排序方式: 共有54条查询结果,搜索用时 0 毫秒
31.
Florent?BatyEmail author Michel?P?Bihl Guy?Perrière Aedín?C?Culhane Martin?H?Brutsche 《BMC bioinformatics》2005,6(1):239
Background
A recent publication described a supervised classification method for microarray data: Between Group Analysis (BGA). This method which is based on performing multivariate ordination of groups proved to be very efficient for both classification of samples into pre-defined groups and disease class prediction of new unknown samples. Classification and prediction with BGA are classically performed using the whole set of genes and no variable selection is required. We hypothesize that an optimized selection of highly discriminating genes might improve the prediction power of BGA. 相似文献32.
BACKGROUND: Benzo(a)pyrene (BaP), anthracene (ANTH) and chrysene (CHRY) are polynuclear aromatic hydrocarbons (PAHs) implicated in renal toxicity and carcinogenesis. These PAHs elicit cell type-specific effects that help predict toxicity outcomes in vitro and in vivo. While BaP and ANTH selectively injure glomerular mesangial cells, and CHRY targets cortico-tubular epithelial cells, binary or ternary mixtures of these hydrocarbons markedly reduce the overall cytotoxic potential of individual hydrocarbons. METHODS: To study the biochemical basis of these antagonistic interactions, renal glomerular mesangial cells were challenged with BaP alone (0.03 - 30 microM) or in the presence of ANTH (3 microM) or CHRY (3 microM) for 24 hr. Total RNA and protein will be harvested for Northern analysis and measurements of aryl hydrocarbon hydroxylase (AHH) and ethoxyresorufin-O-deethylase (EROD) activity, respectively, to evaluate cytochrome P450 mRNA and protein inducibility. Cellular hydrocarbon uptake and metabolic profiles of PAHs were analyzed by high performance liquid chromatography (HPLC). RESULTS: Combined hydrocarbon treatments did not influence the cellular uptake of individual hydrocarbons. ANTH or CHRY strongly repressed BaP-inducible cytochrome P450 mRNA and protein expression, and markedly inhibited oxidative BaP metabolism. CONCLUSION: These findings indicate that antagonistic interactions among nephrocarcinogenic PAHs involve altered expression of cytochrome P450s that modulate bioactivation profiles and nephrotoxic/ nephrocarcinogenic potential. 相似文献
33.
Background
Millions of cells are present in thousands of images created in high-throughput screening (HTS). Biologists could classify each of these cells into a phenotype by visual inspection. But in the presence of millions of cells this visual classification task becomes infeasible. Biologists train classification models on a few thousand visually classified example cells and iteratively improve the training data by visual inspection of the important misclassified phenotypes. Classification methods differ in performance and performance evaluation time. We present a comparative study of computational performance of gentle boosting, joint boosting CellProfiler Analyst (CPA), support vector machines (linear and radial basis function) and linear discriminant analysis (LDA) on two data sets of HT29 and HeLa cancer cells.Results
For the HT29 data set we find that gentle boosting, SVM (linear) and SVM (RBF) are close in performance but SVM (linear) is faster than gentle boosting and SVM (RBF). For the HT29 data set the average performance difference between SVM (RBF) and SVM (linear) is 0.42 %. For the HeLa data set we find that SVM (RBF) outperforms other classification methods and is on average 1.41 % better in performance than SVM (linear).Conclusions
Our study proposes SVM (linear) for iterative improvement of the training data and SVM (RBF) for the final classifier to classify all unlabeled cells in the whole data set.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-342) contains supplementary material, which is available to authorized users. 相似文献34.
Sixteen microsatellite loci are described for the two‐spotted spider mite Tetranychus urticae, which is an agricultural pest. The microsatellite loci were obtained through the construction of an enriched library; these loci exhibited polymorphisms (2–5 alleles per locus) and high levels of observed (0.033–0.667, average 0.415) and expected (0.033–0.602, average 0.336) heterozygosities. The isolated microsatellite markers are expected to be useful for the construction of a linkage map of this species. 相似文献
35.
36.
37.
38.
