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At least 343 records · Page 19Linked to original sources
PubMed2004

Statistical evaporation of rotating clusters. III. Molecular clusters.

Unimolecular evaporation of weakly bound clusters made of rigid molecules is considered from the points of view of statistical theories and molecular dynamics simulations. We explicitly work out expressions for the kinetic energy released and product angular momentum distributions within the sphere+sphere and sphere+linear rigid body assumptions of phase space theory (PST). Various approximations are investigated, including the shape of the interaction potential between the two fragments and the anharmonicity of the vibrational density of states. The comparison between phase space theory and simulation for nitrogen and methane clusters shows a quantitative agreement, thereby suggesting that PST is accurate in predicting statistical observables in a wide range of systems under various physical conditions.

Journal Article↗
PubMed2005

Automated generation of coupled-cluster diagrams: implementation in the multireference state-specific coupled-cluster approach with the complete-active-space reference.

An algorithm for generation of the spin-orbital diagrammatic representation, the corresponding algebraical formulas, and the computer code of the coupled-cluster (CC) method with an arbitrary level of the electronic excitations has been developed. The method was implemented in the general case as well as for specific application in the state-specific multireference coupled-cluster theory (SSMRCC) based on the concept of a "formal reference state." The algorithm was tested in SSMRCC calculations describing dissociation of a single bond and in calculations describing simultaneous dissociation of two single bonds--the problem requiring up to six-particle excitations in the CC operator.

Journal Article↗
PubMed2000

Dynamic scaling in one-dimensional cluster-cluster aggregation

We study the dynamic scaling properties of an aggregation model in which particles obey both diffusive and driven ballistic dynamics. The diffusion constant and the velocity of a cluster of size s follow D(s) approximately s(gamma) and v(s) approximately s(delta), respectively. We determine the dynamic exponent and the phase diagram for the asymptotic aggregation behavior in one dimension in the presence of mixed dynamics. The asymptotic dynamics is dominated by the process that has the largest dynamic exponent with a crossover that is located at delta=gamma-1. The cluster size distributions scale similarly in all cases but the scaling function depends continuously on gamma and delta. For the purely diffusive case the scaling function has a transition from exponential to algebraic behavior at small argument values as gamma changes sign, whereas in the drift dominated case the scaling function always decays exponentially.

Journal Article↗
PubMedDate not supplied

Conserved expression domains for genes upstream and within the HoxA and HoxD clusters suggests a long-range enhancer existed before cluster duplication.

The posterior HoxA and HoxD genes are essential in appendicular development. Studies have demonstrated that a "distal limb enhancer," remotely located upstream of the HoxD complex, is required to drive embryonic autopod expression of the posterior Hox genes as well as the two additional non-Hox genes in the region: Evx2 and Lnp. Our work demonstrates a similar mode of regulation for Hoxa13 and four upstream genes: Evx1, Hibadh, Tax1bp, and Jaz1. These genes all show embryonic (E11.5-E13.5) distal limb and genital bud expression, suggesting the existence of a nearby enhancer influencing the expression of a domain of genes. Comparative sequence analysis between homologous human and mouse genomic sequence upstream of Hoxa13 revealed a remote 2.25-kb conserved noncoding sequence (mmA13CNS) within the fourth intron of the Hibadh gene. mmA13CNS shares a common 131-bp core identity within a conserved noncoding sequence upstream of Hoxd13, which is located within the previously identified distal limb enhancer critical region. To test the function of this conserved sequence, we created mmA13CNS-Hsp86-lacZ transgenic mice. mmA13CNS directed a wide range of tissue expression, including the central nervous system, developing olfactory tissue, limb, and genital bud. Limb and genital bud expression directed by mmA13CNS is not identical to the patterns exhibited by Hoxa13/Evx1/Hibadh/Tax1bp1/Jaz1, suggesting that mmA13CNS is not sufficient to fully recapitulate their expression in those tissues. The Evx1- and Evx2-like central nervous system expression observed in these mice suggests that the long-range regulatory element(s) for the Hox cluster existed before the cluster duplication.

Animals↗
PubMed1997

Analysis of the Bacillus subtilis S10 ribosomal protein gene cluster identifies two promoters that may be responsible for transcription of the entire 15-kilobase S10-spc-alpha cluster.

We have sequenced a previously uncharacterized region of the Bacillus subtilis S10 ribosomal protein gene cluster. The new segment includes genes for S10, L3, L4, L23, L2, S19, L22, S3, and part of L16. These B. subtilis genes map in the same order as the genes in the Escherichia coli S10 ribosomal protein operon. Two potential promoter sequences were identified, one approximately 200 bases and the other approximately 140 bases upstream of the S10 gene. The activities of the two promoters were demonstrated by primer extension analysis, in vitro transcription experiments, and in vivo promoter fusion plasmid studies. In agreement with previous reports, our Northern analysis of exponentially growing cells failed to identify terminators or other active promoters within the S10-spc-alpha region. Our observations suggest that the two S10 promoters reported here are responsible for transcribing a 15-kb-long transcript for all of the genes in the B. subtilis S10, spc, and alpha clusters.

