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  • 1
    Publication Date: 2015-01-25
    Description: We investigate the potential and accuracy of clustering-based redshift estimation using the method proposed by Ménard et al. This technique enables the inference of redshift distributions from measurements of the spatial clustering of arbitrary sources, using a set of reference objects for which redshifts are known. We apply it to a sample of spectroscopic galaxies from the Sloan Digital Sky Survey (SDSS) and show that, after carefully controlling the sampling efficiency over the sky, we can estimate redshift distributions with high accuracy. Probing the full colour space of the SDSS galaxies, we show that we can recover the corresponding mean redshifts with an accuracy ranging from z  = 0.001 to 0.01. We indicate that this mapping can be used to infer the redshift probability distribution of a single galaxy. We show how the lack of information on the galaxy bias limits the accuracy of the inference and show comparisons between clustering redshifts and photometric redshifts for this data set. This analysis demonstrates, using real data, that clustering-based redshift inference provides a powerful data-driven technique to explore the redshift distribution of arbitrary data sets, without any prior knowledge of the spectral energy distribution of the sources.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2015-04-02
    Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2016-06-08
    Description: The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 ± 6. Specific aDNA could be quantified by a newly developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17–19-year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
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  • 4
    Publication Date: 2016-06-17
    Description: We present the effective temperatures ( T eff ), metallicities, and colours in Sloan Digital Sky Survey (SDSS), Two Micron All Sky Survey, and Wide-field Infrared Survey Explorer filters, of a sample of 3834 late-K and early-M dwarfs selected from the SDSS Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectroscopic survey ASPCAP (APOGEE Stellar Parameters and Chemical Abundances Pipeline) catalogue. We confirm that ASPCAP T eff values between 3550 〈 T eff 〈 4200 K are accurate to ~100 K compared to interferometric T eff values. In that same T eff range, ASPCAP metallicities are accurate to 0.18 dex between –1.0 〈[M/H]〈0.2. For these cool dwarfs, nearly every colour is sensitive to both T eff and metallicity. Notably, we find that g – r is not a good indicator of metallicity for near-solar metallicity early-M dwarfs. We confirm that J – K S colour is strongly dependent on metallicity, and find that W 1 – W 2 colour is a promising metallicity indicator. Comparison of the late-K and early-M dwarf colours, metallicities, and T eff to those from three different model grids shows reasonable agreement in r – z and J – K S colours, but poor agreement in u – g , g – r , and W 1 – W 2. Comparison of the metallicities of the KM dwarf sample to those from previous colour–metallicity relations reveals a lack of consensus in photometric metallicity indicators for late-K and early-M dwarfs. We also present empirical relations for T eff as a function of r – z colour combined with either [M/H] or W 1 – W 2 colour, and for [M/H] as a function of r – z and W 1 – W 2 colour. These relations yield T eff to ~100 K and [M/H] to ~0.18 dex precision with colours alone, for T eff in the range of 3550–4200 K and [M/H] in the range of –0.5–0.2.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2016-06-05
    Description: Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus . We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 6
    Publication Date: 2016-08-20
    Description: High-throughput screening (HTS) is an indispensable tool for drug (target) discovery that currently lacks user-friendly software tools for the robust identification of putative hits from HTS experiments and for the interpretation of these findings in the context of systems biology. We developed HiTSeekR as a one-stop solution for chemical compound screens, siRNA knock-down and CRISPR/Cas9 knock-out screens, as well as microRNA inhibitor and -mimics screens. We chose three use cases that demonstrate the potential of HiTSeekR to fully exploit HTS screening data in quite heterogeneous contexts to generate novel hypotheses for follow-up experiments: (i) a genome-wide RNAi screen to uncover modulators of TNFα, (ii) a combined siRNA and miRNA mimics screen on vorinostat resistance and (iii) a small compound screen on KRAS synthetic lethality. HiTSeekR is publicly available at http://hitseekr.compbio.sdu.dk . It is the first approach to close the gap between raw data processing, network enrichment and wet lab target generation for various HTS screen types.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2014-11-28
