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At least 145 records · Page 8Linked to original sources
PubMed2003

Infrared spectroscopy of niobium oxide cluster cations in a molecular beam: identifying the cluster structures.

Infrared spectra of niobium oxide cluster cations are measured via IR multiple photon dissociation spectroscopy in the 400-1650 cm(-1) region. The cluster cations are obtained directly from a laser vaporization source and irradiated with the infrared light emitted by a free electron laser. For those oxide clusters that fragment after excitation, the IR spectra are recorded by measuring the cluster intensity changes as a function of the IR wavelength. The spectra of all examined oxide clusters exhibit two main absorption features that can be assigned to vibrations of terminal (Nb=O) or bridging (Nb-O-Nb) oxide groups. For selected clusters DFT calculations at the B3LYP/LACVP* level have been performed and the calculated vibrational spectra are compared to the experimental data to identify the gas phase structures of the clusters.

Journal Article↗
PubMed2005

Gold cluster carbonyls: saturated adsorption of CO on gold cluster cations, vibrational spectroscopy, and implications for their structures.

We report on the interaction of carbon monoxide with cationic gold clusters in the gas phase. Successive adsorption of CO molecules on the Au(n)(+) clusters proceeds until a cluster size specific saturation coverage is reached. Structural information for the bare gold clusters is obtained by comparing the saturation stoichiometry with the number of available equivalent sites presented by candidate structures of Au(n)(+). Our findings are in agreement with the planar structures of the Au(n)(+) cluster cations with n < or = 7 that are suggested by ion mobility experiments [Gilb, S.; Weis, P.; Furche, F.; Ahlrichs, R.; Kappes, M. M. J. Chem. Phys. 2001, 116, 4094]. By inference we also establish the structure of the saturated Au(n)(CO)(m)(+) complexes. In certain cases we find evidence suggesting that successive adsorption of CO can distort the metal cluster framework. In addition, the vibrational spectra of the Au(n)(CO)(m)(+) complexes in both the CO stretching region and in the region of the Au-C stretch and the Au-C-O bend are measured using infrared photodepletion spectroscopy. The spectra further aid in the structure determination of Au(n)(+), provide information on the structure of the Au(n)(+)-CO complexes, and can be compared with spectra of CO adsorbates on deposited clusters or surfaces.

Journal Article↗
PubMed1989

Expression of the small cell carcinoma antigens of cluster-5 and cluster-5A in primary lung tumours.

The expression of the small cell carcinoma (SCLC) antigens cluster-5 (antibody LAM8) and cluster-5A (antibody SWA20) was examined on a panel of routinely processed biopsy or surgical specimens of 290 lung tumours by immunoperoxidase staining. Antigen expression was largely restricted to SCLC. Of over 150 tissue samples evaluated, moderate or strong antigen expression was found in 49% (cluster-5) and 45% (cluster-5A). Concordance in expression of the two antigens was seen in 71% of SCLC samples, with 35% expressing both antigens strongly, 8% moderately and 28% being negative for both antigens. Antigen expression was independent of the morphological subtype of SCLC. Primary lung tumours of other histology, including squamous cell carcinoma, large cell carcinoma, adenocarcinoma, mesothelioma or carcinoid had no significant antigen expression. Of 135 tumours, strong or moderate expression of both antigens was seen only in two cases. 20%, mostly carcinoids, were weakly positive for cluster 5 and 4% for cluster 5A antigen. The remainder were antigen negative. No significant antigen expression was seen in 25 normal lung tissues. The membrane antigens of SCLC cluster 5 and 5A are markers for SCLC and their expression in tissues is tumour-associated.

Antigens, Neoplasm↗
PubMed2000

Characterization of the O-antigen gene clusters of Yersinia pseudotuberculosis and the cryptic O-antigen gene cluster of Yersinia pestis shows that the plague bacillus is most closely related to and has evolved from Y. pseudotuberculosis serotype O:1b.