Amino Acid Sequence↗
PubMed1999

The mithramycin gene cluster of Streptomyces argillaceus contains a positive regulatory gene and two repeated DNA sequences that are located at both ends of the cluster.

Sequencing of a 4.3-kb DNA region from the chromosome of Streptomyces argillaceus, a mithramycin producer, revealed the presence of two open reading frames (ORFs). The first one (orfA) codes for a protein that resembles several transport proteins. The second one (mtmR) codes for a protein similar to positive regulators involved in antibiotic biosynthesis (DnrI, SnoA, ActII-orf4, CcaR, and RedD) belonging to the Streptomyces antibiotic regulatory protein (SARP) family. Both ORFs are separated by a 1.9-kb, apparently noncoding region. Replacement of the mtmR region by an antibiotic resistance cassette completely abolished mithramycin biosynthesis. Expression of mtmR in a high-copy-number vector in S. argillaceus caused a 16-fold increase in mithramycin production. The mtmR gene restored actinorhodin production in Streptomyces coelicolor JF1 mutant, in which the actinorhodin-specific activator ActII-orf4 is inactive, and also stimulated actinorhodin production by Streptomyces lividans TK21. A 241-bp region located 1.9 kb upstream of mtmR was found to be repeated approximately 50 kb downstream of mtmR at the other end of the mithramycin gene cluster. A model to explain a possible route for the acquisition of the mithramycin gene cluster by S. argillaceus is proposed.

Amino Acid Sequence↗
PubMed2004

Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster.

In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes (leuA, -B, -C, and -D) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the variability in the position of the leucine cluster in the chromosome may be interpreted as resulting from independent insertions from an ancestral plasmid-borne leucine gene. These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome.

Binding Sites↗
PubMed2003

Determination of the optimum cluster parameters in a clustered free-space optical interconnect.

A model for a clustered free-space optical interconnect is developed and is used to determine the maximum array density that can be achieved, together with the optimal cluster parameters that maximize this density. This model includes misalignment tolerance and the impact of multimode vertical-cavity surface-emitting laser beams. We find that for short interconnect distances, the maximum channel density is limited by the speed of the relay lenses, but as the interconnect distance increases, geometric aberrations become the limiting factor. We also determine the interconnect distance below which a micro-channel relay is more suitable and the distance above which a single-lens solution is adequate.

Journal Article↗
PubMed1992

Functional and morphological studies of mitochondria exposed to undecagold clusters: biologic surfaces labeling with gold clusters.

This study reports morphological and functional alterations observed in respiring isolated mitochondria when they are exposed to nonpenetrating, positive electrostatically charged synthetic undecagold clusters. Modification of the undecagold clusters positive charges change or prevent the functional effects and the binding to the outside surface of the mitochondria. The mitochondrial functional alterations are dependent on the oxidative phosphorylation capacity of the isolated organelles. The results of these experiments indicate that artificial undecagold may be useful to explore the molecular mechanisms of biological energy transducers which require electric charges separation, ionic fluxes, and electric surface properties.

Animals↗
PubMed2005

Association Cluster Detector: a tool for heuristic detection of significance clusters in whole-genome scans.

UNLABELLED: Whole genome scans analyze large sets of genetic markers, mainly single nucleotide polymorphisms, over the entire genome in order to find variants and regions associated with complex traits so these can be further investigated. Analyzing the results of such scans becomes difficult due to multiple testing problems and to the genomic distributions of recombination, linkage disequilibrium and true associations, which generate an extremely complex network of dependences between markers. Here we present Association Cluster Detector (ACD), a simple tool aiming to ease the analysis of the results of whole genome scans. ACD facilitates correction for multiple tests using several standard procedures and implements a sliding-window heuristic method that helps in detecting potentially interesting candidate regions by exploiting the property of non-random distribution of significantly associated markers. AVAILABILITY: The tool can be downloaded from http://www.upf.es/cexs/recerca/bioevo/softanddata.htm

Algorithms↗
PubMed1986

The distribution of type I (insulin-dependent) diabetes mellitus by age, sex, secular trend, seasonality, time clusters, and space-time clusters: evidence from Montreal, 1971-1983.

