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  • 1
    Publication Date: 2015-09-30
    Description: Alternative splicing is an important and ancient feature of eukaryotic gene structure, the existence of which has likely facilitated eukaryotic proteome expansions. Here, we have used intron lariat sequencing to generate a comprehensive profile of splicing events in Schizosaccharomyces pombe , amongst the simplest organisms that possess mammalian-like splice site degeneracy. We reveal an unprecedented level of alternative splicing, including alternative splice site selection for over half of all annotated introns, hundreds of novel exon-skipping events, and thousands of novel introns. Moreover, the frequency of these events is far higher than previous estimates, with alternative splice sites on average activated at ~3% the rate of canonical sites. Although a subset of alternative sites are conserved in related species, implying functional potential, the majority are not detectably conserved. Interestingly, the rate of aberrant splicing is inversely related to expression level, with lowly expressed genes more prone to erroneous splicing. Although we validate many events with RNAseq, the proportion of alternative splicing discovered with lariat sequencing is far greater, a difference we attribute to preferential decay of aberrantly spliced transcripts. Together, these data suggest the spliceosome possesses far lower fidelity than previously appreciated, highlighting the potential contributions of alternative splicing in generating novel gene structures.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2014-09-20
    Description: We demonstrate the feasibility and potential of using large integral field spectroscopic surveys to investigate the prevalence of galactic-scale outflows in the local Universe. Using integral field data from the Sydney-AAO Multi-object Integral field spectrograph (SAMI) and the Wide Field Spectrograph, we study the nature of an isolated disc galaxy, SDSS J090005.05+000446.7 ( z  = 0.053 86). In the integral field data sets, the galaxy presents skewed line profiles changing with position in the galaxy. The skewed line profiles are caused by different kinematic components overlapping in the line-of-sight direction. We perform spectral decomposition to separate the line profiles in each spatial pixel as combinations of (1) a narrow kinematic component consistent with H ii regions, (2) a broad kinematic component consistent with shock excitation, and (3) an intermediate component consistent with shock excitation and photoionization mixing. The three kinematic components have distinctly different velocity fields, velocity dispersions, line ratios, and electron densities. We model the line ratios, velocity dispersions, and electron densities with our mappings iv shock and photoionization models, and we reach remarkable agreement between the data and the models. The models demonstrate that the different emission line properties are caused by major galactic outflows that introduce shock excitation in addition to photoionization by star-forming activities. Interstellar shocks embedded in the outflows shock-excite and compress the gas, causing the elevated line ratios, velocity dispersions, and electron densities observed in the broad kinematic component. We argue from energy considerations that, with the lack of a powerful active galactic nucleus, the outflows are likely to be driven by starburst activities. Our results set a benchmark of the type of analysis that can be achieved by the SAMI Galaxy Survey on large numbers of galaxies.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2012-09-22
    Description: Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sugihara, George -- May, Robert -- Ye, Hao -- Hsieh, Chih-hao -- Deyle, Ethan -- Fogarty, Michael -- Munch, Stephan -- New York, N.Y. -- Science. 2012 Oct 26;338(6106):496-500. doi: 10.1126/science.1227079. Epub 2012 Sep 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. gsugihara@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22997134" target="_blank"〉PubMed〈/a〉
    Keywords: *Causality ; Ciliophora ; *Ecosystem ; *Models, Statistical ; Nonlinear Dynamics ; Paramecium
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2020-11-01
    Description: LUX-ZEPLIN (LZ) is a second-generation direct dark matter experiment with spin-independent WIMP-nucleon scattering sensitivity above $${1.4 imes 10^{-48}}, {hbox {cm}}^{2}$$ 1.4 × 10 - 48 cm 2 for a WIMP mass of $${40}, hbox {GeV}/{hbox {c}}^{2}$$ 40 GeV / c 2 and a $${1000}, hbox {days}$$ 1000 days exposure. LZ achieves this sensitivity through a combination of a large $${5.6}, hbox {t}$$ 5.6 t fiducial volume, active inner and outer veto systems, and radio-pure construction using materials with inherently low radioactivity content. The LZ collaboration performed an extensive radioassay campaign over a period of six years to inform material selection for construction and provide an input to the experimental background model against which any possible signal excess may be evaluated. The campaign and its results are described in this paper. We present assays of dust and radon daughters depositing on the surface of components as well as cleanliness controls necessary to maintain background expectations through detector construction and assembly. Finally, examples from the campaign to highlight fixed contaminant radioassays for the LZ photomultiplier tubes, quality control and quality assurance procedures through fabrication, radon emanation measurements of major sub-systems, and bespoke detector systems to assay scintillator are presented.
