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Sample records for clustered yy1 binding

  1. Identification of clustered YY1 binding sites in Imprinting Control Regions

    SciTech Connect

    Kim, J D; Hinz, A; Bergmann, A; Huang, J; Ovcharenko, I; Stubbs, L; Kim, J

    2006-04-19

    Mammalian genomic imprinting is regulated by Imprinting Control Regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In the current study, the sequence features derived from a tandem array of YY1 binding sites of Peg3-DMR (differentially methylated region) led us to identify three additional clustered YY1 binding sites, which are also localized within the DMRs of Xist, Tsix, and Nespas. These regions have been shown to play a critical role as ICRs for the regulation of surrounding genes. These ICRs have maintained a tandem array of YY1 binding sites during mammalian evolution. The in vivo binding of YY1 to these regions is allele-specific and only to the unmethylated active alleles. Promoter/enhancer assays suggest that a tandem array of YY1 binding sites function as a potential orientation-dependent enhancer. Insulator assays revealed that the enhancer-blocking activity is detected only in the YY1 binding sites of Peg3-DMR but not in the YY1 binding sites of other DMRs. Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting.

  2. The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity.

    PubMed

    Wai, Dorothy C C; Shihab, Manar; Low, Jason K K; Mackay, Joel P

    2016-11-02

    Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner.

  3. The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

    PubMed Central

    Wai, Dorothy C.C.; Shihab, Manar; Low, Jason K.K.; Mackay, Joel P.

    2016-01-01

    Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner. PMID:27369384

  4. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

    PubMed Central

    Chen, Chih-yu; Shi, Wenqiang; Balaton, Bradley P.; Matthews, Allison M.; Li, Yifeng; Arenillas, David J.; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R. R.; Brown, Carolyn J.; Wasserman, Wyeth W.

    2016-01-01

    Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors. PMID:27857184

  5. YY1 modulates taxane response in epithelial ovarian cancer

    SciTech Connect

    Matsumura, Noriomi; Huang, Zhiqing; Baba, Tsukasa; Lee, Paula S.; Barnett, Jason C.; Mori, Seiichi; Chang, Jeffrey T.; Kuo, Wen-Lin; Gusberg, Alison H.; Whitaker, Regina S.; Gray, JoeW.; Fujii, Shingo; Berchuck, Andrew; Murphy, Susan K.

    2008-10-10

    The results of this study show that a high YY1 gene signature (characterized by coordinate elevated expression of transcription factor YY1 and putative YY1 target genes) within serous epithelial ovarian cancers is associated with enhanced response to taxane-based chemotherapy and improved survival. If confirmed in a prospective study, these results have important implications for the potential future use of individualized therapy in treating patients with ovarian cancer. Identification of the YY1 gene signature profile within a tumor prior to initiation of chemotherapy may provide valuable information about the anticipated response of these tumors to taxane-based drugs, leading to better informed decisions regarding chemotherapeutic choice. Survival of ovarian cancer patients is largely dictated by their response to chemotherapy, which depends on underlying molecular features of the malignancy. We previously identified YIN YANG 1 (YY1) as a gene whose expression is positively correlated with ovarian cancer survival. Herein we investigated the mechanistic basis of this association. Epigenetic and genetic characteristics of YY1 in serous epithelial ovarian cancer (SEOC) were analyzed along with YY1 mRNA and protein. Patterns of gene expression in primary SEOC and in the NCI60 database were investigated using computational methods. YY1 function and modulation of chemotherapeutic response in vitro was studied using siRNA knockdown. Microarray analysis showed strong positive correlation between expression of YY1 and genes with YY1 and transcription factor E2F binding motifs in SEOC and in the NCI60 cancer cell lines. Clustering of microarray data for these genes revealed that high YY1/E2F3 activity positively correlates with survival of patients treated with the microtubule stabilizing drug paclitaxel. Increased sensitivity to taxanes, but not to DNA crosslinking platinum agents, was also characteristic of NCI60 cancer cell lines with a high YY1/E2F signature. YY1

  6. YY1 Is Required for Germinal Center B Cell Development

    PubMed Central

    Vuyyuru, Raja; Jha, Vibha; Hodewadekar, Suchita; Manser, Tim; Atchison, Michael L.

    2016-01-01

    YY1 has been implicated as a master regulator of germinal center B cell development as YY1 binding sites are frequently present in promoters of germinal center-expressed genes. YY1 is known to be important for other stages of B cell development including the pro-B and pre-B cells stages. To determine if YY1 plays a critical role in germinal center development, we evaluated YY1 expression during B cell development, and used a YY1 conditional knock-out approach for deletion of YY1 in germinal center B cells (CRE driven by the immunoglobulin heavy chain γ1 switch region promoter; γ1-CRE). We found that YY1 is most highly expressed in germinal center B cells and is increased 3 fold in splenic B cells activated by treatment with anti-IgM and anti-CD40. In addition, deletion of the yy1 gene by action of γ1-CRE recombinase resulted in significant loss of GC cells in both un-immunized and immunized contexts with corresponding loss of serum IgG1. Our results show a crucial role for YY1 in the germinal center reaction. PMID:27167731

  7. YY1 Is Required for Germinal Center B Cell Development.

    PubMed

    Banerjee, Anupam; Sindhava, Vishal; Vuyyuru, Raja; Jha, Vibha; Hodewadekar, Suchita; Manser, Tim; Atchison, Michael L

    2016-01-01

    YY1 has been implicated as a master regulator of germinal center B cell development as YY1 binding sites are frequently present in promoters of germinal center-expressed genes. YY1 is known to be important for other stages of B cell development including the pro-B and pre-B cells stages. To determine if YY1 plays a critical role in germinal center development, we evaluated YY1 expression during B cell development, and used a YY1 conditional knock-out approach for deletion of YY1 in germinal center B cells (CRE driven by the immunoglobulin heavy chain γ1 switch region promoter; γ1-CRE). We found that YY1 is most highly expressed in germinal center B cells and is increased 3 fold in splenic B cells activated by treatment with anti-IgM and anti-CD40. In addition, deletion of the yy1 gene by action of γ1-CRE recombinase resulted in significant loss of GC cells in both un-immunized and immunized contexts with corresponding loss of serum IgG1. Our results show a crucial role for YY1 in the germinal center reaction.

  8. CtBP Levels Control Intergenic Transcripts, PHO/YY1 DNA Binding, and PcG Recruitment to DNA

    PubMed Central

    Basu, Arindam; Atchison, Michael L.

    2013-01-01

    Carboxy-terminal binding protein (CtBP) is a well-known corepressor of several DNA binding transcription factors in Drosophila as well as in mammals. CtBP is implicated in Polycomb Group (PcG) complex-mediated transcriptional repression because it can bind to some PcG proteins, and mutation of the ctbp gene in flies results in lost PcG protein recruitment to Polycomb Response Elements (PREs) and lost PcG repression. However, the mechanism of reduced PcG DNA binding in CtBP mutant backgrounds is unknown. We show here that in a Drosophila CtBP mutant background, intergenic transcripts are induced across several PRE sequences and this corresponds to reduced DNA binding by PcG proteins Pleiohomeotic (PHO) and Polycomb (Pc), and reduced trimethylation of histone H3 on lysine 27, a hallmark of PcG repression. Restoration of CtBP levels by expression of a CtBP transgene results in repression of intergenic transcripts, restored PcG binding, and elevated trimethylation of H3 on lysine 27. Our results support a model in which CtBP regulates expression of intergenic transcripts that controls DNA binding by PcG proteins and subsequent histone modifications and transcriptional activity. PMID:20082324

  9. YY1 tethers Xist RNA to the inactive X nucleation center

    PubMed Central

    Jeon, Yesu; Lee, Jeannie T.

    2011-01-01

    SUMMARY The long noncoding Xist RNA inactivates one X-chromosome in the female mammal. Current models posit that Xist induces silencing as it spreads along X and recruits Polycomb complexes. However, the mechanisms for Xist loading and spreading are currently unknown. Here, we define the nucleation center for Xist RNA and show that YY1 docks Xist particles onto the X chromosome. YY1 is a ‘bivalent’ protein, capable of binding both RNA and DNA through different sequence motifs. Xist’s exclusive attachment to the inactive X is determined by an epigenetically regulated trio of YY1 sites as well as allelic origin. Specific YY1-to-RNA and YY1-to-DNA contacts are required to load Xist particles onto X. YY1 interacts with Xist RNA through Repeat C. We propose that YY1 acts as adaptor between regulatory RNA and chromatin targets. PMID:21729784

  10. YY1 positively regulates human UBIAD1 expression

    SciTech Connect

    Funahashi, Nobuaki; Hirota, Yoshihisa; Nakagawa, Kimie; Sawada, Natumi; Watanabe, Masato; Suhara, Yoshitomo; Okano, Toshio

    2015-05-01

    Vitamin K is involved in bone formation and blood coagulation. Natural vitamin K compounds are composed of the plant form phylloquinone (vitamin K{sub 1}) and a series of bacterial menaquionones (MK-n; vitamin K{sub 2}). Menadione (vitamin K{sub 3}) is an artificial vitamin K compound. MK-4 contains 4-isoprenyl as a side group in the 2-methyl-1,4-naphthoquinone common structure and has various bioactivities. UbiA prenyltransferase domain containing 1 (UBIAD1 or TERE1) is the menaquinone-4 biosynthetic enzyme. UBIAD1 transcript expression significantly decreases in patients with prostate carcinoma and overexpressing UBIAD1 inhibits proliferation of a tumour cell line. UBIAD1 mRNA expression is ubiquitous in mouse tissues, and higher UBIAD1 mRNA expression levels are detected in the brain, heart, kidneys and pancreas. Several functions of UBIAD1 have been reported; however, regulation of the human UBIAD1 gene has not been elucidated. Here we report cloning and characterisation of the human UBIAD1 promoter. A 5′ rapid amplification of cDNA ends analysis revealed that the main transcriptional start site was 306 nucleotides upstream of the translation initiation codon. Deletion and mutation analyses revealed the functional importance of the YY1 consensus motif. Electrophoretic gel mobility shift and chromatin immunoprecipitation assays demonstrated that YY1 binds the UBIAD1 promoter in vitro and in vivo. In addition, YY1 small interfering RNA decreased endogenous UBIAD1 mRNA expression and UBIAD1 conversion activity. These results suggest that YY1 up-regulates UBIAD1 expression and UBIAD1 conversion activity through the UBIAD1 promoter. - Highlights: • We cloned the human UBIAD1 promoter. • The functional importance of the YY1 motif was identified in the UBIAD1 promoter. • YY1 binds the UBIAD1 promoter in vitro and in vivo. • Knockdown of YY1 significantly decreased UBIAD1 expression. • YY1 up-regulates UBIAD1 conversion activity through the UBIAD1

  11. The Yin Yang-1 (YY1) protein undergoes a DNA-replication-associated switch in localization from the cytoplasm to the nucleus at the onset of S phase.

    PubMed

    Palko, Linda; Bass, Hank W; Beyrouthy, Maroun J; Hurt, Myra M

    2004-01-26

    The essential Yin Yang-1 gene (YY1) encodes a ubiquitous, conserved, multifunctional zinc-finger transcription factor in animals. The YY1 protein regulates initiation, activation, or repression of transcription from a variety of genes required for cell growth, development, differentiation, or tumor suppression, as well as from genes in some retroviruses and DNA viruses. Among the specific functions attributed to YY1 is a role in cell-cycle-specific upregulation of the replication-dependent histone genes. The YY1 protein binds to the histone alpha element, a regulatory sequence found in all replication-dependent histone genes. We therefore examined the abundance, DNA-binding activity and localization of the YY1 protein throughout the cell cycle in unperturbed, shake-off-synchronized Chinese hamster ovary and HeLa cells. We found that, whereas the DNA-binding activity of YY1 increased dramatically early in S phase, the YY1 mRNA and protein levels did not. YY1 changed subcellular distribution patterns during the cell cycle, from mainly cytoplasmic at G1 to mainly nuclear at early and middle S phase, then back to primarily cytoplasmic later in S phase. Nuclear accumulation of YY1 near the G1/S boundary coincided with both an increase in YY1 DNA-binding activity and the coordinate up-regulation of the replication-dependent histone genes. The DNA synthesis inhibitor aphidicolin caused a nearly complete loss of nuclear YY1, whereas addition of caffeine or 2-aminopurine to aphidicolin-treated cells restored both DNA synthesis and YY1 localization in the nucleus. These findings reveal a mechanism by which YY1 localization is coupled to DNA synthesis and responsive to cell-cycle signaling pathways. Taken together, our results provide insight into how YY1 might participate in the cell-cycle control over a variety of nuclear events required for cell division and proliferation.

  12. Expression of YY1 in Differentiated Thyroid Cancer.

    PubMed

    Arribas, Jéssica; Castellví, Josep; Marcos, Ricard; Zafón, Carles; Velázquez, Antonia

    2015-05-01

    The transcription factor Yin Yang 1 (YY1) has an important regulatory role in tumorigenesis, but its implication in thyroid cancer has not been yet investigated. In the present study, we have analyzed the expression of YY1 in differentiated thyroid cancer and assessed the association of YY1 expression with clinical features. Expression of YY1 was evaluated in human thyroid cancer cell lines, a series of matched normal/tumor thyroid tissues and in a thyroid cancer tissue microarray, using real-time PCR, Western blot, and/or immunohistochemistry. YY1 was overexpressed in thyroid cancer cells, at transcription and protein levels. A significant increase of YY1 mRNA was also observed in tumor thyroid tissues. Moreover, immunohistochemical analysis of the thyroid cancer tissue microarray revealed that both papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC) present increased YY1 protein levels (48 and 19%, respectively). After stratification by the level of YY1 protein, positive YY1 expression identifies 88% of patients with PTC. The association of YY1 expression with clinicopathological features in PTC and FTC showed that YY1 expression was related with age at diagnosis. Our data indicates for the first time overexpression of YY1 in differentiated thyroid cancer, with YY1 being more frequently overexpressed in the PTC subtype.

  13. A prominent and conserved role for YY1 in Xist transcriptional activation

    PubMed Central

    Navarro, Pablo; Neuillet, Damien; Rougeulle, Claire

    2014-01-01

    Accumulation of the non-coding RNA Xist on one X chromosome in female cells is a hallmark of X-chromosome inactivation in eutherians. Here, we uncovered an essential function for the ubiquitous autosomal transcription factor Yin-Yang 1 (YY1) in the transcriptional activation of Xist in both human and mouse. We show that loss of YY1 prevents Xist up-regulation during the initiation and maintenance of X-inactivation, and that YY1 binds directly the Xist 5′ region to trigger the activity of the Xist promoter. Binding of YY1 to the Xist 5′ region prior to X-chromosome inactivation competes with the Xist repressor REX1 while DNA methylation controls mono-allelic fixation of YY1 to Xist at the onset of X-chromosome inactivation. YY1 is thus the first autosomal activating factor involved in a fundamental and conserved pathway of Xist regulation that ensures the asymmetric transcriptional up-regulation of the master regulator of X-chromosome inactivation. PMID:25209548

  14. Epithelial inactivation of Yy1 abrogates lung branching morphogenesis.

    PubMed

    Boucherat, Olivier; Landry-Truchon, Kim; Bérubé-Simard, Félix-Antoine; Houde, Nicolas; Beuret, Laurent; Lezmi, Guillaume; Foulkes, William D; Delacourt, Christophe; Charron, Jean; Jeannotte, Lucie

    2015-09-01

    Yin Yang 1 (YY1) is a multifunctional zinc-finger-containing transcription factor that plays crucial roles in numerous biological processes by selectively activating or repressing transcription, depending upon promoter contextual differences and specific protein interactions. In mice, Yy1 null mutants die early in gestation whereas Yy1 hypomorphs die at birth from lung defects. We studied how the epithelial-specific inactivation of Yy1 impacts on lung development. The Yy1 mutation in lung epithelium resulted in neonatal death due to respiratory failure. It impaired tracheal cartilage formation, altered cell differentiation, abrogated lung branching and caused airway dilation similar to that seen in human congenital cystic lung diseases. The cystic lung phenotype in Yy1 mutants can be partly explained by the reduced expression of Shh, a transcriptional target of YY1, in lung endoderm, and the subsequent derepression of mesenchymal Fgf10 expression. Accordingly, SHH supplementation partially rescued the lung phenotype in vitro. Analysis of human lung tissues revealed decreased YY1 expression in children with pleuropulmonary blastoma (PPB), a rare pediatric lung tumor arising during fetal development and associated with DICER1 mutations. No evidence for a potential genetic interplay between murine Dicer and Yy1 genes during lung morphogenesis was observed. However, the cystic lung phenotype resulting from the epithelial inactivation of Dicer function mimics the Yy1 lung malformations with similar changes in Shh and Fgf10 expression. Together, our data demonstrate the crucial requirement for YY1 in lung morphogenesis and identify Yy1 mutant mice as a potential model for studying the genetic basis of PPB.

  15. YY1 Control of AID-Dependent Lymphomagenesis

    DTIC Science & Technology

    2015-07-01

    AWARD NUMBER: W81XWH-14-1-0171 TITLE: YY1 Control of AID -Dependent Lymphomagenesis PRINCIPAL INVESTIGATOR: Michael Atchison, Ph.D CONTRACTING...W81XWH-14-1-0171 YY1 Control of AID -Dependent Lymphomagenesis 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...SUPPLEMENTARY NOTES 14. ABSTRACT We hypothesize that YY1 levels control AID nuclear accumulation, AID mutation rates, and subsequent AID - mediated B cell

  16. The transcription factor YY1 is a novel substrate for Aurora B kinase at G2/M transition of the cell cycle.

    PubMed

    Kassardjian, Ari; Rizkallah, Raed; Riman, Sarah; Renfro, Samuel H; Alexander, Karen E; Hurt, Myra M

    2012-01-01

    Yin Yang 1 (YY1) is a ubiquitously expressed and highly conserved multifunctional transcription factor that is involved in a variety of cellular processes. Many YY1-regulated genes have crucial roles in cell proliferation, differentiation, apoptosis, and cell cycle regulation. Numerous mechanisms have been shown to regulate the function of YY1, such as DNA binding affinity, subcellular localization, and posttranslational modification including phosphorylation. Polo-like kinase 1(Plk1) and Casein kinase 2α (CK2 α) were the first two kinases identified to phosphorylate YY1. In this study, we identify a third kinase. We report that YY1 is a novel substrate of the Aurora B kinase both in vitro and in vivo. Serine 184 phosphorylation of YY1 by Aurora B is cell cycle regulated and peaks at G2/M and is rapidly dephosphorylated, likely by protein phosphatase 1 (PP1) as the cells enter G1. Aurora A and Aurora C can also phosphorylate YY1 in vitro, but at serine/threonine residues other than serine 184. We present evidence that phosphorylation of YY1 in the central glycine/alanine (G/A)-rich region is important for DNA binding activity, with a potential phosphorylation/acetylation interplay regulating YY1 function. Given their importance in mitosis and overexpression in human cancers, Aurora kinases have been identified as promising therapeutic targets. Increasing our understanding of Aurora substrates will add to the understanding of their signaling pathways.

  17. Phosphorylated C/EBPβ Influences a Complex Network Involving YY1 and USF2 in Lung Epithelial Cells

    PubMed Central

    Viart, Victoria; Varilh, Jessica; Lopez, Estelle; René, Céline; Claustres, Mireille; Taulan-Cadars, Magali

    2013-01-01

    The promoter of the cystic fibrosis transmembrane conductance regulator gene CFTR is tightly controlled by regulators including CCAAT/enhancer binding proteins (C/EBPs). We previously reported that the transcription factors YY1 and USF2 affect CFTR expression. We can now demonstrate that C/EBPβ, a member of the CCAAT family, binds to the CFTR promoter and contributes to its transcriptional activity. Our data reveal that C/EBPβ cooperates with USF2 and acts antagonistically to YY1 in the control of CFTR expression. Interestingly, YY1, a strong repressor, fails to repress the CFTR activation induced by USF2 through DNA binding competition. Collectively, the data strongly suggest a model by which USF2 functionally interacts with YY1 blocking its inhibitory activity, in favour of C/EBPβ transactivation. Further investigation into the interactions between these three proteins revealed that phosphorylation of C/EBPβ influences the DNA occupancy of YY1 and favours the interaction between USF2 and YY1. This phosphorylation process has several implications in the CFTR transcriptional process, thus evoking an additional layer of complexity to the mechanisms influencing CFTR gene regulation. PMID:23560079

  18. Upregulation of miR-146a by YY1 depletion correlates with delayed progression of prostate cancer

    PubMed Central

    Huang, Yeqing; Tao, Tao; Liu, Chunhui; Guan, Han; Zhang, Guangyuan; Ling, Zhixin; Zhang, Lei; Lu, Kai; Chen, Shuqiu; Xu, Bin; Chen, Ming

    2017-01-01

    Previously published studies explained that the excessive expression of miR-146a influences the prostate cancer (PCa) cells in terms of apoptosis, progression, and viability. Although miR-146a acts as a tumor suppressor, current knowledge on the molecular mechanisms that controls its expression in PCa is limited. In this study, gene set enrichment analysis (GSEA) showed negatively enriched expression of miR-146a target gene sets and positively enriched expression of gene sets suppressed by the enhancer of zeste homolog 2 (EZH2) after YY1 depletion in PCa cells. The current results demonstrated that the miR-146a levels in PCa tissues with high Gleason scores (>7) are significantly lower than those in PCa tissues with low Gleason scores (≤7), which were initially observed in the clinical specimens. An inverse relationship between YY1 and miR-146a expression was also observed. Experiments indicated the decrease in cell viability, proliferation, and promoting apoptosis after YY1 depletion, while through inhibiting miR-146a could alleviate the negative effect brought by YY1 depletion. We detected the reversed adjustment of YY1 to accommodate miR-146a transcriptions. On the basis of YY1 depletion, we determined that the expression of miR-146a increased after EZH2 knockdown. We validated the combination of YY1 and its interaction with EZH2 at the miR-146a promoter binding site, thereby prohibiting the transcriptional activity of miR-146a in PCa cells. Our results suggested that YY1 depletion repressed PCa cell viability and proliferation and induced apoptosis at least in a miR-146a-assisted manner. PMID:28101571

  19. NF-kappaB regulation of YY1 inhibits skeletal myogenesis through transcriptional silencing of myofibrillar genes.

    PubMed

    Wang, Huating; Hertlein, Erin; Bakkar, Nadine; Sun, Hao; Acharyya, Swarnali; Wang, Jingxin; Carathers, Micheal; Davuluri, Ramana; Guttridge, Denis C

    2007-06-01

    NF-kappaB signaling is implicated as an important regulator of skeletal muscle homeostasis, but the mechanisms by which this transcription factor contributes to muscle maturation and turnover remain unclear. To gain insight into these mechanisms, gene expression profiling was examined in C2C12 myoblasts devoid of NF-kappaB activity. Interestingly, even in proliferating myoblasts, the absence of NF-kappaB caused the pronounced induction of several myofibrillar genes, suggesting that NF-kappaB functions as a negative regulator of late-stage muscle differentiation. Although several myofibrillar promoters contain predicted NF-kappaB binding sites, functional analysis using the troponin-I2 gene as a model revealed that NF-kappaB-mediated repression does not occur through direct DNA binding. In the search for an indirect mediator, the transcriptional repressor YinYang1 (YY1) was identified. While inducers of NF-kappaB stimulated YY1 expression in multiple cell types, genetic ablation of the RelA/p65 subunit of NF-kappaB in both cultured cells and adult skeletal muscle correlated with reduced YY1 transcripts and protein. NF-kappaB regulation of YY1 occurred at the transcriptional level, mediated by direct binding of the p50/p65 heterodimer complex to the YY1 promoter. Furthermore, YY1 was found associated with multiple myofibrillar promoters in C2C12 myoblasts containing NF-kappaB activity. Based on these results, we propose that NF-kappaB regulation of YY1 and transcriptional silencing of myofibrillar genes represent a new mechanism by which NF-kappaB functions in myoblasts to modulate skeletal muscle differentiation.

  20. NF-κB Regulation of YY1 Inhibits Skeletal Myogenesis through Transcriptional Silencing of Myofibrillar Genes▿ †

    PubMed Central

    Wang, Huating; Hertlein, Erin; Bakkar, Nadine; Sun, Hao; Acharyya, Swarnali; Wang, Jingxin; Carathers, Micheal; Davuluri, Ramana; Guttridge, Denis C.

    2007-01-01

    NF-κB signaling is implicated as an important regulator of skeletal muscle homeostasis, but the mechanisms by which this transcription factor contributes to muscle maturation and turnover remain unclear. To gain insight into these mechanisms, gene expression profiling was examined in C2C12 myoblasts devoid of NF-κB activity. Interestingly, even in proliferating myoblasts, the absence of NF-κB caused the pronounced induction of several myofibrillar genes, suggesting that NF-κB functions as a negative regulator of late-stage muscle differentiation. Although several myofibrillar promoters contain predicted NF-κB binding sites, functional analysis using the troponin-I2 gene as a model revealed that NF-κB-mediated repression does not occur through direct DNA binding. In the search for an indirect mediator, the transcriptional repressor YinYang1 (YY1) was identified. While inducers of NF-κB stimulated YY1 expression in multiple cell types, genetic ablation of the RelA/p65 subunit of NF-κB in both cultured cells and adult skeletal muscle correlated with reduced YY1 transcripts and protein. NF-κB regulation of YY1 occurred at the transcriptional level, mediated by direct binding of the p50/p65 heterodimer complex to the YY1 promoter. Furthermore, YY1 was found associated with multiple myofibrillar promoters in C2C12 myoblasts containing NF-κB activity. Based on these results, we propose that NF-κB regulation of YY1 and transcriptional silencing of myofibrillar genes represent a new mechanism by which NF-κB functions in myoblasts to modulate skeletal muscle differentiation. PMID:17438126

  1. PARP-1 and YY1 are important novel regulators of CXCL12 gene transcription in rat pancreatic beta cells.

    PubMed

    Marković, Jelena; Grdović, Nevena; Dinić, Svetlana; Karan-Djurašević, Teodora; Uskoković, Aleksandra; Arambašić, Jelena; Mihailović, Mirjana; Pavlović, Sonja; Poznanović, Goran; Vidaković, Melita

    2013-01-01

    Despite significant progress, the molecular mechanisms responsible for pancreatic beta cell depletion and development of diabetes remain poorly defined. At present, there is no preventive measure against diabetes. The positive impact of CXCL12 expression on the pancreatic beta cell prosurvival phenotype initiated this study. Our aim was to provide novel insight into the regulation of rat CXCL12 gene (Cxcl12) transcription. The roles of poly(ADP-ribose) polymerase-1 (PARP-1) and transcription factor Yin Yang 1 (YY1) in Cxcl12 transcription were studied by examining their in vitro and in vivo binding affinities for the Cxcl12 promoter in a pancreatic beta cell line by the electrophoretic mobility shift assay and chromatin immunoprecipitation. The regulatory activities of PARP-1 and YY1 were assessed in transfection experiments using a reporter vector with a Cxcl12 promoter sequence driving luciferase gene expression. Experimental evidence for PARP-1 and YY1 revealed their trans-acting potential, wherein PARP-1 displayed an inhibitory, and YY1 a strong activating effect on Cxcl12 transcription. Streptozotocin (STZ)-induced general toxicity in pancreatic beta cells was followed by changes in Cxcl12 promoter regulation. PARP-1 binding to the Cxcl12 promoter during basal and in STZ-compromised conditions led us to conclude that PARP-1 regulates constitutive Cxcl12 expression. During the early stage of oxidative stress, YY1 exhibited less affinity toward the Cxcl12 promoter while PARP-1 displayed strong binding. These interactions were accompanied by Cxcl12 downregulation. In the later stages of oxidative stress and intensive pancreatic beta cell injury, YY1 was highly expressed and firmly bound to Cxcl12 promoter in contrast to PARP-1. These interactions resulted in higher Cxcl12 expression. The observed ability of PARP-1 to downregulate, and of YY1 to upregulate Cxcl12 promoter activity anticipates corresponding effects in the natural context where the functional

  2. Interaction of the Transcription Start Site Core Region and Transcription Factor YY1 Determine Ascorbate Transporter SVCT2 Exon 1a Promoter Activity

    PubMed Central

    Qiao, Huan; May, James M.

    2012-01-01

    Transcription of the ascorbate transporter, SVCT2, is driven by two distinct promoters in exon 1 of the transporter sequence. The exon 1a promoter lacks a classical transcription start site and little is known about regulation of promoter activity in the transcription start site core (TSSC) region. Here we present evidence that the TSSC binds the multifunctional initiator-binding protein YY1. Electrophoresis shift assays using YY1 antibody showed that YY1 is present as one of two major complexes that specifically bind to the TSSC. The other complex contains the transcription factor NF-Y. Mutations in the TSSC that decreased YY1 binding also impaired the exon 1a promoter activity despite the presence of an upstream activating NF-Y/USF complex, suggesting that YY1 is involved in the regulation of the exon 1a transcription. Furthermore, YY1 interaction with NF-Y and/or USF synergistically enhanced the exon 1a promoter activity in transient transfections and co-activator p300 enhanced their synergistic activation. We propose that the TSSC plays a vital role in the exon 1a transcription and that this function is partially carried out by the transcription factor YY1. Moreover, co-activator p300 might be able to synergistically enhance the TSSC function via a “bridge” mechanism with upstream sequences. PMID:22532872

  3. YY1 and GATA-1 interaction modulate the chicken 3'-side alpha-globin enhancer activity.

    PubMed

    Rincón-Arano, Héctor; Valadez-Graham, Viviana; Guerrero, Georgina; Escamilla-Del-Arenal, Martín; Recillas-Targa, Félix

    2005-06-24

    Studying the chicken alpha-globin domain as a model system of gene regulation, we have previously identified contiguous silencer-enhancer elements located on the 3'-side of the domain. To better characterize the enhancer we performed a systematic functional analysis to define its expression influence range and the ubiquitous and stage-specific transcriptional regulators interacting with this control element. In contrast to previous reports, we found that, in addition to a core element that includes three GATA-1 binding sites, the enhancer incorporates a 120 base-pair DNA fragment where EKLF, NF-E2 and a fourth GATA-1 factor could interact. Functional experiments demonstrate that the enhancer activity over the adult alpha(D) promoter is differentially regulated. We found that the transcriptional factor Ying Yang 1 (YY1) binds to the 120 base-pair DNA fragment and its effect over the enhancer activity is GATA-1-dependent. In addition, we characterize a novel physical interaction between GATA-1 and YY1 that influences the enhancer function. Experiments using a histone deacetylation inhibitor indicate that, in pre-erythroblasts, the enhancer down-regulation could be influenced by a closed chromatin conformation. Our observations show that the originally defined enhancer possesses a more complex composition than previously assumed. We propose that its activity is modulated through differential nuclear factor interactions and chromatin modifications at distinct erythroid stages.

  4. The Role of YY1 in Prostate Cancer

    DTIC Science & Technology

    2010-03-01

    activator protein 1. Cancer Res 2007;67:4816-26. 54. Delehouzee S, Yoshikawa T, Sawa C, et al. GABP, HCF-1 and YY1 are involved in Rb gene...expression during myogenesis. Genes Cells 2005;10:717-31. 55. Santiago FS, Ishii H, Shafi S, et al. Yin Yang-1 inhibits vascular smooth muscle cell growth... Ishii H, Shafi S, Khurana R, Kanellakis P, Bhindi R, et al. Yin Yang-1 inhibits vascular smooth muscle cell growth and intimal thickening by

  5. Transcriptional Regulation of the Astrocytic Excitatory Amino Acid Transporter 1 (EAAT1) via NF-κB and Yin Yang 1 (YY1)*

    PubMed Central

    Karki, Pratap; Kim, Clifford; Smith, Keisha; Son, Deok-Soo; Aschner, Michael; Lee, Eunsook

    2015-01-01

    Astrocytic glutamate transporter excitatory amino acid transporter (EAAT) 1, also known as glutamate aspartate transporter (GLAST) in rodents, is one of two glial glutamate transporters that are responsible for removing excess glutamate from synaptic clefts to prevent excitotoxic neuronal death. Despite its important role in neurophysiological functions, the molecular mechanisms of EAAT1 regulation at the transcriptional level remain to be established. Here, we report that NF-κB is a main positive transcription factor for EAAT1, supported by the following: 1) EAAT1 contains two consensus sites for NF-κB, 2) mutation of NF-κB binding sites decreased EAAT1 promoter activity, and 3) activation of NF-κB increased, whereas inhibition of NF-κB decreased EAAT1 promoter activity and mRNA/protein levels. EGF increased EAAT1 mRNA/protein levels and glutamate uptake via NF-κB. The transcription factor yin yang 1 (YY1) plays a role as a critical negative regulator of EAAT1, supported by the following: 1) the EAAT1 promoter contains multiple consensus sites for YY1, 2) overexpression of YY1 decreased EAAT1 promoter activity and mRNA/protein levels, and 3) knockdown of YY1 increased EAAT1 promoter activity and mRNA/protein levels. Manganese decreased EAAT1 expression via YY1. Epigenetic modifiers histone deacetylases (HDACs) served as co-repressors of YY1 to further decrease EAAT1 promoter activity, whereas inhibition of HDACs reversed manganese-induced decrease of EAAT1 expression. Taken together, our findings suggest that NF-κB is a critical positive regulator of EAAT1, mediating the stimulatory effects of EGF, whereas YY1 is a negative regulator of EAAT1 with HDACs as co-repressors, mediating the inhibitory effects of manganese on EAAT1 regulation. PMID:26269591

  6. The Yin and Yang of YY1 in the nervous system.

    PubMed

    He, Ye; Casaccia-Bonnefil, Patrizia

    2008-08-01

    The transcription factor Yin Yang 1 (YY1) is a multifunctional protein that can activate or repress gene expression depending on the cellular context. YY1 is ubiquitously expressed and highly conserved between species. However, its role varies in diverse cell types and includes proliferation, differentiation, and apoptosis. This review will focus on the function of YY1 in the nervous system including its role in neural development, neuronal function, developmental myelination, and neurological disease. The multiple functions of YY1 in distinct cell types are reviewed and the possible mechanisms underlying the cell specificity for these functions are discussed.

  7. IL-13 Induces YY1 through the AKT Pathway in Lung Fibroblasts

    PubMed Central

    Guo, Jia; Yao, Hongwei; Lin, Xin; Xu, Haodong; Dean, David; Zhu, Zhou; Liu, Gang; Sime, Patricia

    2015-01-01

    A key feature of lung fibrosis is the accumulation of myofibroblasts. Interleukin 13 (IL-13) is a pro-fibrotic mediator that directly and indirectly influences the activation of myofibroblasts. Transforming growth factor beta (TGF-β) promotes the differentiation of fibroblasts into myofibroblasts, and can be regulated by IL-13. However, IL-13’s downstream signaling pathways are not completely understood. We previously reported that the transcription factor Yin Yang 1 (YY1) is upregulated in fibroblasts treated with TGF-β and in the lungs of mice and patients with pulmonary fibrosis. Moreover, YY1 directly regulates collagen and alpha smooth muscle actin (α-SMA) expression in fibroblasts. However, it is not known if IL-13 regulates fibroblast activation through YY1 expression. We hypothesize that IL-13 up-regulates YY1 expression through regulation of AKT activation, leading to fibroblast activation. In this study we found that YY1 was upregulated by IL-13 in lung fibroblasts in a dose- and time-dependent manner, resulting in increased α-SMA. Conversely, knockdown of YY1 blocked IL-13-induced α-SMA expression in fibroblasts. Furthermore, AKT phosphorylation was increased in fibroblasts treated with IL-13, and AKT overexpression upregulated YY1, whereas blockade of AKT phosphorylation suppressed the induction of YY1 by IL-13 in vitro. In vivo YY1 was upregulated in fibrotic lungs from CC10-IL-13 transgenic mice compared to that from wild-type littermates, which was associated with increased AKT phosphorylation. Taken together, these findings demonstrate that IL-13 is a potent stimulator and activator of fibroblasts, at least in part, through AKT-mediated YY1 activation. PMID:25775215

  8. The developmental regulator protein Gon4l associates with protein YY1, co-repressor Sin3a, and histone deacetylase 1 and mediates transcriptional repression.

    PubMed

    Lu, Ping; Hankel, Isaiah L; Hostager, Bruce S; Swartzendruber, Julie A; Friedman, Ann D; Brenton, Janet L; Rothman, Paul B; Colgan, John D

    2011-05-20

    Genetic studies involving zebrafish and mice have demonstrated that the protein Gon4l (Gon4-like) is essential for hematopoiesis. These studies also suggested that Gon4l regulates gene expression during hematopoietic development, yet the biochemical function of Gon4l has not been defined. Here, we describe the identification of factors that interact with Gon4l and may cooperate with this protein to regulate gene expression. As predicted by polypeptide sequence conservation, Gon4l interacted and co-localized with the DNA-binding protein YY1 (Yin Yang 1). Density gradient sedimentation analysis of protein lysates from mouse M12 B cells showed that Gon4l and YY1 co-sediment with the transcriptional co-repressor Sin3a and its functional partner histone deacetylase (HDAC) 1. Consistent with these results, immunoprecipitation studies showed that Gon4l associates with Sin3a, HDAC1, and YY1 as a part of complexes that form in M12 cells. Sequential immunoprecipitation studies demonstrated that Gon4l, YY1, Sin3a, and HDAC1 could all associate as components of a single complex and that a conserved domain spanning the central portion of Gon4l was required for formation of this complex. When targeted to DNA, Gon4l repressed the activity of a nearby promoter, which correlated with the ability to interact with Sin3a and HDAC1. Our data suggest that Sin3a, HDAC1, and YY1 are co-factors for Gon4l and that Gon4l may function as a platform for the assembly of complexes that regulate gene expression.

  9. Transgenic over-expression of YY1 induces pathologic cardiac hypertrophy in a sex-specific manner

    PubMed Central

    Stauffer, Brian L.; Dockstader, Karen; Russell, Gloria; Hijmans, Jamie; Walker, Lisa; Cecil, Mackenzie; Demos-Davies, Kimberly; Medway, Allen; McKinsey, Timothy A.; Sucharov, Carmen C.

    2015-01-01

    YY1 can activate or repress transcription of various genes. In cardiac myocytes in culture YY1 has been shown to regulate expression of several genes involved in myocyte pathology. YY1 can also acutely protect the heart against detrimental changes in gene expression. In this study we show that cardiac over-expression of YY1 induces pathologic cardiac hypertrophy in male mice, measured by changes in gene expression and lower ejection fraction/fractional shortening. In contrast, female animals are protected against pathologic gene expression changes and cardiac dysfunction. Furthermore, we show that YY1 regulates, in a sex-specific manner, the expression of mammalian enable (Mena), a factor that regulates cytoskeletal actin dynamics and whose expression is increased in several models of cardiac pathology, and that Mena expression in humans with heart failure is sex-dependent. Finally, we show that sex differences in YY1 expression are also observed in human heart failure. In summary, this is the first work to show that YY1 has a sex-specific effect in the regulation of cardiac pathology. PMID:25935483

  10. Nicotine Suppressed Fetal Adrenal StAR Expression via YY1 Mediated-Histone Deacetylation Modification Mechanism.

    PubMed

    Liu, Lian; Wang, Jian-Fei; Fan, Jie; Rao, Yi-Song; Liu, Fang; Yan, You-E; Wang, Hui

    2016-09-03

    Steroidogenic acute regulatory (StAR) protein plays a pivotal role in steroidogenesis. Previously, we have demonstrated that prenatal nicotine exposure suppressed fetal adrenal steroidogenesis via steroidogenic factor 1 deacetylation. This study further explored the potential role of the transcriptional repressor Yin Yang 1 (YY1) in nicotine-mediated StAR inhibition. Nicotine was subcutaneously administered (1.0 mg/kg) to pregnant rats twice per day and NCI-H295A cells were treated with nicotine. StAR and YY1 expression were analyzed by real-time PCR, immunohistochemistry, and Western blotting. Histone modifications and the interactions between the YY1 and StAR promoter were assessed using chromatin immunoprecipitation (ChIP). Prenatal nicotine exposure increased YY1 expression and suppressed StAR expression. ChIP assay showed that there was a decreasing trend for histone acetylation at the StAR promoter in fetal adrenal glands, whereas H3 acetyl-K14 at the YY1 promoter presented an increasing trend following nicotine exposure. Furthermore, in nicotine-treated NCI-H295A cells, nicotine enhanced YY1 expression and inhibited StAR expression. ChIP assay showed that histone acetylation decreased at the StAR promoter in NCI-H295A cells and that the interaction between the YY1 and StAR promoter increased. These data indicated that YY1-medicated histone deacetylation modification in StAR promoters might play an important role in the inhibitory effect of nicotine on StAR expression.

  11. Nicotine Suppressed Fetal Adrenal StAR Expression via YY1 Mediated-Histone Deacetylation Modification Mechanism

    PubMed Central

    Liu, Lian; Wang, Jian-Fei; Fan, Jie; Rao, Yi-Song; Liu, Fang; Yan, You-E; Wang, Hui

    2016-01-01

    Steroidogenic acute regulatory (StAR) protein plays a pivotal role in steroidogenesis. Previously, we have demonstrated that prenatal nicotine exposure suppressed fetal adrenal steroidogenesis via steroidogenic factor 1 deacetylation. This study further explored the potential role of the transcriptional repressor Yin Yang 1 (YY1) in nicotine-mediated StAR inhibition. Nicotine was subcutaneously administered (1.0 mg/kg) to pregnant rats twice per day and NCI-H295A cells were treated with nicotine. StAR and YY1 expression were analyzed by real-time PCR, immunohistochemistry, and Western blotting. Histone modifications and the interactions between the YY1 and StAR promoter were assessed using chromatin immunoprecipitation (ChIP). Prenatal nicotine exposure increased YY1 expression and suppressed StAR expression. ChIP assay showed that there was a decreasing trend for histone acetylation at the StAR promoter in fetal adrenal glands, whereas H3 acetyl-K14 at the YY1 promoter presented an increasing trend following nicotine exposure. Furthermore, in nicotine-treated NCI-H295A cells, nicotine enhanced YY1 expression and inhibited StAR expression. ChIP assay showed that histone acetylation decreased at the StAR promoter in NCI-H295A cells and that the interaction between the YY1 and StAR promoter increased. These data indicated that YY1-medicated histone deacetylation modification in StAR promoters might play an important role in the inhibitory effect of nicotine on StAR expression. PMID:27598153

  12. New Cross-Talk Layer between Ultraconserved Non-Coding RNAs, MicroRNAs and Polycomb Protein YY1 in Bladder Cancer

    PubMed Central

    Terreri, Sara; Durso, Montano; Colonna, Vincenza; Romanelli, Alessandra; Terracciano, Daniela; Ferro, Matteo; Perdonà, Sisto; Castaldo, Luigi; Febbraio, Ferdinando; de Nigris, Filomena; Cimmino, Amelia

    2016-01-01

    MicroRNAs (miRNAs) are highly conserved elements in mammals, and exert key regulatory functions. Growing evidence shows that miRNAs can interact with another class of non-coding RNAs, so-called transcribed ultraconserved regions (T-UCRs), which take part in transcriptional, post-transcriptional and epigenetic regulation processes. We report here the interaction of miRNAs and T-UCRs as a network modulating the availability of these non-coding RNAs in bladder cancer cells. In our cell system, antagomiR-596 increased the expression of T-UCR 201+. Moreover, T-UCR 8+ silencing increased miR-596 expression, which in turn reduced total T-UCR 283+, showing that the perturbation of one element in this network changes the expression of other interactors. In addition, we identify the polycomb protein Yin Yang 1 (YY1) as mediator of binding between miR-596 and T-UCR 8+. These new findings describe for the first time a network between T-UCRs, miRNAs and YY1 protein, highlighting the existence of an additional layer of gene expression regulation. PMID:27983635

  13. A Casein Kinase II Phosphorylation Site in AtYY1 Affects Its Activity, Stability, and Function in the ABA Response

    PubMed Central

    Wu, Xiu-Yun; Li, Tian

    2017-01-01

    The phosphorylation and dephosphorylation of proteins are crucial in the regulation of protein activity and stability in various signaling pathways. In this study, we identified an ABA repressor, Arabidopsis Ying Yang 1 (AtYY1) as a potential target of casein kinase II (CKII). AtYY1 physically interacts with two regulatory subunits of CKII, CKB3, and CKB4. Moreover, AtYY1 can be phosphorylated by CKII in vitro, and the S284 site is the major CKII phosphorylation site. Further analyses indicated that S284 phosphorylation can enhance the transcriptional activity and protein stability of AtYY1 and hence strengthen the effect of AtYY1 as a negative regulator in the ABA response. Our study provides novel insights into the regulatory mechanism of AtYY1 mediated by CKII phosphorylation. PMID:28348572

  14. Events at the transition between cell cycle exit and oligodendrocyte progenitor differentiation: the role of HDAC and YY1.

    PubMed

    He, Ye; Sandoval, Juan; Casaccia-Bonnefil, Patrizia

    2007-08-01

    The complexity of the adult brain is the result of an integrated series of developmental events that depends on appropriate timing of differentiation. The importance of transcriptional regulatory networks and epigenetic mechanisms of regulation of gene expression is becoming increasingly evident. Among these mechanisms, previous work has revealed the importance of histone deacetylation in oligodendrocyte differentiation. In this manuscript we define the region of interaction between transcription factor Yin-Yang 1 (YY1) and histone deacetylase 1, and characterize the functional consequences of YY1 overexpression on the differentiation of oligodendrocyte progenitors.

  15. Promoter-region hypermethylation and expression downregulation of Yy1 (Yin yang 1) in preneoplastic liver lesions in a thioacetamide rat hepatocarcinogenesis model

    SciTech Connect

    Abe, Hajime; Ogawa, Takashi; Wang, Liyun; Kimura, Masayuki; Tanaka, Takeshi; Morita, Reiko; Yoshida, Toshinori; Shibutani, Makoto

    2014-11-01

    Thioacetamide (TAA) has been used to develop a rodent model for hepatocarcinogenesis. To determine the genes with epigenetic modifications in early hepatocarcinogenesis, we did a genome-wide scan for hypermethylated promoter regions using CpG island microarrays in TAA-promoted rat liver tissue. Eight genes were selected based on the microarray profile; of these, Yy1 and Wdr45b were confirmed to be hypermethylated by methylation-specific polymerase chain reaction (PCR) and pyrosequencing and downregulated by real-time reverse transcription PCR. Non-neoplastic liver cells had nuclear Yy1 immunoreactivity, while preneoplastic foci with glutathione S-transferase placental form (GST-P) immunoreactivity had decreased Yy1 immunoreactivity. The incidence of these foci was proportional to the dose of TAA administered. Co-expression analysis of gene products downstream of Yy1 revealed increased nuclear phospho-c-Myc{sup +} foci as well as nuclear and cytoplasmic p21{sup Cip1+} foci in Yy1{sup −} or GST-P{sup +} foci in response to TAA-promotion dose. Although the absolute number of cells was low, the incidence of death receptor 5{sup −} foci was increased in Yy1{sup −} foci in proportion to the TAA dose. Yy1{sup −}/GST-P{sup +} foci revealed a higher number of proliferating cell nuclear antigen (PCNA)-immunoreactive cells than Yy1{sup +}/GST-P{sup +} foci, while cleaved caspase-3{sup +} cells were unchanged between Yy1{sup –}/GST-P{sup +} and Yy1{sup +}/GST-P{sup +} foci. In the case of Wdr45b, most GST-P{sup +} foci were Wdr45b{sup –} and were not increased by TAA promotion. These results suggest involvement of Yy1 in the epigenetic gene regulation at the early stages of TAA promoted cell proliferation and concomitant cell cycle arrest in preneoplastic lesions. - Highlights: • Epigenetically downregulated genes were searched in TAA-promnoted rat livers. • Yy1 and Wdr45b showed promoter-region hypermethylation and mRNA downregulation. • TAA promoted

  16. Regulation of the microRNA processor DGCR8 by hepatitis B virus proteins via the transcription factor YY1.

    PubMed

    Shan, Xuefeng; Ren, Min; Chen, Ke; Huang, Ailong; Tang, Hua

    2015-03-01

    MicroRNAs (miRNAs) are a new class of well-conserved small noncoding RNAs that mediate posttranscriptional gene regulation. Hepatitis B virus (HBV) causes various liver diseases, including chronic hepatitis, liver cirrhosis and hepatocellular cancer. Recent data have indicated HBV alters miRNAs expression patterns, but the underlying mechanisms have not been fully established so far. Here, we provide a hypothesis that HBV alters the expressions of miRNAs by playing a role in the microRNA production process. In this study, we demonstrate that HBV downregulates miRNAs processor DGCR8 mRNA and protein expression in stable and transient HBV-expressing cells. HBV downregulates DGCR8 expression by inhibiting its promoter activity, and HBs and HBx may be involved in this process. Ectopic expression and knockdown of YY1 revealed that YY1 suppresses the activity of the DGCR8 promoter, while YY1 expression is significantly upregulated by HBV. In conclusion, our data show that HBV proteins repress DGCR8 promoter activity by upregulating the expression of transcription factor YY1. This provides a new insight into the mechanism of HBV-induced miRNA dysregulation.

  17. Brown Adipose YY1 Deficiency Activates Expression of Secreted Proteins Linked to Energy Expenditure and Prevents Diet-Induced Obesity

    PubMed Central

    Verdeguer, Francisco; Soustek, Meghan S.; Hatting, Maximilian; Blättler, Sharon M.; McDonald, Devin; Barrow, Joeva J.

    2015-01-01

    Mitochondrial oxidative and thermogenic functions in brown and beige adipose tissues modulate rates of energy expenditure. It is unclear, however, how beige or white adipose tissue contributes to brown fat thermogenic function or compensates for partial deficiencies in this tissue and protects against obesity. Here, we show that the transcription factor Yin Yang 1 (YY1) in brown adipose tissue activates the canonical thermogenic and uncoupling gene expression program. In contrast, YY1 represses a series of secreted proteins, including fibroblast growth factor 21 (FGF21), bone morphogenetic protein 8b (BMP8b), growth differentiation factor 15 (GDF15), angiopoietin-like 6 (Angptl6), neuromedin B, and nesfatin, linked to energy expenditure. Despite substantial decreases in mitochondrial thermogenic proteins in brown fat, mice lacking YY1 in this tissue are strongly protected against diet-induced obesity and exhibit increased energy expenditure and oxygen consumption in beige and white fat depots. The increased expression of secreted proteins correlates with elevation of energy expenditure and promotion of beige and white fat activation. These results indicate that YY1 in brown adipose tissue controls antagonistic gene expression programs associated with energy balance and maintenance of body weight. PMID:26503783

  18. Loss-of-Function Mutations in YY1AP1 Lead to Grange Syndrome and a Fibromuscular Dysplasia-Like Vascular Disease.

    PubMed

    Guo, Dong-Chuan; Duan, Xue-Yan; Regalado, Ellen S; Mellor-Crummey, Lauren; Kwartler, Callie S; Kim, Dong; Lieberman, Kenneth; de Vries, Bert B A; Pfundt, Rolph; Schinzel, Albert; Kotzot, Dieter; Shen, Xuetong; Yang, Min-Lee; Bamshad, Michael J; Nickerson, Deborah A; Gornik, Heather L; Ganesh, Santhi K; Braverman, Alan C; Grange, Dorothy K; Milewicz, Dianna M

    2017-01-05

    Fibromuscular dysplasia (FMD) is a heterogeneous group of non-atherosclerotic and non-inflammatory arterial diseases that primarily involves the renal and cerebrovascular arteries. Grange syndrome is an autosomal-recessive condition characterized by severe and early-onset vascular disease similar to FMD and variable penetrance of brachydactyly, syndactyly, bone fragility, and learning disabilities. Exome-sequencing analysis of DNA from three affected siblings with Grange syndrome identified compound heterozygous nonsense variants in YY1AP1, and homozygous nonsense or frameshift YY1AP1 variants were subsequently identified in additional unrelated probands with Grange syndrome. YY1AP1 encodes yin yang 1 (YY1)-associated protein 1 and is an activator of the YY1 transcription factor. We determined that YY1AP1 localizes to the nucleus and is a component of the INO80 chromatin remodeling complex, which is responsible for transcriptional regulation, DNA repair, and replication. Molecular studies revealed that loss of YY1AP1 in vascular smooth muscle cells leads to cell cycle arrest with decreased proliferation and increased levels of the cell cycle regulator p21/WAF/CDKN1A and disrupts TGF-β-driven differentiation of smooth muscle cells. Identification of YY1AP1 mutations as a cause of FMD indicates that this condition can result from underlying genetic variants that significantly alter the phenotype of vascular smooth muscle cells.

  19. Human INO80/YY1 chromatin remodeling complex transcriptionally regulates the BRCA2- and CDKN1A-interacting protein (BCCIP) in cells.

    PubMed

    Su, Jiaming; Sui, Yi; Ding, Jian; Li, Fuqiang; Shen, Shuang; Yang, Yang; Lu, Zeming; Wang, Fei; Cao, Lingling; Liu, Xiaoxia; Jin, Jingji; Cai, Yong

    2016-10-01

    The BCCIP (BRCA2- and CDKN1A-interacting protein) is an important cofactor for BRCA2 in tumor suppression. Although the low expression of BCCIP is observed in multiple clinically diagnosed primary tumor tissues such as ovarian cancer, renal cell carcinoma and colorectal carcinoma, the mechanism of how BCCIP is regulated in cells is still unclear. The human INO80/YY1 chromatin remodeling complex composed of 15 subunits catalyzes ATP-dependent sliding of nucleosomes along DNA. Here, we first report that BCCIP is a novel target gene of the INO80/YY1 complex by presenting a series of experimental evidence. Gene expression studies combined with siRNA knockdown data locked candidate genes including BCCIP of the INO80/YY1 complex. Silencing or over-expressing the subunits of the INO80/YY1 complex regulates the expression level of BCCIP both in mRNA and proteins in cells. Also, the functions of INO80/YY1 complex in regulating the transactivation of BCCIP were confirmed by luciferase reporter assays. Chromatin immunoprecipitation (ChIP) experiments clarify the enrichment of INO80 and YY1 at +0.17 kb downstream of the BCCIP transcriptional start site. However, this enrichment is significantly inhibited by either knocking down INO80 or YY1, suggesting the existence of both INO80 and YY1 is required for recruiting the INO80/YY1 complex to BCCIP promoter region. Our findings strongly indicate that BCCIP is a potential target gene of the INO80/YY1 complex.

  20. Reciprocal localization of transcription factors YY1 and CP2c in spermatogonial stem cells and their putative roles during spermatogenesis.

    PubMed

    Kim, Ji Sook; Chae, Ji Hyung; Cheon, Yong-Pil; Kim, Chul Geun

    2016-09-01

    Maintaining stemness and permitting differentiation mediated by combinations of transcription factors (TFs) are key aspects of mammalian spermatogenesis. It has been established that yin yang 1 (YY1), a target factor of mammalian polycomb repressive complex 2 (PRC2) and a regulator of stemness, is involved in the stable maintenance of prophase stage spermatocytes. Recently, we have demonstrated that the TF CP2c partners with YY1 in some cells to antagonistically regulate the other protein's function. To date, the functional roles of YY1 and CP2c in spermatogonial stem cells and their derived germ cells remain unclear. Here, we investigated the expression of YY1 and CP2c in mouse gonocytes and germ cells using tissue immunohistochemical and immunofluorescence analyses. At E14.5, both YY1 and CP2c were stained in gonocytes and Sertoli cells in testicular cords, showing different proportion and density of immunoreactivity. However, in adult testes, YY1 was localized in the nuclei of spermatogonial stem cells and spermatocytes, but not in spermatozoa. It was also detected in spermatogonia and spermatids in a stage-specific manner during spermatogenic cycle. CP2c could be detected mostly in the cytoplasm of spermatocytes but not at all in spermatogonial stem cells, indicating mutually exclusive expression of CP2c and YY1. Interestingly, however, CP2c was stained in the cytoplasm and nucleus of spermatogonia at elongation and release stages, and co-localized with YY1 in the nucleus at grouping, maturation, and releasing stages. Neither YY1 nor CP2c was expressed in spermatozoa. Our data indicate that YY1 strongly localizes in the spermatogonial stem cells and co-localizes heterogeneously with CP2c to permit spermatogenesis, and also suggest that YY1 is essential for stemness of spermatogonial stem cells (SCs) whereas CP2c is critical for the commitment of spermatogonia and during the progression of spermatogonia to spermatids. This evaluation expands our understanding of

  1. Effect of clustered peptide binding on DNA condensation.

    PubMed

    Haley, Jennifer; Kabiru, Paul; Geng, Yan

    2010-01-01

    DNA condensation in-vitro has been studied as a model system to reveal common principles underlying gene packaging in biology, and as the critical first step towards the development of non-viral gene delivery vectors. In this study, we use a bio-inspired approach, where small DNA-binding peptides are controllably clustered by an amphiphilic block copolymer scaffold, to reveal the effect of clustered peptide binding on the energetics, size, shape and physical properties of DNA condensation in-vitro. This provides insights into the general architectural effect of gene-binding proteins on DNA condensation process. Moreover, the versatility afforded by regulating the clustering density and composition of peptides may provide a novel design platform for gene delivery applications in the future.

  2. Predicting Ca2+-binding Sites Using Refined Carbon Clusters

    PubMed Central

    Zhao, Kun; Wang, Xue; Wong, Hing C.; Wohlhueter, Robert; Kirberger, Michael P.; Chen, Guantao; Yang, Jenny J.

    2012-01-01

    Identifying Ca2+-binding sites in proteins is the first step towards understanding the molecular basis of diseases related to Ca2+-binding proteins. Currently, these sites are identified in structures either through X-ray crystallography or NMR analysis. However, Ca2+-binding sites are not always visible in X-ray structures due to flexibility in the binding region or low occupancy in a Ca2+-binding site. Similarly, both Ca2+ and its ligand oxygens are not directly observed in NMR structures. To improve our ability to predict Ca2+-binding sites in both X-ray and NMR structures, we report a new graph theory algorithm (MUGC) to predict Ca2+-binding sites. Using carbon atoms covalently bonded to the chelating oxygen atoms, and without explicit reference to side-chain oxygen ligand coordinates, MUGC is able to achieve 94% sensitivity with 76% selectivity on a dataset of X-ray structures comprised of 43 Ca2+-binding proteins. Additionally, prediction of Ca2+-binding sites in NMR structures were obtained by MUGC using a different set of parameters determined by analysis of both Ca2+-constrained and unconstrained Ca2+-loaded structures derived from NMR data. MUGC identified 20 out of 21 Ca2+-binding sites in NMR structures inferred without the use of Ca2+ constraints. MUGC predictions are also highly-selective for Ca2+-binding sites as analyses of binding sites for Mg2+, Zn2+, and Pb2+ were not identified as Ca2+-binding sites. These results indicate that the geometric arrangement of the second-shell carbon cluster is sufficient for both accurate identification of Ca2+-binding sites in NMR and X-ray structures, and for selective differentiation between Ca2+ and other relevant divalent cations. PMID:22821762

  3. Modulation of cluster incorporation specificity in a de novo iron-sulfur cluster binding peptide.

    PubMed

    Sommer, Dayn Joseph; Roy, Anindya; Astashkin, Andrei; Ghirlanda, Giovanna

    2015-07-01

    iron-sulfur cluster binding proteins perform an astounding variety of functions, and represent one of the most abundant classes of metalloproteins. Most often, they constitute pairs or chains and act as electron transfer modules either within complex redox enzymes or within small diffusible proteins. We have previously described the design of a three-helix bundle that can bind two clusters within its hydrophobic core. Here, we use single-point mutations to exchange one of the Cys ligands coordinating the cluster to either Leu or Ser. We show that the mutants modulate the redox potential of the clusters and stabilize the [3Fe-4S] form over the [4Fe-4S] form, supporting the use of model iron-sulfur cluster proteins as modules in the design of complex redox enzymes.