The etiology of insulin-dependent diabetes mellitus remains obscure. In an attempt to clarify some aspects of the epidemiology, including its compatibility with an acute infectious process, the authors undertook in-depth analyses of childhood cases accumulated in a population-based register in Montreal during the period from 1971-1983. Incidence rates increased with age until puberty, at which point they plateaued and decreased. There was no overall difference in incidence between males and females; however, the rate for females peaked approximately two years before the rate for males. While there was some variation over time, there was no evidence of a long-term trend, nor was the yearly variation impressive in magnitude. The findings further indicate that the disease is not characterized by explosive outbreaks. There was slight seasonality, with a 28% higher rate of onset in fall and winter than in spring and summer. There was some evidence of space-time clustering in 1971-1973, but not thereafter. Taken as a whole, these findings do not support the hypothesis that a significant portion of insulin-dependent diabetes is caused by an acute infectious process.

Adolescent↗
PubMed2005

Familial cluster headache. Is atypical cluster headache in family members part of the clinical spectrum?

Familial cluster headache (CH) was analysed in 21 Swedish families. Diagnosis was made according to The International Classification of Headache Disorders 2004. We identified 55 affected, of whom 42 had episodic or chronic CH, one had probable CH and 12 had atypical symptoms. The atypical cases did not fulfil the diagnostic criteria for CH, but had clinical symptoms with more resemblance to CH than to migraine or other trigeminal autonomic cephalgia syndromes. The overall male : female ratio was 1.8:1. The overall mean age at onset was significantly lower in the second/third generation than in the first generation (mean age at onset 22 vs. 31 years, SD +/- 7 vs. 13 years; P < 0.01). This may be anticipation or selection bias, since individuals with late age at onset from the second/third generation may not yet have symptoms. The prevalence of migraine was 24% (13/55), i.e. similar to the prevalence in the general population. The high incidence of atypical CH cases in the Swedish families with other members affected with CH may suggest that the spectrum of CH is broader than previously thought. We suggest that atypical CH in CH families may represent an expanded spectrum of the disease with a common aetiology, i.e. a common genetic background.

Adult↗
PubMed1995

Case-control study on the epidemiology of cluster headache. I: Etiological factors and associated conditions. Italian Cooperative Study Group on the Epidemiology of Cluster Headache (ICECH).

The etiological and physiopathological mechanisms of cluster headache (CH) are still largely unknown. The majority of the studies published on the possible risk factors and conditions associated with CH rely on either anecdotal observations or generalizations and have not been supported by serious epidemiological investigations. The aim of this case-control study was to evaluate the real association of life habits and general risk factors with CH. CH was associated only with cigarette smoking, head trauma and a positive family history for headache. Further epidemiologic studies are probably necessary in order to find clues to CH etiology.

Adult↗
PubMed2004

Probing ionic association on metal oxide clusters by pulsed field gradient NMR spectroscopy: the example of Sn12-oxo clusters.

Pulsed field gradient (1)H NMR spectroscopy has been applied to investigate the association behavior of the Sn(12)-oxo cluster macrocation [(BuSn)(12)O(14)(OH)(6)](2+) with two different and smaller anions, p-toluenesulfonate (PTS(-)) and diphenylphosphinate (Ph(2)PO(2) (-)). By monitoring the translational diffusion coefficients of the various species involved, it is shown that the association depends on the anion involved and on the solvent used. Moreover, the possibility to individually monitor the diffusion characteristics of multiple anionic and cationic species in mixtures, by virtue of resolved (1)H resonances available from each species, allows us to evidence the occurrence of ion exchange in such systems. Thus when [(BuSn)(12)O(14)(OH)(6)](PTS)(2) is mixed with two equivalents of Ph(2)PO(2)NMe(4), PTS(-) is displaced by Ph(2)PO(2) (-), highlighting the greater affinity of the organotin macrocation for the diphenylphosphinate. This example clearly illustrates the potential of pulsed field gradient (1)H NMR spectroscopy in inorganic/organometallic chemistry, to follow preferential ion pairing in multi-ion systems at the level of each individually charged species.

Hydroxides↗
PubMed2005

Reactivity of alkynes containing alpha-hydrogen atoms with a triruthenium hydrido carbonyl cluster: alkenyl versus allyl cluster derivatives.