One of the most virulent and feared bacterial pathogens is Yersinia pestis, the aetiologic agent of bubonic plague. Characterization of the O-antigen gene clusters of 21 serotypes of Yersinia pseudotuberculosis and the cryptic O-antigen gene cluster of Y. pestis showed that the plague bacillus is most closely related to and has evolved from Y. pseudotuberculosis serotype O:1b. The nucleotide sequences of both gene clusters (about 20.5 kb each) were determined and compared to identify the differences that caused the silencing of the Y. pestis gene cluster. At the nucleotide sequence level, the loci were 98.9% identical and, of the 17 biosynthetic genes identified from the O:1b gene cluster, five were inactivated in the Y. pestis cluster, four by insertions or deletions of one nucleotide and one by a deletion of 62 nucleotides. Apparently, the expression of the O-antigen is not beneficial for the virulence or to the lifestyle of Y. pestis and, therefore, as one step in the evolution of Y. pestis, the O-antigen gene cluster was inactivated.

Amino Acid Sequence↗
PubMed2004

Strongly cluster size dependent reaction behavior of CO with O2 on free silver cluster anions.

Reactions of free silver anions Agn- (n = 1 - 13) with O2, CO, and their mixtures are investigated in a temperature controlled radio frequency ion trap setup. Cluster anions Agn- (n = 1 - 11) readily react with molecular oxygen to yield AgnOm- (m = 2, 4, or 6) oxide products. In contrast, no reaction of the silver cluster anions with carbon monoxide is detected. However, if silver cluster anions are exposed to the mixture of O2 and CO, new reaction products and a pronounced, discontinuous size dependence in the reaction behavior is observed. In particular, coadsorption complexes Agn(CO)O2- are detected for cluster sizes with n = 4 and 6 and, the most striking observation, in the case of the larger odd atom number clusters Ag7-, Ag9-, and Ag11-, the oxide product concentration decreases while a reappearance of the bare metal cluster signal is observed. This leads to the conclusion that carbon monoxide reacts with the activated oxygen on these silver clusters and indicates the prevalence of a catalytic reaction cycle.

Journal Article↗
PubMed2006

Electron transfer processes on Ag and Au clusters supported on TiO2(110) and cluster size effects.

The results of a detailed study of Li(+) neutralization in scattering on Ag and Au clusters and thin films supported on TiO(2) are presented. A very efficient neutralization is observed on small clusters with a decrease for the smallest clusters. These results closely follow the size-effects observed in the reactivity of these systems. The energy dependence of the neutralization was studied for the larger clusters (>4 nm) and observed to be similar in trend to the one observed on films and bulk (111) crystals. A general discussion of possible reasons of the enhancement in neutralization is presented and these changes are then tentatively discussed in terms of progressive modifications in the electronic structure of clusters as a function of reduction in size and as it evolves from metallic-like to discretised states. The highest neutralization efficiency would appear to correspond to clusters sizes for which a metal to nonmetal transition occurs. The relative position of the Li level and the highest occupied molecular orbital in the molecular cluster can be expected to strongly affect the electron transfer processes, which in this case should be described in a molecular framework.

Journal Article↗
PubMed2003

Subcellular compartmentalization of human Nfu, an iron-sulfur cluster scaffold protein, and its ability to assemble a [4Fe-4S] cluster.