Inhibition of the vacuolating and anion channel activities of the VacA toxin of Helicobacter pylori. 总被引:6,自引:0,他引:6
F Tombola F Oregna S Brutsche I Szabò G Del Giudice R Rappuoli C Montecucco E Papini M Zoratti 《FEBS letters》1999,460(2):221-225
VacA, the vacuolating cytotoxin secreted by Helicobacter pylori, is believed to be a major causative factor in the development of gastroduodenal ulcers. This toxin causes vacuolation of cultured cells and it has recently been found to form anion-selective channels upon insertion into planar bilayers as well as in the plasma membrane of HeLa cells. Here, we identify a series of inhibitors of VacA channels and we compare their effectiveness as channel blockers and as inhibitors of VacA-induced vacuolation, confirming that the two phenomena are linked. This characterization opens the way to studies in other experimental systems and to the search for a specific inhibitor of VacA action. 相似文献
39.
Patterns of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) variation
were studied in 378 populations of oak trees sampled throughout the
southern half of France. Six cpDNA haplotypes detected in a previous
European survey and three new cpDNA haplotypes were found in this region.
Two mitochondrial polymorphisms detected earlier by restriction analysis of
PCR-amplified fragments alone, or in combination with single-strand
conformation polymorphism (SSCP), were compared with the cpDNA data.
Sequencing revealed the nature of the two mitochondrial mutations: a
single-base substitution and a 4-bp inversion associated with a 22-bp
hairpin secondary structure. The single-base substitution was then analyzed
by allele-specific amplification. Results for the two cytoplasmic genomes
were combined, which allowed the identification of 12 cpDNA-mtDNA
haplotypes. The 4-bp mtDNA inversion has appeared independently in
different cpDNA lineages. Given the peculiar nature of this mtDNA mutation,
we suggest that intramolecular recombination leading to repeated inversions
of the 4-bp sequence (rather than paternal leakage of one of the two
genomes) is responsible for this pattern. Furthermore, the geographic
locations of the unusual cpDNA-mtDNA associations (due to the inversion)
usually do not match the zones of contact between divergent haplotypes. In
addition, in southern France, the groupings of populations based on the
mtDNA substitution were strictly congruent with those based on cpDNA.
Because many populations that are polymorphic for both cpDNA and mtDNA have
remained in contact since postglacial recolonization in this area without
producing any new combination of cytoplasms involving the mitochondrial
substitution, we conclude that paternal leakage is not a significant factor
at this timescale. Such results confirm and expand our earlier conclusions
based on controlled crosses.
相似文献
40.
Formation of anion-selective channels in the cell plasma membrane by the toxin VacA of Helicobacter pylori is required for its biological activity. 总被引:7,自引:0,他引:7 下载免费PDF全文
I Szabò S Brutsche F Tombola M Moschioni B Satin J L Telford R Rappuoli C Montecucco E Papini M Zoratti 《The EMBO journal》1999,18(20):5517-5527
The vacuolating toxin VacA, a major determinant of Helicobacter pylori-associated gastric diseases, forms anion-selective channels in artificial planar lipid bilayers. Here we show that VacA increases the anion permeability of the HeLa cell plasma membrane and determines membrane depolarization. Electrophysiological and pharmacological approaches indicated that this effect is due to the formation of low-conductance VacA pores in the cell plasma membrane and not to the opening of Ca(2+)- or volume-activated chloride channels. VacA-dependent increase of current conduction both in artificial planar lipid bilayers and in the cellular system was effectively inhibited by the chloride channel blocker 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB), while2-[(2-cyclopentenyl-6,7dichloro-2, 3-dihydro-2-methyl-1-oxo-1H-inden-5-yl)oxy]acetic acid (IAA-94) was less effective. NPPB inhibited and partially reversed the vacuolation of HeLa cells and the increase of ion conductivity of polarized Madine Darby canine kidney cell monolayers induced by VacA, while IAA-94 had a weaker effect. We conclude that pore formation by VacA accounts for plasma membrane permeabilization and is required for both cell vacuolation and increase of trans-epithelial conductivity. 相似文献