1,427 research outputs found
Methylation Status of Imprinted Genes and Repetitive Elements in Sperm DNA from Infertile Males
Stochastic, environmentally and/or genetically induced disturbances in the genome-wide epigenetic reprogramming processes during male germ-cell development may contribute to male infertility. To test this hypothesis, we have studied the methylation levels of 2 paternally (H19 and GTL2) and 5 maternally methylated (LIT1, MEST, NESPAS, PEG3, and SNRPN) imprinted genes, as well as of ALU and LINE1 repetitive elements in 141 sperm samples, which were used for assisted reproductive technologies (ART), including 106 couples with strictly male-factor or combined male and female infertility and 28 couples with strictly female-factor infertility. Aberrant methylation imprints showed a significant association with abnormal semen parameters, but did not seem to influence ART outcome. Repeat methylation also differed significantly between sperm samples from infertile and presumably fertile males. However, in contrast to imprinted genes, ALU methylation had a significant impact on pregnancy and live-birth rate in couples with male-factor or combined infertility. ALU methylation was significantly high-er in sperm samples leading to pregnancy and live-birth than in those that did not. Sperm samples leading to abortions showed significantly lower ALU methylation levels than those leading to the birth of a baby. Copyright (C) 2011 S. Karger AG, Base
Global DNA hypomethylation prevents consolidation of differentiation programs and allows reversion to the embryonic stem cell state.
DNA methylation patterns change dynamically during mammalian development and lineage specification, yet scarce information is available about how DNA methylation affects gene expression profiles upon differentiation. Here we determine genome-wide transcription profiles during undirected differentiation of severely hypomethylated (Dnmt1â»/â») embryonic stem cells (ESCs) as well as ESCs completely devoid of DNA methylation (Dnmt1â»/â»;Dnmt3aâ»/â»;Dnmt3bâ»/â» or TKO) and assay their potential to transit in and out of the ESC state. We find that the expression of only few genes mainly associated with germ line function and the X chromosome is affected in undifferentiated TKO ESCs. Upon initial differentiation as embryoid bodies (EBs) wild type, Dnmt1â»/â» and TKO cells downregulate pluripotency associated genes and upregulate lineage specific genes, but their transcription profiles progressively diverge upon prolonged EB culture. While Oct4 protein levels are completely and homogeneously suppressed, transcription of Oct4 and Nanog is not completely silenced even at late stages in both Dnmt1â»/â» and TKO EBs. Despite late wild type and Dnmt1â»/â» EBs showing a much higher degree of concordant expression, after EB dissociation and replating under pluripotency promoting conditions both Dnmt1â»/â» and TKO cells, but not wild type cells rapidly revert to expression profiles typical of undifferentiated ESCs. Thus, while DNA methylation seems not to be critical for initial activation of differentiation programs, it is crucial for permanent restriction of developmental fate during differentiation
37 years of forest monitoring in Switzerland: drought effects on; Fagus sylvatica
European beech is one of the most important deciduous tree species in natural forest ecosystems in Central Europe. Its dominance is now being questioned by the emerging drought damages due to the increased incidence of severe summer droughts. In Switzerland, Fagus sylvatica have been observed in the Intercantonal Forest Observation Program since 1984. The dataset presented here includes 179176 annual observations of beech trees on 102 plots during 37 years. The plots cover gradients in drought, nitrogen deposition, ozone, age, altitude, and soil chemistry. In dry regions of Switzerland, the dry and hot summer of 2018 caused a serious branch dieback, increased mortality in Fagus sylvatica and increased yellowing of leaves. Beech trees recovered less after 2018 than after the dry summer 2003 which had been similar in drought intensity except that the drought in 2018 started earlier in spring. Our data analyses suggest the importance of drought in subsequent years for crown transparency and mortality in beech. The drought in 2018 followed previous dry years of 2015 and 2017 which pre-weakened the trees. Our long-term data indicate that the drought from up to three previous years were significant predictors for both tree mortality and for the proportion of trees with serious (>60%) crown transparency. The delay in mortality after the weakening event suggests also the importance of weakness parasites. The staining of active vessels with safranine revealed that the cavitation caused by the low tree water potentials in 2018 persisted at least partially in 2019. Thus, the ability of the branches to conduct water was reduced and the branches dried out. Furthermore, photooxidation in light-exposed leaves has increased strongly since 2011. This phenomenon was related to low concentrations of foliar phosphorus (P) and hot temperatures before leaf harvest. The observed drought effects can be categorized as (i) hydraulic failure (branch dieback), (ii) energy starvation as a consequence of closed stomata and P deficiency (photooxidation) and (iii) infestation with weakness parasites (beech bark disease and root rots)
