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  • 1
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    Modulation of glacier ablation by tephra coverage from Eyjafjallajökull and Grimsvötn volcanoes, Iceland: an automated field experiment (2017)
    Copernicus
    Details
    Publication Date: 2017-07-06
    Description: This Article reports results from a field experiment investigating the influence of volcanic tephra coverage on glacier ablation. These influences are known to be significantly different from those of moraine debris on glaciers due to the contrasting grain size distribution and thermal conductivity. Influences of tephra deposits on glacier ablation have hardly been studied so far. For the experiment, artificial plots of two different tephra types from Eyjafjallajökull and Grimsvötn volcanoes were installed on a snow-covered glacier surface of Vatnajökull ice cap, Iceland.Ablation was automatically monitored along with atmospheric variables and ablation on a non-tephra covered reference site over the summer season 2015. For each of the two volcanic tephra types, three plots (~ 1.5 mm, ~ 8.5 mm and ~ 80 mm) were monitored. After limiting the records to a period of reliable measurements, a 50-days dataset of hourly records was obtained, which can be downloaded from the Pangaea data repository (https://www.pangaea.de; https://doi.org/10.1594/PANGAEA.876656). The experiment shows a substantial increase of ablation under the ~ 1.5 mm and ~ 8.5 mm tephra plots when compared to uncovered conditions. Only under the thick tephra cover some insulating effects could be observed. This result is in contrast to other studies which depicted insulating effects for much thinner tephra coverson bare-ice glacier surfaces. Differences between the influences of the two different petrological types of tephra exist but are small.
    Electronic ISSN: 1866-3591
    Topics: Geosciences
    Published by Copernicus
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  • 2
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    Modulation of glacier ablation by tephra coverage from Eyjafjallajökull and Grímsvötn volcanoes, Iceland: an automated field experiment (2018)
    Copernicus
    Details
    Publication Date: 2018-01-10
    Description: We report results from a field experiment investigating the influence of volcanic tephra coverage on glacier ablation. These influences are known to be significantly different from those of moraine debris on glaciers due to the contrasting grain size distribution and thermal conductivity. Thus far, the influences of tephra deposits on glacier ablation have rarely been studied. For the experiment, artificial plots of two different tephra types from Eyjafjallajökull and Grímsvötn volcanoes were installed on a snow-covered glacier surface of Vatnajökull ice cap, Iceland. Snow-surface lowering and atmospheric conditions were monitored in summer 2015 and compared to a tephra-free reference site. For each of the two volcanic tephra types, three plots of variable thickness (∼ 1.5, ∼ 8.5 and ∼ 80 mm) were monitored. After limiting the records to a period of reliable measurements, a 50-day data set of hourly records was obtained, which can be downloaded from the Pangaea data repository (https://www.pangaea.de; doi:10.1594/PANGAEA.876656). The experiment shows a substantial increase in snow-surface lowering rates under the ∼ 1.5 and ∼ 8.5 mm tephra plots when compared to uncovered conditions. Under the thick tephra cover some insulating effects could be observed. These results are in contrast to other studies which depicted insulating effects for much thinner tephra coverage on bare-ice glacier surfaces. Differences between the influences of the two different petrological types of tephra exist but are negligible compared to the effect of tephra coverage overall.
    Print ISSN: 1866-3508
    Electronic ISSN: 1866-3516
    Topics: Geosciences
    Published by Copernicus
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  • 3
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    Snow cover variability across glaciers in Nordenskiöldland (Svalbard) from point measurements in 2014–2016 (2019)
    Copernicus
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    Publication Date: 2019-01-02
    Description: Snow depths and bulk densities of the annual snow layer were measured at 69 different locations on glaciers across Nordenskiöldland, Svalbard, during the spring seasons of the period 2014–2016. Sampling locations lie along nine transects extending over 17 individual glaciers. Several of the locations were visited repeatedly, leading to a total of 109 point measurements, on which we report in this study. Snow water equivalents were calculated for each point measurement. In the dataset, snow depth and density measurements are accompanied by appropriate uncertainties which are rigorously transferred to the calculated snow water equivalents using a straightforward Monte Carlo simulation-style procedure. The final dataset can be downloaded from the Pangaea data repository (https://www.pangaea.de; https://doi.org/10.1594/PANGAEA.896581). Snow cover data indicate a general and statistically significant increase of snow depths and water equivalents with terrain elevation. A significant increase of both quantities with decreasing distance towards the east coast of Nordenskiöldland is also evident, but shows distinct interannual variability. Snow density does not show any characteristic spatial pattern.
