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PubMed2000

Genome fingerprinting by pulsed-field gel electrophoresis of isolates of Burkholderia pseudomallei from patients with melioidosis in Thailand.

A total of 95 isolates of Burkholderia pseudomallei from 53 sporadic cases in Thailand were examined by pulsed-field gel electrophoresis. Digestion of genomic DNA of all isolates by NcoI generated a macrorestriction pattern similar to that of B. pseudomallei which cannot assimilate L-arabinose. Analysis using restriction enzymes SpeI and AvrII demonstrated greater sensitivity than NcoI digestion in the differentiation of B. pseudomallei and could be used for epidemiological groupings. Four cluster groups were evident among 37 isolates tested and the majority of isolates within each cluster displayed more than 65% similarity. Furthermore, multiple isolates from 18 and 35 patients with single and recurrent episodes of melioidosis, respectively, were examined. All patients with a single episode yielded genetically identical isolates and four of 35 patients with recurrent episodes were infected with strains of different genotypic patterns from the primary isolate(s). Hence, most repeated episodes of infection in melioidosis are as a result of the original infecting strains.

Bacterial Typing Techniques↗
PubMed1993

An x-ray absorption near edge structure spectroscopy study of metal coordination in Co(II)-substituted Carcinus maenas hemocyanin.

High-resolution x-ray absorption near edge structure spectroscopy was used to characterize the metal sites in three different cobalt-substituted derivatives of Carcinus maenas hemocyanin (Hc), including a mononuclear cobalt, a dinuclear cobalt and a copper-cobalt hybrid derivative. Co(II) model complexes with structures exemplifying octahedral, trigonal bipyramidal, pseudo-tetrahedral, and square planar geometries were also studied. The results provide structural information about the metal binding site(s) in the Co-Hcs that extend earlier results from EPR and optical spectroscopy (Bubacco et al. 1992. Biochemistry. 31: 9294-9303). Experimental spectra were compared to those calculated for atomic clusters of idealized geometry, generated using a multiple scattering approach. The energy of the dipole forbidden 1s-->3d transition and of the absorption edge in the spectra for all cobalt Hc derivatives confirmed the cobaltous oxidation state which rules out the presence of an oxygenated site. Comparisons between data and simulations showed that the mononuclear and dinuclear Co(II) derivatives, as well as the hybrid derivative, contain four-coordinate Co(II) in distorted tetrahedral sites. Although the spectra for Co(II) in dinuclear metal sites more closely resemble the simulated spectrum for a tetrahedral complex than do spectra for the mononuclear derivative, the Co(II) sites in all derivatives are very similar. The Cu K-edge high resolution x-ray absorption near edge structure spectrum of the hybrid Cu-Co-Hc resembles that of deoxy-Hc demonstrating the presence of three-coordinate Cu(I).

Absorptiometry, Photon↗
PubMed1991

Case report: primary systemic amyloidosis presenting as breast masses, mammographically simulating carcinoma.

A case of primary systemic amyloidosis presenting as bilateral breast masses is described. The mammographic appearance was of multiple ill-defined masses associated with clustered microcalcifications simulating carcinoma. This is the first case of amyloid of breast reported in the radiological literature. Other available literature of breast involvement in systemic amyloidosis is reviewed.

Aged↗
PubMed1998

The conjoint trait of low high-density lipoprotein cholesterol and high triglycerides in adolescent black and white males.

