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Combined Analysis (combined + analysis)
Selected AbstractsPhylogeny and Systematic Position of Opiliones: A Combined Analysis of Chelicerate Relationships Using Morphological and Molecular Data,CLADISTICS, Issue 1 2002Gonzalo Giribet The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones. [source] Systems biology analysis of sjögren's syndrome and mucosa-associated lymphoid tissue lymphoma in parotid glandsARTHRITIS & RHEUMATISM, Issue 1 2009Shen Hu Objective To identify key target genes and activated signaling pathways associated with the pathogenesis of Sjögren's syndrome (SS) by conducting a systems analysis of parotid glands manifesting primary SS or primary SS/mucosa-associated lymphoid tissue (MALT) lymphoma phenotypes. Methods A systems biology approach was used to analyze parotid gland tissue samples obtained from patients with primary SS, patients with primary SS/MALT lymphoma, and subjects without primary SS (non,primary SS controls). The tissue samples were assessed concurrently by gene-expression microarray profiling and proteomics analysis, followed by weighted gene-coexpression network analysis. Results Gene-coexpression modules related to primary SS and primary SS/MALT lymphoma were significantly enriched with genes known to be involved in the immune/defense response, apoptosis, cell signaling, gene regulation, and oxidative stress. Detailed functional pathway analyses indicated that primary SS,associated modules were enriched with genes involved in proteasome degradation, apoptosis, signal peptides of the class I major histocompatibility complex (MHC), complement activation, cell growth and death, and integrin-mediated cell adhesion, while primary SS/MALT lymphoma,associated modules were enriched with genes involved in translation, ribosome biogenesis and assembly, proteasome degradation, class I MHC signal peptides, the G13 signaling pathway, complement activation, and integrin-mediated cell adhesion. Combined analyses of gene expression and proteomics data implicated 6 highly connected "hub" genes for distinguishing primary SS from non,primary SS, and 8 hub genes for distinguishing primary SS/MALT lymphoma from primary SS. Conclusion Systems biology analyses of the parotid glands from patients with primary SS and those with primary SS/MALT lymphoma revealed pathways and molecular targets associated with disease pathogenesis. The identified gene modules/pathways provide further insights into the molecular mechanisms of primary SS and primary SS/MALT lymphoma. The identified disease-hub genes represent promising targets for therapeutic intervention, diagnosis, and prognosis. [source] Search for new biomarkers of gastric cancer through serial analysis of gene expression and its clinical implicationsCANCER SCIENCE, Issue 5 2004Wataru Yasui Gastric cancer is one of the most common human cancers and is the second most frequent cause of cancer-related death in the world. Serial analysis of gene expression (SAGE) is a powerful technique to allow genome-wide analysis of gene expression in a quantitative manner without prior knowledge of the gene sequences. SAGE on 5 samples of gastric cancer with different histology and clinical stages have created large SAGE libraries of gastric cancer that enable us to identify new cancer biomarkers. Commonly up-regulated genes in gastric cancer in comparison with normal gastric epithelia included CEACAM6, APOC1 and YF13H12. By comparing gene expression profiles of gastric cancers at early and advanced stages, several genes differentially expressed by tumor stage were also identified, including FUS, CDH17, COL1A1 and COL1A2, which should be novel genetic markers for high-grade malignancy. Regenerating gene type IV (REGIV) is one of the most up-regulated genes in a SAGE library of a scirrhous-type gastric cancer. In vitro studies using RegIV-transfected cells revealed that RegIV is secreted by cancer cells and inhibits apoptosis, suggesting that RegIV may serve as a novel biomarker and therapeutic target for gastric cancer. Production of RNA aptamers could be a useful approach to establish a detection system in blood. A custom-made array, named Ex-STO-MACHIP, consisting of 395 genes, including highly differentially expressed genes identified by our SAGE and other known genes related to carcinogenesis and chemosensitivity, is useful to study the molecular pathogenesis of gastric cancer and to obtain information about biological behavior and sensitivity to therapy in the clinical setting. Combined analyses of gene expression profile, genetic polymorphism and genetic instability will aid not only cancer detection, but also characterization of individual cancers and patients, leading to personalized medicine and cancer prevention. [source] The 40-mg dose of eletriptan: comparative efficacy and tolerability versus sumatriptan 100 mgEUROPEAN JOURNAL OF NEUROLOGY, Issue 2 2004Hans-Christoph Diener Meta-analysis provides valuable information regarding relative efficacies of triptans, but head-to-head comparator studies remain the gold standard. Three similar head-to-head trials comparing eletriptan 40 mg (E40) with sumatriptan 100 mg (S100) provide a rare opportunity and sufficient power, for robust comparisons of efficacy. Data were combined from three double-blind, placebo-controlled, first-dose, first-attack acute migraine treatment studies comparing E40 (n = 1132), S100 (n = 1129), and placebo (n = 645). The primary outcome was headache response at 2 h. Secondary outcomes included headache response at 1 h, pain-free and functional responses, and sustained headache and pain-free responses. Odds ratios were calculated for summary estimates of probability of response. There were higher headache response rates with eletriptan versus sumatriptan at 2 h (67% vs. 57%; P < 0.0001) and 1 h (34% vs. 26%; P < 0.0001). Eletriptan also had higher 2 h pain-free (35% vs. 25%; P < 0.0001) and functional responses (67% vs. 58%; P < 0.0001). Sustained headache (42%) and pain-free (22%) response rates were higher for eletriptan versus sumatriptan (34%, P < 0.0001; 15%, P < 0.0001). The probability of response for eletriptan versus sumatriptan ranged from 36% higher (relief of nausea) to 64% higher (sustained pain-free rate). Combined analysis demonstrates that E40 has superior efficacy versus S100 across all clinically relevant outcomes. [source] Characterization of amplicons in neuroblastoma: High-resolution mapping using DNA microarrays, relationship with outcome, and identification of overexpressed genesGENES, CHROMOSOMES AND CANCER, Issue 10 2008Anne