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  • 1
    Publication Date: 2017-01-10
    Description: Trimethylation of histone H3K36 is a chromatin mark associated with active gene expression, which has been implicated in coupling transcription with mRNA splicing and DNA damage response. SETD2 is a major H3K36 trimethyltransferase, which has been implicated as a tumor suppressor in mammals. Here, we report the regulation of SETD2 protein stability by the proteasome system, and the identification of SPOP, a key subunit of the CUL3 ubiquitin E3 ligase complex, as a SETD2-interacting protein. We demonstrate that SPOP is critically involved in SETD2 stability control and that the SPOP/CUL3 complex is responsible for SETD2 polyubiquitination both in vivo and in vitro . ChIP-Seq analysis and biochemical experiments demonstrate that modulation of SPOP expression confers differential H3K36me3 on SETD2 target genes, and induce H3K36me3-coupled alternative splicing events. Together, these findings establish a functional connection between oncogenic SPOP and tumor suppressive SETD2 in the dynamic regulation of gene expression on chromatin.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2017-01-05
    Description: We describe LincSNP 2.0 ( http://bioinfo.hrbmu.edu.cn/LincSNP ), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. Furthermore, we developed three flexible online tools to retrieve and analyze the data. Linc-Mart is a convenient way for users to customize their own data. Linc-Browse is a tool for all data visualization. Linc-Score predicts the associations between lncRNA and disease. In addition, we provided users a newly designed, user-friendly interface to search and download all the data in LincSNP 2.0 and we also provided an interface to submit novel data into the database. LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2016-12-13
    Description: We present a timing analysis of two Rossi X-ray Timing Explorer observations of the microquasar GRS 1915+105 during the heartbeat state. The phase–frequency–power maps show that the intermediate-frequency aperiodic X-ray variability weakens as the source softens in the slow rise phase, and when the quasi-periodic oscillation disappears in the rise phase of the pulse of the double-peaked class, its sub-harmonic is still present with a hard phase lag. In the slow rise phase, the energy–frequency–power maps show that most of the aperiodic variability is produced in the corona, and may also induce the aperiodic variability observed at low energies from an accretion disc, which is further supported by the soft phase lag especially in the intermediate-frequency range (with a time delay up to 20 ms). In the rise phase of the pulse, the low-frequency aperiodic variability is enhanced significantly and there is a prominent hard lag (with a time delay up to 50 ms), indicating that the variability is induced by extension of the disc towards small radii as implied by the increase in flux and propagates into the corona. However, during the hard pulse of the double-peaked class, the variability shows no significant lag, which may be attributed to an optically thick corona. These timing results are generally consistent with the spectral results presented by Neilsen, Remillard & Lee which indicated that the slow rise phase corresponds to a local Eddington limit and the rise phase of the pulse corresponds to a radiation pressure instability in the disc.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 4
    Publication Date: 2016-02-28
    Description: We use the evolutionary population synthesis method to investigate the statistical properties of the wind-fed neutron-star (NS) compact ( P orb 〈 10 d) high-mass X-ray binaries (HMXBs) in our Galaxy, based on different spin-down models. Model 1 assumes that the surrounding material is treated as forming a quasi-static atmosphere. Model 2 assumes that the characteristic velocity of matter and the typical Alfvén velocity of material in the magnetospheric boundary layer are comparable to the sound speed in the external medium. We find that the spin-down rate in the supersonic propeller phase in either model 1 or model 2 is too low to produce the observed number of compact HMXBs. Model 3 assumes that the infalling material is ejected with the corotation velocity at the magnetospheric radius when the magnetospheric radius is larger than the corotation radius. Model 4 uses simple integration of the magnetic torque over the magnetosphere. Both models 3 and 4 have a larger spin down rate than that given by model 1 or 2. We also find that models 3 and 4 can predict a reasonable number of observed wind-fed NS compact HMXBs. By comparing our calculated results with the observed particular distributions of wind-fed NS compact HMXBs in a P s versus P orb diagram, we find that the subsonic propeller phase may not exist at all. However, the spin-down rates in models 3 and 4 both seem reasonable to produce the observed distribution of wind-fed NS compact HMXBs in the P s versus P orb diagram. We cannot find which spin-down rate seems more reasonable from our calculations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2016-01-29
