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  • 1
    Publication Date: 2016-08-26
    Description: Author(s): Tim Johannsen, Carlos Wang, Avery E. Broderick, Sheperd S. Doeleman, Vincent L. Fish, Abraham Loeb, and Dimitrios Psaltis The Event Horizon Telescope is a global, very long baseline interferometer capable of probing potential deviations from the Kerr metric, which is believed to provide the unique description of astrophysical black holes. Here, we report an updated constraint on the quadrupolar deviation of Sagittarius… [Phys. Rev. Lett. 117, 091101] Published Wed Aug 24, 2016
    Keywords: Gravitation and Astrophysics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 2
    Publication Date: 2016-01-21
    Description: Author(s): Tim Johannsen, Avery E. Broderick, Philipp M. Plewa, Sotiris Chatzopoulos, Sheperd S. Doeleman, Frank Eisenhauer, Vincent L. Fish, Reinhard Genzel, Ortwin Gerhard, and Michael D. Johnson Deviations in the shadow of our Galaxy’s supermassive black hole could reveal violations of general relativity. [Phys. Rev. Lett. 116, 031101] Published Tue Jan 19, 2016
    Keywords: Gravitation and Astrophysics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 3
    Publication Date: 2012-09-29
    Description: Approximately 10% of active galactic nuclei exhibit relativistic jets, which are powered by the accretion of matter onto supermassive black holes. Although the measured width profiles of such jets on large scales agree with theories of magnetic collimation, the predicted structure on accretion disk scales at the jet launch point has not been detected. We report radio interferometry observations, at a wavelength of 1.3 millimeters, of the elliptical galaxy M87 that spatially resolve the base of the jet in this source. The derived size of 5.5 +/- 0.4 Schwarzschild radii is significantly smaller than the innermost edge of a retrograde accretion disk, suggesting that the M87 jet is powered by an accretion disk in a prograde orbit around a spinning black hole.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doeleman, Sheperd S -- Fish, Vincent L -- Schenck, David E -- Beaudoin, Christopher -- Blundell, Ray -- Bower, Geoffrey C -- Broderick, Avery E -- Chamberlin, Richard -- Freund, Robert -- Friberg, Per -- Gurwell, Mark A -- Ho, Paul T P -- Honma, Mareki -- Inoue, Makoto -- Krichbaum, Thomas P -- Lamb, James -- Loeb, Abraham -- Lonsdale, Colin -- Marrone, Daniel P -- Moran, James M -- Oyama, Tomoaki -- Plambeck, Richard -- Primiani, Rurik A -- Rogers, Alan E E -- Smythe, Daniel L -- SooHoo, Jason -- Strittmatter, Peter -- Tilanus, Remo P J -- Titus, Michael -- Weintroub, Jonathan -- Wright, Melvyn -- Young, Ken H -- Ziurys, Lucy M -- New York, N.Y. -- Science. 2012 Oct 19;338(6105):355-8. doi: 10.1126/science.1224768. Epub 2012 Sep 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MIT Haystack Observatory, Off Route 40, Westford, MA 01886, USA. sdoeleman@haystack.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019611" 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
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2006-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spalding, Mark -- Kelleher, Graeme -- Boucher, Timothy -- Fish, Lucy -- New York, N.Y. -- Science. 2006 Nov 3;314(5800):757-60; author reply 757-60.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17086635" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa ; *Conservation of Natural Resources ; *Ecosystem
    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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  • 5
    Publication Date: 2014-07-22
    Description: Aberrant regulation of RNA stability has an important role in many disease states. Deregulated post-transcriptional modulation, such as that governed by microRNAs targeting linear sequence elements in messenger RNAs, has been implicated in the progression of many cancer types. A defining feature of RNA is its ability to fold into structures. However, the roles of structural mRNA elements in cancer progression remain unexplored. Here we performed an unbiased search for post-transcriptional modulators of mRNA stability in breast cancer by conducting whole-genome transcript stability measurements in poorly and highly metastatic isogenic human breast cancer lines. Using a computational framework that searches RNA sequence and structure space, we discovered a family of GC-rich structural cis-regulatory RNA elements, termed sRSEs for structural RNA stability elements, which are significantly overrepresented in transcripts displaying reduced stability in highly metastatic cells. By integrating computational and biochemical approaches, we identified TARBP2, a double-stranded RNA-binding protein implicated in microRNA processing, as the trans factor that binds the sRSE family and similar structural elements--collectively termed TARBP2-binding structural elements (TBSEs)--in transcripts. TARBP2 is overexpressed in metastatic cells and metastatic human breast tumours and destabilizes transcripts containing TBSEs. Endogenous TARBP2 promotes metastatic cell invasion and colonization by destabilizing amyloid precursor protein (APP) and ZNF395 transcripts, two genes previously associated with Alzheimer's and Huntington's disease, respectively. We