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  • 1
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    Architecture of the Mediator head module (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-05
    Description: Mediator is a key regulator of eukaryotic transcription, connecting activators and repressors bound to regulatory DNA elements with RNA polymerase II (Pol II). In the yeast Saccharomyces cerevisiae, Mediator comprises 25 subunits with a total mass of more than one megadalton (refs 5, 6) and is organized into three modules, called head, middle/arm and tail. Our understanding of Mediator assembly and its role in regulating transcription has been impeded so far by limited structural information. Here we report the crystal structure of the essential Mediator head module (seven subunits, with a mass of 223 kilodaltons) at a resolution of 4.3 angstroms. Our structure reveals three distinct domains, with the integrity of the complex centred on a bundle of ten helices from five different head subunits. An intricate pattern of interactions within this helical bundle ensures the stable assembly of the head subunits and provides the binding sites for general transcription factors and Pol II. Our structural and functional data suggest that the head module juxtaposes transcription factor IIH and the carboxy-terminal domain of the largest subunit of Pol II, thereby facilitating phosphorylation of the carboxy-terminal domain of Pol II. Our results reveal architectural principles underlying the role of Mediator in the regulation of gene expression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109712/" 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/PMC4109712/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Imasaki, Tsuyoshi -- Calero, Guillermo -- Cai, Gang -- Tsai, Kuang-Lei -- Yamada, Kentaro -- Cardelli, Francesco -- Erdjument-Bromage, Hediye -- Tempst, Paul -- Berger, Imre -- Kornberg, Guy Lorch -- Asturias, Francisco J -- Kornberg, Roger D -- Takagi, Yuichiro -- GM36659/GM/NIGMS NIH HHS/ -- P30 CA008748/CA/NCI NIH HHS/ -- P30 CA08748/CA/NCI NIH HHS/ -- R01 GM036659/GM/NIGMS NIH HHS/ -- R01 GM067167/GM/NIGMS NIH HHS/ -- R01GM67167/GM/NIGMS NIH HHS/ -- Y01 CO1020-11/CO/NCI NIH HHS/ -- Y01 GM1104-11/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21725323" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Mediator Complex/*chemistry/*metabolism ; Models, Molecular ; Phosphorylation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; RNA Polymerase II/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry/enzymology ; Structure-Activity Relationship ; Transcription Factor TFIIH/chemistry/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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  • 2
    Electronic Resource
    Electronic Resource
    The study of emitter thickness effect on the heterostructure emitter bipolar transistors (1993)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 74 (1993), S. 1398-1402 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: AlGaAs/GaAs heterostructure emitter bipolar transistors were grown with emitter thicknesses varied from 300 to 900 A(ring) and the emitter thickness effects on the current gain and offset voltage were studied. It was found that both the current gain and offset voltage are strongly dependent on the emitter thickness. The current gain decreases with increasing emitter thickness. For an emitter thickness smaller than 500 A(ring), the offset voltage decreases with increasing emitter thickness, but for an emitter thickness larger than 500 A(ring), the offset voltage stays at a nearly constant value. Offset voltage as low as 55 mV was obtained for an emitter thickness of 700 A(ring). This low offset voltage, mostly contributed by the geometric effect, indicates that the base-emitter junction is a homojunction. From the current gain and offset voltage considerations, the optimal emitter thickness was found to be about 300–500 A(ring).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.354898
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  • 3
    Electronic Resource
    Electronic Resource
    Influence of thin protective InAs layers on the optical quality of AlGaAs and quantum wells (1992)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 72 (1992), S. 2449-2452 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Influence of a thin protective but subsequently evaporated InAs layer on the regrowth of AlGaAs has been studied. It was found that although most of the InAs could be evaporated by thermal desorption, some would react with Al0.36Ga0.64As to form InAlGaAs. These InAlGaAs islands act as potential wells for carrier recombination and dominate the photoluminescence spectrum. Transmission electron microscopy photographs show that dislocations are formed near the islands. These defects are caused by lattice mismatch between AlGaAs and InAlGaAs. These islands and defects strongly affect the optical quality of surrounding Al0.36Ga0.64As and quantum wells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.351590
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  • 4
    Electronic Resource
    Electronic Resource
    Fundamental mode operation of high-power InGaAs/GaAs/AlGaAs laser arrays (1993)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 73 (1993), S. 4706-4708 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A new ridge waveguide laser array with stable fundamental mode operation has been fabricated. By introducing absorption regions in all the laser stripes except for the central one, the electric field distribution of the laser arrays and the modal gains of the array supermodes are changed, resulting in fundamental mode operation. The threshold current of an array with five elements is typically 40 mA and the maximum output power is higher than 150 mW. The single-lobed far-field pattern centered at 0° with full width at half maximum of 2° is obtained at 1.5 times of the threshold current (Ith).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.352741
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  • 5
    Electronic Resource
    Electronic Resource
