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Several Clusters (several + cluster)
Selected AbstractsGene diversity of CYP153A and AlkB alkane hydroxylases in oil-degrading bacteria isolated from the Atlantic OceanENVIRONMENTAL MICROBIOLOGY, Issue 5 2010Liping Wang Summary Alkane hydroxylases, including the integral-membrane non-haem iron monooxygenase (AlkB) and cytochrome P450 CYP153 family, are key enzymes in bacterial alkane oxidation. Although both genes have been detected in a number of bacteria and environments, knowledge about the diversity of these genes in marine alkane-degrading bacteria is still limited, especially in pelagic areas. In this report, 177 bacterial isolates, comprising 43 genera, were obtained from 18 oil-degrading consortia enriched from surface seawater samples collected from the Atlantic Ocean. Many isolates were confirmed to be the first oil-degraders in their affiliated genera including Brachybacterium, Idiomarina, Leifsonia, Martelella, Kordiimonas, Parvibaculum and Tistrella. Using degenerate PCR primers, alkB and CYP153A P450 genes were surveyed in these bacteria. In total, 82 P450 and 52 alkB gene fragments were obtained from 80 of the isolates. These isolates mainly belonged to Alcanivorax, Bacillus, Erythrobacter, Martelella, Parvibaculum and Salinisphaera, some of which were reported, for the first time, to encode alkane hydroxylases. Phylogenetic analysis showed that both genes were quite diverse and formed several clusters, most of which were generated from various Alcanivorax bacteria. Noticeably, some sequences, such as those from the Salinisphaera genus, were grouped into a distantly related novel cluster. Inspection of the linkage between gene and host revealed that alkB and P450 tend to coexist in Alcanivorax and Salinisphaera, while in all isolates of Parvibaculum, only P450 genes were found, but of multiple homologues. Multiple homologues of alkB mostly cooccurred in Alcanivorax isolates. Conversely, distantly related isolates contained similar or even identical sequences. In summary, various oil-degrading bacteria, which harboured diverse P450 and alkB genes, were found in the surface water of Atlantic Ocean. Our results help to show the diversity of P450 and alkB genes in prokaryotes, and to portray the geographic distribution of oil-degrading bacteria in marine environments. [source] Identification of a distinct family of genes encoding atypical odorant-binding proteins in the malaria vector mosquito, Anopheles gambiaeINSECT MOLECULAR BIOLOGY, Issue 6 2003P. X. Xu Abstract We performed a genome-wide analysis for candidate odorant-binding protein (OBP) genes in the malaria vector Anopheles gambiae (Ag). We identified fifty-seven putative genes including sixteen genes predicted to encode distinct, higher molecular weight proteins that lack orthologues in Drosophila. Expression analysis indicates that several of these atypical AgOBPs are transcribed in chemosensory organs in adult and immature stages. Phylogenetic analysis of the Anopheles and Drosophila OBP families reveals these proteins fall into several clusters based on sequence similarity and suggests the atypical AgOBP genes arose in the mosquito lineage after the divergence of mosquitoes and flies. The identification of these AgOBP genes is the first step towards determining their biological roles in this economically and medically important insect. [source] Phenotypic study by numerical taxonomy of strains belonging to the genus AeromonasJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2002L. Valera Aims: ,This study was undertaken to cluster and identify a large collection of Aeromonas strains. Methods and Results: ,Numerical taxonomy was used to analyse phenotypic data obtained on 54 new isolates taken from water, fish, snails, sputum and 99 type and reference strains. Each strain was tested for 121 characters but only the data for 71 were analysed using the `SSM' and `SJ' coefficients, and the UPGMA clustering algorithm. At SJ values of , 81·6% the strains clustered into 22 phenons which were identified as Aer. jandaei, Aer. hydrophila, Aer. encheleia, Aer. veronii biogroup veronii, Aer. trota, Aer. caviae, Aer. eucrenophila, Aer. ichthiosmia, Aer. sobria, Aer. allosaccharophila, Aer. media, Aer. schubertii and Aer. salmonicida. The species Aer. veronii biogroup sobria was represented by several clusters which formed two phenotypic cores, the first related to reference strain CECT 4246 and the second related to CECT 4835. A good correlation was generally observed among this phenotypic clustering and previous genomic and phylogenetic data. In addition, three new phenotypic groups were found, which may represent new Aeromonas species. Conclusions: ,The phenetic approach was found to be a necessary tool to delimitate and identify the Aeromonas species. Significance and Impact of the Study: ,Valuable traits for identifying Aeromonas as well as the possible existence of new Aeromonas