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  • 1
    Publication Date: 2015-09-16
    Description: We present the third data release from the Australia Telescope Large Area Survey. These data combine the observations at 1.4 GHz before and after upgrades to the Australia Telescope Compact Array reaching a sensitivity of 14 μJy beam –1 in 3.6 deg 2 over the Chandra Deep Field South (CDFS) and of 17 μJy beam –1 in 2.7 deg 2 over the European Large Area ISO Survey South 1 (ELAIS-S1). We used a variety of array configurations to maximize the uv coverage resulting in a resolution of 16 by 7 arcsec in CDFS and of 12 by 8 arcsec in ELAIS-S1. After correcting for peak bias and bandwidth smearing, we find a total of 3034 radio source components above 5 in CDFS, of which 514 (17 per cent) are considered to be extended. The number of components detected above 5 in ELAIS-S1 is 2084, of which 392 (19 per cent) are classified as extended. The catalogues include reliable spectral indices (α 〈 0.2) between 1.40 and 1.71 GHz for ~350 of the brightest components.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2015-09-27
    Description: We present the third data release from the Australia Telescope Large Area Survey. These data combine the observations at 1.4 GHz before and after upgrades to the Australia Telescope Compact Array reaching a sensitivity of 14 μJy beam –1 in 3.6 deg 2 over the Chandra Deep Field South (CDFS) and of 17 μJy beam –1 in 2.7 deg 2 over the European Large Area ISO Survey South 1 (ELAIS-S1). We used a variety of array configurations to maximize the uv coverage resulting in a resolution of 16 by 7 arcsec in CDFS and of 12 by 8 arcsec in ELAIS-S1. After correcting for peak bias and bandwidth smearing, we find a total of 3034 radio source components above 5 in CDFS, of which 514 (17 per cent) are considered to be extended. The number of components detected above 5 in ELAIS-S1 is 2084, of which 392 (19 per cent) are classified as extended. The catalogues include reliable spectral indices (α 〈 0.2) between 1.40 and 1.71 GHz for ~350 of the brightest components.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2016-04-06
    Description: The mono-epi (ME) exact structure on the morphisms of an exact category $(\mathcal {A}; \mathcal {E})$ is introduced and used to prove ideal versions of Salce's Lemma, Christensen's (Ghost) Lemma, and Wakamatsu's Lemma for an exact category. Salce's Lemma establishes a bijective correspondence $\mathcal {I} \mapsto \mathcal {I}^{\perp }$ between the class of special precovering ideals of $(\mathcal {A}; \mathcal {E})$ and that of its special preenveloping ideals. ME-extensions of morphisms are used to define an extension $\mathcal {I} \diamond \mathcal {J}$ of ideals. Christensen's Lemma asserts that the class of special precovering (respectively, special preenveloping) ideals is closed under products and extensions and that the bijective correspondence of Salce's Lemma satisfies $(\mathcal {I} \mathcal {J})^{\perp } = \mathcal {J}^{\perp } \diamond \mathcal {I}^{\perp }$ and $(\mathcal {I} \diamond \mathcal {J})^{\perp } = \mathcal {J}^{\perp } \mathcal {I}^{\perp }.$ Wakamatsu's Lemma asserts that if a covering ideal $\mathcal {I}$ is closed under ME-extensions, then it is a special precovering ideal. As an application, it is proved that if $G$ is a finite group and $\Phi $ is the ideal of phantom morphisms in the category $k[G]$ - $\rm Mod,$ then $\Phi ^{n-1}$ is the object ideal generated by projective modules, where $n$ is the nilpotency index of the Jacobson radical $J.$ If $R$ is a semiprimary ring, with $J^n =0,$ then $\Phi ^n$ is generated by projective modules. For a right coherent ring $R$ over which every cotorsion left $R$ -module has a coresolution of length $n$ by pure injective modules, $\Phi ^{n+1}$ is generated by flat modules.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
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  • 4
    Publication Date: 2016-08-20
    Description: Inducible defenses are a common phenotypically plastic response to a heterogeneous predation risk. Once induced, these defenses cannot only lose their benefit, but even become costly, should the predator disappear. Consequently, some organisms have developed the ability to reverse their defensive traits. However, despite extensive research on inducible defenses, reports on reversibility are rare and mostly concentrate on defensive behavior. In our study, we investigated the reversibility of morphological defenses in the freshwater crustacean Daphnia barbata . This species responds to Notonecta glauca and Triops cancriformis with two distinctively defended morphotypes. Within the numerous defensive traits, we found both trait- and predator-specific reversibility. Body torsion and tail-spine-related traits were highly reversible, whereas helmet-related traits remained stable, suggesting different physiological constraints. However, in general, we found the defenses against Triops mostly reversible, while Notonecta -induced defenses were persistent and grew further, even in the absence of a predator.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
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  • 5
    Publication Date: 2015-07-02
