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  • 1
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    Diversity and complexity in DNA recognition by transcription factors (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-05-16
    Description: Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905877/" 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/PMC2905877/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Badis, Gwenael -- Berger, Michael F -- Philippakis, Anthony A -- Talukder, Shaheynoor -- Gehrke, Andrew R -- Jaeger, Savina A -- Chan, Esther T -- Metzler, Genita -- Vedenko, Anastasia -- Chen, Xiaoyu -- Kuznetsov, Hanna -- Wang, Chi-Fong -- Coburn, David -- Newburger, Daniel E -- Morris, Quaid -- Hughes, Timothy R -- Bulyk, Martha L -- R01 HG003985/HG/NHGRI NIH HHS/ -- R01 HG003985-01/HG/NHGRI NIH HHS/ -- R01 HG003985-02/HG/NHGRI NIH HHS/ -- R01 HG003985-03/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19443739" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; DNA/chemistry/*metabolism ; Electrophoretic Mobility Shift Assay ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; Mice ; Protein Array Analysis ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism ; Transcription Factors/*chemistry/*metabolism
    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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  • 2
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    The kinase domain of titin controls muscle gene expression and protein turnover (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-02
    Description: The giant sarcomeric protein titin contains a protein kinase domain (TK) ideally positioned to sense mechanical load. We identified a signaling complex where TK interacts with the zinc-finger protein nbr1 through a mechanically inducible conformation. Nbr1 targets the ubiquitin-associated p62/SQSTM1 to sarcomeres, and p62 in turn interacts with MuRF2, a muscle-specific RING-B-box E3 ligase and ligand of the transactivation domain of the serum response transcription factor (SRF). Nuclear translocation of MuRF2 was induced by mechanical inactivity and caused reduction of nuclear SRF and repression of transcription. A human mutation in the titin protein kinase domain causes hereditary muscle disease by disrupting this pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lange, Stephan -- Xiang, Fengqing -- Yakovenko, Andrey -- Vihola, Anna -- Hackman, Peter -- Rostkova, Elena -- Kristensen, Jakob -- Brandmeier, Birgit -- Franzen, Gereon -- Hedberg, Birgitta -- Gunnarsson, Lars Gunnar -- Hughes, Simon M -- Marchand, Sylvie -- Sejersen, Thomas -- Richard, Isabelle -- Edstrom, Lars -- Ehler, Elisabeth -- Udd, Bjarne -- Gautel, Mathias -- G0200496(63216)/Medical Research Council/United Kingdom -- G0300213/Medical Research Council/United Kingdom -- PG/03/049/15364/British Heart Foundation/United Kingdom -- New York, N.Y. -- Science. 2005 Jun 10;308(5728):1599-603. Epub 2005 Mar 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Muscle Signalling and Development, Randall Division, King's College London, London SE1 1UL, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15802564" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Catalytic Domain ; Cell Line ; Cell Nucleus/metabolism ; Connectin ; *Gene Expression Regulation ; Heat-Shock Proteins/metabolism ; Humans ; Ligands ; Mice ; Mice, Inbred C3H ; Molecular Sequence Data ; Muscle Proteins/*chemistry/genetics/*metabolism ; Muscle, Skeletal/*metabolism ; Muscular Diseases/genetics ; Mutation ; Myocytes, Cardiac/*metabolism ; Protein Binding ; Protein Conformation ; Protein Kinases/*chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Proteins/metabolism ; Rats ; Respiratory Insufficiency/genetics/metabolism ; Sarcomeres/metabolism ; Serum Response Factor/metabolism ; Signal Transduction ; Two-Hybrid System Techniques ; Ubiquitin-Protein Ligases/metabolism
    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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  • 3
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    Targeting QseC signaling and virulence for antibiotic development (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-23
    Description: Many bacterial pathogens rely on a conserved membrane histidine sensor kinase, QseC, to respond to host adrenergic signaling molecules and bacterial signals in order to promote the expression of virulence factors. Using a high-throughput screen, we identified a small molecule, LED209, that inhibits the binding of signals to QseC, preventing its autophosphorylation and consequently inhibiting QseC-mediated activation of virulence gene expression. LED209 is not toxic and does not inhibit pathogen growth; however, this compound markedly inhibits the virulence of several pathogens in vitro and in vivo in animals. Inhibition of signaling offers a strategy for the development of broad-spectrum antimicrobial drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605406/" 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/PMC2605406/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rasko, David A -- Moreira, Cristiano G -- Li, De Run -- Reading, Nicola C -- Ritchie, Jennifer M -- Waldor, Matthew K -- Williams, Noelle -- Taussig, Ron -- Wei, Shuguang -- Roth, Michael -- Hughes, David T -- Huntley, Jason F -- Fina, Maggy W -- Falck, John R -- Sperandio, Vanessa -- P01 AI055637/AI/NIAID NIH HHS/ -- P01 AI055637-010005/AI/NIAID NIH HHS/ -- P01-AI055637-03/AI/NIAID NIH HHS/ -- R01 AI053067/AI/NIAID NIH HHS/ -- R01 AI053067-06/AI/NIAID NIH HHS/ -- R01 GM31278/GM/NIGMS NIH HHS/ -- R03 NS053582/NS/NINDS NIH HHS/ -- R03 NS053582-01/NS/NINDS NIH HHS/ -- R21 AI067827/AI/NIAID NIH HHS/ -- U01 AI077853/AI/NIAID NIH HHS/ -- U01 AI077853-01/AI/NIAID NIH HHS/ -- UO1-AI77853/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Aug 22;321(5892):1078-80. doi: 10.1126/science.1160354.