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  • Oxford University Press  (21)
  • American Association for the Advancement of Science (AAAS)  (4)
  • Hindawi
  • 2010-2014  (21)
  • 1985-1989  (5)
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  • 1
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    Domain-wall dynamics in 4C pyrrhotite at low temperature (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-10
    Description: Monoclinic 4C pyrrhotite (Fe 7 S 8 ) is ferrimagnetic due to an ordered defect structure with alternating vacancy and vacancy-free sublattices. Its low-temperature magnetic transition near 35 K is characterized by the distinct increase in coercivity and remanent magnetization. The increase of these parameters has been attributed to changes in the domain wall structure. We present static and dynamic magnetization data of a powder sample to study the domain-wall dynamics across the low-temperature transition. The amplitude-dependent ac susceptibility and the ferromagnetic resonance spectroscopy indicate that the hardening of the domain-wall pinning at the transition occurs simultaneously with the decrease in initial saturation remanent magnetization. These two effects are explained by the enhanced inhomogeneity of the bulk material caused by the persistency of the ordered vacancies and by newly formed defects due to localized distortion of Fe(II) sites in the vacancy-free sublattice. The generated localized defects are the link between the domain wall dynamics and the low-temperature transition in 4C pyrrhotite.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 2
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    Rock magnetic techniques complemented by ferromagnetic resonance spectroscopy to analyse a sediment record (2012)
    Oxford University Press
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    Publication Date: 2012-08-24
    Description: SUMMARY Environmental magnetism uses the spatial and temporal occurrence of magnetic carriers as diagnostic tools to detect environmental changes. Concentration, composition, grain size and configuration of the carriers inferred from magnetic properties are key parameters, because they are indicative of the formation conditions of magnetic phases, and/or of processes such as diagenesis and weathering. We present a detailed ferromagnetic resonance (FMR) spectroscopy analysis in concert with routinely used rock magnetic measurements to determine these parameters in a sediment record that documents the development of Lake Soppensee (Central Switzerland) since latest Pleistocene. FMR spectroscopy monitors varying concentration of the predominant magnetite/maghemite by the spectral signal intensity, whereas the stable single domain and superparamagnetic states are determined by the signal shape at room and low temperature. Fitting and simulation of FMR spectra are successfully applied to samples with well-defined magnetite components in the sediment matrix. Clear evidence for the colonization of magnetotactic bacteria (MTB) in Lake Soppensee was possible by applying empirical spectral separation to measured FMR signals that yield two magnetite populations differing in their configuration, that is, dispersed and aligned in chains. Low temperature measurements showed that these MTB can be preserved as pure or oxidized magnetite. The FMR data set confirms and completes rock magnetic information obtained from the lacustrine sedimentary record. The advanced application of FMR spectroscopy in the presented study critically highlights the benefit of this rapid and non-destructive method for future analysis of magnetic properties in environmental studies.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
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    Fe–Ti–O exchange at high temperature and thermal hysteresis (2011)
    Oxford University Press
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    Publication Date: 2011-03-10
    Description: SUMMARY In this study, the Fe–Ti–O exchange behaviour between the systems hemo-ilmenite ( y )FeTiO 3 –( 1 − y )Fe 2 O 3 and titano-magnetite ( x )Fe 2 TiO 4 –( 1 − x )Fe 3 O 4 was investigated in the temperature range from 900 to 1400 K in an inert Ar atmosphere. Starting from a mixture of hematite and ilmenite with a fixed mol per cent, heat treatment generates a self-adjusting chemical equilibrium between hemo-ilmenite and titano-magnetite solid solution by means of interdiffusion and Fe 3+ → Fe 2+ reduction. Structural and magnetic characterization reveals that hemo-ilmenite is stable at all temperatures, whereas titano-magnetite shows increasing Ti-content with increasing treatment temperature. Heating–cooling cycles were performed for a sample to mimic slow cooling and study its effects on the two solid solutions. The magnetic properties of that sample exhibit thermal hysteresis during these cycles, as the Ti departs from titano-magnetite and thus leads to a new chemical equilibrium. The experimental data provide insight into the dynamics of the formation of Fe–Ti–O phases formed under varying conditions in geological systems.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
