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At least 307 records · Page 17Linked to original sources
PubMed1995

Genetic analysis of the dTDP-rhamnose biosynthesis region of the Escherichia coli VW187 (O7:K1) rfb gene cluster: identification of functional homologs of rfbB and rfbA in the rff cluster and correct location of the rffE gene.

The O-repeating unit of the Escherichia coli O7-specific lipopolysaccharide is made of galactose, mannose, rhamnose, 4-acetamido-4,6-dideoxyglucose, and N-acetyglucosamine. We have recently characterized the genes involved in the biosynthesis of the sugar precursor GDP-mannose occurring in the E. coli O7:K1 strain VW187 (C. L. Marolda and M. A. Valvano, J. Bacteriol. 175:148-158, 1993). In the present study, we identified and sequenced the rfbBDAC genes encoding the enzymes for the biosynthesis of another precursor, dTDP-rhamnose. These genes are localized on the upstream end of the rfbEcO7 region, and they are strongly conserved compared with similar genes found in various enteric and nonenteric bacteria. Upstream of rfbB we identified a DNA segment containing the rfb promoter and a highly conserved untranslated leader sequence also present in the promoter regions of other surface polysaccharide gene clusters. Also, we have determined that rfbB and rfbA have homologs, rffG (o355) and rffH (o292), respectively, located on the rff cluster, which is involved in the synthesis of enterobacterial common antigen. We provide biochemical evidence that rffG and rffH encode dTDP-glucose dehydratase and glucose-1-phosphate thymidylyltransferase activities, respectively, and we also show that rffG complemented the rfbB defect in the O7+ cosmid pJHCV32. We also demonstrate that rffG is distinct from rffE and map the rffE gene to the second gene of the rff cluster.

Antigens, Bacterial↗
PubMed2000

Regulation of the Escherichia coli K5 capsule gene cluster: evidence for the roles of H-NS, BipA, and integration host factor in regulation of group 2 capsule gene clusters in pathogenic E. coli.

The expression of Escherichia coli group 2 capsules (K antigens) is temperature dependent, with capsules only being expressed at temperatures above 20 degrees C. Thermoregulation is at the level of transcription, with no detectable transcription at 20 degrees C. Using the E. coli K5 capsule gene cluster as a model system, we have shown that the nucleoid-associated protein H-NS plays a dual role in regulating transcription of group 2 capsule gene clusters at 37 and 20 degrees C. At 37 degrees C H-NS is required for maximal transcription of group 2 capsule gene clusters, whereas at 20 degrees C H-NS functions to repress transcription. The BipA protein, previously identified as a tyrosine-phosphorylated GTPase and essential for virulence in enteropathogenic E. coli, was shown to play a similar role to H-NS in regulating transcription at 37 and 20 degrees C. The binding of integration host factor (IHF) to the region 1 promoter was necessary to potentiate transcription at 37 degrees C and IHF binding demonstrated by bandshift assays. The IHF binding site was 3' to the site of transcription initiation, suggesting that sequences in the 5' end of the first gene (kpsF) in region 1 may play a role in regulating transcription from this promoter at 37 degrees C. Two additional cis-acting sequences, conserved in both the region 1 and 3 promoters, were identified, suggesting a role for these sequences in the coordinate regulation of transcription from these promoters. These results indicate that a complex regulatory network involving a number of global regulators exists for the control of expression of group 2 capsules in E. coli.

Bacterial Capsules↗
PubMed2000

The Escherichia coli O111 and Salmonella enterica O35 gene clusters: gene clusters encoding the same colitose-containing O antigen are highly conserved.

O antigen is part of the lipopolysaccharide present in the outer membrane of gram-negative bacteria. Escherichia coli and Salmonella enterica each have many forms of O antigen, but only three are common to the two species. It has been found that, in general, O-antigen genes are of low GC content. This deviation in GC content from that of typical S. enterica or E. coli genes (51%) is thought to indicate that the O-antigen DNA originated in species other than S. enterica or E. coli and was captured by lateral transfer. The O-antigen structure of Salmonella enterica O35 is identical to that of E. coli O111, commonly found in enteropathogenic E. coli strains. This O antigen, which has been shown to be a virulence factor in E. coli, contains colitose, a 3,6-dideoxyhexose found only rarely in the Enterobacteriaceae. Sequencing of the O35-antigen gene cluster of S. enterica serovar Adelaide revealed the same gene order and flanking genes as in E. coli O111. The divergence between corresponding genes of these two gene clusters at the nucleotide level ranges from 21.8 to 11.7%, within the normal range of divergence between S. enterica and E. coli. We conclude that the ancestor of E. coli and S. enterica had an O antigen identical to the O111 and O35 antigens, respectively, of these species and that the gene cluster encoding it has survived in both species.

