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PubMed1996

A metabolic syndrome in whites and African-Americans. The Atherosclerosis Risk in Communities baseline study.

OBJECTIVE: To describe clustering of hypertriglyceridemia, low HDL cholesterol, hypertension, diabetes, and hyperuricemia and its association with fasting insulin, waist-to-hip ratio (WHR), and BMI for African-American and white men and women. RESEARCH DESIGN AND METHODS: Observed frequencies of clusters were compared with those expected in 14,481 participants, 45-64 years of age, of the Atherosclerosis Risk in Communities (ARIC) baseline survey, 1987-1989. Associations of clusters with insulin, central adiposity, and overall obesity, as well as with abnormalities, were analyzed through multiple logistic regression. RESULTS: Clustering beyond chance was observed in all four sex/ethnic groups (P < 0.001), with 7% of the sample presenting 30% of the abnormalities in large clusters (> or = 3 abnormalities per individual). The odds ratio (OR) for the association of each abnormality with clustering of the remaining four ranged from 1.6 to 8.8 (P < 0.01). These odds of clustering were notably large in white women. Of the abnormalities, hypertriglyceridemia demonstrated the highest OR (5.0-8.8) and diabetes had the lower OR in African-American subjects than in white subjects (P < 0.001). Insulin, WHR, and BMI were statistically associated with clustering in all groups (P < 0.001, except for BMI in African-Americans.

Arteriosclerosis↗
PubMed2005

Bioinformatic analyses of bacterial HPr kinase/phosphorylase homologues.

HPr kinase/phosphorylases (HprKs) regulate catabolite repression and sugar transport in Gram-positive bacteria by phosphorylating the small phosphotransferase system (PTS) protein HPr on a serine residue. We identified homologues of HprK in currently sequenced genomes and multiply aligned their sequences in order to perform phylogenetic and motif analyses. Seventy-eight homologues from bacteria and one from an archaeon comprise nine phylogenetic clusters. Some homologues come from bacteria whose genomes contain multiple highly divergent paralogues that cluster loosely together. Many of these proteins are truncated or show little or no identifiable similarity outside of the Walker A nucleotide binding domain. HprK homologues were identified in Gram-negative bacteria that appear to lack PTS permeases, suggesting modes of action and substrates that differ from those characterized in Gram-positive bacteria.

Amino Acid Sequence↗
PubMed2005

Isomer selective infrared spectroscopy of neutral metal clusters.

We report experimental infrared spectra of neutral metal clusters in the gas phase. Multiple photon dissociation of the argon complexes of niobium clusters is used to obtain vibrational spectra in the 80-400 cm(-1) region. The observed spectra for Nb(9)Ar(n) (n=1-4) are different for different values of n. This is explained by the presence of two isomers of Nb(9) that have different affinities towards Ar and the isomer specific infrared spectra are obtained. The structures of the isomers are determined by comparing the observed spectra with the outcome of density-functional theory calculations.

Journal Article↗
PubMed2005

Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm.

In eukaryotes, the primary components of the ribosome are encoded by multicopy nuclear ribosomal RNA (rRNA) genes: 28/26S, 18S, 5.8S, and 5S. Copies of these genes are typically localized within tandem arrays and homogenized within a genome. As a result, nuclear rRNA gene families have become a paradigm of concerted evolution. In filamentous fungi of the subphylum Pezizomycotina, 5S rRNA genes exist as a large and dispersed multigene family, with between 50 and 100 copies per genome. To determine whether these genes defy the concerted evolution paradigm, we examined the patterns of evolution of these genes by using sequences from the complete genomes of four species. Analyses of these sequences revealed (i) multiple 5S gene types within a genome, (ii) interspecies clustering of gene types, (iii) multiple identical gene types shared among species, (iv) multiple pseudogenes within a genome, and (v) presence/absence variation of individual 5S copies in comparisons of closely related species. These results demonstrate that the 5S family in these species is characterized by birth-and-death evolution under strong purifying selection. Furthermore, our results suggest that birth-and-death evolution occurs at different rates in the genera examined, and that the multiplication and movement of 5S genes across the genome are highly dynamic. As such, we hypothesize that a mechanism resembling retroposition controls 5S rRNA gene amplification, dispersal, and integration in the genomes of filamentous fungi.

Aspergillus nidulans↗
PubMed2006

Germ-cell cluster formation in the telotrophic meroistic ovary of Tribolium castaneum (Coleoptera, Polyphaga, Tenebrionidae) and its implication on insect phylogeny.