    Print ISSN: 1434-6044
    Electronic ISSN: 1434-6052
    Topics: Physics
    Published by Springer
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  • 5
    ISSN: 1432-1793
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Fish scales from seven species of demersal fish in an archival collection were analyzed for stable isotopic compositions of carbon and nitrogen to study long-term changes in trophic structure of the Georges Bank food web. Nitrogen isotopic compositions are often used to infer trophic level. In the case of haddock, Melanogrammus aeglefinus (Linnaeus), there was a trend towards feeding at 2/3 of one trophic level (2.45% in δ15N) lower in 1987 than in 1929. Values of °13C, frequently employed to identify sources of organic carbon to consumers, declined by 1.5‰ from 1929 to 1960, and then increased again toward the present, suggesting changes in the food web at the level of the primary producers. Superimposed on long-term isotopic trends were short-term variations (1 to 10 yr).To identify potential causes for these isotopic trends, canonical correlation analysis was performed between isotopic data and a suite of environmental and population factors including sea surface temperature, the Greenland Regional Pressure Anomaly (GRPA), the North Atlantic Oscillation (NAO), and the following haddock stock parameters; stock size, fishing mortality, recruitment, and weight-at-age-2 (a measure of growth rate). Isotopic variation was significantly correlated with a combination of environmental and population variables: GRPA, NAO, weight-at-age-2, stock size, and fishing mortality. On the basis of published gut content analyses, the seven fish species were predicted to vary in trophic level (TL) from American plaice, Hippoglossoides platessoides (Fabricius), (TL 2.9) to summer flounder, Paralichthys dentatus (Linnaeus), (TL 4.5), whereas measured °15N values suggested smaller differences in the trophic levels of these species (less than one TL). Four species showed good agreement between gut-predicted and measured δ15N values, while three species did not. Inclusion of information on ontogenetic dietary shifts in our predictions improved the agreement in some cases but not in other. Differences between stable isotope analysis and gut content analysis in terms of what they measure, i.e., integrated assimilated diet vs short-term ingested diet, respectively, may account for some of the differences in results. Based on our analyses and previous studies, feeding habits of these fish may undergo considerable year-to-year and geographic variation, some of which may have been missed in gut content analyses. To the extent that these fish are representative members of the food web, trophic variation in these fish may indicate more general changes in the food web.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Human evolution 2 (1987), S. 311-319 
    ISSN: 1824-310X
    Keywords: climatic reconstruction ; North Africa ; origin of modern Europeans ; later human evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A critical evaluation of a replacementist hypothesis regarding the origin of modernH. sapiens in Europe as suggested byN. T. Boaz D. Ninkovitch & M. Rossignol-Strick (1982) is presented. These authors have contended that harsh desertic conditions in North Africa between 40 ky — 30 ky B. P. resulted in the movement of modern humans from this region around the Mediterranean littoral into Europe. Two additional tenets of this hypothesis are the claim that Neandertals were islated in Europe during the first half of the Würm and also the assertion that formation of a landbridge at the Dardanelles ca. 34 ky B. P. ended this isolation and facilitated an influx of modern humans into Europe at this time. This hypothesis is found to be unsupported by the balance of the available data. The specific points discussed include the following: a) climatic and archaeological indicators of a hospitable environment in North Africa between 40 ky — 30 ky B.P., b) the likelihood of landbridge formation at the Dardanelles throughout the last glacial cycle, c) the technological capabilities and uncertain taxonomic identity of the North African source group and d) the similarities between west Asian and European Neandertals which indicate that a prolonged separation of the two groups is unlikely.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 4 (1981), S. 561-568 
    ISSN: 0935-6304
    Keywords: HPLC ; Video fluorometry ; Fluorescence detector for HPLC ; Data reduction ; Polynuclear aromatic compounds ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A rapid scanning, two-dimensional fluorometer has been used to obtain Emission-Excitation Matrices (EEMs) of the effluent of an HPLC column. These spectra, obtained “on the fly”, provide qualitative as well as quantitative information about unknown samples. An in-depth discussion of the instrumentation developed and an account of data processing alternatives are presented.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 4 (1981), S. 616-626 
    ISSN: 0935-6304
    Keywords: HPLC ; Video fluorometry ; Emission-excitation matrix ; Spectral deconvolution ; Spectral interpretation ; Polynuclear aromatic hydrocarbons ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A video fluorometer is used as a detector for HPLC to characterize highly complex samples. Data selection and evaluation techniques are discussed so as to speed the spectral identification process. Several well-known polynuclear aromatic hydrocarbons are found in the samples.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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  • 9
  • 10
    Publication Date: 2013-03-27
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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