. Methods/Design The proposed multi-center, cluster-randomized controlled trial will be stratified by the baseline prevalence of smoking in schools. Municipalities with fewer than 100,000 inhabitants will be randomly assigned to a control or intervention group. One secondary school will be randomly selected from each municipality. These schools will be randomized to two groups: the students of one will receive any existing educational course regarding smoking, while those of the other school will receive a four-year, class-based curriculum intervention (22 classroom lessons) aimed at reinforcing a smoke-free school policy and encouraging smoking cessation in parents, pupils, and teachers. The intervention will also include annual meetings with parents and efforts to empower adolescents to change the smoking-related attitudes and behaviors in their homes, classrooms and communities. We will enroll children aged 12-13 years as they enter secondary school during two consecutive school years (to obtain sufficient enrolled subjects). We will follow them for five years, until two years after they leave secondary school. All external evaluators and analysts will be blinded to school allocation. The aim of this study is to analyze the effectiveness of a complex intervention in reducing the prevalence of smoking in the third year of compulsory secondary education (ESO) and two years after secondary school, when the participants are 14-15 and 17-18 years old, respectively. Discussion Most interventions aimed at preventing smoking among adolescents yield little to no positive long-term effects. This clinical trial will analyze the effectiveness of a complex intervention aimed at reducing the incidence and prevalence of smoking in this vulnerable age group. Trial

  20. Increasing chlamydia screening tests in general practice: a modified Zelen prospective Cluster Randomised Controlled Trial evaluating a complex intervention based on the Theory of Planned Behaviour.

    PubMed

    McNulty, Cliodna A M; Hogan, Angela H; Ricketts, Ellie J; Wallace, Louise; Oliver, Isabel; Campbell, Rona; Kalwij, Sebastian; O'Connell, Elaine; Charlett, Andre

    2014-05-01

    To determine if a structured complex intervention increases opportunistic chlamydia screening testing of patients aged 15-24 years attending English general practitioner (GP) practices. A prospective, Cluster Randomised Controlled Trial with a modified Zelen design involving 160 practices in South West England in 2010. The intervention was based on the Theory of Planned Behaviour (TPB). It comprised of practice-based education with up to two additional contacts to increase the importance of screening to GP staff and their confidence to offer tests through skill development (including videos). Practical resources (targets, posters, invitation cards, computer reminders, newsletters including feedback) aimed to actively influence social cognitions of staff, increasing their testing intention. Data from 76 intervention and 81 control practices were analysed. In intervention practices, chlamydia screening test rates were 2.43/100 15-24-year-olds registered preintervention, 4.34 during intervention and 3.46 postintervention; controls testing rates were 2.61/100 registered patients prior intervention, 3.0 during intervention and 2.82 postintervention. During the intervention period, testing in intervention practices was 1.76 times as great (CI 1.24 to 2.48) as controls; this persisted for 9 months postintervention (1.57 times as great, CI 1.27 to 2.30). Chlamydia infections detected increased in intervention practices from 2.1/1000 registered 15-24-year-olds prior intervention to 2.5 during the intervention compared with 2.0 and 2.3/1000 in controls (Estimated Rate Ratio intervention versus controls 1.4 (CI 1.01 to 1.93). This complex intervention doubled chlamydia screening tests in fully engaged practices. The modified Zelen design gave realistic measures of practice full engagement (63%) and efficacy of this educational intervention in general practice; it should be used more often. The trial was registered on the UK Clinical Research Network Study Portfolio database

  1. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363.

    PubMed

    Peters, Daniel T; Fung, Herman K H; Levdikov, Vladimir M; Irmscher, Tobias; Warrander, Fiona C; Greive, Sandra J; Kovalevskiy, Oleg; Isaacs, Harry V; Coles, Mark; Antson, Alfred A

    2016-09-13

    Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein-RNA complex are unknown. Characterization of human Lin28's interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions.

  2. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363

    PubMed Central

    2016-01-01

    Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein–RNA complex are unknown. Characterization of human Lin28’s interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions. PMID:27559824

  3. An unsupervised two-stage clustering approach for forest structure classification based on X-band InSAR data - A case study in complex temperate forest stands

    NASA Astrophysics Data System (ADS)

    Abdullahi, Sahra; Schardt, Mathias; Pretzsch, Hans

    2017-05-01

    Forest structure at stand level plays a key role for sustainable forest management, since the biodiversity, productivity, growth and stability of the forest can be positively influenced by managing its structural diversity. In contrast to field-based measurements, remote sensing techniques offer a cost-efficient opportunity to collect area-wide information about forest stand structure with high spatial and temporal resolution. Especially Interferometric Synthetic Aperture Radar (InSAR), which facilitates worldwide acquisition of 3d information independent from weather conditions and illumination, is convenient to capture forest stand structure. This study purposes an unsupervised two-stage clustering approach for forest structure classification based on height information derived from interferometric X-band SAR data which was performed in complex temperate forest stands of Traunstein forest (South Germany). In particular, a four dimensional input data set composed of first-order height statistics was non-linearly projected on a two-dimensional Self-Organizing Map, spatially ordered according to similarity (based on the Euclidean distance) in the first stage and classified using the k-means algorithm in the second stage. The study demonstrated that X-band InSAR data exhibits considerable capabilities for forest structure classification. Moreover, the unsupervised classification approach achieved meaningful and reasonable results by means of comparison to aerial imagery and LiDAR data.

  4. Unusual self-assembled 1D tape of tetramers and water-nitrate clusters trapped in a zinc(II) complex: Synthesis, characterization, luminescence and catalytic properties

    NASA Astrophysics Data System (ADS)

    Ma, De-Yun; Guo, Hai-Fu; Dong, Ji; Xu, Jun

    2013-12-01

    Unusual tetramers and water-nitrate clusters have been observed in a mononuclear zinc(II) complex of [Zn(4-cpa)(phen)2(H2O)]·(H2O)·(NO3)] (1), (4-Hcpa = 4-chlorophenoxyacetic acid, phen = 1,10-phenanthroline), which was synthesized under hydrothermal conditions and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis (TGA), powder X-ray diffraction, UV-vis absorption spectra and single-crystal X-ray diffraction. The crystal structure analysis of 1, reveals that the nitrate anions, water molecules and carboxylate oxygen atoms (O3) pack to form a one-dimensional infinite tape parallel to the c-axis. The uncoordinated carboxylate oxygen atoms (O3) of 4-cpa ligands, water molecules and nitrate anions interact via hydrogen bonds and extend 1 into a water-anion-cation tape, which are finally connected into a 3D supramolecular structure via π⋯π stacking interactions. Excitation (λex = 310 nm) and luminescence data observed at room temperature show that 1 emits bright blue fluorescence. Moreover, 1 has a remarkable activity for degradation of methyl orange in a photo-assisted Fenton-like process.

  5. N-Heterocyclic Carbene Coinage Metal Complexes of the Germanium-Rich Metalloid Clusters [Ge₉R₃](-) and [Ge₉R(I)₂]²(-) with R = Si((i)Pr)₃ and R(I) = Si(TMS)₃.

    PubMed

    Geitner, Felix S; Giebel, Michael A; Pöthig, Alexander; Fässler, Thomas F

    2017-07-19

    We report on the synthesis of novel coinage metal NHC (N-heterocyclic carbene) compounds of the germanium-rich metalloid clusters [Ge₉R₃](-) and [Ge₉R(I)₂]²(-) with R = Si((i)Pr)₃ and R(I) = Si(TMS)₃. NHC(Dipp)Cu{η³Ge₉R₃} with R = Si((i)Pr)₃ (1) represents a less bulky silyl group-substituted derivative of the known analogous compounds with R = Si((i)Bu)₃ or Si(TMS)₃. The coordination of the [NHC(Dipp)Cu]⁺ moiety to the cluster unit occurs via one triangular face of the tri-capped trigonal prismatic [Ge₉] cluster. Furthermore, a series of novel Zintl cluster coinage metal NHC compounds of the type (NHCM)₂{η³Ge₉R(I)₂} (R(I) = Si(TMS)₃ M = Cu, Ag and Au; NHC = NHC(Dipp) or NHC(Mes)) is presented. These novel compounds represent a new class of neutral dinuclear Zintl cluster coinage metal NHC compounds, which are obtained either by the stepwise reaction of a suspension of K12Ge17 with Si(TMS)₃Cl and the coinage metal carbene complexes NHCMCl (M = Cu, Ag, Au), or via a homogenous reaction using the preformed bis-silylated cluster K₂[Ge₉(Si(TMS)₃)₂] and the corresponding NHCMCl (M = Cu, Ag, Au) complex. The molecular structures of NHC(Dipp)Cu{η³Ge₉(Si((i)Pr)₃)₃} (1) and (NHC(Dipp)Cu)₂{η³-Ge₉(Si(TMS)₃)₂} (2) were determined by single crystal X-ray diffraction methods. In 2, the coordination of the [NHC(Dipp)Cu]⁺ moieties to the cluster unit takes place via both open triangular faces of the [Ge₉] entity. Furthermore, all compounds were characterized by means of NMR spectroscopy (¹H, (13)C, (29)Si) and ESI-MS.

  6. Designing of the Information Advising System to Assess the Potential of Creation and Development of Cluster Agglomeration in the Industrial Complex of the Region

    NASA Astrophysics Data System (ADS)

    Averchenkova, E. E.; Averchenkov, A. V.; Kulagina, N. A.

    2017-01-01

    The theoretical aspects of creation of the information advising system to assess the potential of development of the cluster agglomeration are described in this article. The algorithm provided in the article estimates possibilities of creation and development of the regional industrial cluster agglomeration. This article describes the possible use of the information advising system of the evaluation and diagnostic type in making managerial decisions by the participants of the technology innovation cluster.

  7. Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis*

    PubMed Central

    Hirabayashi, Kei; Yuda, Eiki; Tanaka, Naoyuki; Katayama, Sumie; Iwasaki, Kenji; Matsumoto, Takashi; Kurisu, Genji; Outten, F. Wayne; Fukuyama, Keiichi; Takahashi, Yasuhiro; Wada, Kei

    2015-01-01

    ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex. PMID:26472926

  8. The CareWell-primary care program: design of a cluster controlled trial and process evaluation of a complex intervention targeting community-dwelling frail elderly.

    PubMed

    Ruikes, Franca G H; Meys, Antoinette R M; van de Wetering, Gijs; Akkermans, Reinier P; van Gaal, Betsie G I; Zuidema, Sytse U; Schers, Henk J; van Achterberg, Theo; Koopmans, Raymond T C M

    2012-12-05

    With increasing age and longevity, the rising number of frail elders with complex and numerous health-related needs demands a coordinated health care delivery system integrating cure, care and welfare. Studies on the effectiveness of such comprehensive chronic care models targeting frail elders show inconclusive results. The CareWell-primary care program is a complex intervention targeting community-dwelling frail elderly people, that aims to prevent functional decline, improve quality of life, and reduce or postpone hospital and nursing home admissions of community dwelling frail elderly. The CareWell-primary care study includes a (cost-) effectiveness study and a comprehensive process evaluation. In a one-year pragmatic, cluster controlled trial, six general practices are non-randomly recruited to adopt the CareWell-primary care program and six control practices will deliver 'care as usual'. Each practice includes a random sample of fifty frail elders aged 70 years or above in the cost-effectiveness study. A sample of patients and informal caregivers and all health care professionals participating in the CareWell-primary care program are included in the process evaluation. In the cost-effectiveness study, the primary outcome is the level of functional abilities as measured with the Katz-15 index. Hierarchical mixed-effects regression models/multilevel modeling approach will be used, since the study participants are nested within the general practices. Furthermore, incremental cost-effectiveness ratios will be calculated as costs per QALY gained and as costs weighed against functional abilities. In the process evaluation, mixed methods will be used to provide insight in the implementation degree of the program, patients' and professionals' approval of the program, and the barriers and facilitators to implementation. The CareWell-primary care study will provide new insights into the (cost-) effectiveness, feasibility, and barriers and facilitators for

  9. Partnered pharmacist charting on admission in the General Medical and Emergency Short-stay Unit - a cluster-randomised controlled trial in patients with complex medication regimens.

    PubMed

    Tong, E Y; Roman, C; Mitra, B; Yip, G; Gibbs, H; Newnham, H; Smit, D P; Galbraith, K; Dooley, M J

    2016-08-01

    Patients admitted to general medical units and emergency short-stay units are often complex with multiple comorbidities, polypharmacy and at risk for drug-related problems associated with increased morbidity and mortality. The aim of this study was to evaluate the effectiveness of a partnered pharmacist charting model completed at the time of admission to prevent medication errors. We conducted an unblinded cluster randomized controlled trial comparing partnered pharmacist charting to standard medical charting among patients admitted to general medical units and emergency short-stay units with complex medication regimens or polypharmacy. This trial was conducted at an adult major referral hospital in metropolitan Melbourne, Australia, with an annual emergency department attendance of approximately 60 000 patients. The evaluation included patients' medication charts written in the period of 16 March 2015 to 27 July 2015. Patients randomized to the intervention were managed using the partnered pharmacist charting model. The primary outcome variable was a medication error identified by an independent assessor within 24 h of admission, who was not part of the patient's admission process. Of the 473 patients who received standard medical staff charting during the study period, 372 (78·7%) had at least one medication error identified compared to 15 patients (3·7%) on the partnered pharmacist charting arm (P < 0·001). The relative risk of an error with standard medical charting was 21·4 (95% CI: 13·0-35·0) with a number needed to treat (NNT) to prevent one error of 1·3 (95% CI: 1·3-1·4), and the relative risk of a high or extreme risk error with standard medical charting was 150·9 (95% CI: 21·2-1072·9) with a NNT to prevent one high or extreme error of 2·7 (95% CI 2·4-3·1). Partnering between medical staff and pharmacists to jointly chart initial medications on admission significantly reduced inpatient medication errors (including errors of high and extreme

  10. Rhenium Complexes and Clusters Supported on c-Al2O3: Effects of Rhenium Oxidation State and Rhenium Cluster Size on Catalytic Activity for n-butane Hydrogenolysis

    SciTech Connect

    Lobo Lapidus, R.; Gates, B

    2009-01-01

    Supported metals prepared from H{sub 3}Re{sub 3}(CO){sub 12} on {gamma}-Al{sub 2}O{sub 3} were treated under conditions that led to various rhenium structures on the support and were tested as catalysts for n-butane conversion in the presence of H{sub 2} in a flow reactor at 533 K and 1 atm. After use, two samples were characterized by X-ray absorption edge positions of approximately 5.6 eV (relative to rhenium metal), indicating that the rhenium was cationic and essentially in the same average oxidation state in each. But the Re-Re coordination numbers found by extended X-ray absorption fine structure spectroscopy (2.2 and 5.1) show that the clusters in the two samples were significantly different in average nuclearity despite their indistinguishable rhenium oxidation states. Spectra of a third sample after catalysis indicate approximately Re{sub 3} clusters, on average, and an edge position of 4.5 eV. Thus, two samples contained clusters approximated as Re{sub 3} (on the basis of the Re-Re coordination number), on average, with different average rhenium oxidation states. The data allow resolution of the effects of rhenium oxidation state and cluster size, both of which affect the catalytic activity; larger clusters and a greater degree of reduction lead to increased activity.

  11. The food choice at work study: effectiveness of complex workplace dietary interventions on dietary behaviours and diet-related disease risk - study protocol for a clustered controlled trial

    PubMed Central

    2013-01-01

    Background Dietary behaviour interventions have the potential to reduce diet-related disease. Ample opportunity exists to implement these interventions in the workplace. The overall aim is to assess the effectiveness and cost-effectiveness of complex dietary interventions focused on environmental dietary modification alone or in combination with nutrition education in large manufacturing workplace settings. Methods/design A clustered controlled trial involving four large multinational manufacturing workplaces in Cork will be conducted. The complex intervention design has been developed using the Medical Research Council’s framework and the National Institute for Health and Clinical Excellence (NICE) guidelines and will be reported using the TREND statement for the transparent reporting of evaluations with non-randomized designs. It will draw on a soft paternalistic “nudge” theoretical perspective. Nutrition education will include three elements: group presentations, individual nutrition consultations and detailed nutrition information. Environmental dietary modification will consist of five elements: (a) restriction of fat, saturated fat, sugar and salt, (b) increase in fibre, fruit and vegetables, (c) price discounts for whole fresh fruit, (d) strategic positioning of healthier alternatives and (e) portion size control. No intervention will be offered in workplace A (control). Workplace B will receive nutrition education. Workplace C will receive nutrition education and environmental dietary modification. Workplace D will receive environmental dietary modification alone. A total of 448 participants aged 18 to 64 years will be selected randomly. All permanent, full-time employees, purchasing at least one main meal in the workplace daily, will be eligible. Changes in dietary behaviours, nutrition knowledge, health status with measurements obtained at baseline and at intervals of 3 to 4 months, 7 to 9 months and 13 to 16 months will be recorded. A process

  12. A Cluster of Four Homologous Small RNAs Modulates C1 Metabolism and the Pyruvate Dehydrogenase Complex in Rhodobacter sphaeroides under Various Stress Conditions

    PubMed Central

    Billenkamp, Fabian; Peng, Tao; Berghoff, Bork A.