Tribolium castaneum has telotrophic meroistic ovarioles of the Polyphaga type. During larval stages, germ cells multiply in a first mitotic cycle forming many small, irregularly branched germ-cell clusters which colonize between the anterior and posterior somatic tissues in each ovariole. Because germ-cell multiplication is accompanied by cluster splitting, we assume a very low number of germ cells per ovariole at the beginning of ovariole development. In the late larval and early pupal stages, we found programmed cell death of germ-cell clusters that are located in anterior and middle regions of the ovarioles. Only those clusters survive that rest on posterior somatic tissue. The germ cells that are in direct contact with posterior somatic cells transform into morphologically distinct pro-oocytes. Intercellular bridges interconnecting pro-oocytes are located posteriorly and are filled with fusomes that regularly fuse to form polyfusomes. Intercellular bridges connecting pro-oocytes to pro-nurse cells are always positioned anteriorly and contain small fusomal plugs. During pupal stages, a second wave of metasynchronous mitoses is initiated by the pro-oocytes, leading to linear subclusters with few bifurcations. We assume that the pro-oocytes together with posterior somatic cells build the center of determination and differentiation of germ cells throughout the larval, pupal, and adult stages. The early developmental pattern of germ-cell multiplication is highly similar to the events known from the telotrophic ovary of the Sialis type. We conclude that among the common ancestors of Neuropterida and Coleoptera, a telotrophic meroistic ovary of the Sialis type evolved, which still exists in Sialidae, Raphidioptera, and a myxophagan Coleoptera family, the Hydroscaphidae. Consequently, the telotrophic ovary of the Polyphaga type evolved from the Sialis type.

Animals↗
PubMed2004

Cooperative effects in the activation of molecular oxygen by anionic silver clusters.

A novel size dependence in the adsorption reaction of multiple O2 molecules onto anionic silver clusters Agn- (n = 1-5) is revealed by gas-phase reaction studies in an rf-ion trap. Ab initio theoretical modeling based on DFT method provides insight into the reaction mechanism and finds cooperative electronic and structural effects to be responsible for the size selective reactivity of Agn- clusters toward one or more O2. In particular, Agn- clusters with odd n have paired electrons and therefore bind one O2 only weakly, but they are simultaneously activated to adsorb a strongly bound second oxygen molecule. For the clusters Ag3O4- and Ag5O4-, this cooperative effect results in a superoxo-like, doubly bound O2 subunit with potentially high activity in catalytic silver cluster oxidation processes.

Journal Article↗
PubMed2002

Geographical and seasonal correlation of multiple sclerosis to sporadic schizophrenia.

BACKGROUND: Clusters by season and locality reveal a striking epidemiological overlap between sporadic schizophrenia and multiple sclerosis (MS). As the birth excesses of those individuals who later in life develop schizophrenia mirror the seasonal distribution of Ixodid ticks, a meta analysis has been performed between all neuropsychiatric birth excesses including MS and the epidemiology of spirochaetal infectious diseases. RESULTS: The prevalence of MS and schizophrenic birth excesses entirely spares the tropical belt where human treponematoses are endemic, whereas in more temperate climates infection rates of Borrelia garinii in ticks collected from seabirds match the global geographic distribution of MS. If the seasonal fluctuations of Lyme borreliosis in Europe are taken into account, the birth excesses of MS and those of schizophrenia are nine months apart, reflecting the activity of Ixodes ricinus at the time of embryonic implantation and birth. In America, this nine months' shift between MS and schizophrenic births is also reflected by the periodicity of Borrelia burgdorferi transmitting Ixodes pacificus ticks along the West Coast and the periodicity of Ixodes scapularis along the East Coast. With respect to Ixodid tick activity, amongst the neuropsychiatric birth excesses only amyotrophic lateral sclerosis (ALS) shows a similar seasonal trend. CONCLUSION: It cannot be excluded at present that maternal infection by Borrelia burgdorferi poses a risk to the unborn. The seasonal and geographical overlap between schizophrenia, MS and neuroborreliosis rather emphasises a causal relation that derives from exposure to a flagellar virulence factor at conception and delivery. It is hoped that the pathogenic correlation of spirochaetal virulence to temperature and heat shock proteins (HSP) might encourage a new direction of research in molecular epidemiology.

Journal Article↗
PubMed1994

Complete genomic sequence and patterns of transcription of a member of an unusual family of closely related, chromosomally dispersed Ig gene clusters in Raja.