    Electronic ISSN: 1866-3591
    Topics: Geosciences
    Published by Copernicus
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  • 4
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    Chicken or egg? The PVAR econometrics of transportation (2015)
    Oxford University Press
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    Publication Date: 2015-10-14
    Description: To analyse the mutually dependent relationship between local economic performance, demand for and supply of transport services, we employ the structural panel VAR method that is popular in the macroeconomic literature, but has not previously been applied to the modelling of the within-city dynamics of transportation. We focus on a within-city panel of Berlin, Germany during the heyday of the construction of its dense public transit network (1890–1914). Our results suggest that economic outcomes and a supply of transport infrastructure mutually determine each other. We find a short-run (long-run) elasticity of property prices with respect to transport supply of 2% (8.5%). Both transport demand and supply seem to be driven more by firms than by residents.
    Keywords: N73 - Europe: Pre-1913, N74 - Europe: 1913-, R12 - Size and Spatial Distributions of Regional Economic Activity, R14 - Land Use Patterns, R41 - Transportation: Demand, Supply, and Congestion ; Safety and Accidents ; Transportation Noise
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
    Published by Oxford University Press
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  • 5
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    Translational read-through of the RP2 Arg120stop mutation in patient iPSC-derived retinal pigment epithelium cells (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-25
    Description: Mutations in the RP2 gene lead to a severe form of X-linked retinitis pigmentosa. RP2 patients frequently present with nonsense mutations and no treatments are currently available to restore RP2 function. In this study, we reprogrammed fibroblasts from an RP2 patient carrying the nonsense mutation c.519C〉T (p.R120X) into induced pluripotent stem cells (iPSC), and differentiated these cells into retinal pigment epithelial cells (RPE) to study the mechanisms of disease and test potential therapies. RP2 protein was undetectable in the RP2 R120X patient cells, suggesting a disease mechanism caused by complete lack of RP2 protein. The RP2 patient fibroblasts and iPSC-derived RPE cells showed phenotypic defects in IFT20 localization, Golgi cohesion and Gβ1 trafficking. These phenotypes were corrected by over-expressing GFP-tagged RP2. Using the translational read-through inducing drugs (TRIDs) G418 and PTC124 (Ataluren), we were able to restore up to 20% of endogenous, full-length RP2 protein in R120X cells. This level of restored RP2 was sufficient to reverse the cellular phenotypic defects observed in both the R120X patient fibroblasts and iPSC-RPE cells. This is the first proof-of-concept study to demonstrate successful read-through and restoration of RP2 function for the R120X nonsense mutation. The ability of the restored RP2 protein level to reverse the observed cellular phenotypes in cells lacking RP2 indicates that translational read-through could be clinically beneficial for patients.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Identification of a conserved 5'-dRP lyase activity in bacterial DNA repair ligase D and its potential role in base excision repair (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-01
    Description: Bacillus subtilis is one of the bacterial members provided with a nonhomologous end joining (NHEJ) system constituted by the DNA-binding Ku homodimer that recruits the ATP-dependent DNA Ligase D ( Bsu LigD) to the double-stranded DNA breaks (DSBs) ends. Bsu LigD has inherent polymerization and ligase activities that allow it to fill the short gaps that can arise after realignment of the broken ends and to seal the resulting nicks, contributing to genome stability during the stationary phase and germination of spores. Here we show that Bsu LigD also has an intrinsic 5'-2-deoxyribose-5-phosphate (dRP) lyase activity located at the N-terminal ligase domain that in coordination with the polymerization and ligase activities allows efficient repairing of 2'-deoxyuridine-containing DNA in an in vitro reconstituted Base Excision Repair (BER) reaction. The requirement of a polymerization, a dRP removal and a final sealing step in BER, together with the joint participation of Bsu LigD with the spore specific AP endonuclease in conferring spore resistance to ultrahigh vacuum desiccation suggest that Bsu LigD could actively participate in this pathway. We demonstrate the presence of the dRP lyase activity also in the homolog protein from the distantly related bacterium Pseudomonas aeruginosa , allowing us to expand our results to other bacterial LigDs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    SSX2 is a novel DNA-binding protein that antagonizes polycomb group body formation and gene repression (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-10