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    NKAP is a novel RS-related protein that interacts with RNA and RNA binding proteins (2014)
    Oxford University Press
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    Publication Date: 2014-03-13
    Description: NKAP is a highly conserved protein with roles in transcriptional repression, T-cell development, maturation and acquisition of functional competency and maintenance and survival of adult hematopoietic stem cells. Here we report the novel role of NKAP in splicing. With NKAP-specific antibodies we found that NKAP localizes to nuclear speckles. NKAP has an RS motif at the N-terminus followed by a highly basic domain and a DUF 926 domain at the C-terminal region. Deletion analysis showed that the basic domain is important for speckle localization. In pull-down experiments, we identified RNA-binding proteins, RNA helicases and splicing factors as interaction partners of NKAP, among them FUS/TLS. The FUS/TLS–NKAP interaction takes place through the RS domain of NKAP and the RGG1 and RGG3 domains of FUS/TLS. We analyzed the ability of NKAP to interact with RNA using in vitro splicing assays and found that NKAP bound both spliced messenger RNA (mRNA) and unspliced pre-mRNA. Genome-wide analysis using crosslinking and immunoprecipitation-seq revealed NKAP association with U1, U4 and U5 small nuclear RNA, and we also demonstrated that knockdown of NKAP led to an increase in pre-mRNA percentage. Our results reveal NKAP as nuclear speckle protein with roles in RNA splicing and processing.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Structural and functional analysis of the three MIF4G domains of nonsense-mediated decay factor UPF2 (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-28
    Description: Nonsense-mediated decay (NMD) is a eukaryotic quality control pathway, involving conserved proteins UPF1, UPF2 and UPF3b, which detects and degrades mRNAs with premature stop codons. Human UPF2 comprises three tandem MIF4G domains and a C-terminal UPF1 binding region. MIF4G-3 binds UPF3b, but the specific functions of MIF4G-1 and MIF4G-2 are unknown. Crystal structures show that both MIF4G-1 and MIF4G-2 contain N-terminal capping helices essential for stabilization of the 10-helix MIF4G core and that MIF4G-2 interacts with MIF4G-3, forming a rigid assembly. The UPF2/UPF3b/SMG1 complex is thought to activate the kinase SMG1 to phosphorylate UPF1 in vivo . We identify MIF4G-3 as the binding site and in vitro substrate of SMG1 kinase and show that a ternary UPF2 MIF4G-3/UPF3b/SMG1 complex can form in vitro . Whereas in vivo complementation assays show that MIF4G-1 and MIF4G-2 are essential for NMD, tethering assays reveal that UPF2 truncated to only MIF4G-3 and the UPF1-binding region can still partially accomplish NMD. Thus UPF2 MIF4G-1 and MIF4G-2 appear to have a crucial scaffolding role, while MIF4G-3 is the key module required for triggering NMD.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Magnetic anisotropy and Verwey transition of magnetosome chains in Magnetospirillum gryphiswaldense (2011)
    Oxford University Press
    Details
    Publication Date: 2011-10-06
    Description: SUMMARY Magnetotactic bacteria (MTB) are characterized by cellular magnetic dipoles formed by the 1-D assembly of magnetite and/or greigite particles aligned along their magnetic easy axes. This alignment creates strong interaction-induced shape anisotropy. Ferromagnetic resonance (FMR) spectroscopy is applied to study the changes in anisotropy of the MTB Magnetospirillum gryphiswaldense between room temperature and 10 K. The Verwey transition is found at about 100 K. The characteristic FMR signal of the cellular dipole at room temperature vanishes upon cooling to the isotropic point at T i ≈ 130 K, where the magnetocrystalline anisotropy constant K 1 becomes zero. Monitoring of the FMR response of intact MTB as a function of temperature is taken to discuss theoretically the reduction of the interaction-induced shape anisotropy in magnetofossils because of diagenetic processes. It is concluded that there is a similarity in the FMR response between magnetofossils at room temperature and intact MTB near T i . This is because the critical effect of the magnetocrystalline anisotropy constant K 1 and of the alignment of magnetic easy axes on the cellular dipole. Low-temperature FMR results of intact MTB can thus be used as a guideline for detecting magnetofossils in geological environments.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
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    Complex multicolor tilings and critical phenomena in tetraphilic liquid crystals (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-03-12