Iron-sulfur (Fe-S) clusters serve as cofactors in many proteins that have important redox, catalytic, and regulatory functions. In bacteria, biogenesis of Fe-S clusters is mediated by multiple gene products encoded by the isc and nif operons. In particular, genetic and biochemical studies suggest that IscU, Nfu, and IscA function as scaffold proteins for assembly and delivery of rudimentary Fe-S clusters to target proteins. Here we report the characterization of human Nfu. A combination of biochemical and spectroscopic techniques, including UV-visible absorption and 57Fe Mössbauer spectroscopies, have been used to investigate the ability of purified human Nfu to assemble Fe-S clusters. The results suggest that Nfu can assemble approximately one labile [4Fe-4S] cluster per two Nfu monomers, and support the proposal that Nfu is an alternative scaffold protein for assembly of clusters that are subsequently used for maturation of targeted Fe-S proteins. Analyses of genomic DNA, transcripts, and translation products indicate that alternative splicing of a common pre-mRNA results in synthesis of two Nfu isoforms with distinct subcellular localizations. Isoform I is localized in the mitochondria, whereas isoform II is present in the cytosol and the nucleus. These results, together with previous reports of subcellular distributions of isoforms of human IscS and IscU in mitochondria, cytosol, and nucleus suggest that the Fe-S cluster assembly machineries are compartmentalized in higher eukaryotes.

Alternative Splicing↗
PubMed2001

IscR, an Fe-S cluster-containing transcription factor, represses expression of Escherichia coli genes encoding Fe-S cluster assembly proteins.

IscR (iron-sulfur cluster regulator) is encoded by an ORF located immediately upstream of genes coding for the Escherichia coli Fe-S cluster assembly proteins, IscS, IscU, and IscA. IscR shares amino acid similarity with MarA, a member of the MarA/SoxS/Rob family of transcription factors. In this study, we found that IscR functions as a repressor of the iscRSUA operon, because strains deleted for iscR have increased expression of this operon. In addition, in vitro transcription reactions established a direct role for IscR in repression of the iscR promoter. Analysis of IscR by electron paramagnetic resonance showed that the anaerobically isolated protein contains a [2Fe-2S](1+) cluster. The Fe-S cluster appears to be important for IscR function, because repression of iscR expression is significantly reduced in strains containing null mutations of the Fe-S cluster assembly genes iscS or hscA. The finding that IscR activity is decreased in strain backgrounds in which Fe-S cluster assembly is impaired suggests that this protein may be part of a novel autoregulatory mechanism that senses the Fe-S cluster assembly status of cells.

Amino Acid Sequence↗
PubMed1977

Dependence of the rates of dissolution of the Fe4S4 clusters of Chromatium vinosum high-potential iron protein and ferredoxin on cluster oxidation state.

The influence of oxidation state on the pH dependence of the dissolution of the Fe(4)S(4) clusters of Chromatium vinosum ferredoxin and high-potential iron protein (HIPIP) has been studied. The first-order rate constants (k(obs)) for dissolution of both the Fe(4)S(4)(S-Cys)(4) (2-) and Fe(4)S(4)(S-Cys)(4) (3-) clusters of the ferredoxin follow the same overall kinetic equation but with differing specific rate and equilibrium constants. The dependence of rate and equilibrium constants upon oxidation state may be rationalized on the basis of the accompanying change in electrostatic affinity of a cluster toward H(+) and HO(-). A more drastic change in the pH dependence of the kinetics of dissolution of the Fe(4)S(4) cluster of the HIPIP accompanies its change in oxidation state. Whereas the values of k(obs) for dissolution of HIPIP containing the Fe(4)S(4)(S-Cys)(4) (2-) cluster are strictly second order to [H(+)] and [HO(-)], the pH dependence for dissolution of the HIPIP Fe(4)S(4)(S-Cys)(4) (1-) cluster indicates a first-order dependence upon [H(+)], a second-order dependence upon [HO(-)], and a spontaneous or water rate. These reactivity differences may be related to changes in cluster charge density. Mechanisms of dissolution involve preequilibrium protonation at acidic pH and preequilibrium ligand exchange at basic pH.

Chromatium↗
PubMed2001

Detection of a [3Fe-4S] cluster intermediate of cytosolic aconitase in yeast expressing iron regulatory protein 1. Insights into the mechanism of Fe-S cluster cycling.