Fix Somatically acquired chromosomal imbalances are a key feature of neuroblastoma, a heterogeneous pediatric solid tumor. Among these alterations, genomic amplification targeting the MYCN oncogene and observed in about 25,30% of the cases, strongly correlates with advanced stage and poor outcome. In this work, we have used BAC and SNP arrays as well as gene expression arrays to characterize amplifications in neuroblastoma. Eighty-eight distinct BACs defining high-level amplification events were identified in 65 samples, including 43 tumors and 22 cell lines. Although the highest recurrence was observed on chromosome 2, clones on chromosomes 8, 12, 16, and 17 also revealed genomic amplification in several samples. A detailed analysis of the 2p22-2p25 MYCN containing region indicated highly complex patterns in a number of cases. Coamplifications involving MYCN and other regions were explored by FISH in three cell lines. High-resolution arrays then allowed us to further refine the mapping of 25 amplicons in 19 samples, either reducing the size of a single continuous amplicon or increasing the complexity by highlighting multiple noncontiguous regions of amplification. Combined analysis of gene expression profiling and array-CGH data indicated that 12 to 25% of the genes that are targeted by genomic amplification are actually over-expressed in tumor cells, several of them having already been implicated in cancer. Finally, our results suggest that the presence of amplicons localized outside of chromosome 2, in addition to MYCN amplification, may be linked to a particularly severe outcome in neuroblastoma patients. © 2008 Wiley-Liss, Inc. [source] Combined analysis of specific KRAS mutation, BRAF and microsatellite instability identifies prognostic subgroups of sporadic and hereditary colorectal cancerINTERNATIONAL JOURNAL OF CANCER, Issue 11 2010Inti Zlobec Abstract Confounding effects of specific KRAS gene alterations on colorectal cancer (CRC) prognosis stratified by microsatellite instability (MSI) and BRAFV600E have not yet been investigated. The aim of our study was to evaluate the combined effects of MSI, BRAFV600E and specific KRAS mutation (Gly , Asp; G12D, Gly , Asp, G13D; Gly , Val; G12V) on prognosis in 404 sporadic and 94 hereditary CRC patients. MSI status was determined according to the Bethesda guidelines. Mutational status of KRAS and BRAFV600E was assessed by direct DNA sequencing. In sporadic CRC, KRAS G12D mutations had a negative prognostic effect compared to G13D and wild-type cancers (p = 0.038). With MSI, specific KRAS and BRAFV600E mutations, 3 distinct prognostic subgroups were observed in univariate (p = 0.006) and multivariable (p = 0.051) analysis: patients with (i) KRAS mutation G12D, G12V or BRAFV600E mutation, (ii) KRAS/BRAFV600E wild-type or KRAS G13D mutations in MSS/MSI-L and (iii) MSI-H and KRAS G13D mutations. Moreover, none of the sporadic MSI-H or hereditary patients with KRAS G13 mutations had a fatal outcome. Specific KRAS mutation is an informative prognostic factor in both sporadic and hereditary CRC and applied in an algorithm with BRAFV600E and MSI may identify sporadic CRC patients with poor clinical outcome. [source] Identification of Candidate Genes for Alcohol Preference by Expression Profiling of Congenic Rat StrainsALCOHOLISM, Issue 7 2007Lucinda G. Carr Background: A highly significant quantitative trait locus (QTL) on chromosome 4 that influenced alcohol preference was identified by analyzing crosses between the iP and iNP rats. Congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP (NP.P) exhibited the expected increase in alcohol consumption compared with the iNP background strain. This study was undertaken to identify genes in the chromosome 4 QTL interval that might contribute to the differences in alcohol consumption between the alcohol-naïve congenic and background strains. Methods: RNA from 5 brain regions from each of 6 NP.P and 6 iNP rats was labeled and analyzed separately on an Affymetrix Rat Genome 230 2.0 microarray to look for both cis -regulated and trans -regulated genes. Expression levels were normalized using robust multi-chip average (RMA). Differential gene expression was validated using quantitative real-time polymerase chain reaction. Five individual brain regions (nucleus accumbens, frontal cortex, amygdala, hippocampus, and striatum) were analyzed to detect differential expression of genes within the introgressed QTL interval, as well as genes outside that region. To increase the power to detect differentially expressed genes, combined analyses (averaging data from the 5 discrete brain regions of each animal) were also carried out. Results: Analyses within individual brain regions that focused on genes within the QTL interval detected differential expression in all 5 brain regions; a total of 35 genes were detected in at least 1 region, ranging from 6 genes in the nucleus accumbens to 22 in the frontal cortex. Analysis of the whole genome detected very few differentially expressed genes outside the QTL. Combined analysis across brain regions was more powerful. Analysis focused on the genes within the QTL interval confirmed 19 of the genes detected in individual regions and detected 15 additional genes. Whole genome analysis detected 1 differentially expressed gene outside the interval. Conclusions: Cis -regulated candidate genes for alcohol consumption were identified using microarray profiling of gene expression differences in congenic animals carrying a QTL for alcohol preference. [source] Combined analysis of three crossover clinical pharmacology studies of effects of rabeprazole and esomeprazole on 24-h intragastric pH in healthy volunteersALIMENTARY PHARMACOLOGY & THERAPEUTICS, Issue 4 2007V. NORRIS Summary Aim To compare antisecretory effects of rabeprazole and esomeprazole after single and repeat dosing in Helicobacter pylori -negative healthy volunteers. Methods Results were pooled from three smaller, open, crossover, randomized studies to obtain data from 80 subjects. The studies compared: (a) 5 days' dosing of 20 mg rabeprazole and esomeprazole (n = 24); (b) single doses of rabeprazole 20 mg and esomeprazole 40 mg (n = 27) and (c) 5 days' dosing of rabeprazole 10 mg and esomeprazole 20 mg (n = 29). Washout periods were ,14 days. Intragastric pH was recorded continuously for 24 h on days 0, 1 and 5. Results Single doses of rabeprazole 20 mg maintained 24-h intragastric pH >4 for longer than esomeprazole 20 mg (45% vs. 32%; P < 0.001); rabeprazole 20 mg and esomeprazole 40 mg were equivalent in their effects. After 5 days' dosing, rabeprazole 20 mg