    Description: T-shaped molecules with a rod-like aromatic core and a flexible side chain form liquid crystal honeycombs with aromatic cell walls and a cell interior filled with the side chains. Here, we show how the addition of a second chain, incompatible with the first (X-shaped molecules), can form honeycombs with highly complex tiling patterns, with cells of up to five different compositions ("colors") and polygonal shapes. The complexity is caused by the inability of the side chains to separate cleanly because of geometric frustration. Furthermore, a thermoreversible transition was observed between a multicolor (phase-separated) and a single-color (mixed) honeycomb phase. This is analogous to the Curie transition in simple and frustrated ferro- and antiferromagnets; here spin flips are replaced by 180 degrees reorientations of the molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zeng, Xiangbing -- Kieffer, Robert -- Glettner, Benjamin -- Nurnberger, Constance -- Liu, Feng -- Pelz, Karsten -- Prehm, Marko -- Baumeister, Ute -- Hahn, Harald -- Lang, Heinrich -- Gehring, Gillian A -- Weber, Christa H M -- Hobbs, Jamie K -- Tschierske, Carsten -- Ungar, Goran -- New York, N.Y. -- Science. 2011 Mar 11;331(6022):1302-6. doi: 10.1126/science.1193052.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21393540" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Structure of parkin reveals mechanisms for ubiquitin ligase activation (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-05-11
    Description: Mutations in the PARK2 (parkin) gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-in-between-RING E3 ubiquitin ligase that exhibits low basal activity. We describe the crystal structure of full-length rat parkin. The structure shows parkin in an autoinhibited state and provides insight into how it is activated. RING0 occludes the ubiquitin acceptor site Cys(431) in RING2, whereas a repressor element of parkin binds RING1 and blocks its E2-binding site. Mutations that disrupted these inhibitory interactions activated parkin both in vitro and in cells. Parkin is neuroprotective, and these findings may provide a structural and mechanistic framework for enhancing parkin activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Trempe, Jean-Francois -- Sauve, Veronique -- Grenier, Karl -- Seirafi, Marjan -- Tang, Matthew Y -- Menade, Marie -- Al-Abdul-Wahid, Sameer -- Krett, Jonathan -- Wong, Kathy -- Kozlov, Guennadi -- Nagar, Bhushan -- Fon, Edward A -- Gehring, Kalle -- MOP-14219/Canadian Institutes of Health Research/Canada -- MOP-62714/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 Jun 21;340(6139):1451-5. doi: 10.1126/science.1237908. Epub 2013 May 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23661642" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Activation ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Parkinson Disease ; Parkinsonian Disorders ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Rats ; Ubiquitin-Protein Ligases/*chemistry/genetics/*metabolism ; Ubiquitination ; Zinc Fingers
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    TSSi--an R package for transcription start site identification from 5' mRNA tag data (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-12
    Description: : High-throughput sequencing has become an essential experimental approach for the investigation of transcriptional mechanisms. For some applications like ChIP-seq, several approaches for the prediction of peak locations exist. However, these methods are not designed for the identification of transcription start sites (TSSs) because such datasets contain qualitatively different noise. In this application note, the R package TSSi is presented which provides a heuristic framework for the identification of TSSs based on 5' mRNA tag data. Probabilistic assumptions for the distribution of the data, i.e. for the observed positions of the mapped reads, as well as for systematic errors, i.e. for reads which map closely but not exactly to a real TSS, are made and can be adapted by the user. The framework also comprises a regularization procedure which can be applied as a preprocessing step to decrease the noise and thereby reduce the number of false predictions. Availability: The R package TSSi is available from the Bioconductor web site: www.bioconductor.org/packages/release/bioc/html/TSSi.html . Contact: ckreutz@fdm.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Homeo boxes in the study of development (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-06-05
    Description: The body plan of Drosophila is determined to a large extent by homeotic genes, which specify the identity and spatial arrangement of the body segments. Homeotic genes share a characteristic DNA segment, the homeo box, which encodes a defined domain of the homeotic proteins. The homeo domain seems to mediate the binding to specific DNA sequences, whereby the homeotic proteins exert a gene regulatory function. By isolating the normal Antennapedia gene, fusing its protein-coding sequences to an inducible promoter, and reintroducing this fusion gene into the germline of flies, it has been possible to transform head structures into thoracic structures and to alter the body plan in a predicted way. Sequence homologies suggest that similar genetic mechanisms may control development in higher organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gehring, W J -- New York, N.Y. -- Science. 1987 Jun 5;236(4806):1245-52.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2884726" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Blastoderm/ultrastructure ; Drosophila/embryology/*genetics ; Embryonic and Fetal Development ; *Genes, Homeobox ; Mutation ; Ovum/ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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