To evaluate the interrelationships among body composition, blood pressure, and lipid phenotypes in adolescent black and white boys, we assessed racial distributions of lipids, blood pressure, and obesity and their joint occurrence in black and white boys aged 10 to 15 years. Subjects were recruited from Cincinnati (OH) schools. Because the differences in high-density lipoprotein cholesterol (HDL-C) and triglycerides (TGs) are the most profound coronary heart disease (CHD) risk factor differences between black and white males, we assigned subjects to one of four low-HDL-C and high-TG categories (normal and increased risk) using the age/race-specific 25th (HDL-C) and 75th (TG) percentiles. We then assessed racial distributions of lipids, blood pressure, and obesity by these phenotypes. Age differences between the black and white participants were significant, with the former about 3 months younger (P=.03), but black boys were more mature and were significantly taller and heavier and had a greater body mass index ([BMI] weight in kilograms divided by height in centimeters squared). Differences in the sum of the triceps, subscapular, and suprailiac skinfolds were not significant. Blacks had significantly higher HDL-C, lower TG, and higher diastolic blood pressure (DBP), but differences in systolic blood pressure (SBP) were not significant. In both racial groups, the body composition measures were significantly correlated with HDL-C, TG, and blood pressure levels; the correlations between HDL-C and both weight and BMI were significantly stronger in white boys. The proportion of boys of each race with low HDL-C and high TG was similar by design. In both racial groups, subjects with the conjoint trait had a significantly greater BMI, triceps skinfold, and sum of skinfolds than subjects in the other phenotypic groups. For white boys, participants with the conjoint trait had the highest SBP and DBP; differences in SBP were significant for comparisons to the normal- and high-TG group alone, and differences in DBP were significant for the comparison between normal and low HDL-C alone. For black boys, subjects with both normal HDL-C and TG had significantly lower SBP than boys with either the conjoint trait or high TG alone; none of the group differences in DBP were significant. Black had significantly less dense LDL (more LDL-C per apolipoprotein [apo] B). In each racial group, boys with the conjoint trait had the most dense LDL, significantly more dense than in any of the other phenotypes in black boys and significantly more dense than in boys with low HDL-C alone and normal boys in the white group. In both racial groups, the occurrence of no risk factors (>75th percentile TG, BMI, SBP, and DBP or <25th percentile HDL-C) and three or more risk factors was greater than expected by chance alone, and the occurrence of exactly one risk factor and two factors was less. When examined by phenotypic groups within race, boys in each racial group with the normal phenotype had a greater than expected percentage with no risk factors, and white boys with the conjoint trait were more likely to have a marked increase in multiple risk factors. Possible mechanisms for this clustering of risk factors and for the racial differences in the patterns are discussed.

Adolescent↗
PubMed2003

Assessment of the surface water quality in Northern Greece.

The application of different multivariate statistical approaches for the interpretation of a large and complex data matrix obtained during a monitoring program of surface waters in Northern Greece is presented in this study. The dataset consists of analytical results from a 3-yr survey conducted in the major river systems (Aliakmon, Axios, Gallikos, Loudias and Strymon) as well as streams, tributaries and ditches. Twenty-seven parameters have been monitored on 25 key sampling sites on monthly basis (total of 22,350 observations). The dataset was treated using cluster analysis (CA), principal component analysis and multiple regression analysis on principal components. CA showed four different groups of similarity between the sampling sites reflecting the different physicochemical characteristics and pollution levels of the studied water systems. Six latent factors were identified as responsible for the data structure explaining 90% of the total variance of the dataset and are conditionally named organic, nutrient, physicochemical, weathering, soil-leaching and toxic-anthropogenic factors. A multivariate receptor model was also applied for source apportionment estimating the contribution of identified sources to the concentration of the physicochemical parameters. This study presents the necessity and usefulness of multivariate statistical assessment of large and complex databases in order to get better information about the quality of surface water, the design of sampling and analytical protocols and the effective pollution control/management of the surface waters.

Environmental Monitoring↗
PubMed2000

Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases.

The alpha-amylase sequences contained in databanks were screened for the presence of amino acid residues Arg195, Asn298 and Arg/Lys337 forming the chloride-binding site of several specialized alpha-amylases allosterically activated by this anion. This search provides 38 alpha-amylases potentially binding a chloride ion. All belong to animals, including mammals, birds, insects, acari, nematodes, molluscs, crustaceans and are also found in three extremophilic Gram-negative bacteria. An evolutionary distance tree based on complete amino acid sequences was constructed, revealing four distinct clusters of species. On the basis of multiple sequence alignment and homology modeling, invariable structural elements were defined, corresponding to the active site, the substrate binding site, the accessory binding sites, the Ca(2+) and Cl(-) binding sites, a protease-like catalytic triad and disulfide bonds. The sequence variations within functional elements allowed engineering strategies to be proposed, aimed at identifying and modifying the specificity, activity and stability of chloride-dependent alpha-amylases.