Base Composition↗
PubMed2004

The relationship between physical fitness and clustered risk, and tracking of clustered risk from adolescence to young adulthood: eight years follow-up in the Danish Youth and Sport Study.

INTRODUCTION: Cardiovascular disease (CVD) is usually caused by high levels of many risk factors simultaneously over many years. Therefore, it is of great interest to study if subjects stay within rank order over time in both the biological risk factors and the behaviour that influences these risk factors. Many studies have described stability (tracking) in single risk factors, especially in children where hard endpoints are lacking, but few have analysed tracking in clustered risk. METHODS: Two examinations were conducted 8 years apart. The first time, 133 males and 172 females were 16-19 years of age. Eight years later, 98 males and 137 females participated. They were each time ranked into quartiles by sex in four CVD risk factors all related to the metabolic syndrome. Risk factors were the ratio between total cholesterol and HDL, triglyceride, systolic BP and body fat. The upper quartile was defined as being at risk, and if a subject had two or more risk factors, he/she was defined as a case (15-20 % of the subjects). Odds ratios (OR) for being a case was calculated between quartiles of fitness in both cross-sectional studies. The stability of combined risk was calculated as the OR between cases and non-cases at the first examination to be a case at the second examination. RESULTS: ORs for having two or more risk factors between quartiles of fitness were 3.1, 3.8 and 4.9 for quartiles two to four, respectively. At the second examination, OR were 0.7, 3.5 and 4.9, respectively. The probability for "a case" at the first examination to be "a case" at the second was 6.0. CONCLUSIONS: The relationship between an exposure like physical fitness and CVD risk factors is much stronger when clustering of risk factors are analysed compared to the relationship to single risk factors. The stability over time in multiple risk factors analysed together is strong. This relationship should be seen in the light of moderate or weak tracking of single risk factors, and is strong evidence for early intervention in children where risk factors cluster.

Journal Article↗
PubMed1978

A note on cluster analysis and depression: disparities in results produced by the application of different clustering methods.

Cluster analysis is the most logically suited method for establishing psychiatric classifications. Different mathematical methods of clustering do, however, produce disparate results when applied to the same set of data. This study attempted to quantify the extent of such disparities, and found them to be marked. It was concluded that until cluster analysis has undergone further mathematical and statistical development, it should be used with caution.

Adult↗
PubMed1982

Resonance Raman and electron paramagnetic resonance studies on oxidized and ferricyanide-treated Clostridium pasteurianum ferredoxin. Vibrational assignments from 34S shifts and evidence for conversion of 4 to 3 iron-sulfur clusters via oxidative damage. Vibrational assignments from 34S shifts and evidence for conversion of 4 to 3 iron-sulfur clusters via oxidative damage.

Resonance Raman spectra are reported for oxidized ferredoxin from Clostridium pasteurianum and for protein reconstituted with 34S2-, using 4579 A laser excitation. The spectra are of much higher quality than that previously reported, and the 34S shifts provide assignments of the Fe-S modes. After treatment with ferricyanide, the resonance Raman spectrum closely resembles that of the [3Fe-3S] protein, ferredoxin II from D. gigas; the 34S shifts aid in assignments of the [3Fe-3S] modes. The epr signal associated with the [3Fe-3S] cluster (g = 2.01) corresponds maximally to 0.80 spin/molecule. Anaerobic addition of excess sulfide to the reduced, ferricyanide-treated protein regenerates a [4Fe-4S]1+ epr spectrum, equivalent in intensity to the [3Fe-3S] signal. The ubiquitous occurrence of a g = 2.01 signal in preparations of [4Fe-4S] proteins can be attributed to variable amounts of [3Fe-3S] cluster generated by adventitious oxidation. The ready conversion of [4Fe-4S] to [3Fe-3S] clusters in C. pasterianum raises the possibility that some [3Fe-3S] proteins may actually arise by oxidative damage of [4Fe-4S] proteins during aerobic isolation.

