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151.
Maja Klug Sandra Schmidhofer Claudia Gebhard Reinhard Andreesen Michael Rehli 《Genome biology》2013,14(5):R46
Background
Cytosine methylation is a frequent epigenetic modification restricting the activity of gene regulatory elements. Whereas DNA methylation patterns are generally inherited during replication, both embryonic and somatic differentiation processes require the removal of cytosine methylation at specific gene loci to activate lineage-restricted elements. However, the exact mechanisms facilitating the erasure of DNA methylation remain unclear in many cases.Results
We previously established human post-proliferative monocytes as a model to study active DNA demethylation. We now show, for several previously identified genomic sites, that the loss of DNA methylation during the differentiation of primary, post-proliferative human monocytes into dendritic cells is preceded by the local appearance of 5-hydroxymethylcytosine. Monocytes were found to express the methylcytosine dioxygenase Ten-Eleven Translocation (TET) 2, which is frequently mutated in myeloid malignancies. The siRNA-mediated knockdown of this enzyme in primary monocytes prevented active DNA demethylation, suggesting that TET2 is essential for the proper execution of this process in human monocytes.Conclusions
The work described here provides definite evidence that TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine initiates targeted, active DNA demethylation in a mature postmitotic myeloid cell type. 相似文献152.
Eva C. Schulte Immanuel Stahl Darina Czamara Daniel C. Ellwanger Sebastian Eck Elisabeth Graf Brit Mollenhauer Alexander Zimprich Peter Lichtner Dietrich Haubenberger Walter Pirker Thomas Brücke Benjamin Bereznai Maria J. Molnar Annette Peters Christian Gieger Bertram Müller-Myhsok Claudia Trenkwalder Juliane Winkelmann 《PloS one》2013,8(11)
Approximately 20% of individuals with Parkinson’s disease (PD) report a positive family history. Yet, a large portion of causal and disease-modifying variants is still unknown. We used exome sequencing in two affected individuals from a family with late-onset familial PD followed by frequency assessment in 975 PD cases and 1014 ethnically-matched controls and linkage analysis to identify potentially causal variants. Based on the predicted penetrance and the frequencies, a variant in PLXNA4 proved to be the best candidate and PLXNA4 was screened for additional variants in 862 PD cases and 940 controls, revealing an excess of rare non-synonymous coding variants in PLXNA4 in individuals with PD. Although we cannot conclude that the variant in PLXNA4 is indeed the causative variant, these findings are interesting in the light of a surfacing role of axonal guidance mechanisms in neurodegenerative disorders but, at the same time, highlight the difficulties encountered in the study of rare variants identified by next-generation sequencing in diseases with autosomal dominant or complex patterns of inheritance. 相似文献
153.
Sara Montanari Munazza Saeed Mareike Kn?bel YoonKyeong Kim Michela Troggio Mickael Malnoy Riccardo Velasco Paolo Fontana KyungHo Won Charles-Eric Durel Laure Perchepied Robert Schaffer Claudia Wiedow Vincent Bus Lester Brewer Susan E. Gardiner Ross N. Crowhurst David Chagné 《PloS one》2013,8(10)
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (‘Old Home’בLouise Bon Jersey’) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality. 相似文献
154.
Claudia Palladino Verónica Briz José María Bellón Inês Bártolo Patrícia Carvalho Ricardo Camacho M. ángeles Mu?oz-Fernández Rui Bastos Rolanda Manuel José Casanovas Nuno Taveira 《PloS one》2013,8(12)
In Mozambique, the evaluation of retention in HIV care and ART programmes is limited. To assess rate and predictors of attrition (no retention in care) and HAART effectiveness in HIV-1 infected patients who pay for medication and laboratory testing in Mozambique, we conducted a multicenter survey of HIV-1-infected patients who started HAART during 2002–2006. Cox proportional hazard models were used to assess risk of attrition and of therapy failure. Overall, 142 patients from 16 healthcare centers located in the capital city Maputo were followed-up for 22.2 months (12.1–46.7). The retention rate was 75%, 48% and 37% after one, two and three years, respectively. Risk of attrition was lower in patients with higher baseline CD4 count (P = 0.022) and attending healthcare center 1 (HCC1) (P = 0.013). The proportion of individuals with CD4 count ≤200 cells/µL was 55% (78/142) at baseline and decreased to 6% (3/52) at 36 months. Among the patients with available VL, 86% (64/74) achieved undetectable VL levels. The rate of immunologic failure was 17.2% (95% CI: 12.6–22.9) per 100 person-years. Risk of failure was associated to higher baseline CD4 count (P = 0.002), likely reflecting low adherence levels, and decreased with baseline VL ≥10,000 copies/mL (P = 0.033). These results suggest that HAART can be effective in HIV-1 infected patients from Mozambique that pay for their medication and laboratory testing. Further studies are required to identify the causes for low retention rates in patients with low CD4 counts and to better understand the association between healthcare setting and attrition rate. 相似文献
155.