Amino Acid Sequence↗
PubMed2000

Control of dendritic field formation in Drosophila: the roles of flamingo and competition between homologous neurons.

Neurons elaborate dendrites with stereotypic branching patterns, thereby defining their receptive fields. These branching patterns may arise from properties intrinsic to the neurons or competition between neighboring neurons. Genetic and laser ablation studies reported here reveal that different multiple dendritic neurons in the same dorsal cluster in the Drosophila embryonic PNS do not compete with one another for dendritic fields. In contrast, when dendrites from homologous neurons in the two hemisegments meet at the dorsal midline in larval stages, they appear to repel each other. The formation of normal dendritic fields and the competition between dendrites of homologous neurons require the proper expression level of Flamingo, a G protein-coupled receptor-like protein, in embryonic neurons. Whereas Flamingo functions downstream of Frizzled in specifying planar polarity, Flamingo-dependent dendritic outgrowth is independent of Frizzled.

Animals↗
PubMed2026

Hyperlactate-Associated Lysine Lactylome Remodeling in Laryngeal Squamous Cell Carcinoma.

Laryngeal squamous cell carcinoma (LSCC) lacks reliable biomarkers, and the roles of lactate metabolism and lysine lactylation (Kla) remain largely unknown. We profiled the lysine lactylome of LSCC, paired it with adjacent normal tissues, and integrated the data with quantitative proteomic and transcriptomic analyses. LSCC exhibited a hyperlactate-associated phenotype characterized by dysregulated lactate-related genes (LRGs), altered protein abundance, increased tissue lactate, and globally increased Kla levels. Data-independent acquisition mass spectrometry (DIA-MS) identified 1616 Kla sites on 1468 peptides from 688 proteins, with most differential sites being upregulated in tumors. Differentially lactylated proteins were enriched in cell-matrix adhesion, cell migration, chromatin remodeling, and gene-regulatory processes and were clustered into cytoskeletal and nuclear regulatory modules. Multiple Kla sites were also detected on the core histones. Immunoblotting and tissue microarray analyses confirmed increased pan-Kla expression in the LSCC. Pan-Kla levels were independent of sex and age but positively correlated with the tumor stage and lymph-node metastasis. These findings provide a systematic resource for hyperlactate-associated lactylome remodeling in LSCCs and identify candidate Kla-related molecular features associated with clinicopathological progression for future functional and clinical evaluation.

Humans↗
PubMed1992

Structure and stability of sodium and potassium complexes of dT4G4 and dT4G4T.

The ends of eukaryotic chromosomes contain specialized structures that include DNA with multiple tandem repeats of simple sequences containing clusters of G on one strand, together with proteins which synthesize and bind to these sequences. The unit repeat in the protozoan Oxytricha with the cluster dT4G4 can form structures containing tetrads of guanine residues, referred to G4 DNA, in the presence of metal ions such as Na+ or K+. We show here that, in the presence of Na+, dT4G4 forms a tetramer with parallel strands by means of a UV cross-linking assay. In the presence of K+, two further interactions are observed: at low temperature, higher order complexes are formed, provided the 3' end of the strand is G; a single 3'T inhibits this association in dT4G4T. At high temperature, these complexes dissociate, leading to a tetramer with a different ordered structure that melts only at very high temperatures. These results suggest that the cohesive properties of DNA containing G clusters might depend on associative interactions driven by a free 3'G terminus in the presence of K+, as well as by connecting antiparallel G hairpins as has been postulated.

Circular Dichroism↗
PubMed1996

Identity of prokaryotic and eukaryotic tRNA(Asp) for aminoacylation by aspartyl-tRNA synthetase from Thermus thermophilus.