Ig genes in cartilaginous fish are organized in clusters. This unique form of organization suggests major differences in the regulation of the segmental rearrangement mechanism from that found in mammals and other higher vertebrates. The complete DNA sequence of an IgX-type cluster in the species Raja eglanteria is defined, and shown to consist of four rearranging segmental elements and three constant region exons. Using fluorescence in situ hybridization it is shown that Raja clusters are present at multiple sites within the genome, and that there is no apparent relationship between the chromosomally dispersed IgX clusters and a second isotype (IgM type) in this species. Comprehensive examination of sequence motifs associated with transcription regulation reveals an abundance of short sequences closely resembling those found in higher vertebrate Ig and other genes. However, the linear relationship of these motifs differs markedly from that associated with regulation of expression of the mammalian Ig gene locus. Additional studies of the transcription products of the IgX gene loci emphasize the diversity of transcription and processing of these genes. Considerable variation was noted in the processing of putative IgX transcripts, including the detection of a heretofore unrecognized form containing at least four additional Ig-like domains. These results have profound significance in terms of understanding the selective expression and the evolutionary diversification of Ig genes.

Animals↗
PubMed2002

Predictors of clustering of tuberculosis in Greater Vancouver: a molecular epidemiologic study.

BACKGROUND: The understanding of how tuberculosis is transmitted can be improved by combining DNA fingerprinting of Mycobacterium tuberculosis with conventional epidemiologic methods. We used such techniques to determine the predictors of clustering of identical isolates from tuberculosis patients in Vancouver. METHODS: We used the restriction fragment length polymorphism (RFLP) technique and, if necessary, spoligotyping to determine DNA patterns of M. tuberculosis isolates from all patients with newly diagnosed tuberculosis in Greater Vancouver reported to the Division of Tuberculosis Control from January 1995 to March 1999. Isolates were considered to be part of a cluster if they had an identical DNA pattern. We also collected demographic and epidemiologic data. Predictors associated with being in a cluster were analyzed in a multivariate logistic regression model. RESULTS: Isolates from 793 patients (430 men) were identified; 137 (17.3%) were considered to be in clusters. After adjustment for multiple potential predictors, we found that the following patients were more likely to be part of a cluster: Canadian-born Aboriginals (v. foreign-born patients) (adjusted odds ratio [OR] 6.0, 95% confidence interval [CI] 3.0-11.7), Canadian-born non-Aboriginals (v. foreign-born patients) (adjusted OR 3.6, 95% CI 2.1-6.3), and injection drug users (v. patients who did not inject drugs) (adjusted OR 3.9, 95% CI 1.9-8.1). Patients with a prior history of tuberculosis were less likely to be part of a cluster than were patients with no history of tuberculosis (adjusted OR 0.3, 95% CI 0.1-0.8). INTERPRETATION: Our findings indicate the need to target groups at high risk of tuberculosis more aggressively to prevent transmission and to treat latent infection. DNA fingerprinting may be a useful adjunct to conventional epidemiologic methods to monitor the transmission of tuberculosis in an inner-city setting.

Adult↗
PubMed2006

Computational study of multiple-decker sandwich and rice-ball structures of neutral titanium-benzene clusters.

Density functional theory calculations were applied to systematically and directly compare the relative energetic stability of multiple-decker sandwich and rice-ball structures for a variety of neutral Ti(m)Bz(n) clusters (m = 1-4, n = 1-5). Almost all structures favored the multiple-decker sandwich structure, as observed experimentally for early transition metals. The strength of each metal-benzene interaction averages 37 kcal/mol and remains relatively constant for sandwiches with three or more Ti atoms. The most stable smaller rice-ball structures did not have eta(6)-Bz bound to a single metal atom. Instead, the preferred coordination was having the plane of the benzene molecule parallel to a Ti(2) bond or a Ti(3) face, leading to some distortion of the benzene ring. The larger rice-ball structures, on the other hand, preferred to weaken the metal-metal bonds and retain eta(6)-Bz bound to a single metal atom, a structural motif shared with sandwiches.

Benzene↗
PubMed2002

Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.