Aldo Scarpa Katarzyna Sikora Matteo Fassan Anna Maria Rachiglio Rocco Cappellesso Davide Antonello Eliana Amato Andrea Mafficini Matilde Lambiase Claudia Esposito Emilio Bria Francesca Simonato Maria Scardoni Giona Turri Marco Chilosi Giampaolo Tortora Ambrogio Fassina Nicola Normanno 《PloS one》2013,8(11)
Identification of driver mutations in lung adenocarcinoma has led to development of targeted agents that are already approved for clinical use or are in clinical trials. Therefore, the number of biomarkers that will be needed to assess is expected to rapidly increase. This calls for the implementation of methods probing the mutational status of multiple genes for inoperable cases, for which limited cytological or bioptic material is available. Cytology specimens from 38 lung adenocarcinomas were subjected to the simultaneous assessment of 504 mutational hotspots of 22 lung cancer-associated genes using 10 nanograms of DNA and Ion Torrent PGM next-generation sequencing. Thirty-six cases were successfully sequenced (95%). In 24/36 cases (67%) at least one mutated gene was observed, including EGFR, KRAS, PIK3CA, BRAF, TP53, PTEN, MET, SMAD4, FGFR3, STK11, MAP2K1. EGFR and KRAS mutations, respectively found in 6/36 (16%) and 10/36 (28%) cases, were mutually exclusive. Nine samples (25%) showed concurrent alterations in different genes. The next-generation sequencing test used is superior to current standard methodologies, as it interrogates multiple genes and requires limited amounts of DNA. Its applicability to routine cytology samples might allow a significant increase in the fraction of lung cancer patients eligible for personalized therapy. 相似文献
156.
Matheus Balduíno Goncalves dos Reis Letícia Correa Manjolin Claudia do Carmo Maquiaveli Osvaldo Andrade Santos-Filho Edson Roberto da Silva 《PloS one》2013,8(11)
Epigallocatechin-3-gallate (EGCG), a dietary polyphenol (flavanol) from green tea, possesses leishmanicidal and antitrypanosomal activity. Mitochondrial damage was observed in Leishmania treated with EGCG, and it contributed to the lethal effect. However, the molecular target has not been defined. In this study, EGCG, (+)-catechin and (−)-epicatechin were tested against recombinant arginase from Leishmania amazonensis (ARG-L) and rat liver arginase (ARG-1). The compounds inhibit ARG-L and ARG-1 but are more active against the parasite enzyme. Enzyme kinetics reveal that EGCG is a mixed inhibitor of the ARG-L while (+)-catechin and (−)-epicatechin are competitive inhibitors. The most potent arginase inhibitor is (+)-catechin (IC50 = 0.8 µM) followed by (−)-epicatechin (IC50 = 1.8 µM), gallic acid (IC50 = 2.2 µM) and EGCG (IC50 = 3.8 µM). Docking analyses showed different modes of interaction of the compounds with the active sites of ARG-L and ARG-1. Due to the low IC50 values obtained for ARG-L, flavanols can be used as a supplement for leishmaniasis treatment. 相似文献
157.
Lorena Esposito-Bauer Tobias Saam Iman Ghodrati Jaroslav Pelisek Peter Heider Matthias Bauer Petra Wolf Angelina Bockelbrink Regina Feurer Dominik Sepp Claudia Winkler Peter Zepper Tobias Boeckh-Behrens Matthias Riemenschneider Bernhard Hemmer Holger Poppert 《PloS one》2013,8(7)
Purpose
The aim of this study was to investigate prospectively whether MRI plaque imaging can identify patients with asymptomatic carotid artery stenosis who have an increased risk for future cerebral events. MRI plaque imaging allows categorization of carotid stenosis into different lesion types (I–VIII). Within these lesion types, lesion types IV–V and VI are regarded as rupture-prone plaques, whereas the other lesion types represent stable ones.Methods
Eighty-three consecutive patients (45 male (54.2%); age 54–88 years (mean 73.2 years)) presenting with an asymptomatic carotid stenosis of 50–99% according to ECST-criteria were recruited. Patients were imaged with a 1.5-T scanner. T1-, T2-, time-of-flight-, and proton-density weighted studies were performed. The carotid plaques were classified as lesion type I–VIII. Clinical endpoints were ischemic stroke, TIA or amaurosis fugax. Survival analysis and log rank test were used to ascertain statistical significance.Results
Six out of 83 patients (7.2%) were excluded: 4 patients had insufficient MR image quality; 1 patient was lost-to-follow-up; 1 patient died shortly after the baseline MRI plaque imaging. The following results were obtained by analyzing the remaining 77 patients. The mean time of follow-up was 41.1 months.During follow-up, n = 9 (11.7%) ipsilateral ischemic cerebrovascular events occurred. Only patients presenting with the high-risk lesion types IV–V and VI developed an ipsilateral cerebrovascular event versus none of the patients presenting with the stable lesion types III, VII, and VIII (n = 9 (11.7%) vs. n = 0 (0%) during follow-up). Event-free survival was higher among patients with the MRI-defined stable lesion types (III, VII, and VIII) than in patients with the high-risk lesion types (IV–V and VI) (log rank test P<0.0001).Conclusions
MRI plaque imaging has the potential to identify patients with asymptomatic carotid stenosis who are particularly at risk of developing future cerebral ischemia. MRI could improve selection criteria for invasive therapy in the future. 相似文献158.