The aspartate identity of tRNA for AspRS from Thermus thermophilus has been investigated by kinetic analysis of the aspartylation reaction of different tRNA molecules and their variants as well as of tRNAPhe variants with transplanted aspartate identity elements. It is shown that G10, G34, U35, C36, C38, and G73 determine recognition and aspartylation of yeast and T.thermophilus tRNA(Asp) by the thermophilic AspRS. This set of nucleotides specifies also tRNA aspartylation in the homologous yeast and Escherichia coli systems. Structural considerations indicate that the major aspartate identity elements interact with amino acids conserved in all AspRSs. It follows that the structural features of tRNA and synthetase specifying aspartylation are mainly conserved in various structural contexts and in organisms adapted to different life conditions. Mutations of tRNA identity elements provoke drastic losses of charging in the heterologous system involving yeast tRNA(Asp) and T. thermophilus AspRS. In the homologous systems, the mutational effects are less pronounced. However, effects in E. coli and T. thermophilus exceed those in yeast which are particularly moderate, indicating variations in the individual contributions of identity elements for aspartylation in prokaryotes and eukaryotes. Analysis of multiple tRNA mutants reveals cooperativity between the cluster of determinants of the anticodon loop and the additional determinants G10 and G73 for efficient aspartylation in the thermophilic system, suggesting that conformational changes trigger formation of the functional tRNA/synthetase complex.

Amino Acid Sequence↗
PubMed1999

Pathobiologic identification of two distinct breast carcinoma subsets with diverging clinical behaviors.

Many different pathological and biological variables which characterize breast carcinomas have been found to be associated. The aim of this work was to analyze the complex relationship among these parameters. The pathologic, biologic, and clinical characteristics of a series of primary breast carcinomas from 676 patients were retrospectively investigated. Multiple correspondence analysis of 13 factors revealed clustering of eight pathobiologic variables, that is histologic grade, necrosis, lymphoid infiltration, number of mitoses, c-erbB-2 overexpression, p53, progesterone receptor, and bcl2 expression. An index for each tumor calculated on the basis of these eight factors served to distinguish two different tumor phenotypes, designated A and B. Phenotype A is represented by tumors sharing most of the biologic features of normal breast tissues: indeed, these tumors are characterized by a relatively high degree of differentiation, low proliferation, no necrosis or leukocyte infiltration, and no gene alterations. By contrast, phenotype B is quite divergent from the normal tissue because of its poor differentiation, high proliferation, frequent gene alterations and evidence of a host immune reaction. As regards the disease progression, these two subsets showed marked differences: phenotype A tumors had a low recurrence rate per year that remained constant over time and affected more frequently elderly patients, whereas group B tumors showed high aggressivity in the first years after surgery followed by a low long-term recurrence rate and were more frequently seen in younger patients. These data suggest that breast carcinoma consists of two different subsets that can be identified on the basis of pathobiologic features.

Adult↗
PubMed2003

Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism.

The isoprenoid biosynthetic pathway provides intermediates for the synthesis of a multitude of natural products which serve numerous biochemical functions in plants: sterols (isoprenoids with a C30 backbone) are essential components of membranes; carotenoids (C40) and chlorophylls (which contain a C20 isoprenoid side-chain) act as photosynthetic pigments; plastoquinone, phylloquinone and ubiquinone (all of which contain long isoprenoid side-chains) participate in electron transport chains; gibberellins (C20), brassinosteroids (C30) and abscisic acid (C15) are phytohormones derived from isoprenoid intermediates; prenylation of proteins (with C15 or C20 isoprenoid moieties) may mediate subcellular targeting and regulation of activity; and several monoterpenes (C10), sesquiterpenes (C15) and diterpenes (C20) have been demonstrated to be involved in plant defense. Here we present a comprehensive analysis of genes coding for enzymes involved in the metabolism of isoprenoid-derived compounds in Arabidopsis thaliana. By combining homology and sequence motif searches with knowledge regarding the phylogenetic distribution of pathways of isoprenoid metabolism across species, candidate genes for these pathways in A. thaliana were obtained. A detailed analysis of the vicinity of chromosome loci for genes of isoprenoid metabolism in A. thaliana provided evidence for the clustering of genes involved in common pathways. Multiple sequence alignments were used to estimate the number of genes in gene families and sequence relationship trees were utilized to classify their individual members. The integration of all these datasets allows the generation of a knowledge-based metabolic map of isoprenoid metabolic pathways in A. thaliana and provides a substantial improvement of the currently available gene annotation.