  4. Yin Yang 1 Intronic Binding Sequences and Splicing Elicit Intron-Mediated Enhancement of Ubiquitin C Gene Expression

    PubMed Central

    Bianchi, Marzia; Crinelli, Rita; Giacomini, Elisa; Carloni, Elisa; Radici, Lucia; Magnani, Mauro

    2013-01-01

    In a number of organisms, introns affect expression of the gene in which they are contained. Our previous studies revealed that the 5′-UTR intron of human ubiquitin C (UbC) gene is responsible for the boost of reporter gene expression and is able to bind, in vitro, Yin Yang 1 (YY1) trans-acting factor. In this work, we demonstrate that intact YY1 binding sequences are required for maximal promoter activity and YY1 silencing causes downregulation of luciferase mRNA levels. However, YY1 motifs fail to enhance gene expression when the intron is moved upstream of the proximal promoter, excluding the typical enhancer hypothesis and supporting a context-dependent action, like intron-mediated enhancement (IME). Yet, almost no expression is seen in the construct containing an unspliceable version of UbC intron, indicating that splicing is essential for promoter activity. Moreover, mutagenesis of YY1 binding sites and YY1 knockdown negatively affect UbC intron removal from both endogenous and reporter transcripts. Modulation of splicing efficiency by YY1 cis-elements and protein factor may thus be part of the mechanism(s) by which YY1 controls UbC promoter activity. Our data highlight the first evidence of the involvement of a sequence-specific DNA binding factor in IME. PMID:23776572

  5. Repression of PDGF-R-α after cellular injury involves TNF-α, formation of a c-Fos-YY1 complex, and negative regulation by HDAC.

    PubMed

    Zhang, Ning; Chan, Cecilia W S; Sanchez-Guerrero, Estella; Khachigian, Levon M

    2012-06-01

    Wound healing is a complex dynamic process involving a variety of cell types, including fibroblasts that express and respond to cytokines and growth factors in the local microenvironment. The mechanisms controlling gene expression after injury at a transcriptional level are poorly understood. Here we show that decreased expression of a key receptor, PDGF-receptor (R)-α, after fibroblast injury is due to the release and paracrine activity of TNF-α. TNF-α inhibits PDGF-R-α expression and this involves formation of a c-Fos-Yin Yang 1 (YY1) complex and histone deacetylase (HDAC) activity. c-Fos, induced by TNF-α, negatively regulates PDGF-R-α transcription. Small interfering RNA (siRNA) targeting c-Fos or the zinc finger transcription factor YY1 inhibits TNF-α suppression of PDGF-R-α expression. Coimmunoprecipitation studies show that TNF-α stimulates the formation of a complex between c-Fos with YY1. Furthermore, chromatin immunoprecipitation (ChIP) analysis reveals the enrichment of c-Fos, YY1, and HDAC-1 at the PDGF-R-α promoter in cells exposed to TNF-α. With suberoylanilide hydroxamic acid (SAHA) and HDAC-1 siRNA, we demonstrate that HDAC mediates TNF-α repression of PDGF-R-α. These findings demonstrate that transcriptional repression of PDGF-R-α after fibroblast injury involves paracrine activity of endogenous TNF-α, the formation of a c-Fos-YY1 complex, and negative regulatory activity by HDAC.

  6. The MeCP2/YY1 interaction regulates ANT1 expression at 4q35: novel hints for Rett syndrome pathogenesis.

    PubMed

    Forlani, Greta; Giarda, Elisa; Ala, Ugo; Di Cunto, Ferdinando; Salani, Monica; Tupler, Rossella; Kilstrup-Nielsen, Charlotte; Landsberger, Nicoletta

    2010-08-15

    Rett syndrome is a severe neurodevelopmental disorder mainly caused by mutations in the transcriptional regulator MeCP2. Although there is no effective therapy for Rett syndrome, the recently discovered disease reversibility in mice suggests that there are therapeutic possibilities. Identification of MeCP2 targets or modifiers of the phenotype can facilitate the design of curative strategies. To identify possible novel MeCP2 interactors, we exploited a bioinformatic approach and selected Ying Yang 1 (YY1) as an interesting candidate. We demonstrate that MeCP2 interacts in vitro and in vivo with YY1, a ubiquitous zinc-finger epigenetic factor regulating the expression of several genes. We show that MeCP2 cooperates with YY1 in repressing the ANT1 gene encoding a mitochondrial adenine nucleotide translocase. Importantly, ANT1 mRNA levels are increased in human and mouse cell lines devoid of MeCP2, in Rett patient fibroblasts and in the brain of Mecp2-null mice. We further demonstrate that ANT1 protein levels are upregulated in Mecp2-null mice. Finally, the identified MeCP2-YY1 interaction, together with the well-known involvement of YY1 in the regulation of D4Z4-associated genes at 4q35, led us to discover the anomalous depression of FRG2, a subtelomeric gene of unknown function, in Rett fibroblasts. Collectively, our data indicate that mutations in MeCP2 might cause the aberrant overexpression of genes located at a specific locus, thus providing new candidates for the pathogenesis of Rett syndrome. As both ANT1 mutations and overexpression have been associated with human diseases, we consider it highly relevant to address the consequences of ANT1 deregulation in Rett syndrome.

  7. NLRP7 affects trophoblast lineage differentiation, binds to overexpressed YY1 and alters CpG methylation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maternal-effect mutations in NLRP7 cause rare biparentally inherited hydatidiform moles (BiHMs), abnormal pregnancies containing hypertrophic vesicular trophoblast but no embryo. BiHM trophoblasts display abnormal DNA methylation patterns affecting maternally methylated germline differentially methy...

  8. Complete genome sequence and transcriptomics analyses reveal pigment biosynthesis and regulatory mechanisms in an industrial strain, Monascus purpureus YY-1.

    PubMed

    Yang, Yue; Liu, Bin; Du, Xinjun; Li, Ping; Liang, Bin; Cheng, Xiaozhen; Du, Liangcheng; Huang, Di; Wang, Lei; Wang, Shuo

    2015-02-09

    Monascus has been used to produce natural colorants and food supplements for more than one thousand years, and approximately more than one billion people eat Monascus-fermented products during their daily life. In this study, using next-generation sequencing and optical mapping approaches, a 24.1-Mb complete genome of an industrial strain, Monascus purpureus YY-1, was obtained. This genome consists of eight chromosomes and 7,491 genes. Phylogenetic analysis at the genome level provides convincing evidence for the evolutionary position of M. purpureus. We provide the first comprehensive prediction of the biosynthetic pathway for Monascus pigment. Comparative genomic analyses show that the genome of M. purpureus is 13.6-40% smaller than those of closely related filamentous fungi and has undergone significant gene losses, most of which likely occurred during its specialized adaptation to starch-based foods. Comparative transcriptome analysis reveals that carbon starvation stress, resulting from the use of relatively low-quality carbon sources, contributes to the high yield of pigments by repressing central carbon metabolism and augmenting the acetyl-CoA pool. Our work provides important insights into the evolution of this economically important fungus and lays a foundation for future genetic manipulation and engineering of this strain.

  9. How do small water clusters bind an excess electron?

    PubMed

    Hammer, Nathan I; Shin, Joong-Won; Headrick, Jeffrey M; Diken, Eric G; Roscioli, Joseph R; Weddle, Gary H; Johnson, Mark A

    2004-10-22

    The arrangement of water molecules around a hydrated electron has eluded explanation for more than 40 years. Here we report sharp vibrational bands for small gas-phase water cluster anions, (H2O)(4-6)- and (D2O)(4-6)-. Analysis of these bands reveals a detailed picture of the diffuse electron-binding site. The electron is closely associated with a single water molecule attached to the supporting network through a double H-bond acceptor motif. The local OH stretching bands of this molecule are dramatically distorted in the pentamer and smaller clusters because the excited vibrational levels are strongly coupled to the electron continuum. The vibration-to-electronic energy transfer rates, as revealed by line shape analysis, are mode-specific and remarkably fast, with the symmetric stretching mode surviving for less than 10 vibrational periods [50 fs in (H2O)4-].

  10. The glycocalyx promotes cooperative binding and clustering of adhesion receptors.

    PubMed

    Xu, Guang-Kui; Qian, Jin; Hu, Jinglei

    2016-05-18

    Cell adhesion plays a pivotal role in various biological processes, e.g., immune responses, cancer metastasis, and stem cell differentiation. The adhesion behaviors depend subtly on the binding kinetics of receptors and ligands restricted at the cell-substrate interfaces. Although much effort has been directed toward investigating the kinetics of adhesion molecules, the role of the glycocalyx, anchored on cell surfaces as an exterior layer, is still unclear. In this paper, we propose a theoretical approach to study the collective binding kinetics of a few and a large number of binders in the presence of the glycocalyx, representing the cases of initial and mature adhesions of cells, respectively. The analytical results are validated by finding good agreement with our Monte Carlo simulations. In the force loading case, the on-rate and affinity increase as more bonds form, whereas this cooperative effect is not observed in the displacement loading case. The increased thickness and stiffness of the glycocalyx tend to decrease the affinity for a few bonds, while they have less influence on the affinity for a large number of bonds. Moreover, for a flexible membrane with thermally-excited shape fluctuations, the glycocalyx is exhibited to promote the formation of bond clusters, mainly due to the cooperative binding of binders. This study helps to understand the cooperative kinetics of adhesion receptors under physiologically relevant loading conditions and sheds light on the novel role of the glycocalyx in cell adhesion.

  11. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

    PubMed

    Vockley, Christopher M; D'Ippolito, Anthony M; McDowell, Ian C; Majoros, William H; Safi, Alexias; Song, Lingyun; Crawford, Gregory E; Reddy, Timothy E

    2016-08-25

    The glucocorticoid receptor (GR) binds the human genome at >10,000 sites but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter-gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady-state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs and may therefore play a major role in driving gene activation in response to GCs.

  12. Density functional study of hydrogen binding on gold and silver-gold clusters.

    PubMed

    Zhao, Shuang; Ren, YunLi; Ren, YunLai; Wang, JianJi; Yin, WeiPing

    2010-04-15

    A theoretical study was carried out on the binding of hydrogen on small bimetallic Ag(m)Au(n) (m + n < or = 5) and pure Au(n) (n < or = 5) clusters with neutral, negative, and positive charge state. It is found that the composition and charge state of clusters have strong influence on the most favorable binding site. The adiabatic ionization potentials, electron affinities, and hydrogen binding energies of cluster hydrides increase with the Au content increasing for the given cluster size. The cationic silver-gold cluster hydrides prefer ejection of Au-containing products whereas the anionic silver-gold cluster hydrides prefer ejection of Ag-containing products. The magnitude of metal-H frequency in combination with the metal-H bond length indicates that, with the same type of the binding site, the Au-H interaction is stronger than the Ag-H interaction.

  13. A novel NF-κB/YY1/microRNA-10a regulatory circuit in fibroblast-like synoviocytes regulates inflammation in rheumatoid arthritis

    PubMed Central

    Mu, Nan; Gu, Jintao; Huang, Tonglie; Zhang, Cun; Shu, Zhen; Li, Meng; Hao, Qiang; Li, Weina; Zhang, Wangqian; Zhao, Jinkang; Zhang, Yong; Huang, Luyu; Wang, Shuning; Jin, Xiaohang; Xue, Xiaochang; Zhang, Wei; Zhang, Yingqi

    2016-01-01

    The main etiopathogenesis of rheumatoid arthritis (RA) is overexpressed inflammatory cytokines and tissue injury mediated by persistent NF-κB activation. MicroRNAs widely participate in the regulation of target gene expression and play important roles in various diseases. Here, we explored the mechanisms of microRNAs in RA. We found that microRNA (miR)-10a was downregulated in the fibroblast-like synoviocytes (FLSs) of RA patients compared with osteoarthritis (OA) controls, and this downregulation could be triggered by TNF-α and IL-1β in an NF-κB-dependent manner through promoting the expression of the YingYang 1 (YY1) transcription factor. Downregulated miR-10a could accelerate IκB degradation and NF-κB activation by targeting IRAK4, TAK1 and BTRC. This miR-10a-mediated NF-κB activation then significantly promoted the production of various inflammatory cytokines, including TNF-α, IL-1β, IL-6, IL-8, and MCP-1, and matrix metalloproteinase (MMP)-1 and MMP-13. In addition, transfection of a miR-10a inhibitor accelerated the proliferation and migration of FLSs. Collectively, our data demonstrates the existence of a novel NF-κB/YY1/miR-10a/NF-κB regulatory circuit that promotes the excessive secretion of NF-κB-mediated inflammatory cytokines and the proliferation and migration of RA FLSs. Thus, miR-10a acts as a switch to control this regulatory circuit and may serve as a diagnostic and therapeutic target for RA treatment. PMID:26821827

  14. Ferromagnetism and Borromean binding in three-fermion clusters.

    PubMed

    Kornilovitch, Pavel

    2014-02-21

    A three-particle spin-12 fermion problem with on-site repulsion and nearest-neighbor attraction is solved on the two-dimensional square lattice by discretizing a Schrödinger equation in momentum space. Energies of bound complexes (trions) and their binding conditions are obtained. For total spin S=1/2, a wide region of trion instability toward decaying into a stable singlet pair plus a free fermion is identified. The instability is attributed to the formation of a wave function node upon addition of the third fermion. In the S=3/2 sector, trions are found to form in the absence of bound pairs indicating Borromean binding. In the strong coupling limit the system transitions from an S=1/2 ground state to a ferromagnetic S=3/2 ground state in agreement with the Nagaoka theorem for a four-site plaquette.

  15. Discovery of Fur binding site clusters in Escherichia coli by information theory models

    PubMed Central

    Chen, Zehua; Lewis, Karen A.; Shultzaberger, Ryan K.; Lyakhov, Ilya G.; Zheng, Ming; Doan, Bernard; Storz, Gisela; Schneider, Thomas D.

    2007-01-01

    Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence walkers, which are visual depictions of predicted binding sites, frequently appeared in clusters that fit the footprints (∼83% coverage). This indicated that the model can accurately predict Fur binding. Within the clusters, individual walkers were separated from their neighbors by exactly 3 or 6 bases, consistent with models in which Fur dimers bind on different faces of the DNA helix. When the E. coli genome was scanned, we found 363 unique clusters, which includes all known Fur-repressed genes that are involved in iron metabolism. In contrast, only a few of the known Fur-activated genes have predicted Fur binding sites at their promoters. These observations suggest that Fur is either a direct repressor or an indirect activator. The Pseudomonas aeruginosa and Bacillus subtilis Fur models are highly similar to the E. coli Fur model, suggesting that the Fur–DNA recognition mechanism may be conserved for even distantly related bacteria. PMID:17921503

  16. Perlecan is recruited by dystroglycan to nodes of Ranvier and binds the clustering molecule gliomedin

    PubMed Central

    Colombelli, Cristina; Palmisano, Marilena; Eshed-Eisenbach, Yael; Zambroni, Desirée; Pavoni, Ernesto; Ferri, Cinzia; Saccucci, Stefania; Nicole, Sophie; Soininen, Raija; McKee, Karen K.; Yurchenco, Peter D.; Peles, Elior; Wrabetz, Lawrence

    2015-01-01

    Fast neural conduction requires accumulation of Na+ channels at nodes of Ranvier. Dedicated adhesion molecules on myelinating cells and axons govern node organization. Among those, specific laminins and dystroglycan complexes contribute to Na+ channel clustering at peripheral nodes by unknown mechanisms. We show that in addition to facing the basal lamina, dystroglycan is found near the nodal matrix around axons, binds matrix components, and participates in initial events of nodogenesis. We identify the dystroglycan-ligand perlecan as a novel nodal component and show that dystroglycan is required for the selective accumulation of perlecan at nodes. Perlecan binds the clustering molecule gliomedin and enhances clustering of node of Ranvier components. These data show that proteoglycans have specific roles in peripheral nodes and indicate that peripheral and central axons use similar strategies but different molecules to form nodes of Ranvier. Further, our data indicate that dystroglycan binds free matrix that is not organized in a basal lamina. PMID:25646087

  17. Monoclonal antibody binding-site diversity assessment with a cell-based clustering assay.

    PubMed

    Liao-Chan, Sindy; Zachwieja, Joseph; Gomez, Steven; Duey, Dana; Lippincott, John; Theunissen, Jan-Willem

    2014-03-01

    The diversity of a panel of antibodies that target a specific antigen can be established in various assay formats. In conventional epitope binning assays purified antibodies are tested in a pairwise manner: two antibodies that compete with each other for binding to an antigen are grouped into the same cluster or bin, while they are assigned to two different clusters when they do not compete. Here we present a high through put assay that enables grouping of crude hybridoma supernatants without a need for antibody purification. In addition, the assay does not require recombinant protein, because it is conducted on cells that express the antigen of interest. Hence, one can use the antibody-clustering assay for cell surface proteins that are not amenable to purification. Heavy chain variable region (VH) sequencing shows that VH composition within clusters is conserved. Finally, the assay is in good agreement with a conventional epitope binning assay with purified antigen.

  18. Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions

    PubMed Central

    Lim, Ji-Hyun; Latysheva, Natasha S.; Iggo, Richard D.; Barker, Daniel

    2016-01-01

    p53 is an important regulator of cell cycle arrest, senescence, apoptosis and metabolism, and is frequently mutated in tumors. It functions as a tetramer, where each component dimer binds to a decameric DNA region known as a response element. We identify p53 binding site subtypes and examine the functional and evolutionary properties of these subtypes. We start with over 1700 known binding sites and, with no prior labeling, identify two sets of response elements by unsupervised clustering. When combined, they give rise to three types of p53 binding sites. We find that probabilistic and alignment-based assessments of cross-species conservation show no strong evidence of differential conservation between types of binding sites. In contrast, functional analysis of the genes most proximal to the binding sites provides strong bioinformatic evidence of functional differentiation between the three types of binding sites. Our results are consistent with recent structural data identifying two conformations of the L1 loop in the DNA binding domain, suggesting that they reflect biologically meaningful groups imposed by the p53 protein structure. PMID:27812278

  19. Vibrations of small cobalt clusters on low-index surfaces of copper: Tight-binding simulations

    NASA Astrophysics Data System (ADS)

    Borisova, S. D.; Eremeev, S. V.; Rusina, G. G.; Stepanyuk, V. S.; Bruno, P.; Chulkov, E. V.

    2008-08-01

    Vibrational properties (frequencies, polarizations, and lifetimes) of a single adatom, dimer, and trimer of Co on low-index Cu surfaces, Cu(111), Cu(001), and Cu(110) are studied by using tight-binding second moment approximation interatomic interaction potentials. We show that structural and vibrational properties of the Co clusters strongly depend on the substrate orientation. The longest lifetimes of 1-2.5 ps have been found for high-frequency z -polarized vibrations in all the Co clusters considered. The shortest lifetimes of 0.1-0.8 ps have been obtained for low-frequency horizontal (frustrated translation) vibrational modes.

  20. Renormalized coupled cluster approaches in the cluster-in-molecule framework: predicting vertical electron binding energies of the anionic water clusters (H2O)(n)(-).

    PubMed

    Xu, Peng; Gordon, Mark S

    2014-09-04

    Anionic water clusters are generally considered to be extremely challenging to model using fragmentation approaches due to the diffuse nature of the excess electron distribution. The local correlation coupled cluster (CC) framework cluster-in-molecule (CIM) approach combined with the completely renormalized CR-CC(2,3) method [abbreviated CIM/CR-CC(2,3)] is shown to be a viable alternative for computing the vertical electron binding energies (VEBE). CIM/CR-CC(2,3) with the threshold parameter ζ set to 0.001, as a trade-off between accuracy and computational cost, demonstrates the reliability of predicting the VEBE, with an average percentage error of ∼15% compared to the full ab initio calculation at the same level of theory. The errors are predominantly from the electron correlation energy. The CIM/CR-CC(2,3) approach provides the ease of a black-box type calculation with few threshold parameters to manipulate. The cluster sizes that can be studied by high-level ab initio methods are significantly increased in comparison with full CC calculations. Therefore, the VEBE computed by the CIM/CR-CC(2,3) method can be used as benchmarks for testing model potential approaches in small-to-intermediate-sized water clusters.

  1. Cargo binding promotes KDEL receptor clustering at the mammalian cell surface

    NASA Astrophysics Data System (ADS)

    Becker, Björn; Shaebani, M. Reza; Rammo, Domenik; Bubel, Tobias; Santen, Ludger; Schmitt, Manfred J.

    2016-06-01

    Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand (eGFP-RTAH/KDEL), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface.

  2. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

    PubMed

    Mahony, Shaun; Auron, Philip E; Benos, Panayiotis V

    2007-03-30

    Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been the subject of a number of recent studies, in which generalized binding profiles have been introduced and used to improve the prediction of new target sites. Generalized profiles are generated by aligning and merging the individual profiles of related TFs. However, the distance metrics and alignment algorithms used to compare the binding profiles have not yet been fully explored or optimized. As a result, binding profiles depend on TF structural information and sometimes may ignore important distinctions between subfamilies. Prediction of the identity or the structural class of a protein that binds to a given DNA pattern will enhance the analysis of microarray and ChIP-chip data where frequently multiple putative targets of usually unknown TFs are predicted. Various comparison metrics and alignment algorithms are evaluated (a total of 105 combinations). We find that local alignments are generally better than global alignments at detecting eukaryotic DNA motif similarities, especially when combined with the sum of squared distances or Pearson's correlation coefficient comparison metrics. In addition, multiple-alignment strategies for binding profiles and tree-building methods are tested for their efficiency in constructing generalized binding models. A new method for automatic determination of the optimal number of clusters is developed and applied in the construction of a new set of familial binding profiles which improves upon TF classification accuracy. A software tool, STAMP, is developed to host all tested methods and make them publicly available. This work provides a high quality reference set of familial binding profiles and the first comprehensive platform for analysis of DNA profiles. Detecting similarities between DNA motifs is a key step in the comparative study

  3. Determination of binding energy in molecular clusters by ion imaging methods: A test on the phenol-water 1:1 cluster

    NASA Astrophysics Data System (ADS)

    Mazzoni, F.; Pasquini, M.; Pietraperzia, G.; Becucci, M.

    2015-06-01

    In this paper we present a test on the velocity mapping imaging approach for the experimental direct determination of the binding energy in clusters formed by strongly interacting polyatomic molecules. The method is applied to the phenol-water cluster, a system for which the binding energies were already determined in different experiments. The binding energy values that we obtained, 1975 cm-1 in the S0 state, 2327 cm-1 in the S1 state and 6586 cm-1 in the ionic D0 state, are in very good agreement with the previous determinations. We report our results and we discuss advantages and limitations resulting from our experience.

  4. Cationic Gold Clusters Ligated with Differently Substituted Phosphines: Effect of Substitution on Ligand Reactivity and Binding

    SciTech Connect

    Johnson, Grant E.; Olivares, Astrid M.; Hill, David E.; Laskin, Julia

    2015-01-01

    We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using ligand exchange reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cy ligands. The efficiency of ligand exchange decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of ligand-exchanged gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh¬3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3< PPh2Cy < PPhCy2< PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh3-mMem or PPh3-mCym ligands (L) exchanged onto each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important

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

    PubMed

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

    2013-03-07

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

  6. Mcl-1 and YY1 inhibition and induction of DR5 by the BH3-mimetic Obatoclax (GX15-070) contribute in the sensitization of B-NHL cells to TRAIL apoptosis

    PubMed Central

    Martínez-Paniagua, Melisa A; Baritaki, Stavroula; Huerta-Yepez, Sara; Ortiz-Navarrete, Vianney F; González-Bonilla, Cesar

    2011-01-01

    The pan Bcl-2 family antagonist Obatoclax (GX15-070), currently in clinical trials, was shown to sensitize TRAIL-resistant tumors to TRAIL-mediated apoptosis via the release of Bak and Bim from Mcl-1 or Bcl-2/Bcl-XL complexes or by the activation of Bax, though other mechanisms were not examined. Herein, we hypothesize that Obatoclax-mediated sensitization to TRAIL apoptosis may also result from alterations of the apoptotic pathways. The TRAIL-resistant B-cell line Ramos was used as a model for investigation. Treatment of Ramos cells with obatoclax significantly inhibited the expression of several members of the Bcl-2 family, dissociated Bak from Mcl-1 and inhibited the NFκB activity. Cells treated with Mcl-1 siRNA were sensitized to TRAIL apoptosis. We examined whether the sensitization of Ramos to TRAIL by Obatoclax resulted from signaling of the DR4 and/or DR5. Transfection with DR5 siRNA, but not with DR4 siRNA, sensitized the cells to apoptosis following treatment with Obatoclax and TRAIL. The signaling via DR5 correlated with Obatoclax-induced inhibition of the DR5 repressor Yin Yang 1 (YY1). Transfection with YY1 siRNA sensitized the cells to TRAIL apoptosis following treatment with Obatoclax and TRAIL. Overall, the present findings reveal a new mechanism of Obatoclax-induced sensitization to TRAIL apoptosis and the involvement of the inhibition of NFκB activity and downstream Mcl-1 and YY1 expressions and activities. PMID:21822052

  7. Self-consistent field tight-binding model for neutral and (multi-) charged carbon clusters

    NASA Astrophysics Data System (ADS)

    Montagnon, Laurent; Spiegelman, Fernand

    2007-08-01

    A semiempirical model for carbon clusters modeling is presented, along with structural and dynamical applications. The model is a tight-binding scheme with additional one- and two-center distance-dependent electrostatic interactions treated self-consistently. This approach, which explicitly accounts for charge relaxation, allows us to treat neutral and (multi-) charged clusters not only at equilibrium but also in dissociative regions. The equilibrium properties, geometries, harmonic spectra, and relative stabilities of the stable isomers of neutral and singly charged clusters in the range n =1-14, for C20 and C60, are found to reproduce the results of ab initio calculations. The model is also shown to be successful in describing the stability and fragmentation energies of dictations in the range n =2-10 and allows the determination of their Coulomb barriers, as examplified for the smallest sizes (C22+,C32+,C42+). We also present time-dependent mean-field and linear response optical spectra for the C8 and C60 clusters and discuss their relevance with respect to existing calculations.

  8. Small Al clusters. II - Structure and binding in Al(n) (n = 2-6, 13)

    NASA Technical Reports Server (NTRS)

    Pettersson, Lars G. M.; Bauschlicher, Charles W., Jr.; Halicioglu, Timur

    1987-01-01

    The structure and stability of aluminum clusters containing up to six atoms have been studied using correlated wave functions and extended basis sets. The lowest energy structure is planar for Al4 and Al5, but three dimensional for Al6. The icosahedral, hcp, fcc, and two planar structures of Al13 were considered at the SCF level. The lowest energy structure is the icosahedron, but the planar structures are fairly low lying even in this case. A simplified description using two- and three-body interaction potentials is found to agree well with the ab initio structures and binding energies.

  9. Triple and quadruple excitation contributions to the binding in Be clusters: Calibration calculations on Be3

    NASA Technical Reports Server (NTRS)

    Watts, John D.; Cernusak, Ivan; Noga, Jozef; Bartlett, Rodney J.; Bauschlicher, Charles W., Jr.; Lee, Timothy J.; Rendell, Alistair P.; Taylor, Peter R.

    1991-01-01

    The contribution of connected triple and quadruple excitations to the binding in Be3 is investigated by comparing various coupled-cluster (CC) and truncated configuration interaction (CI) treatments with multireference CI (MRCI) and full CI(FCI) calculations. The CC method with single and double excitations (CCSD) produces results that differ substantially from more elaborate treatments, but most extensions to CCSD that account approximately for connected triple excitations perform very well. In constrast, good agreement with FCI for Be2 can be achieved only with the highest level CC and MRCI methods.

  10. Accurate structures and binding energies for small water clusters: The water trimer

    SciTech Connect

    Nielsen, I.M.; Seidl, E.T.; Janssen, C.L.

    1999-05-01

    The global minimum on the water trimer potential energy surface has been investigated by means of second-order Mo/ller-Plesset (MP2) perturbation theory employing the series of correlation-consistent basis sets aug-cc-pVXZ (X = D, T, Q, 5, 6), the largest of which contains 1329 basis functions. Definitive predictions are made for the binding energy and equilibrium structure, and improved values are presented for the harmonic vibrational frequencies. A value of 15.82{plus_minus}0.05 kcal mol{sup {minus}1} is advanced for the infinite basis set frozen core MP2 binding energy, obtained by extrapolation of MP2 correlation energies computed at the aug-cc-pVQZ MP2 geometry. Inclusion of core correlation, using the aug-cc-pCV5Z basis set, has been found to increase the binding energy by 0.08 kcal mol{sup {minus}1}, and after consideration of core correlation and higher-order correlation effects, the classical binding energy for the water trimer is estimated to be 15.9{plus_minus}0.2 kcal mol{sup {minus}1}. A zero-point vibrational correction of {minus}5.43 kcal mol{sup {minus}1} has been computed from aug-cc-pVTZ MP2 harmonic vibrational frequencies. The accuracy of different computational schemes for obtaining the binding energies of the water dimer and trimer has been investigated, and computationally feasible methods are suggested for obtaining accurate structures and binding energies for larger water clusters.{copyright} {ital 1999 American Institute of Physics.}

  11. Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.

    PubMed

    Li, Xiaolu; Zhuo, Wei; Yu, Jie; Ge, Jingpeng; Gu, Jinke; Feng, Yue; Yang, Maojun; Wang, Linfang; Wang, Na

    2013-02-01

    Dipeptide permease (Dpp), which belongs to an ABC transport system, imports peptides consisting of two or three L-amino acids from the matrix to the cytoplasm in microbes. Previous studies have indicated that haem competes with dipeptides to bind DppA in vitro and in vivo and that the Dpp system can also translocate haem. Here, the crystal structure of DppD, the nucleotide-binding domain (NBD) of the ABC-type dipeptide/oligopeptide/nickel-transport system from Thermoanaerobacter tengcongensis, bound with ATP, Mg(2+) and a [4Fe-4S] iron-sulfur cluster is reported. The N-terminal domain of DppD shares a similar structural fold with the NBDs of other ABC transporters. Interestingly, the C-terminal domain of DppD contains a [4Fe-4S] cluster. The UV-visible absorbance spectrum of DppD was consistent with the presence of a [4Fe-4S] cluster. A search with DALI revealed that the [4Fe-4S] cluster-binding domain is a novel structural fold. Structural analysis and comparisons with other ABC transporters revealed that this iron-sulfur cluster may act as a mediator in substrate (dipeptide or haem) binding by electron transfer and may regulate the transport process in Dpp ABC transport systems. The crystal structure provides a basis for understanding the properties of ABC transporters and will be helpful in investigating the functions of NBDs in the regulation of ABC transporter activity.

  12. Human CLEC18 Gene Cluster Contains C-type Lectins with Differential Glycan-binding Specificity*

    PubMed Central

    Huang, Ya-Lang; Pai, Feng-Shuo; Tsou, Yun-Ting; Mon, Hsien-Chen; Hsu, Tsui-Ling; Wu, Chung-Yi; Chou, Teh-Ying; Yang, Wen-Bin; Chen, Chung-Hsuan; Wong, Chi-Huey; Hsieh, Shie-Liang

    2015-01-01

    The human C-type lectin 18 (clec18) gene cluster, which contains three clec18a, clec18b, and clec18c loci, is located in human chromosome 16q22. Although the amino acid sequences of CLEC18A, CLEC18B, and CLEC18C are almost identical, several amino acid residues located in the C-type lectin-like domain (CTLD) and the sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) domain, also known as the cysteine-rich secretory proteins/antigen 5/pathogenesis-related 1 proteins (CAP) domain, are distinct from each other. Genotyping by real-time PCR and sequencing further shows the presence of multiple alleles in clec18a/b/c loci. Flow cytometry analysis demonstrates that CLEC18 (CLEC18A, -B, and -C) are expressed abundantly in human peripheral blood cells. Moreover, CLEC18 expression is further up-regulated when monocytes differentiate into macrophages and dendritic cells. Immunofluorescence staining reveals that CLEC18 are localized in the endoplasmic reticulum, Golgi apparatus, and endosome. Interestingly, CLEC18 are also detectable in human sera and culture supernatants from primary cells and 293T cells overexpressing CLEC18. Moreover, CLEC18 bind polysaccharide in Ca2+-independent manner, and amino acid residues Ser/Arg339 and Asp/Asn421 in CTLD domain contribute to their differential binding abilities to polysaccharides isolated from Ganoderma lucidum (GLPS-F3). The Ser339 (CLEC18A) → Arg339 (CLEC18A-1) mutation completely abolishes CLEC18A-1 binding to GLPS-F3, and a sugar competition assay shows that CLEC18 preferentially binds to fucoidan, β-glucans, and galactans. Because proteins with the SCP/TAPS/CAP domain are able to bind sterol and acidic glycolipid, and are involved in sterol transport and β-amyloid aggregation, it would be interesting to investigate whether CLEC18 modulates host immunity via binding to glycolipids, and are also involved in glycolipid transportation and protein aggregation in the future. PMID:26170455

  13. Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen

    PubMed Central

    Di Rienzo, Lorenzo; Milanetti, Edoardo; Lepore, Rosalba; Olimpieri, Pier Paolo; Tramontano, Anna

    2017-01-01

    We describe here a superposition free method for comparing the surfaces of antibody binding sites based on the Zernike moments and show that they can be used to quickly compare and cluster sets of antibodies. The clusters provide information about the nature of the bound antigen that, when combined with a method for predicting the number of direct antibody antigen contacts, allows the discrimination between protein and non-protein binding antibodies with an accuracy of 76%. This is of relevance in several aspects of antibody science, for example to select the framework to be used for a combinatorial antibody library. PMID:28338016

  14. Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen.

    PubMed

    Di Rienzo, Lorenzo; Milanetti, Edoardo; Lepore, Rosalba; Olimpieri, Pier Paolo; Tramontano, Anna

    2017-03-24

    We describe here a superposition free method for comparing the surfaces of antibody binding sites based on the Zernike moments and show that they can be used to quickly compare and cluster sets of antibodies. The clusters provide information about the nature of the bound antigen that, when combined with a method for predicting the number of direct antibody antigen contacts, allows the discrimination between protein and non-protein binding antibodies with an accuracy of 76%. This is of relevance in several aspects of antibody science, for example to select the framework to be used for a combinatorial antibody library.

  15. In silico genomic analysis of the human and murine guanylate-binding protein (GBP) gene clusters.

    PubMed

    Olszewski, Maureen A; Gray, John; Vestal, Deborah J

    2006-05-01

    The guanylate-binding proteins (GBPs) were among the first interferon (IFN)-stimulated genes (ISGs) discovered, but until recently, little was known about their functions and even less about the composition of the gene family. Analysis of the promoter of human GBP-1 contributed significantly toward the understanding of Jak-Stat signaling and the delineation of the IFN-gamma activation site (GAS) and IFN-stimulated response element (ISRE) promoter elements. In this study, we have examined the genomic arrangement and composition of the GBPs in both mouse and humans. There are seven GBP paralogs in humans and at least one pseudogene, all of which are located in a cluster of genes on chromosome 1. Five of the six MuGBPs and a GBP pseudogene are clustered in a syntenic region on chromosome 3. The sixth MuGBP, MuGBP-4, and three GBP pseudogenes are located on chromosome 5. As might be expected, the GBPs share similar genomic organizations of introns and exons. Five of the MuGBPs had previously been shown to be coordinately induced by IFNs, and as expected, all of the MuGBPs have GAS and ISRE elements in their promoters. Interestingly, not all of the HuGBPs have GAS and ISRE elements, suggesting that not all GBPs are IFN responsive in humans.

  16. The binding of CO molecule with small Wn(n = 2-9) clusters: a DFT investigation

    NASA Astrophysics Data System (ADS)

    Sun, Xiyuan; Du, Jiguang

    2014-08-01

    The hybrid DFT functional has been utilized to investigate CO adsorption on small W n ( n = 2-9) clusters. The reactivity-selectivity descriptor Δf( r) is proved to be an appropriate tool for predicting the local adsorption site. Our results indicate that the binding of CO to tungsten cluster prefers terminal adsorption mode except for W3 trimer. The Wiberg bond index can predict the interaction between W atoms and CO molecule to a good accuracy using a linear fit. The dependency on number of adsorbate and charge state of host clusters is also investigated. The high CO coverage seriously weakens the W-CO interaction. The anion cluster reveals the stronger interaction with CO molecule than cation and neutral ones. Moreover, the interesting coverage-dependence is revealed for anion cluster.

  17. The platelet fibrinogen receptor: an immunogold-surface replica study of agonist-induced ligand binding and receptor clustering

    PubMed Central

    1987-01-01

    Platelet aggregation requires the binding of fibrinogen to its receptor, a heterodimer consisting of the plasma-membrane glycoproteins (GP) IIb and IIIa. Although the GPIIb-IIIa complex is present on the surface of unstimulated platelets, it binds fibrinogen only after platelet activation. We have used an immunogold-surface replica technique to study the distribution of GPIIb-IIIa and bound fibrinogen over broad areas of surface membranes in unstimulated, as well as thrombin-activated and ADP-activated human platelets. We found that the immunogold-labeled GPIIb-IIIa was monodispersed over the surface of unstimulated platelets, although the cell surface lacked immunoreactive fibrinogen. On thrombin-stimulated platelets, approximately 65% of the GPIIb-IIIa molecules were in clusters within the plane of the membrane. Fibrinogen, which had been released from the alpha-granules of these cells, bound to GPIIb-IIIa on the cell surface and was similarly clustered. To determine whether the receptors clustered before ligand binding, or as a consequence thereof, we studied the surface distribution of GPIIb-IIIa after stimulation with ADP, which causes activation of the fibrinogen receptor function of GPIIb-IIIa without inducing the release of fibrinogen. In the absence of added fibrinogen, the unoccupied, yet binding-competent receptors on ADP-stimulated platelets were monodispersed. The addition of fibrinogen caused the GPIIb-IIIa molecules to cluster on the cell surface. Clustering was also induced by the addition of the GPIIb-IIIa-binding domains of fibrinogen, namely the tetrapeptide Arg-Gly-Asp-Ser on the alpha-chain or the gamma-chain decapeptide gamma 402-411. These results show that receptor occupancy causes clustering of GPIIb-IIIa in activated platelets. PMID:3584243

  18. A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans

    PubMed Central

    Fox, Ellen M.; Gardiner, Donald M.; Keller, Nancy P.; Howlett, Barbara J.

    2008-01-01

    A gene, sirZ, encoding a Zn(II)2Cys6 DNA binding protein is present in a cluster of genes responsible for the biosynthesis of the epipolythiodioxopiperazine (ETP) toxin, sirodesmin PL in the ascomycete plant pathogen, Leptosphaeria maculans. RNA-mediated silencing of sirZ gives rise to transformants that produce only residual amounts of sirodesmin PL and display a decrease in the transcription of several sirodesmin PL biosynthetic genes. This indicates that SirZ is a major regulator of this gene cluster. Proteins similar to SirZ are encoded in the gliotoxin biosynthetic gene cluster of Aspergillus fumigatus (gliZ) and in an ETP-like cluster in Penicillium lilacinoechinulatum (PlgliZ). Despite its high level of sequence similarity to gliZ, PlgliZ is unable to complement the gliotoxin-deficiency of a mutant of gliZ in A. fumigatus. Putative binding sites for these regulatory proteins in the promoters of genes in these clusters were predicted using bioinformatic analysis. These sites are similar to those commonly bound by other proteins with Zn(II)2Cys6 DNA binding domains. PMID:18023597

  19. Mutations in the ligand-binding domain of the androgen receptor gene cluster in two regions of the gene.

    PubMed

    McPhaul, M J; Marcelli, M; Zoppi, S; Wilson, C M; Griffin, J E; Wilson, J D

    1992-11-01

    We have analyzed the nucleotide sequence of the androgen receptor from 22 unrelated subjects with substitution mutations of the hormone-binding domain. Eleven had the phenotype of complete testicular feminization, four had incomplete testicular feminization, and seven had Reifenstein syndrome. The underlying functional defect in cultured skin fibroblasts included individuals with absent, qualitative, or quantitative defects in ligand binding. 19 of the 21 substitution mutations (90%) cluster in two regions that account for approximately 35% of the hormone-binding domain, namely, between amino acids 726 and 772 and between amino acids 826 and 864. The fact that one of these regions is homologous to a region of the human thyroid hormone receptor (hTR-beta) which is a known cluster site for mutations that cause thyroid hormone resistance implies that this localization of mutations is not a coincidence. These regions of the androgen receptor may be of particular importance for the formation and function of the hormone-receptor complex.

  20. Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions

    SciTech Connect

    Johnson, Grant E.; Priest, Thomas A.; Laskin, Julia

    2014-01-01

    The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

  1. Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies

    PubMed Central

    Colebatch, Andrew J.; Di Stefano, Leon; Wong, Stephen Q.; Hannan, Ross D.; Waring, Paul M.; Dobrovic, Alexander

    2016-01-01

    Most cancer DNA sequencing studies have prioritized recurrent non-synonymous coding mutations in order to identify novel cancer-related mutations. Although attention is increasingly being paid to mutations in non-coding regions, standard approaches to identifying significant mutations may not be appropriate and there has been limited analysis of mutational clusters in functionally annotated non-coding regions. We sought to identify clustered somatic mutations (hotspot regions across samples) in functionally annotated regions in melanoma and other cutaneous malignancies (cutaneous squamous cell carcinoma, basal cell carcinoma and Merkel cell carcinoma). Sliding window analyses revealed numerous recurrent clustered hotspot mutations in proximal promoters, with some specific clusters present in up to 25% of cases. Mutations in melanoma were clustered within ETS and Sp1 transcription factor binding motifs, had a UV signature and were identified in other cutaneous malignancies. Clinicopathologic correlation and mutation analysis support a causal role for chronic UV irradiation generating somatic mutations in transcription factor binding motifs of proximal promoters. PMID:27611953

  2. A point mutation in the [2Fe–2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties

    SciTech Connect

    Tamir, Sagi; Eisenberg-Domovich, Yael; Conlan, Andrea R.; Stofleth, Jason T.; Lipper, Colin H.; Paddock, Mark L.; Mittler, Ron; Jennings, Patricia A.; Livnah, Oded Nechushtai, Rachel

    2014-06-01

    NAF-1 has been shown to be related with human health and disease, is upregulated in epithelial breast cancer and suppression of its expression significantly suppresses tumor growth. It is shown that replacement of the single His ligand with Cys resulted in dramatic changes to the properties of its 2Fe-2S clusters without any global crystal structural changes. NAF-1 is an important [2Fe–2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, and suppression of NAF-1 expression by knockdown significantly suppresses tumor growth. Key to NAF-1 function is the NEET fold with its [2Fe–2S] cluster. In this work, the high-resolution structure of native NAF-1 was determined to 1.65 Å resolution (R factor = 13.5%) together with that of a mutant in which the single His ligand of its [2Fe–2S] cluster, His114, was replaced by Cys. The NAF-1 H114C mutant structure was determined to 1.58 Å resolution (R factor = 16.0%). All structural differences were localized to the cluster binding site. Compared with native NAF-1, the [2Fe–2S] clusters of the H114C mutant were found to (i) be 25-fold more stable, (ii) have a redox potential that is 300 mV more negative and (iii) have their cluster donation/transfer function abolished. Because no global structural differences were found between the mutant and the native (wild-type) NAF-1 proteins, yet significant functional differences exist between them, the NAF-1 H114C mutant is an excellent tool to decipher the underlying biological importance of the [2Fe–2S] cluster of NAF-1 in vivo.

  3. Differential palmitoylation directs the AMPA receptor-binding protein ABP to spines or to intracellular clusters.

    PubMed

    DeSouza, Sunita; Fu, Jie; States, Bradley A; Ziff, Edward B

    2002-05-01

    Long-term changes in excitatory synapse strength are thought to reflect changes in synaptic abundance of AMPA receptors mediated by receptor trafficking. AMPA receptor-binding protein (ABP) and glutamate receptor-interacting protein (GRIP) are two similar PDZ (postsynaptic density 95/Discs large/zona occludens 1) proteins that interact with glutamate receptors 2 and 3 (GluR2 and GluR3) subunits. Both proteins have proposed roles during long-term potentiation and long-term depression in the delivery and anchorage of AMPA receptors at synapses. Here we report a variant of ABP-L (seven PDZ form of ABP) called pABP-L that is palmitoylated at a cysteine residue at position 11 within a novel 18 amino acid N-terminal leader sequence encoded through differential splicing. In cultured hippocampal neurons, nonpalmitoylated ABP-L localizes with internal GluR2 pools expressed from a Sindbis virus vector, whereas pABP-L is membrane targeted and associates with surface-localized GluR2 receptors at the plasma membrane in spines. Mutation of Cys-11 to alanine blocks the palmitoylation of pABP-L and targets the protein to intracellular clusters, confirming that targeting the protein to spines is dependent on palmitoylation. Non-palmitoylated GRIP is primarily intracellular, but a chimera with the pABP-L N-terminal palmitoylation sequence linked to the body of the GRIP protein is targeted to spines. We suggest that pABP-L and ABP-L provide, respectively, synaptic and intracellular sites for the anchorage of AMPA receptors during receptor trafficking to and from the synapse.

  4. Possible mechanism of BN fullerene formation from a boron cluster: Density-functional tight-binding molecular dynamics simulations.

    PubMed

    Ohta, Y

    2016-04-15

    We simulate the formation of a BN fullerene from an amorphous B cluster at 2000 K by quantum mechanical molecular dynamics based on the density-functional tight-binding method. We run 30 trajectories 200 ps in length, where N atoms are supplied around the target cluster, which is initially an amorphous B36 cluster. Most of the incident N atoms are promptly incorporated into the target cluster to form B-N-B bridges or NB3 pyramidal local substructures. BN fullerene formation is initiated by alternating BN ring condensation. Spontaneous atomic rearrangement and N2 dissociation lead to the construction of an sp(2) single-shelled structure, during which the BN cluster undergoes a transition from a liquid-like to a solid-like state. Continual atomic rearrangement and sporadic N2 dissociation decrease the number of defective rings in the BN cluster and increase the number of six-membered rings, forming a more regular shell structure. The number of four-membered rings tends to remain constant, and contributes to more ordered isolated-tetragon-rule ring placement.

  5. Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein

    PubMed Central

    Thompson, Michael C.; Wheatley, Nicole M.; Jorda, Julien; Sawaya, Michael R.; Gidaniyan, Soheil D.; Ahmed, Hoda; Yang, Zhongyu; McCarty, Krystal N.; Whitelegge, Julian P.; Yeates, Todd O.

    2014-01-01

    Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein, whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date. PMID:25102080

  6. Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein.

    PubMed

    Thompson, Michael C; Wheatley, Nicole M; Jorda, Julien; Sawaya, Michael R; Gidaniyan, Soheil D; Ahmed, Hoda; Yang, Zhongyu; McCarty, Krystal N; Whitelegge, Julian P; Yeates, Todd O

    2014-09-23

    Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins [bacterial microcompartment (in reference to the shell protein domain)] assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date.

  7. Iron–Sulfur Cluster Binding by Mitochondrial Monothiol Glutaredoxin-1 of Trypanosoma brucei: Molecular Basis of Iron–Sulfur Cluster Coordination and Relevance for Parasite Infectivity

    PubMed Central

    Manta, Bruno; Pavan, Carlo; Sturlese, Mattia; Medeiros, Andrea; Crispo, Martina; Berndt, Carsten; Krauth-Siegel, R. Luise; Bellanda, Massimo

    2013-01-01

    Abstract Aims: Monothiol glutaredoxins (1-C-Grxs) are small proteins linked to the cellular iron and redox metabolism. Trypanosoma brucei brucei, model organism for human African trypanosomiasis, expresses three 1-C-Grxs. 1-C-Grx1 is a highly abundant mitochondrial protein capable to bind an iron–sulfur cluster (ISC) in vitro using glutathione (GSH) as cofactor. We here report on the functional and structural analysis of 1-C-Grx1 in relation to its ISC-binding properties. Results: An N-terminal extension unique to 1-C-Grx1 from trypanosomatids affects the oligomeric structure and the ISC-binding capacity of the protein. The active-site Cys104 is essential for ISC binding, and the parasite-specific glutathionylspermidine and trypanothione can replace GSH as the ligands of the ISC. Interestingly, trypanothione forms stable protein-free ISC species that in vitro are incorporated into the dithiol T. brucei 2-C-Grx1, but not 1-C-Grx1. Overexpression of the C104S mutant of 1-C-Grx1 impairs disease progression in a mouse model. The structure of the Grx-domain of 1-C-Grx1 was solved by nuclear magnetic resonance spectroscopy. Despite the fact that several residues—which in other 1-C-Grxs are involved in the noncovalent binding of GSH—are conserved, different physicochemical approaches did not reveal any specific interaction between 1-C-Grx1 and free thiol ligands. Innovation: Parasite Grxs are able to coordinate an ISC formed with trypanothione, suggesting a new mechanism of ISC binding and a novel function for the parasite-specific dithiol. The first 3D structure and in vivo relevance of a 1-C-Grx from a pathogenic protozoan are reported. Conclusion: T. brucei 1-C-Grx1 is indispensable for mammalian parasitism and utilizes a new mechanism for ISC binding. Antioxid. Redox Signal. 19, 665–682. PMID:23259530

  8. Attractant binding induces distinct structural changes to the polar and lateral signaling clusters in Bacillus subtilis chemotaxis.

    PubMed

    Wu, Kang; Walukiewicz, Hanna E; Glekas, George D; Ordal, George W; Rao, Christopher V

    2011-01-28

    Bacteria employ a modified two-component system for chemotaxis, where the receptors form ternary complexes with CheA histidine kinases and CheW adaptor proteins. These complexes are arranged in semi-ordered arrays clustered predominantly at the cell poles. The prevailing models assume that these arrays are static and reorganize only locally in response to attractant binding. Recent studies have shown, however, that these structures may in fact be much more fluid. We investigated the localization of the chemotaxis signaling arrays in Bacillus subtilis using immunofluorescence and live cell fluorescence microscopy. We found that the receptors were localized in clusters at the poles in most cells. However, when the cells were exposed to attractant, the number exhibiting polar clusters was reduced roughly 2-fold, whereas the number exhibiting lateral clusters distinct from the poles increased significantly. These changes in receptor clustering were reversible as polar localization was reestablished in adapted cells. We also investigated the dynamic localization of CheV, a hybrid protein consisting of an N-terminal CheW-like adaptor domain and a C-terminal response regulator domain that is known to be phosphorylated by CheA, using immunofluorescence. Interestingly, we found that CheV was localized predominantly at lateral clusters in unstimulated cells. However, upon exposure to attractant, CheV was found to be predominantly localized to the cell poles. Moreover, changes in CheV localization are phosphorylation-dependent. Collectively, these results suggest that the chemotaxis signaling arrays in B. subtilis are dynamic structures and that feedback loops involving phosphorylation may regulate the positioning of individual proteins.

  9. Influence of Molecular Structure on O2-Binding Properties and Blood Circulation of Hemoglobin‒Albumin Clusters

    PubMed Central

    Yamada, Kana; Yokomaku, Kyoko; Haruki, Risa; Taguchi, Kazuaki; Nagao, Saori; Maruyama, Toru; Otagiri, Masaki; Komatsu, Teruyuki

    2016-01-01

    A hemoglobin wrapped covalently by three human serum albumins, a Hb-HSA3 cluster, is an artificial O2-carrier with the potential to function as a red blood cell substitute. This paper describes the synthesis and O2-binding properties of new hemoglobin‒albumin clusters (i) bearing four HSA units at the periphery (Hb-HSA4, large-size variant) and (ii) containing an intramolecularly crosslinked Hb in the center (XLHb-HSA3, high O2-affinity variant). Dynamic light scattering measurements revealed that the Hb-HSA4 diameter is greater than that of either Hb-HSA3 or XLHb-HSA3. The XLHb-HSA3 showed moderately high O2-affinity compared to the others because of the chemical linkage between the Cys-93(β) residues in Hb. Furthermore, the blood circulation behavior of 125I-labeled clusters was investigated by assay of blood retention and tissue distribution after intravenous administration into anesthetized rats. The XLHb-HSA3 was metabolized faster than Hb-HSA3 and Hb-HSA4. Results suggest that the molecular structure of the protein cluster is a factor that can influence in vivo circulation behavior. PMID:26895315

  10. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

    PubMed

    De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D A; Norberto de Souza, Osmar

    2015-01-01

    Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill

  11. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features

    PubMed Central

    Ruiz, Duncan D. A.; Norberto de Souza, Osmar

    2015-01-01

    Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward’s, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill

  12. The nature and evolution of excess electron binding in cluster anions studied via negative ion photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Hendricks, Jay H.

    1997-07-01

    The technique of negative ion photoelectron spectroscopy (NIPES) has been used to study a variety of cluster anion systems with the aim of elucidating the nature and evolution of excess electron binding in clusters. The systems studied include molecular and cluster dipole- bound anions, conventional valence molecular anions, ion- molecule cluster anions, solvated electron cluster anions, metal cluster anions, metal oxide anions, and metal hydride anions. The generation and characterization of nanophase Lunsford catalyst, and the study of gas- phase anionic polymerization reactions were also conducted. The studies of dipole-bound anions, (Uracil)/sp-, (Uracil...Xe)/sp-, (Thymine)/sp-, (1- Methylcytosine)/sp-, (HF)2-, (H2O)2-, (EG)2-, where EG = Ethylene Glycol, (CH3CN[/cdots]H2O)/sp-,/ (HCl[/cdots] H2O)/sp-,/ (HCN[/cdots]H2O)/sp-, and (H2S)4- provide some of the best experimental evidence to date confirming the long standing predictions of theory that an excess electron can be bound to a dipole field if the dipole moment of the neutral molecule or cluster exceeds a critical minimum value. The photodetachment of the conventional valence anions /[(2,4,6-tricyanobenzene)/sp-, (CAN3-3HCl)/sp-, where CAN = 2- choloracrylonitrile, (CH3NO2)/sp-/], metal cluster anions /[Lin=1-7-/], metal oxide anions /[NaO/sp-,/ KO/sp-,/ RbO/sp-, and CsO/sp-/] and metal hydride anions /[LiH/sp-,/ LiD/sp-/] enabled the first time determinations of vertical detachment energies, and adiabatic election affinities. The studies of ion-molecule cluster anions /[O/sp- (Ar)n=1-26,34,/ NO/sp-(Ar)n=1-14,/ O/sp- (Kr)n=1-4,/ O/sp-(Xe)n=1-4,/ O/sp-(N2),/ NO/sp-(Kr),/ NO/sp-(Xe)n=1-3,/ NO/sp- (N2O)n=1-5, and NO/sp-(EG),/ (Uracil[/cdots]H2O)/sp-,/ (Uracil[/cdots]Xe)/sp-/] permitted the energetics and structure of microscopic ion solvation to be examined as a function of cluster size and cluster solvent. The photodetachment of solvated the electron clusters anions /[(H2O)n-,/ [(H2O)x[/cdots](NH3)y

  13. POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster.

    PubMed

    Farley, Brian M; Ryder, Sean P

    2012-12-01

    RNA-binding proteins (RBPs) coordinate cell fate specification and differentiation in a variety of systems. RNA regulation is critical during oocyte development and early embryogenesis, in which RBPs control expression from maternal mRNAs encoding key cell fate determinants. The Caenorhabditis elegans Notch homologue glp-1 coordinates germline progenitor cell proliferation and anterior fate specification in embryos. A network of sequence-specific RBPs is required to pattern GLP-1 translation. Here, we map the cis-regulatory elements that guide glp-1 regulation by the CCCH-type tandem zinc finger protein POS-1 and the STAR-domain protein GLD-1. Our results demonstrate that both proteins recognize the glp-1 3' untranslated region (UTR) through adjacent, overlapping binding sites and that POS-1 binding excludes GLD-1 binding. Both factors are required to repress glp-1 translation in the embryo, suggesting that they function in parallel regulatory pathways. It is intriguing that two equivalent POS-1-binding sites are present in the glp-1 3' UTR, but only one, which overlaps with a translational derepression element, is functional in vivo. We propose that POS-1 regulates glp-1 mRNA translation by blocking access of other RBPs to a key regulatory sequence.

  14. Photoelectron spectroscopy of s-triazine anion clusters: Polarization-induced electron binding in aza-aromatic molecule

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Hyun; Song, Jae Kyu; Park, Hyokeun; Lee, Sang Hak; Han, Sang Yun; Kim, Seong Keun

    2003-08-01

    Photoelectron spectroscopy was carried out for the mass-selected cluster anions of s-triazine molecule, Tzn- (n=1-6). The mass spectrum and vibrationally resolved photoelectron spectrum of Tz- showed that unlike pyridine and pyrazine, Tz binds an electron and thus becomes the first molecule in the azabenzene series with a positive electron affinity (0.03 eV). This indicates that the local charge polarization in the aromatic ring by the three nitrogen atoms is large enough to facilitate electron binding to a homologue of benzene. A Jahn-Teller distortion was proposed to explain the vibrational progressions of the photoelectron spectrum of Tz-. A series of Ar-solvated clusters of Tz-, Tz-ṡArm (m=1-7), have been also studied. Their photoelectron spectra showed a drop in the incremental electron binding energy when going from m=4 to 5, indicating the closure of a solvation shell with four Ar atoms. In the mass abundance spectrum of Tzn-, a distinctly high intensity for Tz2- indicated its exceptional stability, which was also manifested by the large increase by more than 0.5 eV in the vertical detachment energy of the photoelectron spectrum. Theoretical calculations were carried out to obtain optimized geometries of the neutral and anion of Tz and Tz2. We confirmed the Jahn-Teller distortion in Tz- and also addressed the role of hydrogen bonding in determining the geometries of Tz2-. A common feature for the two most stable forms of Tz2- with comparable energies was that they achieve their unique stability through equal sharing of the negative charge between their two molecular constituents. A new photoelectron band was found to emerge from Tzn- for n⩾2 by the 355 nm light, in addition to the photoelectron band at lower electron binding energy observed for n⩾1 at 532 nm. The relative intensity of this new band decreased as n increased, and its position was 1.6-1.8 eV above the first band. Photodetachment to an electronically excited state was suggested to give

  15. Comparative Study on the Noble-Gas Binding Ability of BeX Clusters (X = SO4, CO3, O).

    PubMed

    Saha, Ranajit; Pan, Sudip; Merino, Gabriel; Chattaraj, Pratim K

    2015-06-25

    Ab initio computations are carried out to assess the noble gas (Ng) binding capability of BeSO4 cluster. We have further compared the stability of NgBeSO4 with that of the recently detected NgBeCO3 cluster. The Ng-Be bond in NgBeCO3 is somewhat weaker than that in NgBeO cluster. In NgBeSO4, the Ng-Be bond is found to be stronger compared with not only the Ng-Be bond in NgBeCO3 but also that in NgBeO, except the He case. The Ar-Rn-bound BeSO4 analogues are viable even at room temperature. The Wiberg bond indices of Be-Ng bonds and the degree of electron transfer from Ng to Be are somewhat larger in NgBeSO4 than those in NgBeCO3 and NgBeO. Electron density and energy decomposition analyses are performed in search of the nature of interaction in the Be-Ng bond in NgBeSO4. The orbital energy term (ΔE(orb)) contributes the maximum (ca. 80-90%) to the total attraction energy. The Ar/Kr/Xe/Rn-Be bonds in NgBeSO4 could be of partial covalent type with a gradual increase in covalency along Ar to Rn.