The reactions of the hydrido-triruthenium cluster complex [Ru3(mu-H)(mu3-kappa(2)-HNNMe2)(CO)9] (1; H2NNMe2 = 1,1-dimethylhydrazine) with alkynes that have alpha-hydrogen atoms give trinuclear derivatives containing edge-bridging allyl or face-capping alkenyl ligands. Under mild conditions (THF, 70 degrees C) the isolated products are as follows: [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(3)-1-syn-Me-3-anti-EtC3H3)(mu-CO)2(CO)6] (2) and [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(3)-1-syn-Me-3-syn-EtC3H3)(mu-CO)2(CO)6] (3) from 3-hexyne; [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(3)-3-anti-PhC3H4)(mu-CO)2(CO)6] (4), [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(2)-MeCCHPh)(mu-CO)2(CO)6] (5) and [Ru3(mu3-kappa(2)-HNNMe2)(mu3-kappa(2)-PhCCHMe)(mu-CO)2(CO)6] (6) from 1-phenyl-1-propyne; [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(2)-3-anti-PrC3H4)(mu-CO)2(CO)6] (7), [Ru3(mu3-kappa(2)-HNNMe2)(mu3-kappa(2)-BuCCH2)(mu-CO)2(CO)6] (8), and [Ru3(mu3-kappa(2)-HNNMe2)(mu3-kappa(2)-HCCHBu)(mu-CO)2(CO)6] (9) from 1-hexyne; [Ru3(mu3-kappa(2)-HNNMe2)(mu3-kappa(2)-HOH2CCCH2)(mu-CO)2(CO)6] (10) from propargyl alcohol; and [Ru3(mu3-kappa(2)-HNNMe2)(mu3-kappa(2)-MeOCH2CCH2)(mu-CO)2(CO)6] (11) from 3-methoxy-1-propyne. The regioselectivity of these reactions depends upon the nature of the alkyne reagent, which affects considerably the kinetic barriers of important reaction steps and the stability of the final products. It has been established that the face-capped alkenyl derivatives are not precursors to the allyl products, which are formed via edge-bridged alkenyl intermediates. At higher temperature (toluene, 110 degrees C), the complexes that have allyl ligands with an anti substituent are isomerized into allyl derivatives with that substituent in the syn position, for example, 4 into [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(3)-3-syn-PhC3H4)(mu-CO)2(CO)6] (14). The diene complex [Ru3(mu-H)(mu3-kappa(2)-HNNMe2)(mu-kappa(4)-trans-EtC4H5)(CO)7] (13) has been obtained from the thermolysis of compounds 2 and 7 at 110 degrees C (3 and [Ru3(mu3-kappa(2)-HNNMe2)(mu-kappa(2)-3-syn-PrC3H4)(mu-CO)2(CO)6] (12) are also formed in these reactions). A DFT theoretical study has allowed a comparison of the thermodynamic stabilities of isomeric compounds and has helped rationalize the experimental results. Mechanistic proposals for the synthesis of the allyl complexes and their isomerization processes are also provided.

Journal Article↗
PubMed1992

A second gene (qutH) within the Aspergillus nidulans-quinic-acid utilisation gene cluster encodes a protein with a putative zinc-cluster motif.

A sequence of 3299 nt, contiguous with the previously sequenced quinate permease-encoding (qutD) gene and encompassing the dehydroshikimate dehydratase-encoding (qutC) gene, has been determined. Northern-blot analysis detected (i) a quinate-inducible mRNA of the expected size for the qutC gene, and (ii) a quinate-inducible mRNA of 1.45 kb divergently transcribed away from qutC towards qutD. Computer-aided sequence analysis identified an ORF of 1047 nt corresponding to the qutC gene encoding dehydroshikimate dehydratase. In addition, a genetically uncharacterized 1188-nt gene, designated qutH and containing a putative intron of 61 nt, was identified between qutC and qutD. The inferred protein sequence encoded by qutH contains a putative 'zinc cluster' motif and has a low (16%) but significant similarity with the DNA-directed DNA polymerase of hepatitis B virus. The results are interpreted as being consistent with the view that the qutH gene encodes a DNA-binding protein, possibly involved in the regulation of genes essential for the utilisation of protocatechuic acid.

Alcohol Oxidoreductases↗
PubMed1999

Metabolic diversity in myxobacteria: identification of the myxalamid and the stigmatellin biosynthetic gene cluster of Stigmatella aurantiaca Sg a15 and a combined polyketide-(poly)peptide gene cluster from the epothilone producing strain Sorangium cellulosum So ce90.

Myxobacterial strains producing polyketides (PKs) assumed to be biosynthesized by a type I polyketide synthase (PKS) were analysed. Myxobacteria also produce a variety of polypeptides (PP) and PKs with incorporated amino acids ('mixed PK-PP'). In order to be able to identify the biosynthetic gene clusters for these metabolites a PCR based approach has been developed to clone ketosynthase (KS) domains of PKS genes from these organisms. Conserved regions of peptide synthetases of the non-ribosomal type (NRPS) were also amplified via PCR. KS fragments from Stigmatella aurantiaca Sg a15 were used for chromosomal gene inactivation experiments resulting in a series of mutants including such that were unable to produce stigmatellins and myxalamids. A NRPS fragment and PKS fragments from Sorangium cellulosum So ce90 were used to identify cosmids hybridizing with both types of probes from a genomic library. Both a NRPS and a PKS fragment were cloned and sequenced from a relatively short restriction fragment of one of these cosmids. The method described here should be very useful to clone and identify PKS, NRPS and mixed PKS-NRPS from myxobacteria in general and thereby open opportunities to use the biochemical diversity of these bacteria for genetic engineering and combinatorial biosynthesis.

Amino Acid Sequence↗