Abscisic Acid↗
PubMed1995

Lethal beta-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF.

Globin genes are regulated in a tissue-specific and developmental stage-specific manner, with the beta-globin gene being the last to be activated in the beta-gene cluster. CACCC-nucleotide sequences, which bind multiple nuclear proteins, including ubiquitously expressed Sp1 and erythroid Krüppel-like factor (EKLF), are among the cis-regulatory sequences critical for transcription of globin and non-globin erythroid-expressed genes. To determine the function of EKLF in vivo, we created mice deficient in EKLF by gene targeting. These embryos die of anaemia during fetal liver erythropoiesis and show the molecular and haematological features of beta-globin deficiency, found in beta-thalassaemia. Although it is expressed at all stages, EKLF is not required for yolk sac erythropoiesis, erythroid commitment or expression of other potential target genes. Its stage-specific and beta-globin-gene-specific requirement suggests that EKLF may facilitate completion of the fetal-to-adult (haemoglobin gamma to beta) switch in humans.

Anemia↗
PubMed1993

Analysis of individual positron emission tomography activation maps by detection of high signal-to-noise-ratio pixel clusters.

We present a new method for the analysis of individual brain positron emission tomography (PET) activation maps that looks for activated areas of a certain size rather than pixels with maximum values. High signal-to-noise-ratio pixel clusters (HSC) are identified and their sizes are statistically tested with respect to a Monte-Carlo-derived distribution of cluster sizes in pure noise images. From multiple HSC size tests, a strategy is proposed for control of the overall type I error. The sensitivity and specificity of this method have been assessed using realistic Monte Carlo simulations of brain activation maps. When compared with the gamma 2 statistic of the local maxima distribution, the proposed method showed enhanced sensitivity, particularly for signals of low magnitude and/or large size. Its potential for the individual analysis of PET activation studies is presented in two sets of subjects who underwent two cognitive protocols. Although it can be viewed as an alternative to the classical stereotactic averaging approach, this new method is intended to be a first step toward the analysis of single-subject PET activation studies.

Brain↗
PubMed2006

Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray.

Understanding the molecular mechanisms underlying fatty liver disease (FLD) in humans is of major importance. We used high-density oligonucleotide microarrays (22.3 K) to assess the mechanisms responsible for the development of human liver steatosis. We compared global gene expression in normal (n=9) and steatotic (n=9) livers without histological signs of inflammation or fibrosis. A total of 34 additional human samples including normal (n=11), steatosis (n=11), HCV-related steatosis (n=4) or steatohepatitis associated with alcohol consumption (n=4) or obesity (n=4) were used for immunohistochemistry or quantitative real-time PCR studies. With unsupervised classification (no gene selection), all steatotic liver samples clustered together. Using step-down maxT multiple testing procedure for controlling the Family-Wise Error-Rate at level 5%, 110 cDNAs (100 over- and 10 underexpressed) were found to be differentially expressed in steatotic and normal livers. Of them were genes involved in mitochondrial phosphorylative and oxidative metabolism. The mean ratio of mitochondrial DNA to nuclear DNA content was higher in liver steatosis compared to normal liver biopsies (1.12+/-0.14 vs 0.67+/-0.10; P=0.01). An increased expression of genes involved in inflammation (IL-1R family, TGFB) was also observed and confirmed by quantitative RT-PCR or immunochemistry. In steatohepatitis, an increase of the protein expression of mitochondrial antigens, IL-1R1, IGF2 and TGFB1 was also observed, interleukin 1 receptor being always strongly expressed in steatohepatitis linked to alcohol or obesity. In conclusion, mitochondrial alterations play a major role in the development of steatosis per se. Activation of inflammatory pathways is present at a very early stage of steatosis, even if no morphological sign of inflammation is observed.