    2015-01-01

    ABSTRACT In bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs, trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacterium Rhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1–4) for conserved CCUCCUCCC motif stress-induced RNAs 1 to 4. Increased CcsR1–4 expression decreases the expression of genes involved in C1 metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1–4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress. IMPORTANCE Phototrophic organisms have to cope with photo-oxidative stress due to the function of chlorophylls as photosensitizers for the formation of singlet oxygen. Our study assigns an important role in photo-oxidative stress resistance to a

  13. Increasing chlamydia screening tests in general practice: a modified Zelen prospective Cluster Randomised Controlled Trial evaluating a complex intervention based on the Theory of Planned Behaviour

    PubMed Central

    McNulty, Cliodna A M; Hogan, Angela H; Ricketts, Ellie J; Wallace, Louise; Oliver, Isabel; Campbell, Rona; Kalwij, Sebastian; O'Connell, Elaine; Charlett, Andre

    2014-01-01

    Objective To determine if a structured complex intervention increases opportunistic chlamydia screening testing of patients aged 15–24 years attending English general practitioner (GP) practices. Methods A prospective, Cluster Randomised Controlled Trial with a modified Zelen design involving 160 practices in South West England in 2010. The intervention was based on the Theory of Planned Behaviour (TPB). It comprised of practice-based education with up to two additional contacts to increase the importance of screening to GP staff and their confidence to offer tests through skill development (including videos). Practical resources (targets, posters, invitation cards, computer reminders, newsletters including feedback) aimed to actively influence social cognitions of staff, increasing their testing intention. Results Data from 76 intervention and 81 control practices were analysed. In intervention practices, chlamydia screening test rates were 2.43/100 15–24-year-olds registered preintervention, 4.34 during intervention and 3.46 postintervention; controls testing rates were 2.61/100 registered patients prior intervention, 3.0 during intervention and 2.82 postintervention. During the intervention period, testing in intervention practices was 1.76 times as great (CI 1.24 to 2.48) as controls; this persisted for 9 months postintervention (1.57 times as great, CI 1.27 to 2.30). Chlamydia infections detected increased in intervention practices from 2.1/1000 registered 15–24-year-olds prior intervention to 2.5 during the intervention compared with 2.0 and 2.3/1000 in controls (Estimated Rate Ratio intervention versus controls 1.4 (CI 1.01 to 1.93). Conclusions This complex intervention doubled chlamydia screening tests in fully engaged practices. The modified Zelen design gave realistic measures of practice full engagement (63%) and efficacy of this educational intervention in general practice; it should be used more often. Trial registration The trial was

  14. Effectiveness of a primary care based complex intervention to promote self-management in patients presenting psychiatric symptoms: study protocol of a cluster-randomized controlled trial

    PubMed Central

    2014-01-01

    Background Anxiety, Depression and Somatoform (ADSom) disorders are highly prevalent in primary care. Managing these disorders is time-consuming and requires strong commitment on behalf of the General Practitioners (GPs). Furthermore, the management of these patients is restricted by the high patient turnover rates in primary care practices, especially in the German health care system. In order to address this problem, we implement a complex, low-threshold intervention by an Advanced Practice Nurse (APN) using a mixture of case management and counseling techniques to promote self-management in these patients. Here we present the protocol of the “Self-Management Support for Anxiety, Depression and Somatoform Disorders in Primary Care” (SMADS)-Study. Methods/Design The study is designed as a cluster-randomized controlled trial, comparing an intervention and a control group of 10 primary care practices in each case. We will compare the effectiveness of the intervention applied by an APN with usual GP-care. A total of 340 participants will be enrolled in the study, 170 in either arm. We use the Patient Health Questionnaire-German version (PHQ-D) as a screening tool for psychiatric symptoms, including patients with a score above 5 on any of the three symptom scales. The primary outcome is self-efficacy, measured by the General Self-Efficacy Scale (GSE), here used as a proxy for self-management. As secondary outcomes we include the PHQ-D symptom load and questionnaires regarding coping with illness and health related quality of life. Outcome assessments will be applied 8 weeks and 12 months after the baseline assessment. Discussion The SMADS-study evaluates a complex, low threshold intervention for ambulatory patients presenting ADSom-symptoms, empowering them to better manage their condition, as well as improving their motivation to engage in self-help and health-seeking behaviour. The benefit of the intervention will be substantiated, when patients can enhance

  15. The food choice at work study: effectiveness of complex workplace dietary interventions on dietary behaviours and diet-related disease risk - study protocol for a clustered controlled trial.

    PubMed

    Geaney, Fiona; Scotto Di Marrazzo, Jessica; Kelly, Clare; Fitzgerald, Anthony P; Harrington, Janas M; Kirby, Ann; McKenzie, Ken; Greiner, Birgit; Perry, Ivan J

    2013-11-06

    Dietary behaviour interventions have the potential to reduce diet-related disease. Ample opportunity exists to implement these interventions in the workplace. The overall aim is to assess the effectiveness and cost-effectiveness of complex dietary interventions focused on environmental dietary modification alone or in combination with nutrition education in large manufacturing workplace settings. A clustered controlled trial involving four large multinational manufacturing workplaces in Cork will be conducted. The complex intervention design has been developed using the Medical Research Council's framework and the National Institute for Health and Clinical Excellence (NICE) guidelines and will be reported using the TREND statement for the transparent reporting of evaluations with non-randomized designs. It will draw on a soft paternalistic 'nudge' theoretical perspective. It will draw on a soft paternalistic "nudge" theoretical perspective. Nutrition education will include three elements: group presentations, individual nutrition consultations and detailed nutrition information. Environmental dietary modification will consist of five elements: (a) restriction of fat, saturated fat, sugar and salt, (b) increase in fibre, fruit and vegetables, (c) price discounts for whole fresh fruit, (d) strategic positioning of healthier alternatives and (e) portion size control. No intervention will be offered in workplace A (control). Workplace B will receive nutrition education. Workplace C will receive nutrition education and environmental dietary modification. Workplace D will receive environmental dietary modification alone. A total of 448 participants aged 18 to 64 years will be selected randomly. All permanent, full-time employees, purchasing at least one main meal in the workplace daily, will be eligible. Changes in dietary behaviours, nutrition knowledge, health status with measurements obtained at baseline and at intervals of 3 to 4 months, 7 to 9 months and 13 to 16

  16. A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions.

    PubMed

    Billenkamp, Fabian; Peng, Tao; Berghoff, Bork A; Klug, Gabriele

    2015-05-01

    In bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs, trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacterium Rhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1-4) for conserved CCUCCUCCC motif stress-induced RNAs 1 to 4. Increased CcsR1-4 expression decreases the expression of genes involved in C1 metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1-4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress. Phototrophic organisms have to cope with photo-oxidative stress due to the function of chlorophylls as photosensitizers for the formation of singlet oxygen. Our study assigns an important role in photo-oxidative stress resistance to a cluster of four homologous s

  17. 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.

  18. A Chandra Study of the Rosette Star-forming Complex. III. The NGC 2237 Cluster and the Region's Star Formation History

    NASA Astrophysics Data System (ADS)

    Wang, Junfeng; Feigelson, Eric D.; Townsley, Leisa K.; Broos, Patrick S.; Román-Zúñiga, Carlos G.; Lada, Elizabeth; Garmire, Gordon

    2010-06-01

    We present high spatial resolution Chandra X-ray images of the NGC 2237 young stellar cluster on the periphery of the Rosette Nebula. We detect 168 X-ray sources, 80% of which have stellar counterparts in USNO, Two Micron All Sky Survey, and deep FLAMINGOS images. These constitute the first census of the cluster members with 0.2 <~ M <~ 2 M sun. Star locations in near-infrared color-magnitude diagrams indicate a cluster age around 2 Myr with a visual extinction of 1 <~ AV <~ 3 at 1.4 kpc, the distance of the Rosette Nebula's main cluster NGC 2244. We derive the K-band luminosity function and the X-ray luminosity function of the cluster, which indicate a population ~400-600 stars. The X-ray-selected sample shows a K-excess disk frequency of 13%. The young Class II counterparts are aligned in an arc ~3 pc long suggestive of a triggered formation process induced by the O stars in NGC 2244. The diskless Class III sources are more dispersed. Several X-ray emitting stars are located inside the molecular cloud and around gaseous pillars projecting from the cloud. These stars, together with a previously unreported optical outflow originating inside the cloud, indicate that star formation is continuing at a low level and the cluster is still growing. This X-ray view of young stars on the western side of the Rosette Nebula complements our earlier studies of the central cluster NGC 2244 and the embedded clusters on the eastern side of the Nebula. The large-scale distribution of the clusters and molecular material is consistent with a scenario in which the rich central NGC 2244 cluster formed first, and its expanding H II region triggered the formation of the now-unobscured satellite clusters Rosette Molecular Cloud (RMC) XA and NGC 2237. A large swept-up shell material around the H II region is now in a second phase of collect-and-collapse fragmentation, leading to the recent formation of subclusters. Other clusters deeper in the molecular cloud appear unaffected by the

  19. A CHANDRA STUDY OF THE ROSETTE STAR-FORMING COMPLEX. III. THE NGC 2237 CLUSTER AND THE REGION'S STAR FORMATION HISTORY

    SciTech Connect

    Wang Junfeng; Feigelson, Eric D.; Townsley, Leisa K.; Broos, Patrick S.; Garmire, Gordon; Roman-Zuniga, Carlos G.; Lada, Elizabeth

    2010-06-10

    We present high spatial resolution Chandra X-ray images of the NGC 2237 young stellar cluster on the periphery of the Rosette Nebula. We detect 168 X-ray sources, 80% of which have stellar counterparts in USNO, Two Micron All Sky Survey, and deep FLAMINGOS images. These constitute the first census of the cluster members with 0.2 {approx}< M {approx}< 2 M {sub sun}. Star locations in near-infrared color-magnitude diagrams indicate a cluster age around 2 Myr with a visual extinction of 1 {approx}< A{sub V} {approx}< 3 at 1.4 kpc, the distance of the Rosette Nebula's main cluster NGC 2244. We derive the K-band luminosity function and the X-ray luminosity function of the cluster, which indicate a population {approx}400-600 stars. The X-ray-selected sample shows a K-excess disk frequency of 13%. The young Class II counterparts are aligned in an arc {approx}3 pc long suggestive of a triggered formation process induced by the O stars in NGC 2244. The diskless Class III sources are more dispersed. Several X-ray emitting stars are located inside the molecular cloud and around gaseous pillars projecting from the cloud. These stars, together with a previously unreported optical outflow originating inside the cloud, indicate that star formation is continuing at a low level and the cluster is still growing. This X-ray view of young stars on the western side of the Rosette Nebula complements our earlier studies of the central cluster NGC 2244 and the embedded clusters on the eastern side of the Nebula. The large-scale distribution of the clusters and molecular material is consistent with a scenario in which the rich central NGC 2244 cluster formed first, and its expanding H II region triggered the formation of the now-unobscured satellite clusters Rosette Molecular Cloud (RMC) XA and NGC 2237. A large swept-up shell material around the H II region is now in a second phase of collect-and-collapse fragmentation, leading to the recent formation of subclusters. Other clusters deeper

  20. Structures and magnetic properties of an antiferromagnetically coupled polymeric copper(II) complex and ferromagnetically coupled hexanuclear nickel(II) clusters.

    PubMed

    Tandon, Santokh S; Bunge, Scott D; Sanchiz, Joaquin; Thompson, Laurence K

    2012-03-05

    Reactions between 2,6-diformyl-4-methylphenol (DFMF) and tris(hydroxymethyl) aminomethane (THMAM = H(3)L2) in the presence of copper(II) salts, CuX(2) (X = CH(3)CO(2)(-), BF(4)(-), ClO(4)(-), Cl(-), NO(3)(-)) and Ni(CH(3)CO(2))(2) or Ni(ClO(4))(2)/NaC(6)H(5)CO(2), sodium azide (NaN(3)), and triethylamine (TEA), in one pot self-assemble giving a coordination polymer consisting of repeating pentanuclear copper(II) clusters {[Cu(2)(H(5)L(2-))(μ-N(3))](2)[Cu(N(3))(4)]·2CH(3)OH}(n) (1) and hexanuclear Ni(II) complexes [Ni(6)(H(3)L1(-))(2)(HL2(2-))(2)(μ-N(3))(4)(CH(3)CO(2))(2)]·6C(3)H(7)NO·C(2)H(5)OH (2) and [Ni(6)(H(3)L1(-))(2)(HL2(2-))(2)(μ-N(3))(4)(C(6)H(5)CO(2))(2)]·3C(3)H(7)NO·3H(2)O·CH(3)OH (3). In 1, H(5)L(2-) and in 2 and 3 H(3)L1(-) and HL2(2-) represent doubly deprotonated, singly deprotonated, and doubly deprotonated Schiff-base ligands H(7)L and H(4)L1 and a tripodal ligand H(3)L2, respectively. 1 has a novel double-stranded ladder-like structure in which [Cu(N(3))(4)](2-) anions link single chains comprised of dinuclear cationic subunits [Cu(2)(H(5)L(2-))(μ-N(3))](+), forming a 3D structure of interconnected ladders through H bonding. Nickel(II) clusters 2 and 3 have very similar neutral hexanuclear cores in which six nickel(II) ions are bonded to two H(4)L1, two H(3)L2, four μ-azido, and two μ-CH(3)CO(2)(-)/μ-C(6)H(5)CO(2)(-) ligands. In each structure two terminal dinickel (Ni(2)) units are connected to the central dinickel unit through four doubly bridging end-on (EO) μ-azido and four triply bridging μ(3)-methoxy bridges organizing into hexanuclear units. In each terminal dinuclear unit two nickel centers are bridged through one μ-phenolate oxygen from H(3)L1(-), one μ(3)-methoxy oxygen from HL2(2-), and one μ-CH(3)CO(2)(-) (2)/μ-C(6)H(5)CO(2)(-) (3) ion. Bulk magnetization measurements on 1 show moderately strong antiferromagnetic coupling within the [Cu(2)] building block (J(1) = -113.5 cm(-1)). Bulk magnetization measurements on 2

  1. The first hexanuclear tungsten telluride clusters [W{sub 6}Te{sub 8}L{sub 6}]{sup n{minus}} as amine complexes with L = piperidine (n = 0) and L = pyridine (n = 1)

    SciTech Connect

    Xie, Xiaobing; McCarley, R.E.

    1996-05-08

    The authors wished to examine the W{sub 6}Te{sub 8} complexes with the idea that the W{sub 6}Te{sub 8} binary compound might be more stable toward disproportionation than the W{sub 6}S{sub 8}{sup 6a} and W{sub 6}Se{sub 8} examples. In this paper, the authors report the synthesis and structures of the first two molecular telluride complexes with M{sub 6}Te{sub 8}{sup {minus}} and M{sub 6}Te{sub 8} (M = Mo, W) cluster cores.

  2. Charge transfer initiated nitroxyl chemistry on free silver clusters Ag{sub 2-5}{sup-} : size effects and magic complexes.

    SciTech Connect

    Hagen, J.; Socaciu-Sieberg, L. D.; LeRoux, J.; Popolan, D.; Vajda, S.; Bernhardt, T. M.; Woste, L.; Chemistry; Freie Univ.; Univ. Ulm

    2007-01-01

    The reactivity of small silver cluster anions Ag{sub 2--5}- toward nitric oxide and mixtures of nitric oxide with carbon monoxide is investigated under multi-collision conditions in a radio frequency octopole ion trap at temperatures of 100 and 300 K. A strongly cluster size dependent reaction behavior is observed, where reactive fragmentation dominates for clusters with four or fewer atoms and only Ag{sub 5}- is able to form reaction products without dissociation of the metal cluster. The decisive role of charge transfer in the NO bond breakage, NO oxidation, and the formation of free NO{sub 2}{sup -} and N{sub 2}O{sub 4}{sup -} ions, as well as NxO(y>x)-ligands on the silver clusters is discussed. The mass spectrometric data reveal the particular stability of the reaction products AgN{sub 2}O{sub 4}{sup -} and Ag{sub 3}NO{sup -}. The reaction product mass spectra obtained for Ag{sub 5}{sup -} in the presence of NO and CO show the depletion of the NxO(y>x)-ligands on the metal cluster possibly involving the oxidation of CO to CO2.