  16. Electrical resistivity anomaly, valence shift of Pr ion, and magnetic behavior in epitaxial (Pr1-yYy)1-xCaxCoO3 thin films under compressive strain

    NASA Astrophysics Data System (ADS)

    Fujishiro, H.; Noda, Y.; Akuzawa, K.; Naito, T.; Ito, A.; Goto, T.; Marysko, M.; Jirak, Z.; Hejtmanek, J.; Nitta, K.

    2017-03-01

    We have fabricated (Pr1-yYy)1-xCaxCoO3 (PYCCO) epitaxial films with various thicknesses by pulsed laser deposition on the SrLaAlO4 (SLAO) substrate that applied an in-plane compressive stress to the film, and investigated the temperature dependence of the electrical resistivity, ρ(T), of the films. An anomalous ρ(T) upturn with a broad hysteresis could be clearly observed only for the thinnest film (d = 50 nm), and the ρ(T) anomaly decreased by increasing film thickness, d. The temperature dependence of the X-ray absorption near-edge structure (XANES) spectra at Pr L2-edge was measured for the films, and the valence states of praseodymium (Pr) ion were determined using the analysis of the XANES spectra. As a result, the average valence of the Pr ion in the d = 50 nm film slightly increases with decreasing temperature from the common value of 3.0+ around room temperature to 3.15+ at 8 K. The valence shift of Pr is thus similar to what was observed on the PYCCO polycrystalline bulks with an abrupt metal-insulator transition, accompanied by a spin-state (SS) transition of Co ions. Furthermore, the low-temperature SQUID measurements evidenced a paramagnetic behavior down to the lowest temperature, which suggests that the dominant part of Co3+ ions in the film grown on the SLAO substrate tends to be in the low spin state characteristic for the insulating ground state. These results strongly suggest that the anomalous ρ(T) upturn in the thin films on the SrLaAlO4 (SLAO) substrate is closely related to the SS transition of Co ions. On the other hand, PYCCO films grown on the LaAlO3 (LAO) substrate that applied an in-plane tensile stress showed no valence shift of Pr ions and developed a long range ferromagnetic order, which points to a complete suppression of the low-temperature transition. The behaviors of the epitaxial films are discussed in terms of the in-plane stress exerted by different substrates and accumulated elastic energy.

  17. Structure and functional analysis of the siderophore periplasmic binding protein from the fuscachelin gene cluster of Thermobifida fusca.

    PubMed

    Li, Kunhua; Bruner, Steven D

    2016-01-01

    Iron acquisition is a complex, multicomponent process critical for most organisms' survival and virulence. Small iron chelating molecules, siderophores, mediate transport as key components of common pathways for iron assimilation in many microorganisms. The chemistry and biology of the extraordinary tight and specific metal binding siderophores is of general interest in terms of host/guest chemistry and is a potential target toward the development of therapeutic treatments for microbial virulence. The siderophore pathway of the moderate thermophile, Thermobifida fusca, is an excellent model system to study the process in Gram-positive bacteria. Here we describe the structure and characterization of the siderophore periplasmic binding protein, FscJ from the fuscachelin gene cluster of T. fusca. The structure shows a di-domain arrangement connected with a long α-helix hinge. Several X-ray structures detail ligand-free conformational changes at different pH values, illustrating complex interdomain flexibility of the siderophore receptors. We demonstrated that FscJ has a unique recognition mechanism and details the binding interaction with ferric-fuscachelin A through ITC and docking analysis. The presented work provides a structural basis for the complex molecular mechanisms of siderophore recognition and transportation.

  18. Calcium waves in a grid of clustered channels with synchronous IP3 binding and unbinding.

    PubMed

    Rückl, M; Rüdiger, S

    2016-11-01

    Calcium signals in cells occur at multiple spatial scales and variable temporal duration. However, a physical explanation for transitions between long-lasting global oscillations and localized short-term elevations (puffs) of cytoplasmic Ca(2+) is still lacking. Here we introduce a phenomenological, coarse-grained model for the calcium variable, which is represented by ordinary differential equations. Due to its small number of parameters, and its simplicity, this model allows us to numerically study the interplay of multi-scale calcium concentrations with stochastic ion channel gating dynamics even in larger systems. We apply this model to a single cluster of inositol trisphosphate (IP 3) receptor channels and find further evidence for the results presented in earlier work: a single cluster may be capable of producing different calcium release types, where long-lasting events are accompanied by unbinding of IP 3 from the receptor (Rückl et al., PLoS Comput. Biol. 11, e1003965 (2015)). Finally, we show the practicability of the model in a grid of 64 clusters which is computationally intractable with previous high-resolution models. Here long-lasting events can lead to synchronized oscillations and waves, while short events stay localized. The frequency of calcium releases as well as their coherence can thereby be regulated by the amplitude of IP 3 stimulation. Finally the model allows for a new explanation of oscillating [IP 3], which is not based on metabolic production and degradation of IP 3.

  19. N2O binding at a [4Cu:2S] copper-sulphur cluster in nitrous oxide reductase.

    PubMed

    Pomowski, Anja; Zumft, Walter G; Kroneck, Peter M H; Einsle, Oliver

    2011-08-14

    Nitrous oxide (N(2)O) is generated by natural and anthropogenic processes and has a critical role in environmental chemistry. It has an ozone-depleting potential similar to that of hydrochlorofluorocarbons as well as a global warming potential exceeding that of CO(2) 300-fold. In bacterial denitrification, N(2)O is reduced to N(2) by the copper-dependent nitrous oxide reductase (N(2)OR). This enzyme carries the mixed-valent Cu(A) centre and the unique, tetranuclear Cu(Z) site. Previous structural data were obtained with enzyme isolated in the presence of air that is catalytically inactive without prior reduction. Its Cu(Z) site was described as a [4Cu:S] centre, and the substrate-binding mode and reduction mechanism remained elusive. Here we report the structure of purple N(2)OR from Pseudomonas stutzeri, handled under the exclusion of dioxygen, and locate the substrate in N(2)O-pressurized crystals. The active Cu(Z) cluster contains two sulphur atoms, yielding a [4Cu:2S] stoichiometry; and N(2)O bound side-on at Cu(Z), in close proximity to Cu(A). With the substrate located between the two clusters, electrons are transferred directly from Cu(A) to N(2)O, which is activated by side-on binding in a specific binding pocket on the face of the [4Cu:2S] centre. These results reconcile a multitude of available biochemical data on N(2)OR that could not be explained by earlier structures, and outline a mechanistic pathway in which both metal centres and the intervening protein act in concert to achieve catalysis. This structure represents the first direct observation, to our knowledge, of N(2)O bound to its reductase, and sheds light on the functionality of metalloenzymes that activate inert small-molecule substrates. The principle of using distinct clusters for substrate activation and for reduction may be relevant for similar systems, in particular nitrogen-fixing nitrogenase.

  20. Binding of IgG-opsonized particles to Fc gamma R is an active stage of phagocytosis that involves receptor clustering and phosphorylation.

    PubMed

    Sobota, Andrzej; Strzelecka-Kiliszek, Agnieszka; Gładkowska, Ewelina; Yoshida, Kiyotsugu; Mrozińska, Kazimiera; Kwiatkowska, Katarzyna

    2005-10-01

    Fc gammaR mediate the phagocytosis of IgG-coated particles and the clearance of IgG immune complexes. By dissecting binding from internalization of the particles, we found that the binding stage, rather than particle internalization, triggered tyrosine phosphorylation of Fc gammaR and accompanying proteins. High amounts of Lyn kinase were found to associate with particles isolated at the binding stage from J774 cells. PP2 (4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine), an Src kinase inhibitor, but not piceatannol, an inhibitor of Syk kinase, reduced the amount of Lyn associated with the bound particles and simultaneously diminished the binding of IgG-coated particles. Studies of baby hamster kidney cells transfected with wild-type and mutant Fc gammaRIIA revealed that the ability of the receptor to bind particles was significantly reduced when phosphorylation of the receptor was abrogated by Y298F substitution in the receptor signaling motif. Under these conditions, binding of immune complexes of aggregated IgG was depressed to a lesser extent. A similar effect was exerted on the binding ability of wild-type Fc gammaRIIA by PP2. Moreover, expression of mutant kinase-inactive Lyn K275R inhibited both Fc gammaRIIA phosphorylation and IgG-opsonized particle binding. To gain insight into the mechanism by which protein tyrosine phosphorylation can control Fc gammaR-mediated binding, we investigated the efficiency of clustering of wild-type and Y298F-substituted Fc gammaRIIA upon binding of immune complexes. We found that a lack of Fc gammaRIIA phosphorylation led to an impairment of receptor clustering. The results indicate that phosphorylation of Fc gammaR and accompanying proteins, dependent on Src kinase activity, facilitates the clustering of activated receptors that is required for efficient particle binding.

  1. Theoretical investigations of the structures and binding energies of Be(sub n) and Mg(sub n) (n = 3-5) clusters

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rendell, Alistair P.; Taylor, Peter R.

    1989-01-01

    Researchers determined the equilibrium geometries and binding energies of Be and Mg trimers, tetramers and pentamers using single and double excitation coupled cluster (CCSD) and complete active space self-consistent-field (CASSCF) multireference configuration interaction (MRCI) wave functions in conjunction with extended atomic basis sets. Best estimates of the cluster binding energies are 24, 83 and 110 kcal/mole for Be3, Be4 and Be5; and 9, 31 and 41 kcal/mole for Mg3, Mg4 and Mg5, respectively. A comparison of the MRCI and CCSD results shows that even the best single-reference approach (limited to single and double excitations) is not capable of quantitative accuracy in determining the binding energies of Be and Mg clusters.

  2. Effect of medium dependent binding energies on inferring the temperatures and freeze-out density of disassembling hot nuclear matter from cluster yields

    NASA Astrophysics Data System (ADS)

    Shlomo, S.; Röpke, G.; Natowitz, J. B.; Qin, L.; Hagel, K.; Wada, R.; Bonasera, A.

    2009-03-01

    We explore the abundance of light clusters in asymmetric nuclear matter at subsaturation density. With increasing density, binding energies and wave functions are modified due to medium effects. The method of Albergo, Costa, Costanzo, and Rubbino (ACCR) for determining the temperature and free nucleon density of a disassembling hot nuclear source from fragment yields is modified to include, in addition to Coulomb effects and flow, also effects of medium modifications of cluster properties, which become of importance when the nuclear matter density is above 10-3fm-3. We show how the analysis of cluster yields, to infer temperature and nucleon densities, is modified if the shifts in binding energies of in medium clusters are included. Although, at low densities, the temperature calculated from given yields changes only modestly if medium effects are taken into account, larger discrepancies are observed when the nucleon densities are determined from measured yields.

  3. Ion channel clustering by membrane-associated guanylate kinases. Differential regulation by N-terminal lipid and metal binding motifs.

    PubMed

    El-Husseini, A E; Topinka, J R; Lehrer-Graiwer, J E; Firestein, B L; Craven, S E; Aoki, C; Bredt, D S

    2000-08-04

    The postsynaptic density protein PSD-95 and related membrane-associated guanylate kinase (MAGUK) proteins assemble signal transduction complexes at sites of cell-cell contact including synapses. Whereas PSD-95 and PSD-93 occur only at postsynaptic sites in hippocampal neurons, SAP-102 also occurs in axons. In heterologous cells, PSD-95 and PSD-93 mediate cell surface ion channel clustering, but SAP-102 and SAP-97 do not. This selective ion channel clustering activity by MAGUKs is explained by differential palmitoylation, as PSD-93 and PSD-95 are palmitoylated though SAP-97, and SAP-102 are not. Rather than being palmitoylated, we find that N-terminal cysteines from SAP-102 tightly bind to zinc. And, appending the N terminus of SAP-102 to PSD-95 results in localization of the chimera to both axons and dendrites. These data suggest that lipid modifications and heavy metal associations with the N termini of MAGUKs mediate differential functions and subcellular localizations of these synaptic scaffolds.

  4. Halide binding and inhibition of laccase copper clusters: the role of reorganization energy.

    PubMed

    Kepp, Kasper P

    2015-01-20

    Laccase-like proteins are multicopper oxidases involved in several biological and industrial processes. Their application is commonly limited due to inhibition by fluoride and chloride, and as-isolated proteins are often substantially activated by heat, suggesting that multiple redox states can complicate characterization. Understanding these processes at the molecular level is thus desirable but theoretically unexplored. This paper reports systematic calculations of geometries, reorganization energies, and ionization energies for all partly oxidized states of the trinuclear copper clusters in realistic models with ∼200 atoms. Corrections for scalar-relativistic effects, dispersion, and thermal effects were estimated. Fluoride, chloride, hydroxide, or water was bound to the T2 copper site of the oxidized resting state, and the peroxo intermediate was also computed for reference. Antiferromagnetic coupling, assigned oxidation states, and general structures were consistent with known spectroscopic data. The computations show that (i) ligands bound to the T2 site substantially increase the reorganization energy of the second reduction of the resting state and reduce the redox potentials, providing a possible mechanism for inhibition; (ii) the reorganization energy is particularly large for F(-) but also high for Cl(-), consistent with the experimental tendency of inhibition; (iii) reduction leads to release of Cl(-) from the T2 site, suggesting a mechanism for heat/reduction activation of laccases by dissociation of inhibiting halides or hydroxide from T2.

  5. The role of a basic amino acid cluster in target site selection and non-specific binding of bZIP peptides to DNA.

    PubMed Central

    Metallo, S J; Paolella, D N; Schepartz, A

    1997-01-01

    The ability of a transcription factor to locate and bind its cognate DNA site in the presence of closely related sites and a vast array of non-specific DNA is crucial for cell survival. The CREB/ATF family of transcription factors is an important group of basic region leucine zipper (bZIP) proteins that display high affinity for the CRE site and low affinity for the closely related AP-1 site. Members of the CREB/ATF family share in common a cluster of basic amino acids at the N-terminus of their bZIP element. This basic cluster is necessary and sufficient to cause the CRE site to bend upon binding of a CREB/ATF protein. The possibility that DNA bending and CRE/AP-1 specificity were linked in CREB/ATF proteins was investigated using chimeric peptides derived from human CRE-BP1 (a member of the CREB/ATF family) and yeast GCN4, which lacks both a basic cluster and CRE/AP-1 specificity. Gain of function and loss of function experiments demonstrated that the basic cluster was not responsible for the CRE/AP-1 specificity displayed by all characterized CREB/ATF proteins. The basic cluster was, however, responsible for inducing very high affinity for non- specific DNA. It was further shown that basic cluster-containing peptides bind non-specific DNA in a random coil conformation. We postulate that the high non- specific DNA affinities of basic cluster-containing peptides result from cooperative electrostatic interactions with the phosphate backbone that do not require peptide organization. PMID:9224594

  6. IDENTIFICATION OF A MEMBRANE-LOCALIZED CYSTEINE CLUSTER NEAR THE SUBSTRATE BINDING SITES OF THE STREPTOCOCCUS EQUISIMILIS HYALURONAN SYNTHASE

    PubMed Central

    Kumari, Kshama; Weigel, Paul H.

    2005-01-01

    The membrane-bound hyaluronan synthase (HAS) from Streptococcus equisimilis (seHAS), which is the smallest Class I HAS, has four cysteine residues (positions 226, 262, 281, and 367) that are generally conserved within this family. Although Cys-null seHAS is still active, chemical modification of cysteine residues causes inhibition of wildtype enzyme (Kumari et al., J. Biol. Chem. 277, 13943, 2002). Here we studied the effects of N-ethylmaleimide (NEM) treatment on a panel of seHAS Cys-mutants to examine the structural and functional roles of the four cysteine residues in the activity of the enzyme. We found that Cys226, Cys262, and Cys281 are reactive with NEM, but that Cys367 is not. Substrate protection studies of wildtype seHAS and a variety of Cys-mutants revealed that binding of UDP-GlcUA, UDP-GlcNAc or UDP can protect Cys226 and Cys262 from NEM inhibition. Inhibition of the six double Cys-mutants of seHAS by sodium arsenite, which can crosslink vicinyl sulfhydryl groups, also supported the conclusion that Cys262 and Cys281 are close enough to be crosslinked. Similar results indicated that Cys281 and Cys367 are also very close in the active enzyme. We conclude that three of the four Cys residues in seHAS (Cys262, Cys281, and Cys367 ) are clustered very close together, that these Cys residues and Cys226 are located at the inner surface of the cell membrane, and that Cys226 and Cys262 are located in or near a UDP binding site. PMID:15616126

  7. SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster

    PubMed Central

    Mathai, Jinumary; Mittal, Smriti P. K.; Alam, Aftab; Ranade, Payal; Mogare, Devraj; Patel, Sonal; Saxena, Smita; Ghorai, Suvankar; Kulkarni, Abhijeet P.; Chattopadhyay, Samit

    2016-01-01

    Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-373. PMID:27671416

  8. The mouse salivary androgen-binding protein (ABP) gene cluster on chromosomes 7: characterization and evolutionary relationships.

    PubMed

    Laukaitis, Christina M; Dlouhy, Stephen R; Karn, Robert C

    2003-10-01

    Mouse salivary androgen-binding protein (ABP) is a pair of dimers, composed of an alpha subunit disulfide bridged to either a beta or a gamma subunit. It has been proposed that each subunit is encoded by a distinct gene: Abpa, Abpb, and Abpg for the alpha, beta, and gamma subunits, respectively. We report here the structures and sequences of the genes that encode these three subunits. Each gene has three exons separated by two introns. Mouse salivary ABP is a member of the secretoglobin family, and we compare the structure of the three ABP subunit genes to those of 18 other mammalian secretoglobins. We map the three genes as a gene cluster located 10 cM from the centromere of Chromosome (Chr) 7 and show that Abpa is the closest of the three to the gene for glucose phosphate isomerase (GPI) and that Abpg is the closest to the centromere, with Abpb mapping between them. Abpa is oriented in the opposite direction to Abpb and Abpg, with its 5' end directed toward their 5' ends. We compare the location of these genes with other secretoglobin genes in the mouse genome and with the known locations of secretoglobin genes in the human genome and present evidence that strong positive selection has driven the divergence of the coding regions of Abpb and Abpg since the putative duplication event that created them.

  9. FORMATION AND PROPERTIES OF ASTROPHYSICAL CARBONACEOUS DUST. I. AB-INITIO CALCULATIONS OF THE CONFIGURATION AND BINDING ENERGIES OF SMALL CARBON CLUSTERS

    SciTech Connect

    Mauney, Christopher; Lazzati, Davide; Buongiorno Nardelli, Marco

    2015-02-10

    The binding energies of n < 100 carbon clusters are calculated using the ab initio density functional theory code Quantum Espresso. Carbon cluster geometries are determined using several levels of classical techniques and further refined using density functional theory. The resulting energies are used to compute the work of cluster formation and the nucleation rate in a saturated, hydrogen-poor carbon gas. Compared to classical calculations that adopt the capillary approximation, we find that nucleation of carbon clusters is enhanced at low temperatures and depressed at high temperatures. This difference is ascribed to the different behavior of the critical cluster size. We find that the critical cluster size is at n = 27 or n = 8 for a broad range of temperatures and saturations, instead of being a smooth function of such parameters. The results of our calculations can be used to follow carbonaceous cluster/grain formation, stability, and growth in hydrogen-poor environments, such as the inner layers of core-collapse supernovae and supernova remnants.

  10. Binding of phosphoinositide-specific phospholipase C-zeta (PLC-zeta) to phospholipid membranes: potential role of an unstructured cluster of basic residues.

    PubMed

    Nomikos, Michail; Mulgrew-Nesbitt, Anna; Pallavi, Payal; Mihalyne, Gyongyi; Zaitseva, Irina; Swann, Karl; Lai, F Anthony; Murray, Diana; McLaughlin, Stuart

    2007-06-01

    Phospholipase C-zeta (PLC-zeta) is a sperm-specific enzyme that initiates the Ca2+ oscillations in mammalian eggs that activate embryo development. It shares considerable sequence homology with PLC-delta1, but lacks the PH domain that anchors PLC-delta1 to phosphatidylinositol 4,5-bisphosphate, PIP2. Thus it is unclear how PLC-zeta interacts with membranes. The linker region between the X and Y catalytic domains of PLC-zeta, however, contains a cluster of basic residues not present in PLC-delta1. Application of electrostatic theory to a homology model of PLC-zeta suggests this basic cluster could interact with acidic lipids. We measured the binding of catalytically competent mouse PLC-zeta to phospholipid vesicles: for 2:1 phosphatidylcholine/phosphatidylserine (PC/PS) vesicles, the molar partition coefficient, K, is too weak to be of physiological significance. Incorporating 1% PIP2 into the 2:1 PC/PS vesicles increases K about 10-fold, to 5x10(3) M-1, a biologically relevant value. Expressed fragments corresponding to the PLC-zeta X-Y linker region also bind with higher affinity to polyvalent than monovalent phosphoinositides on nitrocellulose filters. A peptide corresponding to the basic cluster (charge=+7) within the linker region, PLC-zeta-(374-385), binds to PC/PS vesicles with higher affinity than PLC-zeta, but its binding is less sensitive to incorporating PIP2. The acidic residues flanking this basic cluster in PLC-zeta may account for both these phenomena. FRET experiments suggest the basic cluster could not only anchor the protein to the membrane, but also enhance the local concentration of PIP2 adjacent to the catalytic domain.

  11. Dissection of RAP-LRP interactions: binding of RAP and RAP fragments to complement-like repeats 7 and 8 from ligand binding cluster II of LRP.

    PubMed

    Lazic, Ana; Dolmer, Klavs; Strickland, Dudley K; Gettins, Peter G W

    2006-06-15

    The receptor associated protein (RAP) is a three domain 38kDa ER-resident chaperone that helps folding of LRP and other LDL receptor family members and prevents premature binding of protein ligands. It competes strongly with all known LRP ligands. To further understanding of the specificity of RAP-LRP interactions, the binding of RAP and RAP fragments to two domains (CR7-CR8) from one of the main ligand-binding regions of LRP has been examined by 2D HSQC NMR spectroscopy and isothermal titration calorimetry. We found that RAP contains two binding sites for CR7-CR8, with the higher affinity site (K(d) approximately 1microM) located in the C-terminal two-thirds and the weaker site (K(d) approximately 5microM) in the N-terminal third of RAP. Residues from both CR7 and CR8 are involved in binding at each RAP site. The presence of more than one binding site on RAP for CR domains from LRP, together with the previous demonstration by others that RAP can bind to CR5-CR6 with comparably low affinities suggest an explanation for the dual roles of RAP as a folding chaperone and a tight competitive inhibitor of ligand binding.

  12. Pichia pastoris Fep1 is a [2Fe-2S] protein with a Zn finger that displays an unusual oxygen-dependent role in cluster binding

    PubMed Central

    Cutone, Antimo; Howes, Barry D.; Miele, Adriana E.; Miele, Rossella; Giorgi, Alessandra; Battistoni, Andrea; Smulevich, Giulietta; Musci, Giovanni; di Patti, Maria Carmela Bonaccorsi

    2016-01-01

    Fep1, the iron-responsive GATA factor from the methylotrophic yeast Pichia pastoris, has been characterised both in vivo and in vitro. This protein has two Cys2-Cys2 type zinc fingers and a set of four conserved cysteines arranged in a Cys-X5-Cys-X8-Cys-X2-Cys motif located between the two zinc fingers. Electronic absorption and resonance Raman spectroscopic analyses in anaerobic and aerobic conditions indicate that Fep1 binds iron in the form of a [2Fe-2S] cluster. Site-directed mutagenesis shows that replacement of the four cysteines with serine inactivates this transcriptional repressor. Unexpectedly, the inactive mutant is still able to bind a [2Fe-2S] cluster, employing two cysteine residues belonging to the first zinc finger. These two cysteine residues can act as alternative cluster ligands selectively in aerobically purified Fep1 wild type, suggesting that oxygen could play a role in Fep1 function by causing differential localization of the [Fe-S] cluster. PMID:27546548

  13. Human Mitochondrial Ferredoxin 1 (FDX1) and Ferredoxin 2 (FDX2) Both Bind Cysteine Desulfurase and Donate Electrons for Iron–Sulfur Cluster Biosynthesis

    PubMed Central

    2016-01-01

    Ferredoxins play an important role as an electron donor in iron–sulfur (Fe–S) cluster biosynthesis. Two ferredoxins, human mitochondrial ferredoxin 1 (FDX1) and human mitochondrial ferredoxin 2 (FDX2), are present in the matrix of human mitochondria. Conflicting results have been reported regarding their respective function in mitochondrial iron–sulfur cluster biogenesis. We report here biophysical studies of the interaction of these two ferredoxins with other proteins involved in mitochondrial iron–sulfur cluster assembly. Results from nuclear magnetic resonance spectroscopy show that both FDX1 and FDX2 (in both their reduced and oxidized states) interact with the protein complex responsible for cluster assembly, which contains cysteine desulfurase (NFS1), ISD11 (also known as LYRM4), and acyl carrier protein (Acp). In all cases, ferredoxin residues close to the Fe–S cluster are involved in the interaction with this complex. Isothermal titration calorimetry results showed that FDX2 binds more tightly to the cysteine desulfurase complex than FDX1 does. The reduced form of each ferredoxin became oxidized in the presence of the cysteine desulfurase complex when l-cysteine was added, leading to its conversion to l-alanine and the generation of sulfide. In an in vitro reaction, the reduced form of each ferredoxin was found to support Fe–S cluster assembly on ISCU; the rate of cluster assembly was faster with FDX2 than with FDX1. Taken together, these results show that both FDX1 and FDX2 can function in Fe–S cluster assembly in vitro. PMID:28001042

  14. Human Mitochondrial Ferredoxin 1 (FDX1) and Ferredoxin 2 (FDX2) Both Bind Cysteine Desulfurase and Donate Electrons for Iron-Sulfur Cluster Biosynthesis.

    PubMed

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

    2017-01-24

    Ferredoxins play an important role as an electron donor in iron-sulfur (Fe-S) cluster biosynthesis. Two ferredoxins, human mitochondrial ferredoxin 1 (FDX1) and human mitochondrial ferredoxin 2 (FDX2), are present in the matrix of human mitochondria. Conflicting results have been reported regarding their respective function in mitochondrial iron-sulfur cluster biogenesis. We report here biophysical studies of the interaction of these two ferredoxins with other proteins involved in mitochondrial iron-sulfur cluster assembly. Results from nuclear magnetic resonance spectroscopy show that both FDX1 and FDX2 (in both their reduced and oxidized states) interact with the protein complex responsible for cluster assembly, which contains cysteine desulfurase (NFS1), ISD11 (also known as LYRM4), and acyl carrier protein (Acp). In all cases, ferredoxin residues close to the Fe-S cluster are involved in the interaction with this complex. Isothermal titration calorimetry results showed that FDX2 binds more tightly to the cysteine desulfurase complex than FDX1 does. The reduced form of each ferredoxin became oxidized in the presence of the cysteine desulfurase complex when l-cysteine was added, leading to its conversion to l-alanine and the generation of sulfide. In an in vitro reaction, the reduced form of each ferredoxin was found to support Fe-S cluster assembly on ISCU; the rate of cluster assembly was faster with FDX2 than with FDX1. Taken together, these results show that both FDX1 and FDX2 can function in Fe-S cluster assembly in vitro.

  15. Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe–2S cluster

    PubMed Central

    Shimberg, Geoffrey D.; Michalek, Jamie L.; Oluyadi, Abdulafeez A.; Rodrigues, Andria V.; Zucconi, Beth E.; Neu, Heather M.; Ghosh, Shanchari; Sureschandra, Kanisha; Wilson, Gerald M.; Stemmler, Timothy L.; Michel, Sarah L. J.

    2016-01-01

    Cleavage and polyadenylation specificity factor 30 (CPSF30) is a key protein involved in pre-mRNA processing. CPSF30 contains five Cys3His domains (annotated as “zinc-finger” domains). Using inductively coupled plasma mass spectrometry, X-ray absorption spectroscopy, and UV-visible spectroscopy, we report that CPSF30 is isolated with iron, in addition to zinc. Iron is present in CPSF30 as a 2Fe–2S cluster and uses one of the Cys3His domains; 2Fe–2S clusters with a Cys3His ligand set are rare and notably have also been identified in MitoNEET, a protein that was also annotated as a zinc finger. These findings support a role for iron in some zinc-finger proteins. Using electrophoretic mobility shift assays and fluorescence anisotropy, we report that CPSF30 selectively recognizes the AU-rich hexamer (AAUAAA) sequence present in pre-mRNA, providing the first molecular-based evidence to our knowledge for CPSF30/RNA binding. Removal of zinc, or both zinc and iron, abrogates binding, whereas removal of just iron significantly lessens binding. From these data we propose a model for RNA recognition that involves a metal-dependent cooperative binding mechanism. PMID:27071088

  16. Characterization of Streptokinases from Group A Streptococci Reveals a Strong Functional Relationship That Supports the Coinheritance of Plasminogen-binding M Protein and Cluster 2b Streptokinase*

    PubMed Central

    Zhang, Yueling; Liang, Zhong; Hsueh, Hsing-Tse; Ploplis, Victoria A.; Castellino, Francis J.

    2012-01-01

    Group A streptococcus (GAS) strains secrete the protein streptokinase (SK), which functions by activating host human plasminogen (hPg) to plasmin (hPm), thus providing a proteolytic framework for invasive GAS strains. The types of SK secreted by GAS have been grouped into two clusters (SK1 and SK2) and one subcluster (SK2a and SK2b). SKs from cluster 1 (SK1) and cluster 2b (SK2b) display significant evolutionary and functional differences, and attempts to relate these properties to GAS skin or pharynx tropism and invasiveness are of great interest. In this study, using four purified SKs from each cluster, new relationships between plasminogen-binding group A streptococcal M (PAM) protein and SK2b have been revealed. All SK1 proteins efficiently activated hPg, whereas all subclass SK2b proteins only weakly activated hPg in the absence of PAM. Surface plasmon resonance studies revealed that the lower affinity of SK2b to hPg served as the basis for the attenuated activation of hPg by SK2b. Binding of hPg to either human fibrinogen (hFg) or PAM greatly enhanced activation of hPg by SK2b but minimally influenced the already effective activation of hPg by SK1. Activation of hPg in the presence of GAS cells containing PAM demonstrated that PAM is the only factor on the surface of SK2b-expressing cells that enabled the direct activation of hPg by SK2b. As the binding of hPg to PAM is necessary for hPg activation by SK2b, this dependence explains the coinherant relationship between PAM and SK2b and the ability of these particular strains to generate the proteolytic activity that disrupts the innate barriers that limit invasiveness. PMID:23086939

  17. From Function to Phenotype: Impaired DNA Binding and Clustering Correlates with Clinical Severity in Males with Missense Mutations in MECP2

    PubMed Central

    Sheikh, Taimoor I.; Ausió, Juan; Faghfoury, Hannah; Silver, Josh; Lane, Jane B.; Eubanks, James H.; MacLeod, Patrick; Percy, Alan K.; Vincent, John B.

    2016-01-01

    Mutations in the MECP2 gene cause Rett syndrome (RTT). MeCP2 binds to chromocentric DNA through its methyl CpG-binding domain (MBD) to regulate gene expression. In heterozygous females the variable phenotypic severity is modulated by non-random X-inactivation, thus making genotype-phenotype comparisons unreliable. However, genotype-phenotype correlations in males with hemizygousMECP2 mutations can provide more accurate insights in to the true biological effect of specific mutations. Here, we compared chromatin organization and binding dynamics for twelve MeCP2 missense mutations (including two novel and the five most common MBD missense RTT mutations) and identifiedacorrelation with phenotype in hemizygous males. We observed impaired interaction of MeCP2-DNA for mutations around the MBD-DNA binding interface, and defective chromatin clustering for distal MBD mutations. Furthermore, binding and mobility dynamics show a gradient of impairment depending on the amino acid properties and tertiary structure within the MBD. Interestingly, a wide range of phenotypic/clinical severity, ranging from neonatal encephalopathy to mild psychiatric abnormalities were observed and all are consistent with our functional/molecular results. Overall, clinical severity showed a direct correlation with the functional impairment of MeCP2. These mechanistic and phenotypic correlations of MeCP2 mutations will enable improved and individualized diagnostics, and may lead to personalized therapeutic interventions. PMID:27929079

  18. Detection and quantitative analysis of two independent binding modes of a small ligand responsible for DC-SIGN clustering.

    PubMed

    Guzzi, C; Alfarano, P; Sutkeviciute, I; Sattin, S; Ribeiro-Viana, R; Fieschi, F; Bernardi, A; Weiser, J; Rojo, J; Angulo, J; Nieto, P M

    2016-01-07

    DC-SIGN (dendritic cell-specific ICAM-3 grabbing non-integrin) is a C-type lectin receptor (CLR) present, mainly in dendritic cells (DCs), as one of the major pattern recognition receptors (PRRs). This receptor has a relevant role in viral infection processes. Recent approaches aiming to block DC-SIGN have been presented as attractive anti-HIV strategies. DC-SIGN binds mannose or fucose-containing carbohydrates from viral proteins such as the HIV envelope glycoprotein gp120. We have previously demonstrated that multivalent dendrons bearing multiple copies of glycomimetic ligands were able to inhibit DC-SIGN-dependent HIV infection in cervical explant models. Optimization of glycomimetic ligands requires detailed characterization and analysis of their binding modes because they notably influence binding affinities. In a previous study we characterized the binding mode of DC-SIGN with ligand 1, which shows a single binding mode as demonstrated by NMR and X-ray crystallography. In this work we report the binding studies of DC-SIGN with pseudotrisaccharide 2, which has a larger affinity. Their binding was analysed by TR-NOESY and STD NMR experiments, combined with the CORCEMA-ST protocol and molecular modelling. These studies demonstrate that in solution the complex cannot be explained by a single binding mode. We describe the ensemble of ligand bound modes that best fit the experimental data and explain the higher inhibition values found for ligand 2.

  19. A Histidine Cluster in the Cytoplasmic Domain of the Na-H Exchanger NHE1 Confers pH-sensitive Phospholipid Binding and Regulates Transporter Activity.

    PubMed

    Webb, Bradley A; White, Katharine A; Grillo-Hill, Bree K; Schönichen, André; Choi, Changhoon; Barber, Diane L

    2016-11-11

    The Na-H exchanger NHE1 contributes to intracellular pH (pHi) homeostasis in normal cells and the constitutively increased pHi in cancer. NHE1 activity is allosterically regulated by intracellular protons, with greater activity at lower pHi However, the molecular mechanism for pH-dependent NHE1 activity remains incompletely resolved. We report that an evolutionarily conserved cluster of histidine residues located in the C-terminal cytoplasmic domain between two phosphatidylinositol 4,5-bisphosphate binding sites (PI(4,5)P2) of NHE1 confers pH-dependent PI(4,5)P2 binding and regulates NHE1 activity. A GST fusion of the wild type C-terminal cytoplasmic domain of NHE1 showed increased maximum PI(4,5)P2 binding at pH 7.0 compared with pH 7.5. However, pH-sensitive binding is abolished by substitutions of the His-rich cluster to arginine (RXXR3) or alanine (AXXA3), mimicking protonated and neutral histidine residues, respectively, and the RXXR3 mutant had significantly greater PI(4,5)P2 binding than AXXA3. When expressed in cells, NHE1 activity and pHi were significantly increased with NHE1-RXXR3 and decreased with NHE1-AXXA3 compared with wild type NHE1. Additionally, fibroblasts expressing NHE1-RXXR3 had significantly more contractile actin filaments and focal adhesions compared with fibroblasts expressing wild type NHE1, consistent with increased pHi enabling cytoskeletal remodeling. These data identify a molecular mechanism for pH-sensitive PI(4,5)P2 binding regulating NHE1 activity and suggest that the evolutionarily conserved cluster of four histidines in the proximal cytoplasmic domain of NHE1 may constitute a proton modifier site. Moreover, a constitutively activated NHE1-RXXR3 mutant is a new tool that will be useful for studying how increased pHi contributes to cell behaviors, most notably the biology of cancer cells.

  20. Binding water to a PEG-linked flexible bichromophore: IR spectra of diphenoxyethane-(H{sub 2}O){sub n} clusters, n = 2-4

    SciTech Connect

    Walsh, Patrick S.; Buchanan, Evan G.; Gord, Joseph R.; Zwier, Timothy S.

    2015-04-21

    The single-conformation infrared (IR) and ultraviolet (UV) spectroscopies of neutral 1,2-diphenoxyethane-(H{sub 2}O){sub n} clusters with n = 2-4 (labeled henceforth as 1:n) have been studied in a molecular beam using a combination of resonant two-photon ionization, IR-UV holeburning, and resonant ion-dip infrared (RIDIR) spectroscopies. Ground state RIDIR spectra in the OH and CH stretch regions were used to provide firm assignments for the structures of the clusters by comparing the experimental spectra with the predictions of calculations carried out at the density functional M05-2X/6-31+G(d) level of theory. At all sizes in this range, the water molecules form water clusters in which all water molecules engage in a single H-bonded network. Selective binding to the tgt monomer conformer of 1,2-diphenoxyethane (C{sub 6}H{sub 5}-O-CH{sub 2}-CH{sub 2}-O-C{sub 6}H{sub 5}, DPOE) occurs, since this conformer provides a binding pocket in which the two ether oxygens and two phenyl ring π clouds can be involved in stabilizing the water cluster. The 1:2 cluster incorporates a water dimer “chain” bound to DPOE much as it is in the 1:1 complex [E. G. Buchanan et al., J. Phys. Chem. Lett. 4, 1644 (2013)], with primary attachment via a double-donor water that bridges the ether oxygen of one phenoxy group and the π cloud of the other. Two conformers of the 1:3 cluster are observed and characterized, one that extends the water chain to a third molecule (1:3 chain) and the other incorporating a water trimer cycle (1:3 cycle). A cyclic water structure is also observed for the 1:4 cluster. These structural characterizations provide a necessary foundation for studies of the perturbations imposed on the two close-lying S{sub 1}/S{sub 2} excited states of DPOE considered in the adjoining paper [P. S. Walsh et al., J. Chem. Phys. 142, 154304 (2015)].

  1. Binding water clusters to an aromatic-rich hydrophobic pocket: [2.2.2]paracyclophane-(H2O)n, n = 1-5.

    PubMed

    Buchanan, Evan G; Zwier, Timothy S

    2014-09-18

    [2.2.2]Paracylcophane (tricyclophane, TCP) is a macrocycle with three phenyl substituents linked by ethyl bridges (-CH2CH2-) in the para-position, forming an aromatic-rich pocket capable of binding various substituents, including nature's solvent, water. Building on previous work [Buchanan, E. G.; et al. J. Chem. Phys. 2013, 138, 064308] that reported on the ground state conformational preferences of TCP, the focus of the present study is on the infrared and ultraviolet spectroscopy of TCP-(H2O)n clusters with n = 1-5. Resonant two-photon ionization (R2PI) was used to interrogate the mass selected electronic spectrum of the clusters, reporting on the perturbations imposed on the electronic states of TCP as the size of the water clusters bound to it vary in size from n = 1-5. The TCP-(H2O)n S0-S1 origins are shifted to lower frequency from the monomer, indicating an increased binding energy of the water or water network in the excited state. Ground state resonant ion-dip infrared (RIDIR) spectra of TCP-(H2O)n (n = 1-5) clusters were recorded in the OH stretch region, which probes the H-bonded water networks present and the perturbations imposed on them by TCP. The experimental frequencies are compared with harmonic vibrational frequencies calculated using density functional theory (DFT) with the dispersion-corrected functional ωB97X-D and a 6-311+g(d,p) basis set, providing firm assignments for their H-bonding structures. The H2O molecule in TCP-(H2O)1 sits on top of the binding pocket, donating both of its hydrogen atoms to the aromatic-rich interior of the monomer. The antisymmetric stretch fundamental of H2O in the complex is composed of a closely spaced set of transitions that likely reflect contributions from both para- and ortho-forms of H2O due to internal rotation of the H2O in the binding pocket. TCP-(H2O)2 also exists in a single conformational isomer that retains the same double-donor binding motif for the first water molecule, with the second H2O acting

  2. Breaking the bottleneck: Use of molecular tailoring approach for the estimation of binding energies at MP2/CBS limit for large water clusters

    NASA Astrophysics Data System (ADS)

    Singh, Gurmeet; Nandi, Apurba; Gadre, Shridhar R.

    2016-03-01

    A pragmatic method based on the molecular tailoring approach (MTA) for estimating the complete basis set (CBS) limit at Møller-Plesset second order perturbation (MP2) theory accurately for large molecular clusters with limited computational resources is developed. It is applied to water clusters, (H2O)n (n = 7, 8, 10, 16, 17, and 25) optimized employing aug-cc-pVDZ (aVDZ) basis-set. Binding energies (BEs) of these clusters are estimated at the MP2/aug-cc-pVNZ (aVNZ) [N = T, Q, and 5 (whenever possible)] levels of theory employing grafted MTA (GMTA) methodology and are found to lie within 0.2 kcal/mol of the corresponding full calculation MP2 BE, wherever available. The results are extrapolated to CBS limit using a three point formula. The GMTA-MP2 calculations are feasible on off-the-shelf hardware and show around 50%-65% saving of computational time. The methodology has a potential for application to molecular clusters containing ˜100 atoms.

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

    PubMed Central

    2012-01-01

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

  4. Unconventional ionic hydrogen bonds: CH +⋯π (C tbnd C) binding energies and structures of benzene + rad (acetylene) 1-4 clusters

    NASA Astrophysics Data System (ADS)

    Soliman, Abdel-Rahman; Hamid, Ahmed M.; Abrash, Samuel A.; El-Shall, M. Samy

    2012-01-01

    Rapid condensation of acetylene onto the benzene cation with the addition of up to eight acetylene molecules is observed in the gas phase at 120-140 K forming the C6D6rad +(C2H2)n clusters. The binding energies and entropy changes of the stepwise condensation of the first four acetylene molecules onto the benzene cation have been measured and correlated with the calculated lowest energy isomers. The measured binding energies (3-4 kcal/mol) reflect weak charge-induced dipole and (benzene) Csbnd Hδ+⋯π Ctbnd C (acetylene) hydrogen bonding interactions. Associative charge transfer is suggested to activate the cyclization of three acetylene molecules to form a benzene molecule (C6H6).

  5. Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster.

    PubMed

    Lee, Brian M; Buck-Koehntop, Bethany A; Martinez-Yamout, Maria A; Dyson, H Jane; Wright, Peter E

    2007-08-31

    Churchill is a zinc-containing protein that is involved in neural induction during embryogenesis. At the time of its discovery, it was thought on the basis of sequence alignment to contain two zinc fingers of the C4 type. Further, binding of an N-terminal GST-Churchill fusion protein to a particular DNA sequence was demonstrated by immunoprecipitation selection assay, suggesting that Churchill may function as a transcriptional regulator by sequence-specific DNA binding. We show by NMR solution structure determination that, far from containing canonical C4 zinc fingers, the protein contains three bound zinc ions in novel coordination sites, including an unusual binuclear zinc cluster. The secondary structure of Churchill is also unusual, consisting of a highly solvent-exposed single-layer beta-sheet. Hydrogen-deuterium exchange and backbone relaxation measurements reveal that Churchill is unusually dynamic on a number of time scales, with the exception of regions surrounding the zinc coordinating sites, which serve to stabilize the otherwise unstructured N terminus and the single-layer beta-sheet. No binding of Churchill to the previously identified DNA sequence could be detected, and extensive searches using DNA sequence selection techniques could find no other DNA sequence that was bound by Churchill. Since the N-terminal amino acids of Churchill form part of the zinc-binding motif, the addition of a fusion protein at the N terminus causes loss of zinc and unfolding of Churchill. This observation most likely explains the published DNA-binding results, which would arise due to non-specific interaction of the unfolded protein in the immunoprecipitation selection assay. Since Churchill does not appear to bind DNA, we suggest that it may function in embryogenesis as a protein-interaction factor.

  6. Strategies for maximizing ATP supply in the microsporidian Encephalitozoon cuniculi: direct binding of mitochondria to the parasitophorous vacuole and clustering of the mitochondrial porin VDAC.

    PubMed

    Hacker, Christian; Howell, Matthew; Bhella, David; Lucocq, John

    2014-04-01

    Microsporidia are obligate intracellular parasites with extremely reduced genomes and a dependence on host-derived ATP. The microsporidium Encephalitozoon cuniculi proliferates within a membranous vacuole and we investigated how the ATP supply is optimized at the vacuole-host interface. Using spatial EM quantification (stereology), we found a single layer of mitochondria coating substantial proportions of the parasitophorous vacuole. Mitochondrial binding occurred preferentially over the vegetative 'meront' stages of the parasite, which bulged into the cytoplasm, thereby increasing the membrane surface available for mitochondrial interaction. In a broken cell system mitochondrial binding was maintained and was typified by electron dense structures (< 10 nm long) bridging between outer mitochondrial and vacuole membranes. In broken cells mitochondrial binding was sensitive to a range of protease treatments. The function of directly bound mitochondria, as measured by the membrane potential sensitive dye JC-1, was indistinguishable from other mitochondria in the cell although there was a generalized depression of the membrane potential in infected cells. Finally, quantitative immuno-EM revealed that the ATP-delivering mitochondrial porin, VDAC, was concentrated atthe mitochondria-vacuole interaction site. Thus E. cuniculi appears to maximize ATP supply by direct binding of mitochondria to the parasitophorous vacuole bringing this organelle within 0.020 microns of the growing vegetative form of the parasite. ATP-delivery is further enhanced by clustering of ATP transporting porins in those regions of the outer mitochondrial membrane lying closest to the parasite.

  7. Interaction of frataxin, an iron binding protein, with IscU of Fe-S clusters biogenesis pathway and its upregulation in AmpB resistant Leishmania donovani.

    PubMed

    Zaidi, Amir; Singh, Krishn Pratap; Anwar, Shadab; Suman, Shashi S; Equbal, Asif; Singh, Kuljit; Dikhit, Manas R; Bimal, Sanjeeva; Pandey, Krishna; Das, Pradeep; Ali, Vahab

    2015-08-01

    Leishmania donovani is a unicellular protozoon parasite that causes visceral leishmaniasis (VL), which is a fatal disease if left untreated. Certain Fe-S proteins of the TCA cycle and respiratory chain have been found in the Leishmania parasite but the precise mechanisms for their biogenesis and the maturation of Fe-S clusters remains unknown. Fe-S clusters are ubiquitous cofactors of proteins that perform critical cellular functions. The clusters are biosynthesized by the mitochondrial Iron-Sulphur Cluster (ISC) machinery with core protein components that include the catalytic cysteine desulphurase IscS, the scaffold proteins IscU and IscA, and frataxin as an iron carrier/donor. However, no information regarding frataxin, its regulation, or its role in drug resistance is available for the Leishmania parasite. In this study, we characterized Ld-frataxin to investigate its role in the ISC machinery of L. donovani. We expressed and purified the recombinant Ld-frataxin protein and observed its interaction with Ld-IscU by co-purification and pull-down assay. Furthermore, we observed that the cysteine desulphurase activity of the purified Ld-IscS protein was stimulated in the presence of Ld-frataxin and Ld-IscU, particularly in the presence of iron; neither Ld-frataxin nor Ld-IscU alone had significant effects on Ld-IscS activity. Interestingly, RT-PCR and western blotting showed that Ld-frataxin is upregulated in AmpB-resistant isolates compared to sensitive strains, which may support higher Fe-S protein activity in AmpB-resistant L. donovani. Additionally, Ld-frataxin was localized in the mitochondria, as revealed by digitonin fractionation and indirect immunofluorescence. Thus, our results suggest the role of Ld-frataxin as an iron binding/carrier protein for Fe-S cluster biogenesis that physically interacts with other core components of the ISC machinery within the mitochondria.

  8. Asp1 from Schizosaccharomyces pombe binds a [2Fe-2S](2+) cluster which inhibits inositol pyrophosphate 1-phosphatase activity.

    PubMed

    Wang, Huanchen; Nair, Vasudha S; Holland, Ashley A; Capolicchio, Samanta; Jessen, Henning J; Johnson, Michael K; Shears, Stephen B

    2015-10-27

    Iron-sulfur (Fe-S) clusters are widely distributed protein cofactors that are vital to cellular biochemistry and the maintenance of bioenergetic homeostasis, but to our knowledge, they have never been identified in any phosphatase. Here, we describe an iron-sulfur cluster in Asp1, a dual-function kinase/phosphatase that regulates cell morphogenesis in Schizosaccharomyces pombe. Full-length Asp1, and its phosphatase domain (Asp1(371-920)), were each heterologously expressed in Escherichia coli. The phosphatase activity is exquisitely specific: it hydrolyzes the 1-diphosphate from just two members of the inositol pyrophosphate (PP-InsP) signaling family, namely, 1-InsP7 and 1,5-InsP8. We demonstrate that Asp1 does not hydrolyze either InsP6, 2-InsP7, 3-InsP7, 4-InsP7, 5-InsP7, 6-InsP7, or 3,5-InsP8. We also recorded 1-phosphatase activity in a human homologue of Asp1, hPPIP5K1, which was heterologously expressed in Drosophila S3 cells with a biotinylated N-terminal tag, and then isolated from cell lysates with avidin beads. Purified, recombinant Asp1(371-920) contained iron and acid-labile sulfide, but the stoichiometry (0.8 atoms of each per protein molecule) indicates incomplete iron-sulfur cluster assembly. We reconstituted the Fe-S cluster in vitro under anaerobic conditions, which increased the stoichiometry to approximately 2 atoms of iron and acid-labile sulfide per Asp1 molecule. The presence of a [2Fe-2S](2+) cluster in Asp1(371-920) was demonstrated by UV-visible absorption, resonance Raman spectroscopy, and electron paramagnetic resonance spectroscopy. We determined that this [2Fe-2S](2+) cluster is unlikely to participate in redox chemistry, since it rapidly degraded upon reduction by dithionite. Biochemical and mutagenic studies demonstrated that the [2Fe-2S](2+) cluster substantially inhibits the phosphatase activity of Asp1, thereby increasing its net kinase activity.

  9. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential.

    PubMed

    Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand

    2015-03-19

    The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the

  10. Binding of Hyaluronan to the Native Lymphatic Vessel Endothelial Receptor LYVE-1 Is Critically Dependent on Receptor Clustering and Hyaluronan Organization*

    PubMed Central

    Lawrance, William; Banerji, Suneale; Day, Anthony J.; Bhattacharjee, Shaumick; Jackson, David G.

    2016-01-01

    The lymphatic endothelial receptor LYVE-1 has been implicated in both uptake of hyaluronan (HA) from tissue matrix and in facilitating transit of leukocytes and tumor cells through lymphatic vessels based largely on in vitro studies with recombinant receptor in transfected fibroblasts. Curiously, however, LYVE-1 in lymphatic endothelium displays little if any binding to HA in vitro, and this has led to the conclusion that the native receptor is functionally silenced, a feature that is difficult to reconcile with its proposed in vivo functions. Nonetheless, as we reported recently, LYVE-1 can function as a receptor for HA-encapsulated Group A streptococci and mediate lymphatic dissemination in mice. Here we resolve these paradoxical findings and show that the capacity of LYVE-1 to bind HA is strictly dependent on avidity, demanding appropriate receptor self-association and/or HA multimerization. In particular, we demonstrate the prerequisite of a critical LYVE-1 threshold density and show that HA binding may be elicited in lymphatic endothelium by surface clustering with divalent LYVE-1 mAbs. In addition, we show that cross-linking of biotinylated HA in streptavidin multimers or supramolecular complexes with the inflammation-induced protein TSG-6 enables binding even in the absence of LYVE-1 cross-linking. Finally, we show that endogenous HA on the surface of macrophages can engage LYVE-1, facilitating their adhesion and transit across lymphatic endothelium. These results reveal LYVE-1 as a low affinity receptor tuned to discriminate between different HA configurations through avidity and establish a new mechanistic basis for the functions ascribed to LYVE-1 in matrix HA binding and leukocyte trafficking in vivo. PMID:26823460

  11. Binding of Hyaluronan to the Native Lymphatic Vessel Endothelial Receptor LYVE-1 Is Critically Dependent on Receptor Clustering and Hyaluronan Organization.

    PubMed

    Lawrance, William; Banerji, Suneale; Day, Anthony J; Bhattacharjee, Shaumick; Jackson, David G

    2016-04-08

    The lymphatic endothelial receptor LYVE-1 has been implicated in both uptake of hyaluronan (HA) from tissue matrix and in facilitating transit of leukocytes and tumor cells through lymphatic vessels based largely onin vitrostudies with recombinant receptor in transfected fibroblasts. Curiously, however, LYVE-1 in lymphatic endothelium displays little if any binding to HAin vitro, and this has led to the conclusion that the native receptor is functionally silenced, a feature that is difficult to reconcile with its proposedin vivofunctions. Nonetheless, as we reported recently, LYVE-1 can function as a receptor for HA-encapsulated Group A streptococci and mediate lymphatic dissemination in mice. Here we resolve these paradoxical findings and show that the capacity of LYVE-1 to bind HA is strictly dependent on avidity, demanding appropriate receptor self-association and/or HA multimerization. In particular, we demonstrate the prerequisite of a critical LYVE-1 threshold density and show that HA binding may be elicited in lymphatic endothelium by surface clustering with divalent LYVE-1 mAbs. In addition, we show that cross-linking of biotinylated HA in streptavidin multimers or supramolecular complexes with the inflammation-induced protein TSG-6 enables binding even in the absence of LYVE-1 cross-linking. Finally, we show that endogenous HA on the surface of macrophages can engage LYVE-1, facilitating their adhesion and transit across lymphatic endothelium. These results reveal LYVE-1 as a low affinity receptor tuned to discriminate between different HA configurations through avidity and establish a new mechanistic basis for the functions ascribed to LYVE-1 in matrix HA binding and leukocyte traffickingin vivo.

  12. A coupled-cluster study on the noble gas binding ability of metal cyanides versus metal halides (metal = Cu, Ag, Au).

    PubMed

    Pan, Sudip; Gupta, Ashutosh; Saha, Ranajit; Merino, Gabriel; Chattaraj, Pratim K

    2015-11-05

    A coupled-cluster study is carried out to investigate the efficacy of metal(I) cyanide (MCN; M = Cu, Ag, Au) compounds to bind with noble gas (Ng) atoms. The M-Ng bond dissociation energy, enthalpy change, and Gibbs free energy change for the dissociation processes producing Ng and MCN are computed to assess the stability of NgMCN compounds. The Ng binding ability of MCN is then compared with the experimentally detected NgMX (X = F, Cl, Br) compounds. While CuCN and AgCN have larger Ng binding ability than those of MCl and MBr (M = Cu, Ag), AuCN shows larger efficacy toward bond formation with Ng than that of AuBr. Natural bond orbital analysis, energy decomposition analysis in conjunction with the natural orbital for chemical valence theory, and the topological analysis of the electron density are performed to understand the nature of interaction occurring in between Ng and MCN. The Ng-M bonds in NgMCN are found comprise an almost equal contribution from covalent and electrostatic types of interactions. The different electron density descriptors also reveal the partial covalent character in the concerned bonds.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2010-12-15

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

  15. Probing the C-H⋅⋅⋅π weak hydrogen bond in anesthetic binding: the sevoflurane-benzene cluster.

    PubMed

    Seifert, Nathan A; Zaleski, Daniel P; Pérez, Cristóbal; Neill, Justin L; Pate, Brooks H; Vallejo-López, Montserrat; Lesarri, Alberto; Cocinero, Emilio J; Castaño, Fernando; Kleiner, Isabelle

    2014-03-17

    Cooperativity between weak hydrogen bonds can be revealed in molecular clusters isolated in the gas phase. Here we examine the structure, internal dynamics, and origin of the weak intermolecular forces between sevoflurane and a benzene molecule, using multi-isotopic broadband rotational spectra. This heterodimer is held together by a primary C-H⋅⋅⋅π hydrogen bond, assisted by multiple weak C-H⋅⋅⋅F interactions. The multiple nonbonding forces hinder the internal rotation of benzene around the isopropyl C-H bond in sevoflurane, producing detectable quantum tunneling effects in the rotational spectrum.

  16. Conformational landscape of the human immunodeficiency virus type 1 reverse transcriptase non-nucleoside inhibitor binding pocket: lessons for inhibitor design from a cluster analysis of many crystal structures.

    PubMed

    Paris, Kristina A; Haq, Omar; Felts, Anthony K; Das, Kalyan; Arnold, Eddy; Levy, Ronald M

    2009-10-22

    Clustering of 99 available X-ray crystal structures of HIV-1 reverse transcriptase (RT) at the flexible non-nucleoside inhibitor binding pocket (NNIBP) provides information about features of the conformational landscape for binding non-nucleoside inhibitors (NNRTIs), including effects of mutation and crystal forms. The ensemble of NNIBP conformations is separated into eight discrete clusters based primarily on the position of the functionally important primer grip, the displacement of which is believed to be one of the mechanisms of inhibition of RT. Two of these clusters are populated by structures in which the primer grip exhibits novel conformations that differ from the predominant cluster by over 4 A and are induced by the unique inhibitors capravirine and rilpivirine/TMC278. This work identifies a new conformation of the NNIBP that may be used to design NNRTIs. It can also be used to guide more complete exploration of the NNIBP free energy landscape using advanced sampling techniques.