Clostridium↗
PubMed1995

Interbilayer cluster-cluster interaction in multilamellar vesicles: thermodynamic approach.

A simple thermodynamic model of the main transition in pure lipid bilayers is presented. The basic relations for cooperativity, aggregation degree and fractional number of molecules are derived. The experimental heat capacity measurements of uni- and multilamellar phospholipid vesicles are analysed within the context of this model, and the transition characteristics are obtained. It is demonstrated that they differ from each other, and these differences are discussed according to the system configuration. The derived cluster configuration entropy supports the idea of strong interbilayer cluster-cluster cooperation.

Entropy↗
PubMed1996

HOXB cluster genes in activated natural killer lymphocytes: expression from 3'-->5' cluster side and proliferative function.

The expression of HOXB cluster genes (i.e., B1 through B9) was evaluated in purified IL-2/IL-1 beta-activated NK lymphocytes from normal adult peripheral blood by RNase protection and reverse transcription-PCR. In quiescent NK cells these genes are essentially not expressed. After IL-2/IL-1 beta addition, we observed a coordinate induction wave in the 3'-5' HOXB cluster direction, i.e., from B1 through B9. As notable exceptions, B8 is silent, while B9 RNA is detected starting from 6 h through day 11. Furthermore, the 3' located B2/B3/B4 are expressed earlier and at higher level than the 5' located B5/B6/B7/B8. In IL-2/IL-1 beta-activated NK cells, treatment with antisense oligonucleotides targeting B2 mRNA causes a significant inhibition of both cell proliferation and expression of activation markers (i.e., IL-2R alpha-chain and transferrin receptor). These studies provide novel evidence of the role of HOX genes in adult NK cell proliferation. Thus, 1) a coordinate activation of HOXB genes from the 3'-->5' cluster side apparently underlies IL-2/IL-1 beta-induced NK cell activation. 2) Since NK cell activation and survival induced by IL-12 and c-kit ligand, respectively, are not associated with cell proliferation of HOXB gene expression, it is apparent that HOXB gene induction is specifically associated with IL-2-induced NK cell proliferation. 3) Studies with antisense oligomer targeting HOXB2 mRNA suggest an important role for 82 in NK cell proliferation, possibly in part via the IL-2R.

Adult↗
PubMed2003

Expression profiling of 68 glycosyltransferase genes in 27 different human tissues by the systematic multiplex reverse transcription-polymerase chain reaction method revealed clustering of sexually related tissues in hierarchical clustering algorithm analysis.

We have developed an experimental system to study the expression of 68 human glycosyltransferase genes. Using this system, we examined the expression of those genes in 27 different tissues by the technique which we named systematic multiplex reverse transcription-polymerase chain reaction (SM RT-PCR). The panoramic view of a total of 1836 (68 x 27) expression data demonstrates that some glycosyltransferase genes are differentially expressed whereas some others are ubiquitously expressed. The data gathered provide more information on glycosyltransferase gene expression in tissues than any other paper published, and surpass in quantity all the information combined from previous publications. Although the expression profiling of glycosyltransferase genes alone may not directly explain the repertoires of oligosaccharides synthesized, it is an important step toward a better understanding of the gene expression network involved in oligosaccharide synthesis/degradation. Our modestly high-throughput gene expression study and the data analysis using a hierarchical clustering algorithm have allowed us to investigate the correlation between tissues and glycosyltransferase gene expression. Similar patterns of glycosyltransferase gene expression were observed in functionally and anatomically related tissues. All, but one, sexually related tissues formed a cluster in a tissue dendrogram, suggesting the involvement of sex hormones in the transcriptional control of many glycosyltransferase genes. Once established, the SM RT-PCR is cost- and time-efficient and requires small amounts of RNA as template. It is especially useful for the simultaneous analyses of multiple samples. Because of its simple design, the SM RT-PCR may offer an easy alternative in studying the expression of many other families of genes, as well as groups of related/unrelated genes, in various biological phenomena.

Algorithms↗
PubMed2004

Elusive amines and cluster headache: mutational analysis of trace amine receptor cluster on chromosome 6q23.