  3. Meaningful Clusters

    SciTech Connect

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

    2004-05-26

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

  4. Photoelectron spectroscopy of molecular clusters

    NASA Astrophysics Data System (ADS)

    Zhang, Xu; Pitts, Jonathan; Zheng, Chaowen; Knee, Joseph L.

    1995-09-01

    High resolution photoelectron spectroscopy is applied to the study of molecular clusters. The primary species studied are fluorene-Arn complexes. Spectroscopy of the neutral S1 state has been performed on clusters as large as n equals 30. In order to study the photoelectron spectra of the clusters size selectively mass analyzed threshold ionization (MATI) is used which is a mass resolved version of the ZEKE technique. MATI spectroscopy has been applied to clusters up to n equals 5. The spectral shifts in the S1 origin and ion threshold are used as a measure of the relative stability of the different clusters. Using previous experimental and theoretical work on related clusters the structures of the clusters are inferred from the observed spectral shifts. In some cases multiple conformations of a particular cluster size are identified.

  5. Application of Balanced Scorecard in the Evaluation of a Complex Health System Intervention: 12 Months Post Intervention Findings from the BHOMA Intervention: A Cluster Randomised Trial in Zambia

    PubMed Central

    Mutale, Wilbroad; Stringer, Jeffrey; Chintu, Namwinga; Chilengi, Roma; Mwanamwenge, Margaret Tembo; Kasese, Nkatya; Balabanova, Dina; Spicer, Neil; Lewis, James; Ayles, Helen

    2014-01-01

    Introduction In many low income countries, the delivery of quality health services is hampered by health system-wide barriers which are often interlinked, however empirical evidence on how to assess the level and scope of these barriers is scarce. A balanced scorecard is a tool that allows for wider analysis of domains that are deemed important in achieving the overall vision of the health system. We present the quantitative results of the 12 months follow-up study applying the balanced scorecard approach in the BHOMA intervention with the aim of demonstrating the utility of the balanced scorecard in evaluating multiple building blocks in a trial setting. Methods The BHOMA is a cluster randomised trial that aims to strengthen the health system in three rural districts in Zambia. The intervention aims to improve clinical care quality by implementing practical tools that establish clear clinical care standards through intensive clinic implementations. This paper reports the findings of the follow-up health facility survey that was conducted after 12 months of intervention implementation. Comparisons were made between those facilities in the intervention and control sites. STATA version 12 was used for analysis. Results The study found significant mean differences between intervention(I) and control (C) sites in the following domains: Training domain (Mean I:C; 87.5.vs 61.1, mean difference 23.3, p = 0.031), adult clinical observation domain (mean I:C; 73.3 vs.58.0, mean difference 10.9, p = 0.02 ) and health information domain (mean I:C; 63.6 vs.56.1, mean difference 6.8, p = 0.01. There was no gender differences in adult service satisfaction. Governance and motivation scores did not differ between control and intervention sites. Conclusion This study demonstrates the utility of the balanced scorecard in assessing multiple elements of the health system. Using system wide approaches and triangulating data collection methods seems to be key to successful

  6. Stormy weather in galaxy clusters

    PubMed

    Burns

    1998-04-17

    Recent x-ray, optical, and radio observations coupled with particle and gas dynamics numerical simulations reveal an unexpectedly complex environment within clusters of galaxies, driven by ongoing accretion of matter from large-scale supercluster filaments. Mergers between clusters and continuous infall of dark matter and baryons from the cluster periphery produce long-lived "stormy weather" within the gaseous cluster atmosphere-shocks, turbulence, and winds of more than 1000 kilometers per second. This weather may be responsible for shaping a rich variety of extended radio sources, which in turn act as "barometers" and "anemometers" of cluster weather.

  7. Health- and disease-associated species clusters in complex natural biofilms determine the innate immune response in oral epithelial cells during biofilm maturation.

    PubMed

    Langfeldt, Daniela; Neulinger, Sven C; Stiesch, Meike; Stumpp, Nico; Bang, Corinna; Schmitz, Ruth A; Eberhard, Jörg

    2014-11-01

    The aim of the present study was to verify our hypothesis concerning the differential induction of various antimicrobial and immunomodulatory responses in oral epithelial cells by diverse bacterial species clusters. For this purpose, oral biofilms between 1 and 14 days of maturation (36 volunteers) were co-incubated with gingival epithelial cells. Subsequently, human β-defensin (hBD)-2, hBD-3, LL-37, interleukin (IL)-1β, IL-6, IL-8 and IL-10 mRNA expression profiles were quantified by quantitative reverse transcription PCR. The correlation between bacterial species and the host innate immune response was determined by relating these results to existing 16S rRNA phylogenetic analysis by amplicon sequencing (Langfeldt et al. 2014. PLoS One 9: e87449). Data were analysed by multiple factor analysis. Transcription of hBD-2 and hBD-3 was significantly associated with the abundance of species of the Prevotella cluster and the absence of species of the Streptococcus cluster. IL-1β, -6, -8 and -10 mRNA syntheses were significant correlated with Leptotrichia species [Leptotrichia 302H02 (0.448, P < 0.0001), Leptotrichia nbw822e09c1 (0.214, P = 0.008) and Leptotrichia wadei (0.218, P = 0.007)] of the Prevotella cluster. In the third dimension IL-10 and members of the Prevotella cluster were negatively correlated, whereas hBD-3 and IL-1β, IL-6 and IL-8 were positive correlated to axis 3, like members of the Proteobacteria cluster. In conclusion, distinct species of health- and disease-associated bacterial clusters induce antibacterial or immunomodulatory reactions in oral epithelial cells during early stages of bacteria-host interactions.

  8. About the Clusters Program

    EPA Pesticide Factsheets

    The Environmental Technology Innovation Clusters Program advises cluster organizations, encourages collaboration between clusters, tracks U.S. environmental technology clusters, and connects EPA programs to cluster needs.

  9. Investigations of the effect of the non-manganese metal in heterometallic-oxido cluster models of the oxygen evolving complex of photosystem II: lanthanides as substitutes for calcium.

    PubMed

    Lin, Po-Heng; Takase, Michael K; Agapie, Theodor

    2015-01-05

    We report the syntheses and electrochemical properties of nine new clusters ([LLnMn(IV)3O4(OAc)3(DMF)n](+) (Ln = La(3+), Ce(3+), Nd(3+), Eu(3+), Gd(3+), Tb(3+), Dy(3+), Yb(3+), and Lu(3+), n = 2 or 3)) supported by a ligand (L(3-)) based on a 1,3,5-triarylbenzene motif appended with alkoxide and pyridine donors. All complexes were obtained by metal substitution of Ca(2+) with lanthanides upon treatment of previously reported LMn3CaO4(OAc)3(THF) with Ln(OTf)3. Structural characterization confirmed that the clusters contain the [LnMn3O4] cubane motif. The effect of the redox-inactive centers on the electronic properties of the Mn3O4 cores was investigated by cyclic voltammetry. A linear correlation between the redox potential of the cluster and the ionic radii or pKa of the lanthanide metal ion was observed. Chemical reduction of the LMn(IV)3GdO4(OAc)3(DMF)2 cluster with decamethylferrocene, resulted in the formation of LGdMn(IV)2Mn(III)O4(OAc)3(DMF)2, a rare example of mixed-valence [MMn3O4] cubane. The lanthanide-coordinated ligands can be substituted with other donors, including water, the biological substrate.

  10. Data Clustering

    NASA Astrophysics Data System (ADS)

    Wagstaff, Kiri L.

    2012-03-01

    On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained

  11. Clustered protocadherins and neuronal diversity.

    PubMed

    Hirayama, Teruyoshi; Yagi, Takeshi

    2013-01-01

    Neuronal diversity is a fundamental requirement for complex neuronal networks and brain function. The clustered protocadherin (Pcdh) family possesses several characteristic features that are important for the molecular basis of neuronal diversity. Clustered Pcdhs are expressed predominantly in the central nervous system, in neurites, growth cones, and synapses. They consist of about 60 isoforms, and their expression is stochastically and combinatorially regulated in individual neurons. The multiple clustered Pcdhs expressed in individual neurons form heteromultimeric protein complexes that exhibit homophilic adhesion properties. Theoretically, the clustered Pcdhs could generate more than 3×10(10) possible variations in each neuron and 12,720 types of cis-tetramers per neuron. The clustered Pcdhs are important for normal neuronal development. The clustered Pcdh genes have also attracted attention as a target for epigenetic regulation.

  12. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa.

    PubMed

    van Duijn, Esther; Barbu, Ioana M; Barendregt, Arjan; Jore, Matthijs M; Wiedenheft, Blake; Lundgren, Magnus; Westra, Edze R; Brouns, Stan J J; Doudna, Jennifer A; van der Oost, John; Heck, Albert J R

    2012-11-01

    The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA. Recently, a cryo-electron microscopy structure of Cascade revealed that the CRISPR RNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes.

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

    PubMed

    Yan, Robert; Adinolfi, Salvatore; Pastore, Annalisa

    2015-09-01

    Fe-S cluster biogenesis is an essential pathway coordinated by a network of protein-protein interactions whose functions include desulfurase activity, substrate delivery, electron transfer and product transfer. In an effort to understand the intricacies of the pathway, we have developed an in vitro assay to follow the ferredoxin role in electron transfer during Fe-S cluster assembly. Previously, assays have relied upon the non-physiological reducing agents dithionite and dithiothreitol to assess function. We have addressed this shortcoming by using electron transfer between NADPH and ferredoxin-NADP-reductase to reduce ferredoxin. Our results show that this trio of electron transfer partners are sufficient to sustain the reaction in in vitro studies, albeit with a rate slower compared with DTT-mediated cluster assembly. We also show that, despite overlapping with the CyaY protein in binding to IscS, Fdx does not interfere with the inhibitory activity of this protein. We suggest explanations for these observations which have important consequences for understanding the mechanism of cluster formation. Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. Copyright © 2015. Published by Elsevier B.V.

  14. Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures.

    PubMed

    Shoji, Mitsuo; Isobe, Hiroshi; Nakajima, Takahito; Shigeta, Yasuteru; Suga, Michihiro; Akita, Fusamichi; Shen, Jian-Ren; Yamaguchi, Kizashi

    2017-03-09

    Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mna(4)-Mnd(1) distance determined by QM/MM was about 5.0 Å for the S3 structure without an inserted hydroxide anion, but this is elongated by 0.2-0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O-O bond formation in water oxidation by the OEC of PSII.

  15. Light cluster production at NICA

    NASA Astrophysics Data System (ADS)

    Bastian, N.-U.; Batyuk, P.; Blaschke, D.; Danielewicz, P.; Ivanov, Yu. B.; Karpenko, Iu.; Röpke, G.; Rogachevsky, O.; Wolter, H. H.

    2016-08-01

    Light cluster production at the NICA accelerator complex offers unique possibilities to use these states as "rare probes" of in-medium characteristics such as phase space occupation and early flow. In order to explain this statement, in this contribution theoretical considerations from the nuclear statistical equilibrium model and from a quantum statistical model of cluster production are supplemented with a discussion of a transport model for light cluster formation and with results from hydrodynamic simulations combined with the coalescence model.

  16. Hierarchical clustering in minimum spanning trees

    NASA Astrophysics Data System (ADS)

    Yu, Meichen; Hillebrand, Arjan; Tewarie, Prejaas; Meier, Jil; van Dijk, Bob; Van Mieghem, Piet; Stam, Cornelis Jan

    2015-02-01

    The identification of clusters or communities in complex networks is a reappearing problem. The minimum spanning tree (MST), the tree connecting all nodes with minimum total weight, is regarded as an important transport backbone of the original weighted graph. We hypothesize that the clustering of the MST reveals insight in the hierarchical structure of weighted graphs. However, existing theories and algorithms have difficulties to define and identify clusters in trees. Here, we first define clustering in trees and then propose a tree agglomerative hierarchical clustering (TAHC) method for the detection of clusters in MSTs. We then demonstrate that the TAHC method can detect clusters in artificial trees, and also in MSTs of weighted social networks, for which the clusters are in agreement with the previously reported clusters of the original weighted networks. Our results therefore not only indicate that clusters can be found in MSTs, but also that the MSTs contain information about the underlying clusters of the original weighted network.

  17. Cool Cluster Correctly Correlated

    SciTech Connect

    Varganov, Sergey Aleksandrovich

    2005-01-01

    Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, since empirical and semiempirical methods rely on simple models with many parameters, it is often difficult to estimate the quantitative and even qualitative accuracy of the results. On the other hand, because of significant advances in quantum chemical methods and computer capabilities, it is now possible to do high quality ab-initio calculations not only on systems of few atoms but on clusters of practical interest as well. In addition to accurate results for specific clusters, such methods can be used for benchmarking of different empirical and semiempirical approaches. The atomic clusters studied in this work contain from a few atoms to

  18. A series of novel gallium and indium borates constructed from [B{sub 5}O{sub 8}(OH){sub 2}]{sup 3-} clusters and metal complex linkers

    SciTech Connect

    Cheng, Lin; Yang, Guo-Yu

    2013-02-15

    Four novel gallium and indium borates, [M(en){sub 2}][B{sub 5}O{sub 8}(OH){sub 2}]{center_dot}H{sub 2}O (M=Ga (1), In (2); en=ethylenediamine), [In(dap){sub 2}][B{sub 5}O{sub 8}(OH){sub 2}]{center_dot}H{sub 2}O (3, dap=1,2-diaminopropane), [In(dien)][B{sub 5}O{sub 8}(OH){sub 2}] (4, dien=diethylenetriamine), have been hydrothermally synthesized and characterized by IR spectra, elemental analyses, powder X-ray diffraction, single crystal X-ray diffraction, and thermogravimetric analyses. Compounds 1, 2 and 3 are isostructural and consist of one-dimensional (1-D) chains built up from [B{sub 5}O{sub 8}(OH){sub 2}]{sup 3-} clusters and Ga-/In-complex linkers. The structure of compound 4 features a 1-D chain containing 8-member rings built by [B{sub 5}O{sub 8}(OH){sub 2}]{sup 3-} clusters and {l_brace}In{sub 2}O{sub 4}{r_brace} dimeric cluster linkers which have never observed in the structural chemistry of borates to date. The H-bonding interactions between adjacent chains lead to 3-D supramolecular network structure. - Graphical abstract: Four novel gallium and indium borates with one-dimensional structures built by B{sub 5}O{sub 8}(OH){sub 2}{sup 3+} clusters and metal complex linkers have been successfully synthesized under hydrothermal conditions. Highlights: Black-Right-Pointing-Pointer Four new Ga/In borates have been hydrothermally made. Black-Right-Pointing-Pointer The helical/ribbon-like chains made of B{sub 5}O{sub 8}(OH){sub 2}{sup 3+} clusters and Ga-/In-complex linkers. Black-Right-Pointing-Pointer The chains form novel 3-D supermolecule framework via H-bonds.

  19. Acid clusters

    SciTech Connect

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

    1986-04-01

    Molecular clusters can be considered to be the smallest size range of an aerosol particle size distribution. Nucleation from the gas phase to particles or droplets involves the formation of clusters in the initial stages. Consequently, knowledge of the properties and formation of clusters containing acids contribute to an understanding of acid rain. This paper presents an overview of results obtained in the laboratory on the formation and stability of both neutral and ionized acid clusters. With free jet expansion techniques, the authors have produced clusters of aqueous nitric acid, aqueous hydrochloric acid, aqueous sulfuric acid, acetic acid and aqueous sulfur dioxide. For analogy to buffering, the formation of clusters containing ammonia have also been examined. These have included ammonia with aqueous nitric acid, hydrogen sulfide and sulfur dioxide. The basic experiment involves expansion of vapor through a nozzle, collimation of the jet with a skimmer to form a well-directed molecular beam, and detection of clusters via electron impact ionization and mass spectrometry. Some variations include the introduction of a reactive gas into vacuum near the expansion as described elsewhere and the implementation of an electrostatic quadrupolar field to examine the polarity of the neutral clusters.

  20. Synthesis, characterization, and electronic structures of a series of two-dimensional trimetallic cluster complexes, Ru3(CO)9(mu-SnPh2)3[Pt(PBu(t)3)]x, x = 0-3.