    Description: Currently, there are 24 black hole (BH) X-ray binary systems that have been dynamically confirmed in the Galaxy. Most of them are low-mass X-ray binaries (LMXBs) comprised of a stellar-mass BH and a low-mass donor star. Although the formation of these systems has been extensively investigated, some crucial issues remain unresolved. The most noticeable one is that, the low-mass companion has difficulties in ejecting the tightly bound envelope of the massive primary during the spiral-in process. While initially intermediate-mass binaries are more likely to survive the common envelope (CE) evolution, the resultant BH LMXBs mismatch the observations. In this paper, we use both stellar evolution and binary population synthesis to study the evolutionary history of BH LMXBs. We test various assumptions and prescriptions for the supernova mechanisms that produce BHs, the binding energy parameter, the CE efficiency and the initial mass distributions of the companion stars. We obtain the birthrate and the distributions of the donor mass, effective temperature and orbital period for the BH LMXBs in each case. By comparing the calculated results with the observations, we put useful constraints on the aforementioned parameters. In particular, we show that it is possible to form BH LMXBs with the standard CE scenario if most BHs are born through failed supernovae.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2015-12-13
    Description: Because of the lack of long-term pulsed emission in quiescence and the strong timing noise, it is impossible to directly measure the braking index n of a magnetar. Based on the estimated ages of their potentially associated supernova remnants (SNRs), we estimate the values of the mean braking indices of eight magnetars with SNRs, and find that they cluster in the range of 1–42. Five magnetars have smaller mean braking indices of 1 〈  n  〈 3, and we interpret them within a combination of magneto-dipole radiation and wind-aided braking. The larger mean braking indices of n  〉 3 for the other three magnetars are attributed to the decay of external braking torque, which might be caused by magnetic field decay. We estimate the possible wind luminosities for the magnetars with 1 〈  n  〈 3, and the dipolar magnetic field decay rates for the magnetars with n  〉 3, within the updated magneto-thermal evolution models. Although the constrained range of the magnetars’ braking indices is tentative, as a result of the uncertainties in the SNR ages due to distance uncertainties and the unknown conditions of the expanding shells, our method provides an effective way to constrain the magnetars’ braking indices if the measurements of the SNR ages are reliable, which can be improved by future observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2015-11-06
    Description: Recent timing observation reported that the radio pulsar PSR J1734–3333 with a rotating period P = 1.17 s is slowing down with a period derivative $\dot{P}=2.28\times 10^{-12}\ \rm s\,s^{-1}$ . Its derived braking index n  = 0.9 ± 0.2 is the lowest value among young radio pulsars with the measured braking indices. In this Letter, we attempt to investigate the influence of the braking torque caused by the interaction between the fall-back disc and the strong magnetic field of the pulsar on the spin evolution of PSR J1734–3333. Analytical result show that this braking torque is obviously far more than that by magnetic dipole radiation for pulsars with spin period of 〉0.1 s, and play an important role during the spin-down of the pulsars. Our simulated results indicate that, for some typical neutron star parameters, the braking index and the period derivative approximately in agreement with the measured value of PSR J1734–3333 if the material inflow rate in the fall-back disc is 2 x 10 17 g s – 1 . In addition, our scenario can account for the measured braking indices of four young pulsars. However, our predicted X-ray luminosity are one to two order of magnitude higher than the observation. We proposed that this discrepancy may originate from the instability of fall-back disc.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
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  • 8
    Publication Date: 2015-04-23
    Description: We propose a method using the redshift dependence of the Alcock–Paczynski (AP) test and volume effect to measure the cosmic expansion history. The galaxy two-point correlation function as a function of angle, (μ), is measured at different redshifts. Assuming an incorrect cosmological model to convert galaxy redshifts to distances, the shape of (μ) appears anisotropic due to the AP effect, and the amplitude is shifted by the change in comoving volume. Due to the redshift dependence of the AP and volume effect, both the shape and amplitude of (μ) exhibit redshift dependence. Similar to Li et al. ( 2014 ), we find that the redshift-space distortions (RSD) caused by galaxy peculiar velocities, although significantly distorting (μ), exhibit much less redshift evolution compared to the AP and volume effects. By focusing on the redshift dependence of (μ), we can correctly recover the cosmological parameters despite the contamination of RSD. The method is tested by using the Horizon Run 3 N -body simulation, from which we made a series of 1/8-sky mock surveys having eight million physically self-bound haloes and sampled to have roughly a uniform number density in z  = 0–1.5. We find the AP effect results in tight, unbiased constraints on the density parameter and dark energy equation of state, with 68.3% CL intervals m  ~ 0.03 and w  ~ 0.1, and the volume effect leads to much tighter constraints of m  ~ 0.007 and w  ~ 0.035.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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