936 research outputs found

    Dysregulated methylation at imprinted genes in prostate tumor tissue detected by methylation microarray.

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    BACKGROUND: Imprinting is an important epigenetic regulator of gene expression that is often disrupted in cancer. While loss of imprinting (LOI) has been reported for two genes in prostate cancer (IGF2 and TFPI2), disease-related changes in methylation across all imprinted gene regions has not been investigated. METHODS: Using an Illumina Infinium Methylation Assay, we analyzed methylation of 396 CpG sites in the promoter regions of 56 genes in a pooled sample of 12 pairs of prostate tumor and adjacent normal tissue. Selected LOI identified from the array was validated using the Sequenom EpiTYPER assay for individual samples and further confirmed by expression data from publicly available datasets. RESULTS: Methylation significantly increased in 52 sites and significantly decreased in 17 sites across 28 unique genes (P \u3c 0.05), and the strongest evidence for loss of imprinting was demonstrated in tumor suppressor genes DLK1, PLAGL1, SLC22A18, TP73, and WT1. Differential expression of these five genes in prostate tumor versus normal tissue using array data from a publicly available database were consistent with the observed LOI patterns, and WT1 hypermethylation was confirmed using quantitative DNA methylation analysis. CONCLUSIONS: Together, these findings suggest a more widespread dysregulation of genetic imprinting in prostate cancer than previously reported and warrant further investigation

    Mechanism of age-dependent susceptibility and novel treatment strategy in glutaric acidemia type I

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    Glutaric acidemia type I (GA-I) is an inherited disorder of lysine and tryptophan metabolism presenting with striatal lesions anatomically and symptomatically similar to Huntington disease. Affected children commonly suffer acute brain injury in the context of a catabolic state associated with nonspecific illness. The mechanisms underlying injury and age-dependent susceptibility have been unknown, and lack of a diagnostic marker heralding brain injury has impeded intervention efforts. Using a mouse model of GA-I, we show that pathologic events began in the neuronal compartment while enhanced lysine accumulation in the immature brain allowed increased glutaric acid production resulting in age-dependent injury. Glutamate and GABA depletion correlated with brain glutaric acid accumulation and could be monitored in vivo by proton nuclear magnetic resonance (1H NMR) spectroscopy as a diagnostic marker. Blocking brain lysine uptake reduced glutaric acid levels and brain injury. These findings provide what we believe are new monitoring and treatment strategies that may translate for use in human GA-I

    Dynamic phase transition properties and hysteretic behavior of a ferrimagnetic core-shell nanoparticle in the presence of a time dependent magnetic field

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    We have presented dynamic phase transition features and stationary-state behavior of a ferrimagnetic small nanoparticle system with a core-shell structure. By means of detailed Monte Carlo simulations, a complete picture of the phase diagrams and magnetization profiles have been presented and the conditions for the occurrence of a compensation point TcompT_{comp} in the system have been investigated. According to N\'{e}el nomenclature, the magnetization curves of the particle have been found to obey P-type, N-type and Q-type classification schemes under certain conditions. Much effort has been devoted to investigation of hysteretic response of the particle and we observed the existence of triple hysteresis loop behavior which originates from the existence of a weak ferromagnetic core coupling Jc/JshJ_{c}/J_{sh}, as well as a strong antiferromagnetic interface exchange interaction Jint/JshJ_{int}/J_{sh}. Most of the calculations have been performed for a particle in the presence of oscillating fields of very high frequencies and high amplitudes in comparison with exchange interactions which resembles a magnetic system under the influence of ultrafast switching fields. Particular attention has also been paid on the influence of the particle size on the thermal and magnetic properties, as well as magnetic features such as coercivity, remanence and compensation temperature of the particle. We have found that in the presence of ultrafast switching fields, the particle may exhibit a dynamic phase transition from paramagnetic to a dynamically ordered phase with increasing ferromagnetic shell thickness.Comment: 12 pages, 12 figure

    Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set

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    Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^>0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations
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