  17. A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL.

    PubMed

    Cantalapiedra, Carlos P; Contreras-Moreira, Bruno; Silvar, Cristina; Perovic, Dragan; Ordon, Frank; Gracia, María Pilar; Igartua, Ernesto; Casas, Ana M

    2016-07-01

    Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site-leucine-rich repeat containing protein) genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation) in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of NGS (next-generation sequencing) tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.

  18. Profiling the binding motif between Be and Mg in the ground state via a single-reference coupled cluster method

    NASA Astrophysics Data System (ADS)

    Sinha Mahapatra, Uttam; Banerjee, Debi; Chaudhuri, Rajat K.; Chattopadhyay, Sudip

    2015-06-01

    We present a study on the performance of our iterative triples correction for the coupled cluster singles and doubles excitations (CCSDT-1a+d) method for computation of potential energy surface (PES), spectroscopic constants, and vibrational spectrum for the ground state (X1Σ+) BeMg, where the ostensible inadequacy of the CCSD and CCSD(T) methods is quite expected. We compare our results with those obtained using state-of-the-art multireference configuration interaction (MRCI) investigations reported earlier by Kerkines and Nicolaides. Our estimated dissociation energy (417.37 cm-1), equilibrium distance (3.285 Å), and vibrational frequency (82.32 cm-1) are in good agreement with recent results of advanced MRCI calculations for X1Σ+ BeMg PES, which exhibits a shallow well of 469.4 cm-1 with a minimum at 3.241 Å and a harmonic vibrational frequency of 85.7 cm-1. Very weakly bound nature of X1Σ+ BeMg is clearly reflected from these values. In accord with MRCI studies, a comparison of BeMg with iso-valence weakly bound ground-state species, Be2 and Mg2, suggests that its characteristics do not exhibit any resemblance to Be2 rather, it shows a close kinship to Mg2. The agreement of our derived vibrational levels with those obtained via the high-level MRCI calculations is very encouraging reflecting the potential of the suitably modified single-reference coupled cluster (SRCC) method, CCSDT-1a+d as a tool for the study of multireference van der Waals systems.

  19. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    SciTech Connect

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  20. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    PubMed Central

    2016-01-01

    Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons. PMID:27698666

  1. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    PubMed

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

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

    PubMed Central

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

    2012-01-01

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

  3. The role of synaptotagmin I C2A calcium-binding domain in synaptic vesicle clustering during synapse formation

    PubMed Central

    Gardzinski, Peter; Lee, David W K; Fei, Guang-He; Hui, Kwokyin; Huang, Guan J; Sun, Hong-Shuo; Feng, Zhong-Ping

    2007-01-01

    Synaptic vesicles aggregate at the presynaptic terminal during synapse formation via mechanisms that are poorly understood. Here we have investigated the role of the putative calcium sensor synaptotagmin I in vesicle aggregation during the formation of soma–soma synapses between identified partner cells using a simple in vitro synapse model in the mollusc Lymnaea stagnalis. Immunocytochemistry, optical imaging and electrophysiological recording techniques were used to monitor synapse formation and vesicle localization. Within 6 h, contact between appropriate synaptic partner cells up-regulated global synaptotagmin I expression, and induced a localized aggregation of synaptotagmin I at the contact site. Cell contacts between non-synaptic partner cells did not affect synaptotagmin I expression. Application of an human immunodeficiency virus type-1 transactivator (HIV-1 TAT)-tagged peptide corresponding to loop 3 of the synaptotagmin I C2A domain prevented synaptic vesicle aggregation and synapse formation. By contrast, a TAT-tagged peptide containing the calcium-binding motif of the C2B domain did not affect synaptic vesicle aggregation or synapse formation. Calcium imaging with Fura-2 demonstrated that TAT–C2 peptides did not alter either basal or evoked intracellular calcium levels. These results demonstrate that contact with an appropriate target cell is necessary to initiate synaptic vesicle aggregation during nascent synapse formation and that the initial aggregation of synaptic vesicles is dependent on loop 3 of the C2A domain of synaptotagmin I. PMID:17317745

  4. Exploring the correlation between network structure and electron binding energy in the (H2O)7- cluster through isomer-photoselected vibrational predissociation spectroscopy and ab initio calculations: Addressing complexity beyond types I-III

    NASA Astrophysics Data System (ADS)

    Roscioli, Joseph R.; Hammer, Nathan I.; Johnson, Mark A.; Diri, Kadir; Jordan, Kenneth D.

    2008-03-01

    We report a combined photoelectron and vibrational spectroscopy study of the (H2O)7- cluster anions in order to correlate structural changes with the observed differences in electron binding energies of the various isomers. Photoelectron spectra of the (H2O)7-ṡArm clusters are obtained over the range of m =0-10. These spectra reveal the formation of a new isomer (I') for m >5, the electron binding energy of which is about 0.15eV higher than that of the type I form previously reported to be the highest binding energy species [Coe et al., J. Chem. Phys. 92, 3980 (1990)]. Isomer-selective vibrational predissociation spectra are obtained using both the Ar dependence of the isomer distribution and photochemical depopulation of the more weakly (electron) binding isomers. The likely structures of the isomers at play are identified with the aid of electronic structure calculations, and the electron binding energies, as well as harmonic vibrational spectra, are calculated for 28 low-lying forms for comparison with the experimental results. The HOH bending spectrum of the low binding type II form is dominated by a band that is moderately redshifted relative to the bending origin of the bare water molecule. Calculations trace this feature primarily to the bending vibration localized on a water molecule in which a dangling H atom points toward the electron cloud. Both higher binding forms (I and I') display the characteristic patterns in the bending and OH stretching regions signaling electron attachment primarily to a water molecule in an AA binding site, a persistent motif found in non-isomer-selective spectra of the clusters up to (H2O)50-.

  5. Surface plasmon resonance and NMR analyses of anti Tn-antigen MLS128 monoclonal antibody binding to two or three consecutive Tn-antigen clusters.

    PubMed

    Matsumoto-Takasaki, Ayano; Hanashima, Shinya; Aoki, Ami; Yuasa, Noriyuki; Ogawa, Haruhiko; Sato, Reiko; Kawakami, Hiroko; Mizuno, Mamoru; Nakada, Hiroshi; Yamaguchi, Yoshiki; Fujita-Yamaguchi, Yoko

    2012-03-01

    Tn-antigens are tumour-associated carbohydrate antigens that are involved in metastatic processes and are associated with a poor prognosis. MLS128 monoclonal antibody recognizes the structures of two or three consecutive Tn-antigens (Tn2 or Tn3). Since MLS128 treatment inhibits colon and breast cancer cell growth [Morita, N., Yajima, Y., Asanuma, H., Nakada, H., and Fujita-Yamaguchi, Y. (2009) Inhibition of cancer cell growth by anti-Tn monoclonal antibody MLS128. Biosci. Trends 3, 32-37.], understanding the interaction between MLS128 and Tn-clusters may allow us to the development of novel cancer therapeutics. Although MLS128 was previously reported to have specificity for Tn3 rather than Tn2, similar levels of Tn2/Tn3 binding were unexpectedly observed at 37°C. Thus, thermodynamic analyses were performed via surface plasmon resonance (SPR) using synthetic Tn2- and Tn3-peptides at 10, 15, 20, 25 and 30°C. SPR results revealed that MLS128's association constants for both antigens were highly temperature dependent. Below 25°C MLS128's association constant for Tn3-peptide was clearly higher than that for Tn2-peptide. At 30°C, however, the association constant for Tn2-peptide was higher than that for Tn3-peptide. This reversal of affinity is due to the sharp increase in K(d) for Tn3. These results were confirmed by NMR, which directly measured MLS128-Tn binding in solution. This study suggested that thermodynamic control plays a critical role in the interaction between MLS128/Tn2 and MLS128/Tn3.

  6. The Amyloid Precursor Protein of Alzheimer’s Disease Clusters at the Organelle/Microtubule Interface on Organelles that Bind Microtubules in an ATP Dependent Manner

    PubMed Central

    Stevenson, James W.; Conaty, Eliza A.; Walsh, Rylie B.; Poidomani, Paul J.; Samoriski, Colin M.; Scollins, Brianne J.; DeGiorgis, Joseph A.

    2016-01-01

    The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer’s protein tau has a microtubule-based function. PMID:26814888

  7. Identification of okadaic acid binding protein 2 in reconstituted sponge cell clusters from Halichondria okadai and its contribution to the detoxification of okadaic acid.

    PubMed

    Konoki, Keiichi; Okada, Kayo; Kohama, Mami; Matsuura, Hiroki; Saito, Kaori; Cho, Yuko; Nishitani, Goh; Miyamoto, Tomofumi; Fukuzawa, Seketsu; Tachibana, Kazuo; Yotsu-Yamashita, Mari

    2015-12-15

    Okadaic acid (OA) and OA binding protein 2 (OABP2) were previously isolated from the marine sponge Halichondria okadai. Because the amino acid sequence of OABP2 is completely different from that of protein phosphatase 2A, a well-known target of OA, we have been investigating the production and function of OABP2. In the present study, we hypothesized that OABP2 plays a role in the detoxification of OA in H. okadai and that the OA concentrations are in proportional to the OABP2 concentrations in the sponge specimens. Based on the OA concentrations and the OABP2 concentrations in the sponge specimens collected in various places and in different seasons, however, we could not determine a positive correlation between OA and OABP2. We then attempted to determine distribution of OA and OABP2 in the sponge specimen. When the mixture of dissociated sponge cells and symbiotic species were separated with various pore-sized nylon meshes, most of the OA and OABP2 was detected from the same 0-10 μm fraction. Next, when sponge cell clusters were prepared from a mixture of dissociated sponge cells and symbiotic species in the presence of penicillin and streptomycin, we identified the 18S rDNA of H. okadai and the gene of OABP2 in the analysis of genomic DNA but could not detect OA by LC-MS/MS. We thus concluded that the sponge cells express OABP2, and that OA was not apparently present in the sponge cells but could be colocalized with OABP2 in the sponge cells at a concentration less than the limit of detection.

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

    SciTech Connect

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

    2009-06-01

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

  9. A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced from Studies with Subunit B of Heterodisulfide Reductase from Methanothermobacter marburgensis†

    PubMed Central

    Hamann, Nils; Mander, Gerd J.; Shokes, Jacob E.; Scott, Robert A.; Bennati, Marina; Hedderich, Reiner

    2013-01-01

    Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]3+ cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX31–39CCX35–36CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusual [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron–sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (gzyx= 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. 57Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with 57Fe hyperfine couplings very similar to that of CoM-HDR. CoM-33SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S3(O/N)1 geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn site. PMID:17929940

  10. Kinetic evaluation of highly active supported gold catalysts prepared from monolayer-protected clusters: an experimental Michaelis-Menten approach for determining the oxygen binding constant during CO oxidation catalysis.

    PubMed

    Long, Cormac G; Gilbertson, John D; Vijayaraghavan, Ganesh; Stevenson, Keith J; Pursell, Christopher J; Chandler, Bert D

    2008-08-06

    Thiol monolayer-protected Au clusters (MPCs) were prepared using dendrimer templates, deposited onto a high-surface-area titania, and then the thiol stabilizers were removed under H2/N2. The resulting Au catalysts were characterized with transmission electron microscopy, X-ray photoelectron spectroscopy, and infrared spectroscopy of adsorbed CO. The Au catalysts prepared via this route displayed minimal particle agglomeration during the deposition and activation steps. Structural data obtained from the physical characterization of the Au catalysts were comparable to features exhibited from a traditionally prepared standard Au catalyst obtained from the World Gold Council (WGC). A differential kinetic study of CO oxidation catalysis by the MPC-prepared Au and the standard WGC catalyst showed that these two catalyst systems have essentially the same reaction order and Arrhenius apparent activation energies (28 kJ/mol). However, the MPC-prepared Au catalyst shows 50% greater activity for CO oxidation. Using a Michaelis-Menten approach, the oxygen binding constants for the two catalyst systems were determined and found to be essentially the same within experimental error. To our knowledge, this kinetic evaluation is the first experimental determination of oxygen binding by supported Au nanoparticle catalysts under working conditions. The values for the oxygen binding equilibrium constant obtained from the Michaelis-Menten treatment (ca. 29-39) are consistent with ultra-high-vacuum measurements on model catalyst systems and support density functional theory calculations for oxygen binding at corner or edge atoms on Au nanoparticles and clusters.

  11. 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.

  12. 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

  13. High mannose-binding lectin with preference for the cluster of alpha1-2-mannose from the green alga Boodlea coacta is a potent entry inhibitor of HIV-1 and influenza viruses.

    PubMed

    Sato, Yuichiro; Hirayama, Makoto; Morimoto, Kinjiro; Yamamoto, Naoki; Okuyama, Satomi; Hori, Kanji

    2011-06-03

    The complete amino acid sequence of a lectin from the green alga Boodlea coacta (BCA), which was determined by a combination of Edman degradation of its peptide fragments and cDNA cloning, revealed the following: 1) B. coacta used a noncanonical genetic code (where TAA and TAG codons encode glutamine rather than a translation termination), and 2) BCA consisted of three internal tandem-repeated domains, each of which contains the sequence motif similar to the carbohydrate-binding site of Galanthus nivalis agglutinin-related lectins. Carbohydrate binding specificity of BCA was examined by a centrifugal ultrafiltration-HPLC assay using 42 pyridylaminated oligosaccharides. BCA bound to high mannose-type N-glycans but not to the complex-type, hybrid-type core structure of N-glycans or oligosaccharides from glycolipids. This lectin had exclusive specificity for α1-2-linked mannose at the nonreducing terminus. The binding activity was enhanced as the number of terminal α1-2-linked mannose substitutions increased. Mannobiose, mannotriose, and mannopentaose were incapable of binding to BCA. Thus, BCA preferentially recognized the nonreducing terminal α1-2-mannose cluster as a primary target. As predicted from carbohydrate-binding propensity, this lectin inhibited the HIV-1 entry into the host cells at a half-maximal effective concentration of 8.2 nm. A high association constant (3.71 × 10(8) M(-1)) of BCA with the HIV envelope glycoprotein gp120 was demonstrated by surface plasmon resonance analysis. Moreover, BCA showed the potent anti-influenza activity by directly binding to viral envelope hemagglutinin against various strains, including a clinical isolate of pandemic H1N1-2009 virus, revealing its potential as an antiviral reagent.

  14. Specific binding of the regulatory protein ExpG to promoter regions of the galactoglucan biosynthesis gene cluster of Sinorhizobium meliloti--a combined molecular biology and force spectroscopy investigation.

    PubMed

    Bartels, Frank Wilco; Baumgarth, Birgit; Anselmetti, Dario; Ros, Robert; Becker, Anke

    2003-08-01

    Specific protein-DNA interaction is fundamental for all aspects of gene transcription. We focus on a regulatory DNA-binding protein in the Gram-negative soil bacterium Sinorhizobium meliloti 2011, which is capable of fixing molecular nitrogen in a symbiotic interaction with alfalfa plants. The ExpG protein plays a central role in regulation of the biosynthesis of the exopolysaccharide galactoglucan, which promotes the establishment of symbiosis. ExpG is a transcriptional activator of exp gene expression. We investigated the molecular mechanism of binding of ExpG to three associated target sequences in the exp gene cluster with standard biochemical methods and single molecule force spectroscopy based on the atomic force microscope (AFM). Binding of ExpG to expA1, expG-expD1, and expE1 promoter fragments in a sequence specific manner was demonstrated, and a 28 bp conserved region was found. AFM force spectroscopy experiments confirmed the specific binding of ExpG to the promoter regions, with unbinding forces ranging from 50 to 165 pN in a logarithmic dependence from the loading rates of 70-79000 pN/s. Two different regimes of loading rate-dependent behaviour were identified. Thermal off-rates in the range of k(off)=(1.2+/-1.0) x 10(-3)s(-1) were derived from the lower loading rate regime for all promoter regions. In the upper loading rate regime, however, these fragments exhibited distinct differences which are attributed to the molecular binding mechanism.

  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 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

  16. (S)-2-Amino-6-nitrohexanoic Acid Binds to Human Arginase I through Multiple Nitro−Metal Coordination Interactions in the Binuclear Manganese Cluster

    SciTech Connect

    Zakharian, T.; Di Costanzo, L; Christianson, D

    2008-01-01

    The binding affinity of (S)-2-amino-6-nitrohexanoic acid to human arginase I was studied using surface plasmon resonance (K{sub d} = 60 {mu}M), and the X-ray crystal structure of the enzyme-inhibitor complex was determined at 1.6 {angstrom} resolution to reveal multiple nitro-metal coordination interactions.

  17. In Silico Analysis for Transcription Factors With Zn(II)2C6 Binuclear Cluster DNA-Binding Domains in Candida albicans

    PubMed Central

    Maicas, Sergi; Moreno, Inmaculada; Nieto, Almudena; Gómez, Micaela; Sentandreu, Rafael

    2005-01-01

    A total of 6047 open reading frames in the Candida albicans genome were screened for Zn(II)2C6-type zinc cluster proteins (or binuclear cluster proteins) involved in DNA recognition. These fungal proteins are transcription regulators of genes involved in a wide range of cellular processes, including metabolism of different compounds such as sugars or amino acids, as well as multi-drug resistance, control of meiosis, cell wall architecture, etc. The selection criteria used in the sequence analysis were the presence of the CysX2CysX6CysX5-16CysX2CysX6-8Cys motif and a putative nuclear localization signal. Using this approach, 70 putative Zn(II)2C6 transcription factors have been found in the genome of C. albicans. PMID:18629206

  18. Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy

    PubMed Central

    Schrapers, Peer; Ilina, Julia; Gregg, Christina M.; Mebs, Stefan; Jeoung, Jae-Hun; Dau, Holger; Dobbek, Holger; Haumann, Michael

    2017-01-01

    Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely. PMID:28178309

  19. Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy.

    PubMed

    Schrapers, Peer; Ilina, Julia; Gregg, Christina M; Mebs, Stefan; Jeoung, Jae-Hun; Dau, Holger; Dobbek, Holger; Haumann, Michael

    2017-01-01

    Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.

  20. Two-Step Membrane Binding of NDPK-B Induces Membrane Fluidity Decrease and Changes in Lipid Lateral Organization and Protein Cluster Formation.

    PubMed

    Francois-Moutal, Liberty; Ouberai, Myriam M; Maniti, Ofelia; Welland, Mark E; Strzelecka-Kiliszek, Agnieszka; Wos, Marcin; Pikula, Slawomir; Bandorowicz-Pikula, Joanna; Marcillat, Olivier; Granjon, Thierry

    2016-12-06

    Nucleoside diphosphate kinases (NDPKs) are crucial elements in a wide array of cellular physiological or pathophysiological processes such as apoptosis, proliferation, or metastasis formation. Among the NDPK isoenzymes, NDPK-B, a cytoplasmic protein, was reported to be associated with several biological membranes such as plasma or endoplasmic reticulum membranes. Using several membrane models (liposomes, lipid monolayers, and supported lipid bilayers) associated with biophysical approaches, we show that lipid membrane binding occurs in a two-step process: first, initiation by a strong electrostatic adsorption process and followed by shallow penetration of the protein within the membrane. The NDPK-B binding leads to a decrease in membrane fluidity and formation of protein patches. The ability of NDPK-B to form microdomains at the membrane level may be related to protein-protein interactions triggered by its association with anionic phospholipids. Such accumulation of NDPK-B would amplify its effects in functional platform formation and protein recruitment at the membrane.

  1. Cluster Headache

    MedlinePlus

    Cluster headache Overview By Mayo Clinic Staff Cluster headaches, which occur in cyclical patterns or clusters, are one of the most painful types of headache. A cluster headache commonly awakens you ...

  2. Two genes encoding an endoglucanase and a cellulose-binding protein are clustered and co-regulated by a TTA codon in Streptomyces halstedii JM8.

    PubMed Central

    Garda, A L; Fernández-Abalos, J M; Sánchez, P; Ruiz-Arribas, A; Santamaría, R I

    1997-01-01

    Streptomyces halstedii JM8 Cel2 is an endoglucanase of 28 kDa that is first produced as a protein of 42 kDa (p42) and is later processed at its C-terminus. Cel2 displays optimal activity towards CM-cellulose at pH6 and 50 degrees C and shows no activity against crystalline cellulose or xylan. The N-terminus of p42 shares similarity with cellulases included in family 12 of the beta-glycanases and the C-terminus shares similarity with bacterial cellulose-binding domains included in family II. This latter domain enables the precursor to bind so tightly to Avicel that it can only be eluted by boiling in 10% (w/v) SDS. Another open reading frame (ORF) situated 216 bp downstream from the p42 ORF encodes a protein of 40 kDa (p40) that does not have any clear hydrolytic activity against cellulosic or xylanosic compounds, but shows high affinity for Avicel (crystalline cellulose). The p40 protein is processed in old cultures to give a protein of 35 kDa that does not bind to Avicel. Translation of both ORFs is impaired in Streptomyces coelicolor bldA mutants, suggesting that a TTA codon situated at the fourth position of the first ORF is responsible for this regulation. S1 nuclease protection experiments demonstrate that both ORFs are co-transcribed. PMID:9182697

  3. Human Leukocyte Antigen (HLA) B27 Allotype-Specific Binding and Candidate Arthritogenic Peptides Revealed through Heuristic Clustering of Data-independent Acquisition Mass Spectrometry (DIA-MS) Data.

    PubMed

    Schittenhelm, Ralf B; Sivaneswaran, Saranjah; Lim Kam Sian, Terry C C; Croft, Nathan P; Purcell, Anthony W

    2016-06-01

    Expression of HLA-B27 is strongly associated with ankylosing spondylitis (AS) and other spondyloarthropathies. While this is true for the majority of HLA-B27 allotypes, HLA-B*27:06 and HLA-B*27:09 are not associated with AS. These two subtypes contain polymorphisms that are ideally positioned to influence the bound peptide repertoire. The existence of disease-inducing peptides (so-called arthritogenic peptides) has therefore been proposed that are exclusively presented by disease-associated HLA-B27 allotypes. However, we have recently demonstrated that this segregation of allotype-bound peptides is not the case and that many peptides that display sequence features predicted to favor binding to disease-associated subtypes are also capable of being presented naturally by protective alleles. To further probe more subtle quantitative changes in peptide presentation, we have used a combination of data-independent acquisition (DIA) and multiple reaction monitoring (MRM) mass spectrometry to quantify the abundance of 1646 HLA-B27 restricted peptides across the eight most frequent HLA-B27 allotypes (HLA-B*27:02-HLA-B*27:09). We utilized K means cluster analysis to group peptides with similar allelic binding preferences across the eight HLA-B27 allotypes, which enabled us to identify the most-stringent binding characteristics for each HLA-B27 allotype and further refined their existing consensus-binding motifs. Moreover, a thorough analysis of this quantitative dataset led to the identification of 26 peptides, which are presented in lower abundance by HLA-B*27:06 and HLA-B*27:09 compared with disease-associated HLA-B27 subtypes. Although these differences were observed to be very subtle, these 26 peptides might encompass the sought-after arthritogenic peptide(s).

  4. Diffusion Monte Carlo studies of MB-pol (H2O)2-6 and (D2O)2-6 clusters: Structures and binding energies

    NASA Astrophysics Data System (ADS)

    Mallory, Joel D.; Mandelshtam, Vladimir A.

    2016-08-01

    We employ the diffusion Monte Carlo (DMC) method in conjunction with the recently developed, ab initio-based MB-pol potential energy surface to characterize the ground states of small (H2O)2-6 clusters and their deuterated isotopomers. Observables, other than the ground state energies, are computed using the descendant weighting approach. Among those are various spatial correlation functions and relative isomer fractions. Interestingly, the ground states of all clusters considered in this study, except for the dimer, are delocalized over at least two conformations that differ by the orientation of one or more water monomers with the relative isomer populations being sensitive to the isotope substitution. Most remarkably, the ground state of the (H2O)6 hexamer is represented by four distinct cage structures, while that of (D2O)6 is dominated by the prism, i.e., the global minimum geometry, with a very small contribution from a prism-book geometry. In addition, for (H2O)6 and (D2O)6, we performed DMC calculations to compute the ground states constrained to the cage and prism geometries. These calculations compared results for three different potentials, MB-pol, TTM3/F, and q-TIP4P/F.

  5. Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast.

    PubMed

    Chatterjee, Debashree; Sanchez, Ana M; Goldgur, Yehuda; Shuman, Stewart; Schwer, Beate

    2016-07-01

    Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt-pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 Å crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m(6)A-modified RNA.

  6. The modular adaptor protein ARH is required for low density lipoprotein (LDL) binding and internalization but not for LDL receptor clustering in coated pits.

    PubMed

    Michaely, Peter; Li, Wei-Ping; Anderson, Richard G W; Cohen, Jonathan C; Hobbs, Helen H

    2004-08-06

    ARH is an adaptor protein required for efficient endocytosis of low density lipoprotein (LDL) receptors (LDLRs) in selected tissues. Individuals lacking ARH (ARH-/-) have severe hypercholesterolemia due to impaired hepatic clearance of LDL. Immortalized lymphocytes, but not fibroblasts, from ARH-deficient subjects fail to internalize LDL. To further define the role of ARH in LDLR function, we compared the subcellular distribution of the LDLR in lymphocytes from normal and ARH-/- subjects. In normal lymphocytes LDLRs were predominantly located in intracellular compartments, whereas in ARH-/- cells the receptors were almost exclusively on the plasma membrane. Biochemical assays and quantification of LDLR by electron microscopy indicated that ARH-/- lymphocytes had >20-fold more LDLR on the cell surface and a approximately 27-fold excess of LDLR outside of coated pits. The accumulation of LDLR on the cell surface was not due to failure of receptors to localize in coated pits since the number of LDLRs in coated pits was similar in ARH-/- and normal cells. Despite the dramatic increase in cell surface receptors, LDL binding was only 2-fold higher in the ARH-/- lymphocytes. These findings indicate that ARH is required not only for internalization of the LDL.LDLR complex but also for efficient binding of LDL to the receptor and suggest that ARH stabilizes the associations of the receptor with LDL and with the invaginating portion of the budding pit, thereby increasing the efficiency of LDL internalization.

  7. Binding of ligands containing carbonyl and phenol groups to iron(iii): new Fe6, Fe10 and Fe12 coordination clusters.

    PubMed

    Kitos, Alexandros A; Papatriantafyllopoulou, Constantina; Tasiopoulos, Anastasios J; Perlepes, Spyros P; Escuer, Albert; Nastopoulos, Vassilios

    2017-03-07

    The initial use of ligands 2'-hydroxyacetophenone (HL(1)), 2-hydroxybenzophenone (HL(2)) and 2,2'-dihydroxybenzophenone (H2L(3)) in iron(iii) chemistry is described. The syntheses and crystal structures are reported for five iron(iii) clusters: [Fe10O4(OMe)14(L(1))6(MeOH)2](NO3)2·3MeOH (1·3MeOH), [Fe12O4(OH)(OMe)17(L(1))8](ClO4)2·2H2O (2·2H2O), [Fe10O4(OMe)14Cl4(L(2))4(MeOH)2] (3), [Fe10O4(OMe)14(L(2))6(py)2](ClO4)2·MeOH (4·MeOH), where py = pyridine, and [Fe6O2(OEt)6(O2CMe)2(L(3))2(HL(3))2] (5). The molecular structures of the decanuclear clusters 1, 3 and 4 are organized around a {Fe10(μ4-O)4(μ3-OMe)2(μ-OMe)12}(8+) core consisting of ten {Fe3O4} face-sharing defective cubane units. The core of 2 consists of a {Fe12(μ4-O)4(μ3-OMe)4(μ-OH)(μ-OMe)13}(10+) unit composed of twelve {Fe3O4} face-sharing defective cubanes. The ligands (L(1))(-) and (L(2))(-) in 1-4 adopt the O,O'-bidentate chelating coordination mode and their roles are to terminate the further aggregation of the Fe(III)/O(2-)/RO(-) cores. Complex 5 contains the {Fe6(μ4-O)2(μ-OEt)6(μ-Ocarbonyl)2}(4+) core, where the μ-Ocarbonyl atoms are the bridging carbonyl oxygens of the two η(1):η(2):η(1):μ (L(3))(2-) ligands; the (HL(3))(-) groups behave as Ophenolate, Ocarbonyl-bidentate chelating ligands with the neutral hydroxyl group being unbound to the Fe(III) atoms. The core is composed of four {Fe3O4} face-sharing defective cubanes. The Fe(III) atoms in 1-5 are all six-coordinate with distorted octahedral geometries. The IR spectra of the complexes are discussed in terms of the known coordination modes of the ligands and the ionic character of nitrates and perchlorates. Variable-temperature magnetic susceptibility and variable-field magnetization measurements establish that 2, 3 and 5 have S = 3, 0 and 5 ground states, respectively. The susceptibility data for 5 were fitted using a 3-J model indicating the simultaneous presence of both antiferromagnetic and ferromagnetic Fe

  8. Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21: Rationale for a new nomenclature of the S100 calcium-binding protein family

    SciTech Connect

    Schaefer, B.W.; Wicki, R.; Engelkamp, D.

    1995-02-10

    S100 proteins are low-molecular-weight calcium-binding proteins of the EF- hand superfamily and appear to be involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. More than 10 members of the S100 protein family have been described from human sources so far. We have now isolated a YAC clone from human chromosome 1q21, on which 9 different genes coding for S100 calcium-binding proteins could be localized. Moreover, we have mapped the gene coding for S100P to human chromosome 4p16 and thereby completed the chromosomal assignments of all known human S100 genes. The clustered organization of S100 genes in the 1q21 region allows us to introduce a new logical nomenclature for these genes, which is based on the physical arrangement on the chromosomes. The new nomenclature should facilitate the further the understanding of this protein family and be easily expandable to other species. 31 refs., 4 figs., 1 tab.

  9. The Lon protease from the haloalkaliphilic archaeon Natrialba magadii is transcriptionally linked to a cluster of putative membrane proteases and displays DNA-binding activity.

    PubMed

    Sastre, Diego E; Paggi, Roberto A; De Castro, Rosana E

    2011-05-20

    The ATP-dependent Lon protease is universally distributed in bacteria, eukaryotic organelles and archaea. In comparison with bacterial and eukaryal Lon proteases, the biology of the archaeal Lon has been studied to a limited extent. In this study, the gene encoding the Lon protease of the alkaliphilic haloarchaeon Natrialba magadii (Nmlon) was cloned and sequenced, and the genetic organization of Nmlon was examined at the transcriptional level. Nmlon encodes a 84 kDa polypeptide with a pI of 4.42 which contains the ATPase, protease and membrane targeting domains of the archaeal-type LonB proteases. Nmlon is part of an operon that encodes membrane proteases and it is transcribed as a polycistronic mRNA in N. magadii cells at different growth stages. Accordingly, NmLon was detected in cell membranes of N. magadii throughout growth by Western blot analysis using specific anti-NmLon antibodies. Interestingly, in electrophoretic mobility shift assays, purified NmLon bound double stranded as well as single stranded DNA in the presence of elevated salt concentrations. This finding shows that DNA-binding is conserved in the LonA and LonB subfamilies and suggests that Lon-DNA interaction may be relevant for its function in haloarchaea.

  10. 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.

  11. Alkali Metal Cluster Theory.

    NASA Astrophysics Data System (ADS)

    Chen, Jian

    Available from UMI in association with The British Library. Requires signed TDF. In this thesis, we apply the tight-binding Hubbard model to alkali metal clusters with Hartree-Fock self-consistent methods and perturbation methods for the numerical calculations. We have studied the relation between the equilibrium structures and the range of the hopping matrix elements in the Hubbard Hamiltonian. The results show that the structures are not sensitive to the interaction range but are determined by the number of valence electrons each atom has. Inertia tensors are used to analyse the symmetries of the clusters. The principal axes of the clusters are determined and they are the axes of rotational symmetries of clusters if the clusters have any. The eigenvalues of inertia tensors which are the indication of the deformation of clusters are compared between our model and the ellipsoidal jellium model. The agreement is good for large clusters. At a finite temperature, the thermal motion fluctuates the structures. We defined a fluctuation function with the distance matrix of a cluster. The fluctuation has been studied with the Monte-Carlo simulation method. Our studies show that the clusters remain in the solid state when temperature is low. The small values of fluctuation functions indicates the thermal vibration of atoms around their equilibrium positions. If the temperature is high, the atoms are delocalized. The cluster melts and enters the liquid region. The cluster melting is simulated by the Monte-Carlo simulation with the fluctuation function we defined. Energy levels of clusters are calculated from the Hubbard model. Ionization potentials and magic numbers are also obtained from these energy levels. The results confirm that the Hubbard model is a good approximation for a small cluster. The excitation energy is presented by the difference between the original level and excited level, and the electron-hole interactions. We also have studied cooling of clusters

  12. Carbamate-linked lactose: design of clusters and evidence for selectivity to block binding of human lectins to (neo)glycoproteins with increasing degree of branching and to tumor cells.

    PubMed

    André, Sabine; Specker, Daniel; Bovin, Nicolai V; Lensch, Martin; Kaltner, Herbert; Gabius, Hans-Joachim; Wittmann, Valentin

    2009-09-01

    Various pathogenic processes are driven by protein(lectin)-glycan interactions, especially involving beta-galactosides at branch ends of cellular glycans. These emerging insights fuel the interest to design potent inhibitors to block lectins. As a step toward this aim, we prepared a series of ten mono- to tetravalent glycocompounds with lactose as a common headgroup. To obtain activated carbonate for ensuing carbamate formation, conditions for the facile synthesis of pure isomers from anomerically unprotected lactose were identified. To probe for the often encountered intrafamily diversity of human lectins, we selected representative members from the three subgroups of adhesion/growth-regulatory galectins as receptors. Diversity of the glycan display was accounted for by using four (neo)glycoproteins with different degrees of glycan branching as matrices in solid-phase assays. Cases of increased inhibitory potency of lactose clusters compared to free lactose were revealed. Extent of relative inhibition was not directly associated with valency in the glycocompound and depended on the lectin type. Of note for screening protocols, efficacy of blocking appeared to decrease with increased degree of glycan branching in matrix glycoproteins. Binding to tumor cells was impaired with selectivity for galectins-3 and -4. Representative compounds did not impair growth of carcinoma cells up to a concentration of 5 mM of lactose moieties (valence-corrected value) per assay. The reported bioactivity and the delineation of its modulation by structural parameters of lectins and glycans set instructive examples for the further design of selective inhibitors and assay procedures.

  13. Role of Litopenaeus vannamei Yin Yang 1 in the Regulation of the White Spot Syndrome Virus Immediate Early Gene ie1.

    PubMed

    Huang, Ping-Han; Huang, Ting-Yi; Cai, Pei-Si; Chang, Li-Kwan

    2017-03-15

    Yin Yang 1 (YY1) is a multifunctional zinc finger transcription factor that regulates many key cellular processes. In this study, we report the cloning of YY1 from Litopenaeus vannamei shrimp (LvYY1). This study shows that LvYY1 is ubiquitously expressed in shrimp tissues, and knockdown of LvYY1 expression by double-stranded RNA (dsRNA) injection in white spot syndrome virus (WSSV)-infected shrimp reduced both mRNA levels of the WSSV immediate early gene ie1 as well as overall copy numbers of the WSSV genome. The cumulative mortality rate of infected shrimp also declined with LvYY1 dsRNA injection. Using an insect cell model, we observed that LvYY1 activates ie1 expression, and a mutation introduced into the ie1 promoter subsequently repressed this capability. Moreover, reporter assay results suggested that LvYY1 is involved in basal transcriptional regulation via an interaction with L. vannamei TATA-binding protein (LvTBP). Electrophoretic mobility shift assay (EMSA) results further indicated that LvYY1 binds to a YY1-binding site in the region between positions -119 and -126 in the ie1 promoter. Chromatin immunoprecipitation analysis also confirmed that LvYY1 binds to the ie1 promoter in WSSV-infected shrimp. Taken together, these results indicate that WSSV uses host LvYY1 to enhance ie1 expression via a YY1-binding site and the TATA box in the ie1 promoter, thereby facilitating lytic activation and viral replication.IMPORTANCE WSSV has long been a scourge of the shrimp industry and remains a serious global threat. Thus, there is a pressing need to understand how the interactions between WSSV and its host drive infection, lytic development, pathogenesis, and mortality. Our successful cloning of L. vannamei YY1 (LvYY1) led to the elucidation of a critical virus-host interaction between LvYY1 and the WSSV immediate early gene ie1 We observed that LvYY1 regulates ie1 expression via a consensus YY1-binding site and TATA box. LvYY1 was also found to interact with L

  14. Modular Insulators: Genome Wide Search for Composite CTCF/Thyroid Hormone Receptor Binding Sites

    PubMed Central

    Weth, Oliver; Weth, Christine; Bartkuhn, Marek; Leers, Joerg; Uhle, Florian; Renkawitz, Rainer

    2010-01-01

    The conserved 11 zinc-finger protein CTCF is involved in several transcriptional mechanisms, including insulation and enhancer blocking. We had previously identified two composite elements consisting of a CTCF and a TR binding site at the chicken lysozyme and the human c-myc genes. Using these it has been demonstrated that thyroid hormone mediates the relief of enhancer blocking even though CTCF remains bound to its binding site. Here we wished to determine whether CTCF and TR combined sites are representative of a general feature of the genome, and whether such sites are functional in regulating enhancer blocking. Genome wide analysis revealed that about 18% of the CTCF regions harbored at least one of the four different palindromic or repeated sequence arrangements typical for the binding of TR homodimers or TR/RXR heterodimers. Functional analysis of 10 different composite elements of thyroid hormone responsive genes was performed using episomal constructs. The episomal system allowed recapitulating CTCF mediated enhancer blocking function to be dependent on poly (ADP)-ribose modification and to mediate histone deacetylation. Furthermore, thyroid hormone sensitive enhancer blocking could be shown for one of these new composite elements. Remarkably, not only did the regulation of enhancer blocking require functional TR binding, but also the basal enhancer blocking activity of CTCF was dependent on the binding of the unliganded TR. Thus, a number of composite CTCF/TR binding sites may represent a subset of other modular CTCF composite sites, such as groups of multiple CTCF sites or of CTCF/Oct4, CTCF/Kaiso or CTCF/Yy1 combinations. PMID:20404925

  15. Cluster headache

    MedlinePlus

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... be related to the body's sudden release of histamine (chemical in the body released during an allergic ...

  16. 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.

  17. The Blast Resistance Gene Pi37 Encodes a Nucleotide Binding Site–Leucine-Rich Repeat Protein and Is a Member of a Resistance Gene Cluster on Rice Chromosome 1

    PubMed Central

    Lin, Fei; Chen, Shen; Que, Zhiqun; Wang, Ling; Liu, Xinqiong; Pan, Qinghua

    2007-01-01

    The resistance (R) gene Pi37, present in the rice cultivar St. No. 1, was isolated by an in silico map-based cloning procedure. The equivalent genetic region in Nipponbare contains four nucleotide binding site–leucine-rich repeat (NBS–LRR) type loci. These four candidates for Pi37 (Pi37-1, -2, -3, and -4) were amplified separately from St. No. 1 via long-range PCR, and cloned into a binary vector. Each construct was individually transformed into the highly blast susceptible cultivar Q1063. The subsequent complementation analysis revealed Pi37-3 to be the functional gene, while -1, -2, and -4 are probably pseudogenes. Pi37 encodes a 1290 peptide NBS–LRR product, and the presence of substitutions at two sites in the NBS region (V239A and I247M) is associated with the resistance phenotype. Semiquantitative expression analysis showed that in St. No. 1, Pi37 was constitutively expressed and only slightly induced by blast infection. Transient expression experiments indicated that the Pi37 product is restricted to the cytoplasm. Pi37-3 is thought to have evolved recently from -2, which in turn was derived from an ancestral -1 sequence. Pi37-4 is likely the most recently evolved member of the cluster and probably represents a duplication of -3. The four Pi37 paralogs are more closely related to maize rp1 than to any of the currently isolated rice blast R genes Pita, Pib, Pi9, Pi2, Piz-t, and Pi36. PMID:17947408

  18. 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.

  19. 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

  20. Thermodynamic prediction of glass formation tendency, cluster-in-jellium model for metallic glasses, ab initio tight-binding calculations, and new density functional theory development for systems with strong electron correlation

    SciTech Connect

    Yao, Yongxin

    2009-01-01

    Solidification of liquid is a very rich and complicated field, although there is always a famous homogeneous nucleation theory in a standard physics or materials science text book. Depending on the material and processing condition, liquid may solidify to single crystalline, polycrystalline with different texture, quasi-crystalline, amorphous solid or glass (Glass is a kind of amorphous solid in general, which has short-range and medium-range order). Traditional oxide glass may easily be formed since the covalent directional bonded network is apt to be disturbed. In other words, the energy landcape of the oxide glass is so complicated that system need extremely long time to explore the whole configuration space. On the other hand, metallic liquid usually crystalize upon cooling because of the metallic bonding nature. However, Klement et.al., (1960) reported that Au-Si liquid underwent an amorphous or “glassy” phase transformation with rapid quenching. In recent two decades, bulk metallic glasses have also been found in several multicomponent alloys[Inoue et al., (2002)]. Both thermodynamic factors (e.g., free energy of various competitive phase, interfacial free energy, free energy of local clusters, etc.) and kinetic factors (e.g., long range mass transport, local atomic position rearrangement, etc.) play important roles in the metallic glass formation process. Metallic glass is fundamentally different from nanocrystalline alloys. Metallic glasses have to undergo a nucleation process upon heating in order to crystallize. Thus the short-range and medium-range order of metallic glasses have to be completely different from crystal. Hence a method to calculate the energetics of different local clusters in the undercooled liquid or glasses become important to set up a statistic model to describe metalllic glass formation. Scattering techniques like x-ray and neutron have widely been used to study the structues of metallic glasses. Meanwhile, computer simulation

  1. Kaempferol suppresses lipid accumulation in macrophages through the downregulation of cluster of differentiation 36 and the upregulation of scavenger receptor class B type I and ATP-binding cassette transporters A1 and G1.

    PubMed

    Li, Xiu-Ying; Kong, Ling-Xi; Li, Juan; He, Hai-Xia; Zhou, Yuan-Da

    2013-02-01

    The accumulation of foam cells in atherosclerotic lesions is a hallmark of early-stage atherosclerosis. Kaempferol has been shown to inhibit oxidized low-density lipoprotein (oxLDL) uptake by macrophages; however, the underlying molecular mechanisms are not yet fully investigated. In this study, we shown that treatment with kaempferol markedly suppresses oxLDL-induced macrophage foam cell formation, which occurs due to a decrease in lipid accumulation and an increase in cholesterol efflux from THP-1-derived macrophages. Additionally, the kaempferol treatment of macrophages led to the downregulation of cluster of differentiation 36 (CD36) protein levels, the upregulation of ATP-binding cassette (ABC) transporter A1 (ABCA1), scavenger receptor class B type I (SR-BI) and ABCG1 protein levels, while no effects on scavenger receptor A (SR-A) expression were observed. Kaempferol had similar effects on the mRNA and protein expression of ABCA1, SR-BI, SR-A, CD36 and ABCG1. The reduced CD36 expression following kaempferol treatment involved the inhibition of c-Jun-activator protein-1 (AP-1) nuclear translocation. The inhibition of AP-1 using the inhibitor, SP600125, confirmed this involvement, as the AP-1 inhibition significantly augmented the kaempferol-induced reduction in CD36 expression. Accordingly, the kaempferol-mediated suppression of lipid accumulation in macrophages was also augmented by SP600125. The increased expression of ABCA1, SR-BI and ABCG1 following kaempferol treatment was accompanied by the enhanced protein expression of heme oxygenase-1 (HO-1). This increase was reversed following the knockdown of the HO-1 gene using small hairpin RNA (shRNA). Moreover, the kaempferol-mediated attenuation of lipid accumulation and the promotion of cholesterol efflux was also inhibited by HO-1 shRNA. In conclusion, the c-Jun-AP‑1-dependent downregulation of CD36 and the HO-1-dependent upregulation of ABCG1, SR-BI and ABCA1 may mediate the beneficial effects of

  2. 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.

  3. Binding Procurement

    NASA Technical Reports Server (NTRS)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  4. 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

  5. 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

  6. 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.

  7. 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…

  8. 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.

  9. Hydrated hydride anion clusters

    NASA Astrophysics Data System (ADS)

    Lee, Han Myoung; Kim, Dongwook; Singh, N. Jiten; Kołaski, Maciej; Kim, Kwang S.

    2007-10-01

    On the basis of density functional theory (DFT) and high level ab initio theory, we report the structures, binding energies, thermodynamic quantities, IR spectra, and electronic properties of the hydride anion hydrated by up to six water molecules. Ground state DFT molecular dynamics simulations (based on the Born-Oppenheimer potential surface) show that as the temperature increases, the surface-bound hydride anion changes to the internally bound structure. Car-Parrinello molecular dynamics simulations are also carried out for the spectral analysis of the monohydrated hydride. Excited-state ab initio molecular dynamics simulations show that the photoinduced charge-transfer-to-solvent phenomena are accompanied by the formation of the excess electron-water clusters and the detachment of the H radical from the clusters. The dynamics of the detachment process of a hydrogen radical upon the excitation is discussed.

  10. An accurate and efficient computational protocol for obtaining the complete basis set limits of the binding energies of water clusters at the MP2 and CCSD(T) levels of theory: Application to (H2O)m, m = 2-6, 8, 11, 16, and 17

    NASA Astrophysics Data System (ADS)

    Miliordos, Evangelos; Xantheas, Sotiris S.

    2015-06-01

    We report MP2 and Coupled Cluster Singles, Doubles, and perturbative Triples [CCSD(T)] binding energies with basis sets up to pentuple zeta quality for the (H2O)m=2-6,8 water clusters. Our best CCSD(T)/Complete Basis Set (CBS) estimates are -4.99 ± 0.04 kcal/mol (dimer), -15.8 ± 0.1 kcal/mol (trimer), -27.4 ± 0.1 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D2d octamer), and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (De) and basis set superposition error-corrected ( De CP ) binding energies recovered with respect to the CBS limit falls into a narrow range on either sides of the CBS limit for each basis set for all clusters. In addition, this range decreases upon increasing the basis set. Relatively accurate estimates (within <0.5%) of the CBS limits can be obtained when using the " 2 3 , 1 3 " (for the AVDZ set) or the " 1 2 , 1 2 " (for the AVTZ, AVQZ, and AV5Z sets) mixing ratio between De and De CP . These mixing rations are determined via a least-mean-squares approach from a dataset that encompasses clusters of various sizes. Based on those findings, we propose an accurate and efficient computational protocol that can be presently used to estimate accurate binding energies of water clusters containing up to 30 molecules (for CCSD(T)) and up to 100 molecules (for MP2).

  11. 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.

  12. INTERACTION OF INTERSTITIAL CLUSTERS WITH RHENIUM, OSMIUM, AND TANTALUM IN TUNGSTEN

    SciTech Connect

    Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

    2016-09-01

    In the previous semi annual report, we explored the stability of interstitial clusters in W up to size seven. In this report, we study the binding of those clusters to Re, Os, and Ta atoms. For each cluster size, the three most stable configurations are considered to average the binding property. The average binding energy to a Re decreases from 0.79 eV for a size-1 cluster (a [111] dumbbell) to 0.65 eV for a size-7 cluster. For Os, the binding decreases from 1.61 eV for a [111] dumbbell to 1.34 eV for a size-7 cluster. Tantalum is repulsive to interstitial clusters with binding energy ranges from -0.61 eV for a [111] dumbbell to -0.5 eV for a size-7 cluster.

  13. Microbial starch-binding domain.

    PubMed

    Rodríguez-Sanoja, Romina; Oviedo, Norma; Sánchez, Sergio

    2005-06-01

    Glucosidic bonds from different non-soluble polysaccharides such as starch, cellulose and xylan are hydrolyzed by amylases, cellulases and xylanases, respectively. These enzymes are produced by microorganisms. They have a modular structure that is composed of a catalytic domain and at least one non-catalytic domain that is involved in polysaccharide binding. Starch-binding modules are present in microbial enzymes that are involved in starch metabolism; these are classified into several different families on the basis of their amino acid sequence similarities. Such binding domains promote attachment to the substrate and increase its concentration at the active site of the enzyme, which allows microorganisms to degrade non-soluble starch. Fold similarities are better conserved than sequences; nevertheless, it is possible to notice two evolutionary clusters of microbial starch-binding domains. These domains have enormous potential as tags for protein immobilization, as well as for the tailoring of enzymes that play a part in polysaccharide metabolism.

  14. Stepwise association of hydrogen cyanide and acetonitrile with the benzene radical cation: structures and binding energies of (C6H6•+)(HCN)n, n = 1-6, and (C6H6•+)(CH3CN)n, n = 1-4, clusters.

    PubMed

    Hamid, Ahmed M; Soliman, Abdel-Rahman; El-Shall, M Samy

    2013-02-14

    Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise association of HCN and CH(3)CN molecules with the benzene radical cation in the C(6)H(6)(•+)(HCN)(n) and C(6)H(6)(•+)(CH(3)CN)(n) clusters with n = 1-6 and 1-4, respectively. The binding energy of CH(3)CN to the benzene cation (14 kcal/mol) is stronger than that of HCN (9 kcal/mol) mostly due to a stronger ion-dipole interaction because of the large dipole moment of acetonitrile (3.9 D). However, HCN can form hydrogen bonds with the hydrogen atoms of the benzene cation (CH(δ+)···NCH) and linear hydrogen bonding chains involving HCN···HCN interaction. HCN molecules tend to form externally solvated structures with the benzene cation where the ion is hydrogen bonded to the exterior of HCN chains. For the C(6)H(6)(•+)(CH(3)CN)(n) clusters, internally solvated structures are formed where the acetonitrile molecules are directly interacting with the benzene cation through ion-dipole and hydrogen bonding interactions. The lack of formation of higher clusters with n > 4, in contrast to HCN, suggests the formation of a solvent shell at n = 4, which is attributed to steric interactions among the acetonitrile molecules attached to the benzene cation and to the presence of the blocking CH(3) groups, both effects make the addition of more than four acetonitrile molecules less favorable.

  15. Quantum Dynamics of Helium Clusters

    DTIC Science & Technology

    1993-03-01

    helium clusters [10-12]. (10) DMC starts with the time - dependent Schr ~ dinger equation in imaginary time and has been employed most- The approximate...bound. (For example, the binding values may be computed by the Metropolis approach . energy of He 3 is five times greater than that of 1l1lie I We first...or four times for computational effort. If this is also the case with the the larger clusters) its original size. If the maximum en- DMC approach

  16. 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.

  17. Nature of multiple-nucleus cluster galaxies

    SciTech Connect

    Merritt, D.

    1984-05-01

    In models for the evolution of galaxy clusters which include dynamical friction with the dark binding matter, the distribution of galaxies becomes more concentrated to the cluster center with time. In a cluster like Coma, this evolution could increase by a factor of approximately 3 the probability of finding a galaxy very close to the cluster center, without decreasing the typical velocity of such a galaxy significantly below the cluster mean. Such an enhancement is roughly what is needed to explain the large number of first-ranked cluster galaxies which are observed to have extra ''nuclei''; it is also consistent with the high velocities typically measured for these ''nuclei.'' Unlike the cannibalism model, this model predicts that the majority of multiple-nucleus systems are transient phenomena, and not galaxies in the process of merging.

  18. Evidence for chemoreceptors with bimodular ligand-binding regions harboring two signal-binding sites

    PubMed Central

    Pineda-Molina, Estela; Reyes-Darias, José-Antonio; Lacal, Jesús; Ramos, Juan L.; García-Ruiz, Juan Manuel; Gavira, Jose A.; Krell, Tino

    2012-01-01

    Chemoreceptor-based signaling is a central mechanism in bacterial signal transduction. Receptors are classified according to the size of their ligand-binding region. The well-studied cluster I proteins have a 100- to 150-residue ligand-binding region that contains a single site for chemoattractant recognition. Cluster II receptors, which contain a 220- to 300-residue ligand-binding region and which are almost as abundant as cluster I receptors, remain largely uncharacterized. Here, we report high-resolution structures of the ligand-binding region of the cluster II McpS chemotaxis receptor (McpS-LBR) of Pseudomonas putida KT2440 in complex with different chemoattractants. The structure of McpS-LBR represents a small-molecule binding domain composed of two modules, each able to bind different signal molecules. Malate and succinate were found to bind to the membrane-proximal module, whereas acetate binds to the membrane-distal module. A structural alignment of the two modules revealed that the ligand-binding sites could be superimposed and that amino acids involved in ligand recognition are conserved in both binding sites. Ligand binding to both modules was shown to trigger chemotactic responses. Further analysis showed that McpS-like receptors were found in different classes of proteobacteria, indicating that this mode of response to different carbon sources may be universally distributed. The physiological relevance of the McpS architecture may lie in its capacity to respond with high sensitivity to the preferred carbon sources malate and succinate and, at the same time, mediate lower sensitivity responses to the less preferred but very abundant carbon source acetate. PMID:23112148

  19. Universality in Molecular Halo Clusters

    NASA Astrophysics Data System (ADS)

    Stipanović, P.; Markić, L. Vranješ; Bešlić, I.; Boronat, J.

    2014-12-01

    The ground state of weakly bound dimers and trimers with a radius extending well into the classically forbidden region is explored, with the goal to test the predicted universality of quantum halo states. The focus of the study is molecules consisting of T ↓ , D ↓ , 3He, 4He, and alkali atoms, where the interaction between particles is much better known than in the case of nuclei, which are traditional examples of quantum halos. The study of realistic systems is supplemented by model calculations in order to analyze how low-energy properties depend on the interaction potential. The use of variational and diffusion Monte Carlo methods enabled a very precise calculation of both the size and binding energy of the trimers. In the quantum halo regime, and for large values of scaled binding energies, all clusters follow almost the same universal line. As the scaled binding energy decreases, Borromean states separate from tango trimers.

  20. Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity

    PubMed Central

    Jose, Davis; Weitzel, Steven E.; Baase, Walter A.; Michael, Miya M.; von Hippel, Peter H.

    2015-01-01

    We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5′-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex. PMID:26275774

  1. Coupled Cluster Evaluation of the Stability of Atmospheric Acid-Base Clusters with up to 10 Molecules.

    PubMed

    Myllys, Nanna; Elm, Jonas; Halonen, Roope; Kurtén, Theo; Vehkamäki, Hanna

    2016-02-04

    We investigate the utilization of the domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method for calculating binding energies of atmospherical molecular clusters. Applied to small complexes of atmospherical relevance we find that the DLPNO method significantly reduces the scatter in the binding energy, which is commonly present in DFT calculations. For medium sized clusters consisting of sulfuric acid and bases the DLPNO method yields a systematic underestimation of the binding energy compared to canonical coupled cluster results. The errors in the DFT binding energies appear to be more random, while the systematic nature of the DLPNO results allows the establishment of a scaling factor, to better mimic the canonical coupled cluster calculations. Based on the trends identified for the small and medium sized systems, we further extend the application of the DLPNO method to large acid - base clusters consisting of up to 10 molecules, which have previously been out of reach with accurate coupled cluster methods. Using the Atmospheric Cluster Dynamics Code (ACDC) we compare the sulfuric acid dimer formation based on the new DLPNO binding energies with previously published RI-CC2/aug-cc-pV(T+d)Z results. We also compare the simulated sulfuric acid dimer concentration as a function of the base concentration with measurement data from the CLOUD chamber and flow tube experiments. The DLPNO method, even after scaling, underpredicts the dimer concentration significantly. Reasons for this are discussed.

  2. Molecular-dynamics simulations of lead clusters

    NASA Astrophysics Data System (ADS)

    Hendy, S. C.; Hall, B. D.

    2001-08-01

    Molecular-dynamics simulations of nanometer-sized lead clusters have been performed using the Lim-Ong-Ercolessi glue potential [Surf. Sci. 269/270, 1109 (1992)]. The binding energies of clusters forming crystalline (fcc), decahedron and icosahedron structures are compared, showing that fcc cuboctahedra are the most energetically favored of these polyhedral model structures. However, simulations of the freezing of liquid droplets produced a characteristic form of surface-reconstructed ``shaved'' icosahedron, in which atoms are absent at the edges and apexes of the polyhedron. This arrangement is energetically favored for 600-4000 atom clusters. Larger clusters favor crystalline structures. Indeed, simulated freezing of a 6525-atom liquid droplet produced an imperfect fcc Wulff particle, containing a number of parallel stacking faults. The effects of temperature on the preferred structure of crystalline clusters below the melting point have been considered. The implications of these results for the interpretation of experimental data is discussed.

  3. Computer simulation of the interaction of ringlike carbon clusters with nanographene

    NASA Astrophysics Data System (ADS)

    Dzhurakhalov, A. A.; Stelmakh, V. G.; Yadgarov, I. D.

    2015-09-01

    Various cases of interaction of ringlike carbon clusters C7, C12 and C13 with a rectangular nanographene consisting of 272 atoms were studied and presented. It was found that this interaction results in the structural change in these clusters and in the local part of nanographene. The cohesive energies of these clusters in the isolated (free) state and their binding energies with nanographene have been calculated. The results show that despite this interaction the atoms of cluster are hold together as a single cluster thanks to the significantly higher cohesive energy of cluster the its binding energy with nanographene.

  4. 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

  5. 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.

  6. Preferential site occupancy observed in coexpanded argon-krypton clusters

    SciTech Connect

    Lundwall, M.; Bergersen, H.; Lindblad, A.; Oehrwall, G.; Svensson, S.; Bjoerneholm, O.; Tchaplyguine, M.

    2006-10-15

    Free heterogeneous argon-krypton clusters have been produced by coexpansion and investigated by means of x-ray photoelectron spectroscopy. By examining cluster surface and bulk binding energy shifts, relative intensities, and peak widths, we show that in the mixed argon-krypton clusters the krypton atoms favor the bulk and argon atoms are pushed to the surface. Furthermore, we show that krypton atoms in the surface layer occupy high-coordination sites and that heterogeneous argon-krypton clusters produced by coexpansion show the same surface structure as argon host clusters doped with krypton. These observations are supported by site-dependent calculations of chemical shifts.

  7. Quantum Monte Carlo methods and lithium cluster properties. [Atomic clusters

    SciTech Connect

    Owen, R.K.

    1990-12-01

    Properties of small lithium clusters with sizes ranging from n = 1 to 5 atoms were investigated using quantum Monte Carlo (QMC) methods. Cluster geometries were found from complete active space self consistent field (CASSCF) calculations. A detailed development of the QMC method leading to the variational QMC (V-QMC) and diffusion QMC (D-QMC) methods is shown. The many-body aspect of electron correlation is introduced into the QMC importance sampling electron-electron correlation functions by using density dependent parameters, and are shown to increase the amount of correlation energy obtained in V-QMC calculations. A detailed analysis of D-QMC time-step bias is made and is found to be at least linear with respect to the time-step. The D-QMC calculations determined the lithium cluster ionization potentials to be 0.1982(14) (0.1981), 0.1895(9) (0.1874(4)), 0.1530(34) (0.1599(73)), 0.1664(37) (0.1724(110)), 0.1613(43) (0.1675(110)) Hartrees for lithium clusters n = 1 through 5, respectively; in good agreement with experimental results shown in the brackets. Also, the binding energies per atom was computed to be 0.0177(8) (0.0203(12)), 0.0188(10) (0.0220(21)), 0.0247(8) (0.0310(12)), 0.0253(8) (0.0351(8)) Hartrees for lithium clusters n = 2 through 5, respectively. The lithium cluster one-electron density is shown to have charge concentrations corresponding to nonnuclear attractors. The overall shape of the electronic charge density also bears a remarkable similarity with the anisotropic harmonic oscillator model shape for the given number of valence electrons.