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle
DNA replication, transcription and repair involve the recruitment of protein complexes that change their composition as they progress along the genome in a directed or strand-specific manner. Chromatin immunoprecipitation in conjunction with hidden Markov models (HMMs) has been instrumental in understanding these processes, as they segment the genome into discrete states that can be related to DNA-associated protein complexes. However, current HMM-based approaches are not able to assign forward or reverse direction to states or properly integrate strand-specific (e.g.,RNA expression) with non-strand-specific (e.g.,ChIP) data, which is indispensable to accurately characterize directed processes. To overcome these limitations, we introduce bidirectional HMMs which infer directed genomic states from occupancy profiles de novo. Application to RNA polymerase II-associated factors in yeast and chromatin modifications in human T cells recovers the majority of transcribed loci, reveals gene-specific variations in the yeast transcription cycle and indicates the existence of directed chromatin state patterns at transcribed, but not at repressed, regions in the human genome. In yeast, we identify 32 new transcribed loci, a regulated initiation-elongation transition, the absence of elongation factors Ctk1 and Paf1 from a class of genes, a distinct transcription mechanism for highly expressed genes and novel DNA sequence motifs associated with transcription termination. We anticipate bidirectional HMMs to significantly improve the analyses of genome-associated directed processes
EP-1180: Postoperative IMRT with helical tomotherapy for breast cancer: outcome and toxicity analysis
A Synergistic Behavior Underpins Human Hand Grasping Force Control During Environmental Constraint Exploitation
Despite the complex nature of human hands, neuroscientific studies suggested a simplified kinematic control underpinning motion generation, resulting in principal joint angle co-variation patterns, usually called postural hand synergies. Such a low dimensional description was observed in common grasping tasks, and was proven to be preserved also for grasps performed by exploiting the external environment (e.g., picking up a key by sliding it on a table). In this paper, we extend this analysis to the force domain. To do so, we performed experiments with six subjects, who were asked to grasp objects from a flat surface while force/torque measures were acquired at fingertip level through wearable sensors. The set of objects was chosen so that participants were forced to interact with the table to achieve a successful grasp. Principal component analysis was applied to force measurements to investigate the existence of co-variation schemes, i.e. a synergistic behavior. Results show that one principal component explains most of the hand force distribution. Applications to clinical assessment and robotic sensing are finally discussed
Angular analysis of the decay in the low- region
An angular analysis of the decay is performed using a data sample, corresponding to an integrated luminosity of 3.0 {\mbox{fb}^{-1}}, collected by the LHCb experiment in collisions at centre-of-mass energies of 7 and 8 TeV during 2011 and 2012. For the first time several observables are measured in the dielectron mass squared () interval between 0.002 and 1.120. The angular observables and which are related to the polarisation and to the lepton forward-backward asymmetry, are measured to be and , where the first uncertainty is statistical and the second systematic. The angular observables and which are sensitive to the photon polarisation in this range, are found to be and . The results are
consistent with Standard Model predictions
Coordinate-space Faddeev-Hahn-type approach to three-body charge-transfer reactions involving exotic particles
Measurement of asymmetries and polarisation fractions in decays
An angular analysis of the decay is performed using collisions corresponding to an integrated luminosity of collected by the LHCb experiment at a centre-of-mass energy TeV. A combined angular and mass analysis separates six helicity amplitudes and allows the measurement of the longitudinal polarisation fraction for the decay. A large scalar contribution from the and resonances is found, allowing the determination of additional asymmetries. Triple product and direct asymmetries are determined to be compatible with the Standard Model expectations. The branching fraction is measured to be
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