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Texas (UT) Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719281" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anti-Bacterial Agents/administration & dosage/*pharmacology/therapeutic use ; Enterohemorrhagic Escherichia coli/drug ; effects/genetics/metabolism/*pathogenicity ; Escherichia coli Infections/drug therapy ; Escherichia coli Proteins/antagonists & inhibitors/genetics/*metabolism ; Francisella tularensis/drug effects/genetics/metabolism/*pathogenicity ; Gene Expression Regulation, Bacterial/drug effects ; Gram-Negative Bacterial Infections/*drug therapy ; Mice ; Norepinephrine/metabolism ; Phosphorylation ; Protein Kinases/genetics/*metabolism ; Rabbits ; Salmonella Infections, Animal/drug therapy ; Salmonella typhimurium/drug effects/genetics/metabolism/*pathogenicity ; Signal Transduction/drug effects ; Small Molecule Libraries ; Sulfonamides/administration & dosage/chemistry/*pharmacology/therapeutic use ; Tularemia/drug therapy ; Virulence Factors/genetics
    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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    A Suzaku Observation of the Neutral Fe-line Emission from RCW 86 (2007)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: The newly operational X-ray satellite Suzaku observed the supernova remnant (SNR) RCW 86 in February 2006 to study the nature of the 6.4 keV emission line first detected with the Advanced Satellite for Cosmology and Astronomy (ASCA). The new data confirms the existence of the line, localizing it for the first time inside a low temperature emission region and not at the locus of the continuum hard X-ray emission. We also report the first detection of a 7.1 keV line that we interpret as the K(beta) emission from neutral or low-ionized iron. The Fe-K line features are consistent with a non-equilibrium plasma of Fe-rich ejecta with n(sub e) less than or approx. equal to 10(exp 9)/cu cm s and kT(sub e) 〉 1 keV. We found a sign that Fe K(alpha) line is intrinsically broadened 47 (35-57) eV (99% error region). Cr-K line is also marginally detected, which is supporting the ejecta origin for the Fe-K line. By showing that the hard continuum above 3 keV has different spatial distribution from the Fe-K line, we confirmed it to be synchrotron X-ray emission.
    Keywords: Astronomy
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  • 5
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    Hubble Space Telescope Observations of Oxygen-rich Supernova Remnants in the Magellanic Clouds. III. WFPC2 Imaging of the Young, Crab-like Supernova Remnant SNRO540-69.3 (2006)
    In:  CASI
    Details
    Publication Date: 2019-07-11
    Description: Hubble Space Telescope images with the Wide Field Planetary Camera 2 of the young, oxygen-rich, Crab-like supernova remnant SNR0540-69.3 in the Large Magellanic Cloud (LMC) reveal details of the emission distribution and the relationship between the expanding ejecta and synchrotron nebula. The emission distributions appear very similar to those seen in the Crab nebula, with the ejecta located in a thin envelope surrounding the synchrotron nebula. The [O III] emission is more extended than other tracers, forming a faint "skin" around the denser filaments and synchrotron nebula, as also observed in the Crab. The [O III] exhibits somewhat different kinematic structure in long-slit spectra, including a more extended high-velocity emission halo not seen in images. Yet even the fastest expansion speeds in SNR 0540 s halo are slow when compared to most other young supernova remnants, though the Crab nebula has similar slow expansion speeds. We show a striking correspondence between the morphology of the synchrotron nebula observed in an optical continuum filter with that recently resolved in Chandra X-ray images. We argue that the multi-component kinematics and filamentary morphology of the optical emission-line features likely result from magnetic Rayleigh-Taylor instabilities that form as the synchrotron nebula expands and sweeps up ejecta, as seen in the Crab nebula. Our images and spectra help to refine our understanding of SNR 0540 in several more detailed respects: they confirm the identification of H(alpha)+[N II] in the red spectrum, they show that the systemic velocity of SNR 0540 is not significantly different from that of the LMC, and they hint at a lower Ne abundance than the Crab (potentially indicating a more massive progenitor star).
    Keywords: Astronomy
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  • 6
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    Investigations into Gravitational Wave Emission from Compact Body Inspiral into Massive Black Holes (2005)
    In:  CASI
    Details
    Publication Date: 2019-08-15
    Description: In contrast to year 1 (when much of the activity associated with this grant focused upon developing our group at MIT), year 2 was a period of very focused attention on research problems. We made significant progress developing relativistic waveforms for the extreme mass ratio inspiral problem; we have pushed forward a formalism our group developed for mapping the spacetimes of massive compact objects; and, in collaboration with the Caltech group, we began to develop a framework for addressing issues in LISA data analysis for extreme mass ratio systems.
    Keywords: Astronomy
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