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PubMed2004

Comparative genomic analysis of vertebrate Hox3 and Hox4 genes.

We used a comparative genomic approach to identify putative cis-acting regulatory sequences of the zebrafish hoxb3a and hoxb4a genes. We aligned genomic sequences spanning the clustered Hoxb1 to Hoxb5 genes from pufferfish, mice, and humans with the zebrafish hoxba and hoxbb cluster sequences. We identified multiple blocks of conserved sequences in non-coding regions within and surrounding the Hoxb3/b4 gene locus; a subset of these blocks are conserved in the zebrafish hoxbb cluster, despite loss of hoxb3/b4 genes. Overall, we find that the architecture of the Hoxb3/b4 loci and of the conserved sequence elements is very similar in teleosts and mammals. Our analyses also revealed two alternative transcripts of the zebrafish hoxb3a gene and an exon sequence unusually located 10 kb upstream of adjacent hoxb4a; an equivalent murine Hoxb3 exon has not yet been confirmed. We show that many of the Hoxb3/b4 conserved non-coding sequences correlate with functional neural enhancers previously described in the mouse. Further, within the conserved non-coding sequences we have identified binding sites for transcription factors, including Kreisler/Valentino, Krox20, Hox, and Pbx, some of which had not been previously described for the mouse. Finally, we demonstrate that the regulatory sequences of zebrafish hoxa3a are divergent with respect to the mouse ortholog Hoxa3, or the paralog hoxb3a. Despite limited conservation of regulatory sequences, zebrafish hoxa3a and hoxb3a genes share very similar expression profiles.

Animals↗
PubMed2026

Comparative transcriptomics reveals hormone signaling and MADS-box genes in divergent development of inflorescences and tendrils in grapevine lateral shoots.

Hormone signaling and MADS-box genes regulate grapevine tendril and inflorescence growth divergence, offering molecular insights for managing tendril growth. Grapevine (Vitis vinifera L.) tendrils and inflorescences are homologous organs; however, their divergent development has important agronomic consequences because excessive tendril growth increases vineyard management costs. To explore the regulatory mechanisms, we compared the inflorescence-prone cultivar 'Einset Seedless' (ENT) with the tendril-prone cultivar 'Pinot Noir' (PN) using anatomical observation, transcriptome analysis of specific tendril nodes, and functional characterization of MADS-box genes. ENT exhibited a higher flowering rate at tendril nodes 1-4 than PN. Transcriptome profiling of specific tendril nodes uncovered 549 differentially expressed genes (DEGs) through an intersection/exclusion strategy, with Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicating that hormone and mitogen-activated protein kinase (MAPK) signaling were the primary candidates driving the divergence. To assess the spatiotemporal dynamics of these DEGs, we performed Mfuzz clustering, which revealed that multiple expression trajectories were highly consistent with the flowering gradient across different ENT and PN nodes. Plant hormone signal transduction was the predominantly enriched pathway across all dynamic clusters, highlighting the centrality of phytohormones in this process. Guided by this transcriptional evidence, we measured endogenous zeatin and gibberellin (GA₃) contents in the nodal tissues. Remarkably, the zeatin-to-GA₃ ratio not only paralleled the flowering gradient but also correlated with the cluster expression trajectories, providing physiological evidence for a cytokinin-gibberellin interaction model governing organ divergence. Additionally, we analyzed the differentially expressed transcription factors among the DEGs and identified a MADS-box gene, FRUITFULL-LIKE (VvFUL-L), which was markedly upregulated in PN tendrils. Heterologous overexpression of VvFUL-L in arabidopsis promoted early flowering and reduced inflorescence branching, suggesting its potential role in regulating lateral meristem development and affecting tendril formation. Collectively, these findings establish that Hormone Signaling, particularly cytokinin-GA crosstalk, and MADS-box regulators, such as VvFUL-L, are key regulators of inflorescence versus tendril growth in grapevines, providing a basis for future molecular and breeding studies.

Vitis↗
PubMed2006

Variation in the type I interferon gene cluster on 9p21 influences susceptibility to asthma and atopy.