maintained pH >4 for longer than esomeprazole 20 mg (62% vs. 56%; P = 0.046); the reverse was true for esomeprazole 20 mg vs. rabeprazole 10 mg (56% vs. 48%; P = 0.035). In general, intragastric pH AUC during 0,5 h after dosing was higher after esomeprazole than rabeprazole, whereas the reverse was true during the night. Conclusions The order of effects on 24-h pH was: rabeprazole 10 mg , esomeprazole 20 mg < rabeprazole 20 mg = esomeprazole 40 mg. Esomeprazole acts faster, whereas rabeprazole's effect lasts longer. [source] A hybrid zone provides evidence for incipient ecological speciation in Heliconius butterfliesMOLECULAR ECOLOGY, Issue 21 2008CARLOS F. ARIAS Abstract In Heliconius butterflies, it has been proposed that speciation occurs through a combination of divergence in ecological habitat preferences and mimetic colour patterns. Here we test this hypothesis by investigating a parapatric form of the widespread species Heliconius erato. Mendelian (colour patterns) and molecular genetic data permit us to address hypotheses about introgression and genetic differentiation between different populations. Combined analysis of colour pattern, microsatellite loci and mitochondrial DNA showed that Heliconius erato venus and Heliconius erato chestertonii form a bimodal hybrid zone implying partial reproductive isolation. In a sample of 121 individuals collected in sympatry, 25% were hybrids representing a significant deficit of heterozygotes compared to the Hardy,Weinberg expectation. Seven microsatellite loci, analysed for a subset of these individuals, showed marked differentiation between the parental taxa, and unambiguously identified two genotypic clusters concordant with our phenotypic classification of individuals. Mitochondrial DNA analysis showed H. erato venus as a monophyletic group well differentiated from H. erato chestertonii, implying a lack of historical introgression between the populations. Heliconius erato chestertonii is therefore an incipient species that maintains its integrity despite high levels of hybridization. Moreover, H. erato chestertonii is found at higher altitudes than other races of H. erato and has a distinct colour pattern and mimetic relationship. Hence, there are now two examples of parapatric incipient species related to H. erato, H. himera and H. erato chestertonii, both of which are associated with higher altitudes, more arid habitats and distinct mimetic relationships. This implies that parapatric habitat adaptation is a likely cause of speciation in this group. [source] Interferon-stimulated gene 15 (ISG15) conjugates proteins in dermatomyositis muscle with perifascicular atrophyANNALS OF NEUROLOGY, Issue 1 2010Mohammad Salajegheh MD Objective We investigated interferon-stimulated gene 15 (ISG15), a poorly understood ubiquitin-like modifier, and its enzymatic pathway in dermatomyositis (DM), an autoimmune disease primarily involving muscle and skin. Methods We generated microarray data measuring transcript abundance for approximately 18,000 genes in each of 113 human muscle biopsy specimens, and studied biopsy specimens and cultured skeletal muscle using immunohistochemistry, immunoblotting proteomics, real-time quantitative polymerase chain reaction, and laser-capture microdissection. Results Transcripts encoding ISG15-conjugation pathway proteins were markedly upregulated in DM with perifascicular atrophy (DM-PFA) muscle (ISG15 339-fold, HERC5 62-fold, and USP18 68-fold) compared with 99 non-DM samples. Combined analysis with publicly available microarray datasets showed that >50-fold ISG15 transcript elevation had 100% sensitivity and specificity for 28 biopsies from adult DM-PFA and juvenile DM patients compared with 199 muscle samples from other muscle diseases. Free ISG15 and ISG15-conjugated proteins were only found on immunoblots from DM-PFA muscle. Cultured human skeletal muscle exposed to type 1 interferons produced similar transcripts and ISG15 protein and conjugates. Laser-capture microdissection followed by proteomic analysis showed deficiency of titin in DM perifascicular atrophic myofibers. Interpretation A large-scale microarray study of muscle samples demonstrated that among a diverse group of muscle diseases DM was uniquely associated with upregulation of the ISG15 conjugation pathway. Exposure of human skeletal muscle cell culture to type 1 interferons produced a molecular picture highly similar to that seen in human DM muscle. Perifascicular atrophic myofibers in DM were deficient in a number of skeletal muscle proteins including titin. ANN NEUROL 2010;67:53,63 [source] Cartilage degradation biomarkers predict efficacy of a novel, highly selective matrix metalloproteinase 13 inhibitor in a dog model of osteoarthritis: Confirmation by multivariate analysis that modulation of type ii collagen and aggrecan degradation peptides parallels pathologic changesARTHRITIS & RHEUMATISM, Issue 10 2010Steven Settle Objective To demonstrate that the novel highly selective matrix metalloproteinase 13 (MMP-13) inhibitor PF152 reduces joint lesions in adult dogs with osteoarthritis (OA) and decreases biomarkers of cartilage degradation. Methods The potency and selectivity of PF152 were evaluated in vitro using 16 MMPs, TACE, and ADAMTS-4 and ADAMTS-5, as well as ex vivo in human cartilage explants. In vivo effects were evaluated at 3 concentrations in mature beagles with partial medial meniscectomy. Gross and histologic changes in the femorotibial joints were evaluated using various measures of cartilage degeneration. Biomarkers of cartilage turnover were examined in serum, urine, or synovial fluid. Results were analyzed individually and in combination using multivariate analysis. Results The potent and selective MMP-13 inhibitor PF152 decreased human cartilage degradation ex vivo in a dose-dependent manner. PF152 treatment of dogs with OA reduced cartilage lesions and decreased biomarkers of type II collagen (type II collagen neoepitope) and aggrecan (peptides ending in ARGN or AGEG) degradation. The dose required for significant inhibition varied with the measure used, but multivariate analysis of 6 gross and histologic measures indicated that all doses differed significantly from vehicle but not from each other. Combined analysis of cartilage degradation markers showed similar results. Conclusion This highly selective MMP-13 inhibitor exhibits chondroprotective effects in mature animals. Biomarkers of cartilage degradation, when evaluated in combination, parallel the joint structural changes induced by the MMP-13 inhibitor. These data support the potential therapeutic value of selective