    PubMed

    Adams, Richard D; Captain, Burjor; Hall, Michael B; Trufan, Eszter; Yang, Xinzheng

    2007-10-10

    The triruthenium-tritin cluster complex, Ru3(CO)9(mu-SnPh2)3, 13 was obtained from the reaction of Ru3(CO)12 with Ph3SnH. Compound 13 reacts with Pt(PBut3)2 to yield three new Pt(PBut3) adducts of 13 Ru3(CO)9(mu-SnPh2)3[Pt(PBut3)]x, 14-16 x = 1 - 3 formed by the addition of Pt(PBut3) groups to the Ru-Sn bonds. The new complexes form a novel series of trimetallic complexes having planar arrangements of the metal atoms. The UV-vis absorptions of the four complexes shift progressively to longer wavelengths as the number of platinum atoms is added to the cluster. The electronic structures of these complexes have been investigated in the ground and excited states by density functional theory and time-dependent density functional theory, and this has provided a detailed understanding of the metal-metal bonding and electronic transitions that are responsible for their UV-vis absorption properties. The predicted absorption maximum for the model structures for 13, 14, 15, and 16 at 465, 508, 556, and 585 nm differ only 4-18 nm from the experimental values of 474, 490, 552, and 576 nm. The shift of principal UV-vis absorption can be explained by a lowering of the HOMO-LUMO energy gap due to interactions of the platinum atoms with the HOMO and LUMO of the Ru3Sn3 core.

  1. Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes

    SciTech Connect

    Serrano, Pauline N.; Wang, Hongxin; Crack, Jason; Prior, Christopher; Hutchings, Matthew; Thompson, Andrew; Kamali, Seed; Yoda, Yoshitaka; Zhao, Jiyong; Hu, Michael; Alp, Ercan E.; Oganesyan, Vasily; Le Brun, Nick

    2016-11-14

    The reaction of protein-bound iron–sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2(NO)4(Cys)2]) and Roussin's Black Salt (RBS, [Fe4(NO)7S3]. In the latter case, the absence of 32S/34S shifts in the Fe−S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates.

  2. Photoionization Spectroscopy of Clusters

    NASA Astrophysics Data System (ADS)

    Dao, Phan Danh

    Studies of the electronic energies in van der Waals molecules (sometimes referred to as clusters or complexes) help one unravel the microscopic details of the condensed state. Furthermore, they provide the connection between gas-phase and condensed-phase sciences. To achieve this goal, we undertake (1) the spectroscopic studies of van der Waals complexes; (2) the determination of the ionization energies of van der Waals complexes, as well as of mixed alkali metal clusters (e.g., K(,n)O); and (3) the studies of processes that occur upon and after the ionization of van der Waals molecules (namely, dissociation and intracluster reactions). A brief discussion of the non-equilibrium synthesis of weakly bound molecules is given. The operation and performance of the pulsed supersonic jet are described along with some theoretical considerations. The characteristic features of the technique of laser ionization are presented with emphasis on its performance as a spectroscopic tool. Resonance two-photon ionization and time-of-flight mass spectrometry provide us with the tool to measure the perturbed electronic excited state of van der Waals complexes. In these studies, the chromophore species is an aromatic molecule having a single ring (phenylacetylene and para-xylene); and the "solvent" species are rare gas atoms, as well as a variey of molecules. In the case of chromophore-rare gas complexes, the S(,1) excited state is red-shifted, with respect to the nascent chromophore, and the magnitude of the shift shows a definite dependence on the atomic polarizability. Other salient trends of the measured spectral shifts are also discussed. In the measurement of complex ionization energies, the use of two tunable UV lasers is required. With p-xylene(.)Ar(,n) complexes (n = 1-6), these energies vary almost linearly with the number of atoms. Also discussed in the text are the effects of ionization in a weak DC field. A simple hydrogenic model of field-ionization is experimentally

  3. CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

    PubMed

    Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

    2017-08-31

    Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

  4. Structural transitions in clusters.

    PubMed

    Hartke, Bernd

    2002-05-03

    If one adds more particles to a cluster, the energetically optimal structure is neither preserved nor does it change in a continuous fashion. Instead, one finds several cluster size regions where one structural principle dominates almost without exception, and rather narrow boundary regions in-between. The structure of the solid is usually reached only at relatively large sizes, after more than one structural transition. The occurrence of this general phenomenon of size-dependent structural transitions does not seem to depend on the nature of the particles, it is found for atomic, molecular, homogeneous, and heterogeneous clusters alike. Clearly, it is a collective many-body phenomenon which can in principle be calculated but not understood in a fully reductionistic manner. Actual calculations with sufficient accuracy are not feasible today, because of the enormous computational expense, even when unconventional evolutionary algorithms are employed for global geometry optimization. Therefore, simple rules for cluster structures are highly desirable. In fact, we are dealing here not just with the academic quest for linkages between cluster structure and features of the potential energy surface, but structural transitions in clusters are also of immediate relevance for many natural and industrial processes, ranging from crystal growth all the way to nanotechnology. This article provides an exemplary overview of research on this topic, from simple model systems where first qualitative explanations start to be successful, up to more realistic complex systems which are still beyond our understanding.

  5. Quintuplet Cluster

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.

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

    PubMed

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

    2010-10-28

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

  7. Spitzer Clusters

    NASA Astrophysics Data System (ADS)

    Krick, Kessica

    This proposal is a specific response to the strategic goal of NASA's research program to "discover how the universe works and explore how the universe evolved into its present form." Towards this goal, we propose to mine the Spitzer archive for all observations of galaxy groups and clusters for the purpose of studying galaxy evolution in clusters, contamination rates for Sunyaev Zeldovich cluster surveys, and to provide a database of Spitzer observed clusters to the broader community. Funding from this proposal will go towards two years of support for a Postdoc to do this work. After searching the Spitzer Heritage Archive, we have found 194 unique galaxy groups and clusters that have data from both the Infrared array camera (IRAC; Fazio et al. 2004) at 3.6 - 8 microns and the multiband imaging photometer for Spitzer (MIPS; Rieke et al. 2004) at 24microns. This large sample will add value beyond the individual datasets because it will be a larger sample of IR clusters than ever before and will have sufficient diversity in mass, redshift, and dynamical state to allow us to differentiate amongst the effects of these cluster properties. An infrared sample is important because it is unaffected by dust extinction while at the same time is an excellent measure of both stellar mass (IRAC wavelengths) and star formation rate (MIPS wavelengths). Additionally, IRAC can be used to differentiate star forming galaxies (SFG) from active galactic nuclei (AGN), due to their different spectral shapes in this wavelength regime. Specifically, we intend to identify SFG and AGN in galaxy groups and clusters. Groups and clusters differ from the field because the galaxy densities are higher, there is a large potential well due mainly to the mass of the dark matter, and there is hot X-ray gas (the intracluster medium; ICM). We will examine the impact of these differences in environment on galaxy formation by comparing cluster properties of AGN and SFG to those in the field. Also, we will

  8. Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Miller, Christopher J. Miller

    2012-03-01

    There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

  9. Correlation between structure and magnetic spin state of the manganese cluster in the oxygen-evolving complex of photosystem II in the S2 state: determination by X-ray absorption spectroscopy.

    PubMed

    Liang, W; Latimer, M J; Dau, H; Roelofs, T A; Yachandra, V K; Sauer, K; Klein, M P

    1994-04-26

    The structure of the manganese cluster in the S2 state with the g approximately 4 EPR signal (S2-g4 state) generated by 130 K illumination of photosystem II (PSII) membranes prepared from spinach has been investigated by X-ray absorption spectroscopy. The Mn X-ray absorption K-edge spectra of the S2-g4 state not only show a shift of the inflection point to higher energy from the S1 state but also reveal a different edge shape from that of the S2 state with the multiline signal (S2-MLS state). Extended X-ray absorption fine structure (EXAFS) studies of the Mn K-edge show that the structure of the Mn cluster in the S2-g4 state is distinctly different from those in the S2-MLS or S1 states. In the S2-g4 state, the second shell of back-scatters from the Mn absorber is found to contain two Mn-Mn distances of 2.73 and 2.85 A. We interpret this to indicate the presence of two nonequivalent di-mu-oxo-bridged Mn binuclear structures in the Mn cluster of the S2-g4 state. The third shell of the S2-g4 state at about 3.3 A also contains increased heterogeneity. By contrast, very little distance disorder was found to exist in the second shell of the S1 or S2-MLS states. A mechanism is proposed to explain these results in the context of our model for the Mn cluster and the EPR properties of the Mn complex in the S2 state.

  10. X-ray Absorption and Emission Spectroscopic Studies of [L2Fe2S2]n Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters

    PubMed Central

    2016-01-01

    Herein, a systematic study of [L2Fe2S2]n model complexes (where L = bis(benzimidazolato) and n = 2-, 3-, 4-) has been carried out using iron and sulfur K-edge X-ray absorption (XAS) and iron Kβ and valence-to-core X-ray emission spectroscopies (XES). These data are used as a test set to evaluate the relative strengths and weaknesses of X-ray core level spectroscopies in assessing redox changes in iron–sulfur clusters. The results are correlated to density functional theory (DFT) calculations of the spectra in order to further support the quantitative information that can be extracted from the experimental data. It is demonstrated that due to canceling effects of covalency and spin state, the information that can be extracted from Fe Kβ XES mainlines is limited. However, a careful analysis of the Fe K-edge XAS data shows that localized valence vs delocalized valence species may be differentiated on the basis of the pre-edge and K-edge energies. These findings are then applied to existing literature Fe K-edge XAS data on the iron protein, P-cluster, and FeMoco sites of nitrogenase. The ability to assess the extent of delocalization in the iron protein vs the P-cluster is highlighted. In addition, possible charge states for FeMoco on the basis of Fe K-edge XAS data are discussed. This study provides an important reference for future X-ray spectroscopic studies of iron–sulfur clusters. PMID:27097289

  11. A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) in Haloferax volcanii*

    PubMed Central

    Brendel, Jutta; Stoll, Britta; Lange, Sita J.; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A.; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

    2014-01-01

    The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA. PMID:24459147

  12. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in Haloferax volcanii.

    PubMed

    Brendel, Jutta; Stoll, Britta; Lange, Sita J; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita

    2014-03-07

    The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1-8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.

  13. Single-step co-deposition of nanostructured tungsten oxide supported gold nanoparticles using a gold-phosphine cluster complex as the gold precursor

    NASA Astrophysics Data System (ADS)

    Molkenova, Anara; Sarip, Rozie; Sathasivam, Sanjay; Umek, Polona; Vallejos, Stella; Blackman, Chris; Hogarth, Graeme; Sankar, Gopinathan

    2014-12-01

    The use of a molecular gold organometallic cluster in chemical vapour deposition is reported, and it is utilized, together with a tungsten oxide precursor, for the single-step co-deposition of (nanostructured) tungsten oxide supported gold nanoparticles (NPs). The deposited gold-NP and tungsten oxide supported gold-NP are highly active catalysts for benzyl alcohol oxidation; both show higher activity than SiO2 supported gold-NP synthesized via a solution-phase method, and tungsten oxide supported gold-NP show excellent selectivity for conversion to benzaldehyde.

  14. Star clusters

    NASA Astrophysics Data System (ADS)

    Labhardt, Lukas; Binggeli, Bruno

    Star clusters are at the heart of astronomy, being key objects for our understanding of stellar evolution and galactic structure. Observations with the Hubble Space Telescope and other modern equipment have revealed fascinating new facts about these galactic building blocks. This book provides two comprehensive and up-to-date, pedagogically designed reviews on star clusters by two well-known experts in the field. Bruce Carney presents our current knowledge of the relative and absolute ages of globular clusters and the chemical history of our Galaxy. Bill Harris addresses globular clusters in external galaxies and their use as tracers of galaxy formation and cosmic distance indicators. The book is written for graduate students as well as professionals in astronomy and astrophysics.

  15. Occupational Clusters.

    ERIC Educational Resources Information Center

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  16. Cluster generator

    DOEpatents

    Donchev, Todor I.; Petrov, Ivan G.

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  17. The simulation model of the computer cluster

    NASA Astrophysics Data System (ADS)

    Sokolova, V. V.; Zamyatina, O. M.

    2017-01-01

    Simulation is often used in cases when it is impossible to carry out experiments with real complex objects. The article represents the description of the computer cluster simulation model. Parameters, which affect the cluster performance, were selected, a simulation model was designed, and experiments were conducted. The obtained model allowed finding the optimal variant of the cluster performance, which consists of five computers.

  18. Insight into genome variability in the Fusarium Incarnatum-equiseti species complex through comparative analysis of secondary metabolic biosynthetic gene clusters

    USDA-ARS?s Scientific Manuscript database

    The genus Fusarium comprises 22 species complexes that together include approximately 300 phylogenetically distinct species. A major focus in Fusarium literature is to understand the genetic basis of niche specialization, secondary metabolites (SM) production, and host interactions in closely relate...

  19. A Complex Insertion Sequence Cluster at a Point of Interaction between the Linear Plasmid SCP1 and the Linear Chromosome of Streptomyces coelicolor A3(2)

    PubMed Central

    Yamasaki, Masayuki; Miyashita, Kiyotaka; Cullum, John; Kinashi, Haruyasu

    2000-01-01

    The giant linear plasmid SCP1 can integrate into the central region of the linear chromosome of Streptomyces coelicolor A3(2). Nucleotide sequence analysis around the target site for SCP1 integration in strain M145 identified a total of five copies of four insertion sequences (ISs) in a 6.5-kb DNA stretch. Three of the four (IS468, IS469, and IS470) are new IS elements, and the other is IS466. All of these elements contain one open reading frame which encodes a transposase-like protein. Two copies of IS468 (IS468A and -B) are tandemly aligned at the left end of the cluster. Following these, IS469 and IS466 are located in a tail-to-tail orientation with 69.3% identity to each other. IS470 is located at the right end of the cluster. The activities of IS466 and IS468 were demonstrated by transposition experiments and sequence comparison of several copies, respectively. PMID:10809688

  20. K-means cluster analysis of rehabilitation service users in the Home Health Care System of Ontario: examining the heterogeneity of a complex geriatric population.

    PubMed

    Armstrong, Joshua J; Zhu, Mu; Hirdes, John P; Stolee, Paul

    2012-12-01

    To examine the heterogeneity of home care clients who use rehabilitation services by using the K-means algorithm to identify previously unknown patterns of clinical characteristics. Observational study of secondary data. Home care system. Assessment information was collected on 150,253 home care clients using the provincially mandated Resident Assessment Instrument-Home Care (RAI-HC) data system. Not applicable. Assessment information from every long-stay (>60 d) home care client that entered the home care system between 2005 and 2008 and used rehabilitation services within 3 months of their initial assessment was analyzed. The K-means clustering algorithm was applied using 37 variables from the RAI-HC assessment. The K-means cluster analysis resulted in the identification of 7 relatively homogeneous subgroups that differed on characteristics such as age, sex, cognition, and functional impairment. Client profiles were created to illustrate the diversity of this geriatric population. The K-means algorithm provided a useful way to segment a heterogeneous rehabilitation client population into more homogeneous subgroups. This analysis provides an enhanced understanding of client characteristics and needs, and could enable more appropriate targeting of rehabilitation services for home care clients. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  1. First principle-based AKMC modelling of the formation and medium-term evolution of point defect and solute-rich clusters in a neutron irradiated complex Fe-CuMnNiSiP alloy representative of reactor pressure vessel steels

    NASA Astrophysics Data System (ADS)

    Ngayam-Happy, R.; Becquart, C. S.; Domain, C.

    2013-09-01

    The formation and medium-term evolution of point defect and solute-rich clusters under neutron irradiation have been modelled in a complex Fe-CuMnNiSiP alloy representative of RPV steels, by means of first principle-based atomistic kinetic Monte Carlo simulations. The results obtained reproduce most features observed in available experimental studies, highlighting the very good agreement between both series. According to simulation, solute-rich clusters form and develop via an induced segregation mechanism on either the vacancy or interstitial clusters, and these point defect clusters are efficiently generated only in cascade debris and not Frenkel pair flux. The results have revealed the existence of two distinct populations of clusters with different characteristic features. Solute-rich clusters in the first group are bound essentially to interstitial clusters and they are enriched in Mn mostly, but also Ni to a lesser extent. Over the low dose regime, their density increases in the alloy as a result of the accumulation of highly stable interstitial clusters. In the second group, the solute-rich clusters are merged with vacancy clusters, and they contain mostly Cu and Si, but also substantial amount of Mn and Ni. The formation of a sub-population of pure solute clusters has been observed, which results from annihilation of the low stable vacancy clusters on sinks. The results indicate finally that the Mn content in clusters is up to 50%, Cu, Si, and Ni sharing the other half in more or less equivalent amounts. This composition has not demonstrated any noticeable modification with increasing dose over irradiation.