species or biotypes are indicated. [source] Phylogenetic analyses and molecular epidemiology of European salmonid alphaviruses (SAV) based on partial E2 and nsP3 gene nucleotide sequencesJOURNAL OF FISH DISEASES, Issue 11 2008E Fringuelli Abstract Sequence data were generated for portions of the E2 and nsP3 genes of 48 salmonid alphaviruses from farmed Atlantic salmon (AS), Salmo salar L., and rainbow trout (RT), Oncorhynchus mykiss (Walbaum), in marine and freshwater environments, respectively, from the Republic of Ireland, Northern Ireland, England, Scotland, Norway, France, Italy and Spain between 1991 and 2007. Based on these sequences, and those of six previously published reference strains, phylogenetic trees were constructed using the parsimony method. Trees generated with both gene segments were similar. Clades corresponding to the three previously recognized subtypes were generated and in addition, two further new clades of viruses were identified. A single further strain (F96-1045) was found to be distinct from all of the other strains in the study. The percentage of nucleotide divergence within clades was generally low (0,4.8% for E2, 0,6.6% for nsP3). Interclade divergence tended to be higher (3.4,19.7% for E2, 6.5,28.1% for nsP3). Based on these results and using current SAV terminology, the two new clades and F96-1045 were termed SAV subtypes 4, 5 and 6, respectively. SAV4 contained AS strains from Ireland and Scotland, while SAV5 contained only Scottish AS strains. Recently identified SAV strains from RT in Italy and Spain were shown to belong to SAV2. In addition, marine AS strains belonging to SAV2 were identified for the first time. Analysis of the origin of several clusters of strains with identical E2 and nsP3 sequences strongly support horizontal transmission of virus between farms and aquaculture companies. Evidence in support of vertical transmission was not found. [source] Genome-Wide Association Study of Alcohol Dependence Implicates a Region on Chromosome 11ALCOHOLISM, Issue 5 2010Howard J. Edenberg Background:, Alcohol dependence is a complex disease, and although linkage and candidate gene studies have identified several genes associated with the risk for alcoholism, these explain only a portion of the risk. Methods:, We carried out a genome-wide association study (GWAS) on a case,control sample drawn from the families in the Collaborative Study on the Genetics of Alcoholism. The cases all met diagnostic criteria for alcohol dependence according to the Diagnostic and Statistical Manual of Mental Disorders,Fourth Edition; controls all consumed alcohol but were not dependent on alcohol or illicit drugs. To prioritize among the strongest candidates, we genotyped most of the top 199 single nucleotide polymorphisms (SNPs) (p , 2.1 × 10,4) in a sample of alcohol-dependent families and performed pedigree-based association analysis. We also examined whether the genes harboring the top SNPs were expressed in human brain or were differentially expressed in the presence of ethanol in lymphoblastoid cells. Results:, Although no single SNP met genome-wide criteria for significance, there were several clusters of SNPs that provided mutual support. Combining evidence from the case,control study, the follow-up in families, and gene expression provided strongest support for the association of a cluster of genes on chromosome 11 (SLC22A18, PHLDA2, NAP1L4, SNORA54, CARS, and OSBPL5) with alcohol dependence. Several SNPs nominated as candidates in earlier GWAS studies replicated in ours, including CPE, DNASE2B, SLC10A2, ARL6IP5, ID4, GATA4, SYNE1, and ADCY3. Conclusions:, We have identified several promising associations that warrant further examination in independent samples. [source] A robust clustering approach for NMR spectra of natural product extractsMAGNETIC RESONANCE IN CHEMISTRY, Issue 5 2005Gregory K. Pierens Abstract A robust method was developed to cluster similar NMR spectra from partially purified extracts obtained from a range of marine sponges and a plant biota. The NMR data were acquired using microtiter plate NMR (VAST) in protonated solvents. A sample data set which contained several clusters was used to optimize the protocol. The evaluation of the robustness was performed using three different clustering methods: tree clustering analysis, K-means clustering and multidimensional scaling. These methods were compared for consistency using the sample data set and the optimized methodology was applied to clustering of a set of spectra from partially purified biota extracts. Copyright © 2005 John Wiley & Sons, Ltd. [source] What is the largest Einstein radius in the universe?MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2009Masamune Oguri ABSTRACT The Einstein radius plays a central role in lens studies as it characterizes the strength of gravitational lensing. In particular, the distribution of Einstein radii near the upper cut-off should probe the probability distribution