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Same Cluster (same + cluster)
Selected AbstractsIdentification of Cephalopod Species (Ommastrephidae and Loliginidae) in Seafood Products by Forensically Informative Nucleotide Sequencing (FINS)JOURNAL OF FOOD SCIENCE, Issue 5 2002M.J. Chapela ABSTRACT: An identification technique of commercially important cephalopods based on 16s RNA analysis was developed. A set of primers was designed to amplify a fragment of approximately 200 bp that presents enough variability for reliable species identification. Sequences from this fragment of 9 different authentic species were studied, genetic distances were measured, and a phylogenetic tree was constructed, with individuals of the same species grouped within the same cluster. Eight different types of commercial seafood products, mainly labelled as "squid rings", were analyzed and sequences were employed for species identification showing that FINS is a suitable technique for identification of processed cephalopods. [source] Discrepancies between the phenotypic and genotypic characterization of Lactococcus lactis cheese isolatesLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2006M. De La Plaza Abstract Aims:, The use of randomly amplified polymorphic DNA (RAPD)-PCR fingerprinting and plasmid profiles to determine at the strain level, the similarity of Lactococcus lactis isolates obtained during sampling of traditional cheeses and to verify its correspondence to the selected phenotypic characteristics. Methods and Results:, A total of 45 L. lactis isolates were genotypically analysed by RAPD-PCR fingerprinting and plasmid patterns. Phenotypic traits used to compare strains were proteolytic, acidifying, aminotransferase (aromatic and branched chain aminotransferase) and , -ketoisovalerate decarboxylase (Kivd) activities. The results show that 23 isolates could be grouped in clusters that exhibited 100% identity in both their RAPD and plasmid patterns, indicating the probable isolation of dominant strains during the cheese sampling process. However, there were phenotypic differences between isolates within the same cluster that included the loss of relevant technological properties such as proteinase activity and acidifying capacity or high variation in their amino acid converting enzyme activities. Likewise, the analysis of a specific attribute, Kivd activity, indicated that 7 of 15 isolates showed no detectable activity despite the presence of the encoding (kivd) gene. Conclusion:, Phenotypic differences found between genotypically similar strains of L. lactis strains could be linked to differences in enzymatic expression. Significance and Impact of the Study:, Phenotypic analysis of L. lactis isolates should be considered when selecting strains with new cheese flavour forming capabilities. [source] Allosteric transition pathways in the lactose repressor protein core domains: Asymmetric motions in a homodimerPROTEIN SCIENCE, Issue 11 2003Terence C. Flynn Abstract The crystal structures of lactose repressor protein (LacI) provide static endpoint views of the allosteric transition between DNA- and IPTG-bound states. To obtain an atom-by-atom description of the pathway between these two conformations, motions were simulated with targeted molecular dynamics (TMD). Strikingly, this homodimer exhibited asymmetric dynamics. All asymmetries observed in this simulation are reproducible and can begin on either of the two monomers. Asymmetry in the simulation originates around D149 and was traced back to the pre-TMD equilibrations of both conformations. In particular, hydrogen bonds between D149 and S193 adopt a variety of configurations during repetitions of this process. Changes in this region propagate through the structure via noncovalent interactions of three interconnected pathways. The changes of pathway 1 occur first on one monomer. Alterations move from the inducer-binding pocket, through the N-subdomain ,-sheet, to a hydrophobic cluster at the top of this region and then to the same cluster on the second monomer. These motions result in changes at (1) side chains that form an interface with the DNA-binding domains and (2) K84 and K84', which participate in the monomer,monomer interface. Pathway 2 reflects consequent reorganization across this subunit interface, most notably formation of a H74-H74rsquo; ,-stacking intermediate. Pathway 3 extends from the rear of the inducer-binding pocket, across a hydrogen-bond network at the bottom of the pocket, and transverses the monomer,monomer interface via changes in H74 and H74rsquo;. In general, intermediates detected in this study are not apparent in the crystal structures. Observations from the simulations are in good agreement with biochemical data and provide a spatial and sequential framework for interpreting existing genetic data. [source] Cloning and Sequencing of the Biosynthetic Gene Cluster for Saquayamycin Z and Galtamycin B and the Elucidation of the Assembly of Their Saccharide ChainsCHEMBIOCHEM, Issue 8 2009Annette Erb Abstract Sweet ways: We have investigated the glycosyltransferase genes of the saquayamycin Z (shown) and galtamycin B biosynthetic gene cluster from Micromonospora sp. Tü6368. The results unambiguously show that both compounds are derived from the same cluster. Furthermore, the function of five glycosyltransferases was elucidated, and the results have shed light on the assembly of the sugar chains. The Gram-positive bacterium, Micromonospora sp. Tü6368 produces the angucyclic antibiotic saquayamycin Z and the tetracenequinone galtamycin B. The structural similarity of both compounds suggests a common biosynthetic pathway. The entire biosynthetic gene cluster (saq gene cluster) was cloned and characterized. DNA sequence analysis of a 36.7 kb region revealed the presence of 31 genes that are probably involved in saquayamycin Z and galtamycin B formation. Heterologous expression experiments and targeted gene inactivations were carried out to specifically manipulate the saquayamycin Z and galtamycin B pathways; this demonstrated unambiguously that both