    Description: Genome-wide assessment of protein–DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify ‘hyper ChIPable regions’ as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2014-12-03
    Description: Cross-correlating the Planck High Frequency Instrument maps against quasars from the Sloan Digital Sky Survey DR7, we estimate the intensity distribution of the cosmic infrared background (CIB) over the redshift range 0 〈  z  〈 5. We detect redshift-dependent spatial cross-correlations between the two data sets using the 857, 545, and 353 GHz channels and we obtain upper limits at 217 GHz consistent with expectations. At all frequencies with detectable signal we infer a redshift distribution peaking around z  ~ 1.2 and find the recovered spectrum to be consistent with emission arising from star-forming galaxies. By assuming simple modified blackbody and Kennicutt relations, we estimate dust and star formation rate density as a function of redshift, finding results consistent with earlier multiwavelength measurements over a large portion of cosmic history. However, we note that, lacking mid-infrared coverage, we are not able to make an accurate determination of the mean temperature for the dust responsible for the CIB. Our results demonstrate that clustering-based redshift inference is a valuable tool for measuring the entire evolution history of the cosmic star formation rate from a single and homogeneous data set.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2012-11-09
    Description: Apple proliferation (AP) represents a serious threat to several fruit-growing areas and is responsible for great economic losses. Several studies have highlighted the key role played by the cell wall in response to pathogen attack. The existence of a cell wall integrity signaling pathway which senses perturbations in the cell wall architecture upon abiotic/biotic stresses and activates specific defence responses has been widely demonstrated in plants. More recently a role played by cell wall-related genes has also been reported in plants infected by phytoplasmas. With the aim of shedding light on the cell wall response to AP disease in the economically relevant fruit-tree Malus x domestica Borkh., we investigated the expression of the cellulose ( CesA ) and callose synthase ( CalS ) genes in different organs (i.e., leaves, roots and branch phloem) of healthy and infected symptomatic outdoor-grown trees, sampled over the course of two time points (i.e., spring and autumn 2011), as well as in in vitro micropropagated control and infected plantlets. A strong up-regulation in the expression of cell wall biosynthetic genes was recorded in roots from infected trees. Secondary cell wall CesA s showed up-regulation in the phloem tissue from branches of infected plants, while either a down-regulation of some genes or no major changes were observed in the leaves. Micropropagated plantlets also showed an increase in cell wall-related genes and constitute a useful system for a general assessment of gene expression analysis upon phytoplasma infection. Finally, we also report the presence of several ‘knot’-like structures along the roots of infected apple trees and discuss the occurrence of this interesting phenotype in relation to the gene expression results and the modalities of phytoplasma diffusion.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 10
    Publication Date: 2013-12-07
    Description: Non-LTR retrotransposons are mobile genetic elements and play a major role in eukaryotic genome evolution and disease. Similar to retroviruses they encode a reverse transcriptase, but their genomic integration mechanism is fundamentally different, and they lack homologs of the retroviral nucleocapsid-forming protein Gag. Instead, their first open reading frames encode distinct multi-domain proteins (ORF1ps) presumed to package the retrotransposon-encoded RNA into ribonucleoprotein particles (RNPs). The mechanistic roles of ORF1ps are poorly understood, particularly of ORF1ps that appear to harbor an enzymatic function in the form of an SGNH-type lipolytic acetylesterase. We determined the crystal structures of the coiled coil and esterase domains of the ORF1p from the Danio rerio ZfL2-1 element. We demonstrate a dimerization of the coiled coil and a hydrolytic activity of the esterase. Furthermore, the esterase binds negatively charged phospholipids and liposomes, but not oligo-(A) RNA. Unexpectedly, the esterase can split into two dynamic half-domains, suited to engulf long fatty acid substrates extending from the active site. These properties indicate a role for lipids and membranes in non-LTR retrotransposition. We speculate that Gag-like membrane targeting properties of ORF1ps could play a role in RNP assembly and in membrane-dependent transport or localization processes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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