of the largest mass concentrations in the universe. Adopting a triaxial halo model, we compute expected distributions of large Einstein radii. To assess the cosmic variance, we generate a number of Monte Carlo realizations of all-sky catalogues of massive clusters. We find that the expected largest Einstein radius in the universe is sensitive to parameters characterizing the cosmological model, especially ,8: for a source redshift of unity, they are 42+9,7, 35+8,6 and 54+12,7 arcsec (errors denote 1, cosmic variance), assuming best-fitting cosmological parameters of the Wilkinson Microwave Anisotropy Probe five-year (WMAP5), three-year (WMAP3) and one-year (WMAP1) data, respectively. These values are broadly consistent with current observations given their incompleteness. The mass of the largest lens cluster can be as small as , 1015 M,. For the same source redshift, we expect in all sky ,35 (WMAP5), ,15 (WMAP3) and ,150 (WMAP1) clusters that have Einstein radii larger than 20 arcsec. For a larger source redshift of 7, the largest Einstein radii grow approximately twice as large. Whilst the values of the largest Einstein radii are almost unaffected by the level of the primordial non-Gaussianity currently of interest, the measurement of the abundance of moderately large lens clusters should probe non-Gaussianity competitively with cosmic microwave background experiments, but only if other cosmological parameters are well measured. These semi-analytic predictions are based on a rather simple representation of clusters, and hence calibrating them with N -body simulations will help to improve the accuracy. We also find that these ,superlens' clusters constitute a highly biased population. For instance, a substantial fraction of these superlens clusters have major axes preferentially aligned with the line-of-sight. As a consequence, the projected mass distributions of the clusters are rounder by an ellipticity of ,0.2 and have , 40,60 per cent larger concentrations compared with typical clusters with similar redshifts and masses. We argue that the large concentration measured in A1689 is consistent with our model prediction at the 1.2, level. A combined analysis of several clusters will be needed to see whether or not the observed concentrations conflict with predictions of the flat ,-dominated cold dark matter model. [source] Adenovirus infections within a family cohort in Iran,PEDIATRIC PULMONOLOGY, Issue 8 2009Mohammadreza Naghipour PhD Abstract Background Adenovirus is one of the most frequent viruses associated with acute respiratory infections (ARI). There is limited information of its transmission within the community. Methods Cohorts of 50 families with ,two children were visited weekly for 2 months to ascertain the presence ARI in Rasht, Iran. Nasopharyngeal swabs were obtained from symptomatic participants and at 3,4-day intervals to assess the duration of adenovirus shedding. Adenoviruses were identified by PCR and adenovirus positive amplicons were subjected to DNA sequencing. Results Thirty-three (35%) of 94 ARI episodes in children and 8 (27%) of 30 episodes in adults were due to adenovirus (not significant, NS). 25/50 (50%) families had adenovirus infections. Children had more infections than adults, were more likely to develop symptoms if there was a symptomatic case within the household and episodes had a longer duration (P,<,0.05). Adenoviruses were recovered for a median of 11 (interquartile range 5,26) days of follow up in children and 7 (2,20) days in adults (NS). Adenovirus-7 was the most frequent serotype (12 families), followed by adenovirus-6 (5 families), adenovirus-1 and 2 (4 families each), and adenovirus-5 (3 families). Both adenovirus-5 and 7 amplicons fell into two clusters. No mutations were observed during transmission within a family. Conclusion A substantial proportion of ARI in the community are due to adenovirus with further transmission within the family. Children ,2 years experienced a higher proportion of infections than younger children and adults. Viral shedding was more prolonged in children and adenovirus-7 and 5 predominated with several clusters co-circulating in the same season. Pediatr Pulmonol. 2009; 44:749,753. © 2009 Wiley-Liss, Inc. [source] Gene amplification of the transcription factor DP1 and CTNND1 in human lung cancer,THE JOURNAL OF PATHOLOGY, Issue 1 2010Sandra D. Castillo Abstract The search for novel oncogenes is important because they could be the target of future specific anticancer therapies. In the present paper we report the identification of novel amplified genes in lung cancer by means of global gene expression analysis. To screen for amplicons, we aligned the gene expression data according to the position of transcripts in the human genome and searched for clusters of over-expressed genes. We found several clusters with gene over-expression, suggesting an underlying genomic amplification. FISH and microarray analysis for DNA copy number in