ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Ihre E-Mail wurde erfolgreich gesendet. Bitte prüfen Sie Ihren Maileingang.

Leider ist ein Fehler beim E-Mail-Versand aufgetreten. Bitte versuchen Sie es erneut.

Vorgang fortführen?

Exportieren
Filter
  • Oxford University Press  (56)
  • Nature Publishing Group (NPG)
  • 2010-2014  (68)
Sammlung
Schlagwörter
Verlag/Herausgeber
Erscheinungszeitraum
Jahr
  • 1
    facet.materialart.
    Unbekannt
    MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data (2013)
    Oxford University Press
    Details
    Publikationsdatum: 2013-02-13
    Beschreibung: Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms. Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis. Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html . Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 2
    facet.materialart.
    Unbekannt
    Sequence requirements for RNA binding by HuR and AUF1 (2012)
    Oxford University Press
    Details
    Publikationsdatum: 2012-04-25
    Beschreibung: The stability of RNAs bearing AU-rich elements in their 3'-UTRs, and thus the level of expression of their protein products, is regulated by interactions with cytoplasmic RNA-binding proteins. Binding by HuR generally leads to mRNA stabilization and increased protein production, whereas binding by AUF1 isoforms generally lead to rapid degradation of the mRNA and reduced protein production. The exact nature of the interplay between these and other RNA-binding proteins remains unclear, although recent studies have shown close interactions between them and even suggested competition between the two for binding to their cognate recognition sequences. Other recent reports have suggested that the sequences recognized by the two proteins are different. We therefore performed a detailed in vitro analysis of the binding site(s) for HuR and AUF1 present in androgen receptor mRNA to define their exact target sequences, and show that the same sequence is contacted by both proteins. Furthermore, we analysed a proposed HuR target within the 3'-UTR of MTA1 mRNA, and show that the contacted bases lie outside of the postulated motif and are a better match to a classical ARE than the postulated motif. The defining features of these HuR binding sites are their U-richness and single strandedness.
    Print ISSN: 0021-924X
    Digitale ISSN: 1756-2651
    Thema: Biologie , Chemie und Pharmazie
    Publiziert von Oxford University Press im Namen von The Japanese Biochemical Society (JBS).
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 3
    facet.materialart.
    Unbekannt
    Nitrogen uptake over entire root systems of tree seedlings (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-05-06
    Beschreibung: Uptake of nitrogen (N) by sequential root regions in six tree species was measured in roots of 16- to 26-month-old seedlings at 50 and 1500 µM NH 4 NO 3 concentration, at the cell level using oscillating microelectrodes and at the root region level using enriched 15 N application. Our objective was to determine the root regions making the greatest contribution to total N uptake in each species as measured by the two contrasting techniques. White and condensed tannin zones were the regions with the smallest surface area in all species, but these zones often had the highest net flux of NH 4 + and NO 3 – . For most species, little variation was found among root regions in N flux calculated using a 15 N mass balance approach, but where significant differences existed, high N flux was observed in white, cork or woody zones. When N fluxes measured by each of the two methods were multiplied by the estimated surface area or biomass of each root region, the effect of root region size had the greatest influence on regional N uptake. Root regions of greatest overall N uptake were the cork and woody zones, on average. Total N uptake may thus be greatest in older regions of tree seedling roots, despite low rates of uptake per unit area.
    Print ISSN: 0829-318X
    Digitale ISSN: 1758-4469
    Thema: Land- und Forstwirtschaft, Gartenbau, Fischereiwirtschaft, Hauswirtschaft
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 4
    facet.materialart.
    Unbekannt
    Modelling the ages and metallicities of early-type galaxies in Fundamental Plane space (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-10-26
    Beschreibung: Recent observations have probed the formation histories of nearby elliptical galaxies by tracking correlations between the stellar population parameters, age and metallicity, and the structural parameters that enter the Fundamental Plane, size R e , and velocity dispersion . These studies have found intriguing correlations between these four parameters. In this work, we make use of a semi-analytic model, based on halo merger trees extracted from the Bolshoi cosmological simulation, that predicts the structural properties of spheroid-dominated galaxies based on an analytic model that has been tested and calibrated against an extensive suite of hydrodynamic+ N -body binary merger simulations. We predict the R e , , luminosity, age, and metallicity of spheroid-dominated galaxies, enabling us to compare directly to observations. Our model predicts a strong correlation between age and for early-type galaxies, and no significant correlation between age and radius, in agreement with observations. In addition, we predict a strong correlation between metallicity and , and a weak correlation between metallicity and R e , in qualitative agreement with observations. We find that the correlations with arise as a result of the strong link between and the galaxy's assembly time. Minor mergers produce a large change in radius while leaving nearly the same, which explains the weaker trends with radius.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 5
    facet.materialart.