  8. A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The B4 resistance (R)-gene cluster, located in subtelomeric region of chromosome 4, is one of the largest clusters known in common bean (Phaseolus vulgaris, Pv). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-coil-Nucleotide-Binding-Site-Leucine-Rich...

  9. Yin Yang 1: a multifaceted protein beyond a transcription factor.

    PubMed

    Deng, Zhiyong; Cao, Paul; Wan, Mei Mei; Sui, Guangchao

    2010-01-01

    As a transcription factor, Yin Yang 1 (YY1) regulates the transcription of a dazzling list of genes and the number of its targets still mounts. Recent studies revealed that YY1 possesses functions independent of its DNA binding activity and its regulatory role in tumorigenesis has started to emerge.

  10. Theoretical studies of binding of mannose-binding protein to monosaccharides

    NASA Astrophysics Data System (ADS)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  11. Water may inhibit oxygen binding in hemoprotein models.

    PubMed

    Collman, James P; Decréau, Richard A; Dey, Abhishek; Yang, Ying

    2009-03-17

    Three distal imidazole pickets in a cytochrome c oxidase (CcO) model form a pocket hosting a cluster of water molecules. The cluster makes the ferrous heme low spin, and consequently the O(2) binding slow. The nature of the rigid proximal imidazole tail favors a high spin/low spin cross-over. The O(2) binding rate is enhanced either by removing the water, increasing the hydrophobicity of the gas binding pocket, or inserting a metal ion that coordinates to the 3 distal imidazole pickets.

  12. PREFACE: Nuclear Cluster Conference; Cluster'07

    NASA Astrophysics Data System (ADS)

    Freer, Martin

    2008-05-01

    The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

  13. Silver cluster chromophores for absorption enhancement of peptides.

    PubMed

    Kulesza, Alexander; Mitrić, Roland; Bonacić-Koutecký, Vlasta

    2009-04-23

    We present a theoretical study of the structural and optical properties of tripeptide-silver cluster hybrid systems which shows that silver clusters induce significant absorption enhancement in the spectral region between 225 and 350 nm with respect to the pure peptide. This allows the use of clusters as chromophores for absorption enhancement of peptides and proteins and offers a potential for different applications in biosensing. Furthermore, we demonstrate that cluster binding can change the conformational preference for the secondary structure type leading possibly to new functional properties.

  14. Cluster Physics with Merging Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Molnar, Sandor

    Collisions between galaxy clusters provide a unique opportunity to study matter in a parameter space which cannot be explored in our laboratories on Earth. In the standard ΛCDM model, where the total density is dominated by the cosmological constant (Λ) and the matter density by cold dark matter (CDM), structure formation is hierarchical, and clusters grow mostly by merging. Mergers of two massive clusters are the most energetic events in the universe after the Big Bang, hence they provide a unique laboratory to study cluster physics. The two main mass components in clusters behave differently during collisions: the dark matter is nearly collisionless, responding only to gravity, while the gas is subject to pressure forces and dissipation, and shocks and turbulence are developed during collisions. In the present contribution we review the different methods used to derive the physical properties of merging clusters. Different physical processes leave their signatures on different wavelengths, thus our review is based on a multifrequency analysis. In principle, the best way to analyze multifrequency observations of merging clusters is to model them using N-body/HYDRO numerical simulations. We discuss the results of such detailed analyses. New high spatial and spectral resolution ground and space based telescopes will come online in the near future. Motivated by these new opportunities, we briefly discuss methods which will be feasible in the near future in studying merging clusters.

  15. Structures and stabilities of copper encapsulated within silicon nano-clusters: Cu@Si n ( n = 9-15)

    NASA Astrophysics Data System (ADS)

    Hossain, Delwar; Pittman, Charles U., Jr.; Gwaltney, Steven R.

    2008-01-01

    Density functional electronic-structure calculations were performed for Cu@Si n ( n = 9-15) clusters. The lowest-energy endohedral structure and its stability for each Cu@Si n cluster were determined. The encapsulation of Cu within silicon clusters generates stable neutral Cu@Si n clusters. The binding energies and embedding energies of these clusters indicate that they are likely to be chemically stable. The relative cluster stabilities and other thermodynamic properties alternate with cluster size, with an apparent preference existing for clusters with an even number of Si atoms.

  16. Chemiluminescence in the Agglomeration of Metal Clusters

    PubMed

    König; Rabin; Schulze; Ertl

    1996-11-22

    The agglomeration of copper or silver atoms in a matrix of noble gas atoms to form small clusters may be accompanied by the emission of visible light. Spectral analysis reveals the intermediate formation of electronically excited atoms and dimers as the source of the chemiluminescence. A mechanism is proposed, according to which the gain in binding energy upon cluster formation may even lead to the ejection of excited fragments as a result of unstable intermediate configurations. A similar concept was introduced in the field of nuclear reactions by Niels Bohr 60 years ago.

  17. Photoelectron spectroscopy of nitromethane anion clusters

    NASA Astrophysics Data System (ADS)

    Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

    2016-08-01

    Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

  18. Gold-bismuth clusters.

    PubMed

    Martínez, Ana

    2014-08-07

    Metal clusters have interesting characteristics, such as the relationship between properties and size of the cluster. This is not always apparent, so theoretical studies can provide relevant information. In this report, optimized structures and electron donor-acceptor properties of AunBim clusters are reported (n + m = 2-7, 20). Density functional theory calculations were performed to obtain optimized structures. The ground states of gold clusters formed with up to seven atoms are planar. The presence of Bi modifies the structure, and the clusters become 3-D. Several optimized geometries have at least one Bi atom bonded to gold or bismuth atoms and form structures similar to NH3. This fragment is also present in clusters with 20 atoms, where the formation of Au3Bi stabilizes the structures. Bismuth clusters are better electron donors and worse electron acceptors than gold clusters. Mixed clusters fall in between these two extremes. The presence of Bi atoms in gold clusters modifies the electron donor-acceptor properties of the clusters, but there is no correlation between the number of Bi atoms present in the cluster and the capacity for donating electrons. The effect of planarity in Au19Bi clusters is the same as that in Au20 clusters. The properties of pure gold clusters are certainly interesting, but clusters formed by Bi and Au are more important because the introduction of different atoms modifies the geometry, the stability, and consequently the physical and chemical properties. Apparently, the presence of Bi may increase the reactivity of gold clusters, but further studies are necessary to corroborate this hypothesis.

  19. Nuclear Clusters in Astrophysics

    NASA Astrophysics Data System (ADS)

    Kubono, S.; Binh, Dam N.; Hayakawa, S.; Hashimoto, H.; Kahl, D.; Wakabayashi, Y.; Yamaguchi, H.; Teranishi, T.; Iwasa, N.; Komatsubara, T.; Kato, S.; Khiem, Le H.

    2010-03-01

    The role of nuclear clustering is discussed for nucleosynthesis in stellar evolution with Cluster Nucleosynthesis Diagram (CND) proposed before. Special emphasis is placed on α-induced stellar reactions together with molecular states for O and C burning.

  20. Matlab Cluster Ensemble Toolbox

    SciTech Connect

    Sapio, Vincent De; Kegelmeyer, Philip

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  1. STABILITY OF SMALL SELF-INTERSTITIAL CLUSTERS IN TUNGSTEN

    SciTech Connect

    Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

    2015-12-31

    Density functional theory was employed to explore the stability of interstitial clusters in W up to size seven. For each cluster size, the most stable configuration consists of parallel dumbbells. For clusters larger than size three, parallel dumbbells prefer to form in a multilayer fashion, instead of a planar structure. For size-7 clusters, the most stable configuration is a complete octahedron. The binding energy of a [111] dumbbell to the most stable cluster increases with cluster size, namely 2.49, 3.68, 4.76, 4.82, 5.47, and 6.85 eV for clusters of size 1, 2, 3, 4, 5, and 6, respectively. For a size-2 cluster, collinear dumbbells are still repulsive at the maximum allowable distance of 13.8 Å (the fifth neighbor along [111]). On the other hand, parallel dumbbells are strongly bound together. Two parallel dumbbells in which the axis-to-axis distance is within a cylindrical radius of 5.2 Å still exhibit a considerable binding of 0.28 eV. The most stable cluster in each size will be used to explore interactions with transmutation products.

  2. [Pathophysiology of cluster headache].

    PubMed

    Donnet, Anne

    2015-11-01

    The aetiology of cluster headache is partially unknown. Three areas are involved in the pathogenesis of cluster headache: the trigeminal nociceptive pathways, the autonomic system and the hypothalamus. The cluster headache attack involves activation of the trigeminal autonomic reflex. A dysfunction located in posterior hypothalamic gray matter is probably pivotal in the process. There is a probable association between smoke exposure, a possible genetic predisposition and the development of cluster headache.

  3. Nonpolytropic model for the Coma Cluster

    NASA Technical Reports Server (NTRS)

    Fusco-Femiano, R.; Hughes, John P.

    1994-01-01

    In this article we demonstrate, for the first time, how a physically motivated static model for both the gas and galaxies in the Coma Cluster of galaxies can jointly fit all available X-ray and optical imaging and spectroscopic data. The principal assumption of this nonpolytropic model (Cavaliere & Fusco-Femiano 1981, hereafter CFF), is that the intracluster gas temperature is proportional to the square of the galaxy velocity dispersion everywhere throughout the cluster; no other assumption about the gas temperature distribution is required. After demonstrating that the CFF nonpolytropic model is an adequate representation of the gas and galaxy distributions, the radial velocity dispersion profile, and the gas temperature distribution, we derive the following information about the Coma Cluster: 1. The central temperature is about 9 keV and the central density is 2.8 x 10(exp -3)/cm(exp 3) for the X-ray emitting plasma; 2. The binding mass of the cluster is approximately 2 x 10(exp 15) solar mass within 5 Mpc for (H(sub 0) = 50 km/sec/Mpc), with a mass-to-light ratio of approximately 160 solar mass/solar luminosity; 3. The contribution of the gas to the total virial mass increases with distance from the cluster center, and we estimate that this ratio is no greater than approximately 50% within 5 Mpc. The ability of the CFF nonpolytropic model to describe the current X-ray and optical data for the Coma Cluster suggests that a significant fraction of the thermal energy contained in the hot gas in this as well as other rich galaxy clusters may have come from the interaction between the galaxies and the ambient cluster medium. interaction between the galaxies and the ambient cluster medium.

  4. Clustering algorithm studies

    NASA Astrophysics Data System (ADS)

    Graf, Norman A.

    2001-07-01

    An object-oriented framework for undertaking clustering algorithm studies has been developed. We present here the definitions for the abstract Cells and Clusters as well as the interface for the algorithm. We intend to use this framework to investigate the interplay between various clustering algorithms and the resulting jet reconstruction efficiency and energy resolutions to assist in the design of the calorimeter detector.

  5. Computer simulation structure and vibrations of small metal cluster on the Cu (111) surface

    NASA Astrophysics Data System (ADS)

    Borisova, Svetlana D.; Rusina, Galina G.

    2015-10-01

    Vibrational properties of the small tetrahedral cluster of Co on the Cu (111) surface are studied by using tight-binding second moment approximation interatomic interaction potentials. It was shown that interaction of the clusters with substrate leads to arising of frustrated translation and frustrated rotation in-plane polarized vibrational modes localized on the cluster atoms. The Co4 cluster on the surface the high frequency modes remain strongly localized and mixed with the nearest neighbor atoms vibrations.

  6. Computer simulation structure and vibrations of small metal cluster on the Cu (111) surface

    SciTech Connect

    Borisova, Svetlana D. Rusina, Galina G.

    2015-10-27

    Vibrational properties of the small tetrahedral cluster of Co on the Cu (111) surface are studied by using tight-binding second moment approximation interatomic interaction potentials. It was shown that interaction of the clusters with substrate leads to arising of frustrated translation and frustrated rotation in-plane polarized vibrational modes localized on the cluster atoms. The Co{sub 4} cluster on the surface the high frequency modes remain strongly localized and mixed with the nearest neighbor atoms vibrations.

  7. Tight-Binding and Hueckel Models of Molecular Clusters

    DTIC Science & Technology

    1990-05-01

    Chem. Phys. Lett. 163, 323 (1989); Phys. Rev. Lett. 64, 551 (1990). 16. H. Kupka and K. Jug, Chem. Phys. 130, 23 (1989). 17. Y. Wang , T. F. George...D. M. Lindsay and A. C. Beri, J. Chem. Phys. 86, 3493 (1987). 18. D. M. Lindsay, Y. Wang and T. F. George, J. Chem. Phys. 86, 3500 (1987). 23 Table 1...Department of Chemistry Northwestern University University of California Evanston, IL 60208 Irvine, CA 92717 Professor Frank DiSalvo Professor Roald Hoffmann

  8. A new clustering strategy

    NASA Astrophysics Data System (ADS)

    Feng, Jian-xin; Tang, Jia-fu; Wang, Guang-xing

    2007-04-01

    On the basis of the analysis of clustering algorithm that had been proposed for MANET, a novel clustering strategy was proposed in this paper. With the trust defined by statistical hypothesis in probability theory and the cluster head selected by node trust and node mobility, this strategy can realize the function of the malicious nodes detection which was neglected by other clustering algorithms and overcome the deficiency of being incapable of implementing the relative mobility metric of corresponding nodes in the MOBIC algorithm caused by the fact that the receiving power of two consecutive HELLO packet cannot be measured. It's an effective solution to cluster MANET securely.

  9. Star cluster dynamics.

    PubMed

    Vesperini, Enrico

    2010-02-28

    Dynamical evolution plays a key role in shaping the current properties of star clusters and star cluster systems. A detailed understanding of the effects of evolutionary processes is essential to be able to disentangle the properties that result from dynamical evolution from those imprinted at the time of cluster formation. In this review, I focus my attention on globular clusters, and review the main physical ingredients driving their early and long-term evolution, describe the possible evolutionary routes and show how cluster structure and stellar content are affected by dynamical evolution.

  10. Globular cluster X-ray sources

    NASA Astrophysics Data System (ADS)

    Pooley, D.

    We know from observations that globular clusters are very efficient catalysts in forming unusual binary systems, such as low-mass X-ray binaries (LMXBs), cataclysmic variables (CVs), and millisecond pulsars (MSPs), with formation rates per unit mass exceeding those in the Galactic disk by orders of magnitude. The high stellar densities in globular clusters trigger various dynamical interactions: exchange encounters, direct collisions, destruction of binaries, and tidal capture. This binary population is, in turn, critical to the stabilization of globular clusters against gravitational collapse; the long-term stability of a cluster is thought to depend on tapping into the gravitational binding energy of such close binaries. I will present an overview of the current state of globular cluster X-ray observations, as well as our work on deep Chandra observations of M4, where we reach some of the lowest X-ray luminosities in any globular cluster (comparable to the deep observations of 47 Tuc and NGC 6397). One of M4 X-ray sources previously classified as a white dwarf binary is likely a neutron star binary, and another X-ray source is a sub-subgiant, the nature of which is still unclear. skip=3pt

  11. Preferential site occupancy of krypton atoms on free argon-cluster surfaces.

    PubMed

    Lundwall, M; Lindblad, A; Bergersen, H; Rander, T; Ohrwall, G; Tchaplyguine, M; Svensson, S; Björneholm, O

    2006-07-07

    Argon clusters have been doped with krypton atoms in a pick-up setup and investigated by means of ultraviolet and x-ray photoelectron spectroscopy (UPS and XPS). The width of the krypton surface feature in the XPS spectra from mixed krypton/argon clusters has been studied and found to be narrower than in the case of homogeneous krypton clusters. By considering known spectral broadening mechanisms of the cluster features and the electron binding energy shift of the cluster surface feature relative to the atomic signal, we conclude that krypton ad-atoms preferentially occupy high-coordination surface sites on the argon host-cluster.

  12. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  13. Fuzzy Subspace Clustering

    NASA Astrophysics Data System (ADS)

    Borgelt, Christian

    In clustering we often face the situation that only a subset of the available attributes is relevant for forming clusters, even though this may not be known beforehand. In such cases it is desirable to have a clustering algorithm that automatically weights attributes or even selects a proper subset. In this paper I study such an approach for fuzzy clustering, which is based on the idea to transfer an alternative to the fuzzifier (Klawonn and Höppner, What is fuzzy about fuzzy clustering? Understanding and improving the concept of the fuzzifier, In: Proc. 5th Int. Symp. on Intelligent Data Analysis, 254-264, Springer, Berlin, 2003) to attribute weighting fuzzy clustering (Keller and Klawonn, Int J Uncertain Fuzziness Knowl Based Syst 8:735-746, 2000). In addition, by reformulating Gustafson-Kessel fuzzy clustering, a scheme for weighting and selecting principal axes can be obtained. While in Borgelt (Feature weighting and feature selection in fuzzy clustering, In: Proc. 17th IEEE Int. Conf. on Fuzzy Systems, IEEE Press, Piscataway, NJ, 2008) I already presented such an approach for a global selection of attributes and principal axes, this paper extends it to a cluster-specific selection, thus arriving at a fuzzy subspace clustering algorithm (Parsons, Haque, and Liu, 2004).

  14. Structure and analysis of atomic vibrations in clusters of Cu n ( n ≤ 20)

    NASA Astrophysics Data System (ADS)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2013-02-01

    The binding energy, equilibrium geometry, and vibration frequencies of free clusters Cu n (2 ≤ n ≤ 20) are calculated using the potentials of interatomic interactions found using the tight-binding approximation. The nonmonotonic dependence of the clusters' minimum vibration frequency on their sizes and the extreme values for the number of atoms in a cluster n = 4, 6, 13, and 19 is demonstrated. It is noted that this result agrees with the theoretical and experimental data on stable structures of small and medium metallic clusters.

  15. Nanophase materials assembled from clusters

    SciTech Connect

    Siegel, R.W.

    1992-02-01

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

  16. Infrared spectroscopic probing of dimethylamine clusters in an Ar matrix.

    PubMed

    Li, Siyang; Kjaergaard, Henrik G; Du, Lin

    2016-02-01

    Amines have many atmospheric sources and their clusters play an important role in aerosol nucleation processes. Clusters of a typical amine, dimethylamine (DMA), of different sizes were measured with matrix isolation IR (infrared) and NIR (near infrared) spectroscopy. The NIR vibrations are more separated and therefore it is easier to distinguish different sizes of clusters in this region. The DMA clusters, up to DMA tetramer, have been optimized using density functional methods, and the geometries, binding energies and thermodynamic properties of DMA clusters were obtained. The computed frequencies and intensities of NH-stretching vibrations in the DMA clusters were used to interpret the experimental spectra. We have identified the fundamental transitions of the bonded NH-stretching vibration and the first overtone transitions of the bonded and free NH-stretching vibration in the DMA clusters. Based on the changes in vibrational intensities during the annealing processes, the growth of clusters was clearly observed. The results of annealing processes indicate that DMA molecules tend to form larger clusters with lower energies under matrix temperatures, which is also supported by the calculated reaction energies of cluster formation.

  17. Orientation-dependent binding energy of graphene on palladium

    SciTech Connect

    Kappes, Branden B.; Ebnonnasir, Abbas; Ciobanu, Cristian V.; Kodambaka, Suneel

    2013-02-04

    Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

  18. Information-based clustering

    PubMed Central

    Slonim, Noam; Atwal, Gurinder Singh; Tkačik, Gašper; Bialek, William

    2005-01-01

    In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster “prototype,” does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures. PMID:16352721

  19. Clusters of galaxies

    NASA Astrophysics Data System (ADS)

    Vikhlinin, A. A.; Kravtsov, A. V.; Markevich, M. L.; Sunyaev, R. A.; Churazov, E. M.

    2014-04-01

    Galaxy clusters are formed via nonlinear growth of primordial density fluctuations and are the most massive gravitationally bound objects in the present Universe. Their number density at different epochs and their properties depend strongly on the properties of dark matter and dark energy, making clusters a powerful tool for observational cosmology. Observations of the hot gas filling the gravitational potential well of a cluster allows studying gasdynamic and plasma effects and the effect of supermassive black holes on the heating and cooling of gas on cluster scales. The work of Yakov Borisovich Zeldovich has had a profound impact on virtually all cosmological and astrophysical studies of galaxy clusters, introducing concepts such as the Harrison-Zeldovich spectrum, the Zeldovich approximation, baryon acoustic peaks, and the Sunyaev-Zeldovich effect. Here, we review the most basic properties of clusters and their role in modern astrophysics and cosmology.

  20. Binding energy effects in cascade evolution and sputtering

    SciTech Connect

    Robinson, M.T.

    1995-06-01

    The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced {approximately}8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced {approximately}9% at 1 keV and {approximately}15% at 100 keV. In sputtering, the mean binding energy is reduced {approximately}8% in Cu and {approximately}15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits.

  1. Chemistry Within Molecular Clusters

    DTIC Science & Technology

    1990-01-01

    DME )nCH3OCH 2 +). We speculate that this is due to the fragments being consumed by an ion-molecule reaction within the cluster. One likely candidate is...the ion-molecule reaction of the fragment cations with a neutral DME , within the bulk cluster to form a trimethyloxonlum cation intermediate. This...the observed products. We therefore speculate that the DME cluster reactions leading to the same products, should involve the same mechanism found to

  2. Chemistry Within Molecular Clusters

    DTIC Science & Technology

    1992-06-01

    and ( DME ).CH 3OCH2+). We speculate that this is due to the fragments being consumed by an ion-molecule reaction within the cluster. A likely candidate...is the ion-molecule reaction of the fragment cations with a neutral DME within the bulk cluster, to form a trimethyloxonium cation intermediate...a trimethyloxonium intermediate as the common intermediate for the observed products. We therefore speculate that the DME cluster reactions leading to

  3. Cluster State Quantum Computation

    DTIC Science & Technology

    2014-02-01

    nearest neighbor cluster state has been shown to be a universal resource for MBQC thus we can say our quantum computer is universal. We note that...CLUSTER STATE QUANTUM COMPUTATION FEBRUARY 2014 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED STINFO COPY AIR FORCE...TITLE AND SUBTITLE CLUSTER STATE QUANTUM COMPUTATION 5a. CONTRACT NUMBER IN-HOUSE 5b. GRANT NUMBER N/A 5c. PROGRAM ELEMENT NUMBER 62788F 6

  4. Chemical Reactions in Clusters

    DTIC Science & Technology

    1992-11-04

    NH 3)n, n _> 4, clusters has been attributed to the (solvated) naphtholate anion.3a A single picosecond decay measurement has been reported which...vibrational energy in the cluster Sl state. The data are summarized in Table I. A model to explain these decay results can be constructed based on a proton...11 TITLE (Include Security Classification) Chemical Reactions in Clusters 12 PERSONAL AUTHOR(S) Elliot R. Bernstein 13a TYPE OF REPORT 13b TIME COVERED

  5. 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.

  6. Star Clusters within FIRE

    NASA Astrophysics Data System (ADS)

    Perez, Adrianna; Moreno, Jorge; Naiman, Jill; Ramirez-Ruiz, Enrico; Hopkins, Philip F.

    2017-01-01

    In this work, we analyze the environments surrounding star clusters of simulated merging galaxies. Our framework employs Feedback In Realistic Environments (FIRE) model (Hopkins et al., 2014). The FIRE project is a high resolution cosmological simulation that resolves star forming regions and incorporates stellar feedback in a physically realistic way. The project focuses on analyzing the properties of the star clusters formed in merging galaxies. The locations of these star clusters are identified with astrodendro.py, a publicly available dendrogram algorithm. Once star cluster properties are extracted, they will be used to create a sub-grid (smaller than the resolution scale of FIRE) of gas confinement in these clusters. Then, we can examine how the star clusters interact with these available gas reservoirs (either by accreting this mass or blowing it out via feedback), which will determine many properties of the cluster (star formation history, compact object accretion, etc). These simulations will further our understanding of star formation within stellar clusters during galaxy evolution. In the future, we aim to enhance sub-grid prescriptions for feedback specific to processes within star clusters; such as, interaction with stellar winds and gas accretion onto black holes and neutron stars.

  7. Melting of nickel clusters

    SciTech Connect

    Garzon, I.L.; Jellinek, J.

    1991-12-31

    The meltinglike phenomenon in Ni{sub n}, n = 19,20,55, clusters is studied using microcanonical molecular dynamics simulations. The interaction between the atoms in the clusters is modelled by a size-dependent Gupta-like potential that incorporates many-body effects. The clusters display the ``usual`` stages in their meltinglike transition, which characterize also Lennard-Jones (e.g., noble gas) and ionic clusters. In addition, Ni{sub 20} passes through a so-called premelting stage found earlier also for Ni{sub 14}. 11 ref., 3 figs.

  8. Melting of nickel clusters

    SciTech Connect

    Garzon, I.L. . Inst. de Fisica); Jellinek, J. )

    1991-01-01

    The meltinglike phenomenon in Ni{sub n}, n = 19,20,55, clusters is studied using microcanonical molecular dynamics simulations. The interaction between the atoms in the clusters is modelled by a size-dependent Gupta-like potential that incorporates many-body effects. The clusters display the usual'' stages in their meltinglike transition, which characterize also Lennard-Jones (e.g., noble gas) and ionic clusters. In addition, Ni{sub 20} passes through a so-called premelting stage found earlier also for Ni{sub 14}. 11 ref., 3 figs.

  9. Mini-clusters

    NASA Technical Reports Server (NTRS)

    Chinellato, J. A.; Dobrigkeit, C.; Bellandifilho, J.; Lattes, C. M. G.; Menon, M. J.; Navia, C. E.; Pamilaju, A.; Sawayanagi, K.; Shibuya, E. H.; Turtelli, A., Jr.

    1985-01-01

    Experimental results of mini-clusters observed in Chacaltaya emulsion chamber no.19 are summarized. The study was made on 54 single core shower upper and 91 shower clusters of E(gamma) 10 TeV from 30 families which are visible energy greater than 80 TeV and penetrate through both upper and lower detectors of the two-story chamber. The association of hadrons in mini-cluster is made clear from their penetrative nature and microscopic observation of shower continuation in lower chamber. Small P sub t (gamma) of hadrons in mini-clusters remained in puzzle.

  10. Clustering versus non-clustering phase synchronizations

    SciTech Connect

    Liu, Shuai; Zhan, Meng

    2014-03-15

    Clustering phase synchronization (CPS) is a common scenario to the global phase synchronization of coupled dynamical systems. In this work, a novel scenario, the non-clustering phase synchronization (NPS), is reported. It is found that coupled systems do not transit to the global synchronization until a certain sufficiently large coupling is attained, and there is no clustering prior to the global synchronization. To reveal the relationship between CPS and NPS, we further analyze the noise effect on coupled phase oscillators and find that the coupled oscillator system can change from CPS to NPS with the increase of noise intensity or system disorder. These findings are expected to shed light on the mechanism of various intriguing self-organized behaviors in coupled systems.

  11. Ureaplasma urealyticum binds mannose-binding lectin.

    PubMed

    Benstein, Barbara D; Ourth, Donald D; Crouse, Dennis T; Shanklin, D Radford

    2004-10-01

    Mannose-binding C-type lectin (MBL) is an important component of innate immunity in mammals. Mannose-binding lectin (MBL), an acute phase protein, acts as an opsonin for phagocytosis and also activates the mannan-binding lectin complement pathway. It may play a particularly significant role during infancy before adequate specific protection can be provided by the adaptive immune system. Ureaplasma urealyticum has been linked to several diseases including pneumonia and chronic lung disease (CLD) in premature infants. We therefore investigated the ability of U. urealyticum to bind MBL. A guinea pig IgG anti-rabbit-MBL antiserum was produced. An immunoblot (dot-blot) assay done on nitrocellulose membrane determined that the anti-MBL antibody had specificity against both rabbit and human MBL. Pure cultures of U. urealyticum, serotype 3, were used to make slide preparations. The slides containing the organisms were then incubated with nonimmune rabbit serum containing MBL. Ureaplasma was shown to bind rabbit MBL with an immunocytochemical assay using the guinea pig IgG anti-rabbit MBL antiserum. Horseradish peroxidase (HRP)-labeled anti-guinea pig IgG was used to localize the reaction. The anti-MBL antiserum was also used in an immunocytochemical assay to localize U. urealyticum in histological sections of lungs from mice specifically infected with this organism. The same method also indicated binding of MBL by ureaplasma in human lung tissue obtained at autopsy from culture positive infants. Our results demonstrate that ureaplasma has the capacity to bind MBL. The absence of MBL may play a role in the predisposition of diseases related to this organism.

  12. A nonparametric clustering technique which estimates the number of clusters

    NASA Technical Reports Server (NTRS)

    Ramey, D. B.

    1983-01-01

    In applications of cluster analysis, one usually needs to determine the number of clusters, K, and the assignment of observations to each cluster. A clustering technique based on recursive application of a multivariate test of bimodality which automatically estimates both K and the cluster assignments is presented.

  13. Theoretical studies of the electronic structure of small metal clusters

    NASA Technical Reports Server (NTRS)

    Jordan, K. D.

    1982-01-01

    Theoretical studies of the electronic structure of metal clusters, in particular clusters of Group IIA and IIB atoms were conducted. Early in the project it became clear that electron correlation involving d orbitals plays a more important role in the binding of these clusters than had been previously anticipated. This necessitated that computer codes for calculating two electron integrals and for constructing the resulting CI Hamiltonions be replaced with newer, more efficient procedures. Program modification, interfacing and testing were performed. Results of both plans are reported.

  14. Field Evaporation of Grounded Arsenic Doped Silicon Clusters

    NASA Astrophysics Data System (ADS)

    Deng, Zexiang; She, Juncong; Li, Zhibing; Wang, Weiliang; Chen, Qiang

    2015-08-01

    We have investigated the field evaporation of grounded arsenic (As) doped silicon (Si) clusters composed of 52 atoms with density functional theory (DFT) to mimic Si nano structures of hundreds of nanometers long standing on a substrate. Six cluster structures with different As doping concentrations and dopant locations are studied. The critical evaporation electric fields are found to be lower for clusters with higher doping concentrations and doping sites closer to the surface. We attribute the difference to the difference in binding energies corresponding to the different As-doping concentrations and to the doping locations. Our theoretical study could shed light on the stability of nano apexes under high electric field.

  15. Photoionization of molecular clusters

    NASA Astrophysics Data System (ADS)

    Andres, R. P.; Calo, J. M.

    1981-12-01

    An experimental apparatus consisting of a novel multiple expansion cluster source coupled with a molecular beam system and photoionization mass spectrometer has been designed and constructed. This apparatus has been thoroughly tested and preliminary measurements of the growth kinetics of water clusters and the photoionization cross section of the water dimer have been carried out.

  16. Probability and Cancer Clusters

    ERIC Educational Resources Information Center

    Hamilton-Keene, Rachael; Lenard, Christoper T.; Mills, Terry M.

    2009-01-01

    Recently there have been several news items about possible cancer clusters in the Australian media. The term "cancer cluster" is used when an unusually large number of people in one geographic area, often a workplace, are diagnosed with cancer in a short space of time. In this paper the authors explore this important health issue using…

  17. Coma cluster of galaxies

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Atlas Image mosaic, covering 34' x 34' on the sky, of the Coma cluster, aka Abell 1656. This is a particularly rich cluster of individual galaxies (over 1000 members), most prominently the two giant ellipticals, NGC 4874 (right) and NGC 4889 (left). The remaining members are mostly smaller ellipticals, but spiral galaxies are also evident in the 2MASS image. The cluster is seen toward the constellation Coma Berenices, but is actually at a distance of about 100 Mpc (330 million light years, or a redshift of 0.023) from us. At this distance, the cluster is in what is known as the 'Hubble flow,' or the overall expansion of the Universe. As such, astronomers can measure the Hubble Constant, or the universal expansion rate, based on the distance to this cluster. Large, rich clusters, such as Coma, allow astronomers to measure the 'missing mass,' i.e., the matter in the cluster that we cannot see, since it gravitationally influences the motions of the member galaxies within the cluster. The near-infrared maps the overall luminous mass content of the member galaxies, since the light at these wavelengths is dominated by the more numerous older stellar populations. Galaxies, as seen by 2MASS, look fairly smooth and homogeneous, as can be seen from the Hubble 'tuning fork' diagram of near-infrared galaxy morphology. Image mosaic by S. Van Dyk (IPAC).

  18. Mixed-Initiative Clustering

    ERIC Educational Resources Information Center

    Huang, Yifen

    2010-01-01

    Mixed-initiative clustering is a task where a user and a machine work collaboratively to analyze a large set of documents. We hypothesize that a user and a machine can both learn better clustering models through enriched communication and interactive learning from each other. The first contribution or this thesis is providing a framework of…

  19. Cluster Guide. Accounting Occupations.

    ERIC Educational Resources Information Center

    Beaverton School District 48, OR.

    Based on a recent task inventory of key occupations in the accounting cluster taken in the Portland, Oregon, area, this curriculum guide is intended to assist administrators and teachers in the design and implementation of high school accounting cluster programs. The guide is divided into four major sections: program organization and…

  20. Marketing Occupations. Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    This cluster guide, which is designed to show teachers what specific knowledge and skills qualify high school students for entry-level employment (or postsecondary training) in marketing occupations, is organized into three sections: (1) cluster organization and implementation, (2) instructional emphasis areas, and (3) assessment. The first…

  1. Ultrametric Hierarchical Clustering Algorithms.

    ERIC Educational Resources Information Center

    Milligan, Glenn W.

    1979-01-01

    Johnson has shown that the single linkage and complete linkage hierarchical clustering algorithms induce a metric on the data known as the ultrametric. Johnson's proof is extended to four other common clustering algorithms. Two additional methods also produce hierarchical structures which can violate the ultrametric inequality. (Author/CTM)

  2. [Cluster headache differential diagnosis].

    PubMed

    Guégan-Massardier, Evelyne; Laubier, Cécile

    2015-11-01

    Cluster headache is characterized by disabling stereotyped headache. Early diagnosis allows appropriate treatment, unfortunately diagnostic errors are frequent. The main differential diagnoses are other primary or essential headaches. Migraine, more frequent and whose diagnosis is carried by excess, trigeminal neuralgia or other trigemino-autonomic cephalgia. Vascular or tumoral underlying condition can mimic cluster headache, neck and brain imaging is recommended, ideally MRI.

  3. Targeting Clusters, Achieving Excellence.

    ERIC Educational Resources Information Center

    Rosenfeld, Stuart; Jacobs, Jim; Liston, Cynthia

    2003-01-01

    Suggests that groups, or clusters, of industries form partnerships with community colleges in order to positively impact economic development. Asserts that a cluster-oriented community college system requires innovation, specialized resources and expertise, knowledge of trends, and links to industry. Offers suggestions for developing such a…

  4. Multiple frame cluster tracking

    NASA Astrophysics Data System (ADS)

    Gadaleta, Sabino; Klusman, Mike; Poore, Aubrey; Slocumb, Benjamin J.

    2002-08-01

    Tracking large number of closely spaced objects is a challenging problem for any tracking system. In missile defense systems, countermeasures in the form of debris, chaff, spent fuel, and balloons can overwhelm tracking systems that track only individual objects. Thus, tracking these groups or clusters of objects followed by transitions to individual object tracking (if and when individual objects separate from the groups) is a necessary capability for a robust and real-time tracking system. The objectives of this paper are to describe the group tracking problem in the context of multiple frame target tracking and to formulate a general assignment problem for the multiple frame cluster/group tracking problem. The proposed approach forms multiple clustering hypotheses on each frame of data and base individual frame clustering decisions on the information from multiple frames of data in much the same way that MFA or MHT work for individual object tracking. The formulation of the assignment problem for resolved object tracking and candidate clustering methods for use in multiple frame cluster tracking are briefly reviewed. Then, three different formulations are presented for the combination of multiple clustering hypotheses on each frame of data and the multiple frame assignments of clusters between frames.

  5. Brightest Cluster Galaxy Identification

    NASA Astrophysics Data System (ADS)

    Leisman, Luke; Haarsma, D. B.; Sebald, D. A.; ACCEPT Team

    2011-01-01

    Brightest cluster galaxies (BCGs) play an important role in several fields of astronomical research. The literature includes many different methods and criteria for identifying the BCG in the cluster, such as choosing the brightest galaxy, the galaxy nearest the X-ray peak, or the galaxy with the most extended profile. Here we examine a sample of 75 clusters from the Archive of Chandra Cluster Entropy Profile Tables (ACCEPT) and the Sloan Digital Sky Survey (SDSS), measuring masked magnitudes and profiles for BCG candidates in each cluster. We first identified galaxies by hand; in 15% of clusters at least one team member selected a different galaxy than the others.We also applied 6 other identification methods to the ACCEPT sample; in 30% of clusters at least one of these methods selected a different galaxy than the other methods. We then developed an algorithm that weighs brightness, profile, and proximity to the X-ray peak and centroid. This algorithm incorporates the advantages of by-hand identification (weighing multiple properties) and automated selection (repeatable and consistent). The BCG population chosen by the algorithm is more uniform in its properties than populations selected by other methods, particularly in the relation between absolute magnitude (a proxy for galaxy mass) and average gas temperature (a proxy for cluster mass). This work supported by a Barry M. Goldwater Scholarship and a Sid Jansma Summer Research Fellowship.

  6. Dynamical Analyses of Galaxy Clusters With Large Redshift Samples

    NASA Astrophysics Data System (ADS)

    Mohr, J. J.; Richstone, D. O.; Wegner, G.

    1998-12-01

    We construct equilibrium models of galaxy orbits in five nearby galaxy clusters to study the distribution of binding mass, the nature of galaxy orbits and the kinematic differences between cluster populations of emission-line and non emission-line galaxies. We avail ourselves of 1718 galaxy redshifts (and 1203 cluster member redshifts) in this Jeans analysis; most of these redshifts are new, coming from multifiber spectroscopic runs on the MDM 2.4m with the Decaspec and queue observing on WIYN with Hydra. In addition to the spectroscopic data we have V and R band CCD mosaics (obtained with the MDM 1.3m) of the Abell region in each of these clusters. Our scientific goals include: (i) a quantitative estimate of the range of binding masses M500 consistent with the optical and X-ray data, (ii) an estimate of the typical galaxy oribital anisotropies required to make the galaxy data consistent with the NFW expectation for the cluster potential, (iii) a better understanding of the systematics inherent in the process of rescaling and ``stacking'' galaxy cluster observations, (iv) a reexamination of the recent CNOC results implying that emission-line (blue) galaxies are an equilibrium population with a more extended radial distribution than their non emission-line (red) galaxy counterparts and (v) a measure of the galaxy contribution to the cluster mass of baryons.

  7. Evolving nucleotide binding surfaces

    NASA Technical Reports Server (NTRS)

    Kieber-Emmons, T.; Rein, R.

    1981-01-01

    An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

  8. Hybridization schemes for clusters

    NASA Astrophysics Data System (ADS)

    Wales, David J.

    The concept of an optimum hybridization scheme for cluster compounds is developed with particular reference to electron counting. The prediction of electron counts for clusters and the interpretation of the bonding is shown to depend critically upon the presumed hybridization pattern of the cluster vertex atoms. This fact has not been properly appreciated in previous work, particularly in applications of Stone's tensor surface harmonic (TSH) theory, but is found to be a useful tool when dealt with directly. A quantitative definition is suggested for the optimum cluster hybridization pattern based directly upon the ease of interpretation of the molecular orbitals, and results are given for a range of species. The relationship of this scheme to the detailed cluster geometry is described using Löwdin's partitioned perturbation theory, and the success and range of application of TSH theory are discussed.

  9. 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

  10. Galaxy cluster's rotation

    NASA Astrophysics Data System (ADS)

    Manolopoulou, M.; Plionis, M.

    2017-03-01

    We study the possible rotation of cluster galaxies, developing, testing, and applying a novel algorithm which identifies rotation, if such does exist, as well as its rotational centre, its axis orientation, rotational velocity amplitude, and, finally, the clockwise or counterclockwise direction of rotation on the plane of the sky. To validate our algorithms we construct realistic Monte Carlo mock rotating clusters and confirm that our method provides robust indications of rotation. We then apply our methodology on a sample of Abell clusters with z ≲ 0.1 with member galaxies selected from the Sloan Digital Sky Survey DR10 spectroscopic data base. After excluding a number of substructured clusters, which could provide erroneous indications of rotation, and taking into account the expected fraction of misidentified coherent substructure velocities for rotation, provided by our Monte Carlo simulation analysis, we find that ∼23 per cent of our clusters are rotating under a set of strict criteria. Loosening the strictness of the criteria, on the expense of introducing spurious rotation indications, we find this fraction increasing to ∼28 per cent. We correlate our rotation indicators with the cluster dynamical state, provided either by their Bautz-Morgan type or by their X-ray isophotal shape and find for those clusters showing rotation within 1.5 h^{-1}_{70} Mpc that the significance of their rotation is related to the dynamically younger phases of cluster formation but after the initial anisotropic accretion and merging has been completed. Finally, finding rotational modes in galaxy clusters could lead to the necessity of correcting the dynamical cluster mass calculations.

  11. Metallic clusters on a model surface: Quantum versus geometric effects

    NASA Astrophysics Data System (ADS)

    Blundell, S. A.; Haldar, Soumyajyoti; Kanhere, D. G.

    2011-08-01

    We determine the structure and melting behavior of supported metallic clusters using an ab initio density-functional-based treatment of intracluster interactions and an approximate treatment of the surface as an idealized smooth plane yielding an effective Lennard-Jones interaction with the ions of the cluster. We apply this model to determine the structure of sodium clusters containing from 4 to 22 atoms, treating the cluster-surface interaction strength as a variable parameter. For a strong cluster-surface interaction, the clusters form two-dimensional (2D) monolayer structures; comparisons with calculations of structure and dissociation energy performed with a classical Gupta interatomic potential show clearly the role of quantum shell effects in the metallic binding in this case, and evidence is presented that these shell effects correspond to those for a confined 2D electron gas. The thermodynamics and melting behavior of a supported Na20 cluster is considered in detail using the model for several cluster-surface interaction strengths. We find quantitative differences in the melting temperatures and caloric curve from density-functional and Gupta treatments of the valence electrons. A clear dimensional effect on the melting behavior is also demonstrated, with 2D structures showing melting temperatures above those of the bulk or (at very strong cluster-surface interactions) no clear meltinglike transition.

  12. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.

    PubMed

    Slot, Jason C; Rokas, Antonis

    2011-01-25

    Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK:

  13. Optical binding between dielectric nanowires (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Hanna, Simon; Simpson, Stephen H.

    2016-09-01

    Optical binding occurs when micron-sized particles interact through the exchange of scattered photons. It has been observed both in systems of colloidal dielectric particles and between metallic nanoparticles, and can result in the formation of clusters and coupled dynamical behaviour. Optical binding between spherical particles has been studied in some detail, but little work has appeared in the literature to describe binding effects in lower symmetry systems. In the present paper we discuss recent theoretical work and computer simulations of optical binding effects operating between dielectric nanowires in counter propagating beams. The reduction in symmetry from simple spheres introduces new opportunities for binding, including different types of orientational ordering and anisotropies in the spatial arrangements that are possible for the bound particles. Various ordered configurations are possible, including ladder-like structures and oriented lattices. The stability of these structures to thermal perturbations will be discussed. Asymmetric arrangements of the nanowires are also possible, as a consequence of interactions between the nanowires and the underlying counter-propagating laser field. These configurations lead to a diversity of non-conservative effects, including uniform translation in linearly polarised beams and synchronous rotations in circularly polarised beams, suggesting potential applications of such bound structures in micro-machines.

  14. Small Al clusters on the Cu(111) surface: Atomic relaxation and vibrational properties

    NASA Astrophysics Data System (ADS)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2010-11-01

    The relaxation and vibrational properties of both Al clusters and the (111) surface of a copper sub-strate were studied using the interatomic interaction potentials obtained in a tight-binding approximation. The presence of small aluminum clusters led to modification of the vibrational states of the substrate, a shift of the Rayleigh mode, and excitation of new Z-polarized modes. Hybridized modes localized on the cluster adatoms and the neighboring atoms of the substrate were found in the phonon spectrum. The localized dipole-active modes of the cluster and their strong hybridization with vibrations of the substrate points to desorption stability of the tri- and heptaatomic clusters.

  15. Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

    DOEpatents

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

    2009-12-22

    Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

  16. Evolution Properties of Clusters and AXAF Contributions to understanding Clusters

    NASA Technical Reports Server (NTRS)

    Jones, Christine

    1998-01-01

    Our ROSAT survey for distant clusters of galaxies contains the largest solid angle of all ROSAT pointed surveying and thus has sufficient area to test the previously reported cluster evolution. We find significant negative cluster evolution, i.e,, at high redshifts there are fewer luminous clusters than at present. We compare optical cluster properties for the most distant clusters in the ROSAT survey with those measured for nearby clusters. We also present AXAF capabilities and show how AXAF will significantly extend our understanding of cluster properties and their cosmological evolution.

  17. Studies in clustering theory

    NASA Astrophysics Data System (ADS)

    Stell, George

    In recent years the properties of percolation models have been studied intensively. The purpose of our project was to develop a general theory of percolation and clustering between particles of arbitrary size and shape, with arbitrary correlations between them. The goal of such a theory includes the treatment of continuum percolation as well as a novel treatment of lattice percolation. We made substantial progress toward this goal. The quantities basic to a description of clustering, the mean cluster size, mean number of clusters, etc., were developed. Concise formulas were given for the terms in such series, and proved, at least for sufficiently low densities, that the series are absolutely convergent. These series can now be used to construct Pade approximants that will allow one to probe the percolation transition. A scaled-particle theory of percolation was developed which gives analytic approximants for the mean number of clusters in a large class of two and three dimensional percolation models. Although this quantity is essential in many applications, e.g., explaining colligative properties, and interpreting low-angle light-scattering data, no systematic studies of it have been done before this work. Recently carried out detailed computer simulations show that the mean number of clusters is given to high accuracy by several of there approximations. Extensions of this work will allow calculation of the complete cluster size distribution.

  18. Nuclear Star Clusters

    NASA Astrophysics Data System (ADS)

    Neumayer, Nadine

    2017-03-01

    The centers of galaxies host two distinct, compact components: massive black holes and nuclear star clusters. Nuclear star clusters are the densest stellar systems in the universe, with masses of ~ 107M⊙ and sizes of ~ 5pc. They are almost ubiquitous at the centres of nearby galaxies with masses similar to, or lower than the Milky Way. Their occurrence both in spirals and dwarf elliptical galaxies appears to be a strong function of total galaxy light or mass. Nucleation fractions are up to 100% for total galaxy magnitudes of M B = -19mag or total galaxy luminosities of about L B = 1010 L ⊙ and falling nucleation fractions for both smaller and higher galaxy masses. Although nuclear star clusters are so common, their formation mechanisms are still under debate. The two main formation scenarios proposed are the infall and subsequent merging of star clusters and the in-situ formation of stars at the center of a galaxy. Here, I review the state-of-the-art of nuclear star cluster observations concerning their structure, stellar populations and kinematics. These observations are used to constrain the proposed formation scenarios for nuclear star clusters. Constraints from observations show, that likely both cluster infall and in-situ star formation are at work. The relative importance of these two mechanisms is still subject of investigation.

  19. Allodynia in Cluster Headache.

    PubMed

    Wilbrink, Leopoldine A; Louter, Mark A; Teernstra, Onno Pm; van Zwet, Erik W; Huygen, Frank Jpm; Haan, Joost; Ferrari, Michel D; Terwindt, Gisela M

    2017-03-04

    Cutaneous allodynia is an established marker for central sensitization in migraine. There is debate whether cutaneous allodynia may also occur in cluster headache, another episodic headache disorder. Here we examined the presence and severity of allodynia in a large well-defined nation-wide population of people with cluster headache.Using validated questionnaires we assessed, cross-sectionally, ictal allodynia and comorbid depression and migraine in the nation-wide "Leiden University Cluster headache neuro-Analysis" (LUCA) study. Participants with cluster headache were diagnosed according to the International Classification of Headache Disorders criteria. Multivariate regression models were used, with correction for demographic factors and cluster headache subtype (chronic vs. episodic; recent attacks < 1 month vs. no recent attacks).In total 606/798 (75.9%) participants with cluster headache responded of whom 218/606 (36%) had allodynia during attacks. Female gender (OR 2.05, 95% CI 1.28-3.29), low age at onset (OR 0.98, 95% CI 0.96- 0.99), lifetime depression (OR 1.63; 95% CI 1.06-2.50), comorbid migraine (OR 1.96; 95% CI 1.02-3.79), and having recent attacks (OR 1.80; 95% CI 1.13-2.86), but not duration of attacks and chronic cluster headache, were independent risk factors for allodynia.The high prevalence of cutaneous allodynia with similar risk factors for allodynia as found for migraine suggests that central sensitization, like in migraine, also occurs in cluster headache. In clinical practice, awareness that people with cluster headache may suffer from allodynia can in the future be an important feature in treatment options.

  20. Melanin-binding radiopharmaceuticals

    SciTech Connect

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  1. Extending Beowulf Clusters

    USGS Publications Warehouse

    Steinwand, Daniel R.; Maddox, Brian; Beckmann, Tim; Hamer, George

    2003-01-01

    Beowulf clusters can provide a cost-effective way to compute numerical models and process large amounts of remote sensing image data. Usually a Beowulf cluster is designed to accomplish a specific set of processing goals, and processing is very efficient when the problem remains inside the constraints of the original design. There are cases, however, when one might wish to compute a problem that is beyond the capacity of the local Beowulf system. In these cases, spreading the problem to multiple clusters or to other machines on the network may provide a cost-effective solution.

  2. Dwarfs in Coma Cluster

    NASA Technical Reports Server (NTRS)

    2007-01-01

    [figure removed for brevity, see original site] Click on image for larger poster version

    This false-color mosaic of the central region of the Coma cluster combines infrared and visible-light images to reveal thousands of faint objects (green). Follow-up observations showed that many of these objects, which appear here as faint green smudges, are dwarf galaxies belonging to the cluster. Two large elliptical galaxies, NGC 4889 and NGC 4874, dominate the cluster's center. The mosaic combines visible-light data from the Sloan Digital Sky Survey (color coded blue) with long- and short-wavelength infrared views (red and green, respectively) from NASA's Spitzer Space Telescope.

  3. Magnetization of ferromagnetic clusters

    SciTech Connect

    Onishi, Naoki; Bertsch, G.; Yabana, Kazuhiro

    1995-02-01

    The magnetization and deflection profiles of magnetic clusters in a Stern-Gerlach magnet are calculated for conditions under which the magnetic moment is fixed in the intrinsic frame of the cluster, and the clusters enter the magnetic field adiabatically. The predicted magnetization is monotonic in the Langevin parameter, the ratio of magnetic energy {mu}{sub 0}B to thermal energy k{sub B}T. In low field the average magnetization is 2/3 of the Langevin function. The high-field moment approaches saturation asymptotically as B{sup {minus}1/2} instead of the B{sup {minus}1} dependence in the Langevin function.

  4. H-cluster stars

    NASA Astrophysics Data System (ADS)

    Lai, X. Y.; Gao, C. Y.; Xu, R. X.

    2013-06-01

    The study of dense matter at ultrahigh density has a very long history, which is meaningful for us to understand not only cosmic events in extreme circumstances but also fundamental laws of physics. It is well known that the state of cold matter at supranuclear density depends on the non-perturbative nature of quantum chromodynamics (QCD) and is essential for modelling pulsars. A so-called H-cluster matter is proposed in this paper as the nature of dense matter in reality. In compact stars at only a few nuclear densities but low temperature, quarks could be interacting strongly with each other there. That might render quarks grouped in clusters, although the hypothetical quark clusters in cold dense matter have not been confirmed due to the lack of both theoretical and experimental evidence. Motivated by recent lattice QCD simulations of the H-dibaryons (with structure uuddss), we therefore consider here a possible kind of quark clusters, H-clusters, that could emerge inside compact stars during their initial cooling as the dominant components inside (the degree of freedom could then be H-clusters there). Taking into account the in-medium stiffening effect, we find that at baryon densities of compact stars H-cluster matter could be more stable than nuclear matter. We also find that for the H-cluster matter with lattice structure, the equation of state could be so stiff that it would seem to be `superluminal' in the most dense region. However, the real sound speed for H-cluster matter is in fact difficult to calculate, so at this stage we do not put constraints on our model from the usual requirement of causality. We study the stars composed of H-clusters, i.e. H-cluster stars, and derive the dependence of their maximum mass on the in-medium stiffening effect, showing that the maximum mass could be well above 2 M⊙ as observed and that the resultant mass-radius relation fits the measurement of the rapid burster under reasonable parameters. Besides a general

  5. Atomic cluster collisions

    NASA Astrophysics Data System (ADS)

    Korol, Andrey V.; Solov'yov, Andrey

    2013-01-01

    Atomic cluster collisions are a field of rapidly emerging research interest by both experimentalists and theorists. The international symposium on atomic cluster collisions (ISSAC) is the premier forum to present cutting-edge research in this field. It was established in 2003 and the most recent conference was held in Berlin, Germany in July of 2011. This Topical Issue presents original research results from some of the participants, who attended this conference. This issues specifically focuses on two research areas, namely Clusters and Fullerenes in External Fields and Nanoscale Insights in Radiation Biodamage.

  6. Partially supervised speaker clustering.

    PubMed

    Tang, Hao; Chu, Stephen Mingyu; Hasegawa-Johnson, Mark; Huang, Thomas S

    2012-05-01

    Content-based multimedia indexing, retrieval, and processing as well as multimedia databases demand the structuring of the media content (image, audio, video, text, etc.), one significant goal being to associate the identity of the content to the individual segments of the signals. In this paper, we specifically address the problem of speaker clustering, the task of assigning every speech utterance in an audio stream to its speaker. We offer a complete treatment to the idea of partially supervised speaker clustering, which refers to the use of our prior knowledge of speakers in general to assist the unsupervised speaker clustering process. By means of an independent training data set, we encode the prior knowledge at the various stages of the speaker clustering pipeline via 1) learning a speaker-discriminative acoustic feature transformation, 2) learning a universal speaker prior model, and 3) learning a discriminative speaker subspace, or equivalently, a speaker-discriminative distance metric. We study the directional scattering property of the Gaussian mixture model (GMM) mean supervector representation of utterances in the high-dimensional space, and advocate exploiting this property by using the cosine distance metric instead of the euclidean distance metric for speaker clustering in the GMM mean supervector space. We propose to perform discriminant analysis based on the cosine distance metric, which leads to a novel distance metric learning algorithm—linear spherical discriminant analysis (LSDA). We show that the proposed LSDA formulation can be systematically solved within the elegant graph embedding general dimensionality reduction framework. Our speaker clustering experiments on the GALE database clearly indicate that 1) our speaker clustering methods based on the GMM mean supervector representation and vector-based distance metrics outperform traditional speaker clustering methods based on the “bag of acoustic features” representation and statistical

  7. Stability and Spectra of Small 3He-4He Clusters

    NASA Astrophysics Data System (ADS)

    Navarro, J.; Fantoni, S.; Guardiola, R.; Zuker, A.

    Diffusion Monte Carlo calculations have been systematically performed to analyze the stability of small mixed 3He-4He clusters, as well as their excitation spectra. The picture that emerges is that of systems with strong shell effects whose binding and excitation energies are essentially determined by the monopole properties of an effective Hamiltonian.

  8. Directed Assembly of Hierarchically Ordered Clusters from Anisotropic Microparticles

    NASA Astrophysics Data System (ADS)

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

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

  9. Combining cluster number counts and galaxy clustering

    NASA Astrophysics Data System (ADS)

    Lacasa, Fabien; Rosenfeld, Rogerio

    2016-08-01

    The abundance of clusters and the clustering of galaxies are two of the important cosmological probes for current and future large scale surveys of galaxies, such as the Dark Energy Survey. In order to combine them one has to account for the fact that they are not independent quantities, since they probe the same density field. It is important to develop a good understanding of their correlation in order to extract parameter constraints. We present a detailed modelling of the joint covariance matrix between cluster number counts and the galaxy angular power spectrum. We employ the framework of the halo model complemented by a Halo Occupation Distribution model (HOD). We demonstrate the importance of accounting for non-Gaussianity to produce accurate covariance predictions. Indeed, we show that the non-Gaussian covariance becomes dominant at small scales, low redshifts or high cluster masses. We discuss in particular the case of the super-sample covariance (SSC), including the effects of galaxy shot-noise, halo second order bias and non-local bias. We demonstrate that the SSC obeys mathematical inequalities and positivity. Using the joint covariance matrix and a Fisher matrix methodology, we examine the prospects of combining these two probes to constrain cosmological and HOD parameters. We find that the combination indeed results in noticeably better constraints, with improvements of order 20% on cosmological parameters compared to the best single probe, and even greater improvement on HOD parameters, with reduction of error bars by a factor 1.4-4.8. This happens in particular because the cross-covariance introduces a synergy between the probes on small scales. We conclude that accounting for non-Gaussian effects is required for the joint analysis of these observables in galaxy surveys.

  10. Temporal Clustering and Sequencing in Short-Term Memory and Episodic Memory

    ERIC Educational Resources Information Center

    Farrell, Simon

    2012-01-01

    A model of short-term memory and episodic memory is presented, with the core assumptions that (a) people parse their continuous experience into episodic clusters and (b) items are clustered together in memory as episodes by binding information within an episode to a common temporal context. Along with the additional assumption that information…

  11. Organising Atoms, Clusters and Proteins on Surfaces

    NASA Astrophysics Data System (ADS)

    Palmer, Richard E.