  2. DICON: interactive visual analysis of multidimensional clusters.

    PubMed

    Cao, Nan; Gotz, David; Sun, Jimeng; Qu, Huamin

    2011-12-01

    Clustering as a fundamental data analysis technique has been widely used in many analytic applications. However, it is often difficult for users to understand and evaluate multidimensional clustering results, especially the quality of clusters and their semantics. For large and complex data, high-level statistical information about the clusters is often needed for users to evaluate cluster quality while a detailed display of multidimensional attributes of the data is necessary to understand the meaning of clusters. In this paper, we introduce DICON, an icon-based cluster visualization that embeds statistical information into a multi-attribute display to facilitate cluster interpretation, evaluation, and comparison. We design a treemap-like icon to represent a multidimensional cluster, and the quality of the cluster can be conveniently evaluated with the embedded statistical information. We further develop a novel layout algorithm which can generate similar icons for similar clusters, making comparisons of clusters easier. User interaction and clutter reduction are integrated into the system to help users more effectively analyze and refine clustering results for large datasets. We demonstrate the power of DICON through a user study and a case study in the healthcare domain. Our evaluation shows the benefits of the technique, especially in support of complex multidimensional cluster analysis.

  3. The complex behavior of the Pd 7 cluster supported on TiO 2 (110) during CO oxidation: adsorbate-driven promoting effect

    SciTech Connect

    An, Wei; Liu, Ping

    2016-09-07

    When using the TiO2(110)-supported Pd7 cluster as a model catalyst, we identified the dynamics of supported metal nanoparticles using density functional theory calculations, at the sub-nanometer scale and under reactive environments. Increasing the CO coverage can induce a structural transformation from Pd7-3D/TiO2(110) at low coverage to Pd7-2D/TiO2(110) at the saturation coverage wherein CO saturation-driven Pd7-2D/TiO2(110) structure displays superior CO oxidation activity at the interfacial sites, which are highly active for catalyzing O2 dissociation and CO oxidation via bifunctional synergy.

  4. The complex behavior of the Pd 7 cluster supported on TiO 2 (110) during CO oxidation: adsorbate-driven promoting effect

    DOE PAGES

    An, Wei; Liu, Ping

    2016-09-07

    When using the TiO2(110)-supported Pd7 cluster as a model catalyst, we identified the dynamics of supported metal nanoparticles using density functional theory calculations, at the sub-nanometer scale and under reactive environments. Increasing the CO coverage can induce a structural transformation from Pd7-3D/TiO2(110) at low coverage to Pd7-2D/TiO2(110) at the saturation coverage wherein CO saturation-driven Pd7-2D/TiO2(110) structure displays superior CO oxidation activity at the interfacial sites, which are highly active for catalyzing O2 dissociation and CO oxidation via bifunctional synergy.

  5. The complex behavior of the Pd 7 cluster supported on TiO 2 (110) during CO oxidation: adsorbate-driven promoting effect

    SciTech Connect

    An, Wei; Liu, Ping

    2016-09-07

    When using the TiO2(110)-supported Pd7 cluster as a model catalyst, we identified the dynamics of supported metal nanoparticles using density functional theory calculations, at the sub-nanometer scale and under reactive environments. Increasing the CO coverage can induce a structural transformation from Pd7-3D/TiO2(110) at low coverage to Pd7-2D/TiO2(110) at the saturation coverage wherein CO saturation-driven Pd7-2D/TiO2(110) structure displays superior CO oxidation activity at the interfacial sites, which are highly active for catalyzing O2 dissociation and CO oxidation via bifunctional synergy.

  6. Clusters, factories and domains

    PubMed Central

    Gillespie, Peter J

    2010-01-01

    During S-phase of the cell cycle, chromosomal DNA is replicated according to a complex replication timing program, with megabase-sized domains replicating at different times. DNA fiber analysis reveals that clusters of adjacent replication origins fire near-synchronously. Analysis of replicating cells by light microscopy shows that DNA synthesis occurs in discrete foci or factories. The relationship between timing domains, origin clusters and replication foci is currently unclear. Recent work, using a hybrid Xenopus/hamster replication system, has shown that when CDK levels are manipulated during S-phase the activation of replication factories can be uncoupled from progression through the replication timing program. Here, we use data from this hybrid system to investigate potential relationships between timing domains, origin clusters and replication foci. We suggest that each timing domain typically comprises several replicon clusters, which are usually processed sequentially by replication factories. We discuss how replication might be regulated at different levels to create this complex organization and the potential involvement of CDKs in this process. PMID:20724827

  7. Active matter clusters at interfaces.

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    2016-03-01

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor formation and metastasis, colonies of bacteria in a biofilm, or even flocks of birds and schools of fish at the macro-scale. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit that moves in two dimensions by exerting a force/torque per unit area whose magnitude depends on the nature of the local environment. We find that low speed (overdamped) clusters encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds (underdamped), where inertia dominates, the clusters show more complex behaviors crossing the interface multiple times and deviating from the predictable refraction and reflection for the low velocity clusters. We then present an extreme limit of the model in the absence of rotational damping where clusters can become stuck spiraling along the interface or move in large circular trajectories after leaving the interface. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  8. The SMART CLUSTER METHOD - adaptive earthquake cluster analysis and declustering

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas; Daniell, James; Wenzel, Friedemann

    2016-04-01

    Earthquake declustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity with usual applications comprising of probabilistic seismic hazard assessments (PSHAs) and earthquake prediction methods. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation. Various methods have been developed to address this issue from other researchers. These have differing ranges of complexity ranging from rather simple statistical window methods to complex epidemic models. This study introduces the smart cluster method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal identification. Hereby, an adaptive search algorithm for data point clusters is adopted. It uses the earthquake density in the spatio-temporal neighbourhood of each event to adjust the search properties. The identified clusters are subsequently analysed to determine directional anisotropy, focussing on a strong correlation along the rupture plane and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010/2011 Darfield-Christchurch events, an adaptive classification procedure is applied to disassemble subsequent ruptures which may have been grouped into an individual cluster using near-field searches, support vector machines and temporal splitting. The steering parameters of the search behaviour are linked to local earthquake properties like magnitude of completeness, earthquake density and Gutenberg-Richter parameters. The method is capable of identifying and classifying earthquake clusters in space and time. It is tested and validated using earthquake data from California and New Zealand. As a result of the cluster identification process, each event in

  9. Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II.

    PubMed

    Isobe, H; Shoji, M; Yamanaka, S; Mino, H; Umena, Y; Kawakami, K; Kamiya, N; Shen, J-R; Yamaguchi, K

    2014-06-28

    Full geometry optimizations followed by the vibrational analysis were performed for eight spin configurations of the CaMn4O4X(H2O)3Y (X = O, OH; Y = H2O, OH) cluster in the S1 and S3 states of the oxygen evolution complex (OEC) of photosystem II (PSII). The energy gaps among these configurations obtained by vertical, adiabatic and adiabatic plus zero-point-energy (ZPE) correction procedures have been used for computation of the effective exchange integrals (J) in the spin Hamiltonian model. The J values are calculated by the (1) analytical method and the (2) generalized approximate spin projection (AP) method that eliminates the spin contamination errors of UB3LYP solutions. Using J values derived from these methods, exact diagonalization of the spin Hamiltonian matrix was carried out, yielding excitation energies and spin densities of the ground and lower-excited states of the cluster. The obtained results for the right (R)- and left (L)-opened structures in the S1 and S3 states are found to be consistent with available optical and magnetic experimental results. Implications of the computational results are discussed in relation to (a) the necessity of the exact diagonalization for computations of reliable energy levels, (b) magneto-structural correlations in the CaMn4O5 cluster of the OEC of PSII, (c) structural symmetry breaking in the S1 and S3 states, and (d) the right- and left-handed scenarios for the O-O bond formation for water oxidation.

  10. Iron-sulfur cluster biosynthesis: characterization of IscU-IscS complex formation and a structural model for sulfide delivery to the [2Fe-2S] assembly site.

    PubMed

    Nuth, Manunya; Cowan, J A

    2009-08-01

    Recent work on the bacterial iron-sulfur cluster (isc) family of gene products, and eukaryotic homologs, has advanced the molecular understanding of cellular mechanisms of iron-sulfur cluster biosynthesis. Members of the IscS family are pyridoxyl-5'-phosophate dependent proteins that deliver inorganic sulfide during assembly of the [2Fe-2S] cluster on the IscU scaffold protein. Herein it is demonstrated through calorimetry, fluorescence, and protein stability measurements that Thermotoga maritima IscS forms a 1:1 complex with IscU in a concentration-dependent manner (K(D) varying from 6 to 34 microM, over an IscS concentration range of approximately 2-50 microM). Docking simulations of representative IscU and IscS proteins reveal critical contact surfaces at the N-terminal helix of IscU and a C-terminal loop comprising a chaperone binding domain. Consistent with the isothermal titration calorimetry results described here, an overall dominant contribution of charged surfaces with a change in the molar heat capacity of binding, DeltaC(p) approximately 199.8 kcal K(-1) mol(-1), is observed that accounts for approximately 10% of the total accessible surface area at the binding interface. Both apo and holo IscUs and homologs were found to bind to IscS in an enthalpically driven reaction with comparable K(D) values. Both helix and loop regions are highly conserved among phylogenetically diverse organisms from a pool of archael, bacterial, fungal, and mammalian representatives.

  11. Towards models of the oxygen-evolving complex (OEC) of photosystem II: a Mn4Ca cluster of relevance to low oxidation states of the OEC.

    PubMed

    Koumousi, Evangelia S; Mukherjee, Shreya; Beavers, Christine M; Teat, Simon J; Christou, George; Stamatatos, Theocharis C

    2011-10-21

    Synthetic access has been achieved into high oxidation state Mn/Ca chemistry with the 4 : 1 Mn : Ca stoichiometry of the oxygen-evolving complex (OEC) of plants and cyanobacteria; the anion of (Et(3)NH)(2)[Mn(III)(4)Ca(O(2)CPh)(4)(shi)(4)] has a square pyramidal metal topology and an S = 0 ground state.

  12. A geological explanation for intraplate earthquake clustering complexity: The zeolite-bearing fault/fracture networks in the Adamello Massif (Southern Italian Alps)

    NASA Astrophysics Data System (ADS)

    Dempsey, E. D.; Holdsworth, R. E.; Imber, J.; Bistacchi, A.; Di Toro, G.

    2014-09-01

    Interconnected networks of faults and veins filled with hydrothermal minerals such as zeolite are widespread in many orogenic terrains. These fractures commonly form at relatively low temperatures (e.g. <200 °C) late in the tectonic history and represent significant phases of fluid flow and mineralisation during exhumation. Zeolite-bearing fractures spatially associated with the Gole Larghe Fault Zone in the Southern Italian Alps are preserved along an interconnected network of variably orientated pre-existing structures. They show evidence of repeated episodes of hydraulic tensile fracturing and small magnitude (total offsets <5 m) shear displacements. We use geological observations and Coulomb stress modelling to propose that repeated seismogenic rupturing of larger offset faults led to local stress transfer and reactivation of widely distributed smaller pre-existing structures in the wall rocks. The differing orientations of the pre-existing features within what is assumed to have been a single regional stress field led to the simultaneous development of reverse, strike-slip and extensional faults. The kinematic diversity and cyclic nature of the hydraulically-assisted deformation suggest that the mineralised fracture systems represent a geological manifestation of intraplate micro-earthquake clusters associated with fluid migration episodes in the upper crust. Our observations highlight the role of crustal fluids and structural reactivation during earthquakes.

  13. Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

    PubMed Central

    Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

    2013-01-01

    Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

  14. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    PubMed

    Handfield, Louis-François; Chong, Yolanda T; Simmons, Jibril; Andrews, Brenda J; Moses, Alan M

    2013-01-01

    Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  15. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP-oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution.

    PubMed

    Howard, E I; Guillot, B; Blakeley, M P; Haertlein, M; Moulin, M; Mitschler, A; Cousido-Siah, A; Fadel, F; Valsecchi, W M; Tomizaki, Takashi; Petrova, T; Claudot, J; Podjarny, A

    2016-03-01

    Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

  16. Symmetry Based Automatic Evolution of Clusters: A New Approach to Data Clustering

    PubMed Central

    Vijendra, Singh; Laxman, Sahoo

    2015-01-01

    We present a multiobjective genetic clustering approach, in which data points are assigned to clusters based on new line symmetry distance. The proposed algorithm is called multiobjective line symmetry based genetic clustering (MOLGC). Two objective functions, first the Davies-Bouldin (DB) index and second the line symmetry distance based objective functions, are used. The proposed algorithm evolves near-optimal clustering solutions using multiple clustering criteria, without a priori knowledge of the actual number of clusters. The multiple randomized K dimensional (Kd) trees based nearest neighbor search is used to reduce the complexity of finding the closest symmetric points. Experimental results based on several artificial and real data sets show that proposed clustering algorithm can obtain optimal clustering solutions in terms of different cluster quality measures in comparison to existing SBKM and MOCK clustering algorithms. PMID:26339233

  17. Symmetry Based Automatic Evolution of Clusters: A New Approach to Data Clustering.

    PubMed

    Vijendra, Singh; Laxman, Sahoo

    2015-01-01

    We present a multiobjective genetic clustering approach, in which data points are assigned to clusters based on new line symmetry distance. The proposed algorithm is called multiobjective line symmetry based genetic clustering (MOLGC). Two objective functions, first the Davies-Bouldin (DB) index and second the line symmetry distance based objective functions, are used. The proposed algorithm evolves near-optimal clustering solutions using multiple clustering criteria, without a priori knowledge of the actual number of clusters. The multiple randomized K dimensional (Kd) trees based nearest neighbor search is used to reduce the complexity of finding the closest symmetric points. Experimental results based on several artificial and real data sets show that proposed clustering algorithm can obtain optimal clustering solutions in terms of different cluster quality measures in comparison to existing SBKM and MOCK clustering algorithms.

  18. A band Lanczos approach for calculation of vibrational coupled cluster response functions: simultaneous calculation of IR and Raman anharmonic spectra for the complex of pyridine and a silver cation.

    PubMed

    Godtliebsen, Ian H; Christiansen, Ove

    2013-07-07

    We describe new methods for the calculation of IR and Raman spectra using vibrational response theory. Using damped linear response functions that incorporate a Lorentzian line-shape function from the outset, it is shown how the calculation of Raman spectra can be carried out through the calculation of a set of vibrational response functions in the same manner as described previously for IR spectra. The necessary set of response functions can be calculated for both vibrational coupled cluster (VCC) and vibrational configuration interaction (VCI) anharmonic vibrational wave-functions. For the efficient and simultaneous calculation of the full set of necessary response functions, a non-hermitian band Lanczos algorithm is implemented for VCC, and a hermitian band Lanczos algorithm is implemented for VCI. It is shown that the simultaneous calculation of several response functions is often advantageous. Sample calculations are presented for pyridine and the complex between pyridine and the silver cation.

  19. H-D exchange in metal carbene complexes: Structure of cluster (μ-H)(μ-OCD3)Os3(CO)9{:C(CD3)NC2H8O}

    NASA Astrophysics Data System (ADS)

    Savkov, Boris; Maksakov, Vladimir; Kuratieva, Natalia

    2015-10-01

    X-ray and spectroscopic data for the new complex (μ-H)(μ-OCH3)Os3(CO)9{:C(CD3)NC2H8O} (2) obtained in the reaction of the (μ-H)(μ-Cl)Os3(CO)9{:C(CH3)NC2H8O} (1) with NaOCD3 in CD3OD solution are reported. It is shown that cluster 1 has the property of CH-acidity inherent of Fisher type carbenes. This had demonstrated using hydrogen deuterium exchange reaction in the presence of a strong base. Bridging chlorine to metoxide ligand substitution takes place during the reaction. The molecular structure of 2 is compared with known analogues.