A genome-wide screen for asthma and atopy susceptibility alleles conducted in the Hutterites, a founder population of European descent, reported evidence of linkage with a short tandem repeat polymorphism (STRP) within the type I interferon (IFN) gene cluster on chromosome 9p21. The goal of this study was to identify variation within the IFN gene cluster that influences susceptibility to asthma and atopic phenotypes. We screened approximately 25 kb of sequence, including the flanking sequence of all 15 functional genes and the single coding exon in 12, in Hutterites representing different IFNA-STRP genotypes. We identified 78 polymorphisms, and genotyped 40 of these (in 14 genes) in a large Hutterite pedigree. Modest associations (0.003<P<0.05) with asthma, bronchial hyper-responsiveness (BHR), and atopy were observed with individual variants or genes, spanning the entire 400 kb region. However, pairwise combinations of haplotypes between genes showed highly significant associations with different phenotypes (P<10(-5)) that were localized to specific pairs of genes or regions of this cluster. These results suggest that variation in multiple genes in the type I IFN cluster on 9p22 contribute to asthma and atopy susceptibility, and that not all genes contribute equally to all phenotypes.

Adolescent↗
PubMed1999

A profile analysis of personality disorders: beyond multiple diagnoses.

The authors applied cluster analysis and multidimensional scaling to the analyses of 59 patients with personality pathology. Cluster analysis yielded eight typologies of patients: detached, anankastic, phobic, dramatic, erratic, emotional, milder emotional, and masochistic negativistic. Multidimensional scaling identified the dimensions of classifying patients: anxious rumination versus behavioural acting out, overall severity of personality pathology, and assertiveness versus withdrawal. Considering the distinction between personality disorder (dysfunctional personality) and abnormal personality (extreme personality), the following changes in current classification system are proposed: use of a hierarchy and exclusion criteria in a categorical-type model or use of a personality profile in a dimensional-trait model, in either case, with a dimensional rating for severity of psychopathology to define personality 'disorder'.

Adult↗
PubMed2002

DiffTool: building, visualizing and querying protein clusters.

UNLABELLED: DiffTool is a resource to build and visualize protein clusters computed from a sequence database. The package provides a clustering tool to construct protein families according to sequence similarities and a web interface to query the corresponding clusters. A subtractive genome analysis tool selects protein families specific for a genome or a group of genomes. For each protein cluster, DiffTool includes access to sequences, coloured multiple alignments and phylogenetic trees. AVAILABILITY: A cluster database built from yeast and complete prokaryotic genomes is queryable at http://bioweb.pasteur.fr/seqanal/difftool. All the Perl sources are freely available to non-profit organizations upon request.

Cluster Analysis↗
PubMed1995

Multiple agminated Spitz nevi: report of two cases and review of the literature.

Spitz nevus is most commonly a benign solitary lesion. Multiple lesions arranged in clusters (agminated) are very rare. Malignant degeneration has not been reported. Although spontaneous involution may occur, the nevi are frequently treated by surgical excision. We describe two preschool girls with multiple agminated Spitz nevi, and review the current world literature on multiple Spitz nevi.

Back↗
PubMed1991

Characterization of the Cephalosporium acremonium pcbAB gene encoding alpha-aminoadipyl-cysteinyl-valine synthetase, a large multidomain peptide synthetase: linkage to the pcbC gene as a cluster of early cephalosporin biosynthetic genes and evidence of multiple functional domains.

A 24-kb region of Cephalosporium acremonium C10 DNA was cloned by hybridization with the pcbAB and pcbC genes of Penicillium chrysogenum. A 3.2-kb BamHI fragment of this region complemented the mutation in the structural pcbC gene of the C. acremonium N2 mutant, resulting in cephalosporin production. A functional alpha-aminoadipyl-cysteinyl-valine (ACV) synthetase was encoded by a 15.6-kb EcoRI-BamHI DNA fragment, as shown by complementation of an ACV synthetase-deficient mutant of P. chrysogenum. Two transcripts of 1.15 and 11.4 kb were found by Northern (RNA blot) hybridization with probes internal to the pcbC and pcbAB genes, respectively. An open reading frame of 11,136 bp was located upstream of the pcbC gene that matched the 11.4-kb transcript initiation and termination regions. It encoded a protein of 3,712 amino acids with a deduced Mr of 414,791. The nucleotide sequence of the gene showed 62.9% similarity to the pcbAB gene encoding the ACV synthetase of P. chrysogenum; 54.9% of the amino acids were identical in both ACV synthetases. Three highly repetitive regions occur in the deduced amino acid sequence of C. acremonium ACV synthetase. Each is similar to the three repetitive domains in the deduced sequence of P. chrysogenum ACV synthetase and also to the amino acid sequence of gramicidin synthetase I and tyrocidine synthetase I of Bacillus brevis. These regions probably correspond to amino acid activating domains in the ACV synthetase protein. In addition, a thioesterase domain was present in the ACV synthetases of both fungi. A similarity has been found between the domains existing in multienzyme nonribosomal peptide synthetases and polyketide and fatty acid synthetases. The pcbAB gene is linked to the pcbC gene, forming a cluster of early cephalosporin-biosynthetic genes.