compounds are derived from the same cluster. The inactivation of glycosyltransferase genes led to the production of novel saquayamycin and galtamycin derivatives, provided information on the assembly of the sugar chains, and showed that tetracenequinones are formed from angucyclines. [source] Measuring simultaneous belongingness for sets of objectsINTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 4 2008Vicenç Torra This paper presents the so-called measures of simultaneous belongingness. These measures are used in clustering for establishing in which extent two objects belong to the same clusters. In the case of fuzzy clustering, the measure also takes into account fuzzy membership. In this paper, we establish a more general framework and, in particular, we introduce a definition that permits to compute this measure for sets of objects (instead of only to pairs of them). © 2008 Wiley Periodicals, Inc. [source] Identification of tryptase- and chymase-related gene clusters in human mast cells using microarraysALLERGY, Issue 3 2006C. Dahl Tryptase and chymase are the two major granular proteases present in human mast cell (MC)s. We used oligonucleotide microarray to measure the levels of approximately 22 000 transcripts in cord blood-derived MCs at 4 weeks, 8 weeks, 12 weeks and 18 weeks in culture. Tryptase (TPSB2) was expressed at the highest level among all transcripts and its expression level reached a plateau at 8 weeks. On the other hand, the expression level of chymase (CMAI) doubled every 4,6 weeks. A similar tendency was found at the protein levels with FACS analysis. After filtering the transcripts with MC-specificity, hierarchical clustering analysis identified 494 and 81 transcripts in the same clusters with tryptase and chymase, respectively. MC-specific genes, KIT and HDC were found in the tryptase cluster. In the chymase cluster, a critical suppressor for cell senescence, BMI1 and the several related genes were found, suggesting that chymase expression may be closely related to cell senescence/quiescence events. [source] Probing cosmology and galaxy cluster structure with the Sunyaev,Zel'dovich decrement versus X-ray temperature scaling relationMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2009Cien Shang ABSTRACT Scaling relations among galaxy cluster observables, which will become available in large future samples of galaxy clusters, could be used to constrain not only cluster structure, but also cosmology. We study the utility of this approach, employing a physically motivated parametric model to describe cluster structure and applying it to the expected relation between the Sunyaev,Zel'dovich decrement (S,) and the emission-weighted X-ray temperature (Tew). The slope and normalization of the entropy profile, the concentration of the dark matter potential, the pressure at the virial radius and the level of non-thermal pressure support as well as the mass and redshift dependence of these quantities are described by free parameters. With a suitable choice of fiducial parameter values, the cluster model satisfies several existing observational constraints. We employ a Fisher matrix approach to estimate the joint errors on cosmological and cluster structure parameters from a measurement of S, versus Tew in a future survey. We find that different cosmological parameters affect the scaling relation differently: predominantly through the baryon fraction (,m and ,b), the virial overdensity (w0 and wa for low- z clusters) and the angular diameter distance (w0 and wa for high- z clusters; ,DE and h). We find that the cosmology constraints from the scaling relation are comparable to those expected from the number counts (dN/dz) of the same clusters. The scaling-relation approach is relatively insensitive to selection effects and it offers a valuable consistency check; combining the information from the scaling relation and dN/dz is also useful to break parameter degeneracies and help disentangle cluster physics from cosmology. Our work suggests that scaling relations should be a useful component in extracting cosmological information from large future cluster surveys. [source] Anomalous SZ contribution to three-year WMAP dataMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 3 2007R. M. Bielby ABSTRACT We first show that the new Wilkinson Microwave Anisotropy Probe (WMAP) 3-yr data confirm the detection by Myers et al. of an extended SZ signal centred on 606 Abell (ACO) clusters with richness class, R, 2. Our results also show SZ decrements around APM and 2MASS groups at increased significance than previously detected. We then follow the approach of Lieu, Mittaz & Zhang and compare the stacked WMAP results for the decrement in 31 clusters with ROSAT X-ray profiles where Lieu et al. found on average less SZ decrement in the WMAP 1-yr data than predicted. We confirm that in the 3-yr data these same clusters again show less SZ decrement than the X-ray data predict. We then analysed the WMAP results for the 38 X-ray clusters with OVRO/BIMA measured SZ decrements as presented by Bonamente et al.. We again find that the average decrement is measured to be significantly less (5.5,) than predicted by the Chandra X-ray data. Thus while we confirm the original detection of an extended SZ effect by Myers et al., these X-ray comparisons may now suggest that the central SZ amplitudes detected by WMAP may actually be lower than expected. One possible explanation is that there is contamination of the WMAP SZ signal by radio sources in the clusters but we argue that this appears implausible. We then consider the possibility that the SZ decrement has been lensed away by foreground galaxy groups. Such a model predicts that the SZ decrement should depend on cluster redshift. A reduction in the SZ decrement with redshift is suggested from the ACO cluster sample and also from comparing the samples of Lieu et al. and Bonamente et al.. However, the mass power spectrum would require a far higher amplitude than currently expected if lensing was to explain the SZ deficit in high-redshift clusters. [source] | ||||||||||