  20. Large-scale QM/MM calculations of the CaMn4O5 cluster in the oxygen-evolving complex of photosystem II: Comparisons with EXAFS structures

    NASA Astrophysics Data System (ADS)

    Shoji, Mitsuo; Isobe, Hiroshi; Nakajima, Takahito; Yamaguchi, Kizashi

    2016-08-01

    Large-scale QM/MM calculations including hydrogen-bonding networks in the oxygen evolving complex (OEC) of photosystem II (PSII) were performed to elucidate the geometric structures of the CaMn4O5 cluster in the key catalytic states (Si (i = 0-3)). The optimized Mn-Mn, Ca-Mn and Mn-O distances by the large-scale QM/MM starting from the high-resolution XRD structure were consistent with those of the EXAFS experiments in the dark stable S1 state by the Berkeley and Berlin groups. The optimized geometrical parameters for other Si (i = 0, 2, 3) states were also consistent with those of EXAFS, indicating the importance of the large-scale QM/MM calculations for the PSII-OEC.

  1. Adolescent seasonal allergic rhinitis and the impact of health-care professional training: cluster randomised controlled trial of a complex intervention in primary care.

    PubMed

    Hammersley, Victoria S; Elton, Rob A; Walker, Samantha; Hansen, Christian H; Sheikh, Aziz

    2014-06-05

    Seasonal allergic rhinitis is typically poorly managed, particularly in adolescents, in whom it is responsible for considerable morbidity. Our previous work has demonstrated that if poorly controlled this can impair educational performance. The primary aim of this trial was to assess the impact of a primary care-based professional training intervention on clinical outcomes in adolescents with seasonal allergic rhinitis. Cluster trial in which UK general practice staff were randomised to a short, intensive workshop on the evidence-based management of seasonal allergic rhinitis. The primary outcome measure was the change in the validated Rhinoconjunctivitis Quality of Life Questionnaire with Standardized Activities (RQLQ(S)) score between baseline and 6 weeks post intervention (minimal clinically important difference=0.5). Secondary outcome measures of interest included health-care professionals' knowledge and confidence in managing seasonal allergic rhinitis, number of seasonal allergic rhinitis-related consultations, relevant treatments prescribed and symptom scores. Thirty-eight general practices were randomised (20 in the intervention arm) and 246 patients (50.2% males, mean age 15 years) were included in the primary outcome analysis. Health-care professionals' knowledge and confidence of the clinical management of seasonal allergic rhinitis improved. This did not, however, result in clinically or statistically significant improvements in RQLQ(S): -0.15, (95% confidence interval, -0.5 to +0.2). There were no differences in consultation frequency, treatments issued for seasonal allergic rhinitis or symptom scores. Although associated with increases in professionals' self-assessed confidence and understanding of seasonal allergic rhinitis management, this intensive training workshop did not translate into improvements in adolescents' disease-specific quality of life or a reduction in rhinitis symptoms.

  2. First insertion of NO into a transition-metal cluster-carbon bond: regioselective formation, structure, and reactions of the first alkanenitrile oxide complexes

    SciTech Connect

    Goldhaber, A.; Vollhardt, K.P.C.; Walborsky, E.C.; Wolfgruber, M.

    1986-02-05

    The chemistry of NO in the presence of transition metals is receiving considerable current attention because of its role in air pollution, its potential in organic synthesis by carbon-nitrogen bond formation, and an increasing interest in its basic features. The nitrosyl cation has been reacted with many mono and polynuclear metal systems, leading mainly to substitution and reduction. Insertion into alkyl and aryl metal bonds in mono-metallic complexes is documented. The unprecedented title reaction and some preliminary chemistry of the products are reported here. 27 references, 1 figure.

  3. Cancer symptom clusters: current concepts and controversies.

    PubMed

    Aktas, Aynur

    2013-03-01

    Cluster research examines complex interrelationships between multiple concurrent symptoms and their mechanisms. An individual's varying understanding of the cluster concept and variations in assessment tools results in discrepancies. This article will focus on the conceptual and methodological issues associated with definitions, symptom interrelationships, and outcomes of cancer symptom clusters. An important issue in symptom cluster research is to clarify the definition of a cluster. Some evidence suggests that 'symptom pairs' should be treated as clusters. There is substantial evidence (both qualitative and quantitative) to support a psychoneurological symptom cluster in cancer patients. It has been proposed that consistent clusters are those that have similar 'core' symptoms over time. Research has also shown that a 'sentinel' symptom can predict the presence of other relevant symptoms within a cluster. Identification of patient subgroups with higher symptom severity may be useful in targeting the most needy individuals for intervention. Symptom clusters are predictors of patient outcomes, including decreased functional performance and shorter cancer survival. Additional efforts should refine the cluster definition and elucidate the cluster stability and sentinel symptom. Both conceptual and empirical contributions should advance symptom cluster research. The qualitative approaches can explore the experience of symptom clusters and provide a conceptual basis for future research.

  4. A Robust Open Framework Formed by Decavanadate Clusters and Copper(II) Complexes of Macrocyclic Polyamines: Permanent Microporosity and Catalytic Oxidation of Cycloalkanes.

    PubMed

    Martín-Caballero, Jagoba; San José Wéry, Ana; Reinoso, Santiago; Artetxe, Beñat; San Felices, Leire; El Bakkali, Bouchra; Trautwein, Guido; Alcañiz-Monge, Juan; Vilas, José Luis; Gutiérrez-Zorrilla, Juan M

    2016-05-16

    The first decavanadate-based microporous hybrid, namely, [Cu(cyclam)][{Cu(cyclam)}2(V10O28)]·10H2O (1, cyclam = 1,4,8,11-tetraazacyclotetradecane) was prepared by reaction of (VO3)(-) anions and {Cu(cyclam)}(2+) complexes in NaCl (aq) at pH 4.6-4.7 and characterized by elemental analyses, thermogravimetry, and X-ray diffraction (powder, single-crystal) techniques. Compound 1 exhibits a POMOF-like supramolecular open-framework built of covalent decavanadate/metalorganic layers with square-like voids, the stacking of which is aided by interlamellar cementing complexes and generates water-filled channels with approximate cross sections of 10.4 × 8.8 Å(2). The framework is robust enough to remain virtually unaltered upon thermal evacuation of all water molecules of hydration, as demonstrated through single-crystal X-ray diffraction studies on the anhydrous phase 1a. This permanent microporosity renders interesting functionality to 1, such as selective adsorption of CO2 over N2 and remarkable activity as heterogeneous catalyst toward the H2O2-based oxidation of the highly-stable, tricyclic alkane adamantane.

  5. How often are interventions in cluster-randomised controlled trials of complex interventions in general practices effective and reasons for potential shortcomings? Protocol and results of a feasibility project for a systematic review

    PubMed Central

    Siebenhofer, Andrea; Erckenbrecht, Stefanie; Pregartner, Gudrun; Berghold, Andrea; Muth, Christiane

    2016-01-01

    Introduction Most studies conducted at general practices investigate complex interventions and increasingly use cluster-randomised controlled trail (c-RCT) designs to do so. Our primary objective is to evaluate how frequently complex interventions are shown to be more, equally or less effective than routine care in c-RCTs with a superior design. The secondary aim is to discover whether the quality of a c-RCT determines the likelihood of the complex intervention being effective. Methods and analysis All c-RCTs of any design that have a patient-relevant primary outcome and with a duration of at least 1 year will be included. The search will be performed in three electronic databases (MEDLINE, EMBASE and the Cochrane Database of Systematic Reviews (CDSR)). The screening process, data collection, quality assessment and statistical data analyses (if suitably similar and of adequate quality) will be performed in accordance with requirements of the Cochrane Handbook for Systematic Reviews of Interventions. A feasibility project was carried out that was restricted to a search in MEDLINE and the CCTR for c-RCTs published in 1 of the 8 journals that are most relevant to general practice. The process from trial selection to data collection, assessment and results presentation was piloted. Of the 512 abstracts identified during the feasibility search, 21 studies examined complex interventions in a general practice setting. Extrapolating the preliminary search to include all relevant c-RCTs in three databases, about 5000 abstracts and 150 primary studies are expected to be identified in the main study. 14 studies included in the feasibility project (67%) did not show a positive effect on a primary patient-relevant end point. Ethics and dissemination Ethical approval is not being sought for this review. Findings will be disseminated via peer-reviewed journals that frequently publish articles on the results of c-RCTs and through presentations at international conferences. Trial

  6. An embedded longitudinal multi-faceted qualitative evaluation of a complex cluster randomized controlled trial aiming to reduce clinically important errors in medicines management in general practice.

    PubMed

    Cresswell, Kathrin M; Sadler, Stacey; Rodgers, Sarah; Avery, Anthony; Cantrill, Judith; Murray, Scott A; Sheikh, Aziz

    2012-06-08

    There is a need to shed light on the pathways through which complex interventions mediate their effects in order to enable critical reflection on their transferability. We sought to explore and understand key stakeholder accounts of the acceptability, likely impact and strategies for optimizing and rolling-out a successful pharmacist-led information technology-enabled (PINCER) intervention, which substantially reduced the risk of clinically important errors in medicines management in primary care. Data were collected at two geographical locations in central England through a combination of one-to-one longitudinal semi-structured telephone interviews (one at the beginning of the trial and another when the trial was well underway), relevant documents, and focus group discussions following delivery of the PINCER intervention. Participants included PINCER pharmacists, general practice staff, researchers involved in the running of the trial, and primary care trust staff. PINCER pharmacists were interviewed at three different time-points during the delivery of the PINCER intervention. Analysis was thematic with diffusion of innovation theory providing a theoretical framework. We conducted 52 semi-structured telephone interviews and six focus group discussions with 30 additional participants. In addition, documentary data were collected from six pharmacist diaries, along with notes from four meetings of the PINCER pharmacists and feedback meetings from 34 practices. Key findings that helped to explain the success of the PINCER intervention included the perceived importance of focusing on prescribing errors to all stakeholders, and the credibility and appropriateness of a pharmacist-led intervention to address these shortcomings. Central to this was the face-to-face contact and relationship building between pharmacists and a range of practice staff, and pharmacists' explicitly designated role as a change agent. However, important concerns were identified about the likely

  7. An embedded longitudinal multi-faceted qualitative evaluation of a complex cluster randomized controlled trial aiming to reduce clinically important errors in medicines management in general practice

    PubMed Central

    2012-01-01

    Background There is a need to shed light on the pathways through which complex interventions mediate their effects in order to enable critical reflection on their transferability. We sought to explore and understand key stakeholder accounts of the acceptability, likely impact and strategies for optimizing and rolling-out a successful pharmacist-led information technology-enabled (PINCER) intervention, which substantially reduced the risk of clinically important errors in medicines management in primary care. Methods Data were collected at two geographical locations in central England through a combination of one-to-one longitudinal semi-structured telephone interviews (one at the beginning of the trial and another when the trial was well underway), relevant documents, and focus group discussions following delivery of the PINCER intervention. Participants included PINCER pharmacists, general practice staff, researchers involved in the running of the trial, and primary care trust staff. PINCER pharmacists were interviewed at three different time-points during the delivery of the PINCER intervention. Analysis was thematic with diffusion of innovation theory providing a theoretical framework. Results We conducted 52 semi-structured telephone interviews and six focus group discussions with 30 additional participants. In addition, documentary data were collected from six pharmacist diaries, along with notes from four meetings of the PINCER pharmacists and feedback meetings from 34 practices. Key findings that helped to explain the success of the PINCER intervention included the perceived importance of focusing on prescribing errors to all stakeholders, and the credibility and appropriateness of a pharmacist-led intervention to address these shortcomings. Central to this was the face-to-face contact and relationship building between pharmacists and a range of practice staff, and pharmacists’ explicitly designated role as a change agent. However, important concerns were

  8. Cluster bulleticity

    NASA Astrophysics Data System (ADS)

    Massey, Richard; Kitching, Thomas; Nagai, Daisuke

    2011-05-01

    The unique properties of dark matter are revealed during collisions between clusters of galaxies, such as the bullet cluster (1E 0657-56) and baby bullet (MACS J0025-12). These systems provide evidence for an additional, invisible mass in the separation between the distributions of their total mass, measured via gravitational lensing, and their ordinary 'baryonic' matter, measured via its X-ray emission. Unfortunately, the information available from these systems is limited by their rarity. Constraints on the properties of dark matter, such as its interaction cross-section, are therefore restricted by uncertainties in the individual systems' impact velocity, impact parameter and orientation with respect to the line of sight. Here we develop a complementary, statistical measurement in which every piece of substructure falling into every massive cluster is treated as a bullet. We define 'bulleticity' as the mean separation between dark matter and ordinary matter, and we measure the signal in hydrodynamical simulations. The phase space of substructure orbits also exhibits symmetries that provide an equivalent control test. Any detection of bulleticity in real data would indicate a difference in the interaction cross-sections of baryonic and dark matter that may rule out hypotheses of non-particulate dark matter that are otherwise able to model individual systems. A subsequent measurement of bulleticity could constrain the dark matter cross-section. Even with conservative estimates, the existing Hubble Space Telescope archive should yield an independent constraint tighter than that from the bullet cluster. This technique is then trivially extendable to and benefits enormously from larger, future surveys.

  9. Full geometry optimizations of the CaMn4O4 model cluster for the oxygen evolving complex of photosystem II

    NASA Astrophysics Data System (ADS)

    Shoji, Mitsuo; Isobe, Hiroshi; Nakajima, Takahito; Yamaguchi, Kizashi

    2015-11-01

    Full geometry optimizations of ([CaMn4O4(CH3COO)8(py)(CH3COOH)2], (py: pyridine) (1)) were performed at the UB3LYP theoretical level. 1 is a theoretical model for the synthetic model ([CaMn4O4(ButCOO)8(py)(ButCOOH)2], (But: t-butyl) (2)) which closely mimicks the native oxygen evolving complex (OEC) in photosystem II. It was shown that the X-ray structure of 2 was well reproduced by 1 in the (Mn1(III), Mn2(IV), Mn3(IV), Mn4(III)) valence state with the unprotonated O5 (O5 = O2-), and two different valence states were obtained in the one-electron oxidized state. Importance of the Jahn-Teller effect of the Mn(III) site for the structural deformations was presented.

  10. Active matter clusters at interfaces

    NASA Astrophysics Data System (ADS)

    Copenhagen, Katherine; Gopinathan, Ajay

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development and flocks of birds. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit whose movement depends on the nature of the local environment. We find that low speed clusters which exert forces but no active torques, encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds and clusters with active torques, they show more complex behaviors crossing the interface multiple times, becoming trapped at the interface and deviating from the predictable refraction and reflection of the low velocity clusters. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  11. Toward Parallel Document Clustering

    SciTech Connect

    Mogill, Jace A.; Haglin, David J.

    2011-09-01

    A key challenge to automated clustering of documents in large text corpora is the high cost of comparing documents in a multimillion dimensional document space. The Anchors Hierarchy is a fast data structure and algorithm for localizing data based on a triangle inequality obeying distance metric, the algorithm strives to minimize the number of distance calculations needed to cluster the documents into “anchors” around reference documents called “pivots”. We extend the original algorithm to increase the amount of available parallelism and consider two implementations: a complex data structure which affords efficient searching, and a simple data structure which requires repeated sorting. The sorting implementation is integrated with a text corpora “Bag of Words” program and initial performance results of end-to-end a document processing workflow are reported.

  12. High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution

    PubMed Central

    Howard, E. I.; Guillot, B.; Blakeley, M. P.; Haertlein, M.; Moulin, M.; Mitschler, A.; Cousido-Siah, A.; Fadel, F.; Valsecchi, W. M.; Tomizaki, Takashi; Petrova, T.; Claudot, J.; Podjarny, A.

    2016-01-01

    Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader’s quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H⋯H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface. PMID:27006775

  13. Chiral heteropoly blues and controllable switching of achiral polyoxometalate clusters.

    PubMed

    Wang, Yizhan; Li, Haolong; Wu, Che; Yang, Yang; Shi, Lei; Wu, Lixin

    2013-04-22

    Managing the blues: Chiral heteropoly blues of achiral polyoxometalate clusters were created through an intermolecular interaction with a chiral organic compound. Controllable chiroptical switching of the cluster complexes was possible through reversible photochromism of the polyoxometalates (see picture).

  14. The [Sn(9)Pt(2)(PPh(3))](2)(-) and [Sn(9)Ni(2)(CO)](3)(-) complexes: two markedly different Sn(9)M(2)L transition metal zintl ion clusters and their dynamic behavior.