MMP-13 inhibitors and the use of a set of appropriate biomarkers to predict efficacy in OA clinical trials. [source] Antiretroviral therapy and preterm delivery,a pooled analysis of data from the United States and EuropeBJOG : AN INTERNATIONAL JOURNAL OF OBSTETRICS & GYNAECOLOGY, Issue 11 2010CL Townsend Please cite this paper as: Townsend C, Schulte J, Thorne C, Dominguez K, Tookey P, Cortina-Borja M, Peckham C, Bohannon B, Newell M, for the Pediatric Spectrum of HIV Disease Consortium, the European Collaborative Study and the National Study of HIV in Pregnancy and Childhood. Antiretroviral therapy and preterm delivery,a pooled analysis of data from the United States and Europe. BJOG 2010;117:1399,1410. Objective, To investigate reported differences in the association between highly active antiretroviral therapy (HAART) in pregnancy and the risk of preterm delivery among HIV-infected women. Design, Combined analysis of data from three observational studies. Setting, USA and Europe. Population, A total of 19 585 singleton infants born to HIV-infected women, 1990,2006. Methods, Data from the Pediatric Spectrum of HIV Disease project (PSD), a US monitoring study, the European Collaborative Study (ECS), a consented cohort study, and the National Study of HIV in Pregnancy and Childhood (NSHPC), the United Kingdom and Ireland surveillance study. Main outcome measure, Preterm delivery rate (<37 weeks of gestation). Results, Compared with monotherapy, HAART was associated with increased preterm delivery risk in the ECS (adjusted odds ratio [AOR] 2.40, 95% CI 1.49,3.86) and NSHPC (AOR 1.43, 95% CI 1.10,1.86), but not in the PSD (AOR 0.92, 95% CI 0.67,1.26), after adjusting for relevant covariates. Because of heterogeneity, data were not pooled for this comparison, but heterogeneity disappeared when HAART was compared with dual therapy (P = 0.26). In a pooled analysis, HAART was associated with 1.5-fold increased odds of preterm delivery compared with dual therapy (95% CI 1.19,1.87, P = 0.001), after adjusting for covariates. Conclusions, Heterogeneity in the association between HAART and preterm delivery was not explained by study design, adjustment for confounders or a standard analytical approach, but may have been the result of substantial differences in populations and data collected. The pooled analysis comparing HAART with dual therapy showed an increased risk of preterm delivery associated with HAART. [source] Integrated genomic and expression profiling in mantle cell lymphoma: identification of gene-dosage regulated candidate genesBRITISH JOURNAL OF HAEMATOLOGY, Issue 2 2008Margit Schraders Summary Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) translocation and several other cytogenetic aberrations, including heterozygous loss of chromosomal arms 1p, 6q, 11q and 13q and/or gains of 3q and 8q. The common intervals of chromosomal imbalance have been narrowed down using array-comparative genomic hybridization (CGH). However, the chromosomal intervals still contain many genes potentially involved in MCL pathogeny. Combined analysis of tiling-resolution array-CGH with gene expression profiling on 11 MCL tumours enabled the identification of genomic alterations and their corresponding gene expression profiles. Only subsets of genes located within given cytogenetic anomaly-intervals showed a concomitant change in mRNA expression level. The genes that showed consistent correlation between DNA copy number and RNA expression levels are likely to be important in MCL pathology. Besides several ,anonymous genes', we also identified various fully annotated genes, whose gene products are involved in cyclic adenosine monophosphate-regulated pathways (PRKACB), DNA damage repair, maintenance of chromosome stability and prevention of rereplication (ATM, ERCC5, FBXO5), energy metabolism (such as genes that are involved in the synthesis of proteins encoded by the mitochondrial genome) and signal transduction (ARHGAP29). Deregulation of these gene products may interfere with the signalling pathways that are involved in MCL tumour development and maintenance. [source] The phylogeny of the living and fossil Sphenisciformes (penguins)CLADISTICS, Issue 5 2006Daniel T. Ksepka We present the first phylogenetic analysis of the Sphenisciformes that extensively samples fossil taxa. Combined analysis of 181 morphological characters and sequence fragments from mitochondrial and nuclear genes (12S, 16S, COI, cytochrome b, RAG-1) yields a largely resolved tree. Two species of the New Zealand Waimanu form a trichotomy with all other penguins in our result. The much discussed giant penguins Anthropornis and Pachydyptes are placed in two clades near the base of the tree. Stratigraphic and phylogenetic evidence suggest that some lineages of penguins attained very large body size rapidly and early in the clade's evolutionary history. The only fossil taxa that fall inside the crown clade Spheniscidae are fossil species assigned to the genus Spheniscus. Thus, extant penguin diversity is more accurately viewed as the product of a successful radiation of derived taxa than as an assemblage of survivors belonging to numerous lineages. The success of the Spheniscidae may be due to novel feeding adaptations and a more derived flipper apparatus. We offer a biogeographical scenario for penguins that incorporates fossil distributions and paleogeographic reconstructions of the Southern continent's positions. Our results do not support an expansion of the Spheniscidae from a cooling Continental Antarctica, but instead suggest those species that currently breed in that area are the descendants of colonizers from the Subantarctic. Many important divergence events in the clade Spheniscidae can instead be explained by dispersal along the paths of major ocean currents and the emergence of new islands due to tectonic events. © The Willi Hennig Society 2006. [source] Combined analysis of intracellular signalling and immunophenotype of human peripheral blood basophils by flow cytometry: a proof of conceptCLINICAL & EXPERIMENTAL ALLERGY, Issue 11 2007D. G. Ebo Summary Background The signal transduction pathways and control mechanisms involved in IgE-mediated basophil activation remain incompletely understood. Objectives To investigate whether basophilic intracellular signal transduction and immunophenotype can be analysed simultaneously by flow cytometry. Methods Basophils in whole blood were stimulated with anti-IgE and latex antigen at various concentrations and during different time courses. Phosphorylation of p38 mitogen-activated protein kinase (MAPK) as a representative of the