The subterranean termite Reticulitermes chinensis Snyder is an important pest of trees and buildings in China. Here, we characterized genetic structure and reproductive modes of R. chinensis from China for the first time. A total of 1,875 workers from 75 collection sites in Huanggang, Changsha and Chongqing cities were genotyped at eight microsatellite loci. Analysis of genetic clusters showed two subpopulations in Chongqing city. The Huanggang population showed a uniform genetic pattern and was separated from the other populations by the largest genetic distances (F
ST: 0.17–0.20). In contrast, smaller genetic distances (F
ST: 0.05–0.12) separated Changsha, Chongqing-1 and Chongqing-2 populations. Chongqing-1 was the only population showing a genetic bottleneck. Isolation by distance among colonies in the Huanggang population indicated limited alate dispersal or colony budding. Lack of isolation by distance among colonies within the populations of Changsha, Chongqing-1 and Chongqing-2, suggested long-range dispersal by alates and/or human-mediated transport. Overall, extended family colonies (73.91%) were predominant in all four populations, followed by simple (20.29%), and mixed family colonies (5.80%). Most simple families were headed by inbred related reproductive pairs in the Changsha population, while most simple families in the Chongqing-1 population were headed by outbred unrelated pairs. Simple families in the Huanggang population were a mixture of colonies headed by outbred or inbred reproductive pairs. The sample size of simple families in the Chongqing-2 population was too small to yield significant results. Extended families in all four populations were headed on the average by ≤10 neotenics. Mixed families likely originated from pleometrosis. Presence of heterozygote genotypes showed that all neotenic reproductives collected in addition from five field colonies in Wuhan city were sexually produced, suggesting that these colonies did not undergo parthenogenesis. This study contributes to better understanding of the variance of genetic structure and reproductive mode in the genus Reticulitermes. 相似文献
159.
160.
Claudia Siegl Patricia Hamminger Herbert Jank Uwe Ahting Benedikt Bader Adrian Danek Allison Gregory Monika Hartig Susan Hayflick Andreas Hermann Holger Prokisch Esther M. Sammler Zuhal Yapici Rainer Prohaska Ulrich Salzer 《PloS one》2013,8(10)
Neuroacanthocytosis (NA) refers to a group of heterogenous, rare genetic disorders, namely chorea acanthocytosis (ChAc), McLeod syndrome (MLS), Huntington’s disease-like 2 (HDL2) and pantothenate kinase associated neurodegeneration (PKAN), that mainly affect the basal ganglia and are associated with similar neurological symptoms. PKAN is also assigned to a group of rare neurodegenerative diseases, known as NBIA (neurodegeneration with brain iron accumulation), associated with iron accumulation in the basal ganglia and progressive movement disorder. Acanthocytosis, the occurrence of misshaped erythrocytes with thorny protrusions, is frequently observed in ChAc and MLS patients but less prevalent in PKAN (about 10%) and HDL2 patients. The pathological factors that lead to the formation of the acanthocytic red blood cell shape are currently unknown. The aim of this study was to determine whether NA/NBIA acanthocytes differ in their functionality from normal erythrocytes. Several flow-cytometry-based assays were applied to test the physiological responses of the plasma membrane, namely drug-induced endocytosis, phosphatidylserine exposure and calcium uptake upon treatment with lysophosphatidic acid. ChAc red cell samples clearly showed a reduced response in drug-induced endovesiculation, lysophosphatidic acid-induced phosphatidylserine exposure, and calcium uptake. Impaired responses were also observed in acanthocyte-positive NBIA (PKAN) red cells but not in patient cells without shape abnormalities. These data suggest an “acanthocytic state” of the red cell where alterations in functional and interdependent membrane properties arise together with an acanthocytic cell shape. Further elucidation of the aberrant molecular mechanisms that cause this acanthocytic state may possibly help to evaluate the pathological pathways leading to neurodegeneration. 相似文献