Acremonium↗
PubMed2006

Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data.

Cortical surface-based analysis of fMRI data has proven to be a useful method with several advantages over 3-dimensional volumetric analyses. Many of the statistical methods used in 3D analyses can be adapted for use with surface-based analyses. Operating within the framework of the FreeSurfer software package, we have implemented a surface-based version of the cluster size exclusion method used for multiple comparisons correction. Furthermore, we have a developed a new method for generating regions of interest on the cortical surface using a sliding threshold of cluster exclusion followed by cluster growth. Cluster size limits for multiple probability thresholds were estimated using random field theory and validated with Monte Carlo simulation. A prerequisite of RFT or cluster size simulation is an estimate of the smoothness of the data. In order to estimate the intrinsic smoothness of group analysis statistics, independent of true activations, we conducted a group analysis of simulated noise data sets. Because smoothing on a cortical surface mesh is typically implemented using an iterative method, rather than directly applying a Gaussian blurring kernel, it is also necessary to determine the width of the equivalent Gaussian blurring kernel as a function of smoothing steps. Iterative smoothing has previously been modeled as continuous heat diffusion, providing a theoretical basis for predicting the equivalent kernel width, but the predictions of the model were not empirically tested. We generated an empirical heat diffusion kernel width function by performing surface-based smoothing simulations and found a large disparity between the expected and actual kernel widths.

Cerebral Cortex↗
PubMed2004

Transfer of photosynthesis genes to and from Prochlorococcus viruses.

Comparative genomics gives us a new window into phage-host interactions and their evolutionary implications. Here we report the presence of genes central to oxygenic photosynthesis in the genomes of three phages from two viral families (Myoviridae and Podoviridae) that infect the marine cyanobacterium Prochlorococcus. The genes that encode the photosystem II core reaction center protein D1 (psbA), and a high-light-inducible protein (HLIP) (hli) are present in all three genomes. Both myoviruses contain additional hli gene types, and one of them encodes the second photosystem II core reaction center protein D2 (psbD), whereas the other encodes the photosynthetic electron transport proteins plastocyanin (petE) and ferredoxin (petF). These uninterrupted, full-length genes are conserved in their amino acid sequence, suggesting that they encode functional proteins that may help maintain photosynthetic activity during infection. Phylogenetic analyses show that phage D1, D2, and HLIP proteins cluster with those from Prochlorococcus, indicating that they are of cyanobacterial origin. Their distribution among several Prochlorococcus clades further suggests that the genes encoding these proteins were transferred from host to phage multiple times. Phage HLIPs cluster with multicopy types found exclusively in Prochlorocococus, suggesting that phage may be mediating the expansion of the hli gene family by transferring these genes back to their hosts after a period of evolution in the phage. These gene transfers are likely to play a role in the fitness landscape of hosts and phages in the surface oceans.

Base Sequence↗
PubMed2004

Beta-1 integrin-mediated adhesion may be initiated by multiple incomplete bonds, thus accounting for the functional importance of receptor clustering.