Interconversion of iron regulatory protein 1 (IRP1) with cytosolic aconitase (c-aconitase) occurs via assembly/disassembly of a [4Fe-4S] cluster. Recent evidence implicates oxidants in cluster disassembly. We investigated H(2)O(2)-initiated Fe-S cluster disassembly in c-aconitase expressed in Saccharomyces cerevisiae. A signal for [3Fe-4S] c-aconitase was detected by whole-cell EPR of aerobically grown, aco1 yeast expressing wild-type IRP1 or a S138A-IRP1 mutant (IRP1(S138A)), providing the first direct evidence of a 3Fe intermediate in vivo. Exposure of yeast to H(2)O(2) increased this 3Fe c-aconitase signal up to 5-fold, coincident with inhibition of c-aconitase activity. Untreated yeast expressing IRP1(S138D) or IRP1(S138E), which mimic phosphorylated IRP1, failed to give a 3Fe signal. H(2)O(2) produced a weak 3Fe signal in yeast expressing IRP1(S138D). Yeast expressing IRP1(S138D) or IRP1(S138E) were the most sensitive to inhibition of aconitase-dependent growth by H(2)O(2) and were more responsive to changes in media iron status. Ferricyanide oxidation of anaerobically reconstituted c-aconitase yielded a strong 3Fe EPR signal with wild-type and S138A c-aconitases. Only a weak 3Fe signal was obtained with S138D c-aconitase, and no signal was obtained with S138E c-aconitase. This, paired with loss of c-aconitase activity, strongly argues that the Fe-S clusters of these phosphomimetic c-aconitase mutants undergo more complete disassembly upon oxidation. Our results demonstrate that 3Fe c-aconitase is an intermediate in H(2)O(2)-initiated Fe-S cluster disassembly in vivo and suggest that cluster assembly/disassembly in IRP1 is a dynamic process in aerobically growing yeast. Further, our results support the view that phosphorylation of IRP1 can modulate its response to iron through effects on Fe-S cluster stability and turnover.

Aconitate Hydratase↗
PubMed1997

Laminin-induced clustering of dystroglycan on embryonic muscle cells: comparison with agrin-induced clustering.

The effect of laminin on the distribution of dystroglycan (DG) and other surface proteins was examined by fluorescent staining in cultures of muscle cells derived from Xenopus embryos. Western blotting confirmed that previously characterized antibodies are reactive in Xenopus. In control cultures, alphaDG, betaDG, and laminin binding sites were distributed as microclusters (<1 microm2 in area) over the entire dorsal surface of the muscle cells. Treatment with laminin induced the formation of macroclusters (1-20 microm2), accompanied by a corresponding decline in the density of the microclusters. With 6 nM laminin, clustering was apparent within 150 min and near maximal within 1 d. Laminin was effective at 30 pM, the lowest concentration tested. The laminin fragment E3, which competes with laminin for binding to alphaDG, inhibited laminin-induced clustering but did not itself cluster DG, thereby indicating that other portions of the laminin molecule in addition to its alphaDG binding domain are required for its clustering activity. Laminin-induced clusters also contained dystrophin, but unlike agrin-induced clusters, they did not contain acetylcholine receptors, utrophin, or phosphotyrosine, and their formation was not inhibited by a tyrosine kinase inhibitor. The results reinforce the notion that unclustered DG is mobile on the surface of embryonic muscle cells and suggest that this mobile DG can be trapped by at least two different sets of molecular interactions. Laminin self binding may be the basis for the laminin-induced clustering.

Agrin↗
PubMed2006

Computer simulation of diffusion-limited cluster-cluster aggregation with an Epstein drag force.