    PubMed

    Kesanli, Banu; Fettinger, James; Gardner, Donna R; Eichhorn, Bryan

    2002-05-01

    [Sn(9)Pt(2)(PPh(3))](2)(-) (2) was prepared from Pt(PPh(3))(4), K(4)Sn(9), and 2,2,2-cryptand in en/toluene solvent mixtures. The [K(2,2,2-cryptand)](+) salt is very air and moisture sensitive and has been characterized by ESI-MS, variable-temperature (119)Sn, (31)P, and (195)Pt NMR and single-crystal X-ray diffraction studies. The structure of 2 comprises an elongated tricapped Sn(9) trigonal prism with a capping PtPPh(3), an interstitial Pt atom, a hypercloso electron count (10 vertex, 20 electron) and C(3)(v)() point symmetry. Hydrogenation trapping experiments and deuterium labeling studies showed that the formation of 2 involves a double C-H activation of solvent molecules (en or DMSO) with the elimination of H(2) gas. The ESI-MS analysis of 2 showed the K[Sn(9)Pt(2)(PPh(3))](1)(-) parent ion, an oxidized [Sn(9)Pt(2)(PPh(3))](1)(-) ion, and the protonated binary cluster anion [HSn(9)Pt(2)](1)(-). 2 is highly fluxional in solution giving rise to a single time-averaged (119)Sn NMR signal for all nine Sn atoms but the Pt atoms remain distinct. The exchange is intramolecular and is consistent with a rigid, linear Pt-Pt-PPh(3) rod embedded in a liquidlike Sn(9) matrix. [Sn(9)Ni(2)(CO)](3)(-) (3) was prepared from Ni(CO)(2)(PPh(3))(2), K(4)Sn(9), and 2,2,2-cryptand in en/toluene solvent mixtures. The [K(2,2,2-cryptand)](+) salt is very air and moisture sensitive, is paramagnetic, and has been characterized by ESI-MS, EPR, and single-crystal X-ray diffraction. Complex 3 is a 10-vertex 21-electron polyhedron, a slightly distorted closo-Sn(9)Ni cluster with an additional interstitial Ni atom and overall C(4)(v)() point symmetry. The EPR spectrum showed a five-line pattern due to 4.8-G hyperfine interactions involving all nine tin atoms. The ESI-MS analysis showed weak signals for the potassium complex [K(2)Sn(9)Ni(2)(CO)](1-) and the ligand-free binary ions [K(2)Sn(9)Ni(2)](1)(-), [KSn(9)Ni(2)](1)(-), and [HSn(9)Ni(2)](1)(-).

  15. Iron-Sulphur Cluster Biosynthesis

    PubMed Central

    Bandyopadhyay, Sibali; Chandramouli, Kala; Johnson, Michael K.

    2010-01-01

    Iron-sulphur clusters are present in more than 200 different types of enzymes or proteins and constitute one of the most ancient, ubiquitous and structurally diverse classes of biological prosthetic groups. Hence the process of iron-sulphur biosynthesis is essential to almost all forms of life and is remarkably conserved in prokaryotic and eukaryotic organisms. Three distinct types of iron-sulphur cluster assembly machinery have been established in bacteria, termed the NIF, ISC and SUF systems, and in each case the overall mechanism involves cysteine desulphurase-mediated assembly of transient clusters on scaffold proteins and subsequent transfer of preformed clusters to apo proteins. A molecular level understanding of the complex processes of iron-sulphur cluster assembly and transfer is now beginning to emerge from the combination of in vivo and in vitro approaches. This review highlights recent developments in understanding the mechanism of iron-sulphur cluster assembly and transfer involving the ubiquitous U-type scaffold proteins and the potential roles of accessory proteins such as Nfu proteins and monothiol glutaredoxins in the assembly, storage or transfer of iron-sulphur clusters. PMID:19021507

  16. Stable prenucleation calcium carbonate clusters.

    PubMed

    Gebauer, Denis; Völkel, Antje; Cölfen, Helmut

    2008-12-19

    Calcium carbonate forms scales, geological deposits, biominerals, and ocean sediments. Huge amounts of carbon dioxide are retained as carbonate ions, and calcium ions represent a major contribution to water hardness. Despite its relevance, little is known about the precipitation mechanism of calcium carbonate, and specified complex crystal structures challenge the classical view on nucleation considering the formation of metastable ion clusters. We demonstrate that dissolved calcium carbonate in fact contains stable prenucleation ion clusters forming even in undersaturated solution. The cluster formation can be characterized by means of equilibrium thermodynamics, applying a multiple-binding model, which allows for structural preformation. Stable clusters are the relevant species in calcium carbonate nucleation. Such mechanisms may also be important for the crystallization of other minerals.

  17. Chemical evolution of star clusters.

    PubMed

    van Loon, Jacco Th

    2010-02-28

    I discuss the chemical evolution of star clusters, with emphasis on old Galactic globular clusters (GCs), in relation to their formation histories. GCs are clearly formed in a complex fashion, under markedly different conditions from any younger clusters presently known. Those special conditions must be linked to the early formation epoch of the Galaxy and must not have occurred since. While a link to the formation of GCs in dwarf galaxies has been suggested, present-day dwarf galaxies are not representative of the gravitational potential wells within which the GCs formed. Instead, a formation deep within the proto-Galaxy or within dark-matter mini-haloes might be favoured. Not all GCs may have formed and evolved similarly. In particular, we may need to distinguish Galactic Halo from Galactic Bulge clusters.

  18. Architecture of Eph receptor clusters

    SciTech Connect

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

    2010-10-04

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

  19. Clustering Millions of Faces by Identity.

    PubMed

    Otto, Charles; Wang, Dayong; Jain, Anil

    2017-03-07

    Given a large collection of unlabeled face images, we address the problem of clustering faces into an unknown number of identities. This problem is of interest in social media, law enforcement, and other applications, where the number of faces can be of the order of hundreds of million, while the number of identities (clusters) can range from a few thousand to millions. To address the challenges of run-time complexity and cluster quality, we present an approximate Rank-Order clustering algorithm that performs better than popular clustering algorithms (k-Means and Spectral). Our experiments include clustering up to 123 million face images into over 10 million clusters. Clustering results are analyzed in terms of external (known face labels) and internal (unknown face labels) quality measures, and run-time. Our algorithm achieves an F-measure of 0:87 on the LFW benchmark (13K faces of 5; 749 individuals), which drops to 0:27 on the largest dataset considered (13K faces in LFW + 123M distractor images). Additionally, we show that frames in the YouTube benchmark can be clustered with an F-measure of 0:71. An internal per-cluster quality measure is developed to rank individual clusters for manual exploration of high quality clusters that are compact and isolated.

  20. Contribution of globular clusters to halos

    NASA Astrophysics Data System (ADS)

    Bragaglia, Angela

    2017-03-01

    The contribution of massive star clusters to their hosting halo dramatically depends on their formation mechanism and their early evolution. Massive globular clusters in the Milky Way (and in other galaxies) have been shown to display peculiar chemical patterns (light-elements correlations and anti-correlations) indicative of a complex star formation, confirmed by photometric evidence (spread or split sequences). I use these chemical signatures to try to understand what is the fraction of halo stars originally born in globular clusters.

  1. Expulsion of Dust from Young Stellar Clusters

    NASA Astrophysics Data System (ADS)

    Grosbøl, P.; Dottori, H.

    2013-03-01

    Young stellar clusters were identified on deep near-infrared images of 6 nearby, grand-design spirals observed with HAWK-I/VLT. A 90% completeness was reached for cluster complexes with M K = -11.5m (corresponding to masses around 104 M⊙) while the linear resolution was around 40 pc. The distribution of clusters in the (H-K)-(J-H) diagrams revealed two groups of clusters. Comparing with Starburst99 model tracks, the groups could be interpreted as one old population of clusters with low extinction and one consisting of young clusters with visual extinction as high as AV = 7m. The clear separation between the two groups suggests a rapid expulsion of dust from the young clusters.

  2. ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network.

    PubMed

    Wang, Jianxin; Zhong, Jiancheng; Chen, Gang; Li, Min; Wu, Fang-xiang; Pan, Yi

    2015-01-01

    Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

  3. Astrophysics of galaxy clusters

    NASA Astrophysics Data System (ADS)

    Ettori, Stefano

    2016-07-01

    As the nodes of the cosmic web, clusters of galaxies trace the large-scale distribution of matter in the Universe. They are thus privileged sites in which to investigate the complex physics of structure formation. However, the complete story of how these structures grow, and how they dissipate the gravitational and non-thermal components of their energy budget over cosmic time, is still beyond our grasp. Most of the baryons gravitationally bound to the cluster's halo is in the form of a diffuse, hot, metal-enriched plasma that radiates primarily in the X-ray band. X-ray observations of the evolving cluster population provide a unique opportunity to address such fundamental open questions as: How do hot diffuse baryons accrete and dynamically evolve in dark matter potentials? How and when was the energy that we observe in the ICM generated and distributed? Where and when are heavy elements produced and how are they circulated? We will present the ongoing activities to define the strategy on how an X-ray observatory with large collecting area and an unprecedented combination of high spectral and angular resolution, such as Athena, can address these questions.

  4. Electronic Absorption and MCD Spectra for Pd(AuPPh(3))(8)(2+), Pt(AuPPh(3))(8)(2+), and Related Platinum-Centered Gold Cluster Complexes.

    PubMed

    Adrowski, Michael J.; Mason, W. Roy

    1997-03-26

    Electronic absorption and 7.0 T magnetic circular dichroism (MCD) spectra in the UV-vis region, 1.6 to approximately 4.0 &mgr;m(-)(1) (1 &mgr;m(-)(1) = 10(4) cm(-)(1)) are reported for [Pd(AuPPh(3))(8)](NO(3))(2) and [Pt(AuPPh(3))(8)](NO(3))(2) in acetonitrile solutions at room temperature. The MCD spectra are better resolved than the absorption spectra and consist of both A and B terms. The spectra are interpreted in terms of D(4)(d)() skeletal geometry and MO's that are approximated by 5s and 6s orbitals for Pd and Pt/Au atoms, respectively. The lowest energy excited configurations and states are attributed to intraframework (IF) Au(8)(2+) transitions. Evidence is also presented for Pt 5d --> Au 6s transitions in the MCD spectra for Pt(AuPPh(3))(8)(2+). Acetonitrile solution absorption and MCD spectra for the related Pt-centered cluster complexes [Pt(CO)(AuPPh(3))(8)](NO(3))(2), [Pt(AuP(p-tolyl)(3))(8)](NO(3))(2), [Pt(CuCl)(AuPPh(3))(8)](NO(3))(2), [Pt(AgNO(3))(AuPPh(3))(8)](NO(3))(2), [Pt(Hg)(2)(AuPPh(3))(8)](NO(3))(2), [Pt(HgCl)(2)(AuPPh(3))(8)](BF(4))(2), and [Pt(HgNO(3))(2)(AuPPh(3))(8)](BF(4))(2) are also reported and interpreted within the context of the model developed for the M(AuPPh(3))(8)(2+) complexes.

  5. Clustervision: Visual Supervision of Unsupervised Clustering.

    PubMed

    Kwon, Bum Chul; Eysenbach, Ben; Verma, Janu; Ng, Kenney; deFilippi, Christopher; Stewart, Walter F; Perer, Adam

    2017-08-29

    Clustering, the process of grouping together similar items into distinct partitions, is a common type of unsupervised machine learning that can be useful for summarizing and aggregating complex multi-dimensional data. However, data can be clustered in many ways, and there exist a large body of algorithms designed to reveal different patterns. While having access to a wide variety of algorithms is helpful, in practice, it is quite difficult for data scientists to choose and parameterize algorithms to get the clustering results relevant for their dataset and analytical tasks. To alleviate this problem, we built Clustervision, a visual analytics tool that helps ensure data scientists find the right clustering among the large amount of techniques and parameters available. Our system clusters data using a variety of clustering techniques and parameters and then ranks clustering results utilizing five quality metrics. In addition, users can guide the system to produce more relevant results by providing task-relevant constraints on the data. Our visual user interface allows users to find high quality clustering results, explore the clusters using several coordinated visualization techniques, and select the cluster result that best suits their task. We demonstrate this novel approach using a case study with a team of researchers in the medical domain and showcase that our system empowers users to choose an effective representation of their complex data.

  6. Probing the topography of the photosystem II oxygen evolving complex: PsbO is required for efficient calcium protection of the manganese cluster against dark-inhibition by an artificial reductant.

    PubMed

    Popelkova, Hana; Boswell, Nicholas; Yocum, Charles

    2011-12-01

    The photosystem II (PSII) manganese-stabilizing protein (PsbO) is known to be the essential PSII extrinsic subunit for stabilization and retention of the Mn and Cl(-) cofactors in the oxygen evolving complex (OEC) of PSII, but its function relative to Ca(2+) is less clear. To obtain a better insight into the relationship, if any, between PsbO and Ca(2+) binding in the OEC, samples with altered PsbO-PSII binding properties were probed for their potential to promote the ability of Ca(2+) to protect the Mn cluster against dark-inhibition by an exogenous artificial reductant, N,N-dimethylhydroxylamine. In the absence of the PsbP and PsbQ extrinsic subunits, Ca(2+) and its surrogates (Sr(2+), Cd(2+)) shield Mn atoms from inhibitory reduction (Kuntzleman et al., Phys Chem Chem Phys 6:4897, 2004). The results presented here show that PsbO exhibits a positive effect on Ca(2+) binding in the OEC by facilitating the ability of the metal to prevent inhibition of activity by the reductant. The data presented here suggest that PsbO may have a role in the formation of the OEC-associated Ca(2+) binding site by promoting the equilibrium between bound and free Ca(2+) that favors the bound metal.

  7. Hierarchical Aligned Cluster Analysis for Temporal Clustering of Human Motion.

    PubMed

    Zhou, Feng; De la Torre, Fernando; Hodgins, Jessica K

    2013-03-01

    Temporal segmentation of human motion into plausible motion primitives is central to understanding and building computational models of human motion. Several issues contribute to the challenge of discovering motion primitives: the exponential nature of all possible movement combinations, the variability in the temporal scale of human actions, and the complexity of representing articulated motion. We pose the problem of learning motion primitives as one of temporal clustering, and derive an unsupervised hierarchical bottom-up framework called hierarchical aligned cluster analysis (HACA). HACA finds a partition of a given multidimensional time series into m disjoint segments such that each segment belongs to one of k clusters. HACA combines kernel k-means with the generalized dynamic time alignment kernel to cluster time series data. Moreover, it provides a natural framework to find a low-dimensional embedding for time series. HACA is efficiently optimized with a coordinate descent strategy and dynamic programming. Experimental results on motion capture and video data demonstrate the effectiveness of HACA for segmenting complex motions and as a visualization tool. We also compare the performance of HACA to state-of-the-art algorithms for temporal clustering on data of a honey bee dance. The HACA code is available online.

  8. Oxygen atom transfer reactions from dioxygen to phosphines via a bridging sulfur dioxide in a trinuclear cluster complex of rhenium, [(Ph(3)P)(2)N][Re(3)(mu(3)-S)(mu-S)(2)(mu-SO(2))Cl(6)(PMe(2)Ph)(3)].

    PubMed

    Saito, Taro; Sunaga, Tomoaki; Sakai, Nobuaki; Nakamura, Yoichi; Yamamoto, Saori; Iriuchijima, Daisuke; Yoza, Kenji

    2005-06-13

    A trinuclear rhenium sulfide cluster complex, [(Ph(3)P)(2)N][Re(3)(mu(3)-S)(mu-S)(3)Cl(6)(PMe(2)Ph)(3)], synthesized from Re(3)S(7)Cl(7), dimethylphenylphosphine, and [(Ph(3)P)(2)N]Cl is readily converted to a bridging SO(2) complex, [(Ph(3)P)(2)N][Re(3)(mu(3)-S)(mu-S)(2)(mu-SO(2))Cl(6)(PMe(2)Ph)(3)], by reaction with O(2). The oxygen atoms on the SO(2) ligand react with phosphines or phosphites to form phosphine oxides or phosphates, and the original cluster complex is recovered. The reaction course has been monitored by (31)P NMR as well as by UV-vis spectroscopy. The catalytic oxygenation of PMePh(2) in the presence of the SO(2) complex shows that turnovers are 8 per hour at 23 degrees C in CDCl(3). The X-ray structures of the cluster complexes are described.