reveal these genes to be novel metastasis suppressor genes in breast cancer. The cleavage product of APP, extracellular amyloid-alpha peptide, directly suppresses invasion while ZNF395 transcriptionally represses a pro-metastatic gene expression program. The expression levels of TARBP2, APP and ZNF395 in human breast carcinomas support their experimentally uncovered roles in metastasis. Our findings establish a non-canonical and direct role for TARBP2 in mammalian gene expression regulation and reveal that regulated RNA destabilization through protein-mediated binding of mRNA structural elements can govern cancer progression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440807/" 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/PMC4440807/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goodarzi, Hani -- Zhang, Steven -- Buss, Colin G -- Fish, Lisa -- Tavazoie, Saeed -- Tavazoie, Sohail F -- R01 HG003219/HG/NHGRI NIH HHS/ -- England -- Nature. 2014 Sep 11;513(7517):256-60. doi: 10.1038/nature13466. Epub 2014 Jul 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Systems Cancer Biology, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA. ; Department of Biochemistry and Molecular Biophysics, and Department of Systems Biology, Columbia University, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25043050" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid beta-Protein Precursor/metabolism ; Breast Neoplasms/pathology ; Cell Line, Tumor ; DNA-Binding Proteins/metabolism ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; HEK293 Cells ; Humans ; Neoplasm Metastasis ; Protein Binding ; *RNA Stability ; RNA, Messenger/*metabolism ; RNA-Binding Proteins/genetics/*metabolism ; Transcription Factors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2012-04-13
    Description: Decoding post-transcriptional regulatory programs in RNA is a critical step towards the larger goal of developing predictive dynamical models of cellular behaviour. Despite recent efforts, the vast landscape of RNA regulatory elements remains largely uncharacterized. A long-standing obstacle is the contribution of local RNA secondary structure to the definition of interaction partners in a variety of regulatory contexts, including--but not limited to--transcript stability, alternative splicing and localization. There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (for example, human cardiac troponin T) or affects other aspects of RNA biology. Thus, a full characterization of post-transcriptional regulatory programs requires capturing information provided by both local secondary structures and the underlying sequence. Here we present a computational framework based on context-free grammars and mutual information that systematically explores the immense space of small structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behaviour. By applying this framework to genome-wide human mRNA stability data, we reveal eight highly significant elements with substantial structural information, for the strongest of which we show a major role in global mRNA regulation. Through biochemistry, mass spectrometry and in vivo binding studies, we identified human HNRPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1, also known as HNRNPA2B1) as the key regulator that binds this element and stabilizes a large number of its target genes. We created a global post-transcriptional regulatory map based on the identity of the discovered linear and structural cis-regulatory elements, their regulatory interactions and their target pathways. This approach could also be used to reveal the structural elements that modulate other aspects of RNA behaviour.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350620/" 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/PMC3350620/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goodarzi, Hani -- Najafabadi, Hamed S -- Oikonomou, Panos -- Greco, Todd M -- Fish, Lisa -- Salavati, Reza -- Cristea, Ileana M -- Tavazoie, Saeed -- 2R01HG003219/HG/NHGRI NIH HHS/ -- DP1 DA026192/DA/NIDA NIH HHS/ -- DP1 OD003787/OD/NIH HHS/ -- DP1 OD003787-05/OD/NIH HHS/ -- R01 HG003219/HG/NHGRI NIH HHS/ -- R01 HG003219-08/HG/NHGRI NIH HHS/ -- T32-GM066699/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Apr 8;485(7397):264-8. doi: 10.1038/nature11013.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495308" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics/physiology ; Algorithms ; Animals ; Breast Neoplasms/genetics ; Cell Line, Tumor ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Knockdown Techniques ; Genome, Human/genetics ; Genomics ; Heterogeneous-Nuclear Ribonucleoprotein Group A-B/genetics/metabolism ; Humans ; Mice ; *Nucleic Acid Conformation ; Nucleotide Motifs ; *RNA Stability/genetics ; RNA, Messenger/chemistry/*genetics/*metabolism ; RNA, Small Interfering ; Time Factors ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2016-01-20