    Description: Polycomb group (PcG) complexes regulate cellular identity through epigenetic programming of chromatin. Here, we show that SSX2, a germline-specific protein ectopically expressed in melanoma and other types of human cancers, is a chromatin-associated protein that antagonizes BMI1 and EZH2 PcG body formation and derepresses PcG target genes. SSX2 further negatively regulates the level of the PcG-associated histone mark H3K27me3 in melanoma cells, and there is a clear inverse correlation between SSX2/3 expression and H3K27me3 in spermatogenesis. However, SSX2 does not affect the overall composition and stability of PcG complexes, and there is no direct concordance between SSX2 and BMI1/H3K27me3 presence at regulated genes. This suggests that SSX2 antagonizes PcG function through an indirect mechanism, such as modulation of chromatin structure. SSX2 binds double-stranded DNA in a sequence non-specific manner in agreement with the observed widespread association with chromatin. Our results implicate SSX2 in regulation of chromatin structure and function.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Phage-mediated horizontal gene transfer of both prophage and heterologous DNA by {phi}BB-1, a bacteriophage of Borrelia burgdorferi (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-14
    Description: Horizontal gene transfer (HGT) in Borrelia burgdorferi , the Lyme disease agent, is likely mediated by bacteriophage. Studies of the B. burgdorferi phage, BB-1 and its role in HGT have been hindered by the lack of an assay for readily characterizing phage-mediated DNA movement (transduction). Here we describe an in vitro assay in which a clone of B. burgdorferi strain CA-11.2A encoding kanamycin resistance on a BB-1 prophage is co-cultured with different clones encoding gentamicin resistance on a shuttle vector; transduction is monitored by enumerating colonies selected in the presence of both kanamycin and gentamicin. When both clones used in the assay were derived from CA-11.2A, the frequency of transduction was 1.23 x 10 –6 transductants per cell, and could be increased 5-fold by exposing the phage-producing strain to 5% ethanol. Transduction was also demonstrated between the CA-11.2A clone and clones of both high-passage B. burgdorferi strain B31 and low-passage, virulent B. burgdorferi strain 297, although with lower transduction frequencies. The transductant in the 297 background produced phage capable of transducing another B. burgdorferi clone: this is the first experimental demonstration of transduction from a clone of a virulent strain. In addition to prophage DNA, small Escherichia coli -derived shuttle vectors were also transduced between co-cultured B. burgdorferi strains, suggesting both a broad role for the phage in the HGT of heterologous DNA and a potential use of the phage as a molecular tool. These results enhance our understanding of phage-mediated transduction as a mechanism of HGT in the Lyme disease spirochetes. Furthermore, the reagents and techniques developed herein will facilitate future studies of phage-mediated HGT, especially within the tick vector and vertebrate host.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein (2014)
    Oxford University Press
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    Publication Date: 2014-06-03
    Description: Instead of a classical s ingle- s tranded deoxyribonuleic acid (DNA)- b inding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP- r elated p roteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro . A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Structural and biochemical studies of SLIP1-SLBP identify DBP5 and eIF3g as SLIP1-binding proteins (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-06
    Description: In metazoans, replication-dependent histone mRNAs end in a stem-loop structure instead of the poly(A) tail characteristic of all other mature mRNAs. This specialized 3' end is bound by stem-loop binding protein (SLBP), a protein that participates in the nuclear export and translation of histone mRNAs. The translational activity of SLBP is mediated by interaction with SLIP1, a m iddle domain of i nitiation f actor 4G (MIF4G)-like protein that connects to translation initiation. We determined the 2.5 Å resolution crystal structure of zebrafish SLIP1 bound to the translation–activation domain of SLBP and identified the determinants of the recognition. We discovered a SLIP1-binding motif (SBM) in two additional proteins: the translation initiation factor eIF3g and the mRNA-export factor DBP5. We confirmed the binding of SLIP1 to DBP5 and eIF3g by pull-down assays and determined the 3.25 Å resolution structure of SLIP1 bound to the DBP5 SBM. The SBM-binding and homodimerization residues of SLIP1 are conserved in the MIF4G domain of CBP80/20-dependent translation initiation factor (CTIF). The results suggest how the SLIP1 homodimer or a SLIP1–CTIF heterodimer can function as platforms to bridge SLBP with SBM-containing proteins involved in different steps of mRNA metabolism.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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