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  • Copernicus  (74)
  • Oxford University Press  (67)
  • 2015-2019  (127)
  • 1995-1999  (14)
  • 1
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    Wolbachia megadiversity: 99% of these microorganismic manipulators unknown (2019)
    Oxford University Press
    Details
    Publication Date: 2019-09-30
    Description: Wolbachia (Alphaproteobacteria) are the most widespread endosymbionts of arthropods, manipulating their hosts by various means to maximize the number of host individuals infected. Based on quantitative analyzes of the published literature from Web of Science® and of DNA sequences of arthropod-hosted Wolbachia from GenBank, we made plausible that less than 1% of the expected 100 000 strains of Wolbachia in arthropods is known. Our findings suggest that more and globally better coordinated efforts in screening arthropods are needed to explore the true Wolbachia diversity and to help us understand the ecology and evolution of these host-endosymbiont interactions.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press on behalf of Federation of European Microbiological Societies.
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  • 2
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    On the theoretical framework of magnetized outflows from stellar-mass black holes and related observations (2016)
    Oxford University Press
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    Publication Date: 2016-07-15
    Description: The spins of stellar-mass black holes (BHs) and the power outputs of their jets are measurable quantities. Unfortunately, the currently employed methods do not agree and the results are controversial. Two major issues concern the measurements of BH spin and beam (jet) power. The former issue can be resolved by future observations. But the latter issue can be resolved now, if we pay attention to what is expected from theoretical considerations. The question of whether a correlation has been found between the power outputs of few objects and the spins of their BHs is moot because BH beam power does not scale with the square of the spin of the BH. We show that the theoretical BH beam power is a strongly non-linear function of spin that cannot be approximated by a quadratic relation, as is generally stated when the influence of the magnetic field is not accounted for in the Blandford & Znajek model. The BH beam power of ballistic jets should scale a lot more steeply with BH spin irrespective of the magnetic field assumed to thread the horizon and the spin range considered. This behaviour may already be visible in the analyses of radio observations by Narayan & McClintock and Russell et al. In agreement with previous studies, we also find that the power output that originates in the inner regions of the surrounding accretion discs is higher than that from the BHs and it cannot be ignored in investigations of continuous compact jets from these systems.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    The effects of feeding and withholding food on the canine small intestinal microbiota (2016)
    Oxford University Press
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    Publication Date: 2016-05-11
    Description: Prolonged lack of enteral feeding has a negative impact on gut physiology, potentially via microbiota modulation. The aims were to investigate the impact of fasting and post-prandial changes in canine jejunal microbiota. To study post-prandial effects, jejunal brushings were analyzed in 8 healthy fistulated dogs 15 min before feeding (baseline) and hourly for 8 h after feeding. To study effects of withholding food (WF), daily samples were collected for 15 days from 5 dogs. The first 5 days (PRE) dogs were fed regular diet. Food was withheld the next 5 days (days 6–10). For days 11–15 (POST), the original diet was reintroduced. Microbiota was characterized via denaturing gradient gel electrophoresis and 454-pyrosequencing of 16S rRNA genes. In the post-prandial study, no changes in microbiome structure were seen after feeding (ANOSIM, P  = 0.28), but Betaproteobacteria ( P  = 0.04) and Bacteroidales decreased compared to baseline. Species richness decreased by 300 min ( P  = 0.04). During WF, microbiota structure differed from PRE and POST period ( P  = 0.001). During WF, species richness did not vary over time ( P  = 0.69). In conclusion, a prolonged period of food withholding results in altered jejunal microbiota. How these changes affect the microbiota metabolism warrants further studies.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Analysis of hedgehog signaling in cerebellar granule cell precursors in a conditional Nsdhl allele demonstrates an essential role for cholesterol in postnatal CNS development (2015)
    Oxford University Press
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    Publication Date: 2015-04-23
