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  • 1
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    Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-02
    Description: A distance constrained secondary structural model of the 10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Self-assembly of a nanoscale DNA box with a controllable lid (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-09
    Description: The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a 'bottom-up' approach. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures. Recently, the DNA 'origami' method was used to build two-dimensional addressable DNA structures of arbitrary shape that can be used as platforms to arrange nanomaterials with high precision and specificity. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 x 36 x 36 nm(3) in size that can be opened in the presence of externally supplied DNA 'keys'. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersen, Ebbe S -- Dong, Mingdong -- Nielsen, Morten M -- Jahn, Kasper -- Subramani, Ramesh -- Mamdouh, Wael -- Golas, Monika M -- Sander, Bjoern -- Stark, Holger -- Oliveira, Cristiano L P -- Pedersen, Jan Skov -- Birkedal, Victoria -- Besenbacher, Flemming -- Gothelf, Kurt V -- Kjems, Jorgen -- England -- Nature. 2009 May 7;459(7243):73-6. doi: 10.1038/nature07971.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Danish National Research Foundation: Centre for DNA Nanotechnology.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19424153" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; DNA/*chemistry ; Imaging, Three-Dimensional ; Microscopy, Atomic Force ; Nanostructures/*chemistry ; *Nucleic Acid Conformation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    MicroRNA-128 governs neuronal excitability and motor behavior in mice (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-07
    Description: The control of motor behavior in animals and humans requires constant adaptation of neuronal networks to signals of various types and strengths. We found that microRNA-128 (miR-128), which is expressed in adult neurons, regulates motor behavior by modulating neuronal signaling networks and excitability. miR-128 governs motor activity by suppressing the expression of various ion channels and signaling components of the extracellular signal-regulated kinase ERK2 network that regulate neuronal excitability. In mice, a reduction of miR-128 expression in postnatal neurons causes increased motor activity and fatal epilepsy. Overexpression of miR-128 attenuates neuronal responsiveness, suppresses motor activity, and alleviates motor abnormalities associated with Parkinson's-like disease and seizures in mice. These data suggest a therapeutic potential for miR-128 in the treatment of epilepsy and movement disorders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932786/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932786/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tan, Chan Lek -- Plotkin, Joshua L -- Veno, Morten T -- von Schimmelmann, Melanie -- Feinberg, Philip -- Mann, Silas -- Handler, Annie -- Kjems, Jorgen -- Surmeier, D James -- O'Carroll, Donal -- Greengard, Paul -- Schaefer, Anne -- 1DP2MH100012-01/DP/NCCDPHP CDC HHS/ -- DA025962/DA/NIDA NIH HHS/ -- DA10044/DA/NIDA NIH HHS/ -- DP2 MH100012/MH/NIMH NIH HHS/ -- NS34696/NS/NINDS NIH HHS/ -- P01 DA010044/DA/NIDA NIH HHS/ -- P50 MH090963/MH/NIMH NIH HHS/ -- P50MH090963/MH/NIMH NIH HHS/ -- R01 NS034696/NS/NINDS NIH HHS/ -- R03 DA025962/DA/NIDA NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 6;342(6163):1254-8. doi: 10.1126/science.1244193.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24311694" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Corpus Striatum/cytology ; Dendrites/physiology ; Epilepsy/metabolism ; Hyperkinesis/metabolism ; MAP Kinase Signaling System ; Mice ; MicroRNAs/genetics/*metabolism ; Mitogen-Activated Protein Kinase 1/antagonists & inhibitors/metabolism ; Mitogen-Activated Protein Kinase 3/antagonists & inhibitors/metabolism ; *Motor Activity ; Neurons/*physiology ; Parkinsonian Disorders/metabolism/physiopathology ; Prosencephalon/cytology/*physiology ; RNA, Messenger/genetics/metabolism ; RNA-Induced Silencing Complex/metabolism ; Up-Regulation
    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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  • 4
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    Natural RNA circles function as efficient microRNA sponges (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-03-01
    Description: MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more than 70 selectively conserved miRNA target sites, and it is highly and widely associated with Argonaute (AGO) proteins in a miR-7-dependent manner. Although the circRNA is completely resistant to miRNA-mediated target destabilization, it strongly suppresses miR-7 activity, resulting in increased levels of miR-7 targets. In the mouse brain, we observe overlapping co-expression of ciRS-7 and miR-7, particularly in neocortical and hippocampal neurons, suggesting a high degree of endogenous interaction. We further show that the testis-specific circRNA, sex-determining region Y (Sry), serves as a miR-138 sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hansen, Thomas B -- Jensen, Trine I -- Clausen, Bettina H -- Bramsen, Jesper B -- Finsen, Bente -- Damgaard, Christian K -- Kjems, Jorgen -- England -- Nature. 2013 Mar 21;495(7441):384-8. doi: 10.1038/nature11993. Epub 2013 Feb 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Aarhus University, C.F. Mollers Alle 3, 8000C, Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23446346" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argonaute Proteins/metabolism ; Brain/metabolism ; *Gene Expression Regulation ; HEK293 Cells ; HeLa Cells ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; MicroRNAs/genetics/*metabolism ; RNA/genetics/*metabolism ; Sex-Determining Region Y Protein/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