Dimethyl sulphide dehydrogenase catalyses the oxidation of dimethyl sulphide to dimethyl sulphoxide (DMSO) during photoautotrophic growth of Rhodovulum sulfidophilum. Dimethyl sulphide dehydrogenase was shown to contain bis(molybdopterin guanine dinucleotide)Mo, the form of the pterin molybdenum cofactor unique to enzymes of the DMSO reductase family. Sequence analysis of the ddh gene cluster showed that the ddhA gene encodes a polypeptide with highest sequence similarity to the molybdopterin-containing subunits of selenate reductase, ethylbenzene dehydrogenase. These polypeptides form a distinct clade within the DMSO reductase family. Further sequence analysis of the ddh gene cluster identified three genes, ddhB, ddhD and ddhC. DdhB showed sequence homology to NarH, suggesting that it contains multiple iron-sulphur clusters. Analysis of the N-terminal signal sequence of DdhA suggests that it is secreted via the Tat secretory system in complex with DdhB, whereas DdhC is probably secreted via a Sec-dependent mechanism. Analysis of a ddhA mutant showed that dimethyl sulphide dehydrogenase was essential for photolithotrophic growth of Rv. sulfidophilum on dimethyl sulphide but not for chemo-trophic growth on the same substrate. Mutational analysis showed that cytochrome c2 mediated photosynthetic electron transfer from dimethyl sulphide dehydrogenase to the photochemical reaction centre, although this cytochrome was not essential for photoheterotrophic growth of the bacterium.

Alphaproteobacteria↗
PubMed2000

Occurrence of a Salmonella enterica serovar typhimurium DT104-like antibiotic resistance gene cluster including the floR gene in S. enterica serovar agona.

Recently a chromosomal locus possibly specific for Salmonella enterica serovar Typhimurium DT104 has been reported that contains a multiple antibiotic resistance gene cluster. Evidence is provided that Salmonella enterica serovar Agona strains isolated from poultry harbor a similar gene cluster including the newly described floR gene, conferring cross-resistance to chloramphenicol and florfenicol.

Animals↗
PubMed2006

Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.

Ortholog identification is a crucial first step in comparative genomics. Here, we present a rapid method of ortholog grouping which is effective enough to allow the comparison of many genomes simultaneously. The method takes as input all-against-all similarity data and classifies genes based on the traditional hierarchical clustering algorithm UPGMA. In the course of clustering, the method detects domain fusion or fission events, and splits clusters into domains if required. The subsequent procedure splits the resulting trees such that intra-species paralogous genes are divided into different groups so as to create plausible orthologous groups. As a result, the procedure can split genes into the domains minimally required for ortholog grouping. The procedure, named DomClust, was tested using the COG database as a reference. When comparing several clustering algorithms combined with the conventional bidirectional best-hit (BBH) criterion, we found that our method generally showed better agreement with the COG classification. By comparing the clustering results generated from datasets of different releases, we also found that our method showed relatively good stability in comparison to the BBH-based methods.

Algorithms↗
PubMed2001

Quantum/classical studies of photodissociation and reaction dynamics in clusters.

In this paper, a multiple configurational time-dependent self-consistent field (TDSCF) approach for studying photodissociation and reaction dynamics is described. This approach has been applied to studies of several benchmark systems and is found to provide an accurate description of the reactions. The focus of the present work is on investigations of processes in cluster environments. Specifically, the dynamics of the O(3P) + HCl reaction and H2O photodissociation dynamics in isolation and in Van der Waals complexes with one argon atom are compared. The nature and importance of quantum mechanical effects in these systems are investigated through an analysis of the results of the quantum/classical simulations and a comparison of these results with those obtained from previously reported experimental and classical studies on these systems. It is found that, although the effects of complexation are subtle, they are not negligible. In addition, most of them can be understood in terms of kinematic and steric factors, although electronic effects cannot be dismissed.

Journal Article↗
PubMed2004

White-matter diffusion anisotropy after chemo-irradiation: a statistical parametric mapping study and histogram analysis.

The aim of the study was to evaluate white-matter (WM) diffusion anisotropy in medulloblastoma survivors after cranial irradiation and chemotherapy using voxel-based analysis with SPM99 and fractional anisotropy (FA) histogram-derived indices, and to identify quantitative indices for detecting and monitoring children with treatment-induced white-matter injury. Familywise error rate (FWE) that corrects for multiple comparisons was used to locate statistically significant regions of P < 0.05 in voxel-based analysis. Subsequently, the false discovery rate (FDR) controlling procedure (corrected P < 0.05) was used. FA map histogram analysis of histogram-derived indices, mean FA, mean FA peak height, and peak location was performed. Two-sample t test was used in all analyses. Using FWE-corrected P < 0.05, there was a cluster of reduced anisotropy in the periventricular white matter lateral to the left ventricular atrium. When FDR-corrected P < 0.05 was used, there were multiple clusters of reduced anisotropy in the periventricular white matter, the corpus callosum, and corona radiata. Simplified voxel-based morphometry (VBM)-like analysis of cerebrospinal fluid (CSF) did not show significant differences between patient and control subjects. 'White-matter FA map' histogram showed significant reduction in mean FA and mean FA peak location and significant increase in mean FA peak height in the patient group compared to control subjects (P = 0.003, P = 0.003, and P = 0.014, respectively). This approach of quantifying FA can be applied to characterize anisotropy in the white matter after cranial irradiation and chemotherapy and can potentially be used to detect and monitor treatment-induced neurotoxicity.