    2008-10-01

    This talk will discuss new developments in the creation of nanoscale surface features and their applications in biomedicine. Electron-surface interactions and plasma methods play a crucial role in both the production and analysis of these ``atomic architectures.'' At the extreme limit, electron injection from the tip of a scanning tunnelling microscope (STM) enables bond-selective manipulation of individual polyatomic molecules [1]. On a more practical level, the controlled deposition of size-selected clusters [2], generated by magnetron sputtering and gas condensation followed by mass selection, represents a surprisingly efficient route to the fabrication of surface features of size 1-10 nm, the size scale of biological molecules such as proteins. STM and AFM measurements show the clusters can act as binding sites for individual protein molecules. For example, the pinning of size-selected AuN clusters (N = 1--2000) to the (hydrophobic) graphite surface presents bindings site for sulphur atoms and thus for the cysteine residues in protein molecules. Systematic studies of different proteins [3] provide ``ground rules'' for residue-specific protein immobilisation by clusters and have led to the development of a novel biochip for protein screening by a spin-off company. The 3D atomic structure of the clusters is highly relevant to such applications. We show that measurement of the scattered electron beam intensity - specifically, the high angle annular dark field (HAADF) signal - in the scanning transmission electron microscope (STEM) allows us (a) to count the number of atoms in a cluster on the surface and (b) to determine a 3D atom-density map of the cluster when an aberration-corrected STEM is used [4]. 1. P.A. Sloan and R.E. Palmer, Nature 434 367 (2005). 2. S. Pratontep, P. Preece, C. Xirouchaki, R.E. Palmer, C.F. Sanz-Navarro, S.D. Kenny and R. Smith, Phys. Rev. Lett. 90 055503 (2003). 3. R.E. Palmer, S. Pratontep and H.-G. Boyen, Nature Materials 2 443 (2003

  12. How Clusters Work

    EPA Pesticide Factsheets

    Technology innovation clusters are geographic concentrations of interconnected companies, universities, and other organizations with a focus on environmental technology. They play a key role in addressing the nation’s pressing environmental problems.

  13. [Treatment of cluster headache].

    PubMed

    Fabre, N

    2005-07-01

    Remarkable therapeutic improvements have come forward recently for trigemino-autonomic cephalalgias. Attack treatment in cluster headache is based on sumatriptan and oxygen. Non-vasoconstrictive treatments are opening a new post-triptan era but are not yet applicable. Prophylactic treatment of cluster headache is based on verapamil and lithium. The efficacy of anti-epileptic drugs in cluster headache remains to be demonstrated. Surgical treatment aimed at the parasympathetic pathways and at the trigeminal nerve demonstrates a high rate of recurrence and adverse events and questions about the relevance of a "peripheral" target in cluster headache. The efficacy of continuous hypothalamic stimulation in patients with intractable headache constitutes a breakthrough, but must be demonstrated at a larger scale and the benefice/risk ratio must be carefully evaluated. Indomethacin still remains the gold standard in paroxysmal hemicrania treatment. Until recently SUNCT was considered an intractable condition. However there are some reports of complete relief with lamotrigine, topiramate and gabapentin.

  14. Identification and characterization of four novel peptide motifs that recognize distinct regions of the transcription factor CP2.

    PubMed

    Kang, Ho Chul; Chung, Bo Mee; Chae, Ji Hyung; Yang, Sung-Il; Kim, Chan Gil; Kim, Chul Geun

    2005-03-01

    Although ubiquitously expressed, the transcriptional factor CP2 also exhibits some tissue- or stage-specific activation toward certain genes such as globin in red blood cells and interleukin-4 in T helper cells. Because this specificity may be achieved by interaction with other proteins, we screened a peptide display library and identified four consensus motifs in numerous CP2-binding peptides: HXPR, PHL, ASR and PXHXH. Protein-database searching revealed that RE-1 silencing factor (REST), Yin-Yang1 (YY1) and five other proteins have one or two of these CP2-binding motifs. Glutathione S-transferase pull-down and coimmunoprecipitation assays showed that two HXPR motif-containing proteins REST and YY1 indeed were able to bind CP2. Importantly, this binding to CP2 was almost abolished when a double amino acid substitution was made on the HXPR sequence of REST and YY1 proteins. The suppressing effect of YY1 on CP2's transcriptional activity was lost by this point mutation on the HXPR sequence of YY1 and reduced by an HXPR-containing peptide, further supporting the interaction between CP2 and YY1 via the HXPR sequence. Mapping the sites on CP2 for interaction with the four distinct CP2-binding motifs revealed at least three different regions on CP2. This suggests that CP2 recognizes several distinct binding motifs by virtue of employing different regions, thus being able to interact with and regulate many cellular partners.

  15. Understanding ligand effects in gold clusters using mass spectrometry

    SciTech Connect

    Johnson, Grant E.; Laskin, Julia

    2016-01-01

    This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because “each-atom-counts” toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted that may be compared with the results of high-level theoretical calculations. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well

  16. Clustered frequency comb.

    PubMed

    Matsko, Andrey B; Savchenkov, Anatoliy A; Huang, Shu-Wei; Maleki, Lute

    2016-11-01

    We show theoretically that it is feasible to generate a spectrally broad Kerr frequency comb consisting of several spectral clusters phase matched due to interplay among second- and higher-order group velocity dispersion contributions. We validate the theoretical analysis experimentally by driving a magnesium fluoride resonator, characterized with 110 GHz free spectral range, with a continuous wave light at 1.55 μm and observing two comb clusters separated by nearly two-thirds of an octave.

  17. Cluster State Quantum Computing

    DTIC Science & Technology

    2012-12-01

    implementation of quantum computation,” Fortschr. Phys. 48, 771 (2000). [Dragoman01] D. Dragoman, “Proposal for a three-qubit teleportation experiment”, Phys...CLUSTER STATE QUANTUM COMPUTING DECEMBER 2012 INTERIM TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION...From - To) NOV 2010 – OCT 2012 4. TITLE AND SUBTITLE CLUSTER STATE QUANTUM COMPUTING 5a. CONTRACT NUMBER IN-HOUSE 5b. GRANT NUMBER N/A 5c

  18. Globular clusters with Gaia

    NASA Astrophysics Data System (ADS)

    Pancino, E.; Bellazzini, M.; Giuffrida, G.; Marinoni, S.

    2017-01-01

    The treatment of crowded fields in Gaia data will only be a reality in a few years from now. In particular, for globular clusters, only the end-of-mission data (public in 2022-2023) will have the necessary full crowding treatment and will reach sufficient quality for the faintest stars. As a consequence, the work on the deblending and decontamination pipelines is still ongoing. We describe the present status of the pipelines for different Gaia instruments, and we model the end-of-mission crowding errors on the basis of available information. We then apply the nominal post-launch Gaia performances, appropriately worsened by the estimated crowding errors, to a set of 18 simulated globular clusters with different concentration, distance, and field contamination. We conclude that there will be 103-104 stars with astrometric performances virtually untouched by crowding (contaminated by <1 mmag) in the majoritiy of clusters. The most limiting factor will be field crowding, not cluster crowding: the most contaminated clusters will only contain 10-100 clean stars. We also conclude that: (i) the systemic proper motions and parallaxes will be determined to 1% or better up to ≃15 kpc, and the nearby clusters will have radial velocities to a few km s-1 ; (ii) internal kinematics will be of unprecendented quality, cluster masses will be determined to ≃10% up to 15 kpc and beyond, and it will be possible to identify differences of a few km s-1 or less in the kinematics (if any) of cluster sub-populations up to 10 kpc and beyond; (iii) the brightest stars (V≃17 mag) will have space-quality, wide-field photometry (mmag errors), and all Gaia photometry will have 1-3% errors on the absolute photometric calibration.

  19. Chemistry within Molecular Clusters

    DTIC Science & Technology

    1992-05-29

    molecule reaction of the fragment cations with a neutral DME within the bulk cluster, to form a trimethyloxonium cation intermediate. Similar ion...trimethyloxonium intermediate as the common intermediate for the observed products. We therefore speculate that the DME cluster reactions leading to the same...1982, 20, 51, Ibid. Kinetics of Ion-Molecule Reactions ; Ausloos, P., Ed.; Plenum, New York, 1979; p. 69. (18) Ono, Y.; Ng, C. Y. J. Am. Chem. Soc. 1982

  20. Wild Duck Cluster

    NASA Technical Reports Server (NTRS)

    2005-01-01

    On April 7, 2005, the Deep Impact spacecraft's Impactor Target Sensor camera recorded this image of M11, the Wild Duck cluster, a galactic open cluster located 6 thousand light years away. The camera is located on the impactor spacecraft, which will image comet Tempel 1 beginning 22 hours before impact until about 2 seconds before impact. Impact with comet Tempel 1 is planned for July 4, 2005.

  1. Parallel Wolff Cluster Algorithms

    NASA Astrophysics Data System (ADS)

    Bae, S.; Ko, S. H.; Coddington, P. D.

    The Wolff single-cluster algorithm is the most efficient method known for Monte Carlo simulation of many spin models. Due to the irregular size, shape and position of the Wolff clusters, this method does not easily lend itself to efficient parallel implementation, so that simulations using this method have thus far been confined to workstations and vector machines. Here we present two parallel implementations of this algorithm, and show that one gives fairly good performance on a MIMD parallel computer.

  2. Iron-sulfur cluster exchange reactions mediated by the human Nfu protein.

    PubMed

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

    2016-10-01

    Human Nfu is an iron-sulfur cluster protein that has recently been implicated in multiple mitochondrial dysfunctional syndrome (MMDS1). The Nfu family of proteins shares a highly homologous domain that contains a conserved active site consisting of a CXXC motif. There is less functional conservation between bacterial and human Nfu proteins, particularly concerning their Iron-sulfur cluster binding and transfer roles. Herein, we characterize the cluster exchange chemistry of human Nfu and its capacity to bind and transfer a [2Fe-2S] cluster. The mechanism of cluster uptake from a physiologically relevant [2Fe-2S](GS)4 cluster complex, and extraction of the Nfu-bound iron-sulfur cluster by glutathione are described. Human holo Nfu shows a dimer-tetramer equilibrium with a protein to cluster ratio of 2:1, reflecting the Nfu-bridging [2Fe-2S] cluster. This cluster can be transferred to apo human ferredoxins at relatively fast rates, demonstrating a direct role for human Nfu in the process of [2Fe-2S] cluster trafficking and delivery.

  3. The stabilization mechanism of titanium cluster

    NASA Astrophysics Data System (ADS)

    Sun, Houqian; Ren, Yun; Hao, Yuhua; Wu, Zhaofeng; Xu, Ning

    2015-05-01

    A systematic and comparative theoretical study on the stabilization mechanism of titanium cluster has been performed by selecting the clusters Tin (n=3, 4, 5, 7, 13, 15 and 19) as representatives in the framework of density-functional theory. For small clusters Tin (n=3, 4 and 5), the binding energy gain due to spin polarization is substantially larger than that due to structural distortion. For medium clusters Ti13 and Ti15, both have about the same contribution. For Tin (n=4, 5, 13 and 15), when the undistorted high symmetric structure with spin-polarization is changed into the lowest energy structure, the energy level spelling due to distortion fails to reverse the level order of occupied and unoccupied molecular orbital (MO) of two type spin states, the spin configuration remains unchanged. In spin restricted and undistorted high symmetric structure, d orbitals participate in the hybridization in MOs, usually by way of a less distorted manner, and weak bonds are formed. In contrast, d orbitals take part in the formation of MOs in the ground state structure, usually in a distorted manner, and strong covalent metallic bonds are formed.

  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. Cluster functional renormalization group

    NASA Astrophysics Data System (ADS)

    Reuther, Johannes; Thomale, Ronny

    2014-01-01

    Functional renormalization group (FRG) has become a diverse and powerful tool to derive effective low-energy scattering vertices of interacting many-body systems. Starting from a free expansion point of the action, the flow of the RG parameter Λ allows us to trace the evolution of the effective one- and two-particle vertices towards low energies by taking into account the vertex corrections between all parquet channels in an unbiased fashion. In this work, we generalize the expansion point at which the diagrammatic resummation procedure is initiated from a free UV limit to a cluster product state. We formulate a cluster FRG scheme where the noninteracting building blocks (i.e., decoupled spin clusters) are treated exactly, and the intercluster couplings are addressed via RG. As a benchmark study, we apply our cluster FRG scheme to the spin-1/2 bilayer Heisenberg model (BHM) on a square lattice where the neighboring sites in the two layers form the individual two-site clusters. Comparing with existing numerical evidence for the BHM, we obtain reasonable findings for the spin susceptibility, the spin-triplet excitation energy, and quasiparticle weight even in coupling regimes close to antiferromagnetic order. The concept of cluster FRG promises applications to a large class of interacting electron systems.

  6. Interatomic forces and bonding mechanisms in MgO clusters

    SciTech Connect

    Wright, N.F.; Painter, G.S.

    1990-01-01

    We report results from a first-principles local spin density quantum mechanical study of the energetics and elastic properties of a series of magnesium-oxygen clusters of various morphologies. The role of quantum effects, e.g. covalency, in the bonding character of diatomic MgO is determined by comparison of classical and quantum restoring force curves. The dependence of binding properties on geometry and metal to oxygen ratio is determined by comparison of binding energy curves for a series of clusters. Results show that while gross features of the binding curves may be represented by simple interatomic potentials, details require the many body corrections of a full quantum treatment. 6 refs., 5 figs.

  7. Correlation effects on the properties of small cobalt clusters

    NASA Astrophysics Data System (ADS)

    Hancock, Yvette; Iäs, Mari

    2009-03-01

    Demands for higher-density magnetic storage media and smaller memory devices require atomic-scale magnetic components with stable magnetic properties. One such candidate for this application is a small transition metal cluster. The magnetic properties of transition metal clusters are very sensitive to the geometry of the cluster, the local atomic and structural environments, and to the system size. In this work, the GGA + U DFT approach is used for the first time to study the system properties of small cobalt clusters consisting of 2 to 5 atoms. Previous studies using DFT and tight-binding approaches have been found to overestimate the binding energies, dissociation energies and vibrational frequencies of the clusters against their known experimental values. By including a Hubbard U correction between 2 -- 3 eV, the DFT method can then be fitted to reproduce the experimental results, thereby improving upon previous theoretical descriptions of these systems. The effect of U on the calculated magnetic and structural properties of the clusters is also discussed.

  8. Tidal disruption of open clusters in their parent molecular clouds

    NASA Technical Reports Server (NTRS)

    Long, Kevin

    1989-01-01

    A simple model of tidal encounters has been applied to the problem of an open cluster in a clumpy molecular cloud. The parameters of the clumps are taken from the Blitz, Stark, and Long (1988) catalog of clumps in the Rosette molecular cloud. Encounters are modeled as impulsive, rectilinear collisions between Plummer spheres, but the tidal approximation is not invoked. Mass and binding energy changes during an encounter are computed by considering the velocity impulses given to individual stars in a random realization of a Plummer sphere. Mean rates of mass and binding energy loss are then computed by integrating over many encounters. Self-similar evolutionary calculations using these rates indicate that the disruption process is most sensitive to the cluster radius and relatively insensitive to cluster mass. The calculations indicate that clusters which are born in a cloud similar to the Rosette with a cluster radius greater than about 2.5 pc will not survive long enough to leave the cloud. The majority of clusters, however, have smaller radii and will survive the passage through their parent cloud.

  9. Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein.

    PubMed

    Poppe, Juliane; Warkentin, Eberhard; Demmer, Ulrike; Kowalewski, Björn; Dierks, Thomas; Schneider, Klaus; Ermler, Ulrich

    2014-09-01

    The molybdenum storage protein (MoSto) can store more than 100 Mo or W atoms as discrete polyoxometalate (POM) clusters. Here, we describe the three POM cluster sites along the threefold axis of the protein complex based on four X-ray structures with slightly different polyoxomolybdate compositions between 1.35 and 2 Å resolution. In contrast to the Moα-out binding site occupied by an Mo3 cluster, the Moα-in and Moβ binding sites contain rather weak and non-uniform electron density for the Mo atoms (but clearly identifiable by anomalous data), suggesting the presence of POM cluster ensembles and/or degradation products of larger aggregates. The "Moα-in cluster ensemble" was interpreted as an antiprism-like Mo6 species superimposed with an Mo7 pyramide and the "Moβ cluster ensemble" as an Mo13 cluster (present mostly in a degraded form) composed of a pyramidal Mo7 and a Mo3 building block linked by three spatially separated MoOx units. Inside the ball-shaped Mo13 cluster sits an occluded central atom, perhaps a metal ion. POM cluster formation at the Moα-in and Moβ sites appears to be driven by filtering out and binding/protecting self-assembled transient species complementary to the protein template.

  10. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria.

    PubMed Central

    Tam, R; Saier, M H

    1993-01-01

    Extracellular solute-binding proteins of bacteria serve as chemoreceptors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-binding proteins of gram-negative bacteria and homologous extracytoplasmic lipoproteins of gram-positive bacteria have been analyzed for sequence similarities, and their degrees of relatedness have been determined. Some of these proteins are homologous to cytoplasmic transcriptional regulatory proteins of bacteria; however, with the sole exception of the vitamin B12-binding protein of Escherichia coli, which is homologous to human glutathione peroxidase, they are not demonstrably homologous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Cluster 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 proteins are specific for galactose, ribose, arabinose, and multiple monosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose repressors of E. coli. Cluster 3 proteins are specific for histidine, lysine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleucine-valine, and they are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Cluster 6 proteins are specific for sulfate, thiosulfate, and possibly phosphate. Cluster 7 proteins are specific for dicarboxylates and tricarboxylates, but these two proteins exhibit insufficient sequence similarity to establish homology. Finally, cluster 8 proteins are specific for iron complexes and possibly vitamin B12. Members of each cluster of binding proteins exhibit greater

  11. The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO2 photoreduction

    DOE PAGES

    Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.; ...

    2015-09-04

    In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO2 photoreduction reaction (bent CO2–), we find that flatter (2D-like) Pt clusters that “wet” the TiO2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO2 interfacial sites with geometries that can aid CO2 bond bending and charge transfer processes. Second, binding competitionmore » among each Pt–CO2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO2 surfaces for CO2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO2 on TiO2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.« less

  12. Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast

    PubMed Central

    Ruault, Myriam; De Meyer, Arnaud; Loïodice, Isabelle

    2011-01-01

    A general feature of the nucleus is the organization of repetitive deoxyribonucleic acid sequences in clusters concentrating silencing factors. In budding yeast, we investigated how telomeres cluster in perinuclear foci associated with the silencing complex Sir2–Sir3–Sir4 and found that Sir3 is limiting for telomere clustering. Sir3 overexpression triggers the grouping of telomeric foci into larger foci that relocalize to the nuclear interior and correlate with more stable silencing in subtelomeric regions. Furthermore, we show that Sir3′s ability to mediate telomere clustering can be separated from its role in silencing. Indeed, nonacetylable Sir3, which is unable to spread into subtelomeric regions, can mediate telomere clustering independently of Sir2–Sir4 as long as it is targeted to telomeres by the Rap1 protein. Thus, arrays of Sir3 binding sites at telomeres appeared as the sole requirement to promote trans-interactions between telomeres. We propose that similar mechanisms involving proteins able to oligomerize account for long-range interactions that impact genomic functions in many organisms. PMID:21300849

  13. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters

    NASA Astrophysics Data System (ADS)

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-08-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1–12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms.

  14. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters

    PubMed Central

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-01-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1–12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms. PMID:27534599

  15. Metallochaperones: bind and deliver

    SciTech Connect

    Rosenzweig, A.C.

    2010-03-08

    Metallochaperones deliver metal ions directly to target proteins via specific protein-protein interactions. Recent research has led to a molecular picture of how some metallochaperones bind metal ions, recognize their partner proteins, and accomplish metal ion transfer.

  16. Behavioral Clustering of School Children.

    ERIC Educational Resources Information Center

    Huberty, Carl J.; DiStefano, Christine; Kamphaus, Randy W.

    1997-01-01

    How a cluster analysis is conducted, validated, and interpreted is illustrated using a 14-scale behavioral assessment instrument and a national sample of 1,228 elementary school students. Method, cluster typology, validity, cluster structure, and prediction of cluster membership are discussed. (Author/SLD)

  17. SHBG (Sex Hormone Binding Globulin)

    MedlinePlus

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  18. Electronic structure, stability, and oxidation of boron-magnesium clusters and cluster solids

    SciTech Connect

    Reber, Arthur C.; Khanna, Shiv N.

    2015-02-07

    Electronic structure studies on Mg{sub m}B{sub n}{sup −} (1 ≤ n ≤ 15, 0 ≤ m ≤ 3) clusters have been performed to identify the nature of bonding and the origin of stability in the mixed clusters. Boron clusters are found to have planar structures marked by tangential, radial, and π aromaticity. The maximum stability is achieved for when all three types of aromaticity are quenched. The ring like B{sub n}{sup −} clusters are shown to be electron deficient for n = 6-8, and the addition of Mg atoms is found to enhance the stability of the boron cluster through ionic bonding that quenches the aromaticity and produces umbrella-like structures. Several species including MgB{sub 6}{sup −}, MgB{sub 8}{sup −}, Mg{sub 2}B{sup −}, and Mg{sub 3}B{sub 7}{sup −} are found to have the largest Mg binding energies due to this mechanism. The transfer of a single electron from the Mg atom to the boron cluster results in a Mg atom with a half-filled 3s orbital that may serve as an ignition center for combustion. Studies on the MgB{sub 7} and MgB{sub 4} cluster solids indicate that they are constructed from icosahedral and umbrella-like motifs and are semiconductors with band gap energies of 1.46 eV and 0.41 eV, respectively.

  19. Binding site number variation and high-affinity binding consensus of Myb-SANT-like transcription factor Adf-1 in Drosophilidae

    PubMed Central

    Lang, Michael; Juan, Elvira

    2010-01-01

    There is a growing interest in the evolution of transcription factor binding sites and corresponding functional change of transcriptional regulation. In this context, we have examined the structural changes of the ADF-1 binding sites at the Adh promoters of Drosophila funebris and D. virilis. We detected an expanded footprinted region in D. funebris that contains various adjacent binding sites with different binding affinities. ADF-1 was described to direct sequence-specific DNA binding to sites consisting of the multiple trinucleotide repeat . The ADF-1 recognition sites with high binding affinity differ from this trinucleotide repeat consensus sequence and a new consensus sequence is proposed for the high-affinity ADF-1 binding sites. In vitro transcription experiments with the D. funebris and D. virilis ADF-1 binding regions revealed that stronger ADF-1 binding to the expanded D. funebris ADF-1 binding region only moderately lead to increased transcriptional activity of the Adh gene. The potential of this regional expansion is discussed in the context of different ADF-1 cellular concentrations and maintenance of the ADF-1 stimulus. Altogether, evolutionary change of ADF-1 binding regions involves both, rearrangements of complex binding site cluster and also nucleotide substitutions within sites that lead to different binding affinities. PMID:20542916

  20. Clustered data in sports research.

    PubMed

    Hayen, A

    2006-05-01

    Clustered, or dependent, data, arise commonly in sports medicine and sports science research, particularly in studies of sports injury and biomechanics, particularly in sports injury trials that are randomised at team or club level, in cross-sectional surveys in which groups of individuals are studied and in studies with repeated measures designs. Clustering, or positive correlation among responses, arises because responses and outcomes from the same cluster will usually be more similar than from different clusters. Study designs with clustering will usually required an increased sample size when compared to those without clustering. Ignoring clustering in statistical analyses can also lead to misleading conclusions, including incorrect confidence intervals and p-values. Appropriate statistical analyses for clustered data must be adopted. This paper gives some examples of clustered data and discusses the implications of clustering on the design and analysis of studies in sports medicine and sports science research.

  1. Trends in methanol decomposition on transition metal alloy clusters from scaling and Brønsted–Evans–Polanyi relationships

    SciTech Connect

    Mehmood, Faisal; Rankin, Rees B.; Greeley, Jeffrey; Curtiss, Larry A.

    2012-05-15

    A combination of first principles Density Functional Theory calculations and thermochemical scaling relationships are employed to estimate the thermochemistry and kinetics of methanol decomposition on unsupported subnanometer metal clusters. The approach uses binding energies of various atomic and molecular species, determined on the pure metal clusters, to develop scaling relationships that are then further used to estimate the methanol decomposition thermodynamics for a series of pure and bimetallic clusters with four atoms per cluster. Additionally, activation energy barriers are estimated from Brønsted–Evans–Polanyi plots relating transition and final state energies on these clusters. The energetic results are combined with a simple, microkinetically-inspired rate expression to estimate reaction rates as a function of important catalytic descriptors, including the carbon and atomic oxygen binding energies to the clusters. Finally, based on these analyses, several alloy clusters are identified as promising candidates for the methanol decomposition reaction.

  2. Dust in galaxy clusters

    NASA Astrophysics Data System (ADS)

    Polikarpova, O. L.; Shchekinov, Yu. A.

    2017-02-01

    The conditions for the destruction of dust in hot gas in galaxy clusters are investigated. It is argued that extinction measurements can be subject to selection effects, hindering their use in obtaining trustworthy estimates of dust masses in clusters. It is shown, in particular, that the ratio of the dust mass to the extinction M d / S d increases as dust grains are disrupted, due to the rapid destruction of small grains. Over long times, this ratio can asymptotically reach values a factor of three higher than the mean value in the interstellar medium in the Galaxy. This lowers dust-mass estimates based on measurements of extinction in galaxy clusters. The characteristic lifetime of dust in hot cluster gas is determined by its possible thermal isolation by the denser medium of gas fragments within which the dust is ejected from galaxies, and can reach 100-300 million years, depending on the kinematics and morphology of the fragments. As a result, the mass fraction of dust in hot cluster gas can reach 1-3% of the Galactic value. Over its lifetime, dust can also be manifest through its far-infrared emission. The emission characteristics of the dust change as it is disrupted, and the ratio of the fluxes at 350 and 850 μm can increase appreciably. This can potentially serve as an indicator of the state of the dust and ambient gas.

  3. Spatio-temporal clustering

    NASA Astrophysics Data System (ADS)

    Kisilevich, Slava; Mansmann, Florian; Nanni, Mirco; Rinzivillo, Salvatore

    Spatio-temporal clustering is a process of grouping objects based on their spatial and temporal similarity. It is relatively new subfield of data mining which gained high popularity especially in geographic information sciences due to the pervasiveness of all kinds of location-based or environmental devices that record position, time or/and environmental properties of an object or set of objects in real-time. As a consequence, different types and large amounts of spatio-temporal data became available that introduce new challenges to data analysis and require novel approaches to knowledge discovery. In this chapter we concentrate on the spatio-temporal clustering in geographic space. First, we provide a classification of different types of spatio-temporal data. Then, we focus on one type of spatio-temporal clustering - trajectory clustering, provide an overview of the state-of-the-art approaches and methods of spatio-temporal clustering and finally present several scenarios in different application domains such as movement, cellular networks and environmental studies.

  4. The first intron of the human growth hormone gene contains a binding site for glucocorticoid receptor.

    PubMed

    Moore, D D; Marks, A R; Buckley, D I; Kapler, G; Payvar, F; Goodman, H M

    1985-02-01

    Glucocorticoid receptor (GCR) protein stimulates transcription from a variety of cellular genes. We show here that GCR partially purified from rat liver binds specifically to a site within the first intron of the human growth hormone (hGH) gene, approximately 100 base pairs downstream from the start of hGH transcription. GCR binding is selectively inhibited by methylation of two short, symmetrically arranged clusters of guanine residues within this site. A cloned synthetic 24-base-pair deoxyoligonucleotide containing the predicted GCR binding sequence interacts specifically with GCR. The hGH binding site shares sequence homology with a GCR binding site upstream from the human metallothionein II gene and a subset of GCR binding sites from mouse mammary tumor virus. All of these binding sites for this eukaryotic transcriptional regulatory protein show remarkable similarity in overall geometry to the binding sites for several prokaryotic transcriptional regulatory proteins.

  5. Linked supramolecular building blocks for enhanced cluster formation

    DOE PAGES

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

    2015-01-09

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

  6. Linked supramolecular building blocks for enhanced cluster formation

    SciTech Connect

    McLellan, Ross; Palacios, Maria A.; Beavers, Christine M.; Teat, Simon J.; Piligkos, Stergios; Brechin, Euan K.; Dalgarno, Scott J.

    2015-01-09

    Methylene-bridged calix[4]arenes have emerged as extremely versatile ligand supports in the formation of new polymetallic clusters possessing fascinating magnetic properties. Metal ion binding rules established for this building block allow one to partially rationalise the complex assembly process. The ability to covalently link calix[4]arenes at the methylene bridge provides significantly improved control over the introduction of different metal centres to resulting cluster motifs. Clusters assembled from bis-calix[4]arenes and transition metal ions or 3d-4f combinations display characteristic features of the analogous calix[4]arene supported clusters, thereby demonstrating an enhanced and rational approach towards the targeted synthesis of complex and challenging structures.

  7. Creeping Motion of Self Interstitial Atom Clusters in Tungsten

    NASA Astrophysics Data System (ADS)

    Zhou, Wang Huai; Zhang, Chuan Guo; Li, Yong Gang; Zeng, Zhi

    2014-05-01

    The formation and motion features of self interstitial atom (SIA) clusters in tungsten are studied by molecular dynamics (MD) simulations. The static calculations show that the SIA clusters are stable with binding energy over 2 eV. The SIA clusters exhibit a fast one dimensional (1D) motion along <111>. Through analysis of the change of relative distance between SIAs, we find that SIAs jump in small displacements we call creeping motion, which is a new collective diffusion process different from that of iron. The potential energy surface of SIAs implicates that the creeping motion is due to the strong interaction between SIAs. These imply that several diffusion mechanism for SIA clusters can operate in BCC metals and could help us explore deep insight into the performance of materials under irradiation.

  8. Formation and stability of high-spin alkali clusters.

    PubMed

    Schulz, C P; Claas, P; Schumacher, D; Stienkemeier, F

    2004-01-09

    Helium nanodroplet isolation has been applied to agglomerate alkali clusters at temperatures of 380 mK. The very weak binding to the surface of the droplets allows a selection of only weakly bound, high-spin states. Here we show that larger clusters of alkali atoms in high-spin states can be formed. The lack of strong bonds from pairing electrons makes these systems nonmetallic, van der Waals-like complexes of metal atoms. We find that sodium and potassium readily form such clusters containing up to 25 atoms. In contrast, this process is suppressed for rubidium and cesium. Apparently, for these heavy alkalis, larger high-spin aggregates are not stable and depolarize spontaneously upon cluster formation.

  9. Formation and Stability of High-Spin Alkali Clusters

    NASA Astrophysics Data System (ADS)

    Schulz, C. P.; Claas, P.; Schumacher, D.; Stienkemeier, F.

    2004-01-01

    Helium nanodroplet isolation has been applied to agglomerate alkali clusters at temperatures of 380mK. The very weak binding to the surface of the droplets allows a selection of only weakly bound, high-spin states. Here we show that larger clusters of alkali atoms in high-spin states can be formed. The lack of strong bonds from pairing electrons makes these systems nonmetallic, vanderWaals like complexes of metal atoms. We find that sodium and potassium readily form such clusters containing up to 25atoms. In contrast, this process is suppressed for rubidium and cesium. Apparently, for these heavy alkalis, larger high-spin aggregates are not stable and depolarize spontaneously upon cluster formation.

  10. Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

    PubMed Central

    Han, Gye Won; Yang, Xiang-Lei; McMullan, Daniel; Chong, Yeeting E.; Krishna, S. Sri; Rife, Christopher L.; Weekes, Dana; Brittain, Scott M.; Abdubek, Polat; Ambing, Eileen; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Caruthers, Jonathan; Chiu, Hsiu-Ju; Clayton, Thomas; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Slawomir K.; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Paulsen, Jessica; Reyes, Ron; van den Bedem, Henry; White, Aprilfawn; Wolf, Guenter; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc-André; Schimmel, Paul; Wilson, Ian A.

    2010-01-01

    A novel aminoacyl-tRNA synthetase that contains an iron–sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron–sulfur [4Fe–­4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an l-­tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe–4S] cluster-binding motif (C-x 22-C-x 6-C-x 2-C). It is speculated that the iron–sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon. PMID:20944229

  11. Identification of a common hyaluronan binding motif in the hyaluronan binding proteins RHAMM, CD44 and link protein.

    PubMed Central

    Yang, B; Yang, B L; Savani, R C; Turley, E A

    1994-01-01

    We have previously identified two hyaluronan (HA) binding domains in the HA receptor, RHAMM, that occur near the carboxyl-terminus of this protein. We show here that these two HA binding domains are the only HA binding regions in RHAMM, and that they contribute approximately equally to the HA binding ability of this receptor. Mutation of domain II using recombinant polypeptides of RHAMM demonstrates that K423 and R431, spaced seven amino acids apart, are critical for HA binding activity. Domain I contains two sets of two basic amino acids, each spaced seven residues apart, and mutation of these basic amino acids reduced their binding to HA--Sepharose. These results predict that two basic amino acids flanking a seven amino acid stretch [hereafter called B(X7)B] are minimally required for HA binding activity. To assess whether this motif predicts HA binding in the intact RHAMM protein, we mutated all basic amino acids in domains I and II that form part of these motifs using site-directed mutagenesis and prepared fusion protein from the mutated cDNA. The altered RHAMM protein did not bind HA, confirming that the basic amino acids and their spacing are critical for binding. A specific requirement for arginine or lysine residues was identified since mutation of K430, R431 and K432 to histidine residues abolished binding. Clustering of basic amino acids either within or at either end of the motif enhanced HA binding activity while the occurrence of acidic residues between the basic amino acids reduced binding. The B(X7)B motif, in which B is either R or K and X7 contains no acidic residues and at least one basic amino acid, was found in all HA binding proteins molecularly characterized to date. Recombinant techniques were used to generate chimeric proteins containing either the B(X7)B motifs present in CD44 or link protein, with the amino-terminus of RHAMM (amino acids 1-238) that does not bind HA. All chimeric proteins containing the motif bound HA in transblot analyses

  12. Electronic and magnetic properties of CrGen (15 ⩽ n ⩽ 29) clusters: A DFT study

    NASA Astrophysics Data System (ADS)

    Mahtout, Sofiane; Tariket, Yacine

    2016-06-01

    We report ab initio calculations of electronic and magnetic properties of medium-sized CrGen (15 ⩽ n ⩽ 29) clusters using density functional theory. The encapsulation of Cr atoms within Gen clusters leads to stable Cr encapsulated Gen clusters. The binding energies generally increase while the differences between the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO gaps) generally decrease with the increasing of cluster size. The clusters of CrGen at size 16, 17, 19, 22, 24 and 29 exhibit high stabilities when compared to their neighbors. This has been discussed in terms of their structures, energies and the effect of the position of doping atom. Doping of Gen clusters with one Cr atom leads to CrGen clusters with magnetic moment depending on the structure of the clusters and the position of Cr atom in the clusters. Moreover, vertical ionization potential, vertical electronic affinity, and chemical hardness are also analyzed.

  13. Clustering granulometric features

    NASA Astrophysics Data System (ADS)

    Brun, Marcel; Balagurunathan, Yoganand; Barrera, Junior; Dougherty, Edward R.

    2002-05-01

    Granulometric features have been widely used for classification, segmentation and recently in estimation of parameters in shape models. In this paper we study the inference of clustering based on granulometric features for a collection of structuring probes in the context of random models. We use random Boolean models to represent grains of different shapes and structure. It is known that granulometric features are excellent descriptors of shape and structure of grains. Inference based on clustering these features helps to analyze the consistency of these features and clustering algorithms. This greatly aids in classifier design and feature selection. Features and the order of their addition play a role in reducing the inference errors. We study four different types of feature addition methods and the effect of replication in reducing the inference errors.

  14. Ab initio study of interstitial cluster interaction with Re, Os, and Ta in W

    NASA Astrophysics Data System (ADS)

    Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

    2017-02-01

    The stability of tungsten self-interstitial atom (SIA) clusters is studied using first-principles methods. Clusters from one to seven SIAs are systematically explored from 1264 unique configurations. Finite-size effect of the simulation cell is corrected based on the scaling of formation energy versus inverse volume cell. Furthermore, the accuracy of the calculations is improved by treating the 5p semicore states as valence states. Configurations of the three most stable clusters in each cluster size n are presented, which consist of parallel [111] dumbbells. The evolution of these clusters leading to small dislocation loops is discussed. The binding energy of size-n clusters is analyzed relative to an n → (n-1) + 1 dissociation and is shown to increase with size. Extrapolation for n > 7 is presented using a dislocation loop model. In addition, the interaction of these clusters with a substitutional Re, Os, or Ta solute is explored by replacing one of the dumbbells with the solute. Re and Os strongly attract these clusters, but Ta strongly repels. The strongest interaction is found when the solute is located on the periphery of the cluster rather than in the middle. The magnitude of this interaction decreases with cluster size. Empirical fits to describe the trend of the solute binding energy are presented.

  15. Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

    PubMed

    Manzoor, Dar; Pal, Sourav

    2015-06-18

    Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

  16. Characterisation, degradation and regeneration of luminescent Ag29 clusters in solution.

    PubMed

    van der Linden, Marte; Barendregt, Arjan; van Bunningen, Arnoldus J; Chin, Patrick T K; Thies-Weesie, Dominique; de Groot, Frank M F; Meijerink, Andries

    2016-12-01

    Luminescent Ag clusters are prepared with lipoic acid (LA) as the ligand. Using a combination of mass spectrometry, optical spectroscopy and analytical ultracentrifugation, the clusters are found to be highly monodisperse with mass 5.6 kDa. We assign the chemical composition [Ag29(LA)12](3-) to the clusters, where LA likely binds in a bidentate fashion. The Ag29 clusters show slow degradation, retaining their deep red emission for at least 18 months if stored in the dark. Purification or exposure to light results in faster degradation. No other cluster species are observed during the degradation process. Once degraded, the clusters could easily be regenerated using NaBH4, which is not usually observed for thiolate-capped Ag clusters.

  17. The X-ray emitting gas in poor clusters with central dominant galaxies

    NASA Technical Reports Server (NTRS)

    Kriss, G. A.; Cioffi, D. F.; Canizares, C. R.

    1983-01-01

    The 12 clusters detected in the present study by the Einstein Observatory's X-ray imaging proportional counter show X-ray emission centered on the dominant galaxy in all cases. Comparison of the deduced distribution of binding mass with the light distribution of the central galaxies of four clusters indicates that the mass/luminosity ratio rises to over 200 solar masses/solar luminosity in the galaxy halos. These halos must therefore, like the clusters themselves, posses dark matter. The X-ray data clearly show that the dominant galaxies sit at the bottoms of the poor cluster gravitational potential wells, suggesting a similar origin for dominant galaxies in poor and rich clusters, perhaps through the merger and cannibalism of cluster galaxies. It is the luminosity of the distended cD envelope that reflects the relative wealth of the cluster environment.

  18. First-principles insights into interaction of Au with small Co clusters

    NASA Astrophysics Data System (ADS)

    Aghajani, Mahdieh; Javad Hashemifar, S.; Akbarzadeh, Hadi

    2014-08-01

    The effects of Au doping on structural, electronic, magnetic, and dynamical properties of the Con nano-clusters are investigated by using density functional computations and numeric atom-centered orbitals method. The Au doping that enhances stability of the planar structures of the Con clusters over their 3-dimensional structures is discussed. Doping with the nonmagnetic Au atom is found to decrease the spin moments of the Con clusters. The calculated binding energies and their various derivatives are used to investigate the structural stability of the doped clusters. The electronic energy levels of the clusters are accurately determined and discussed after applying the many body based GW correction. The vibrational and infrared spectra of the doped clusters are calculated to provide spectroscopic finger print of these clusters.

  19. A DFT study on the adsorption of CO and CO{sub 2} molecules on Pt{sub 4} and Ir{sub 4} clusters

    SciTech Connect

    Munieswaran, P.; Seenithurai, S.; Pandyan, R. Kodi; Kumar, S. Vinodh; Saranya, C.; Mahendran, M.

    2015-06-24

    We analyze the electronic structure and adsorption binding energy of CO and CO{sub 2} molecules adsorbed on Ir{sub 4} and Pt{sub 4} clusters by using Density functional theory (DFT). It is found that the Ir{sub 4} cluster has more adsorption binding energy than Pt{sub 4} cluster. We show that the Ir and Ir - supported materials are good catalytic materials and could be useful for gas sensor applications.

  20. Sigma Receptor Binding Assays.

    PubMed

    Chu, Uyen B; Ruoho, Arnold E

    2015-12-08

    Sigma receptors, both Sigma-1(S1R) and Sigma-2 (S2R), are small molecule-regulated, primarily endoplasmic reticulum (ER) membrane-associated sites. A number of drugs bind to sigma receptors, including the antipsychotic haloperidol and (+)-pentazocine, an opioid analgesic. Sigma receptors are implicated in many central nervous system disorders, in particular Alzheimer's disease and conditions associated with motor control, such as Amyotrophic Lateral Sclerosis (ALS). Described in this unit are radioligand binding assays used for the pharmacological characterization of S1R and S2R. Methods detailed include a radioligand saturation binding assay for defining receptor densities and a competitive inhibition binding assay employing [³H]-(+)-pentazocine for identifying and characterizing novel ligands that interact with S1R. Procedures using [³H]-1,3-di(2-tolyl)guanidine ([³H]-DTG), a nonselective sigma receptor ligand, are described for conducting a saturation binding and competitive inhibition assays for the S2R site. These protocols are of value in drug discovery in identifying new sigma ligands and in the characterization of these receptors.

  1. Structure and energetics of nanometer size clusters of sulfuric acid with ammonia and dimethylamine.

    PubMed

    DePalma, Joseph W; Bzdek, Bryan R; Doren, Douglas J; Johnston, Murray V

    2012-01-26

    The structures of positively and negatively charged clusters of sulfuric acid with ammonia and/or dimethylamine ((CH(3))(2)NH or DMA) are investigated using a combination of Monte Carlo configuration sampling, semiempirical calculations, and density functional theory (DFT) calculations. Positively charged clusters of the formula [(NH(4)(+))(x)(HSO(4)(-))(y)](+), where x = y + 1, are studied for 1 ≤ y ≤ 10. These clusters exhibit strong cation-anion interactions, with no contribution to the hydrogen-bonding network from the bisulfate ion protons. A similar hydrogen-bonding network is found for the [(DMAH(+))(5)(HSO(4)(-))(4)](-) cluster. Negatively charged clusters derived from the reaction of DMA with [(H(2)SO(4))(3)(NH(4)(+))(HSO(4)(-))(2)](-) are also studied, up to the fully reacted cluster [(DMAH(+))(4)(HSO(4)(-))(5)](-). These clusters exhibit anion-anion and ion-molecule interactions in addition to cation-anion interactions. While the hydrogen-bonding network is extensive for both positively and negatively charged clusters, the binding energies of ions and molecules in these clusters are determined mostly by electrostatic interactions. The thermodynamics of amine substitution is explored and compared to experimental thermodynamic and kinetic data. Ammonia binds more strongly than DMA to sulfuric acid due to its greater participation in hydrogen bonding and its ability to form a more compact structure that increases electrostatic attraction between oppositely charged ions. However, the greater gas-phase basicity of DMA is sufficient to overcome the stronger binding of ammonia, making substitution of DMA for ammonia thermodynamically favorable. For small clusters of both polarities, substitutions of surface ammonium ions are facile. As the cluster size increases, an ammonium ion becomes encapsulated in the center of the cluster, making it inaccessible to substitution.

  2. STRUCTURAL PARAMETERS FOR 10 HALO GLOBULAR CLUSTERS IN M33

    SciTech Connect

    Ma, Jun

    2015-05-15

    In this paper, we present the properties of 10 halo globular clusters (GCs) with luminosities L ≃ 5–7 × 10{sup 5} L{sub ⊙} in the Local Group galaxy M33 using images from the Hubble Space Telescope WFPC2 in the F555W and F814W bands. We obtained the ellipticities, position angles, and surface brightness profiles for each GC. In general, the ellipticities of the M33 sample clusters are similar to those of the M31 clusters. The structural and dynamical parameters are derived by fitting the profiles to three different models combined with mass-to-light ratios (M/L values) from population-synthesis models. The structural parameters include core radii, concentration, half-light radii, and central surface brightness. The dynamical parameters include the integrated cluster mass, integrated binding energy, central surface mass density, and predicted line of sight velocity dispersion at the cluster center. The velocity dispersions of the four clusters predicted here agree well with the observed dispersions by Larsen et al. The results here showed that the majority of the sample halo GCs are better fitted by both the King model and the Wilson model than the Sérsic model. In general, the properties of the clusters in M33, M31, and the Milky Way fall in the same regions of parameter spaces. The tight correlations of cluster properties indicate a “fundamental plane” for clusters, which reflects some universal physical conditions and processes operating at the epoch of cluster formation.

  3. Fullerene Molecules and Other Clusters of III-V Compounds

    NASA Astrophysics Data System (ADS)

    Hira, Ajit; Auxier, John, II; Lucero, Melinda

    2010-03-01

    The goal of the our work is to derive geometries of fullerene-like cages and other clusters of atoms from groups III and V of the periodic table. Our previous research focused on Carbon Fullerenes and on GanAsn clusters (n = 1 thru 12). Our research group has made an original discovery about GanAsn clusters. In our work on nanotechnology to date, we used the hybrid ab initio methods of quantum chemistry to derive the different geometries for the clusters of interest. We also calculated binding energies, bond-lengths, ionization potentials, electron affinities and HOMO-LUMO gaps, and IR spectra for these geometries. Of particular significance was the magic number for GaAs cluster stability that we found at n = 8. This is important because materials containing controlled III-V nanostructures provide the capability of preparing new classes of materials with enhanced optical, magnetic, chemical sensor and photo-catalytic properties. The second phase of the investigation will examine the effects of confinement on the optical properties the clusters. It will be interesting to observe novel linear as well as nonlinear optical processes in them. The third phase of the investigation will focus on the improved design of solar cells based on the optical properties of the clusters.

  4. Analysis of leukocyte binding to depletion filters: role of passive binding, interaction with platelets, and plasma components.

    PubMed

    Henschler, R; Rüster, B; Steimle, A; Hansmann, H L; Walker, W; Montag, T; Seifried, E

    2005-08-01

    Since limited knowledge exists on the mechanisms which regulate cell binding to leukocyte removal filter surfaces, we investigated the binding patterns of leukocytes to individual layers of leukocyte depletion filters. After passage of 1 unit of whole blood, blotting of isolated filter layers on glass slides or elution of cells from filter layers revealed that most leukocytes were located within the first 10 of a total of 28 filter layers, peaking at layers 6 to 8, with granulocytes binding on average to earlier filter layers than lymphocytes. Leukocytes preincubated with inhibitors of actin activation showed unchanged distribution between filter layers, suggesting that cytoskeletal activation does not significantly contribute to their binding. When leukocytes were directly incubated with single filter layers, binding of up to 30% of input cells was recorded in the absence of Ca(2+). Immunohistological analyses showed colocalization of platelets and leukocytes, with co-clustering of platelets and leukocytes. Monocytes and to some degree lymphocytes but not granulocytes competed with platelets for filter binding. Precoating of filter layers with individual plasma components showed that hyaluronic acid, plasma type fibronectin, and fibrinogen all increased the binding of leukocytes compared with albumin coating. In conclusion, leukocytes can bind passively to filters in a process which does not require Ca(2+), which is independent of cytoskeletal activation and which may depend on individual plasma components. These results are of importance when new selective cell enrichment or depletion strategies through specific filters are envisaged.

  5. Clustering cancer gene expression data by projective clustering ensemble

    PubMed Central

    Yu, Xianxue; Yu, Guoxian

    2017-01-01

    Gene expression data analysis has paramount implications for gene treatments, cancer diagnosis and other domains. Clustering is an important and promising tool to analyze gene expression data. Gene expression data is often characterized by a large amount of genes but with limited samples, thus various projective clustering techniques and ensemble techniques have been suggested to combat with these challenges. However, it is rather challenging to synergy these two kinds of techniques together to avoid the curse of dimensionality problem and to boost the performance of gene expression data clustering. In this paper, we employ a projective clustering ensemble (PCE) to integrate the advantages of projective clustering and ensemble clustering, and to avoid the dilemma of combining multiple projective clusterings. Our experimental results on publicly available cancer gene expression data show PCE can improve the quality of clustering gene expression data by at least 4.5% (on average) than other related techniques, including dimensionality reduction based single clustering and ensemble approaches. The empirical study demonstrates that, to further boost the performance of clustering cancer gene expression data, it is necessary and promising to synergy projective clustering with ensemble clustering. PCE can serve as an effective alternative technique for clustering gene expression data. PMID:28234920

  6. Aluminum binding by humus

    SciTech Connect

    Benedetti, M.F.; Hiemstra, T.; Riemsdijk, W. van; Kinniburgh, D.

    1996-10-01

    The need for qualitative and quantitative description of the chemical speciation of Al, in particular and other metal ions in general, is stressed by the increased mobilization of metal ions in water and soils due to acid rain deposition. In this paper we present new data of Al binding to two humic acids. These new data sets and the some previously published data will be analyzed with the NICA-Donnan model using one set of parameters to describe the Al binding to the different humic substances. Once the experimental data is described with the NICA-Donnan approach, we will show the effect of Ca on Al binding and surface speciation as well as the effect of Al on the charge of the humic particles. The parameters derived from the laboratory experiments will be used to describe the variation of the field based Al partition coefficient.

  7. Whole-genome cartography of estrogen receptor alpha binding sites.

    PubMed

    Lin, Chin-Yo; Vega, Vinsensius B; Thomsen, Jane S; Zhang, Tao; Kong, Say Li; Xie, Min; Chiu, Kuo Ping; Lipovich, Leonard; Barnett, Daniel H; Stossi, Fabio; Yeo, Ailing; George, Joshy; Kuznetsov, Vladimir A; Lee, Yew Kok; Charn, Tze Howe; Palanisamy, Nallasivam; Miller, Lance D; Cheung, Edwin; Katzenellenbogen, Benita S; Ruan, Yijun; Bourque, Guillaume; Wei, Chia-Lin; Liu, Edison T

    2007-06-01

    Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor alpha (ERalpha) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERalpha binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5' and 3' ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERalpha binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERalpha-positive from ERalpha-negative breast tumors. The expression dynamics of the genes adjacent to ERalpha binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERalpha appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERalpha target genes. Unexpectedly, we found that only 22%-24% of the bona fide human ERalpha binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERalpha binding and gene

  8. Health Occupations Cluster.

    ERIC Educational Resources Information Center

    Walraven, Catherine; And Others

    These instructional materials consist of a series of curriculum worksheets that cover tasks to be mastered by students in health occupations cluster programs. Covered in the curriculum worksheets are diagnostic procedures; observing/recording/reporting/planning; safety; nutrition/elimination; hygiene/personal care/comfort;…

  9. Clustering in Bubble Suspensions

    NASA Astrophysics Data System (ADS)

    Zenit, Roberto

    2000-11-01

    A monidisperse bubble suspension is studied experimentally for the limit in which the Weber number is small and the Reynolds number is large. For this regime the suspension can be modeled using potential flow theory to describe the dynamics of the interstitial fluid. Complete theoretical descriptions have been composed (Spelt and Sangani, 1998) to model the behavior of these suspensions. Bubble clustering is a natural instability that arises from the potential flow considerations, in which bubbles tend to align in horizontal rafts as they move upwards. The appearance of bubble clusters was recently corroborated experimentally by Zenit et al. (2000), who found that although clusters did appear, their strength was not as strong as the predictions. Experiments involving gravity driven shear flows are used to explain the nature of the clustering observed in these type of flows. Balances of the bubble phase pressure (in terms of a calculated diffusion coefficient) and the Maxwell pressure (from the potential flow description) are presented to predict the stability of the bubble suspension. The predictions are compared with experimental results.

  10. FUEL ROD CLUSTERS

    DOEpatents

    Schultz, A.B.

    1959-08-01

    A cluster of nuclear fuel rods and a tubular casing therefor through which a coolant flows in heat-exchange contact with the fuel rods is described. The fuel rcds are held in the casing by virtue of the compressive force exerted between longitudinal ribs of the fuel rcds and internal ribs of the casing or the internal surfaces thereof.

  11. Hydrodynamics of Merging Clusters

    NASA Technical Reports Server (NTRS)

    David,Laurence; Mushotzky, Richard F. (Technical Monitor)

    2004-01-01

    With the Chandra X-Ray Observatory, we observed two clusters of galaxies that are undergoing major mergers . All of the analysis is complete and two papers have been accepted for publication. The abstracts of the two papers are presented in the report.

  12. PVM Support for Clusters

    NASA Technical Reports Server (NTRS)

    Springer, P.

    2000-01-01

    The latest version of PVM (3.4.3) now contains support for a PC cluster running Linux, also known as a Beowulf system. A PVM user of a computer outside the Beowulf system can add the Beowulf as a single machine.

  13. Nuclear Cluster Physics

    SciTech Connect

    Kamimura, Masayasu

    2011-05-06

    Predictive power of theory needs good models and accurate calculation methods to solve the Schroedinger equations of the systems concerned. We present some examples of successful predictions based on the nuclear cluster models of light nuclei and hypernuclei and on the calculation methods that have been developed by Kyushu group.

  14. Cluster headaches simulating parasomnias.

    PubMed

    Isik, Ugur; D'Cruz, O 'Neill F

    2002-09-01

    Nocturnal episodes of agitated arousal in otherwise healthy young children are often related to nonrapid eye movement parasomnias (night terrors). However, in patients with acute onset or increased frequency of parasomnias, organic causes of discomfort must be excluded. We report four young children whose parasomnias were caused by nocturnal cluster headaches and who responded to indomethacin dramatically.

  15. Clustered for Success

    ERIC Educational Resources Information Center

    Brulles, Dina; Winebrenner, Susan

    2012-01-01

    Schools need to address the needs of their students with high ability. Not only does this raise achievement levels schoolwide, it also attracts students from surrounding districts and recaptures advanced learners who left the school because their needs weren't being met. One practical intervention--cluster grouping--provides an inclusive…

  16. Health Occupations Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    Intended to assist the vocational teacher in designing and implementing a cluster program in health occupations, this guide suggests ideas for teaching the specific knowledge and skills that qualify students for entry-level employment in the health occupations field. The knowledge and skills are applicable to 12 occupations: dental assistant;…

  17. Buckets, Clusters and Dienst

    NASA Technical Reports Server (NTRS)

    Nelson, Michael L.; Maly, Kurt; Shen, Stewart N. T.

    1997-01-01

    In this paper we describe NCSTRL+, a unified, canonical digital library for scientific and technical information (STI). NCSTRL+ is based on the Networked Computer Science Technical Report Library (NCSTRL), a World Wide Web (WWW) accessible digital library (DL) that provides access to over 80 university departments and laboratories. NCSTRL+ implements two new technologies: cluster functionality and publishing "buckets." We have extended the Dienst protocol, the protocol underlying NCSTRL, to provide the ability to "cluster" independent collections into a logically centralized digital library based upon subject category classification, type of organization, and genres of material. The concept of "buckets" provides a mechanism for publishing and managing logically linked entities with multiple data formats. The NCSTRL+ prototype DL contains the holdings of NCSTRL and the NASA Technical Report Server (NTRS). The prototype demonstrates the feasibility of publishing into a multi-cluster DL, searching across clusters, and storing and presenting buckets of information. We show that the overhead for these additional capabilities is minimal to both the author and the user when compared to the equivalent process within NCSTRL.

  18. Universality of cluster dynamics

    NASA Astrophysics Data System (ADS)

    McFadden, Carson; Bouchard, Louis-S.

    2010-12-01

    We have studied the kinetics of cluster formation for dynamical systems of dimensions up to n=8 interacting through elastic collisions or coalescence. These systems could serve as possible models for gas kinetics, polymerization, and self-assembly. In the case of elastic collisions, we found that the cluster size probability distribution undergoes a phase transition at a critical time which can be predicted from the average time between collisions. This enables forecasting of rare events based on limited statistical sampling of the collision dynamics over short time windows. The analysis was extended to Lp -normed spaces (p=1,…,∞) to allow for some amount of interpenetration or volume exclusion. The results for the elastic collisions are consistent with previously published low-dimensional results in that a power law is observed for the empirical cluster size distribution at the critical time. We found that the same power law also exists for all dimensions n=2,…,8 , two-dimensional Lp norms, and even for coalescing collisions in two dimensions. This broad universality in behavior may be indicative of a more fundamental process governing the growth of clusters.

  19. Curriculum Guide Construction Cluster.

    ERIC Educational Resources Information Center

    Kline, Ken

    As part of a model construction cluster curriculum development project, this guide was developed and implemented in the Beaverton (Oregon) School District. The curriculum guide contains 16 units covering the following topics: introduction to construction jobs; safety and first aid; blueprint readings; basic mathematics; site work; framing; roofing…

  20. Hybrid cluster identification

    NASA Astrophysics Data System (ADS)

    Martín-Herrero, J.

    2004-10-01

    I present a hybrid method for the labelling of clusters in two-dimensional lattices, which combines the recursive approach with iterative scanning to reduce the stack size required by the pure recursive technique, while keeping its benefits: single pass and straightforward cluster characterization and percolation detection parallel to the labelling. While the capacity to hold the entire lattice in memory is usually regarded as the major constraint for the applicability of the recursive technique, the required stack size is the real limiting factor. Resorting to recursion only for the transverse direction greatly reduces the recursion depth and therefore the required stack. It also enhances the overall performance of the recursive technique, as is shown by results on a set of uniform random binary lattices and on a set of samples of the Ising model. I also show how this technique may replace the recursive technique in Wolff's cluster algorithm, decreasing the risk of stack overflow and increasing its speed, and the Hoshen-Kopelman algorithm in the Swendsen-Wang cluster algorithm, allowing effortless characterization during generation of the samples and increasing its speed.

  1. Dynamics and Interactions of Adsorbates on Palladium and Nickel Clusters

    NASA Astrophysics Data System (ADS)

    Hira, Ajit; Pacheco, Jose; Salazar, Justin; Brownrigg, Clifton

    2013-04-01

    We continue our interest on the interactions of different atomic and molecular species with small clusters of metallic elements, by examining the interactions of H, O and F atoms with Pdn and Nin clusters (n = 6 thru 12). The hybrid ab initio methods of quantum chemistry (particularly the DFT-B3LYP model) are used to derive optimal geometries for the clusters of interest. We compare calculated binding energies, bond-lengths, ionization potentials, electron affinities and HOMO-LUMO gaps for the clusters of the two different metals. Of particular interest are the comparisons of binding strengths at the three important types of sites: edge (E) sites, hollow sites (H) site and on-top (T) sites. Effects of crystal symmetries corresponding to the bulk structures for the two metals will also be investigated. Our theoretical results will be compared with the experimental studies where they are available. We will also study the dynamics of the atomic species, and the dynamics and dissociation of the molecular species on the clusters.

  2. The efficiency of star formation in clustered and distributed regions

    NASA Astrophysics Data System (ADS)

    Bonnell, Ian A.; Smith, Rowan J.; Clark, Paul C.; Bate, Matthew R.

    2011-02-01

    We investigate the formation of both clustered and distributed populations of young stars in a single molecular cloud. We present a numerical simulation of a 104 M⊙ elongated, turbulent, molecular cloud and the formation of over 2500 stars. The stars form both in stellar clusters and in a distributed mode, which is determined by the local gravitational binding of the cloud. A density gradient along the major axis of the cloud produces bound regions that form stellar clusters and unbound regions that form a more distributed population. The initial mass function (IMF) also depends on the local gravitational binding of the cloud with bound regions forming full IMFs whereas in the unbound, distributed regions the stellar masses cluster around the local Jeans mass and lack both the high-mass and the low-mass stars. The overall efficiency of star formation is ≈ 15 per cent in the cloud when the calculation is terminated, but varies from less than 1 per cent in the regions of distributed star formation to ≈ 40 per cent in regions containing large stellar clusters. Considering that large-scale surveys are likely to catch clouds at all evolutionary stages, estimates of the (time-averaged) star formation efficiency (SFE) for the giant molecular cloud reported here is only ≈ 4 per cent. This would lead to the erroneous conclusion of slow star formation when in fact it is occurring on a dynamical time-scale.

