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  • 1
    Publication Date: 2015-05-03
    Description: Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet)—initiated oxidative demethylation. The connection of Gadd45a with oxidative demethylation is evidenced by the enhanced activation of a methylated reporter gene in HEK293T cells expressing Gadd45a in combination with catalytically active TDG and Tet. Gadd45a interacts with TDG physically and increases the removal of 5fC and 5caC from genomic and transfected plasmid DNA by TDG. Knockout of both Gadd45a and Gadd45b from mouse ES cells leads to hypermethylation of specific genomic loci most of which are also targets of TDG and show 5fC enrichment in TDG-deficient cells. These observations indicate that the demethylation effect of Gadd45a is mediated by TDG activity. This finding thus unites Gadd45a with the recently defined Tet-initiated demethylation pathway.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2016-08-28
    Description: Chlamydial species are common intracellular parasites that cause various diseases, mainly characterized by persistent infection, which lead to inflammatory responses modulated by pattern recognition receptors (PRRs). The best understood PRRs are the extracellular Toll-like receptors, but recent significant advances have focused on two important proteins, NOD1 and NOD2, which are members of the intracellular nucleotide-binding oligomerization domain receptor family and are capable of triggering the host innate immune signaling pathways. This results in the production of pro-inflammatory cytokines, which is vital for an adequate host defense against intracellular chlamydial infection. NOD1/2 ligands are known to derive from peptidoglycan, and the latest research has resolved the paradox of whether chlamydial species possess this bacterial cell wall component; this finding is likely to promote in-depth investigations into the interaction between the NOD proteins and chlamydial pathogens. In this review, we summarize the basic characteristics and signal transduction functions of NOD1 and NOD2 and highlight the new research on the roles of NOD1 and NOD2 in the host defense against chlamydial infection.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 3
    Publication Date: 2015-12-10
    Description: : Demultiplexing is used after high-throughput sequencing to in silico assign reads to the samples of origin based on the sequenced reads of the indices. Existing demultiplexing tools based on the similarity between the read index and the reference index sequences may fail to provide satisfactory results on low-quality datasets. We developed Bayexer, a Bayesian demultiplexing algorithm for Illumina sequencers. Bayexer uses the information extracted directly from the contaminant sequences of the targeting reads as the training dataset for a naïve Bayes classifier to assign reads. According to our evaluation, Bayexer provides higher capability, accuracy and speed on various real datasets than other tools. Availability and implementation : Bayexer is implemented in Perl and freely available at https://github.com/HaisiYi/Bayexer . Contact: litao@ihb.ac.cn or lizhe@ibcas.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 4
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Finite-difference (FD) methods are widely used for numerical solution of acoustic and elastic wave equations. Temporal high-order FD methods exhibit better accuracy and stability than the methods with second-order differencing in time. Also, the implicit calculation of spatial derivatives can bring significant improvement in accuracy. The present implicit FD methods with high-order accuracy in time are based on centred grids. In this paper, we propose an implicit staggered-grid FD (SFD) scheme with a combined stencil, which is the combination of rhombus/pyramid and cross stencils in 2-D/3-D case, for modelling scalar wave propagation. Our scheme computes the temporal and spatial derivatives using high-order temporal and implicit spatial FD operators based on the combined stencil and the conventional stencil, respectively. We derive the dispersion relations of the FD scheme for 2-D and 3-D scalar wave equations and estimate temporal and implicit spatial FD coefficients by Taylor series expansion (TE) and least squares (LS). According to the kinds of FD coefficients, we formulate four implicit SFD operators: TE–TE, TE–LS, LS–TE and LS–LS operators. We carry out the comparison between our scheme and several existing SFD schemes: the conventional explicit and implicit, optimal explicit and implicit and explicit temporal high-order schemes. 2-D and 3-D dispersion analysis, stability analysis and modelling examples reveal that our implicit scheme has greater accuracy than other schemes and requires slightly stricter stability condition than the explicit temporal high-order SFD schemes. Owing to higher accuracy, our implicit SFD scheme with LS-LS operators allows for shorter FD operators and larger grid spacing, which can increase the computational efficiency.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 5
    Publication Date: 2014-01-16
    Description: We investigated the spectral and timing properties of the type B quasi-periodic oscillations (QPOs) showing up in the transient black hole binary GX 339-4 during its four outbursts observed by Rossi X-ray Timing Explorer (RXTE)/PCA and HEXTE in 2002, 2004, 2007 and 2010. We find that, the dependence on variability of the accretion flow turns out to be similar for the type B QPOs occurring in these four outbursts. We therefore take the results from the 2010 outburst for presentation. Our spectral results obtained from both the energy and time domains show that, the occurrence of the type B QPO is accompanied with sudden increase of hard component flux, relatively smaller inner disk radius, stable disk but variable corona. The latter may be understood in a scenario of variable input of seed photons for Comptonization in the corona. Further clues to probing the possible origination of the type B QPO come from our analysis of time lag and its energy dependence. The energy dependence of type B QPO amplitude suggests that the hard component dominate the variability and the time lag spectral analysis results suggests the type B QPO could be related to inverse Compton scattering. The time lag between hard and soft energy band is about 10 ms and found to depend on frequency in a form of –0.7 for type B QPOs in the rising phase. Finally we put these results in a context of a blob mechanism at work.