    Electronic Resource
    Electronic Resource
    Inelastic neutron scattering studies on 1D near-Heisenberg antiferromagnets: A test of the Haldane conjecture (1987)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 61 (1987), S. 3953-3955 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Our studies of the spin dynamics for two near-Heisenberg antiferromagnets (AFMs) revealed: In CsNiCl3 (S=1) at low T(very-much-less-than)TN we confirm the conclusions given earlier, but disagreement with the spin-wave calculations used is found for the eigenvectors. For T〉TN, the most important result is the observation that all 〈SαSα〉 (α=x,y,z) are identical, demanding another interpretation for the gap observed than the easy axis one. In CsVCl3 (S= (3)/(2) ) we could not observe any inconsistency in the microscopic parameters determined above and below TN. Although there is a striking coincidence with Haldane's conjecture [unexplained gap for S=1 (CsNiCl3), no such gap for S= (3)/(2) (CsVCl3)], it is not clear whether this can be considered a proof for Haldane's conjecture.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.338595
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  • 6
    Electronic Resource
    Electronic Resource
    Neutron scattering studies of heavy fermion systems (invited) (abstract) (1987)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 61 (1987), S. 3909-3909 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We review our results of neutron scattering experiments on the heavy electron systems UPt3, U2Zn17, and URu2Si2. In the superconductor UPt3 we have established the existence of spin fluctuations on an energy scale of 0.5 meV and correlated in the same structure as the antiferromagnetic order in the Th- and Pd-doped systems. In the antiferromagnet U2Zn17 overdamped antiferromagnetically correlated excitations dominate the excitation spectrum above and below TN. However, in an applied field the resonances are induced in the transverse response. In the antiferromagnetic superconductor URu2Si2 the excitations in the ordered phases are propagating, longitudinal and similar to observations in singlet rare-earth ground-state systems. However, the ordered moment of 0.03μB is anomalously small and the transverse response is overdamped. We discuss a simple model of exchange coupled overdamped responses which gives a consistent description of the diffusive spin-fluctuations in several heavy electron systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.338580
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  • 7
    Electronic Resource
    Electronic Resource
    Exchange mechanisms in CsMnxMg1−xBr3 (1985)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 57 (1985), S. 3332-3334 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The inelastic neutron scattering technique was used to measure the excitation spectra of pairs and triads of magnetic Mn2+ ions in the one-dimensional S-state magnet CsMnxMg1−xBr3 (x=0.14, 0.28, 0.5). It turns out that the Heisenberg exchange interactions in pairs and triads are slightly different from each other. In the cluster regime dipolar interactions are negligibly small.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.335086
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  • 8
    Electronic Resource
    Electronic Resource
    Solution structure of human plasma fibronectin using small-angle X-ray and neutron scattering at physiological pH and ionic strength
    Amsterdam : Elsevier
    Archives of Biochemistry and Biophysics 255 (1987), S. 347-353 
    Details
    ISSN: 0003-9861
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0003-9861(87)90402-4
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  • 9
    Electronic Resource
    Electronic Resource
    Iron–germanium multilayer neutron polarizing monochromators (1976)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 9 (1976), S. 454-459 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A new type of thermal neutron polarizing monochromator, consisting of alternate thin layers of iron and germanium, has been constructed and tested. Bragg reflection from such artificial `crystals' in the fully magnetized state yields a highly polarized beam with high reflecting efficiency (0̃.84) for the reflected spin state. These multilayer monochromators have the additional advantage that higher orders in the reflected beam are almost completely suppressed. Since d spacings are typically large (1̃00 Å), they produce a broader wavelength distribution than conventional single-crystal polarizing monochromators. Nevertheless, there are many applications where wavelength resolution is of secondary importance and the large gain in intensity (4̃0-fold) over conventional polarizing crystals can be a considerable advantage. Multilayers can also be used to advantage in combination with good monochromating crystals such as pyrolytic graphite or beryllium to produce polarized beams of high intensity and good wavelength resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889876011916
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  • 10
    Electronic Resource
    Electronic Resource
    Archaeal rRNA operons
    Amsterdam : Elsevier
    Trends in Biochemical Sciences 16 (1991), S. 22-26 
    Details
    ISSN: 0968-0004
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0968-0004(91)90011-J
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