The regulation of cell integrin receptors involves modulation of membrane expression, shift between different affinity states, and topographical redistribution on the cell membrane. Here we attempted to assess quantitatively the functional importance of receptor clustering. We studied beta-1 integrin-mediated attachment of THP-1 cells to fibronectin-coated surfaces under low shear flow. Cells displayed multiple binding events with a half-life of the order of 1 s. The duration of binding events after the first second after arrest was quantitatively accounted for by a model assuming the existence of a short-time intermediate binding state with 3.6 s(-1) dissociation rate and 1.3 s(-1) transition frequency toward a more stable state. Cell binding to surfaces coated with lower fibronectin densities was concluded to be mediated by single molecular interactions, whereas multiple bonds were formed <1 s after contact with higher fibronectin surface densities. Cell treatment with microfilament inhibitors or a neutral antiintegrin antibody decreased bond number without changing aforementioned kinetic parameters whereas a function enhancing antibody increased the rate of bond formation and/or the lifetime of intermediate state. Receptor aggregation was induced by treating cells with neutral antiintegrin antibody and antiimmunoglobulin antibodies. A semiquantitative confocal microscopy study suggested that this treatment increased between 40% and 100% the average number of integrin receptors located in a volume of approximately 0.045 microm(3) surrounding each integrin. This aggregation induced up to 2.7-fold increase of the average number of bonds. Flow cytometric analysis of fluorescent ligand binding showed that THP-1 cells displayed low-affinity beta-1 integrins with a dissociation constant in the micromolar range. It is concluded that the initial step of cell adhesion was mediated by multiple incomplete bonds rather than a single equilibrium-state ligand receptor association. This interpretation accounts for the functional importance of integrin clustering.

Actin Cytoskeleton↗
PubMed1991

Geographic clustering of myeloma in Tokushima.

Between 1978-1988, seven cases of multiple myeloma were found in T Town (population 9,000), which is located at the mouth of a large river within the boundaries of Tokushima City, Japan. This is a significantly high incidence, 7.06 per 100,000 as compared with an incidence of 1.20 in Tokushima City itself and 1.53 in Japan as a whole. The clinical and laboratory features of these patients were typical of myeloma. Although the causes of this small but apparent cluster of multiple myeloma remain obscure, the fact that five of the seven patients had been working for long periods as fishermen was notable.

Adult↗
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↗
PubMed2004

Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.

MOTIVATION: Transcription factor binding sites often differ significantly in their primary sequence and can hardly be aligned. Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences. RESULTS: We developed a novel method for analysis of unaligned sets of sequences based on kernel estimation. The method is able to reveal 'multiple local patterns'-a set of weight matrices. Every weight matrix characterizes a pattern that can be found in a significant subset of sequences under analysis. The method developed has been compared with several other methods of pattern discovery such as Gibbs sampling, MEME, CONSENSUS, MULTIPROFILER and PROJECTION. The kernel method showed the best performance in terms of how close the revealed weight matrices are to the original ones. We applied the kernel method to analyze three samples of promoters (cell-cycle, T-cells and muscle-specific). We compared the multiple patterns revealed with the TRANSFAC library of weight matrices and found a strong similarity to several weight matrices for transcription factors known to be involved in the mentioned specific gene regulation. AVAILABILITY: The program is available for on-line use at: http://www.biobase.de/cgi-bin/biobase/cbs2/bin/template.cgi?template=cbscall.html

Algorithms↗
PubMed1989

An allelic cluster of DQ alpha restriction fragments is associated with multiple sclerosis: evidence that a second haplotype may influence disease susceptibility.

Extensive analysis of restriction fragment length polymorphism using HLA class II and T-cell receptor gene probes has been carried out in an attempt to identify genetic markers more strongly associated with multiple sclerosis than the classically defined antigens DR2, Dw2, and DQw1. The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DP alpha, DP beta, DQ alpha, DQ beta, DR beta) and two T-cell antigen receptor probes. Restriction fragment length polymorphisms which discriminated between multiple sclerosis and control pools were identified with four restriction enzymes: Msp1 (DQ alpha), BamH1, Bgl11, and Taq1 (DQ beta). No discriminatory polymorphism was seen with any of the other enzyme/probe combinations. Subsequent Southern blot analysis of individual DNA samples was carried out using these enzymes and probes in two independently conducted studies, in Northern Ireland and northeast Scotland. Following Msp1-digestion and hybridization to DQ alpha, a 3.25-kb fragment was observed in 31% of Scottish patients but in only 4% of controls from the same population. Furthermore, when only DR2-positive individuals were analyzed, there was a significant excess of this fragment in patients from both Scotland (28, or 2.9%) and Northern Ireland (20, or 3.4%). Although the DQ alpha gene characterized by this fragment remains to be determined, this fragment exhibits apparent allelism to DQw1. Therefore, these data raise the possibility that two different DQ alleles, one on each haplotype, may jointly contribute to disease susceptibility.