intracellular signal transduction pathway and surface expression of CD63 was assessed simultaneously flow cytometrically. The effect of pre-incubation with IL-3 was assessed. Results Stimulation of the basophils with anti-IgE and allergen induces a rapid phosphorylation of p38 MAPK that peaks between 1 and 5 min and returns to baseline levels after 60 min. In contrast, CD63 up-regulation demonstrates a maximal but more continuous expression that peaks approximately 5 min later than phosphorylation of p38 MAPK. Specific inhibition of p38 MAPK reduced or almost completely abrogated up-regulation of CD63. Pre-incubation of the basophils with IL-3 produces a rapid p38 MAPK phosphorylation over basal levels, but this was weaker and shorter than for anti-IgE stimulation. Pre-incubation of the basophils with IL-3 did not potentiate anti-IgE-induced phosphorylation of p38 MAPK and did affect spontaneous or IgE-mediated CD63 up-regulation. Conclusions This study provides the proof that the flow cytometer allows an integrated analysis of basophilic intracellular signalling and immunophenotyping. Owing to its technical simplicity, the low number of cells required and rapid analysis, the technique seems promising for use in the clinic as a diagnostic tool or to monitor therapy. Capsule summary This study is the first to provide evidence for a combined analysis of basophilic intracellular signalling and immunophenotyping by flow cytometry. Owing to its technical simplicity, the low number of cells required and rapid analysis, the technique seems promising for use in the clinic as a diagnostic tool or to monitor therapy. [source] Identification of Candidate Genes for Alcohol Preference by Expression Profiling of Congenic Rat StrainsALCOHOLISM, Issue 7 2007Lucinda G. Carr Background: A highly significant quantitative trait locus (QTL) on chromosome 4 that influenced alcohol preference was identified by analyzing crosses between the iP and iNP rats. Congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP (NP.P) exhibited the expected increase in alcohol consumption compared with the iNP background strain. This study was undertaken to identify genes in the chromosome 4 QTL interval that might contribute to the differences in alcohol consumption between the alcohol-naïve congenic and background strains. Methods: RNA from 5 brain regions from each of 6 NP.P and 6 iNP rats was labeled and analyzed separately on an Affymetrix Rat Genome 230 2.0 microarray to look for both cis -regulated and trans -regulated genes. Expression levels were normalized using robust multi-chip average (RMA). Differential gene expression was validated using quantitative real-time polymerase chain reaction. Five individual brain regions (nucleus accumbens, frontal cortex, amygdala, hippocampus, and striatum) were analyzed to detect differential expression of genes within the introgressed QTL interval, as well as genes outside that region. To increase the power to detect differentially expressed genes, combined analyses (averaging data from the 5 discrete brain regions of each animal) were also carried out. Results: Analyses within individual brain regions that focused on genes within the QTL interval detected differential expression in all 5 brain regions; a total of 35 genes were detected in at least 1 region, ranging from 6 genes in the nucleus accumbens to 22 in the frontal cortex. Analysis of the whole genome detected very few differentially expressed genes outside the QTL. Combined analysis across brain regions was more powerful. Analysis focused on the genes within the QTL interval confirmed 19 of the genes detected in individual regions and detected 15 additional genes. Whole genome analysis detected 1 differentially expressed gene outside the interval. Conclusions: Cis -regulated candidate genes for alcohol consumption were identified using microarray profiling of gene expression differences in congenic animals carrying a QTL for alcohol preference. [source] Alcoholism Susceptibility Loci: Confirmation Studies in a Replicate Sample and Further MappingALCOHOLISM, Issue 7 2000Tatiana Foroud Background: There is substantial evidence for a significant genetic component to the risk for alcoholism. A previous study reported linkage to chromosomes 1, 2, and 7 in a large data set that consisted of 105 families, each with at least three alcoholic members. Methods: Additional, genotyping in the 105 families has been completed in the chromosomal regions identified in the initial analyses, and a replication sample of 157 alcoholic families ascertained under identical criteria has been genotyped. Two hierarchical definitions of alcoholism were employed in the linkage analyses: (1) Individuals who met both Feighner and DSM-III-R criteria for alcohol dependence represented a broad definition of disease; and (2) individuals who met ICD-10 criteria for alcoholism were considered affected under a more severe definition of disease. Results: Genetic analyses of affected sibling pairs supported linkage to chromosome 1 (LOD = 1.6) in the replication data set as well as in a combined analysis of the two samples (LOD = 2.6). Evidence of linkage to chromosome 7 increased in the combined data (LOD = 2.9). The LOD score on chromosome 2 in the initial data set increased after genotyping of additional markers; however, combined analyses of the two data sets resulted in overall lower LOD scores (LOD = 1.8) on chromosome 2. A new finding of linkage to chromosome 3 was identified in the replication data set (LOD = 3.4). Conclusions: Analyses of a second large sample of alcoholic families provided further evidence of genetic susceptibility loci on chromosomes 1 and 7. Genetic analyses also have identified susceptibility loci on chromosomes 2 and 3 that may act only in one of the two data sets. [source] Microsatellite DNA markers for two endemic ground beetles: Carabus punctatoauratus and C. solieriMOLECULAR ECOLOGY RESOURCES, Issue 4 2002S. Garnier Abstract We isolated and characterized nine and five polymorphic microsatellite loci in the respective ground beetles Carabus punctatoauratus and C. solieri. We tested cross-species amplification of all these loci plus six isolated in C. solieri and for which primers sequences were soon published. From these combined analyses, we obtained 14 and 17 polymorphic markers, respectively, for C. punctatoauratus and C. solieri. [source] Variants in Intron 13 of the ELMO1 Gene are Associated with Diabetic Nephropathy in African AmericansANNALS OF HUMAN GENETICS, Issue 2 2009T. S. Leak Summary Variants in the engulfment and cell motility 1 (ELMO1) gene are associated