DNA, Mitochondrial↗
PubMed2004

Evolving nature of the AP2 alpha-appendage hub during clathrin-coated vesicle endocytosis.

Clathrin-mediated endocytosis involves the assembly of a network of proteins that select cargo, modify membrane shape and drive invagination, vesicle scission and uncoating. This network is initially assembled around adaptor protein (AP) appendage domains, which are protein interaction hubs. Using crystallography, we show that FxDxF and WVxF peptide motifs from synaptojanin bind to distinct subdomains on alpha-appendages, called 'top' and 'side' sites. Appendages use both these sites to interact with their binding partners in vitro and in vivo. Occupation of both sites simultaneously results in high-affinity reversible interactions with lone appendages (e.g. eps15 and epsin1). Proteins with multiple copies of only one type of motif bind multiple appendages and so will aid adaptor clustering. These clustered alpha(appendage)-hubs have altered properties where they can sample many different binding partners, which in turn can interact with each other and indirectly with clathrin. In the final coated vesicle, most appendage binding partners are absent and thus the functional status of the appendage domain as an interaction hub is temporal and transitory giving directionality to vesicle assembly.

Adaptor Protein Complex 2↗
PubMed1997

Intra-vascular tumour in pleomorphic adenomas--a report of four cases.

AIMS: The aim of this study was to report four cases of pleomorphic adenoma which were characterized by intra-vascular tumour. METHODS AND RESULTS: The patients ranged in age from 13-43 years, one was male while three were female. The tumours were situated in the parotid gland, submandibular gland and palate (two cases). The intra-vascular tumour consisted of single, clustered and solid cords of cells within multiple muscular walled blood vessels and capillaries both in the capsule and in the tumour. Immunoperoxidase staining confirmed that the intra-vascular cells were phenotypically identical to those of the tumour. The possibility that the intra-vascular tumour represents artefactual 'spillage' has been considered, however there is some histological evidence suggesting that this phenomenon represents true vascular invasion. CONCLUSIONS: The biological significance of intra-vascular tumour in pleomorphic adenomas is unknown. Thus far there has been no correlation with either recurrence or metastases.

Adenoma, Pleomorphic↗
PubMed2002

Identification of novel factors involved in colonization and acid tolerance of Vibrio cholerae.

Despite over 100 years of study, the intestinal pathogen Vibrio cholerae still causes epidemic disease in areas of the world where there is poor sanitation. While cholera toxin and the toxin-coregulated pilus (TCP) are known to be essential for full virulence, the role that other factors play has remained ill-defined. Herein, we describe a large-scale signature-tagged mutagenesis (STM) screen utilizing 100 pools of 96 mutants each to identify factors involved in colonization of the infant mouse small intestine. A total of 164 mutants representing transposition events into 95 different open reading frames were shown to be recovered at greatly reduced numbers from the infant mouse model. Analysis of the sites of insertion revealed multiple independent mutations within the rfb gene cluster, needed for synthesis of lipopolysaccharide (LPS), and the tcp gene cluster, needed for synthesis of the TCP. More importantly, in addition to these previously known colonization factors, we identified many genes whose activity in colonization was not previously appreciated. These can be divided into a number of functional groups, which include production of factors involved in metabolic activities, regulation of cellular processes, transport, adaptation to stress and unknown functions. In addition, we describe the reiterative use of STM, whereby colonization-defective mutants were assembled into virulence-attenuated pools (VAPs), which were used to begin to reveal roles that the identified virulence factors play in the infection process. Nine new factors were shown to be crucial for the V. cholerae acid tolerance response, which has previously been hypothesized to be important for epidemic spread of cholera. Competition assays of these nine acid tolerance response (ATR)-defective mutants revealed that mutations in gshB, hepA and recO result in a 1000-fold reduction in colonization.

Animals↗