    Description: NSDHL is a 3β-hydroxysterol dehydrogenase that is involved in the removal of two C-4 methyl groups in one of the later steps of cholesterol biosynthesis. Mutations in the gene encoding the enzyme are responsible for the X-linked, male lethal mouse mutations bare patches and striated, as well as most cases of human CHILD syndrome. Rare, hypomorphic NSDHL mutations are also associated with X-linked intellectual disability in males with CK syndrome. Since hemizygous male mice with Nsdhl mutations die by midgestation, we generated a conditional targeted Nsdhl mutation ( Nsdhl tm1.1Hrm ) to investigate the essential role of cholesterol in the early postnatal CNS. Ablation of Nsdhl in radial glia using GFAP-cre resulted in live-born, normal appearing affected male pups. However, the pups develop overt ataxia by postnatal day 8–10 and die shortly thereafter. Histological abnormalities include progressive loss of cortical and hippocampal neurons, as well as deficits in the proliferation and migration of cerebellar granule precursors and subsequent massive apoptosis of the cerebellar cortex. We replicated the granule cell precursor proliferation defect in vitro and demonstrate that it results from defective signaling by SHH. Furthermore, this defect is almost completely rescued by supplementation of the culture media with exogenous cholesterol, while methylsterol accumulation above the enzymatic block appears to be associated with increased cell death. These data support the absolute requirement for cholesterol synthesis in situ once the blood-brain-barrier forms and cholesterol transport to the fetus is abolished. They further emphasize the complex ramifications of cholesterogenic enzyme deficiency on cellular metabolism.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Tomography of X-ray Nova Muscae 1991: evidence for ongoing mass transfer and stream-disc overflow (2015)
    Oxford University Press
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    Publication Date: 2015-03-26
    Description: We present a spectroscopic analysis of the black hole binary Nova Muscae 1991 in quiescence using data obtained in 2009 with Magellan Echelette on the Magellan Clay telescope and in 2010 with IMACS on the Magellan Baade telescope at the Las Campanas Observatory. Emission from the disc is observed in Hα, Hβ and Ca  ii (8662). A prominent hotspot is observed in the Doppler maps of all three emission lines. The existence of this spot establishes ongoing mass transfer from the donor star in 2009–2010 and, given its absence in the 1993–1995 observations, demonstrates the presence of a variable hotspot in the system. We find the radial distance to the hotspot from the black hole to be consistent with the circularization radius. Our tomograms are suggestive of stream–disc overflow in the system. We also detect possible Ca  ii (8662) absorption from the donor star.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    The p53-p21-DREAM-CDE/CHR pathway regulates G2/M cell cycle genes (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: The tumor suppressor p53 functions predominantly as a transcription factor by activating and downregulating gene expression, leading to cell cycle arrest or apoptosis. p53 was shown to indirectly repress transcription of the CCNB2 , KIF23 and PLK4 cell cycle genes through the recently discovered p53-p21-DREAM-CDE/CHR pathway. However, it remained unclear whether this pathway is commonly used. Here, we identify genes regulated by p53 through this pathway in a genome-wide computational approach. The bioinformatic analysis is based on genome-wide DREAM complex binding data, p53-depedent mRNA expression data and a genome-wide definition of phylogenetically conserved CHR promoter elements. We find 210 target genes that are expected to be regulated by the p53-p21-DREAM-CDE/CHR pathway. The target gene list was verified by detailed analysis of p53-dependent repression of the cell cycle genes B-MYB ( MYBL2 ), BUB1 , CCNA2 , CCNB1 , CHEK2 , MELK , POLD1 , RAD18 and RAD54L . Most of the 210 target genes are essential regulators of G 2 phase and mitosis. Thus, downregulation of these genes through the p53-p21-DREAM-CDE/CHR pathway appears to be a principal mechanism for G 2 /M cell cycle arrest by p53.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    The effects of high density on the X-ray spectrum reflected from accretion discs around black holes (2016)
    Oxford University Press
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    Publication Date: 2016-08-07
    Description: Current models of the spectrum of X-rays reflected from accretion discs around black holes and other compact objects are commonly calculated assuming that the density of the disc atmosphere is constant within several Thomson depths from the irradiated surface. An important simplifying assumption of these models is that the ionization structure of the gas is completely specified by a single, fixed value of the ionization parameter , which is the ratio of the incident flux to the gas density. The density is typically fixed at n e  = 10 15  cm –3 . Motivated by observations, we consider higher densities in the calculation of the reflected spectrum. We show by computing model spectra for n e 10 17  cm –3 that high-density effects significantly modify reflection spectra. The main effect is to boost the thermal continuum at energies 2 keV. We discuss the implications of these results for interpreting observations of both active galactic nuclei and black hole binaries. We also discuss the limitations of our models imposed by the quality of the atomic data currently available.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation (2016)