Cluster headache (CH) is characterised by unilateral pain and ipsilateral autonomic features. To date, no molecular genetic evidence has been shown for CH. Small pedigrees and low penetrance render the identification of the CH-gene quite difficult. Nonetheless the association of CH and migraine to a new class of amine, namely trace or elusive amines such as tyramine, octopamine and synephrine, has recently been demonstrated. In particular, in comparison to healthy control subjects, all these neurotransmitters have been found to be greatly elevated in CH sufferers in plasma and platelets both in active and remission periods. A cluster of gene-encoding G-protein-coupled receptors that bind and are activated by trace amines was identified in the long arm of chromosome 6q23. We evaluated two families with CH by linkage analysis to 6q23 region and the mutation scanning of the TAR 1, TAR 3, TAR 4, TAR 5, PNR and GPR58 genes by denaturing high liquid chromatography is in progress in 16 familial cases.

Biogenic Amines↗
PubMed1994

Clustering and six year cluster-tracking of serum total cholesterol, HDL-cholesterol and diastolic blood pressure in children and young adults. The Cardiovascular Risk in Young Finns Study.

Clustering and tracking of serum total cholesterol, high-density lipoprotein cholesterol (HDL-C) and diastolic blood pressure were studied in children and young adults. "High-risk" individuals were defined as those having these risk factors at the age and sex specific upper tertile (lowest tertile for HDL-C). Among older boys risk factors occurred at adverse levels more often than expected by chance. Cluster-tracking was assessed as the probability of remaining in the extreme tertiles during follow-up. Approximately 25% of subjects initially at "risk" remained there for 6 years. Subjects who became high-risk individuals during the follow-up expressed greater increase in obesity indices, started to consume more saturated fat and cholesterol and became physically active less often compared to those subjects who were initially at risk, but no longer at the follow-up.

Adolescent↗
PubMed2007

Effect of cluster size in kiloelectronvolt cluster bombardment of solid benzene.

Emission of benzene molecules by 5-keV cluster bombardment of a range of carbon projectiles from C6H6 to C180 is studied by a coarse-grained molecular dynamics (MD) technique. This approach permits calculations that are not feasible using more complicated potential energy functions, particularly as the interesting physics associated with the ion impact event approaches the mesoscale. These calculations show that the highest ejection yields are associated with clusters that deposit their incident energy 15-20 A below the surface. The highest yield for the projectiles is produced by the C20 and C60 projectiles. The results from the MD simulations are also compared favorably to an analytical model based on fluid dynamics to describe the energy deposition. The analytical model is then utilized to extend the range of the calculations to higher incident energies. The issue of the relative amount of chemical fragmentation and intact molecular desorption is also examined for the benzene crystal. These results show that damage accumulation at high-incident fluence should not be problematic and that it should be possible to perform molecular depth profiling via secondary ion mass spectrometry experiments. In general, the approach presented here illustrates the power of combining a simplified MD method with analytical strategies for describing a length scale that is difficult to achieve with traditional MD calculations.

Benzene↗
PubMed1993

Hypothalamic modulation of nociception and reproduction in cluster headache. II. Testosterone-induced increase of sexual activity in males with cluster headache.

Short-lasting chronic testosterone administration did not change the course of cluster headache in seven chronic sufferers, whereas it enhanced sexual excitement in comparison with male control subjects who received the same treatment. We postulate that the sexual excitement induced in cluster headache sufferers by chronic treatment with testosterone relates to an impairment of neuronal modulation in this disorder.

Adult↗
PubMed1995

Cluster headache attacks treated for up to three months with subcutaneous sumatriptan (6 mg). Sumatriptan Cluster Headache Long-term Study Group.

In the first three months of a 24-month open study to assess the safety and efficacy of subcutaneous sumatriptan 6 mg in the long-term acute treatment of cluster headache, 138 patients treated a maximum of two attacks daily each with a single 6 mg injection. A total of 6353 attacks were treated. Adverse events, reported in 28% of sumatriptan-treated attacks, were qualitatively similar to those seen in migraine long-term trials. Their incidence did not increase with frequent use of sumatriptan. There were no clinically significant treatment effects on vital signs, ECG recordings or laboratory parameters. Headache relief (a reduction from very severe, severe or moderate pain to mild or no pain) at 15 min was obtained for a median of 96% of attacks treated. There was no indication of tachyphylaxis, decrease in the speed of response, or increased frequency of attacks with long-term treatment. This study demonstrated that, in long-term use, subcutaneous sumatriptan 6 mg is a well-tolerated and effective acute treatment for cluster headache.