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Finite-difference (FD) methods are widely used for numerical solution of acoustic and elastic wave equations. Temporal high-order FD methods exhibit better accuracy and stability than the methods with second-order differencing in time. Also, the implicit calculation of spatial derivatives can bring significant improvement in accuracy. The present implicit FD methods with high-order accuracy in time are based on centered grids. In this paper, we propose an implicit staggered-grid FD (SFD) scheme with a combined stencil, which is the combination of rhombus/pyramid and cross stencils in 2D/3D case, for modelling scalar wave propagation. Our scheme computes the temporal and spatial derivatives using high-order temporal and implicit spatial FD operators based on the combined stencil and the conventional stencil, respectively. We derive the dispersion relations of the FD scheme for 2D and 3D scalar wave equations and estimate temporal and implicit spatial FD coefficients by Taylor series expansion (TE) and least squares (LS). According to the kinds of FD coefficients, we formulate four implicit SFD operators: TE-TE, TE-LS, LS-TE and LS-LS operators. We carry out the comparison between our scheme and several existing SFD schemes: the conventional explicit and implicit, optimal explicit and implicit, and explicit temporal high-order schemes. 2D and 3D dispersion analysis, stability analysis and modelling examples reveal that our implicit scheme has greater accuracy than other schemes and requires slightly stricter stability condition than the explicit temporal high-order SFD schemes. Owing to higher accuracy, our implicit SFD scheme with LS-LS operators allows for shorter FD operators and larger grid spacing, which can increase the computational efficiency.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
    Publication Date: 2018-03-06
    Description: Flue gas from natural gas boilers contains much water vapor, so the latent heat occupies a large proportion of the total waste heat. This paper introduces a flue gas driven absorption system based on low-pressure regeneration liquid cycle to recover water and waste heat, especially the latent heat. The concentrated liquid desiccant is sprayed into the packed tower to absorb the vapor from the low-temperature flue gas and gets diluted itself. Then the diluted desiccant is heated and concentrated by the high-temperature flue gas in the vacuum regenerator. The evaporated water from the regenerator then releases condensation heat to the return water of the heating network. Based on the thermodynamic model of the new system, the simulation results show that the flue gas (200°C, 120 g/kg) is eventually released to the atmosphere at 53°C with a humidity ratio of 46 g/kg, which means considerable heat is recovered by the system. The heat and water recovery of the new system is not constrained by the dew point of the flue gas. It also lowers the requirement of the generation temperature due to vacuum regeneration. So in terms of heat recovery, the new system outperforms the traditional condensing system and the open-cycle absorption system by 28.3% and 23.1%, respectively. The new system also helps to reduce particulate emissions and recover water, with a recovery of 0.36 tons of water per hour according to the simulation result based on the boiler with a power of 2.8 MW.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 8
    Publication Date: 2016-09-17
    Description: Snub-nosed monkeys (genus Rhinopithecus ) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 9
    Publication Date: 2016-07-30
    Description: In this work, we mainly study the magnification relations of quad lens models for cusp, fold and cross configurations. By dividing and ray-tracing in different image regions, we numerically derive the positions and magnifications of the four images for a point source lying inside of the astroid caustic. Then, based on the magnifications, we calculate the signed cusp and fold relations for the singular isothermal elliptical lenses. The signed fold relation map has positive and negative regions, and the positive region is usually larger than the negative region as has been confirmed before. It can also explain that for many observed fold image pairs, the fluxes of the Fermat minimum images are apt to be larger than those of the saddle images. We define a new quantity cross relation R cross which describes the magnification discrepancy between two minimum images and two saddle images. Distance ratio d sadd / d mini is also defined as the ratio of the distance of two saddle images to that of two minimum images. We calculate the cross relations and distance ratios for nine observed Einstein crosses. In theory, for most of the quad lens models, the cross relations decrease as the distance ratios increase. In observation, the cross relations of the nine samples do not agree with the quad lens models very well, nevertheless, the cross relations of the nine samples do not give obvious evidence for anomalous flux ratio as the cusp and fold types do. Then, we discuss several reasons for the disagreement, and expect good consistencies for more precise observations and better lens models in the future.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 10
    Publication Date: 2016-05-06
    Description: Trimethylated histone H3 lysine 27 (H3K27me3) is linked to gene silencing, whereas H3K4me3 is associated with gene activation. These two marks frequently co-occupy gene promoters, forming bivalent domains. Bivalency signifies repressed but activatable states of gene expression and can be resolved to active, H3K4me3-prevalent states during multiple cellular processes, including differentiation, development and epithelial mesenchymal transition. However, the molecular mechanism underlying bivalency resolution remains largely unknown. Here, we show that the H3K27 demethylase UTX (also called KDM6A) is required for the resolution and activation of numerous retinoic acid (RA)-inducible bivalent genes during the RA-driven differentiation of mouse embryonic stem cells (ESCs). Notably, UTX loss in mouse ESCs inhibited the RA-driven bivalency resolution and activation of most developmentally critical homeobox ( Hox ) a–d genes. The UTX-mediated resolution and activation of many bivalent Hox genes during mouse ESC differentiation were recapitulated during RA-driven differentiation of human NT2/D1 embryonal carcinoma cells. In support of the importance of UTX in bivalency resolution, Utx -null mouse ESCs and UTX-depleted NT2/D1 cells displayed defects in RA-driven cellular differentiation. Our results define UTX as a bivalency-resolving histone modifier necessary for stem cell differentiation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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