    Oxford University Press
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    Publication Date: 2016-09-03
    Description: The modulation of chromatin structure is a key step in transcription regulation in mammalian cells and eventually determines lineage commitment and differentiation. USF1/2, Setd1a and NURF complexes interact to regulate chromatin architecture in erythropoiesis, but the mechanistic basis for this regulation is hitherto unknown. Here we showed that Setd1a and NURF complexes bind to promoters to control chromatin structural alterations and gene activation in a cell context dependent manner. In human primary erythroid cells USF1/2, H3K4me3 and the NURF complex were significantly co-enriched at transcription start sites of erythroid genes, and their binding was associated with promoter/enhancer accessibility that resulted from nucleosome repositioning. Mice deficient for Setd1a , an H3K4 trimethylase, in the erythroid compartment exhibited reduced Ter119/CD71 positive erythroblasts, peripheral blood RBCs and hemoglobin levels. Loss of Setd1a led to a reduction of promoter-associated H3K4 methylation, inhibition of gene transcription and blockade of erythroid differentiation. This was associated with alterations in NURF complex occupancy at erythroid gene promoters and reduced chromatin accessibility. Setd1a deficiency caused decreased associations between enhancer and promoter looped interactions as well as reduced expression of erythroid genes such as the adult β-globin gene. These data indicate that Setd1a and NURF complexes are specifically targeted to and coordinately regulate erythroid promoter chromatin dynamics during erythroid lineage differentiation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    A treatment procedure for VLT/SINFONI data cubes: application to NGC 5643 (2015)
    Oxford University Press
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    Publication Date: 2015-04-18
    Description: In this second paper of a series, we present a treatment procedure for data cubes obtained with the Spectrograph for Integral Field Observations in the Near Infrared of the Very Large Telescope. We verified that the treatment procedure improves significantly the quality of the images of the data cubes, allowing a more detailed analysis. The images of the Br  and H 2 21 218 emission lines from the treated data cube of the nuclear region of NGC 5643 reveal the existence of ionized and molecular-gas clouds around the nucleus, which cannot be seen clearly in the images from the non-treated data cube of this galaxy. The ionized-gas clouds represent the narrow-line region, in the form of a bicone. We observe a good correspondence between the positions of the ionized-gas clouds in the Br  image and in an [O iii ] image, obtained with the Hubble Space Telescope , of the nuclear region of this galaxy convolved with an estimate of the point spread function of the data cube of NGC 5643. The morphologies of the ionized and molecular gas seem to be compatible with the existence of a molecular torus/disc that collimates the active galactic nucleus (AGN) emission. The molecular gas may also flow along this torus/disc, feeding the AGN. This scenario is compatible with the unified model for AGNs.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Digging process in NGC 6951: the molecular disc bumped by the jet (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-29
    Description: We present a study of the central 200 pc of the galaxy NGC 6951, SAB(rs)bc, an active twin of the Milky Way, at a distance of 24 Mpc. Its nucleus has been observed in the optical with the Integral Field Unit of the Gemini Multi-Object Spectrograph, showing an outflow, and with the HST /ACS, revealing two extended structures with similar orientation, suggesting the presence of a collimating and/or obscuring structure. In order to ascertain this hypothesis, adaptive optics assisted NIR integral field spectroscopic observations were obtained with the Near-Infrared Integral Field Spectrograph in the Gemini North telescope. We detected a compact structure of H 2 molecular gas, interpreted as a nearly edge-on disc with diameter of ~47 pc, PA = 124° and velocity range from –40 to +40 km s –1 . This disc is misaligned by 32° with respect to the radio jet and the ionization cones seen in the optical. There are two regions of turbulent gas, with position angles similar to the jet/cones, seen both in molecular and ionized phases; these regions are connected to the edges of the molecular disc and coincide with a high ratio of [N ii ]/H α = 5, suggesting that these regions are shock excited, partially ionized or both. We explain these structures as a consequence of a ‘digging process’ that the jet inflicts on the disc, ejecting the molecular gas towards the ionization cones. The dynamical mass within 17 pc is estimated as 6.3  x  10 6 M . This is an interesting case of an object presenting evidence of a connected feeding-feedback structure.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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