    Description: The identification of crosslinks by mass spectrometry has recently been established as an integral part of the hybrid structural analysis of protein complexes and networks. The crosslinking analysis determines distance restraints between two covalently linked amino acids which are typically summarized in a table format that precludes the immediate and comprehensive interpretation of the topological data. xVis displays crosslinks in clear schematic representations in form of a circular, bar or network diagram. The interactive graphs indicate the linkage sites and identification scores, depict the spatial proximity of structurally and functionally annotated protein regions and the evolutionary conservation of amino acids and facilitate clustering of proteins into subcomplexes according to the crosslink density. Furthermore, xVis offers two options for the qualitative assessment of the crosslink identifications by filtering crosslinks according to identification scores or false discovery rates and by displaying the corresponding fragment ion spectrum of each crosslink for the manual validation of the mass spectrometric data. Our web server provides an easy-to-use tool for the fast topological and functional interpretation of distance information on protein complex architectures and for the evaluation of crosslink fragment ion spectra. xVis is available under a Creative Commons Attribution-ShareAlike 4.0 International license at http://xvis.genzentrum.lmu.de/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2012-08-23
    Description: Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity by still poorly understood mechanisms. Here, we examined the role of histone demethylase Kdm3a during cell differentiation, showing that Kdm3a is essential for differentiation into parietal endoderm-like (PE) cells in the F9 mouse embryonal carcinoma model. We identified a number of target genes regulated by Kdm3a during endoderm differentiation; among the most dysregulated were the three developmental master regulators Dab2, Pdlim4 and FoxQ1 . We show that dysregulation of the expression of these genes correlates with Kdm3a H3K9me2 demethylase activity. We further demonstrate that either Dab2 depletion or Kdm3a depletion prevents F9 cells from fully differentiating into PE cells, but that ectopic expression of Dab2 cannot compensate for Kdm3a knockdown; Dab2 is thus necessary, but insufficient on its own, to promote complete terminal differentiation. We conclude that Kdm3a plays a crucial role in progression through PE differentiation by regulating expression of a set of endoderm differentiation master genes. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the view that histone demethylases are essential to cell differentiation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2015-09-30
    Description: Any profound comprehension of gene function requires detailed information about the subcellular localization, molecular interactions and spatio-temporal dynamics of gene products. We developed a multifunctional integrase (MIN) tag for rapid and versatile genome engineering that serves not only as a genetic entry site for the Bxb1 integrase but also as a novel epitope tag for standardized detection and precipitation. For the systematic study of epigenetic factors, including Dnmt1 , Dnmt3a , Dnmt3b , Tet1 , Tet2 , Tet3 and Uhrf1 , we generated MIN-tagged embryonic stem cell lines and created a toolbox of prefabricated modules that can be integrated via Bxb1-mediated recombination. We used these functional modules to study protein interactions and their spatio-temporal dynamics as well as gene expression and specific mutations during cellular differentiation and in response to external stimuli. Our genome engineering strategy provides a versatile open platform for efficient generation of multiple isogenic cell lines to study gene function under physiological conditions.
    Keywords: Synthetic Biology and Assembly Cloning, Targeted gene modification
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2014-03-13
    Description: TDP-43 is a nuclear protein involved in many aspects of RNA metabolism. To ensure cellular viability, its expression levels within cells must be tightly regulated. We have previously demonstrated that TDP-43 autoregulation occurs through the activation of a normally silent intron in its 3'-UTR sequence that results in the use of alternative polyadenylation sites. In this work, we analyse which is the dominant event in autoregulation: the recognition of the splice sites of 3'-UTR intron 7 or the intrinsic quality of the alternative polyadenylation sites. A panel of minigene constructs was tested for autoregulation functionality, protein production and subcellular messenger RNA localization. Our data clearly indicate that constitutive spliceosome complex formation across intron 7 does not lead to high protein production but, on the contrary, to lower TDP-43 messenger RNA and protein levels. This is due to altered nucleocytoplasmic distribution of the RNA that is mostly retained in the nucleus and degraded. This study provides a novel in-depth characterization of how RNA binding proteins can autoregulate their own levels within cells, an essential regulatory process in maintaining cellular viability.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2014-10-29
    Description: Vascular endothelial cells, in addition to many other mammalian cell types, express proteins that are highly modified with mucin-type O-glycosylation, a specific type of glycosylation that begins with the addition of an N -acetylgalactosamine moiety to serine or threonine residues within the peptide backbone. Recently, it has become evident that O-glycosylation governs the separation of blood and lymphatic vessels throughout life and plays a critical role in maintaining vascular integrity in specific tissues such as the brain and lymph node. This mini-review seeks to highlight some of these recent advances regarding in vivo functions of mucin-type O -glycans.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 10
    Publication Date: 2014-11-26
    Description: : MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public- or user-uploaded reference databases. Availability and implementation: The Web service is freely available at http://bioinformatics.mpi-bn.mpg.de . MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our Web site. Contact: Mario.Looso@mpi-bn.mpg.de 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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