Adolescent↗
PubMed1998

Cortical and subcortical influences on clustering and switching in the performance of verbal fluency tasks.

Impairments on lexical and semantic fluency tasks occur in both cortical and subcortical dementia. Recent reports that the average size of phonemic and semantic clusters is reduced in Alzheimer's disease (AD), but not in Parkinson's disease (PD) could support the hypothesis that in AD verbal fluency deficits arise from degraded memory storage while in PD the same impairments result from defective retrieval. In the present study, patients with AD, PD with dementia, or Huntington's disease produced fewer words, fewer switching responses and smaller semantic cluster sizes. Patients with multiple sclerosis, regardless of whether or not they were demented, produced fewer words and switching responses, but normal size clusters, and patients with PD without dementia performed normally on all fluency measures. These results indicate that reductions in cluster size on verbal fluency tests are best interpreted as changes in the efficiency of access to lexical and semantic memory stores. The findings are also consistent with the idea that patterns of cognitive impairment may differ among diseases that result in subcortical dementia.

Adult↗
PubMed1987

Structural analysis of an HLA-B27 population variant, B27f. Multiple patterns of amino acid changes within a single polypeptide segment generate polymorphism in HLA-B27.

The structure of a new HLA-B27 variant, B27f, distinguishable from other HLA-B27 subtypes by isoelectric focusing and serologic criteria, has been established by comparative peptide mapping and radiochemical sequence analysis. HLA-B27f differs from the major B27.1 subtype in three clustered amino acid replacements: Asp74, Asp77, and Leu81 in B27.1 are changed to Tyr74, Asn77, and Ala81, respectively in B27f. This pattern of differences is analogous to that of HLA-B27.2 in that this subtype also differs from B27.1 in multiple clustered substitutions within the same segment. Thus, polymorphism within the HLA-B27 system is being achieved by introducing different sets of amino acid changes within a particular short segment of the alpha 1 domain. The most likely mechanism for the introduction of multiple changes within this segment is a nonreciprocal recombination event, such as gene conversion. The structural analogies and ethnic distribution of B27f and B27.2 as compared with those of B27.3, and B27.4 support a dynamic model of HLA-B27 evolution in which polymorphism has been created after the separation of the major ethnic groups. In this model, a Caucasian branch would be characterized by subtypes differing from B27.1 in a few changes within the alpha 1 domain, which were probably generated by single genetic steps. An Oriental branch would include those subtypes which differ from B27.1 by changes in both alpha 1 and alpha 2, involving multiple genetic steps for their generation.

Amino Acid Sequence↗
PubMed1995

Susceptibility to multiple sclerosis and the immunoglobulin heavy chain variable region.

A haplotype marker consisting of three biallelic restriction fragment length polymorphism (RFLP) loci from the VH-2 variable gene family was examined in 124 families with sibling pairs concordant for multiple sclerosis, 178 unrelated patients and 159 unaffected controls to investigate the role of the immunoglobulin heavy chain gene cluster in susceptibility to multiple sclerosis. Evidence for linkage was assessed using the affected sibling pair method of identity by descent, modified to allow for haplotype sharing on a probabilistic basis in families where haplotypes could not be assigned with certainty. The estimated probabilities of affected siblings sharing 0, 1 or 2 haplotypes were Z0 = 0.20, Z1 = 0.45, Z2 = 0.35. This deviation from the expected sharing probabilities of Z0 = 0.25, Z1 = 0.5, Z2 = 0.25 provides evidence for weak linkage (P < 0.05; equivalent to a lod score of 0.84); however, no significant allelic or haplotypic association was observed. Linkage without a population association suggests that a gene encoded on 14q confers susceptibility to multiple sclerosis, although this is not any of the existing VH-2 polymorphisms.

Alleles↗