with nephropathy due to type 2 diabetes mellitus (T2DM) in a Japanese cohort. We comprehensively evaluated this gene in African American (AA) T2DM patients with end-stage renal disease (ESRD). Three hundred and nine HapMap tagging SNPs and 9 reportedly associated SNPs were genotyped in 577 AA T2DM-ESRD patients and 596 AA non-diabetic controls, plus 43 non-diabetic European American controls and 45 Yoruba Nigerian samples for admixture adjustment. Replication analyses were conducted in 558 AA with T2DM-ESRD and 564 controls without diabetes. Extension analyses included 328 AA with T2DM lacking nephropathy and 326 with non-diabetic ESRD. The original and replication analyses confirmed association with four SNPs in intron 13 (permutation p-values for combined analyses = 0.001,0.003), one in intron 1 (P = 0.004) and one in intron 5 (P = 0.002) with T2DM-associated ESRD. In a subsequent combined analysis of all 1,135 T2DM-ESRD cases and 1,160 controls, an additional 7 intron 13 SNPs produced evidence of association (P = 3.5 × 10,5, P = 0.05). No associations were seen with these SNPs in those with T2DM lacking nephropathy or with ESRD due to non-diabetic causes. Variants in intron 13 of the ELMO1 gene appear to confer risk for diabetic nephropathy in AA. [source] Genetic variants in the Runt-related transcription factor 3 gene contribute to gastric cancer risk in a Chinese populationCANCER SCIENCE, Issue 9 2009Dongmei Wu Runt-related transcription factor 3 (RUNX3) is a well known gene for its functions in gastric cancer suppression, but the effect of its genetic variations on the risk of gastric cancer remains unclear. In this study, ten tagging single nucleotide polymorphisms (tSNPs) of the RUNX3 gene were selected and genotyped in a hospital-based case-control study of 312 gastric cancer patients and 329 cancer-free controls in a Chinese population. In the single-locus analysis, three RUNX3 intronic tSNPs associated with significantly increased risk of gastric cancer were observed: the SNP3 rs11249206 CC genotype (adjusted odds ratio [OR] = 1.75, 95% confidence interval [CI] = 1.03,2.99), compared with the TT genotype; the SNP7 rs760805 AA genotype (adjusted OR = 1.82, 95% CI = 1.14,2.92), compared with the TT genotype; and the SNP8 rs2236852 GG genotype (adjusted OR = 1.69, 95% CI = 1.05,2.72), compared with the AA genotype. In the combined analyses of these three tSNPs, we found that the combined genotypes with four to six variant (risk) alleles (i.e. SNP3 C, SNP7 A, and SNP8 G alleles) were associated with an increased risk of gastric cancer compared with those with one to three variant (risk) alleles (adjusted OR = 2.00, 95% CI = 1.41,2.85), and this increased risk was more pronounced among subgroups of age ,65 years, never smokers, and never drinkers. However, no significant association was observed in the clinicopathological features analyses. In conclusion, the RUNX3 genetic variants may modulate the risk of gastric cancer in a Chinese population. Further larger and functional studies are warranted to validate the findings. (Cancer Sci 2009; 100: 1688,1694) [source] Higher-level phylogenetics of linyphiid spiders (Araneae, Linyphiidae) based on morphological and molecular evidenceCLADISTICS, Issue 3 2009Miquel A. Arnedo This study infers the higher-level cladistic relationships of linyphiid spiders from five genes (mitochondrial CO1, 16S; nuclear 28S, 18S, histone H3) and morphological data. In total, the character matrix includes 47 taxa: 35 linyphiids representing the currently used subfamilies of Linyphiidae (Stemonyphantinae, Mynogleninae, Erigoninae, and Linyphiinae (Micronetini plus Linyphiini)) and 12 outgroup species representing nine araneoid families (Pimoidae, Theridiidae, Nesticidae, Synotaxidae, Cyatholipidae, Mysmenidae, Theridiosomatidae, Tetragnathidae, and Araneidae). The morphological characters include those used in recent studies of linyphiid phylogenetics, covering both genitalic and somatic morphology. Different sequence alignments and analytical methods produce different cladistic hypotheses. Lack of congruence among different analyses is, in part, due to the shifting placement of Labulla, Pityohyphantes, Notholepthyphantes, and Pocobletus. Almost all combined analyses agree on the monophyly of linyphioids, Pimoidae, Linyphiidae, Erigoninae, Mynogleninae, as well as Stemonyphantes as a basal lineage within Linyphiidae. Our results suggest independent origins of the desmitracheate tracheal system in micronetines and erigonines, and that erigonines were primitively haplotracheate. Cephalothoracic glandular specializations of erigonines and mynoglenines apparently evolved independently. Subocular sulci of mynoglenines and lateral sulci (e.g. Bathyphantes) evolved independently but glandular pores in the prosoma proliferated once. The contribution of different character partitions and their sensitivity to changes in traditional analytical parameters is explored and quantified. ,© The Willi Hennig Society 2009. [source] Phylogenetic relationships of the genera of Theaceae based on morphologyCLADISTICS, Issue 3 2004Isolda Luna This work represents the first phylogenetic analysis of all genera belonging to the plant family Theaceae (sensu lato). The study is based on 60 morphological characters derived from herbarium specimens and an extensive literature review of 37 genera (including the outgroup). In contrast to the results from molecular data, Theaceae is here found to consist of one clade in which the recognition of two families or subfamilies would leave Theaceae s.s. paraphyletic. Within that clade, Ternstroemiaceae is supported as monophyletic and includes Adinandra, Anneslea, Archboldiodendron, Balthasaria, Cleyera, Eurya, Euryodendron, Ficalhoa, Freziera, Symplococarpon, Ternstroemia and Visnea. The paraphyletic Theaceae s.s. includes Apterosperma, Camellia, Dankia, Gordonia, Pyrenaria, Schima, and Stewartia. Tetrameristaceae (Pentamerista and Tetramerista) are supported as a monophyletic family, with Pellicieraceae (Pelliciera) as sister group, and that clade is sister to the rest of the taxa. Bonnetiaceae (Archytaea and Bonnetia) and Kielmeyeroideae of the Clusiaceae (Caraipa, Haploclathra, Kielmeyera, Mahurea, Marila, and Neotatea) are also supported as monophyletic. Given the differences between the results obtained from morphological and molecular data, we consider that there is still a need for further research, including combined analyses. [source] A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genesCLADISTICS, Issue 6 2003Norberto P Giannini The phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) has