  3. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Carolyn

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  4. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    2001-10-09

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  5. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    1999-01-01

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  6. AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application

    PubMed Central

    Hoinka, Jan; Berezhnoy, Alexey; Sauna, Zuben E.; Przytycka, Teresa M.

    2014-01-01

    Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is a well established experimental procedure to identify aptamers - synthetic single-stranded (ribo)nucleic molecules that bind to a given molecular target. Recently, new sequencing technologies have revolutionized the SELEX protocol by allowing for deep sequencing of the selection pools after each cycle. The emergence of High Throughput SELEX (HT-SELEX) has opened the field to new computational opportunities and challenges that are yet to be addressed. To aid the analysis of the results of HT-SELEX and to advance the understanding of the selection process itself, we developed AptaCluster. This algorithm allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets. We performed HT-SELEX with Interleukin 10 receptor alpha chain (IL-10RA) as the target molecule and used AptaCluster to analyze the resulting sequences. AptaCluster allowed for the first survey of the relationships between sequences in different selection rounds and revealed previously not appreciated properties of the SELEX protocol. As the first tool of this kind, AptaCluster enables novel ways to analyze and to optimize the HT-SELEX procedure. Our AptaCluster algorithm is available as a very fast multiprocessor implementation upon request. PMID:25558474

  7. The ACS Survey of Galactic Globular Clusters. VIII. Effects of Environment on Globular Cluster Global Mass Functions

    NASA Astrophysics Data System (ADS)

    Paust, Nathaniel E. Q.; Reid, I. Neill; Piotto, Giampaolo; Aparicio, Antonio; Anderson, Jay; Sarajedini, Ata; Bedin, Luigi R.; Chaboyer, Brian; Dotter, Aaron; Hempel, Maren; Majewski, Steven; Marín-Franch, A.; Milone, Antonino; Rosenberg, Alfred; Siegel, Michael

    2010-02-01

    We have used observations obtained as part of the Hubble Space Telescope/ACS Survey of Galactic Globular Clusters to construct global present-day mass functions for 17 globular clusters utilizing multi-mass King models to extrapolate from our observations to the global cluster behavior. The global present-day mass functions for these clusters are well matched by power laws from the turnoff, ≈0.8 M sun, to 0.2-0.3 M sun on the lower main sequence. The slopes of those power-law fits, α, have been correlated with an extensive set of intrinsic and extrinsic cluster properties to investigate which parameters may influence the form of the present-day mass function. We do not confirm previous suggestions of correlations between α and either metallicity or Galactic location. However, we do find a strong statistical correlation with the related parameters central surface brightness, μ V , and inferred central density, ρ0. The correlation is such that clusters with denser cores (stronger binding energy) tend to have steeper mass functions (a higher proportion of low-mass stars), suggesting that dynamical evolution due to external interactions may have played a key role in determining α. Thus, the present-day mass function may owe more to nurture than to nature. Detailed modeling of external dynamical effects is therefore a requisite for determining the initial mass function for Galactic globular clusters.

  8. THE ACS SURVEY OF GALACTIC GLOBULAR CLUSTERS. VIII. EFFECTS OF ENVIRONMENT ON GLOBULAR CLUSTER GLOBAL MASS FUNCTIONS

    SciTech Connect

    Paust, Nathaniel E. Q.; Reid, I. Neill; Anderson, Jay E-mail: inr@stsci.edu

    2010-02-15

    We have used observations obtained as part of the Hubble Space Telescope/ACS Survey of Galactic Globular Clusters to construct global present-day mass functions for 17 globular clusters utilizing multi-mass King models to extrapolate from our observations to the global cluster behavior. The global present-day mass functions for these clusters are well matched by power laws from the turnoff, {approx}0.8 M {sub sun}, to 0.2-0.3 M {sub sun} on the lower main sequence. The slopes of those power-law fits, {alpha}, have been correlated with an extensive set of intrinsic and extrinsic cluster properties to investigate which parameters may influence the form of the present-day mass function. We do not confirm previous suggestions of correlations between {alpha} and either metallicity or Galactic location. However, we do find a strong statistical correlation with the related parameters central surface brightness, {mu} {sub V}, and inferred central density, {rho}{sub 0}. The correlation is such that clusters with denser cores (stronger binding energy) tend to have steeper mass functions (a higher proportion of low-mass stars), suggesting that dynamical evolution due to external interactions may have played a key role in determining {alpha}. Thus, the present-day mass function may owe more to nurture than to nature. Detailed modeling of external dynamical effects is therefore a requisite for determining the initial mass function for Galactic globular clusters.

  9. PDMS embedded Ag clusters: Coalescence and cluster-matrix interaction

    NASA Astrophysics Data System (ADS)

    Roese, S.; Engemann, D.; Hoffmann, S.; Latussek, K.; Sternemann, C.; Hövel, H.

    2016-05-01

    Polydimethylsiloxane (PDMS) has proven to be a suitable embedding medium for silver clusters to prevent aggregation. In order to investigate the influence of the PDMS on the electronic and local atomic structure of the clusters the measurement of x-ray absorption near edge structure (XANES) spectra for different coverages of silver clusters in PDMS and calculations of corresponding XANES spectra have been performed. The coalescence process and the cluster-PDMS interaction were investigated with XANES.

  10. Excitonic effects and the optical absorption spectrum ofhydrogenated Si clusters

    SciTech Connect

    Rohlfing, Michael; Louie, Steven G.

    1997-10-19

    We calculate the optical absorption spectrum of hydrogen-terminated silicon clusters by solving the Bethe-Salpeter equation for the two-particle Green's function using an ab initio approach. The one-particle Green's function and the electron-hole interaction kernel are calculated within the GW approximation for the electron self-energy operator. Very large exciton binding energies are observed. Our results for the one-particle properties and the optical absorption spectra of the clusters are in very good agreement with available experimental data.

  11. The Rotation of Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Tovmassian, H. M.

    2015-09-01

    The method for detection of the galaxy cluster rotation based on the study of distribution of member galaxies with velocities lower and higher than the cluster mean velocity over the cluster image is proposed. The search for rotation is made for flat clusters with a/b > 1.8 and BMI type clusters which are expected to be rotating. For comparison there were studied also round clusters and clusters of NBMI type, the second by brightness galaxy, which does not differ significantly from the cluster cD galaxy. Seventeen out of studied 65 clusters are found to be rotating. It was found that the detection rate is sufficiently high for flat clusters, over 60%, and clusters of BMI type with dominant cD galaxy, ≈ 35% . The obtained results show that clusters were formed from the huge primordial gas clouds and preserved the rotation of the primordial clouds, unless they did not experience mergings with other clusters and groups of galaxies, as a result of which the rotation was prevented.

  12. Femtosecond dynamics of cluster expansion

    NASA Astrophysics Data System (ADS)

    Gao, Xiaohui; Wang, Xiaoming; Shim, Bonggu; Arefiev, Alexey; Tushentsov, Mikhail; Breizman, Boris; Downer, Mike

    2010-03-01

    Noble gas clusters irradiated by intense ultrafast laser expand quickly and become typical plasma in picosecond time scale. During the expansion, the clustered plasma demonstrates unique optical properties such as strong absorption and positive contribution to the refractive index. Here we studied cluster expansion dynamics by fs-time-resolved refractive index and absorption measurements in cluster gas jets after ionization and heating by an intense pump pulse. The refractive index measured by frequency domain interferometry (FDI) shows the transient positive peak of refractive index due to clustered plasma. By separating it from the negative contribution of the monomer plasma, we are able to determine the cluster fraction. The absorption measured by a delayed probe shows the contribution from clusters of various sizes. The plasma resonances in the cluster explain the enhancement of the absorption in our isothermal expanding cluster model. The cluster size distribution can be determined. A complete understanding of the femtosecond dynamics of cluster expansion is essential in the accurate interpretation and control of laser-cluster experiments such as phase-matched harmonic generation in cluster medium.

  13. Structural properties of small rhodium clusters

    SciTech Connect

    Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    We report a systematic study of the structural properties of rhodium clusters at the atomistic level. A novel global-minimum search algorithm, known as parallel tempering multicanonical basin hopping plus genetic algorithm (PTMBHGA), is used to obtain the geometrical structures with lowest minima at the semi-empirical level where Gupta potential is used to describe the atomic interaction among the rhodium atoms. These structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA). The structures are optimized for different spin multiplicities. The ones with lowest energies will be taken as ground-state structures. In most cases, we observe only minor changes in the geometry and bond length of the clusters as a result of DFT-level re-optimization. Only in some limited cases, the initial geometries obtained from the PTMBHGA are modified by the re-optimization. The variation of structural properties, such as ground-state geometry, symmetry and binding energy, with respect to the cluster size is studied and agreed well with other results available in the literature.

  14. Photoionization of rare gas clusters

    NASA Astrophysics Data System (ADS)

    Zhang, Huaizhen

    This thesis concentrates on the study of photoionization of van der Waals clusters with different cluster sizes. The goal of the experimental investigation is to understand the electronic structure of van der Waals clusters and the electronic dynamics. These studies are fundamental to understand the interaction between UV-X rays and clusters. The experiments were performed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The experimental method employs angle-resolved time-of-flight photoelectron spectrometry, one of the most powerful methods for probing the electronic structure of atoms, molecules, clusters and solids. The van der Waals cluster photoionization studies are focused on probing the evolution of the photoelectron angular distribution parameter as a function of photon energy and cluster size. The angular distribution has been known to be a sensitive probe of the electronic structure in atoms and molecules. However, it has not been used in the case of van der Waals clusters. We carried out outer-valence levels, inner-valence levels and core-levels cluster photoionization experiments. Specifically, this work reports on the first quantitative measurements of the angular distribution parameters of rare gas clusters as a function of average cluster sizes. Our findings for xenon clusters is that the overall photon-energy-dependent behavior of the photoelectrons from the clusters is very similar to that of the corresponding free atoms. However, distinct differences in the angular distribution point at cluster-size-dependent effects were found. For krypton clusters, in the photon energy range where atomic photoelectrons have a high angular anisotropy, our measurements show considerably more isotropic angular distributions for the cluster photoelectrons, especially right above the 3d and 4p thresholds. For the valence electrons, a surprising difference between the two spin-orbit components was found. For argon clusters, we found that the

  15. RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.

    PubMed

    Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

    2009-01-01

    We present a new database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases. The database consists of a classification of binding sites derived from protein-RNA complexes. Each binding site is assigned to a cluster of similar binding sites in other protein-RNA complexes. Cluster members share similar spatial arrangements of physico-chemical properties, thus can reveal novel similarity between proteins and RNAs with different sequences and folds. The clusters provide 3D consensus binding patterns important for protein-nucleotide recognition. The database search engine allows two types of useful queries: first, given a PDB code of a protein-RNA complex, RsiteDB can detail and classify the properties of the protein binding pockets accommodating extruded RNA nucleotides not involved in local RNA base pairing. Second, given an unbound protein structure, RsiteDB can perform an on-line structural search against the constructed database of 3D consensus binding patterns. Regions similar to known patterns are predicted to serve as binding sites. Alignment of the query to these patterns with their corresponding RNA nucleotides allows making unique predictions of the protein-RNA interactions at the atomic level of detail. This database is accessible at http://bioinfo3d.cs.tau.ac.il/RsiteDB.

  16. Choosing the Number of Clusters in K-Means Clustering

    ERIC Educational Resources Information Center

    Steinley, Douglas; Brusco, Michael J.

    2011-01-01

    Steinley (2007) provided a lower bound for the sum-of-squares error criterion function used in K-means clustering. In this article, on the basis of the lower bound, the authors propose a method to distinguish between 1 cluster (i.e., a single distribution) versus more than 1 cluster. Additionally, conditional on indicating there are multiple…

  17. MD-2 binds cholesterol.

    PubMed

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  18. MD-2 binds cholesterol

    PubMed Central

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I.

    2016-01-01

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis. PMID:26806306

  19. Cellulose binding domain proteins

    SciTech Connect

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  20. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  1. Sequential memory: Binding dynamics

    NASA Astrophysics Data System (ADS)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  2. SIGMA RECEPTOR BINDING ASSAYS

    PubMed Central

    CHU, UYEN B.; RUOHO, ARNOLD E.

    2016-01-01

    Sigma receptors belong to a class of small molecule-regulated, primarily endoplasmic reticulum (ER) membrane-associated receptors, of which there are two subtypes: the Sigma-1 receptor (S1R) and the Sigma-2 receptor (S2R). Both S1R and S2R bind to a number of drugs including antipsychotic, haloperidol, and the opioid analgesic, (+)-pentazocine. Sigma receptors are implicated in multiple disease pathologies associated with the nervous system including diseases affecting motor control such as Amyotrophic Lateral Sclerosis (ALS) and Alzeimher's disease. This unit describes methods for the pharmacological characterization of S1R and S2R using radioligand-binding assays. In the first section, radioligand saturation binding assay to determine receptor densities and competitive inhibition assays to characterize affinities of novel compounds are presented for S1R using the selective S1R ligand, [3H]-(+)-pentazocine. The second section describes radioligand saturation binding assay and competitive inhibition assays for the S2R using a non-selective S1R and S2R ligand, [3H]-1,3-di(2-tolyl)guanidine ([3H]-DTG). PMID:26646191

  3. Animation of the Phoenix Cluster

    NASA Video Gallery

    This animation shows how large numbers of stars form in the Phoenix Cluster. It begins by showing several galaxies in the cluster and hot gas (in red). This hot gas contains more normal matter than...

  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. Nuclear Cluster Aspects in Astrophysics

    NASA Astrophysics Data System (ADS)

    Kubono, Shigeru

    2010-03-01

    The role of nuclear clustering is discussed for nucleosynthesis in stellar evolution with Cluster Nucleosynthesis Diagram (CND) proposed before. Special emphasis is placed on α-induced stellar reactions together with molecular states for O and C burning.

  6. Observations of Distant Clusters

    NASA Technical Reports Server (NTRS)

    Donahue, Megan

    2004-01-01

    The is the proceedings and papers supported by the LTSA grant: Homer, D. J.\\& Donahue, M. 2003, in "The Emergence of Cosmic Structure": 13'h Astrophysics Conference Proceedings, Vol. 666,3 1 1-3 14, (AIP). Baumgartner, W. H., Loewenstein, M., Horner, D. J., Mushotzky, R. F. 2003, HEAD- AAS, 35.3503. Homer, D. J. , Donahue, M., Voit G. M. 2003, HEAD-AAS, 35.1309. Nowak, M. A., Smith, B., Donahue, M., Stocke, J. 2003, HEAD-AAS, 35.1316. Scott, D., Borys, C., Chapman, S. C., Donahue, M., Fahlman, G. G., Halpem, M. Newbury, P. 2002, AAS, 128.01. Jones, L. R. et al. 2002, A new era in cosmology, ASP Conference Proceedings, Vol. 283, p. 223 Donahue, M., Daly, R. A., Homer, D. J. 2003, ApJ, 584, 643, Constraints on the Cluster Environments and Hotspot magnetic field strengths for radio sources 3280 and 3254. Donahue, M., et al. 2003, ApJ, 598, 190. The mass, baryonic fraction, and x-ray temperature of the luminous, high-redshift cluster of galaxies MS045 1.6-0305 Perlman, E. S. et al. 2002, ApJS, 140, 256. Smith, B. J., Nowak, M., Donahue, M., Stocke, J. 2003, AJ, 126, 1763. Chandra Observations of the Interacting NGC44 10 Group of Galaxies. Postman, M., Lauer, T. R., Oegerle, W., Donahue, M. 2002, ApJ, 579, 93. The KPNO/deep-range cluster survey I. The catalog and space density of intermediate-redshift clusters. Molnar, S. M., Hughes, J. P., Donahue, M., Joy, M. 2002, ApJ, 573, L91, Chandra Observations of Unresolved X-Ray Sources around Two Clusters of Galaxies. Donahue, M., Mack, J., 2002 NewAR, 46, 155, HST NIcmos and WFPC2 observations of molecular hydrogen and dust around cooling flows. Koekemoer, A. M. et al. 2002 NewAR, 46, 149, Interactions between the A2597 central radio source and dense gas host galaxy. Donahue, M. et al. 2002 ApJ, 569,689, Distant cluster hunting II.

  7. Structures and optical absorptions of PbSe clusters from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Zeng, Qun; Shi, Jing; Jiang, Gang; Yang, Mingli; Wang, Fan; Chen, Jun

    2013-09-01

    Based on the low-lying structures of (PbSe)n (n = 1-10) clusters identified with a first-principles molecular dynamics approach, two growth patterns with distinct structure and energy evolutions were predicted for the even-n and odd-n clusters, respectively. Moreover, the clusters favor a simple cubic and bulk-like growth pattern, unlike the extensively studied II-VI clusters whose structural diversity has been well established. The overlap between 6p of Pb and 4p of Se makes not only the ordered and bulk-like structures but also a stable building block of (PbSe)4. The high stability of (PbSe)4 is recognized in terms of its binding energy, HOMO-LUMO gap, appearance in the structures of larger-size clusters, as well as its appearance in the fragmentation products of PbSe clusters. The geometrical and electronic structures of the PbSe clusters were further studied within the density functional theory framework including spin-orbital (SO) coupling. We found that SO coupling does not change the relative stability of the clusters but reduces their binding energy significantly. Particularly, the SO effect has a great impact on the UV-vis spectra of the clusters, which were simulated with time-dependent density functional theory at SO level of zeroth-order regular approximation.

  8. Chloroplast HCF101 is a scaffold protein for [4Fe-4S] cluster assembly

    PubMed Central

    Schwenkert, Serena; Netz, Daili J. A.; Frazzon, Jeverson; Pierik, Antonio J.; Bill, Eckhard; Gross, Jeferson; Lill, Roland; Meurer, Jörg

    2009-01-01

    Oxygen-evolving chloroplasts possess their own iron-sulfur cluster assembly proteins including members of the SUF (sulfur mobilization) and the NFU family. Recently, the chloroplast protein HCF101 (high chlorophyll fluorescence 101) has been shown to be essential for the accumulation of the membrane complex Photosystem I and the soluble ferredoxin-thioredoxin reductases, both containing [4Fe-4S] clusters. The protein belongs to the FSC-NTPase ([4Fe-4S]-cluster-containing P-loop NTPase) superfamily, several members of which play a crucial role in Fe/S cluster biosynthesis. Although the C-terminal ISC-binding site, conserved in other members of the FSC-NTPase family, is not present in chloroplast HCF101 homologues using Mössbauer and EPR spectroscopy, we provide evidence that HCF101 binds a [4Fe-4S] cluster. 55Fe incorporation studies of mitochondrially targeted HCF101 in Saccharomyces cerevisiae confirmed the assembly of an Fe/S cluster in HCF101 in an Nfs1-dependent manner. Site-directed mutagenesis identified three HCF101-specific cysteine residues required for assembly and/or stability of the cluster. We further demonstrate that the reconstituted cluster is transiently bound and can be transferred from HCF101 to a [4Fe-4S] apoprotein. Together, our findings suggest that HCF101 may serve as a chloroplast scaffold protein that specifically assembles [4Fe-4S] clusters and transfers them to the chloroplast membrane and soluble target proteins. PMID:19817716

  9. Methanethiol chemistry on TiO 2-supported Ni clusters

    NASA Astrophysics Data System (ADS)

    Ozturk, O.; Park, J. B.; Black, T. J.; Rodriguez, J. A.; Hrbek, J.; Chen, D. A.

    2008-10-01

    The thermal decomposition of methanethiol on Ni clusters grown on TiO 2(1 1 0) was studied by temperature programmed desorption (TPD), X-ray photoelectron spectroscopy (XPS) and low energy ion scattering (LEIS). On all of the Ni surfaces investigated, methane and hydrogen were observed as gaseous products in the TPD experiments, and the only sulfur-containing species that desorbed from the surface was methanethiol itself at low temperatures. The two pathways for methanethiol reaction were hydrodesulfurization to produce methane and nonselective decomposition, which leaves atomic carbon and sulfur on the surface. From high resolution XPS studies, methyl thiolate was identified as the surface intermediate for reaction on TiO 2 and on all of the Ni surfaces investigated, similar to what is observed on single-crystal Ni surfaces. However, the binding sites for methyl thiolate on the 1 ML (monolayer) Ni clusters were different from those on the Ni clusters at coverages of 2.5 ML and higher, based on the S(2p) binding energies for methyl thiolate. No distinct changes in activity or selectivity were observed for the smaller Ni clusters grown at low coverage compared to the more film-like Ni surfaces other than what could be accounted for by changes in total surface area. Interactions between the Ni clusters and the TiO 2 support had two main effects on chemical activity. First, carbon was oxidized by oxygen from the TiO 2 lattice to produce CO at temperatures above 800 K. Second, annealing induced encapsulation of the Ni clusters by reduced TiO x and chemisorbed oxygen. At 800 K, the Ni clusters were totally encapsulated, resulting in a complete loss of methanethiol activity; partial encapsulation at 700 K caused a smaller decrease in activity accompanied by increased oxidation of carbon by lattice oxygen.

  10. Methanethiol Chemistry on TiO2-Supported Ni Clusters

    SciTech Connect

    Ozturk,O.; Park, J.; Black, T.; Rodriguez, J.; Hrbek, J.; Chen, D.

    2008-01-01

    The thermal decomposition of methanethiol on Ni clusters grown on TiO2(1 1 0) was studied by temperature programmed desorption (TPD), X-ray photoelectron spectroscopy (XPS) and low energy ion scattering (LEIS). On all of the Ni surfaces investigated, methane and hydrogen were observed as gaseous products in the TPD experiments, and the only sulfur-containing species that desorbed from the surface was methanethiol itself at low temperatures. The two pathways for methanethiol reaction were hydrodesulfurization to produce methane and nonselective decomposition, which leaves atomic carbon and sulfur on the surface. From high resolution XPS studies, methyl thiolate was identified as the surface intermediate for reaction on TiO2 and on all of the Ni surfaces investigated, similar to what is observed on single-crystal Ni surfaces. However, the binding sites for methyl thiolate on the 1 ML (monolayer) Ni clusters were different from those on the Ni clusters at coverages of 2.5 ML and higher, based on the S(2p) binding energies for methyl thiolate. No distinct changes in activity or selectivity were observed for the smaller Ni clusters grown at low coverage compared to the more film-like Ni surfaces other than what could be accounted for by changes in total surface area. Interactions between the Ni clusters and the TiO2 support had two main effects on chemical activity. First, carbon was oxidized by oxygen from the TiO2 lattice to produce CO at temperatures above 800 K. Second, annealing induced encapsulation of the Ni clusters by reduced TiOx and chemisorbed oxygen. At 800 K, the Ni clusters were totally encapsulated, resulting in a complete loss of methanethiol activity; partial encapsulation at 700 K caused a smaller decrease in activity accompanied by increased oxidation of carbon by lattice oxygen.

  11. The Orion nebula star cluster

    NASA Technical Reports Server (NTRS)

    Panek, R. J.

    1982-01-01

    Photography through filters which suppress nebular light reveal a clustering of faint red stars centered on the Trapezium, this evidences a distinct cluster within the larger OB1 association. Stars within about 20 ft of trapezium comprise the Orion Nebula star cluster are considered. Topics discussed re: (1) extinction by dust grains; (2) photometric peculiarities; (3) spectroscopic peculiarities; (4) young variables; (5) the distribution and motion of gas within the cluster.

  12. Massive star clusters in galaxies.

    PubMed

    Harris, William E

    2010-02-28

    The ensemble of all star clusters in a galaxy constitutes its star cluster system. In this review, the focus of the discussion is on the ability of star clusters, particularly the systems of old massive globular clusters (GCs), to mark the early evolutionary history of galaxies. I review current themes and key findings in GC research, and highlight some of the outstanding questions that are emerging from recent work.

  13. Multiple sup 3 H-oxytocin binding sites in rat myometrial plasma membranes

    SciTech Connect

    Crankshaw, D.; Gaspar, V.; Pliska, V. )

    1990-01-01

    The affinity spectrum method has been used to analyse binding isotherms for {sup 3}H-oxytocin to rat myometrial plasma membranes. Three populations of binding sites with dissociation constants (Kd) of 0.6-1.5 x 10(-9), 0.4-1.0 x 10(-7) and 7 x 10(-6) mol/l were identified and their existence verified by cluster analysis based on similarities between Kd, binding capacity and Hill coefficient. When experimental values were compared to theoretical curves constructed using the estimated binding parameters, good fits were obtained. Binding parameters obtained by this method were not influenced by the presence of GTP gamma S (guanosine-5'-O-3-thiotriphosphate) in the incubation medium. The binding parameters agree reasonably well with those found in uterine cells, they support the existence of a medium affinity site and may allow for an explanation of some of the discrepancies between binding and response in this system.

  14. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, James F.; Furuya, Frederic R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab').sub.2 fragments thereof are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy.

  15. Derivatized gold clusters and antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.; Furuya, F.R.

    1994-11-01

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be as small as 5.0 nm. Methods and reagents are disclosed in which antibodies, Fab' or F(ab')[sub 2] fragments are covalently bound to a stable cluster of gold atoms. The gold clusters may contain 6, 8, 9, 11, 13, 55 or 67 gold atoms in their inner core. The clusters may also contain radioactive gold. The antibody-cluster conjugates are useful in electron microscopy applications as well as in clinical applications that include imaging, diagnosis and therapy. 7 figs.

  16. Dynamics of the coronas of open star clusters

    NASA Astrophysics Data System (ADS)

    Danilov, V. M.; Putkov, S. I.; Seleznev, A. F.

    2014-12-01

    A method for distinguishing coronas in models of open star clusters is proposed. The method uses trajectories of stars that do not leave the coronas over time intervals t comparable to the mean lifetime τ of the clusters. Corona models are constructed for six numerical cluster models, and the direction and character of the dynamical evolution of the coronas are determined. Retrograde stellar motions are dominant in the coronas. In spite of some signs of dynamical instability of the coronas (small densities compared to the critical density and accelerated expansion of the coronas), the formation of close-toequilibrium density and phase-density distributions at distances from one to three cluster tidal radii from the cluster center can be seen. Approximations are constructed for the corona and cluster phase density using distributions that depend on three parameters (the parameters of the stellar motion in the Lindblad rotating coordinate system). This temporary equilibrium of the corona is due to balance in the number of starsmoving from the central areas of the cluster to the corona, and from the corona to the corona periphery or beyond. Evidence that corona stars can be gravitationally bound at distances out to four tidal radii from the cluster center is found: the presence of nearly periodic retrograde mean motions of a large number of corona stars in the Galactic plane; 91-99% of corona stars satisfy the gravitational binding criterion of Ross, Mennim and Heggie over time intervals that are close to the mean cluster lifetime. The escape rate from the corona is estimated for t ≥ τ, and found to be from 0.03 to 0.23 of the number of corona stars per violent relaxation time.

  17. THEORETICAL STUDY ON THE INTERACTION BETWEEN XENON AND POSITIVE SILVER CLUSTERS IN GAS PHASE AND ON THE (001) CHABAZITE SURFACE

    SciTech Connect

    Hunter, D.

    2009-03-16

    A systematic study on the adsorption of xenon on silver clusters in the gas phase and on the (001) surface of silver-exchanged chabazite is reported. Density functional theory at the B3LYP level with the cluster model was employed. The results indicate that the dominant part of the binding is the {sigma} donation, which is the charge transfer from the 5p orbital of Xe to the 5s orbital of Ag and is not the previously suggested d{sub {pi}}-d{sub {pi}} back-donation. A correlation between the binding energy and the degree of {sigma} donation is found. Xenon was found to bind strongly to silver cluster cations and not to neutral ones. The binding strength decreases as the cluster size increases for both cases, clusters in the gas-phase and on the chabazite surface. The Ag{sup +} cation is the strongest binding site for xenon both in gas phase and on the chabazite surface with the binding energies of 73.9 and 14.5 kJ/mol, respectively. The results also suggest that the smaller silver clusters contribute to the negative chemical shifts observed in the {sup 129}Xe NMR spectra in experiments.

  18. Adaptive Clustering of Hypermedia Documents.

    ERIC Educational Resources Information Center

    Johnson, Andrew; Fotouhi, Farshad

    1996-01-01

    Discussion of hypermedia systems focuses on a comparison of two types of adaptive algorithm (genetic algorithm and neural network) in clustering hypermedia documents. These clusters allow the user to index into the nodes to find needed information more quickly, since clustering is "personalized" based on the user's paths rather than…

  19. Connecting Remote Clusters with ATM

    SciTech Connect

    Hu, T.C.; Wyckoff, P.S.

    1998-10-01

    Sandia's entry into utilizing clusters of networked workstations is called Computational Plant or CPlant for short. The design of CPlant uses Ethernet to boot the individual nodes, Myrinet to communicate within a node cluster, and ATM to connect between remote clusters. This SAND document covers the work done to enable the use of ATM on the CPlant nodes in the Fall of 1997.

  20. Stellar populations in star clusters

    NASA Astrophysics Data System (ADS)

    Li, Cheng-Yuan; de Grijs, Richard; Deng, Li-Cai

    2016-12-01

    Stellar populations contain the most important information about star cluster formation and evolution. Until several decades ago, star clusters were believed to be ideal laboratories for studies of simple stellar populations (SSPs). However, discoveries of multiple stellar populations in Galactic globular clusters have expanded our view on stellar populations in star clusters. They have simultaneously generated a number of controversies, particularly as to whether young star clusters may have the same origin as old globular clusters. In addition, extensive studies have revealed that the SSP scenario does not seem to hold for some intermediate-age and young star clusters either, thus making the origin of multiple stellar populations in star clusters even more complicated. Stellar population anomalies in numerous star clusters are well-documented, implying that the notion of star clusters as true SSPs faces serious challenges. In this review, we focus on stellar populations in massive clusters with different ages. We present the history and progress of research in this active field, as well as some of the most recent improvements, including observational results and scenarios that have been proposed to explain the observations. Although our current ability to determine the origin of multiple stellar populations in star clusters is unsatisfactory, we propose a number of promising projects that may contribute to a significantly improved understanding of this subject.

  1. Subspace K-means clustering.

    PubMed

    Timmerman, Marieke E; Ceulemans, Eva; De Roover, Kim; Van Leeuwen, Karla

    2013-12-01

    To achieve an insightful clustering of multivariate data, we propose subspace K-means. Its central idea is to model the centroids and cluster residuals in reduced spaces, which allows for dealing with a wide range of cluster types and yields rich interpretations of the clusters. We review the existing related clustering methods, including deterministic, stochastic, and unsupervised learning approaches. To evaluate subspace K-means, we performed a comparative simulation study, in which we manipulated the overlap of subspaces, the between-cluster variance, and the error variance. The study shows that the subspace K-means algorithm is sensitive to local minima but that the problem can be reasonably dealt with by using partitions of various cluster procedures as a starting point for the algorithm. Subspace K-means performs very well in recovering the true clustering across all conditions considered and appears to be superior to its competitor methods: K-means, reduced K-means, factorial K-means, mixtures of factor analyzers (MFA), and MCLUST. The best competitor method, MFA, showed a performance similar to that of subspace K-means in easy conditions but deteriorated in more difficult ones. Using data from a study on parental behavior, we show that subspace K-means analysis provides a rich insight into the cluster characteristics, in terms of both the relative positions of the clusters (via the centroids) and the shape of the clusters (via the within-cluster residuals).

  2. 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.

  3. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-08-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-[3-(triethoxysilyl)propyl]-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  4. Fractal polyzirconosiloxane cluster coatings

    SciTech Connect

    Sugama, T.

    1992-01-01

    Fractal polyzirconosiloxane (PZS) cluster films were prepared through the hydrolysis-polycondensation-pyrolysis synthesis of two-step HCl acid-NaOH base catalyzed sol precursors consisting of N-(3-(triethoxysilyl)propyl)-4,5-dihydroimidazole, Zr(OC{sub 3}H{sub 7}){sub 4}, methanol, and water. When amorphous PZSs were applied to aluminum as protective coatings against NaCl-induced corrosion, the effective film was that derived from the sol having a pH near the isoelectric point in the positive zeta potential region. The following four factors played an important role in assembling the protective PZS coating films: (1) a proper rate of condensation, (2) a moderate ratio of Si-O-Si to Si-O-Zr linkages formed in the PZS network, (3) hydrophobic characteristics, and (4) a specific microstructural geometry, in which large fractal clusters were linked together.

  5. Clusters of Galaxies

    NASA Astrophysics Data System (ADS)

    Huchtmeier, W. K.; Richter, O. G.; Materne, J.

    1981-09-01

    The large-scale structure of the universe is dominated by clustering. Most galaxies seem to be members of pairs, groups, clusters, and superclusters. To that degree we are able to recognize a hierarchical structure of the universe. Our local group of galaxies (LG) is centred on two large spiral galaxies: the Andromeda nebula and our own galaxy. Three sr:naller galaxies - like M 33 - and at least 23 dwarf galaxies (KraanKorteweg and Tammann, 1979, Astronomische Nachrichten, 300, 181) can be found in the evironment of these two large galaxies. Neighbouring groups have comparable sizes (about 1 Mpc in extent) and comparable numbers of bright members. Small dwarf galaxies cannot at present be observed at great distances.

  6. Binaries in globular clusters

    NASA Technical Reports Server (NTRS)

    Hut, Piet; Mcmillan, Steve; Goodman, Jeremy; Mateo, Mario; Phinney, E. S.; Pryor, Carlton; Richer, Harvey B.; Verbunt, Frank; Weinberg, Martin

    1992-01-01

    Recent observations have shown that globular clusters contain a substantial number of binaries most of which are believed to be primordial. We discuss different successful optical search techniques, based on radial-velocity variables, photometric variables, and the positions of stars in the color-magnitude diagram. In addition, we review searches in other wavelengths, which have turned up low-mass X-ray binaries and more recently a variety of radio pulsars. On the theoretical side, we give an overview of the different physical mechanisms through which individual binaries evolve. We discuss the various simulation techniques which recently have been employed to study the effects of a primordial binary population, and the fascinating interplay between stellar evolution and stellar dynamics which drives globular-cluster evolution.

  7. CLUTO - A Clustering Toolkit

    DTIC Science & Technology

    2002-04-23

    061W Y C R 062W spo0 spo30 spo2 spo5 spo7 spo9 spo11 cluster 0 E F B 1 Y A L004W S S A 1 M D M 10 C Y S 3 N T G 1 Y A L018C M A K 16 F U N 19 F U N 12...013C H S P 30 C R Y 1 A R E 1 P W P 2 Y C R 056W P W P 2 Y C R 061W Y C R 062W spo0 spo30 spo2 spo5 spo7 spo9 spo11 cluster 0 (b) (a) Figure 12

  8. Basic cluster compression algorithm

    NASA Technical Reports Server (NTRS)

    Hilbert, E. E.; Lee, J.

    1980-01-01

    Feature extraction and data compression of LANDSAT data is accomplished by BCCA program which reduces costs associated with transmitting, storing, distributing, and interpreting multispectral image data. Algorithm uses spatially local clustering to extract features from image data to describe spectral characteristics of data set. Approach requires only simple repetitive computations, and parallel processing can be used for very high data rates. Program is written in FORTRAN IV for batch execution and has been implemented on SEL 32/55.

  9. Improved graph clustering

    DTIC Science & Technology

    2013-01-01

    optimization problem (2)–(3) is convex and can 1We adopt the convention that yii = 1 for any node i that belongs to a cluster. 2We assume aii = 1 for all i. 3The...relaxations: The formulation (2)–(3) is not the only way to relax the non - convex ML estimator. Instead of the nuclear norm regularizer, a hard constraint ...presented a convex optimization formulation, essentially a convexification of the maximum likelihood estimator. Our theoretic analysis shows that this

  10. Dial-A-Cluster

    SciTech Connect

    Martin, Shawn; Quach, Tu-Toan

    2016-09-14

    Dial-A-Cluster is a web application that can be used to interactively analyze multi-variate time series data. It supports multiple users, DOE markings, and user authentication. It is designed to let the user adjust the influence of particular time series in the dataset, interact with the resulting dimension reduced visualization, interact with the time series themselves, and look for correlations of the data with any available meta-data.

  11. Cosmology, Clusters and Calorimeters

    NASA Technical Reports Server (NTRS)

    Figueroa-Feliciano, Enectali

    2005-01-01

    I will review the current state of Cosmology with Clusters and discuss the application of microcalorimeter arrays to this field. With the launch of Astro-E2 this summer and a slew of new missions being developed, microcalorimeters are the next big thing in x-ray astronomy. I will cover the basics and not-so-basic concepts of microcalorimeter designs and look at the future to see where this technology will go.

  12. SBA Innovation Clusters

    DTIC Science & Technology

    2012-03-02

    Health Information Technology Cluster Health Information Technology 9 FL - Space Coast Clean Energy Jobs Accelerator Clean Energy 10 WI - Milwaukee...helping businesses that develop and commercialize clean energy technology • Helping Manufacturers and Businesses adopt Green Practices with DoC, DoE...serve energy businesses • Since 2010 : 173 Loans totaling $357M • Investments in Clean Energy Businesses – Impact Investment Initiative – Startup America

  13. 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.

  14. Reactivity Control of Rhodium Cluster Ions by Alloying with Tantalum Atoms.

    PubMed

    Mafuné, Fumitaka; Tawaraya, Yuki; Kudoh, Satoshi

    2016-02-18

    Gas phase, bielement rhodium and tantalum clusters, RhnTam(+) (n + m = 6), were prepared by the double laser ablation of Rh and Ta rods in He carrier gas. The clusters were introduced into a reaction gas cell filled with nitric oxide (NO) diluted with He and were subjected to collisions with NO and He at room temperature. The product species were observed by mass spectrometry, demonstrating that the NO molecules were sequentially adsorbed on the RhnTam(+) clusters to form RhnTam(+)NxOx (x = 1, 2, 3, ...) species. In addition, oxide clusters, RhnTam(+)O2, were also observed, suggesting that the NO molecules were dissociatively adsorbed on the cluster, the N atoms migrated on the surface to form N2, and the N2 molecules were released from RhnTam(+)N2O2. The reactivity, leading to oxide formation, was composition dependent: oxide clusters were dominantly formed for the bielement clusters containing both Rh and Ta atoms, whereas such clusters were hardly formed for the single-element Rhn(+) and Tam(+) clusters. DFT calculations indicated that the Ta atoms induce dissociation of NO on the clusters by lowering the dissociation energy, whereas the Rh atoms enable release of N2 by lowering the binding energy of the N atoms on the clusters.

  15. Tungsten Cluster Migration on Nanoparticles: Minimum Energy Pathway and Migration Mechanism

    SciTech Connect

    Chen, Dong; Hu, Wangyu; Gao, Fei; Deng, Huiqiu; Sun, Lixian

    2011-03-02

    Transition state searches have been employed to investigate the migration mechanisms of W clusters on W nanoparticles, and to determine the corresponding migration energies for the possible migration paths of these clusters. The tungsten clusters containing up to four adatoms are found to prefer 2D-compact structures with relatively low binding energies. The effect of interface and vertex regions on the migration behavior of the clusters is significantly strong, as compared to that of nanoparticle size. The migration mechanisms are quite different when the clusters are located at the center of the nanoparticle and near the interface or vertex areas. Near the interfaces and vertex areas, the substrate atoms tend to participate in the migration processes of the clusters, and can join the adatoms to form a larger cluster or lead to the dissociation of a cluster via the exchange mechanism, which results in the adatom crossing the facets. The lowest energy paths are used to be determined the energy barriers for W cluster migrations (from 1- to 4-atoms) on the facets, edges and vertex regions. The calculated energy barriers for the trimers suggest that the concerted migration is more probable than the successive jumping of a single adatom in the clusters. In addition, it of interest to note that the dimer shearing is a dominant migration mechanism for the tetramer, but needs to overcome a relatively higher migration energy than other clusters.

  16. 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.

  17. Wade's rules and the stability of AunGem clusters

    NASA Astrophysics Data System (ADS)

    McDermott, Danielle; Newman, Kathie E.

    2015-03-01

    The properties of clusters formed from two connected Gem cage-like clusters, such as experimentally synthesized Au3Ge{18/5-}, are examined using first-principles DFT methods. We focus particularly on AunGe{12/q-} formed from a Wade-rules stable Ge6 cluster, where n = 0-3 and q = 0,2. The geometries, electronic structure, and thermal excitations of these clusters are examined using the SIESTA code. Cluster stability is tested using short molecular dynamics simulations. We find that intercluster bridges between Ge m cages, formed of either Ge-Ge or Au-Ge bonds, can either bind a cluster together or tear it apart depending on the orientation of the bridging atoms with respect to the cages. The properties of neutrally charged AuGe12 and Au2Ge12 are characterized, and we observe that radially directed molecular orbitals stabilize AuGe12 while a geometric asymmetry stabilizes Au2Ge12 and Au3Ge18. A two-dimensional {2/∞}[Au2Ge6] structure is examined and found to be more stable than other periodic [AunGe6] subunits. While no stable neutral isomers of Au3Ge12 are observed in our calculations, our work suggests additional charge stabilizes isomers of both Au2Ge12 and Au3Ge12.

  18. Novel kinetic trapping in charged colloidal clusters due to self-induced surface charge organization.

    PubMed

    Klix, Christian L; Murata, Ken-ichiro; Tanaka, Hajime; Williams, Stephen R; Malins, Alex; Royall, C Patrick

    2013-01-01

    Colloidal clusters are an unusual state of matter where tunable interactions enable a sufficient reduction in their degrees of freedom that their energy landscapes can become tractable - they form a playground for statistical mechanics and promise unprecedented control of structure on the submicron lengthscale. We study colloidal clusters in a system where a short-ranged polymer-induced attraction drives clustering, while a weak, long-ranged electrostatic repulsion prevents extensive aggregation. We compare experimental yields of cluster structures with theory which assumes simple addition of competing isotropic interactions between the colloids. Here we show that for clusters of size 4 ≤ m ≤ 7, the yield of minimum energy clusters is much less than expected. We attribute this to an anisotropic self-organized surface charge distribution which leads to unexpected kinetic trapping. We introduce a model for the coupling between counterions and binding sites on the colloid surface with which we interpret our findings.

  19. Low energy slowing down of nanosize copper clusters on gold (1 1 1) surfaces

    NASA Astrophysics Data System (ADS)

    Lei, H.; Hou, Q.; Hou, M.

    2000-04-01

    The slowing down of copper clusters formed by 440 atoms on a gold (1 1 1) surface is studied in detail by means of molecular dynamics. The atomic classical molecular dynamics is based on the second moment approximation of the tight binding model and, in addition, accounts for the electron-phonon coupling in the frame of the Sommerfeld theory of metals. The slowing down energy range is 0-1 eV/atom, which is characteristic of low energy cluster beam deposition (LECBD). A pronounced epitaxy of the copper clusters is found. However, their morphology is significantly energy dependent. The structure and the radial pair correlation functions are used to study the details of the epitaxial properties as well as the pronounced relaxation in the interfacial cluster atom positions due to the lattice mismatch between copper and gold. The effect of the cluster and substrate average temperature is investigated and can be distinguished from the kinetic effect of the cluster impact.

  20. Stellar Snowflake Cluster

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Figure 1 Stellar Snowflake Cluster Combined Image [figure removed for brevity, see original site] Figure 2 Infrared Array CameraFigure 3 Multiband Imaging Photometer

    Newborn stars, hidden behind thick dust, are revealed in this image of a section of the Christmas Tree cluster from NASA's Spitzer Space Telescope, created in joint effort between Spitzer's infrared array camera and multiband imaging photometer instruments.

    The newly revealed infant stars appear as pink and red specks toward the center of the combined image (fig. 1). The stars appear to have formed in regularly spaced intervals along linear structures in a configuration that resembles the spokes of a wheel or the pattern of a snowflake. Hence, astronomers have nicknamed this the 'Snowflake' cluster.

    Star-forming clouds like this one are dynamic and evolving structures. Since the stars trace the straight line pattern of spokes of a wheel, scientists believe that these are newborn stars, or 'protostars.' At a mere 100,000 years old, these infant structures have yet to 'crawl' away from their location of birth. Over time, the natural drifting motions of each star will break this order, and the snowflake design will be no more.

    While most of the visible-light stars that give the Christmas Tree cluster its name and triangular shape do not shine brightly in Spitzer's infrared eyes, all of the stars forming from this dusty cloud are considered part of the cluster.

    Like a dusty cosmic finger pointing up to the newborn clusters, Spitzer also illuminates the optically dark and dense Cone nebula, the tip of which can be seen towards the bottom left corner of each image.

    This combined image shows the presence of organic molecules mixed with dust as wisps of green, which have been illuminated by nearby star formation. The larger yellowish dots neighboring the baby red stars in the Snowflake Cluster are massive stellar infants forming

  1. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative.

    PubMed Central

    Adams, C C; Workman, J L

    1995-01-01

    To investigate mechanisms by which multiple transcription factors access complex promoters and enhancers within cellular chromatin, we have analyzed the binding of disparate factors to nucleosome cores. We used a purified in vitro system to analyze binding of four activator proteins, two GAL4 derivatives, USF, and NF-kappa B (KBF1), to reconstituted nucleosome cores containing different combinations of binding sites. Here we show that binding of any two or all three of these factors to nucleosomal DNA is inherently cooperative. Thus, the binuclear Zn clusters of GAL4, the helix-loop-helix/basic domains of USF, and the rel domain of NF-kappa B all participated in cooperative nucleosome binding, illustrating that this effect is not restricted to a particular DNA-binding domain. Simultaneous binding by two factors increased the affinity of individual factors for nucleosomal DNA by up to 2 orders of magnitude. Importantly, cooperative binding resulted in efficient nucleosome binding by factors (USF and NF-kappa B) which independently possess little nucleosome-binding ability. The participation of GAL4 derivatives in cooperative nucleosome binding required only DNA-binding and dimerization domains, indicating that disruption of histone-DNA contacts by factor binding was responsible for the increased affinity of additional factors. Cooperative nucleosome binding required sequence-specific binding of all transcription factors, appeared to have spatial constraints, and was independent of the orientation of the binding sites on the nucleosome. These results indicate that cooperative nucleosome binding is a general mechanism that may play a significant role in loading complex enhancer and promoter elements with multiple diverse factors in chromatin and contribute to the generation of threshold responses and transcriptional synergy by multiple activator sites in vivo. PMID:7862134

  2. Convex Clustering: An Attractive Alternative to Hierarchical Clustering

    PubMed Central

    Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

    2015-01-01

    The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

  3. Conciliating binding efficiency and polypharmacology.

    PubMed

    Mestres, Jordi; Gregori-Puigjané, Elisabet

    2009-09-01

    The association between molecular size and risk of failure has promoted the use of binding efficiency as a prioritization metric in lead selection. Even though by extension it is often referred to as "ligand efficiency", the concept was originally conceived to be strictly applicable to comparing the binding efficiencies of ligands for a single target. With current trends in designing drugs to bind efficiently to multiple targets, a revision of the original binding efficiency definition is carried out. To this aim, the dependency of binding efficiency on polypharmacology is highlighted in a retrospective analysis of a set of antipsychotic drugs. Statistical standardization of target binding efficiencies relative to basal values obtained from a large background of medicinal chemistry compounds is proposed as a means to conciliate the concepts of binding efficiency and polypharmacology. Finally, the interplay between binding efficiency and therapeutic efficacy for optimizing natural products, random hits, and fragments is discussed.

  4. CATCHprofiles: Clustering and Alignment Tool for ChIP Profiles

    PubMed Central

    Nielsen, Fiona G. G.; Markus, Kasper Galschiøt; Friborg, Rune Møllegaard; Favrholdt, Lene Monrad; Stunnenberg, Hendrik G.; Huynen, Martijn

    2012-01-01

    Chromatin Immuno Precipitation (ChIP) profiling detects in vivo protein-DNA binding, and has revealed a large combinatorial complexity in the binding of chromatin associated proteins and their post-translational modifications. To fully explore the spatial and combinatorial patterns in ChIP-profiling data and detect potentially meaningful patterns, the areas of enrichment must be aligned and clustered, which is an algorithmically and computationally challenging task. We have developed CATCHprofiles, a novel tool for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns “ab initio”, and enables the detection of new patterns from ChIP data at a high resolution, exemplified by the detection of asymmetric histone and histone modification patterns around H2A.Z-enriched sites. CATCHprofiles' capability for exhaustive analysis combined with its ease-of-use makes it an invaluable tool for explorative research based on ChIP profiling data. CATCHprofiles and the CATCH algorithm run on all platforms and is available for free through the CATCH website: http://catch.cmbi.ru.nl/. User support is available by subscribing to the mailing list catch-users@bioinformatics.org. PMID:22238575

  5. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    NASA Astrophysics Data System (ADS)

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei

    2015-12-01

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  6. Molecular dynamics modelling of EGCG clusters on ceramide bilayers

    SciTech Connect

    Yeo, Jingjie; Cheng, Yuan; Li, Weifeng; Zhang, Yong-Wei

    2015-12-31

    A novel method of atomistic modelling and characterization of both pure ceramide and mixed lipid bilayers is being developed, using only the General Amber ForceField. Lipid bilayers modelled as pure ceramides adopt hexagonal packing after equilibration, and the area per lipid and bilayer thickness are consistent with previously reported theoretical results. Mixed lipid bilayers are modelled as a combination of ceramides, cholesterol, and free fatty acids. This model is shown to be stable after equilibration. Green tea extract, also known as epigallocatechin-3-gallate, is introduced as a spherical cluster on the surface of the mixed lipid bilayer. It is demonstrated that the cluster is able to bind to the bilayers as a cluster without diffusing into the surrounding water.

  7. CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation.

    PubMed

    Narendra, Varun; Rocha, Pedro P; An, Disi; Raviram, Ramya; Skok, Jane A; Mazzoni, Esteban O; Reinberg, Danny

    2015-02-27

    Polycomb and Trithorax group proteins encode the epigenetic memory of cellular positional identity by establishing inheritable domains of repressive and active chromatin within the Hox clusters. Here we demonstrate that the CCCTC-binding factor (CTCF) functions to insulate these adjacent yet antagonistic chromatin domains during embryonic stem cell differentiation into cervical motor neurons. Deletion of CTCF binding sites within the Hox clusters results in the expansion of active chromatin into the repressive domain. CTCF functions as an insulator by organizing Hox clusters into spatially disjoint domains. Ablation of CTCF binding disrupts topological boundaries such that caudal Hox genes leave the repressed domain and become subject to transcriptional activation. Hence, CTCF is required to insulate facultative heterochromatin from impinging euchromatin to produce discrete positional identities.

  8. Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

    USGS Publications Warehouse

    Leenheer, J.A.; Brown, G.K.; MacCarthy, P.; Cabaniss, S.E.

    1998-01-01

    Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The 'metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-1R spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short- chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The `metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that

  9. Library Binding Manual. Revised Edition.

    ERIC Educational Resources Information Center

    Lakhanpal, S. K.

    This procedural manual is designed to be used in bindery sections in public, university and special libraries. It briefly discusses these general matters: administrative control; selection of a binder; when and what to bind; conventional binding; routines; missing issues; schedule for shipments; temporary binding; rare books, maps and newspapers;…

  10. Sketching Star Clusters

    NASA Astrophysics Data System (ADS)

    Perez, Jeremy

    The next time you plan a quiet evening under a salted sky, with hopes of bathing your eyes in the ancient light of a majestic star cluster, be sure that your sketching kit comes with you! A casual glance at these celestial marvels will not give you a decent appreciation for an object whose history and character are as unique as the fingerprints you should be pressing into the side of your trusty pencil. I can think of no better way to connect with these stellar ballets, to understand their intricacies, and to recall your view later than to spend time sketching the soft glow or blazing pinpricks you see through the eyepiece.

  11. Are Earthquake Magnitudes Clustered?

    SciTech Connect

    Davidsen, Joern; Green, Adam

    2011-03-11

    The question of earthquake predictability is a long-standing and important challenge. Recent results [Phys. Rev. Lett. 98, 098501 (2007); ibid.100, 038501 (2008)] have suggested that earthquake magnitudes are clustered, thus indicating that they are not independent in contrast to what is typically assumed. Here, we present evidence that the observed magnitude correlations are to a large extent, if not entirely, an artifact due to the incompleteness of earthquake catalogs and the well-known modified Omori law. The latter leads to variations in the frequency-magnitude distribution if the distribution is constrained to those earthquakes that are close in space and time to the directly following event.

  12. Clustering with shallow trees

    NASA Astrophysics Data System (ADS)

    Bailly-Bechet, M.; Bradde, S.; Braunstein, A.; Flaxman, A.; Foini, L.; Zecchina, R.

    2009-12-01

    We propose a new method for obtaining hierarchical clustering based on the optimization of a cost function over trees of limited depth, and we derive a message-passing method that allows one to use it efficiently. The method and the associated algorithm can be interpreted as a natural interpolation between two well-known approaches, namely that of single linkage and the recently presented affinity propagation. We analyse using this general scheme three biological/medical structured data sets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.

  13. Circular rogue wave clusters.

    PubMed

    Kedziora, David J; Ankiewicz, Adrian; Akhmediev, Nail

    2011-11-01

    Using the Darboux transformation technique and numerical simulations, we study the hierarchy of rational solutions of the nonlinear Schrödinger equation that can be considered as higher order rogue waves in this model. This analysis reveals the existence of rogue wave clusters with a high level of symmetry in the (x,t) plane. These structures arise naturally when the shifts in the Darboux scheme are taken to be eigenvalue dependent. We have found single-shell structures where a central higher order rogue wave is surrounded by a ring of first order peaks on the (x,t) plane.

  14. The galactic globular cluster system

    NASA Technical Reports Server (NTRS)

    Djorgovski, S.; Meylan, G.

    1994-01-01

    We explore correlations between various properties of Galactic globular clusters, using a database on 143 objects. Our goal is identify correlations and trends which can be used to test and constrain theoretical models of cluster formation and evolution. We use a set of 13 cluster parameters, 9 of which are independently measured. Several arguments suggest that the number of clusters still missing in the obscured regions of the Galaxy is of the order of 10, and thus the selection effects are probably not severe for our sample. Known clusters follow a power-law density distribution with a slope approximately -3.5 to -4, and an apparent core with a core radius approximately 1 kpc. Clusters show a large dynamical range in many of their properties, more so for the core parameters (which are presumably more affected by dynamical evolution) than for the half-light parameters. There are no good correlations with luminosity, although more luminous clusters tend to be more concentrated. When data are binned in luminosity, several trends emerge: more luminous clusters tend to have smaller and denser cores. We interpret this as a differential survival effect, with more massive clusters surviving longer and reaching more evolved dynamical states. Cluster core parameters and concentrations also correlate with the position in the Galaxy, with clusters closer to the Galactic center or plane being more concentrated and having smaller and denser cores. These trends are more pronounced for the fainter (less massive) clusters. This is in agreement with a picture where tidal shocks form disk or bulge passages accelerate dynamical evolution of clusters. Cluster metallicities do not correlate with any other parameter, including luminosity and velocity dispersion; the only detectable trend is with the position in the Galaxy, probably reflecting Zinn's disk-halo dichotomy. This suggests that globular clusters were not self-enriched systems. Velocity dispersions show excellent correlations

  15. Comparative Density Functional Study of Methanol Decomposition on Cu4 and Co4 Clusters

    SciTech Connect

    Mehmood, Faisal; Greeley, Jeffrey P.; Zapol, Peter; Curtiss, Larry A.

    2010-11-18

    A density functional theory study of the decomposition of methanol on Cu4 and Co4 clusters is presented. The reaction intermediates and activation barriers have been determined for reaction steps to form H2 and CO. For both clusters, methanol decomposition initiated by C-H and O-H bond breaking was investigated. In the case of a Cu4 cluster, methanol dehydrogenation through hydroxymethyl (CH2OH), hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO) is found to be slightly more favorable. For a Co4 cluster, the dehydrogenation pathway through methoxy (CH3O) and formaldehyde (CH2O) is slightly more favorable. Each of these pathways results in formation of CO and H2. The Co cluster pathway is very favorable thermodynamically and kinetically for dehydrogenation. However, since CO binds strongly, it is likely to poison methanol decomposition to H2 and CO at low temperatures. In contrast, for the Cu cluster, CO poisoning is not likely to be a problem since it does not bind strongly, but the dehydrogenation steps are not energetically favorable. Pathways involving C-O bond cleavage are even less energetically favorable. The results are compared to our previous study of methanol decomposition on Pd4 and Pd8 clusters. Finally, all reaction energy changes and transition state energies, including those for the Pd clusters, are related in a linear, Broensted-Evans-Polanyi plot.

  16. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters.

    PubMed

    Turi, László

    2016-04-21

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory(DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavitystructure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  17. PHAT Stellar Cluster Survey. II. Andromeda Project Cluster Catalog

    NASA Astrophysics Data System (ADS)

    Johnson, L. Clifton; Seth, Anil C.; Dalcanton, Julianne J.; Wallace, Matthew L.; Simpson, Robert J.; Lintott, Chris J.; Kapadia, Amit; Skillman, Evan D.; Caldwell, Nelson; Fouesneau, Morgan; Weisz, Daniel R.; Williams, Benjamin F.; Beerman, Lori C.; Gouliermis, Dimitrios A.; Sarajedini, Ata

    2015-04-01

    We construct a stellar cluster catalog for the Panchromatic Hubble Andromeda Treasury (PHAT) survey using image classifications collected from the Andromeda Project citizen science website. We identify 2753 clusters and 2270 background galaxies within ˜0.5 deg2 of PHAT imaging searched, or ˜400 kpc2 in deprojected area at the distance of the Andromeda Galaxy (M31). These identifications result from 1.82 million classifications of ˜20,000 individual images (totaling ˜7 gigapixels) by tens of thousands of volunteers. We show that our crowd-sourced approach, which collects >80 classifications per image, provides a robust, repeatable method of cluster identification. The high spatial resolution Hubble Space Telescope images resolve individual stars in each cluster and are instrumental in the factor of ˜6 increase in the number of clusters known within the survey footprint. We measure integrated photometry in six filter passbands, ranging from the near-UV to the near-IR. PHAT clusters span a range of ˜8 magnitudes in F475W (g-band) luminosity, equivalent to ˜4 decades in cluster mass. We perform catalog completeness analysis using >3000 synthetic cluster simulations to determine robust detection limits and demonstrate that the catalog is 50% complete down to ˜500 {{M}⊙ } for ages <100 Myr. We include catalogs of clusters, background galaxies, remaining unselected candidates, and synthetic cluster simulations, making all information publicly available to the community. The catalog published here serves as the definitive base data product for PHAT cluster science, providing a census of star clusters in an {{L}\\star } spiral galaxy with unmatched sensitivity and quality.