    Unbekannt
    Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-09-20
    Beschreibung: Keratoconus, a common inherited ocular disorder resulting in progressive corneal thinning, is the leading indication for corneal transplantation in the developed world. Genome-wide association studies have identified common SNPs 100 kb upstream of ZNF469 strongly associated with corneal thickness. Homozygous mutations in ZNF469 and PR domain-containing protein 5 ( PRDM5 ) genes result in brittle cornea syndrome (BCS) Types 1 and 2, respectively. BCS is an autosomal recessive generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Some individuals with heterozygous PRDM5 mutations demonstrate a carrier ocular phenotype, which includes a mildly reduced corneal thickness, keratoconus and blue sclera. We hypothesized that heterozygous variants in PRDM5 and ZNF469 predispose to the development of isolated keratoconus. We found a significant enrichment of potentially pathologic heterozygous alleles in ZNF469 associated with the development of keratoconus ( P = 0.00102) resulting in a relative risk of 12.0. This enrichment of rare potentially pathogenic alleles in ZNF469 in 12.5% of keratoconus patients represents a significant mutational load and highlights ZNF469 as the most significant genetic factor responsible for keratoconus identified to date.
    Print ISSN: 0964-6906
    Digitale ISSN: 1460-2083
    Thema: Biologie , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 6
    facet.materialart.
    Unbekannt
    Understanding the structural scaling relations of early-type galaxies (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-08-29
    Beschreibung: We use a large suite of hydrodynamical simulations of binary galaxy mergers to construct and calibrate a physical prescription for computing the effective radii and velocity dispersions of spheroids. We implement this prescription within a semi-analytic model embedded in merger trees extracted from the Bolshoi cold dark matter N -body simulation, accounting for spheroid growth via major and minor mergers and disc instabilities. We find that without disc instabilities, our model does not predict sufficient numbers of intermediate-mass early-type galaxies in the local Universe. Spheroids also form earlier in models with spheroid growth via disc instabilities. Our model correctly predicts the normalization, slope, and scatter of the low-redshift size–mass and Fundamental Plane relations for early-type galaxies. It predicts a degree of curvature in the Faber–Jackson relation that is not seen in local observations, but this could be alleviated if higher mass spheroids have more bottom-heavy initial mass functions. The model also correctly predicts the observed strong evolution of the size–mass relation for spheroids out to higher redshifts, as well as the slower evolution in the normalization of the Faber–Jackson relation. We emphasize that these are genuine predictions of the model since it was tuned to match hydrodynamical simulations and not these observations.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 7
    facet.materialart.
    Unbekannt
    Cholesterol homeostatic responses provide biomarkers for monitoring treatment for the neurodegenerative disease Niemann-Pick C1 (NPC1) (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-10-22
    Beschreibung: Niemann–Pick C1 (NPC1) disease is a rare, neurodegenerative lysosomal cholesterol storage disorder, typified by progressive cognitive and motor function impairment. Affected individuals usually succumb to the disease in adolescence. 2-Hydroxypropyl-β-cyclodextrin (HP-β-CD) has emerged as a promising intervention that reduces lipid storage and prolongs survival in NPC1 disease animal models. A barrier to the development of HP-β-CD and other treatments for NPC disease has been the lack of validated biochemical measures to evaluate efficacy. Here we explored whether cholesterol homeostatic responses resulting from HP-β-CD-mediated redistribution of sequestered lysosomal cholesterol could provide biomarkers to monitor treatment. Upon direct CNS delivery of HP-β-CD, we found increases in plasma 24( S )-HC in two independent NPC1 disease animal models, findings that were confirmed in human NPC1 subjects receiving HP-β-CD. Since circulating 24( S )-HC is almost exclusively CNS-derived, the increase in plasma 24( S )-HC provides a peripheral, non-invasive measure of the CNS effect of HP-β-CD. Our findings suggest that plasma 24( S )-HC, along with the other cholesterol-derived markers examined in this study, can serve as biomarkers that will accelerate development of therapeutics for NPC1 disease.
    Print ISSN: 0964-6906
    Digitale ISSN: 1460-2083
    Thema: Biologie , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 8
    facet.materialart.