    Description: Near a black hole, differential rotation of a magnetized accretion disk is thought to produce an instability that amplifies weak magnetic fields, driving accretion and outflow. These magnetic fields would naturally give rise to the observed synchrotron emission in galaxy cores and to the formation of relativistic jets, but no observations to date have been able to resolve the expected horizon-scale magnetic-field structure. We report interferometric observations at 1.3-millimeter wavelength that spatially resolve the linearly polarized emission from the Galactic Center supermassive black hole, Sagittarius A*. We have found evidence for partially ordered magnetic fields near the event horizon, on scales of ~6 Schwarzschild radii, and we have detected and localized the intrahour variability associated with these fields.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, Michael D -- Fish, Vincent L -- Doeleman, Sheperd S -- Marrone, Daniel P -- Plambeck, Richard L -- Wardle, John F C -- Akiyama, Kazunori -- Asada, Keiichi -- Beaudoin, Christopher -- Blackburn, Lindy -- Blundell, Ray -- Bower, Geoffrey C -- Brinkerink, Christiaan -- Broderick, Avery E -- Cappallo, Roger -- Chael, Andrew A -- Crew, Geoffrey B -- Dexter, Jason -- Dexter, Matt -- Freund, Robert -- Friberg, Per -- Gold, Roman -- Gurwell, Mark A -- Ho, Paul T P -- Honma, Mareki -- Inoue, Makoto -- Kosowsky, Michael -- Krichbaum, Thomas P -- Lamb, James -- Loeb, Abraham -- Lu, Ru-Sen -- MacMahon, David -- McKinney, Jonathan C -- Moran, James M -- Narayan, Ramesh -- Primiani, Rurik A -- Psaltis, Dimitrios -- Rogers, Alan E E -- Rosenfeld, Katherine -- SooHoo, Jason -- Tilanus, Remo P J -- Titus, Michael -- Vertatschitsch, Laura -- Weintroub, Jonathan -- Wright, Melvyn -- Young, Ken H -- Zensus, J Anton -- Ziurys, Lucy M -- New York, N.Y. -- Science. 2015 Dec 4;350(6265):1242-5. doi: 10.1126/science.aac7087. Epub 2015 Dec 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA. mjohnson@cfa.harvard.edu. ; Haystack Observatory, Route 40, Massachusetts Institute of Technology, Westford, MA 01886, USA. ; Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA. Haystack Observatory, Route 40, Massachusetts Institute of Technology, Westford, MA 01886, USA. ; Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721-0065, USA. ; Department of Astronomy, Radio Astronomy Laboratory, 501 Campbell, University of California Berkeley, Berkeley, CA 94720-3411, USA. ; Department of Physics MS-057, Brandeis University, Waltham, MA 02454-0911. ; Haystack Observatory, Route 40, Massachusetts Institute of Technology, Westford, MA 01886, USA. National Astronomical Observatory of Japan, Osawa 2-21-1, Mitaka, Tokyo 181-8588, Japan. Department of Astronomy, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. ; Institute of Astronomy and Astrophysics, Academia Sinica, Post Office Box 23-141, Taipei 10617, Taiwan. ; Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA. ; Academia Sinica Institute for Astronomy and Astrophysics (ASIAA), 645 N. A'ohoku Pl. Hilo, HI 96720, USA. ; Department of Astrophysics/Institute for Mathematics, Astrophysics and Particle Physics, Radboud University Nijmegen, Post Office Box 9010, 6500 GL Nijmegen, Netherlands. ; Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, ON N2L 2Y5, Canada. Department of Physics and Astronomy, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada. ; Max Planck Institute for Extraterrestrial Physics, Giessenbachstrasse 1, 85748 Garching, Germany. ; James Clerk Maxwell Telescope, East Asia Observatory, 660 N. A'ohoku Place, University Park, Hilo, HI 96720, USA. ; Department of Physics, Joint Space-Science Institute, University of Maryland at College Park, Physical Sciences Complex, College Park, MD 20742, USA. ; National Astronomical Observatory of Japan, Osawa 2-21-1, Mitaka, Tokyo 181-8588, Japan. Graduate University for Advanced Studies, Mitaka, 2-21-1 Osawa, Mitaka, Tokyo 181-8588. ; Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA. Haystack Observatory, Route 40, Massachusetts Institute of Technology, Westford, MA 01886, USA. Department of Physics MS-057, Brandeis University, Waltham, MA 02454-0911. ; Max-Planck-Institut fur Radioastronomie, Auf dem Hugel 69, D-53121 Bonn, Germany. ; Owens Valley Radio Observatory, California Institute of Technology, 100 Leighton Lane, Big Pine, CA 93513-0968, USA. ; Haystack Observatory, Route 40, Massachusetts Institute of Technology, Westford, MA 01886, USA. Max-Planck-Institut fur Radioastronomie, Auf dem Hugel 69, D-53121 Bonn, Germany. ; Department of Astrophysics/Institute for Mathematics, Astrophysics and Particle Physics, Radboud University Nijmegen, Post Office Box 9010, 6500 GL Nijmegen, Netherlands. Leiden Observatory, Leiden University, Post Office Box 9513, 2300 RA Leiden, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26785487" 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
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  • 8
    Publication Date: 2017-12-07
    Description: Developmental nonlinearity drives phenotypic robustness Developmental nonlinearity drives phenotypic robustness, Published online: 06 December 2017; doi:10.1038/s41467-017-02037-7 Developmental processes often involve nonlinearities, but the consequences for translating genotype to phenotype are not well characterized. Here, Green et al. vary Fgf8 signaling across allelic series of mice and show that phenotypic robustness in craniofacial shape is explained by a nonlinear effect of Fgf8 expression.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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