been investigated using several different molecular datasets. These studies differed widely in taxonomic and locus sampling, and their results tended to lack resolution of internal nodes and were themselves largely incongruent. To address this, we assembled a data set of 5 loci (up to 3.5 kbp from 12S rDNA, 16S rDNA, tDNA-valine, cytochrome b, and the nuclear gene c -mos) for 43 species of megachiropterans and 6 microchiropteran outgroups. We analyzed these data with direct optimization under equal costs for substitutions and indels. We used POY in a parallel setting, and searches consisted of replicated swapping + refinements (ratcheting, tree fusing, and iterative pass optimization). Our results indicate that Megachiroptera and all recognized genera (including Pteropus) are monophyletic, and that Melonycteris is the sister group of the clade containing all the other genera. Clades previously proposed using molecular data, as well as many new and traditional groups, were well-supported, and various sources suggest that the degree of conflict with morphological data may be considerably less marked than previously supposed. Analysis of individual loci suffer 70% loss in the number of compatible groups recovered across all analyses with respect to combined analyses. Our results indicate that, within Megachiroptera, nectarivory and cave-dwelling originated several times, but echolocation (used for obstacle detection) evolved only once. Megachiropterans likely originated in SE Asia-Melanesia, and colonized Africa at least four times. [source] The phylogeny of the Histeroidea (Coleoptera: Staphyliniformia)CLADISTICS, Issue 4 2002Michael S. Caterino For its size (ca. 4000 species) the Histeridae is one of the most ecologically and morphologically diverse families of beetles. Its mostly predaceous members occupy a wide variety of habitats for which their morphologies may be highly modified. Previous attempts to resolve the phylogeny of the family based on morphological data have left many difficult issues unresolved. This study is the first to utilize either larval or molecular (18S rDNA) data in combination with adult morphology in an attempt to resolve these issues. We compare the performance of optimization alignment with a fixed positional homology approach, over a range of parameter space. Optimizing alignment parameters for combined analyses of 18S and morphology for both approaches resulted in very similar topologies. Contrary to previous hypotheses which held the cylindrical, subcortical forms of the family (e.g., Niponius, Trypanaeus, Trypeticus) to be the most primitive, our analyses find these to be highly specialized forms derived from within other more generalized taxa. Basal lineages within the family instead include Onthophilus, Anapleus, and Dendrophilus, all of which are ovoid, mainly generalist forms. [source] On the Initial Stages of Electrooxidation of Aqueous Maleic Acid on Bi-Doped PbO2ELECTROANALYSIS, Issue 15 2007Carlos Borras Abstract Oxidation of maleic acid in aqueous solution on bismuth-doped lead oxide has been studied. The effects of hydrodynamic conditions on the oxidation rate have been identified. The number of electrons transferred during the initial stages of oxidation as well as the apparent heterogeneous rate constant was obtained from the combined analysis of rotating ring-disk currents and the decrease of concentration at constant potential, determined from UV-vis measurements. The number of electrons involved during electrochemical oxidation was found to be 12, indicating full mineralization to CO2, and the heterogeneous rate constant for oxidation at 1.6,V was 9.8×105,cm s,1. [source] A multivariate biomarker-based model predicting population-level responses of Daphnia magnaENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 9 2003Wim M. De Coen Abstract A multivariate model is proposed relating short-term biomarker measurements in Daphnia magna to chronic effects (21-d exposure) occurring at the population level (time to death, mean brood size, mean total young per female, intrinsic rate of natural increase, net reproductive rate, and growth). The results of the short-term exposure (48h-96 h) to eight model toxicants (cadmium, chromium, mercury, tributyl tin, linear alkylsulfonic acid, sodium pentachlorophenolate, lindane, and 2,4-dichloro-phenoxyacetic acid) on the following biomarkers were used for the multivariate model: digestive enzymes (amylase, cellulase, ,-galactosidase, trypsin, and esterase), enzymes of the intermediary metabolism (glycogen phosphorylase, glucose-6-phosphate de-hydrogenase, pyruvate kinase, lactate dehydrogenase, and isocitrate dehydrogenase), cellular energy allocation (CEA) (protein, carbohydrate, and lipid content and electron transport activity), and DNA damage and antioxidative stress activity. Using partial least squares to latent structures (PLS), a two-component model was obtained with R2 of 0.68 and a Q2 value of 0.60 based on the combined analysis of a limited number of the 48- and 96-h biomarker responses. For the individual population-level responses, the R2 values varied from 0.66 to 0.77 and the Q2 values from 0.52 to 0.69. Energy-related biomarkers (cellular energy allocation, lipid contents, anaerobic metabolic activity,pyruvate kinase, and lactate dehydrogenase), combined with parameters related to oxidative stress (catalase) and DNA damage measured after 48 and 96 h of exposure, were able to predict long-term effects at higher levels of biological organization. [source] ACE and angiotensinogen gene genotypes and left ventricular mass in athletesEUROPEAN JOURNAL OF CLINICAL INVESTIGATION, Issue 10 2001F. Diet Background Genetic factors may be important in modifying heart size due to long-term athletic training. The significance of polymorphisms of genes of the renin,angiotensin system in myocardial mass in a population of athletes participating in different disciplines is not known. Methods The angiotensin I-converting enzyme gene insertion/deletion (I/D) polymorphism, angiotensinogen gene M235T polymorphism and angiotensin II type 1 receptor gene A1166C polymorphism were determined in 83 male Caucasian endurance athletes and associated with left ventricular mass. Results No association with left ventricular mass was found for the polymorphisms of angiotensin I-converting enzyme gene I/D, angiotensinogen gene M235T and angiotensin II type 1 gene A1166C when studied separately. However, combined analysis of the angiotensin I-converting enzyme gene I/D polymorphism and angiotensinogen gene M235T polymorphism genotypes suggested an