The motion of particles, dispersed in a medium, between collisions with each other can, in limiting situations, be either ballistic (straight line) or diffusive (random walker). The diffusive regime can be divided into two distinct subregimes. The "continuum regime" exhibits Stokes-Einstein-type diffusion (no-slip surface boundary condition) with a frictional coefficient proportional to the particle size (linear dimension). The "Epstein regime," as we shall refer to it, is characterized by a frictional coefficient proportional to the particle cross-sectional area, hence an Epstein-type diffusion (slip surface). The purpose of the current study is to illuminate the dynamics of dilute-limit aggregation in the Epstein regime. We present results from low volume fraction Monte Carlo simulations of cluster-cluster aggregation in the Epstein regime with the particle motion based on each particle's cross-sectional area. Our findings indicate that aggregates grown under Epstein conditions have a fractal dimension of approximately 1.8, similar to that of diffusion-limited cluster-cluster aggregates (DLCA) in the continuum regime. The kinetic exponent z in the Epstein regime is found to be z approximately 0.8, lower than its value for both the continuum regime DLCA (z = 1) and for the ballistic cluster aggregation regime (z approximately 2). Cluster size distribution data for Epstein systems are found to scale at large cluster sizes with exponents consistent with the kinetic data. A scaling argument for predicting the kinetic exponent and kernel homogeneity based on the mass or size dependence of the particle velocity and collision cross section is presented and is seen to give accurate results for dilute and intermediate values of particle volume fractions not only for the current study, but also for work done by other researchers with various choices for the aggregation kernel.

Journal Article↗
PubMed2004

Kinetic analysis of the oxidative conversion of the [4Fe-4S]2+ cluster of FNR to a [2Fe-2S]2+ Cluster.

The ability of FNR to sense and respond to cellular O(2) levels depends on its [4Fe-4S](2+) cluster. In the presence of O(2), the [4Fe-4S](2+) cluster is converted to a [2Fe-2S](2+) cluster, which inactivates FNR as a transcriptional regulator. In this study, we demonstrate that approximately 2 Fe(2+) ions are released from the reaction of O(2) with the [4Fe-4S](2+) cluster. Fe(2+) release was then used as an assay of reaction progress to investigate the rate of [4Fe-4S](2+) to [2Fe-2S](2+) cluster conversion in vitro. We also found that there was no detectable difference in the rate of O(2)-induced cluster conversion for FNR free in solution compared to its DNA-bound form. In addition, the rate of FNR inactivation was monitored in vivo by measuring the rate at which transcriptional regulation by FNR is lost upon the exposure of cells to O(2); a comparison of the in vitro and in vivo rates of conversion suggests that O(2)-induced cluster conversion is sufficient to explain FNR inactivation in cells. FNR protein levels were also compared for cells grown under aerobic and anaerobic conditions.

DNA↗
PubMed1984

Iron-sulfur cluster 3 of beef heart succinate-ubiquinone oxidoreductase is a 3-iron cluster.

From a study of the magnetic field dependence of the linear electric field effect (LEFE) in EPR spectroscopy, we demonstrate that iron-sulfur cluster 3 in air-oxidized, beef heart succinate-ubiquinone oxidoreductase (Complex II) is a 3-iron cluster. This suggests that cluster 3 may arise by oxidative degradation from a 4-iron cluster originally present in the enzyme and may be reconverted back into a 4-iron cluster under reducing conditions. Linear electric field effect studies of succinate-reduced Complex II are in accord with the view that cluster 1 is a 2-iron cluster.

Animals↗
PubMed2004

Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques.

Although the characterization of proteins cannot solely rely upon sequence similarity, it has been widely proved that all-vs-all massive sequence comparisons may be an effective approach and a good basis for the prediction of biochemical functions or for the delineation of common shared properties. The program Cluster-C presented here enables a stand-alone and efficient construction of protein families within whole proteomes. The algorithm, which is based on the detection of cliques, ensures a high level of connectivity within the clusters. As opposed to the single transitive linkage method, Cluster-C allows a large number of sequences to be classified in such a way that the multidomain proteins do not produce a chain-grouping effect resulting in meaningless clusters. Moreover, some proteins can be present in several different but relevant clusters, which is of help in the determination of their functional domains. In the present analysis we used the Z-value, an evaluation of the significance of the similarity score, as the criterion for connecting sequences (the user can freely define the threshold of the similarity criterion). The clusters built with a rather low threshold (Z= 14) include more than 97% of the sequences and are consistent with known protein families and PROSITE patterns.