Alleles↗
PubMed2000

Oscillatory cluster patterns in a homogeneous chemical system with global feedback

Oscillatory clusters are sets of domains in which nearly all elements in a given domain oscillate with the same amplitude and phase. They play an important role in understanding coupled neuron systems. In the simplest case, a system consists of two clusters that oscillate in antiphase and can each occupy multiple fixed spatial domains. Examples of cluster behaviour in extended chemical systems are rare, but have been shown to resemble standing waves, except that they lack a characteristic wavelength. Here we report the observation of so-called 'localized clusters'--periodic antiphase oscillations in one part of the medium, while the remainder appears uniform--in the Belousov-Zhabotinsky reaction-diffusion system with photochemical global feedback. We also observe standing clusters with fixed spatial domains that oscillate periodically in time and occupy the entire medium, and irregular clusters with no periodicity in either space or time, with standing clusters transforming into irregular clusters and then into localized clusters as the strength of the global negative feedback is gradually increased. By incorporating the effects of global feedback into a model of the reaction, we are able to simulate successfully the experimental data.

Journal Article↗
PubMed1997

Admission examination factors predicting cognitive improvement during acute brain injury rehabilitation.

In this study 46 brain-injured patients admitted to a brain injury inpatient rehabilitation programme after acute care were evaluated at the bedside with a comprehensive mental status examination and physical evaluation. Using multiple regression analysis, elements of the cognitive and physical examinations were studied to determine if any of these items, individually or collectively, had predictive value for discharge functional status. A principal-components analysis identified meaningful clusters of items. Factor I, Simple Cognitive Operations, consisted of word repetition, naming and comprehension of simple commands. Factor IV, Higher Cognitive Operations, consisted of interpretation of similarities and reverse digit span. Other items, including elements of the physical examination such as eye movements, hearing and ambulatory function, were also clustered into factors. Stepwise multiple regression analysis led to a conclusion that only factor IV was a significant predictor of Discharge Rancho Level, with the predictive power of factor I and Admission Rancho Level subsumed by factor IV. This model, using a few items from a bedside mental status examination, accounted for 27% of the variance in Discharge Rancho Level in patients admitted to a brain injury rehabilitation unit after injury. We conclude that a brief mental status examination in a rehabilitation inpatient setting can be useful in predicting outcome in patients with brain injuries. More research is needed to identify additional test items that will add prognostic power to the initial evaluation of patients with brain injuries admitted to a rehabilitation unit.

Acute Disease↗
PubMed2005

Cortical sources of CRF, NKB, and CCK and their effects on pyramidal cells in the neocortex.

In order to investigate how neuropeptide transmission can modulate the neocortical network, we mapped the expression of neurokinin (NK) B, cholecystokinin (CCK), and corticotropin-releasing factor (CRF) and their receptors to neuronal types using patch-clamp and single-cell reverse transcription-polymerase chain reaction in acute slices of rat neocortex. Classification of neurons by unsupervised clustering based on the analysis of multiple electrophysiological and molecular properties disclosed 3 GABAergic interneuron clusters and 1 pyramidal cell cluster. The 3 neuropeptides were expressed in a cluster of interneurons characteristically expressing vasoactive intestinal peptide. CRF was additionally found in a cluster containing almost exclusively somatostatin-expressing interneurons, whereas CCK was present in all clusters. The respective receptors of these peptides, NK-3, CCK-B, and CRF-1, were essentially expressed in pyramidal cells. At -60 mV, pyramidal cells were weakly depolarized by each of these peptides. When pyramidal neurons were maintained to about 5 mV below spike threshold, depolarization induced by each peptide resulted in a long-lasting action potential discharge. Neuropeptide effects were prevented by selective antagonists of NK-3, CCK-B, and CRF-1 receptors. These results suggest that pyramidal neurons are the primary target of NKB, CCK, and CRF in the neocortex. They further indicate that specific interneuron types coordinate the release of these peptides and can induce a long-lasting increase of the excitability of the neocortical network.

Action Potentials↗