  18. Americium binding to humic acid.

    PubMed

    Peters, A J; Hamilton-Taylor, J; Tipping, E

    2001-09-01

    The binding of americium (Am) by peat humic acid (PHA) has been investigated at Am concentrations between 10(-1) and 10(-7) M at pH approximately 2.6 in the presence and absence of Cu as a competing ion. Cu-PHA binding was also investigated in order to derive independent binding constants for use in modeling the competitive binding studies. Humic ion-binding model VI was used to compare the acquired data with previously published binding data and to investigate the importance of high-affinity binding sites in metal-PHA binding. Am was not observed to bind to high-affinity, low-concentration binding sites. The model VI parameter deltaLK2 takes into accountthe small number of strong sites in PHA and was found to be important for Cu-PHA binding but not for Am-PHA binding, regardless of whether Cu was present. Analysis of the PHA sample revealed that it contained a considerable quantity of Fe not removed by the extraction procedure, much of which is believed to be present as Fe(III). Model VI was then used to investigate the possible importance of the presence of Fe(III) in the Am-PHA binding experiments. When Fe(III) was assumed to be present, improved descriptions of the data by model VI were obtained by assuming that all of the metals [Am, Cu, and Fe(III)] undergo strong binding. This highlights the importance of Fe(III) competition in metal-PHA binding studies and possible shortcomings in the extraction procedure used to extract PHA.

  19. Tidal Stripping of Globular Clusters in a Simulated Galaxy Cluster

    NASA Astrophysics Data System (ADS)

    Ramos, F.; Coenda, V.; Muriel, H.; Abadi, M.

    2015-06-01

    Using a cosmological N-body numerical simulation of the formation of a galaxy-cluster-sized halo, we analyze the temporal evolution of its globular cluster population. We follow the dynamical evolution of 38 galactic dark matter halos orbiting in a galaxy cluster that at redshift z = 0 has a virial mass of 1.71 × 1014 M⊙ h-1. In order to mimic both “blue” and “red” populations of globular clusters, for each galactic halo we select two different sets of particles at high redshift (z ≈ 1), constrained by the condition that, at redshift z = 0, their average radial density profiles are similar to the observed profiles. As expected, the general galaxy cluster tidal field removes a significant fraction of the globular cluster populations to feed the intracluster population. On average, halos lost approximately 16% and 29% of their initial red and blue globular cluster populations, respectively. Our results suggest that these fractions strongly depend on the orbital trajectory of the galactic halo, specifically on the number of orbits and on the minimum pericentric distance to the galaxy cluster center that the halo has had. At a given time, these fractions also depend on the current clustercentric distance, just as observations show that the specific frequency of globular clusters SN depends on their clustercentric distance.

  20. TIDAL STRIPPING OF GLOBULAR CLUSTERS IN A SIMULATED GALAXY CLUSTER

    SciTech Connect

    Ramos, F.; Coenda, V.; Muriel, H.; Abadi, M.

    2015-06-20

    Using a cosmological N-body numerical simulation of the formation of a galaxy-cluster-sized halo, we analyze the temporal evolution of its globular cluster population. We follow the dynamical evolution of 38 galactic dark matter halos orbiting in a galaxy cluster that at redshift z = 0 has a virial mass of 1.71 × 10{sup 14} M{sub ⊙} h{sup −1}. In order to mimic both “blue” and “red” populations of globular clusters, for each galactic halo we select two different sets of particles at high redshift (z ≈ 1), constrained by the condition that, at redshift z = 0, their average radial density profiles are similar to the observed profiles. As expected, the general galaxy cluster tidal field removes a significant fraction of the globular cluster populations to feed the intracluster population. On average, halos lost approximately 16% and 29% of their initial red and blue globular cluster populations, respectively. Our results suggest that these fractions strongly depend on the orbital trajectory of the galactic halo, specifically on the number of orbits and on the minimum pericentric distance to the galaxy cluster center that the halo has had. At a given time, these fractions also depend on the current clustercentric distance, just as observations show that the specific frequency of globular clusters S{sub N} depends on their clustercentric distance.

  1. Carboplatin binding to histidine

    SciTech Connect

    Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.; Levy, Colin; Schreurs, Antoine M. M.; Helliwell, John R.

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  2. Glutathione-coordinated [2Fe-2S] cluster is stabilized by intramolecular salt bridges.

    PubMed

    Li, Jingwei; Pearson, Stephen A; Fenk, Kevin D; Cowan, J A

    2015-12-01

    Halide salts of alkali and alkaline earth metals were used to probe the contributions of intramolecular salt bridge formation on the stability of glutathione-coordinated [2Fe-2S] cluster toward hydrolysis. The effect of ionic strength on cluster stability was quantitatively investigated by application of Debye-Hückel theory to the rates of hydrolysis. Results from this study demonstrate that ionic strength influences the stability of the cluster, with the rate of cluster degradation depending on the charge density, hydrated ionic radius, and hydration energy. The identity of the salt ions was also observed to be correlated with the binding affinity toward the cluster. Based on the modified Debye-Hückel equation and counterion screening effect, these results suggest that interactions between glutathione molecules in the [2Fe-2S](GS)4 cluster is via salt bridges, in agreement with our previous results where modifications of glutathione carboxylates and amines prevented solution aggregation and cluster formation. These results not only provide a rationale for the stability of such clusters under physiological conditions, but also suggest that the formation of glutathione-complexed [2Fe-2S] cluster from a glutathione tetramer may be facilitated by salt bridge interactions between glutathione molecules prior to cluster assembly, in a manner consistent with Nature's equivalent of dynamic combinatorial chemistry.

  3. Secondary Globular Cluster populations

    NASA Astrophysics Data System (ADS)

    Fritze-v. Alvensleben, U.

    2004-02-01

    This study is motivated by two facts: 1. The formation of populous star cluster systems is widely observed to accompany violent star formation episodes in gas-rich galaxies as e.g. those triggered by strong interactions or merging. 2. The Globular Cluster (GC) systems of most but not all early-type galaxies show bimodal optical color distributions with fairly universal blue peaks and somewhat variable red peak colors, yet their Luminosity Functions (LFs) look like simple Gaussians with apparently universal turn-over magnitudes that are used for distance measurements and the determination of Ho. Based on a new set of evolutionary synthesis models for Simple (= single burst) Stellar Populations (SSPs) of various metallicities using the latest Padova isochrones I study the color and luminosity evolution of GC populations over the wavelength range from U through K, providing an extensive grid of models for comparison with observations. I assume the intrinsic widths of the color distributions and LFs to be constant in time at the values observed today for the Milky Way or M 31 halo GC populations. Taking the color distributions and LFs of the Milky Way or M 31 halo GC population as a reference for old metal-poor GC populations in general, I study for which combinations of age and metallicity a secondary GC population formed in some violent star formation event in the history of its parent galaxy may or may not be detected in the observed GC color distributions. I also investigate the effect of these secondary GCs on the LFs of the total GC system. Significant differences are found among the diagnostic efficiencies in various wavelength regions. In particular, we predict the NIR to be able to reveal the presence of GC subpopulations with different age - metallicity combinations that may perfectly hide within one inconspicuous optical color peak. If the entire manifold of possible age - metallicity combinations is admitted for a secondary GC population, we find several

  4. 25. Steenbock symposium -- Biosynthesis and function of metal clusters for enzymes: Proceedings

    SciTech Connect

    1997-12-31

    This symposium was held June 10--14, 1997 in Madison, Wisconsin. The purpose of this conference was to provide a multidisciplinary forum for exchange of state-of-the-art information on biochemistry of enzymes that have an affinity for metal clusters. Attention is focused on the following: metal clusters involved in energy conservation and remediation; tungsten, molybdenum, and cobalt-containing enzymes; Fe proteins, and Mo-binding proteins; nickel enzymes; and nitrogenase.

  5. Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains.

    PubMed

    Brackley, Chris A; Liebchen, Benno; Michieletto, Davide; Mouvet, Francois; Cook, Peter R; Marenduzzo, Davide

    2017-03-28

    Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear bodies exchange rapidly with the soluble pool while the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins able to switch between an "on" (binding) and an "off" (nonbinding) state. This system provides a model for any DNA-binding protein that can be posttranslationally modified to change its affinity for DNA (e.g., through phosphorylation). Protein switching is a nonequilibrium process, and it leads to the formation of clusters of self-limiting size, where individual proteins in a cluster exchange with the soluble pool with kinetics similar to those seen in photobleaching experiments. This behavior contrasts sharply with that exhibited by nonswitching proteins, which are permanently in the on-state; when these bind to DNA nonspecifically, they form clusters that grow indefinitely in size. To explain these findings, we propose a mean-field theory from which we obtain a scaling relation between the typical cluster size and the protein switching rate. Protein switching also reshapes intrachromatin contacts to give networks resembling those seen in topologically associating domains, as switching markedly favors local (short-range) contacts over distant ones. Our results point to posttranslational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, nonequilibrium, protein clusters with the properties of nuclear bodies.

  6. Ab initio calculations of cooperativity effects on clusters of methanol, ethanol, 1-propanol, and methanethiol

    SciTech Connect

    Sum, A.K.; Sandler, S.I.

    2000-02-17

    The results of ab initio calculations for cyclic clusters of methanol, ethanol, 1-propanol, and methanethiol are presented. Dimer, trimer, and tetramer clusters of all four compounds are studied, as are pentamer and hexamer clusters of methanol. From optimized clusters at HG/6--31G**, total energies and binding energies were calculated with both the HF and MP2 theories using the aug-cc-pVDZ basis set. Accurate binding energies were also calculated for the dimer and trimer of methanol using symmetry-adapted perturbation theory with the same basis set. Intermolecular and intramolecular distances, charge distribution of binding sites, binding energies, and equilibrium constants were computed to determine the hydrogen bond cooperativity effect for each species. The cooperativity effect, exclusive to hydrogen bonding systems, results form specific forces among the molecules, in particular charge-transfer processes and the greater importance of interactions between molecules not directly hydrogen bonded because of the longer range of the interactions. The ratios of equilibrium constants for forming multimer hydrogen bonds to that for dimer hydrogen bond formation increase rapidly with the cluster size, in contrast to the constant value commonly used in thermodynamic models for hydrogen bonding liquids.

  7. Decaying neutrinos in galaxy clusters

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Splinter, Randall J.; Persic, Massimo; Salucci, Paolo

    1994-01-01

    Davidsen et al. (1991) have argued that the failure to detect UV photons from the dark matter (DM) in cluster A665 excludes the decaying neutrino hypothesis. Sciama et al. (1993) argued that because of high central concentration the DM in that cluster must be baryonic. We study the DM profile in clusters of galaxies simulated using the Harrison-Zel'dovich spectrum of density fluctuations, and an amplitude previously derived from numerical simulations (Melott 1984b; Anninos et al. 1991) and in agreement with microwave background fluctuations (Smoot et al. 1992). We find that with this amplitude normalization cluster neutrino DM densities are comparable to observed cluster DM values. We conclude that given this normalization, the cluster DM should be at least largely composed of neutrinos. The constraint of Davidsen et al. can be somewhat weakened by the presence of baryonic DM; but it cannot be eliminated given our assumptions.

  8. 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.

  9. X-Ray Absorption Spectroscopy of Cuprous-Thiolate Clusters in Saccharomyces Cerevisiae Metallothionein

    SciTech Connect

    Zhang, L.; Pickering, I.J.; Winge, D.R.; George, G.N.

    2009-05-28

    Copper (Cu) metallothioneins are cuprous-thiolate proteins that contain multimetallic clusters, and are thought to have dual functions of Cu storage and Cu detoxification. We have used a combination of X-ray absorption spectroscopy (XAS) and density-functional theory (DFT) to investigate the nature of Cu binding to Saccharomyces cerevisiae metallothionein. We found that the XAS of metallothionein prepared, containing a full complement of Cu, was quantitatively consistent with the crystal structure, and that reconstitution of the apo-metallothionein with stoichiometric Cu results in the formation of a tetracopper cluster, indicating cooperative binding of the Cu ions by the metallothionein.

  10. Restored mutant receptor:Corticoid binding in chaperone complexes by trimethylamine N-oxide

    PubMed Central

    Miller, Aaron L.; Elam, W. Austin; Johnson, Betty H.; Khan, Shagufta H.; Kumar, Raj; Thompson, E. Brad

    2017-01-01

    Without a glucocorticoid (GC) ligand, the transcription factor glucocorticoid receptor (GR) is largely cytoplasmic, with its GC-binding domain held in high affinity conformation by a cluster of chaperones. Binding a GC causes serial dis- and re-associations with chaperones, translocation of the GR to the nucleus, where it binds to DNA sites and associates with coregulatory proteins and basic transcription complexes. Herein, we describe the effects of a potent protective osmolyte, trimethylamine N-oxide (TMAO), on a conditions-dependent “activation-labile” mutant GR (GRact/l), which under GR-activating conditions cannot bind GCs in cells or in cell cytosols. In both cells and cytosols, TMAO restores binding to GRact/l by stabilizing it in complex with chaperones. Cells bathed in much lower concentrations of TMAO than those required in vitro show restoration of GC binding, presumably due to intracellular molecular crowding effects. PMID:28301576

  11. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin.

    PubMed

    Zhu, Yu; Ye, Xin-Hai; Liu, Yang; Yan, Zhi-Chao; Stanley, David; Ye, Gong-Yin; Fang, Qi

    2015-11-30

    Chitin-binding proteins (CBPs) are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP) from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs) of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton.

  12. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin

    PubMed Central

    Zhu, Yu; Ye, Xin-Hai; Liu, Yang; Yan, Zhi-Chao; Stanley, David; Ye, Gong-Yin; Fang, Qi

    2015-01-01

    Chitin-binding proteins (CBPs) are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP) from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs) of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton. PMID:26633500

  13. 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.

  14. Collagen binding to Staphylococcus aureus

    SciTech Connect

    Holderbaum, D.; Hall, G.S.; Ehrhart, L.A.

    1986-11-01

    Staphylococcus aureus can bind soluble collagen in a specific, saturable manner. We have previously shown that some variability exists in the degree of collagen binding between different strains of heat-killed, formaldehyde-fixed S. aureus which are commercially available as immunologic reagents. The present study demonstrates that live S. aureus of the Cowan 1 strain binds amounts of collagen per organism equivalent to those demonstrated previously in heat-killed, formaldehyde-fixed bacteria but has an affinity over 100 times greater, with Kd values of 9.7 X 10(-11) M and 4.3 X 10(-8) M for live and heat-killed organisms, respectively. Studies were also carried out with S. aureus killed by ionizing radiation, since this method of killing the organism seemed less likely to alter the binding moieties on the surface than did heat killing. Bacteria killed by exposure to gamma radiation bound collagen in a manner essentially indistinguishable from that of live organisms. Binding of collagen to irradiated cells of the Cowan 1 strain was rapid, with equilibrium reached by 30 min at 22 degrees C, and was fully reversible. The binding was not inhibited by fibronectin, fibrinogen, C1q, or immunoglobulin G, suggesting a binding site for collagen distinct from those for these proteins. Collagen binding was virtually eliminated in trypsin-treated organisms, indicating that the binding site has a protein component. Of four strains examined, Cowan 1 and S. aureus ATCC 25923 showed saturable, specific binding, while strains Woods and S4 showed a complete lack of binding. These results suggest that some strains of S. aureus contain high-affinity binding sites for collagen. While the number of binding sites per bacterium varied sixfold in the two collagen-binding strains, the apparent affinity was similar.

  15. 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

  16. Common molecular mechanisms in field- and agrin-induced acetylcholine receptor clustering.

    PubMed

    Sabrina, F; Stollberg, J

    1997-04-01

    1. The aggregation of acetylcholine receptors at the developing neuromuscular junction is critical to the development and function of this synapse. In vitro studies have shown that receptor aggregation can be induced by the finding of agrin to the muscle cell surface and by the electric field-induced concentration of a (nonreceptor) molecule at the cathodal cell pole. 2. We report here on the interaction between agrin binding and electric fields with respect to the distribution of receptors and agrin binding sites. 3. (a) Pretreatment of cells with agrin completely blocks the development of field-induced receptor clusters. (b) Field-induced aggregation of receptors precedes the field-induced aggregation of agrin binding sites by approximately 30 min. (c) Electric fields prevent agrin-induced receptor clustering despite the presence of agrin binding sites and freely diffusing receptors. 4. These results indicate that another membrane component-but not the agrin binding site and not the receptor-is required for agrin-induced receptor clustering. They also suggest that electric fields and agrin cause receptor clustering via common molecular mechanisms.

  17. First-principles study on stability, and growth strategies of small AlnZr (n=1-9) clusters

    NASA Astrophysics Data System (ADS)

    Li, Zhi; Zhou, Zhonghao; Wang, Hongbin; Li, Shengli; Zhao, Zhen

    2016-09-01

    The geometries, relative stability as well as growth strategies of the AlnZr (n=1-9) clusters are investigated with spin polarized density functional theory: BLYP. The results reveal that the AlnZr clusters are more likely to form the dense accumulation structures than the AlN (N=1-10) clusters. The average binding energies of AlnZr are higher than those of AlN clusters. The AlnZr (n=3, 5, and 7) clusters are more stable than others by the differences of the total binding energies. Mülliken population analysis for the AlnZr clusters shows that the electron's adsorption ability of Zr is slightly lower than that of Al except for AlZr cluster. Local peaks of the HOMO-LUMO gap curve are found at n=3, 5, and 7. The reaction energies of AlnZr are higher, which means that AlnZr clusters are easier to react with Al clusters. Zr atom preferential reacts with Al2 cluster. Local peaks of the magnetic dipole moments are found at n=2, 5, and 8.

  18. Structure and Stability of GeAu{sub n}, n = 1-10 clusters: A Density Functional Study

    SciTech Connect

    Priyanka,; Dharamvir, Keya; Sharma, Hitesh

    2011-12-12

    The structures of Germanium doped gold clusters GeAu{sub n} (n = 1-10) have been investigated using ab initio calculations based on density functional theory (DFT). We have obtained ground state geometries of GeAu{sub n} clusters and have it compared with Silicon doped gold clusters and pure gold clusters. The ground state geometries of the GeAu{sub n} clusters show patterns similar to silicon doped gold clusters except for n = 5, 6 and 9. The introduction of germanium atom increases the binding energy of gold clusters. The binding energy per atom of germanium doped cluster is smaller than the corresponding silicon doped gold cluster. The HUMO-LOMO gap for Au{sub n}Ge clusters have been found to vary between 0.46 eV-2.09 eV. The mullikan charge analysis indicates that charge of order of 0.1e always transfers from germanium atom to gold atom.

  19. Solute clustering and interfacial tension

    NASA Astrophysics Data System (ADS)

    Larson, M. A.; Garside, John

    1986-07-01

    The effect of surface curvature on surface tension has been included in the theory of homogeneous nucleation to show that, under certain conditions, cluster formation results in a decrease in Gibb's free energy. This cluster formation is thus a spontaneous event and a quasi-equilibrium concentration of clusters of narrow size range may then exist in supersaturated solutions. Previous experimental work suggests the existence of solute clusters in a variety of aqueous solutions. The implications for crystal nucleation and growth theory are discussed.

  20. SIZES OF GALACTIC GLOBULAR CLUSTERS

    SciTech Connect

    Van den Bergh, Sidney

    2012-02-20

    A study is made of deviations from the mean power-law relationship between the Galactocentric distances and the half-light radii of Galactic globular clusters. Surprisingly, deviations from the mean R{sub h} versus R{sub gc} relationship do not appear to correlate with cluster luminosity, cluster metallicity, or horizontal-branch morphology. Differences in orbit shape are found to contribute to the scatter in the R{sub h} versus R{sub gc} relationship of Galactic globular clusters.

  1. 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.

  2. Absolute classification with unsupervised clustering

    NASA Technical Reports Server (NTRS)

    Jeon, Byeungwoo; Landgrebe, D. A.

    1992-01-01

    An absolute classification algorithm is proposed in which the class definition through training samples or otherwise is required only for a particular class of interest. The absolute classification is considered as a problem of unsupervised clustering when one cluster is known initially. The definitions and statistics of the other classes are automatically developed through the weighted unsupervised clustering procedure, which is developed to keep the cluster corresponding to the class of interest from losing its identity as the class of interest. Once all the classes are developed, a conventional relative classifier such as the maximum-likelihood classifier is used in the classification.

  3. Adaptive cluster detection

    NASA Astrophysics Data System (ADS)

    Friedenberg, David

    2010-10-01

    the rate of falsely detected active regions. Additionally we examine the more general field of clustering and develop a framework for clustering algorithms based around diffusion maps. Diffusion maps can be used to project high-dimensional data into a lower dimensional space while preserving much of the structure in the data. We demonstrate how diffusion maps can be used to solve clustering problems and examine the influence of tuning parameters on the results. We introduce two novel methods, the self-tuning diffusion map which replaces the global scaling parameter in the typical diffusion map framework with a local scaling parameter and an algorithm for automatically selecting tuning parameters based on a cross-validation style score called prediction strength. The methods are tested on several example datasets.

  4. Single-cluster dynamics for the random-cluster model

    NASA Astrophysics Data System (ADS)

    Deng, Youjin; Qian, Xiaofeng; Blöte, Henk W. J.

    2009-09-01

    We formulate a single-cluster Monte Carlo algorithm for the simulation of the random-cluster model. This algorithm is a generalization of the Wolff single-cluster method for the q -state Potts model to noninteger values q>1 . Its results for static quantities are in a satisfactory agreement with those of the existing Swendsen-Wang-Chayes-Machta (SWCM) algorithm, which involves a full-cluster decomposition of random-cluster configurations. We explore the critical dynamics of this algorithm for several two-dimensional Potts and random-cluster models. For integer q , the single-cluster algorithm can be reduced to the Wolff algorithm, for which case we find that the autocorrelation functions decay almost purely exponentially, with dynamic exponents zexp=0.07 (1), 0.521 (7), and 1.007 (9) for q=2 , 3, and 4, respectively. For noninteger q , the dynamical behavior of the single-cluster algorithm appears to be very dissimilar to that of the SWCM algorithm. For large critical systems, the autocorrelation function displays a range of power-law behavior as a function of time. The dynamic exponents are relatively large. We provide an explanation for this peculiar dynamic behavior.

  5. Single-cluster dynamics for the random-cluster model.

    PubMed

    Deng, Youjin; Qian, Xiaofeng; Blöte, Henk W J

    2009-09-01

    We formulate a single-cluster Monte Carlo algorithm for the simulation of the random-cluster model. This algorithm is a generalization of the Wolff single-cluster method for the q-state Potts model to noninteger values q>1. Its results for static quantities are in a satisfactory agreement with those of the existing Swendsen-Wang-Chayes-Machta (SWCM) algorithm, which involves a full-cluster decomposition of random-cluster configurations. We explore the critical dynamics of this algorithm for several two-dimensional Potts and random-cluster models. For integer q, the single-cluster algorithm can be reduced to the Wolff algorithm, for which case we find that the autocorrelation functions decay almost purely exponentially, with dynamic exponents z(exp)=0.07 (1), 0.521 (7), and 1.007 (9) for q=2, 3, and 4, respectively. For noninteger q, the dynamical behavior of the single-cluster algorithm appears to be very dissimilar to that of the SWCM algorithm. For large critical systems, the autocorrelation function displays a range of power-law behavior as a function of time. The dynamic exponents are relatively large. We provide an explanation for this peculiar dynamic behavior.

  6. Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides.

    PubMed

    Verkhivker, Gennady M; Bouzida, Djamal; Gehlhaar, Daniel K; Rejto, Paul A; Schaffer, Lana; Arthurs, Sandra; Colson, Anthony B; Freer, Stephan T; Larson, Veda; Luty, Brock A; Marrone, Tami; Rose, Peter W

    2002-01-03

    Structure and energetics of the Src Src Homology 2 (SH2) domain binding with the recognition phosphopeptide pYEEI and its mutants are studied by a hierarchical computational approach. The proposed structure prediction strategy includes equilibrium sampling of the peptide conformational space by simulated tempering dynamics with the simplified, knowledge-based energy function, followed by structural clustering of the resulting conformations and binding free energy evaluation of a single representative from each cluster, a cluster center. This protocol is robust in rapid screening of low-energy conformations and recovers the crystal structure of the pYEEI peptide. Thermodynamics of the peptide-SH2 domain binding is analyzed by computing the average energy contributions over conformations from the clusters, structurally similar to the predicted peptide bound structure. Using this approach, the binding thermodynamics for a panel of studied peptides is predicted in a better agreement with the experiment than previously suggested models. However, the overall correlation between computed and experimental binding affinity remains rather modest. The results of this study show that small differences in binding free energies between the Ala and Gly mutants of the pYEEI peptide are considerably more difficult to predict than the structure of the bound peptides, indicating that accurate computational prediction of binding affinities still remains a major methodological and technical challenge.

  7. Clustered engine study

    NASA Technical Reports Server (NTRS)

    Shepard, Kyle; Sager, Paul; Kusunoki, Sid; Porter, John; Campion, AL; Mouritzan, Gunnar; Glunt, George; Vegter, George; Koontz, Rob

    1993-01-01

    Several topics are presented in viewgraph form which together encompass the preliminary assessment of nuclear thermal rocket engine clustering. The study objectives, schedule, flow, and groundrules are covered. This is followed by the NASA groundrules mission and our interpretation of the associated operational scenario. The NASA reference vehicle is illustrated, then the four propulsion system options are examined. Each propulsion system's preliminary design, fluid systems, operating characteristics, thrust structure, dimensions, and mass properties are detailed as well as the associated key propulsion system/vehicle interfaces. A brief series of systems analysis is also covered including: thrust vector control requirements, engine out possibilities, propulsion system failure modes, surviving system requirements, and technology requirements. An assessment of vehicle/propulsion system impacts due to the lessons learned are presented.

  8. Analyzing geographic clustered response

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1991-08-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm. 21 refs., 15 figs., 2 tabs.

  9. Astronomy from satellite clusters

    NASA Astrophysics Data System (ADS)

    Stachnik, R.; Labeyrie, A.

    1984-03-01

    Attention is called to the accumulating evidence that giant space telescopes, comprising a number of separate mirrors on independent satellites, are a realistic prospect for providing research tools of extraordinary power. The ESA-sponsored group and its counterpart in the US have reached remarkably similar conclusions regarding the basic configuration of extremely large synthetic-aperture devices. Both share the basic view that a cluster of spacecraft is preferable to a single monolithic structure. The emphasis of the US group has been on a mission that sweeps across as many sources as possible in the minimum time; it is referred to as SAMSI (Spacecraft Array for Michelson Spatial Interferometry). The European group has placed more emphasis on obtaining two-dimensional images. Their system is referred to as TRIO because, at least initially, it involves three independent systems. Detailed descriptions are given of the two systems.

  10. Ionized cluster beam deposition

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, A. R.

    1983-01-01

    Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

  11. Penicillin-binding proteins in Actinobacteria.

    PubMed

    Ogawara, Hiroshi

    2015-04-01

    Because some Actinobacteria, especially Streptomyces species, are β-lactam-producing bacteria, they have to have some self-resistant mechanism. The β-lactam biosynthetic gene clusters include genes for β-lactamases and penicillin-binding proteins (PBPs), suggesting that these are involved in self-resistance. However, direct evidence for the involvement of β-lactamases does not exist at the present time. Instead, phylogenetic analysis revealed that PBPs in Streptomyces are distinct in that Streptomyces species have much more PBPs than other Actinobacteria, and that two to three pairs of similar PBPs are present in most Streptomyces species examined. Some of these PBPs bind benzylpenicillin with very low affinity and are highly similar in their amino-acid sequences. Furthermore, other low-affinity PBPs such as SCLAV_4179 in Streptomyces clavuligerus, a β-lactam-producing Actinobacterium, may strengthen further the self-resistance against β-lactams. This review discusses the role of PBPs in resistance to benzylpenicillin in Streptomyces belonging to Actinobacteria.

  12. Characterization of the [2Fe-2S] cluster of the Escherichia coli transcription factor IscR†

    PubMed Central

    Fleischhacker, Angela S.; Stubna, Audria; Hsueh, Kuang-Lung; Guo, Yisong; Teter, Sarah J.; Rose, Justin C.; Brunold, Thomas C.; Markley, John L.; Münck, Eckard; Kiley, Patricia J.

    2012-01-01

    IscR is a Fe-S cluster-containing transcription factor involved in a homeostatic mechanism that controls Fe-S cluster biogenesis in Escherichia coli. Although IscR has been proposed to act as a sensor of the cellular demands for Fe-S cluster biogenesis, the mechanism by which IscR performs this function is not known. In this study, we investigated the biochemical properties of the Fe-S cluster of IscR to gain insight into the proposed sensing activity. Mössbauer studies revealed that IscR contains predominantly a reduced [2Fe-2S]1+ cluster in vivo. However, upon anaerobic isolation of IscR some clusters became oxidized to the [2Fe-2S]2+ form. Cluster oxidation did not, however, alter the affinity of IscR for its binding site within the iscR promoter in vitro, indicating that cluster oxidation state is not important for regulation of DNA binding. Furthermore, characterization of anaerobically isolated IscR using resonance Raman, Mössbauer, and NMR spectroscopies leads to the proposal that the [2Fe-2S] cluster does not have full cysteinyl ligation. Mutagenesis studies indicate that, in addition to the three previously identified cysteine residues (Cys92, Cys98, and Cys104), the highly conserved residue His107 is essential for cluster ligation. Thus, these data suggest that IscR binds the cluster with an atypical ligation scheme of three cysteines and one histidine, a feature that may be relevant to the proposed function of IscR as a sensor of cellular Fe-S cluster status. PMID:22583201

  13. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design

    PubMed Central

    Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html. PMID:27487245

  14. Proton transfer in gas-phase ammonium dinitramide clusters

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Thompson, Donald L.

    2003-02-01

    Proton transfer in gaseous ammonium dinitramide (ADN) clusters up to (ADN)2 is studied by using density-functional theory. Proton transfer between the hydrogen dinitramide and ammonia units does not occur in the ADN monomer, rather the ammonia-hydrogen dinitramide complex is stabilized by strong hydrogen bonding. However, proton transfer between hydrogen dinitramide and ammonia is observed in the ADN dimer [NH3HN(NO2)2]2, ADN solvated with a single ammonia molecule [NH3NH(NO2)2]NH3, and ADN solvated with a hydrogen dinitramide molecule [NH3HN(NO2)2]HN(NO2)2. Structural changes in the complexes relative to the free molecules and the binding energies of the clusters are given. Using population analysis, the total electrostatic interaction energy in each cluster is calculated. The electrostatic energy is a measure that distinguishes between the ionic or hydrogen-bonded nature of the clusters. Some implications of proton transfer in ADN clusters on the decomposition mechanism of ADN are discussed.

  15. Dynamic Clustering of the Bacterial Sensory Kinase BaeS

    PubMed Central

    Koler, Moriah; Frank, Vered; Amartely, Hadar; Friedler, Assaf; Vaknin, Ady

    2016-01-01

    Several bacterial sensory-kinase receptors form clusters on the cell membrane. However, the dynamics of sensory-kinase clustering are largely unclear. Using measurements of fluorescence anisotropy and time-lapse imaging of Escherichia coli cells, we demonstrate that copper ions trigger self-association of BaeS receptors and lead to rapid formation of clusters, which can be reversibly dispersed by a metal chelator. Copper ions did not trigger self-association of other fluorescently tagged sensory kinases, and other divalent metal ions could not elicit self-association of BaeS. The histidine residues in the BaeS periplasmic domain are essential for copper binding in vitro and are important for the copper-induced BaeS responses in vivo. BaeS clustering was triggered also under conditions that directly triggered BaeS-dependent transcriptional responses. Thus, clustering of sensory kinase receptors can be dynamic and context dependent and can be triggered by specific environmental cues. PMID:26950881

  16. Multipose binding in molecular docking.

    PubMed

    Atkovska, Kalina; Samsonov, Sergey A; Paszkowski-Rogacz, Maciej; Pisabarro, M Teresa

    2014-02-14

    Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.

  17. Characterization of Homogeneous, Cooperative Protein-DNA Clusters by Sedimentation Equilibrium Analytical Ultracentrifugation and Atomic Force Microscopy.

    PubMed

    Tessmer, Ingrid; Fried, Michael G

    2015-01-01

    Strong, positively cooperative binding can lead to the clustering of proteins on DNA. Here, we describe one approach to the analysis of such clusters. Our example is based on recent studies of the interactions of O(6)-alkylguanine DNA alkyltransferase (AGT) with high-molecular-weight DNAs (Adams et al., 2009; Tessmer, Melikishvili, & Fried, 2012). Cooperative cluster size distributions are predicted using the simplest homogeneous binding and cooperativity (HBC) model, together with data obtained by sedimentation equilibrium analysis. These predictions are tested using atomic force microscopy imaging; for AGT, measured cluster sizes are found to be significantly smaller than those predicted by the HBC model. A mechanism that may account for cluster size limitation is briefly discussed.

  18. Decoding of lipoprotein – receptor interactions; Properties of ligand binding modules governing interactions with ApoE

    PubMed Central

    Guttman, Miklos; Prieto, J. Helena; Croy, Johnny E.; Komives, Elizabeth A.

    2010-01-01

    Clusters of complement-type ligand binding repeats in the LDL receptor family are thought to mediate the interactions between these receptors and their various ligands. Apolipoprotein E, a key ligand for cholesterol homeostasis, has been shown to interact with LDLR, LRP and VLDLR, through these clusters. LDLR and VLDLR each contain a single ligand-binding repeat cluster, whereas LRP contains three large clusters of ligand binding repeats, each with ligand binding functions. We show that within sLRP3, the three-repeat subcluster CR16-18 recapitulated ligand binding to the isolated receptor binding portion of ApoE (residues 130-149). Binding experiments with LA3-5 of LDLR and CR16-18 showed that a conserved W25/D30 pair appears critical for high affinity binding to ApoE(130-149). The triple repeat LA3-5 showed the expected interaction with ApoE(1-191)•DMPC, but surprisingly CR16-18 did not interact with this form of ApoE. To understand these differences in ApoE binding affinity, we introduced mutations of conserved residues from LA5 into CR18, and produced a CR16-18 variant capable of binding ApoE(1-191)•DMPC. This change cannot fully be accounted for by the interaction with the proposed ApoE receptor binding region, therefore we speculate that LA5 is recognizing a distinct epitope on ApoE that may only exists in the lipid bound form. The combination of avidity effects with this distinct recognition process likely governs the ApoE-LDL receptor interaction. PMID:20030366

  19. Quantum chemical study of the interaction of elemental Hg with small neutral, anionic and cationic Au{sub n} (n = 1–6) clusters

    SciTech Connect

    Siddiqui, Shamoon Ahmad; Bouarissa, Nadir; Rasheed, Tabish; Al-Assiri, M.S.

    2013-03-15

    Graphical abstract: Binding energies as a function of cluster size for Au{sub n}Hg, Au{sub n}Hg{sup +} and Au{sub n}Hg{sup −} complexes. Highlights: ► Hg adsorption of neutral and charged Au{sub n} (n = 1–6) clusters has been discussed. ► Size and charged state of cluster significantly affect the Hg adsorption. ► Transfer of electron mainly found from s orbital of Hg to s orbital of Au. - Abstract: Adsorption of elemental mercury (Hg) on small neutral, cationic and anionic gold clusters (Au{sub n}, n = 1–6) has been studied by using the density functional theory (DFT). Results of this investigation show that frontier molecular orbital theory is a useful tool to predict the selectivity of Hg adsorption. It is found that adsorption of Hg on neutral, cationic and anionic Au{sub n} (n = 1–6) clusters are thermodynamically favorable. The binding energies of Hg on the cationic Au{sub n} clusters are greater than those on the neutral and anionic clusters. Natural bond orbital (NBO) analysis indicates that the flow of electrons in the neutral and charged clusters is mainly due to the s orbitals of Hg and Au. Results of NBO analysis also indicate that the binding energy of Hg with Au{sub n} clusters is directly proportional to the charge transfer, i.e. greater is the charge transfer, higher is the binding energy.

  20. Characterization of Pt-Au and Ni-Au Clusters on TiO2(110)

    SciTech Connect

    S Tenney; W He; J Ratliff; D Mullins; D Chen

    2011-12-31

    The surface composition and properties of Pt-Au and Ni-Au clusters on TiO{sub 2}(110) have been studied by scanning tunneling microscopy (STM), low energy ion scattering (LEIS) and soft X-ray photoelectron spectroscopy (sXPS). STM studies show that bimetallic clusters are formed during sequential deposition of the two metals, regardless of the order of deposition. At the 2 ML of Au/2 ML of Pt or Ni coverages studied here, the second metal contributes to the growth of existing clusters rather than forming new pure metal clusters. LEIS experiments demonstrate that the surfaces of the bimetallic clusters are almost 100% Au when 2 ML of Au is deposited on top of 2 ML of Pt or Ni. However, a much larger fraction of Pt or Ni (50 and 20%, respectively) remains at the surface when 2 ML of Pt or Ni is deposited on 2 ML of Au, most likely due to limited diffusion of atoms within the clusters at room temperature. According to sXPS investigations, the binding energies of the metals in the bimetallic clusters are shifted from those observed for pure metal clusters; the Pt(4f{sub 7/2}) and Ni(3p{sub 3/2}) peaks are shifted to lower binding energies while the position of the Au(4f{sub 7/2}) peak is dominated by surface core level shifts. Pure Pt clusters as well as 0.4 ML of Au on 2 ML of Pt clusters reduce the titania support upon encapsulation after annealing to 800 K, whereas 2 ML of Au on 2 ML of Pt clusters do not reduce titania, presumably because there is no Pt at the surface of the clusters. Pure Ni clusters are also known to become encapsulated upon heating, but the reduction of titania is much less extensive compared to that of pure Pt clusters.

  1. SCOWLP classification: Structural comparison and analysis of protein binding regions

    PubMed Central

    Teyra, Joan; Paszkowski-Rogacz, Maciej; Anders, Gerd; Pisabarro, M Teresa

    2008-01-01

    Background Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Description Protein binding regions (PBRs) might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed. We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions. The hierarchical

  2. Yin Yang 1 cooperates with activator protein 2 to stimulate ERBB2 gene expression in mammary cancer cells.

    PubMed

    Begon, Dominique Y; Delacroix, Laurence; Vernimmen, Douglas; Jackers, Pascale; Winkler, Rosita

    2005-07-01

    Overexpression of the ERBB2 oncogene is observed in about 30% of breast cancers and is generally correlated with a poor prognosis. Previous results from our and other laboratories indicated that elevated transcriptional activity contributes significantly to the overexpression of ERBB2 mRNA in mammary adenocarcinoma cell lines. Activator protein 2 (AP-2) transcription factors account for this overexpression through two recognition sequences located 215 and 500 bp upstream from the transcription start site. Furthermore, AP-2 transcription factors are highly expressed in cancer cell lines overexpressing ERBB2. In this report, we examined the cooperative effect of Yin Yang 1 (YY1) on AP-2-induced activation of ERBB2 promoter activity. We detected high levels of YY1 transcription factor in mammary cancer cell lines. Notably, we showed that YY1 enhances AP-2alpha transcriptional activation of the ERBB2 promoter through an AP-2 site both in HepG2 and in HCT116 cells, whereas a carboxyl-terminal-truncated form of YY1 cannot. Moreover, we demonstrated the interaction between endogenous AP-2 and YY1 factors in the BT-474 mammary adenocarcinoma cell line. In addition, inhibition of endogenous YY1 protein by an antisense decreased the transcription of an AP-2-responsive ERBB2 reporter plasmid in BT-474 breast cancer cells. Finally, we detected in vivo AP-2 and YY1 occupancy of the ERBB2 proximal promoter in chromatin immunoprecipitation assays. Our data thus provide evidence that YY1 cooperates with AP-2 to stimulate ERBB2 promoter activity through the AP-2 binding sites.

  3. Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters

    PubMed Central

    Tellaroli, Paola; Bazzi, Marco; Donato, Michele; Brazzale, Alessandra R.; Drăghici, Sorin

    2016-01-01

    Four of the most common limitations of the many available clustering methods are: i) the lack of a proper strategy to deal with outliers; ii) the need for a good a priori estimate of the number of clusters to obtain reasonable results; iii) the lack of a method able to detect when partitioning of a specific data set is not appropriate; and iv) the dependence of the result on the initialization. Here we propose Cross-clustering (CC), a partial clustering algorithm that overcomes these four limitations by combining the principles of two well established hierarchical clustering algorithms: Ward’s minimum variance and Complete-linkage. We validated CC by comparing it with a number of existing clustering methods, including Ward’s and Complete-linkage. We show on both simulated and real datasets, that CC performs better than the other methods in terms of: the identification of the correct number of clusters, the identification of outliers, and the determination of real cluster memberships. We used CC to cluster samples in order to identify disease subtypes, and on gene profiles, in order to determine groups of genes with the same behavior. Results obtained on a non-biological dataset show that the method is general enough to be successfully used in such diverse applications. The algorithm has been implemented in the statistical language R and is freely available from the CRAN contributed packages repository. PMID:27015427

  4. Catalytic role of boron atoms in self-interstitial clustering in Si

    NASA Astrophysics Data System (ADS)

    Hwang, Gyeong S.; Goddard, William A.

    2003-08-01

    Using density functional theory (DFT) calculations and kinetic simulations, we have investigated the influence of boron atoms on self-interstitial clustering in Si. From DFT calculations of neutral interstitial clusters with a single B atom (BsIn, n⩽4), we find that the binding of B (BsIn→In-1+BsI) becomes substantially weaker than that of an interstitial (BsIn→BsIn-1+I) when n⩾4. This implies boron can be liberated while leaving an interstitial cluster behind. Our kinetic simulations including the boron liberation explain well experimental observations reported by J. L. Benton et al., J. Appl. Phys. 82, 120 (1997).

  5. Gaseous models of globular clusters with stellar evolution

    NASA Astrophysics Data System (ADS)

    Deiters, S.; Spurzem, R.

    Comparing different approaches for modelling the evolution of star clusters, gaseous models have the advantage of high "particle numbers" but --- until now --- the disadvantage of a lack of realism (Giersz & Spurzem 1994, MNRAS 269, 24 1). To improve gaseous models towards a more realistic description of globular clusters one has to take the effects of stellar evolution and many (primordial) binaries into account and add a consistent treatment of the tidal field of the galaxy (Chernoff & Weinberg 1990, ApJ 351, 121; Portegies Zwart 1998, AA in press). We want to present the first steps on our way towards more realistic gaseous models: We show results of the first implementation of stellar evolution in a spherically symmetric anisotropic gaseous model. We subdivide our model in several dynamical components, each with different stellar mass, whose stellar evolution is followed in a parameterized way. Thus we can simulate the effects of the evolution of stars of different masses in the cluster: During their evolution the stars lose a significant amount of their initial mass, which can easily escape from the cluster. Hence the binding energy of the cluster is reduced. We show several models with different initial conditions with and without the effects of stellar evolution. Their evolution is followed into core bounce and during the post-collapse phase. Dynamical properties of the clusters for the different initial conditions are compared. If time allows we will focus briefly on the treatment of a (time-independent) tidal boundary, modelling the gravitational field of the mother galaxy in our models and give an outlook on the next steps towards more realism in our models of globular clusters, e.g. the inclusion of stochastic binaries (Spurzem & Giersz 1996, MNRAS 283, 805) and stellar finite-size effects.

  6. Effect of Graphene with Nanopores on Metal Clusters

    SciTech Connect

    Zhou, Hu; Chen, Xianlang; Wang, Lei; Zhong, Xing; Zhuang, Guilin; Li, Xiaonian; Mei, Donghai; Wang, Jianguo

    2015-10-07

    Porous graphene, which is a novel type of defective graphene, shows excellent potential as a support material for metal clusters. In this work, the stability and electronic structures of metal clusters (Pd, Ir, Rh) supported on pristine graphene and graphene with different sizes of nanopore were investigated by first-principle density functional theory (DFT) calculations. Thereafter, CO adsorption and oxidation reaction on the Pd-graphene system were chosen to evaluate its catalytic performance. Graphene with nanopore can strongly stabilize the metal clusters and cause a substantial downshift of the d-band center of the metal clusters, thus decreasing CO adsorption. All binding energies, d-band centers, and adsorption energies show a linear change with the size of the nanopore: a bigger size of nanopore corresponds to a stronger metal clusters bond to the graphene, lower downshift of the d-band center, and weaker CO adsorption. By using a suitable size nanopore, supported Pd clusters on the graphene will have similar CO and O2 adsorption ability, thus leading to superior CO tolerance. The DFT calculated reaction energy barriers show that graphene with nanopore is a superior catalyst for CO oxidation reaction. These properties can play an important role in instructing graphene-supported metal catalyst preparation to prevent the diffusion or agglomeration of metal clusters and enhance catalytic performance. This work was supported by National Basic Research Program of China (973Program) (2013CB733501), the National Natural Science Foundation of China (NSFC-21176221, 21136001, 21101137, 21306169, and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational

  7. Ambient preparation and reactions of gas phase silver cluster cations and anions.

    PubMed

    Wleklinski, Michael; Sarkar, Depanjan; Hollerbach, Adam; Pradeep, Thalappil; Cooks, R Graham

    2015-07-28

    Electrospray ionization of metal salt solutions followed by ambient heating transforms the resulting salt clusters into new species, primarily naked ionic metal clusters. The experiment is done by passing the clusters through a heated coiled loop outside the mass spectrometer which releases the counter-anion while generating the anionic or cationic naked metal cluster. The nature of the anion in the starting salt determines the type of metal cluster observed. For example, silver acetate upon heating generates only positive silver clusters, Ag(n)(+), but silver fluoride generates both positive and negative silver clusters, Ag(n)(+/-) (3 < n < 20). Both unheated and heated metal salt sprays yield ions with characteristic geometric and electronic magic numbers. There is also a strong odd/even effect in the cationic and anionic silver clusters. Thermochemical control is suggested as the basis for favored formation of the observed clusters, with anhydride elimination occurring from the acetates and fluorine elimination from the fluorides to give cationic and anionic clusters, respectively. Data on the intermediates observed as the temperature is ramped support this. The naked metal clusters react with gaseous reagents in the open air, including methyl substituted pyridines, hydrocarbons, common organic solvents, ozone, ethylene, and propylene. Argentation of hydrocarbons, including saturated hydrocarbons, is shown to occur and serves as a useful analytical ionization method. The new cluster formation methodology allows investigation of ligand-metal binding including in reactions of industrial importance, such as olefin epoxidation. These reactions provide insight into the physicochemical properties of silver cluster anions and cations. The potential use of the ion source in ion soft landing is demonstrated by reproducing the mass spectra of salts heated in air using a custom surface science instrument.

  8. The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO2 photoreduction

    SciTech Connect

    Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.; Joseph, Babu

    2015-09-04

    In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO2 photoreduction reaction (bent CO2), we find that flatter (2D-like) Pt clusters that “wet” the TiO2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO2 interfacial sites with geometries that can aid CO2 bond bending and charge transfer processes. Second, binding competition among each Pt–CO2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO2 surfaces for CO2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO2 on TiO2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.

  9. Measurement of free glucocorticoids: quantifying corticosteroid-binding globulin binding affinity and its variation within and among mammalian species

    PubMed Central

    Delehanty, Brendan; Hossain, Sabrina; Jen, Chao Ching; Crawshaw, Graham J.; Boonstra, Rudy

    2015-01-01

    Plasma glucocorticoids (GCs) are commonly used as measures of stress in wildlife. A great deal of evidence indicates that only free GC (GC not bound by the specific binding protein, corticosteroid-binding globulin, CBG) leaves the circulation and exerts biological effects on GC-sensitive tissues. Free hormone concentrations are difficult to measure directly, so researchers estimate free GC using two measures: the binding affinity and the binding capacity in plasma. We provide an inexpensive saturation binding method for calculating the binding affinity (equilibrium dissociation constant, Kd) of CBG that can be run without specialized laboratory equipment. Given that other plasma proteins, such as albumin, also bind GCs, the method compensates for this non-specific binding. Separation of bound GC from free GC was achieved with dextran-coated charcoal. The method provides repeatable estimates (12% coefficient of variation in the red squirrel, Tamiasciurus hudsonicus), and there is little evidence of inter-individual variation in Kd (range 2.0–7.3 nM for 16 Richardson's ground squirrels, Urocitellus richardsonii). The Kd values of 28 mammalian species we assessed were mostly clustered around a median of 4 nM, but five species had values between 13 and 61 nM. This pattern may be distinct from birds, for which published values are more tightly distributed (1.5–5.1 nM). The charcoal separation method provides a reliable and robust method for measuring the Kd in a wide range of species. It uses basic laboratory equipment to provide rapid results at very low cost. Given the importance of CBG in regulating the biological activity of GCs, this method is a useful tool for physiological ecologists. PMID:27293705

  10. Ensemble Clustering for Result Diversification

    DTIC Science & Technology

    2012-11-01

    different clustering methods for a par- ticular data source. He et al. [8] proposed a framework to combine clusters of external resources to...representations for result diversification. In Proceedings of SIGIR, 2012. [9] D. Hiemstra and C. Hauff. Mapreduce for information retrieval evaluation: ‘let’s

  11. Antibody-gold cluster conjugates

    DOEpatents

    Hainfeld, J.F.

    1988-06-28

    Antibody- or antibody fragment-gold cluster conjugates are shown wherein the conjugate size can be about 5.0 nm. Methods and reagents are disclosed in which antibodies or Fab' fragments thereof are covalently bound to a stable cluster of gold atoms. 2 figs.

  12. Medicolegal issues in cluster headache.

    PubMed

    Loder, Elizabeth; Loder, John

    2004-04-01

    This paper identifies legal issues of relevance to the diagnosis and treatment of cluster headache, including areas of actual and potential malpractice liability. Legal topics that are relevant to cluster headache can be divided into five categories: diagnostic-related issues, risks inherent in the disease process, prescribing and treatment-related problems, research-related issues, and disability determination.

  13. Two generalizations of Kohonen clustering

    NASA Technical Reports Server (NTRS)

    Bezdek, James C.; Pal, Nikhil R.; Tsao, Eric C. K.

    1993-01-01

    The relationship between the sequential hard c-means (SHCM), learning vector quantization (LVQ), and fuzzy c-means (FCM) clustering algorithms is discussed. LVQ and SHCM suffer from several major problems. For example, they depend heavily on initialization. If the initial values of the cluster centers are outside the convex hull of the input data, such algorithms, even if they terminate, may not produce meaningful results in terms of prototypes for cluster representation. This is due in part to the fact that they update only the winning prototype for every input vector. The impact and interaction of these two families with Kohonen's self-organizing feature mapping (SOFM), which is not a clustering method, but which often leads ideas to clustering algorithms is discussed. Then two generalizations of LVQ that are explicitly designed as clustering algorithms are presented; these algorithms are referred to as generalized LVQ = GLVQ; and fuzzy LVQ = FLVQ. Learning rules are derived to optimize an objective function whose goal is to produce 'good clusters'. GLVQ/FLVQ (may) update every node in the clustering net for each input vector. Neither GLVQ nor FLVQ depends upon a choice for the update neighborhood or learning rate distribution - these are taken care of automatically. Segmentation of a gray tone image is used as a typical application of these algorithms to illustrate the performance of GLVQ/FLVQ.

  14. 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.

  15. On the History of Cluster Beams

    NASA Astrophysics Data System (ADS)

    Becker, E. W.

    1986-06-01

    The methods to produce and investigate cluster beams have been developed primarily with the use of permanent gases. A summary is given of related work carried out at Marburg and Karlsruhe. The report deals with the effect of carrier gases on cluster beam production; ionization, electrical acceleration and magnetic deflection of cluster beams; the retarding potential mass spectrometry of cluster beams; cluster size measurement by atomic beam attenuation; reflection of cluster beams at solid surfaces; scattering properties of4He and3He clusters; the application of cluster beams in plasma physics, and the reduction of space charge problems by acceleration of cluster ions.

  16. Structure and atomic vibrations in bimetallic Ni13 - n Al n clusters

    NASA Astrophysics Data System (ADS)

    Rusina, G. G.; Borisova, S. D.; Chulkov, E. V.

    2015-04-01

    The binding energy, equilibrium geometry, and vibration frequencies in bimetallic clusters Ni13 - n Al n ( n = 0-13) have been calculated using the embedded atom method potentials. It has been shown that the icosahedral structure is the most stable in monoatomic and bimetallic clusters. A tendency of Al atoms to segregate on the cluster surface has been revealed in agreement with the experimental data. The calculations of the atomic vibrations have shown the nonmonotonic dependence of the minimum and maximum vibration frequencies of cluster atoms on its composition and the coupling of their extreme values with the most stable atomic configuration. The increase in the number of Al atoms leads to the shift of the frequency spectrum and the substantial redistribution of the localization of vibrations on the cluster atoms.

  17. Vibrational properties of small cobalt clusters on the Cu(111) surface

    NASA Astrophysics Data System (ADS)

    Borisova, S. D.; Rusina, G. G.; Eremeev, S. V.; Chulkov, E. V.

    2009-06-01

    Vibrational properties of small cobalt clusters (dimer and trimer) adsorbed on the Cu(111) surface are studied using interatomic interaction potentials obtained in a tight-binding approximation. The complete (lateral and vertical) relaxation of the surface, the local phonon density of states, and the polarization of vibration modes of clusters and atoms of the substrate are discussed. It is shown that the adsorption of small cobalt clusters leads to a local modification of the vibrational properties of the substrate surface and to excitation of new vibration modes localized on both the cluster adatoms and substrate surface atoms. An increase in the cluster size causes a decrease in the intensity of peaks of the local density of states and their broadening and also a shift in the frequencies of the peaks.

  18. Theoretical Studies on Cluster Compounds

    NASA Astrophysics Data System (ADS)

    Lin, Zhenyang

    Available from UMI in association with The British Library. Requires signed TDF. The Thesis describes some theoretical studies on ligated and bare clusters. Chapter 1 gives a review of the two theoretical models, Tensor Surface Harmonic Theory (TSH) and Jellium Model, accounting for the electronic structures of ligated and bare clusters. The Polyhedral Skeletal Electron Pair Theory (PSEPT), which correlates the structures and electron counts (total number of valence electrons) of main group and transition metal ligated clusters, is briefly described. A structural jellium model is developed in Chapter 2 which accounts for the electronic structures of clusters using a crystal-field perturbation. The zero-order potential we derive is of central-field form, depends on the geometry of the cluster, and has a well-defined relationship to the full nuclear-electron potential. Qualitative arguments suggest that this potential produces different energy level orderings for clusters with a nucleus with large positive charge at the centre of the cluster. Analysis of the effects of the non-spherical perturbation on the spherical jellium shell structures leads to the conclusion that for a cluster with a closed shell electronic structure a high symmetry arrangement which is approximately or precisely close packed will be preferred. It also provides a basis for rationalising those structures of clusters with incomplete shell electronic configurations. In Chapter 3, the geometric conclusions derived in the structural jellium model are developed in more detail. The group theoretical consequences of the Tensor Surface Harmonic Theory are developed in Chapter 4 for (ML_2) _{rm n}, (ML_4) _{rm n} and (ML_5 ) _{rm n} clusters where either the xz and yz or x^2 -y^2 and xy components to L_sp{rm d}{pi } and L_sp{rm d} {delta} do not contribute equally to the bonding. The closed shell requirements for such clusters are defined and the orbital symmetry constraints pertaining to the

  19. Structural and electronic properties of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13): Theoretical investigation based on ab initio molecular orbital theory.

    PubMed

    Nigam, Sandeep; Majumder, Chiranjib; Kulshreshtha, S K

    2006-08-21

    The geometric and electronic structures of Si(n), Si(n)-, and PSi(n-1) clusters (2 < or = n < or = 13) have been investigated using the ab initio molecular orbital theory formalism. The hybrid exchange-correlation energy functional (B3LYP) and a standard split-valence basis set with polarization functions (6-31+G(d)) were employed to optimize geometrical configurations. The total energies of the lowest energy isomers thus obtained were recalculated at the MP2/aug-cc-pVTZ level of theory. Unlike positively charged clusters, which showed similar structural behavior as that of neutral clusters [Nigam et al., J. Chem. Phys. 121, 7756 (2004)], significant geometrical changes were observed between Si(n) and Si(n)- clusters for n = 6, 8, 11, and 13. However, the geometries of P substituted silicon clusters show similar growth as that of negatively charged Si(n) clusters with small local distortions. The relative stability as a function of cluster size has been verified based on their binding energies, second difference in energy (Delta2 E), and fragmentation behavior. In general, the average binding energy of Si(n)- clusters is found to be higher than that of Si(n) clusters. For isoelectronic PSi(n-1) clusters, it is found that although for small clusters (n < 4) substitution of P atom improves the binding energy of Si(n) clusters, for larger clusters (n > or = 4) the effect is opposite. The fragmentation behavior of these clusters reveals that while small clusters prefer to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size. The adiabatic electron affinities of Si(n) clusters and vertical detachment energies of Si(n)- clusters were calculated and compared with available experimental results. Finally, a good agreement between experimental and our theoretical results suggests good prediction of the lowest energy isomeric structures for all clusters calculated in the present study.

  20. Transcriptional regulation of the novobiocin biosynthetic gene cluster.

    PubMed

    Dangel, Volker; Härle, Johannes; Goerke, Christiane; Wolz, Christiane; Gust, Bertolt; Pernodet, Jean-Luc; Heide, Lutz

    2009-12-01

    The aminocoumarin antibiotic novobiocin is a gyrase inhibitor formed by a Streptomyces strain. The biosynthetic gene cluster of novobiocin spans 23.4 kb and contains 20 coding sequences, among them the two regulatory genes novE and novG. We investigated the location of transcriptional promoters within this cluster by insertion of transcriptional terminator cassettes and RT-PCR analysis of the resulting mutants. The cluster was found to contain eight DNA regions with promoter activity. The regulatory protein NovG binds to a previously identified binding site within the promoter region located upstream of novH, but apparently not to any of the other seven promoters. Quantitative real-time PCR was used to compare the number of transcripts in a strain carrying an intact novobiocin cluster with strains carrying mutated clusters. Both in-frame deletion of the regulatory gene novG and insertion of a terminator cassette into the biosynthetic gene novH led to a strong reduction of the number of transcripts of the genes located between novH and novW. This suggested that these 16 biosynthetic genes form a single operon. Three internal promoters are located within this operon but appear to be of minor importance, if any, under our experimental conditions. Transcription of novG was found to depend on the presence of NovE, suggesting that the two regulatory genes, novE and novG, act in a cascade-like mechanism. The resistance gene gyrB(R), encoding an aminocoumarin-resistant gyrase B subunit, may initially be co-transcribed with the genes from novH to novW. However, when the gyrase inhibitor novobiocin accumulates in the cultures, gyrB(R) is transcribed from its own promoter. Previous work has suggested that this promoter is controlled by the superhelical density of chromosomal DNA.