Algorithms↗
PubMed1992

Immunological alterations in cluster headache during remission and cluster period. Comparison with low back pain patients.

Cluster headache is a disorder of unknown origin. Some studies have focused their attention on neuroendocrine derangement, others on immunity. To probe central alterations in cluster headache (CH), immune parameters were investigated in cluster headache patients in comparison to low back pain patients and healthy controls. Increases in peripheral blood monocytes found in remission cluster headache patients may be attributable to chronic central nervous system (hypothalamic?) noradrenergic dysfunction or altered beta-endorphin. Alterations in NK+, CD3+ and CD4+ levels found in cluster period cluster headache and low back pain patients are probably pain or stress-related.

Adult↗
PubMed1990

A statistical method for evaluating suicide clusters and implementing cluster surveillance.

The absence of any standard definition of suicide cluster events hinders understanding of the prevalence of the problem, hinders the development of appropriate public health responses to observed clusters, and ultimately hinders investigation of the mechanisms underlying contagious communication of suicidal behavior. The authors introduce a Poisson mixture model for assessing potential clusters of adolescent suicide, apply that model to the monthly incidence rates of adolescent suicide for one populous US county over the last 11 years, and generate 99% tolerance limits with 95% confidence for the number of suicides which may occur by chance within specific intervals of time in that county. The suicide incidence data showed a remarkable fit to a single Poisson distribution, suggesting it is not unreasonable to consider the cases as randomly-distributed and independent events. The authors conclude that there is no evidence that adolescent suicides occurred in clusters in the place and in the time frame under study, and recommend the Poisson mixture model for ascertaining clusters as well as implementing cluster surveillance.

Adolescent↗
PubMed1999

An empirical comparison of several clustered data approaches under confounding due to cluster effects in the analysis of complications of coronary angioplasty.

In the analysis of binary response data from many types of large studies, the data are likely to have arisen from multiple centers, resulting in a within-center correlation for the response. Such correlation, or clustering, occurs when outcomes within centers tend to be more similar to each other than to outcomes in other centers. In studies where there is also variability among centers with respect to the exposure of interest, analysis of the exposure-outcome association may be confounded, even after accounting for within-center correlations. We apply several analytic methods to compare the risk of major complications associated with two strategies, staged and combined procedures, for performing percutaneous transluminal coronary angioplasty (PTCA), a mechanical means of relieving blockage of blood vessels due to atherosclerosis. Combined procedures are used in some centers as a cost-cutting strategy. We performed a number of population-averaged and cluster-specific (conditional) analyses, which (a) make no adjustments for center effects of any kind; (b) make adjustments for the effect of center on only the response; or (c) make adjustments for both the effect of center on the response and the relationship between center and exposure. The method used for this third approach decomposes the procedure type variable into within-center and among-center components, resulting in two odds ratio estimates. The naive analysis, ignoring clusters, gave a highly significant effect of procedure type (OR = 1.6). Population average models gave marginally to very nonsignificant estimates of the OR for treatment type ranging from 1.6 to 1.2 with adjustment only for the effect of centers on response. These results depended on the assumed correlation structure. Conditional (cluster-specific) models and other methods that decomposed the treatment type variable into among- and within-center components all found no within-center effect of procedure type (OR = 1.02, consistently) and a considerable among-center effect. This among-center variability in outcomes was related to the proportion of patients who receive combined procedures and was found even when conditioned on procedure type (within-center) and other patient- and center-level covariates. This example illustrates the importance of addressing the potential for center effects to confound an outcome-exposure association when average exposure varies across clusters. While conditional approaches provide estimates of the within-cluster effect, they do not provide information about among-center effects. We recommend using the decomposition approach, as it provides both types of estimates.

Angioplasty, Balloon, Coronary↗