two clusters, at chromosomes 11q12 and 13q34, confirmed the presence of amplifications spanning about 0.4 and 1 Mb for 11q12 and 13q34, respectively. Amplification at these regions each occurred at a frequency of 3%. Moreover, quantitative RT,PCR of each individual transcript within the amplicons allowed us to verify the increased in gene expression of several genes. The p120ctn and DP1 proteins, encoded by two candidate oncogenes, CTNND1 and TFDP1, at 11q12 and 13q amplicons, respectively, showed very strong immunostaining in lung tumours with gene amplification. We then focused on the 13q34 amplicon and in the TFDP1 candidate oncogene. To further determine the oncogenic properties of DP1, we searched for lung cancer cell lines carrying TFDP1 amplification. Depletion of TFDP1 expression by small interference RNA in a lung cancer cell line (HCC33) with TFDP1 amplification and protein over-expression reduced cell viability by 50%. In conclusion, we report the identification of two novel amplicons, at 13q34 and 11q12, each occurring at a frequency of 3% of non-small cell lung cancers. TFDP1, which encodes the E2F-associated transcription factor DP1 is a candidate oncogene at 13q34. The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series Accession No. GSE21168. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Genetic structure of a wide-spectrum chicken gene poolANIMAL GENETICS, Issue 5 2009Z. Granevitze Summary The genetic structure of 65 chicken populations was studied using 29 simple sequence repeat loci. Six main clusters which corresponded to geographical origins and histories were identified: Brown Egg Layers; predominantly Broilers; native Chinese breeds or breeds with recent Asian origin; predominantly breeds of European derivation; a small cluster containing populations with no common history and populations that had breeding history with White Leghorn. Another group of populations that shared their genome with several clusters was defined as ,Multi-clusters'. Gallus gallus gallus (Multi-clusters), one of the subspecies of the Red Jungle Fowl, which was previously suggested to be one of the ancestors of the domesticated chicken, has almost no shared loci with European and White Egg layer populations. In a further sub-clustering of the populations, discrimination between all the 65 populations was possible, and relationships between each were suggested. The genetic variation between populations was found to account for about 34% of the total genetic variation, 11% of the variation being between clusters and 23% being between populations within clusters. The suggested clusters may assist in future studies of genetic aspects of the chicken gene pool. [source] Developmental microRNA expression profiling of murine embryonic orofacial tissueBIRTH DEFECTS RESEARCH, Issue 7 2010Partha Mukhopadhyay Abstract BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. METHODS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real-time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. RESULTS: Expression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD-12,GD-14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters wereshown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. Birth Defects Research (Part A), 2010. © 2010 Wiley-Liss, Inc. [source] Birth Defects Cluster Study: A national approach to birth defects cluster investigations,,BIRTH DEFECTS RESEARCH, Issue 11 2008James E. Kucik Abstract BACKGROUND: Investigations of clusters of birth defects have been challenging endeavors that have had only modest success identifying causes or risk factors. Some of the challenges to individual cluster investigations have been small sample size and limited data collection. We describe a novel approach for investigating and analyzing pooled information from a series of birth defects cluster investigations. METHODS: The Birth Defects Cluster Study uses a case-control study design with standardized methods, including a case definition, control selection, data collection methods, and data collected (e.g., maternal interviews, blood samples, and environmental samples). Analyses of pooled data from several clusters of the same defect are conducted for specific hypotheses once a sufficient sample size has been achieved. The feasibility of conducting individual birth defect investigations was evaluated on a cluster of gastroschisis. RESULTS: The pilot investigation of a cluster of gastroschisis demonstrated success in recruiting participants and in collecting data and specimens for eventual inclusion in a pooled analysis. CONCLUSIONS: The Birth Defects Cluster Study offers a unique and effective approach to cluster investigations that improves the likelihood of identifying genetic and environmental causes of birth defects and provides a model for cluster investigations of other noninfectious health outcomes. Birth Defects Research (Part A), 2008. Published 2008 Wiley-Liss, Inc. [source] | |||||||||||||