association with left ventricular mass (g m,2) (P = 0·023). Athletes with the angiotensin I-converting enzyme gene DD/angiotensinogen gene TT genotype combination had greater left ventricular mass compared with all other genotype combinations (179·8 ± 26·1 g m,2 vs. 145·2 ± 27·3 g m,2, P = 0·003). Conclusions These results suggest an association of combined angiotensin I-converting enzyme gene I/D polymorphism genotypes, and angiotensinogen gene M235T polymorphism genotypes with left ventricular hypertrophy due to long-term athletic training. A synergistic effect of angiotensin I-converting enzyme gene DD genotype and angiotensinogen gene TT genotype on left ventricular mass in endurance athletes appears to occur. [source] Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chainsGENETIC EPIDEMIOLOGY, Issue 4 2008Yunjung Kim Abstract A map of the background levels of disequilibrium between nearby markers can be useful for association mapping studies. In order to assess the background levels of linkage disequilibrium (LD), multilocus LD measures are more advantageous than pairwise LD measures because the combined analysis of pairwise LD measures is not adequate to detect simultaneous allele associations among multiple markers. Various multilocus LD measures based on haplotypes have been proposed. However, most of these measures provide a single index of association among multiple markers and does not reveal the complex patterns and different levels of LD structure. In this paper, we employ non-homogeneous, multiple order Markov Chain models as a statistical framework to measure and partition the LD among multiple markers into components due to different orders of marker associations. Using a sliding window of multiple markers on phased haplotype data, we compute corresponding likelihoods for different Markov Chain (MC) orders in each window. The log-likelihood difference between the lowest MC order model (MC0) and the highest MC order model in each window is used as a measure of the total LD or the overall deviation from the gametic equilibrium for the window. Then, we partition the total LD into lower order disequilibria and estimate the effects from two-, three-, and higher order disequilibria. The relationship between different orders of LD and the log-likelihood difference involving two different orders of MC models are explored. By applying our method to the phased haplotype data in the ENCODE regions of the HapMap project, we are able to identify high/low multilocus LD regions. Our results reveal that the most LD in the HapMap data is attributed to the LD between adjacent pairs of markers across the whole region. LD between adjacent pairs of markers appears to be more significant in high multilocus LD regions than in low multilocus LD regions. We also find that as the multilocus total LD increases, the effects of high-order LD tends to get weaker due to the lack of observed multilocus haplotypes. The overall estimates of first, second, third, and fourth order LD across the ENCODE regions are 64, 23, 9, and 3%. Genet. Epidemiol. 2008. © 2008 Wiley-Liss, Inc. [source] SHADOWS OF PLANNING: ON LANDSCAPE/PLANNING HISTORY AND INHERITED LANDSCAPE AMBIGUITIES AT THE URBAN FRINGEGEOGRAFISKA ANNALER SERIES B: HUMAN GEOGRAPHY, Issue 3 2010Mattias Qviström ABSTRACT. The history of vernacular landscapes at the urban fringe is poorly studied, limiting our understanding of the contemporary character of the fringe and our knowledge of the urbanization process. This article argues the necessity of a combined analysis of the legacies of planning and the footprints of former landscape ideals in order to understand the conditions for spatial planning at the urban fringe. After first introducing the methodological use of landscape/planning history, the article focuses on the Swedish discourse on landscape change and landscape planning concerning the urban fringe in the 1930s. Particular focus is placed on the discourse on agricultural landscapes at the urban fringe. The third section of the article presents an examination of the footprints of the ,landscape convention' (i.e. an agreement on the meaning of landscape in relation to law and justice) resulting from the landscape discourse of the 1930s. The article argues that the legacy of the 1930s explains some of the difficulties arising when planners of today aim to utilize the farm landscape as a resource for recreation at the urban fringe. The shadow of the landscape discourse of the 1930s also creates difficulties in dealing with peri-urban landscapes in Swedish planning and Swedish law. With the ongoing discourse on how to implement the European Landscape Convention, such knowledge is particularly useful. [source] Simultaneous assessment of DNA ploidy and biomarker expression in paraffin-embedded tissue sectionsHISTOPATHOLOGY, Issue 1 2010Stijn J H M Fleskens Fleskens S J H M, Takes R P, Otte-Höller I, van Doesburg L, Smeets A, Speel E-J M, Slootweg P J & van der Laak J A W M (2010) Histopathology,57, 14,26 Simultaneous assessment of DNA ploidy and biomarker expression in paraffin-embedded tissue sections Aims:, Aneuploidy is a potential biomarker for predicting progression of premalignancies. Ploidy assessment is mostly performed on nuclei isolated from tissue sections. Ploidy assessment in situ in tissue sections may be a large improvement, enabling selective sampling of nuclei, thus allowing the correlation between ploidy and histology. Existing ploidy analysis methods in sections suffer from limited sensitivity. The aim was to reliably assess ploidy in sections, combined with simultaneous assessment of other markers at the individual cell level. Methods and results:, Ploidy was measured in 22 paraffin-embedded oral premalignancies. The DNA stoichiometric Feulgen procedure was used on isolated nuclei, as well as fluoresence in situ hybridization analysis. In tissue sections, Feulgen was combined with immunohistochemistry for Ki67 proliferation marker, enabling distinction between cycling euploid and aneuploid cells. Aneuploidy was reliably detected in tissue sections (sensitivity 100%, specificity 92%). One section in which aneuploidy was detected was misclassified in isolated nuclei analysis. Sections were also successfully analysed using our model combined with DNA double strand break marker ,-H2AX in fluorescence microscopy, underlining the power of biomarker evaluation on single cells in tissue sections. Conclusions:, The analysis model proposed in this study enables the combined analysis of histology, genotypic and phenotypic information. [source] | |||||||||||||||||||||||||||||||||||||