    Compositional disordering of InGaAs/GaAs heterostructures by low-temperature-grown GaAs layers (1996)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 79 (1996), S. 664-670 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Compositional disordering of InGaAs/GaAs superlattices using a low-temperature-grown GaAs cap layer (LT-GaAs) by molecular beam epitaxy has been studied. The disordering of the superlattice was verified by photoluminescence and double-crystal x-ray rocking curve measurements. The Ga-vacancy-enhanced interdiffusion due to the presence of LT-GaAs was found to be the disordering mechanism. Diffusion equations and the Schrödinger's equation were solved numerically to obtain the composition profile and the transition energies in the disordered quantum well, respectively. The simulated energy shifts for samples under different annealing conditions agreed very well with the experimental results. The calculated effective diffusivity for the In–Ga interdiffusion has an activation energy of 1.63 eV, which is smaller than the activation energy 1.93 eV, for intrinsic interdiffusion. The diffusivity for the enhanced In–Ga interdiffusion due to the presence of LT-GaAs is about two orders of magnitude larger than the intrinsic In–Ga diffusivity. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.360810
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  • 6
    Electronic Resource
    Electronic Resource
    Kinetics of compositional disordering of AlGaAs/GaAs quantum wells induced by low-temperature grown GaAs (1995)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 77 (1995), S. 4302-4306 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Compositional disordering of GaAs/AlGaAs quantum wells due to the presence of low-temperature grown GaAs (by molecular beam epitaxy) was studied. Ga vacancy enhanced interdiffusion was found to be the mechanism underlying the observed intermixing. Diffusion equations were solved numerically to obtain the band profile after intermixing. The transition energies in the quantum wells under various annealing conditions were solved and agree very well with the observed photoluminescence emission peaks. The diffusivity of Ga vacancies and that of induced Al-Ga interdiffusion were obtained. The vacancy induced interdiffusion diffusivity was found to have an activation energy of 4.08 eV, which is smaller than the activation energy of interdiffusion diffusivity of normal temperature grown GaAs/AlGaAs heterostructures. This is a clear indication of enhanced interdiffusion due to the presence of low-temperature grown GaAs. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.359453
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  • 7
    Electronic Resource
    Electronic Resource
    Influence of oxygen on the performance of GaAs/AlGaAs quantum well infrared photodetectors (1994)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 76 (1994), S. 274-277 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The influence of oxygen on the performance of GaAs/AlGaAs quantum well infrared photodetectors (QWIP) has been studied. Photoluminescence and secondary ion mass spectroscopy were used to examine the relationship between the quality of AlGaAs and the oxygen content that were then correlated to the performance of QWIPs. It was found that oxygen is the dominant impurity in the GaAs/AlGaAs superlattice. Because oxygen atoms behave likes electron traps, which effectively reduce the carrier concentration in the material, both of the responsivity and the dark current of QWIP are reduced. The detectivities of QWIPs with lower oxygen concentrations are better than those with higher oxygen concentrations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.358439
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  • 8
    Electronic Resource
    Electronic Resource
    Magnetic properties of Fe clusters in NaY zeolite : The 6th joint magnetism and magnetic materials (MMM)-intermag conference (1994)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 76 (1994), S. 6567-6569 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Clusters of up to 28 Fe0 atoms have been introduced into the "supercages'' of NaY zeolite by ion exchange of Fe+2 for Na+ followed by reduction to Fe0 with solvated electrons and Na−1 ions. The temperature-dependent ac and dc susceptibilities, which exhibit Curie–Weiss behavior before reduction, change to something approximating superparamagnetic behavior afterwards. The blocking temperature, Tb shows a strong dependence on magnetic field but weak dependence on frequency. There is at best a very weak remanence and coercive field while the onset of irreversibility occurs at temperatures well above Tb. In addition, the real and imaginary parts of the ac susceptibility show essentially similar temperature dependence. Some of this anomalous behavior can be attributed to a distribution of particle sizes. To the best of our knowledge these preliminary data—while poorly understood—represent the first measurements of the temperature, frequency, and field dependence of the magnetic properties of such small clusters.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.358196
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  • 9
    Electronic Resource
    Electronic Resource
    Quantum well infrared photodetectors with bi-periodic grating couplers (1992)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 61 (1992), S. 2437-2439 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Multiple quantum well infrared photodetectors (QWIPs) with bi-periodic grating couplers have been demonstrated. The bi-periodic grating consists of two gratings with different periods. The response linewidths of such QWIPs are found to be much wider than those of conventional grating coupled QWIPs. By using bi-periodic gratings for coupling the radiation into QWIPs, the influence of variation of material and grating quality on the performance of QWIP can be largely eliminated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.108189
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  • 10
    Electronic Resource
    Electronic Resource
    Asymmetric dark current in quantum well infrared photodetectors (1994)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 64 (1994), S. 2436-2438 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Asymmetric dark current versus voltage characteristics in quantum well infrared photodetectors have been studied. A model based on asymmetrical potential barriers was proposed. The asymmetrical potential barriers, which are most likely due to the accumulation of oxygen impurities at one of the interfaces, cause the asymmetrical I-V characteristics. The height of the potential spike is found to increase with the Al content in the AlGaAs barriers. Calculations based on our model agree well with experimental results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.111591
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