Adolescent↗
PubMed2003

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP and PVM.

Cluster Analysis↗
PubMed1993

Subcutaneous sumatriptan in the acute treatment of cluster headache: a dose comparison study. The Sumatriptan Cluster Headache Study Group.

This multicentre, double-blind, randomised, crossover study compared the efficacy, safety and tolerability of subcutaneous sumatriptan (6 mg and 12 mg) with placebo in 134 in-patients with cluster headache. Headache improvement to mild or no pain at 5, 10 and 15 min after treatment was recorded. At 10 min, headache relief was reported by 25% (placebo), 49% (6 mg) and 63% (12 mg) of patients and at 15 min the results were 35% (placebo), 75% (6 mg) and 80% (12 mg) (p < 0.001 for all comparisons with placebo). The 12 mg dose was not significantly better than the 6 mg dose and was associated with more adverse events. The 6 mg dose is therefore recommended for the acute treatment of cluster headache.

Adolescent↗
PubMed1994

Immunological evidence for co-expression of cluster-5 and cluster-5A small cell lung cancer antigen on a single molecule.

We have investigated immunologically the molecular association of the cell-surface sialoglycoprotein antigens cluster-5 (CL-5) and cluster-5A (CL-5A), known to be co-expressed in human small-cell lung cancer (SCLC). CL-5 antigen is exclusively defined by IgM antibodies as represented by MAb LAM8, whereas CL-5A antigen is exclusively defined by IgG antibodies as represented by MAbs SWA20 and SEN31. Because of the unavailability of purified antigens, the question of the molecular relationship between these antigens was addressed by immunological studies. We generated an anti-anti-idiotypic MAb of the IgG isotype using a CL-5-antigen-mimicking anti-idiotype defined by rat MAb Ly8-229 as an immunogen to circumvent the avidity problems observed with the IgM MAb LAM8 in binding-competition experiments. In addition, we developed a heterologous double antibody sandwich assay able to identify circulating CL-5/5A antigens in pre-treatment sera of patients with SCLC. The results of both types of immunological studies demonstrated the expression of CL-5 and CL-5A antigens on a single molecule, both in cellular assays and in assays detecting antigens shed into the serum of patients with SCLC.

Animals↗
PubMed2002

Cluster-cluster aggregation kinetics and primary particle growth of soot nanoparticles in flame by light scattering and numerical simulations.

The agglomeration kinetics of growing soot generated in a diffusion atmospheric flame are here studied in situ by light scattering technique to infer cluster morphology and size (fractal dimension D(f) and radius of gyration R(g)). SEM analysis is used as a standard reference to obtain primary particle size D(P) at different residence times. The number N(P) of primary particles per aggregate and the number concentration n(A) of clusters are evaluated on the basis of the measured angular patterns of the scattered light intensity. The major finding is that the kinetics of the coagulation process that yields to the formation of chain-like aggregates by soot primary particles (size 10 to 40 nm) can be described with a constant coagulation kernel beta(c,exp)=2.37x10(-9) cm3/s (coagulation constant tau(c) approximately = 0.28 ms). This result is in nice accord with the Smoluchowski coagulation equation in the free molecular regime, and, vice versa, it is in contrast with previous studies conducted by invasive (ex situ) techniques, which claimed the evidence in flames of coagulation rates much larger than the kinetic theory predictions. Thereafter, a number of numerical simulations is implemented to compare with the experimental results on primary particle growth rate and on the process of aggregate reshaping that is observed by light scattering at later residence times. The restructuring process is conjectured to occur, for not well understood reasons, as a direct consequence of the atomic rearrangement in the solid phase carbon due to the prolonged residence time within the flame. Thus, on one side, it is shown that the numerical simulations of primary size history compare well with the values of primary size from SEM experiment with a growth rate constant of primary diameter about 1 nm/s. On the other side, the evolution of aggregate morphology is found to be predictable by the numerical simulations when the onset of a first-order "thermal" restructuring mechanism is assumed to occur in the flame at about 20 ms residence time leading to aggregates with an asymptotic fractal dimension D(f,infinity) approximately = 2.5.

Journal Article↗