    Unbekannt
    Microarray expression analysis and identification of serum biomarkers for Niemann-Pick disease, type C1 (2012)
    Oxford University Press
    Details
    Publikationsdatum: 2012-07-28
    Beschreibung: Niemann–Pick disease type C (NPC) is a lysosomal storage disorder characterized by liver disease and progressive neurodegeneration. Deficiency of either NPC1 or NPC2 leads to the accumulation of cholesterol and glycosphingolipids in late endosomes and early lysosomes. In order to identify pathological mechanisms underlying NPC and uncover potential biomarkers, we characterized liver gene expression changes in an Npc1 mouse model at six ages spanning the pathological progression of the disease. We identified altered gene expression at all ages, including changes in asymptomatic, 1-week-old mice. Biological pathways showing early altered gene expression included: lipid metabolism, cytochrome P450 enzymes involved in arachidonic acid and drug metabolism, inflammation and immune responses, mitogen-activated protein kinase and G-protein signaling, cell cycle regulation, cell adhesion and cytoskeleton remodeling. In contrast, apoptosis and oxidative stress appeared to be late pathological processes. To identify potential biomarkers that could facilitate monitoring of disease progression, we focused on a subset of 103 differentially expressed genes that encode secreted proteins. Further analysis identified two secreted proteins with increased serum levels in NPC1 patients: galectin-3 (LGALS3), a pro-inflammatory molecule, and cathepsin D (CTSD), a lysosomal aspartic protease. Elevated serum levels of both proteins correlated with neurological disease severity and appeared to be specific for NPC1. Expression of Lgals3 and Ctsd was normalized following treatment with 2-hydroxypropyl-β-cyclodextrin, a therapy that reduces pathological findings and significantly increases Npc1 –/– survival. Both LGALS3 and CTSD have the potential to aid in diagnosis and serve as biomarkers to monitor efficacy in therapeutic trials.
    Print ISSN: 0964-6906
    Digitale ISSN: 1460-2083
    Thema: Biologie , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 9
    facet.materialart.
    Unbekannt
    Radiative cooling II: effects of density and metallicity (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-04-19
    Beschreibung: This work follows Lykins et al. discussion of classic plasma cooling function at low density and solar metallicity. Here, we focus on how the cooling function changes over a wide range of density ( n H 〈10 12 cm –3 ) and metallicity ( Z  〈 30 Z ). We find that high densities enhance the ionization of elements such as hydrogen and helium until they reach local thermodynamic equilibrium. By charge transfer, the metallicity changes the ionization of hydrogen when it is partially ionized. We describe the total cooling function as a sum of four parts: those due to H&He, the heavy elements, electron–electron bremsstrahlung and grains. For the first three parts, we provide a low-density limit cooling function, a density dependence function, and a metallicity-dependent function. These functions are given with numerical tables and analytical fit functions. We discuss grain cooling only in the interstellar medium case. We then obtain a total cooling function that depends on density, metallicity and temperature. As expected, collisional de-excitation suppresses the heavy elements cooling. Finally, we provide a function giving the electron fraction, which can be used to convert the cooling function into a cooling rate.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
  • 10
    facet.materialart.
    Unbekannt
    The {alpha} isoform of topoisomerase II is required for hypercompaction of mitotic chromosomes in human cells (2014)
    Oxford University Press
    Details
    Publikationsdatum: 2014-04-15
    Beschreibung: As proliferating cells transit from interphase into M-phase, chromatin undergoes extensive reorganization, and topoisomerase (topo) IIα, the major isoform of this enzyme present in cycling vertebrate cells, plays a key role in this process. In this study, a human cell line conditional null mutant for topo IIα and a derivative expressing an auxin-inducible degron (AID)-tagged version of the protein have been used to distinguish real mitotic chromosome functions of topo IIα from its more general role in DNA metabolism and to investigate whether topo IIβ makes any contribution to mitotic chromosome formation. We show that topo IIβ does contribute, with endogenous levels being sufficient for the initial stages of axial shortening. However, a significant effect of topo IIα depletion, seen with or without the co-depletion of topo IIβ, is the failure of chromosomes to hypercompact when delayed in M-phase. This requires much higher levels of topo II protein and is impaired by drugs or mutations that affect enzyme activity. A prolonged delay at the G2/M border results in hyperefficient axial shortening, a process that is topo IIα-dependent. Rapid depletion of topo IIα has allowed us to show that its function during late G2 and M-phase is truly required for shaping mitotic chromosomes.
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
    AKTUELLE ARTIKEL
Schließen ⊗
Diese Webseite nutzt Cookies und das Analyse-Tool Matomo. Weitere Informationen finden Sie hier...