  9. Cluster headache

    PubMed Central

    Leroux, Elizabeth; Ducros, Anne

    2008-01-01

    Cluster headache (CH) is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes) of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye). It affects young adults, predominantly males. Prevalence is estimated at 0.5–1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name) in bouts that can occur during specific months of the year. Alcohol is the only dietary trigger of CH, strong odors (mainly solvents and cigarette smoke) and napping may also trigger CH attacks. During bouts, attacks may happen at precise hours, especially during the night. During the attacks, patients tend to be restless. CH may be episodic or chronic, depending on the presence of remission periods. CH is associated with trigeminovascular activation and neuroendocrine and vegetative disturbances, however, the precise cautive mechanisms remain unknown. Involvement of the hypothalamus (a structure regulating endocrine function and sleep-wake rhythms) has been confirmed, explaining, at least in part, the cyclic aspects of CH. The disease is familial in about 10% of cases. Genetic factors play a role in CH susceptibility, and a causative role has been suggested for the hypocretin receptor gene. Diagnosis is clinical. Differential diagnoses include other primary headache diseases such as migraine, paroxysmal hemicrania and SUNCT syndrome. At present, there is no curative treatment. There are efficient treatments to shorten the painful attacks (acute treatments) and to reduce the number of daily attacks (prophylactic treatments). Acute treatment is based on subcutaneous administration of sumatriptan and high-flow oxygen. Verapamil, lithium, methysergide, prednisone, greater occipital nerve blocks and topiramate may be used for prophylaxis. In refractory cases, deep-brain stimulation of the hypothalamus and

  10. Conversion events in gene clusters

    PubMed Central

    2011-01-01

    Background Gene clusters containing multiple similar genomic regions in close proximity are of great interest for biomedical studies because of their associations with inherited diseases. However, such regions are difficult to analyze due to their structural complexity and their complicated evolutionary histories, reflecting a variety of large-scale mutational events. In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments. Results To correct the distorted information generated by such methods, we have developed an automated pipeline called CHAP (Cluster History Analysis Package) for detecting conversion events. We used this pipeline to analyze the conversion events that affected two well-studied gene clusters (α-globin and β-globin) and three gene clusters for which comparative sequence data were generated from seven primate species: CCL (chemokine ligand), IFN (interferon), and CYP2abf (part of cytochrome P450 family 2). CHAP is freely available at http://www.bx.psu.edu/miller_lab. Conclusions These studies reveal the value of characterizing conversion events in the context of studying gene clusters in complex genomes. PMID:21798034

  11. Splitting Methods for Convex Clustering

    PubMed Central

    Chi, Eric C.; Lange, Kenneth

    2016-01-01

    Clustering is a fundamental problem in many scientific applications. Standard methods such as k-means, Gaussian mixture models, and hierarchical clustering, however, are beset by local minima, which are sometimes drastically suboptimal. Recently introduced convex relaxations of k-means and hierarchical clustering shrink cluster centroids toward one another and ensure a unique global minimizer. In this work we present two splitting methods for solving the convex clustering problem. The first is an instance of the alternating direction method of multipliers (ADMM); the second is an instance of the alternating minimization algorithm (AMA). In contrast to previously considered algorithms, our ADMM and AMA formulations provide simple and unified frameworks for solving the convex clustering problem under the previously studied norms and open the door to potentially novel norms. We demonstrate the performance of our algorithm on both simulated and real data examples. While the differences between the two algorithms appear to be minor on the surface, complexity analysis and numerical experiments show AMA to be significantly more efficient. This article has supplemental materials available online. PMID:27087770

  12. Uranyl peroxide closed clusters containing topological squares

    SciTech Connect

    Unruh, Daniel K.; Burtner, Alicia; Pressprich, Laura; Sigmon, Ginger E.; Burns, Peter C

    2010-01-01

    Four self-assembling clusters of uranyl peroxide polyhedra have been formed in alkaline aqueous solutions and structurally characterized. These clusters consist of 28, 30, 36 and 44 uranyl polyhedra and exhibit complex new topologies. Each has a structure that contains topological squares, pentagons and hexagons. Analysis of possible topologies within boundary constraints indicates a tendency for adoption of higher symmetry topologies in these cases. Small angle X-ray scattering data demonstrated that crystals of one of these clusters can be dissolved in ultrapure water and that the clusters remain intact for at least several days.

  13. Star Clusters in the Magellanic Clouds

    NASA Astrophysics Data System (ADS)

    Gallagher, J. S., III

    2014-09-01

    The Magellanic Clouds (MC) are prime locations for studies of star clusters covering a full range in age and mass. This contribution briefly reviews selected properties of Magellanic star clusters, by focusing first on young systems that show evidence for hierarchical star formation. The structures and chemical abundance patterns of older intermediate age star clusters in the Small Magellanic Cloud (SMC) are a second topic. These suggest a complex history has affected the chemical enrichment in the SMC and that low tidal stresses in the SMC foster star cluster survival.

  14. An analysis of hospital brand mark clusters.

    PubMed

    Vollmers, Stacy M; Miller, Darryl W; Kilic, Ozcan

    2010-07-01

    This study analyzed brand mark clusters (i.e., various types of brand marks displayed in combination) used by hospitals in the United States. The brand marks were assessed against several normative criteria for creating brand marks that are memorable and that elicit positive affect. Overall, results show a reasonably high level of adherence to many of these normative criteria. Many of the clusters exhibited pictorial elements that reflected benefits and that were conceptually consistent with the verbal content of the cluster. Also, many clusters featured icons that were balanced and moderately complex. However, only a few contained interactive imagery or taglines communicating benefits.

  15. Formation of [4Fe-4S] clusters in the mitochondrial iron-sulfur cluster assembly machinery.

    PubMed

    Brancaccio, Diego; Gallo, Angelo; Mikolajczyk, Maciej; Zovo, Kairit; Palumaa, Peep; Novellino, Ettore; Piccioli, Mario; Ciofi-Baffoni, Simone; Banci, Lucia

    2014-11-19

    The generation of [4Fe-4S] clusters in mitochondria critically depends, in both yeast and human cells, on two A-type ISC proteins (in mammals named ISCA1 and ISCA2), which perform a nonredundant functional role forming in vivo a heterocomplex. The molecular function of ISCA1 and ISCA2 proteins, i.e., how these proteins help in generating [4Fe-4S] clusters, is still unknown. In this work we have structurally characterized the Fe/S cluster binding properties of human ISCA2 and investigated in vitro whether and how a [4Fe-4S] cluster is assembled when human ISCA1 and ISCA2 interact with the physiological [2Fe-2S](2+) cluster-donor human GRX5. We found that (i) ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state, and (ii) two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex. This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster. The formation of the same [4Fe-4S](2+) cluster-bound heterodimeric species is also observed by having first one [2Fe-2S](2+) cluster transferred from GRX5 to each individual ISCA1 and ISCA2 proteins to form [2Fe-2S](2+) ISCA2 and [2Fe-2S](2+) ISCA1, and then mixing them together. These findings imply that such heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins.

  16. Dimensionality Reduction Particle Swarm Algorithm for High Dimensional Clustering

    SciTech Connect

    Cui, Xiaohui; ST Charles, Jesse Lee; Potok, Thomas E; Beaver, Justin M

    2008-01-01

    The Particle Swarm Optimization (PSO) clustering algorithm can generate more compact clustering results than the traditional K-means clustering algorithm. However, when clustering high dimensional datasets, the PSO clustering algorithm is notoriously slow because its computation cost increases exponentially with the size of the dataset dimension. Dimensionality reduction techniques offer solutions that both significantly improve the computation time, and yield reasonably accurate clustering results in high dimensional data analysis. In this paper, we introduce research that combines different dimensionality reduction techniques with the PSO clustering algorithm in order to reduce the complexity of high dimensional datasets and speed up the PSO clustering process. We report significant improvements in total runtime. Moreover, the clustering accuracy of the dimensionality reduction PSO clustering algorithm is comparable to the one that uses full dimension space.

  17. Geographic clusters of congenital anomalies in Argentina.

    PubMed

    Groisman, Boris; Gili, Juan; Giménez, Lucas; Poletta, Fernando; Bidondo, María Paz; Barbero, Pablo; Liascovich, Rosa; López-Camelo, Jorge

    2017-01-01

    Geographical clusters are defined as the occurrence of an unusual number of cases higher than expected in a given geographical area in a certain period of time. The aim of this study was to identify potential geographical clusters of specific selected congenital anomalies (CA) in Argentina. The cases were ascertained from 703,325 births, examined in 133 maternity hospitals in the 24 provinces of Argentina. We used the spatial scan statistic to determine areas of Argentina which had statistically significant elevations of prevalence. Prenatal diagnosis followed by referral of high-risk pregnancies to high complexity hospitals in a hospital-based surveillance system can create artifactual clusters. We assessed the referral bias by evaluating the prevalence heterogeneity within each cluster. Eight clusters of selected CAs with unusually high birth prevalence were identified: anencephaly, encephalocele, spina bifida, diaphragmatic hernia, talipes equinovarus, omphalocele, Cleft lip with or without cleft palate (CL/P), and Down syndrome. The clusters of Down syndrome and CL/P observed in this study match the previously reported clusters. These findings support local targeted interventions to lower the prevalence of the CAs and/or further research on the cause of each cluster. The clusters of spina bifida, anencephaly, encephalocele, omphalocele, congenital diaphragmatic hernia, and talipes equinovarus may be influenced by prenatal diagnosis and referral to high complexity hospitals.

  18. The longitudinal development of clusters in French.

    PubMed

    Demuth, Katherine; McCullough, Elizabeth

    2009-03-01

    Studies of English and German find that children tend to acquire word-final consonant clusters before word-initial consonant clusters. This order of acquisition is generally attributed to articulatory, frequency and/or morphological factors. This contrasts with recent experimental findings from French, where two-year-olds were better at producing word-initial than word-final clusters (Demuth & Kehoe, 2006). The purpose of the present study was to examine French-speaking children's longitudinal acquisition of clusters to determine if these results replicate developmentally. Analysis of spontaneous speech productions from two French-speaking children between one and three years confirmed the earlier acquisition of initial clusters, even when sonority factors were controlled. The findings suggest that French-speaking children acquire complexity at the beginnings of words before complexity appears word-finally. The role of frequency, morphological, structural and input factors is discussed.

  19. Synthesis and structure of a water-soluble hexanuclear silver(I) nicotinate cluster comprised of a "cyclohexane-chair"-type of framework, showing effective antibacterial and antifungal activities: use of "sparse matrix" techniques for growing crystals of water-soluble inorganic complexes.

    PubMed

    Tsyba, Irina; Mui, Becky Bun-Kit; Bau, Robert; Noguchi, Ryusuke; Nomiya, Kenji

    2003-12-01

    The synthesis of a water-soluble anionic silver 2-mercaptonicotinate complex having effective antibacterial and antifungal properties is described. Its structure has been confirmed to be a hexameric cluster by an X-ray diffraction analysis of a mixed Na(+)/Tris(+) salt (Tris(+) = tris(hydroxymethyl)methylammonium cation). The [Ag(mna)](6)(6-) cluster has a Ag(6)S(6) core and an overall shape of twisted hexagonal cylinder with six sulfur atoms and six silver atoms alternating on a puckered drum-like surface. Each Ag atom is trigonally coordinated by one N and two S ligands. The overall [Ag(mna)](6)(6-).4Na(+).2[(HOCH(2))(3)CNH(3)](+).10H(2)O complex has a layered appearance in the crystal packing diagram, with a [Ag(mna)](6)(-) cluster layer alternating with a solvent layer consisting of sodium atoms, Tris buffer cations, and water molecules. The structure is almost identical to that of a neutral [Ag(Hmna)](6) complex reported earlier. The neutral and charged complexes are both known to possess antimicrobial activities, and some biological properties of these and related compounds are briefly discussed in this paper.

  20. Peptide-bound dinitrosyliron complexes (DNICs) and neutral/reduced-form Roussin's red esters (RREs/rRREs): understanding nitrosylation of [Fe-S] clusters leading to the formation of DNICs and RREs using a de novo design strategy.

    PubMed

    Lin, Zong-Sian; Lo, Feng-Chun; Li, Chih-Hsiang; Chen, Chih-Hao; Huang, Wei-Ning; Hsu, I-Jui; Lee, Jyh-Fu; Horng, Jia-Cherng; Liaw, Wen-Feng

    2011-10-17

    This manuscript describes the interaction of low-molecular-weight DNICs with short peptides designed to explore the stability and structure of DNIC-peptide/RRE-peptide constructs. Although characterization of protein-bound and low-molecular-weight DNICs is possible via EPR, XAS, and NRVS, this study demonstrates that the combination of aqueous IR ν(NO) and UV-vis spectra can serve as an efficient tool to characterize and discriminate peptide-bound DNICs and RREs. The de novo chelate-cysteine-containing peptides KC(A)(n)CK-bound (n = 1-4) dinitrosyliron complexes KC(A)(n)CK-DNIC (CnA-DNIC) and monodentate-cysteine-containing peptides KCAAK-/KCAAHK-bound Roussin's red esters (RREs) KCAAK-RRE/KCAAHK-RRE were synthesized and characterized by aqueous IR, UV-vis, EPR, CD, XAS, and ESI-MS. In contrast to the inertness of chelate-cysteine-containing peptide-bound DNICs toward KCAAK/KCAAHK, transformation of KCAAK-RRE/KCAAHK-RRE into CnA-DNIC triggered by CnA and reversible transformation between CnA-DNIC and CnA-RRE via {Fe(NO)(2)}(9)-{Fe(NO)(2)}(10) reduced-form peptide-bound RREs demonstrate that the {Fe(NO)(2)}(9) motif displays a preference for chelate-cysteine-containing peptides over monodentate-cysteine-containing peptides. Also, this study may signify that nitrosylation of [Fe-S] proteins generating protein-bound RREs, reduced protein-bound RREs, or protein-bound DNICs are modulated by both the oxidation state of iron and the chelating effect of the bound proteins of [Fe-S] clusters.

  1. New insights into the mechanism of proton transfer to hydride complexes: kinetic and theoretical evidence showing the existence of competitive pathways for protonation of the cluster [W3S4H3(dmpe)3]+ with acids.

    PubMed

    Algarra, Andrés G; Basallote, Manuel G; Feliz, Marta; Fernández-Trujillo, M Jesús; Llusar, Rosa; Safont, Vicent S

    2006-02-01

    The reaction of the hydride cluster [W3S4H3(dmpe)3]+ (1, dmpe = 1,2-bis(dimethylphosphanyl)ethane) with acids (HCl, CF3COOH, HBF4) in CH2Cl2 solution under pseudo-first-order conditions of excess acid occurs with three kinetically distinguishable steps that can be interpreted as corresponding to successive formal substitution processes of the coordinated hydrides by the anion of the acid (HCl, CF3COOH) or the solvent (HBF4). Whereas the rate law for the third step changes with the nature of the acid, the first two kinetic steps always show a second-order dependence on acid concentration. In contrast, a single kinetic step with a first-order dependence with respect to the acid is observed when the experiments are carried out with a deficit of acid. The decrease in the T1 values for the hydride NMR signal of 1 in the presence of added HCl suggests the formation of an adduct with a W-H...H-Cl dihydrogen bond. Theoretical calculations for the reaction with HCl indicate that the kinetic results in CH2Cl2 solution can be interpreted on the basis of a mechanism with two competitive pathways. One of the pathways consists of direct proton transfer within the W-H...H-Cl adduct to form W-Cl and H2, whereas the other requires the presence of a second HCl molecule to form a W-H...H-Cl...H-Cl adduct that transforms into W-Cl, H2 and HCl in the rate-determining step. The activation barriers and the structures of the transition states for both pathways were also calculated, and the results indicate that both pathways can be competitive and that the transition states can be described in both cases as a dihydrogen complex hydrogen-bonded to Cl- or HCl2(-).

  2. Scientific Cluster Deployment and Recovery - Using puppet to simplify cluster management

    NASA Astrophysics Data System (ADS)

    Hendrix, Val; Benjamin, Doug; Yao, Yushu

    2012-12-01

    Deployment, maintenance and recovery of a scientific cluster, which has complex, specialized services, can be a time consuming task requiring the assistance of Linux system administrators, network engineers as well as domain experts. Universities and small institutions that have a part-time FTE with limited time for and knowledge of the administration of such clusters can be strained by such maintenance tasks. This current work is the result of an effort to maintain a data analysis cluster (DAC) with minimal effort by a local system administrator. The realized benefit is the scientist, who is the local system administrator, is able to focus on the data analysis instead of the intricacies of managing a cluster. Our work provides a cluster deployment and recovery process (CDRP) based on the puppet configuration engine allowing a part-time FTE to easily deploy and recover entire clusters with minimal effort. Puppet is a configuration management system (CMS) used widely in computing centers for the automatic management of resources. Domain experts use Puppet's declarative language to define reusable modules for service configuration and deployment. Our CDRP has three actors: domain experts, a cluster designer and a cluster manager. The domain experts first write the puppet modules for the cluster services. A