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  • 1
    Publication Date: 2018-12-21
    Description: The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo–electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box–binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
    Keywords: Biochemistry, Online Only
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Keywords: human ; NEW-YORK ; PROTEIN ; USA ; microbiology ; biotechnology
    Type of Publication: Journal article published
    PubMed ID: 18259167
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  • 3
    Publication Date: 2018-10-03
    Description: Obesity is associated with cancer risk and its link with liver cancer is particularly strong. Obesity causes non-alcoholic fatty liver disease (NAFLD) that could progress to hepatocellular carcinoma (HCC). Chronic inflammation likely plays a key role. We carried out a bioassay in the high-fat diet (HFD)-fed C57BL/6J mice to provide insight into the mechanisms of obesity-related HCC by studying -OHPdG, a mutagenic DNA adduct derived from lipid peroxidation. In an 80-week bioassay, mice received a low-fat diet (LFD), high-fat diet (HFD), and HFD with 2% Theaphenon E (TE) (HFD+TE). HFD mice developed a 42% incidence of HCC and LFD mice a 16%. Remarkably, TE, a standardized green tea extract formulation, completely blocked HCC in HFD mice with a 0% incidence. -OHPdG measured in the hepatic DNA of mice fed HFD and HFD+TE showed its levels increased during the early stages of NAFLD in HFD mice and the increases were significantly suppressed by TE, correlating with the tumor data. Whole-exome sequencing showed an increased mutation load in the liver tumors of HFD mice with G〉A and G〉T as the predominant mutations, consistent with the report that -OHPdG induces G〉A and G〉T. Furthermore, the mutation loads were significantly reduced in HFD+TE mice, particularly G〉T, the most common mutation in human HCC. These results demonstrate in a relevant model of obesity-induced HCC that -OHPdG formation during fatty liver disease may be an initiating event for accumulated mutations that leads to HCC and this process can be effectively inhibited by TE. Cancer Prev Res; 11(10); 665–76. ©2018 AACR .
    Print ISSN: 1940-6207
    Electronic ISSN: 1940-6215
    Topics: Medicine
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  • 4
    Publication Date: 2018-06-09
    Description: Soft adaptable materials that change their shapes, volumes, and properties in response to changes under ambient conditions have important applications in tissue engineering, soft robotics, biosensing, and flexible displays. Upon water absorption, most existing soft materials, such as hydrogels, show a positive volume change, corresponding to a positive swelling. By contrast, the negative swelling represents a relatively unusual phenomenon that does not exist in most natural materials. The development of material systems capable of large or anisotropic negative swelling remains a challenge. We combine analytic modeling, finite element analyses, and experiments to design a type of soft mechanical metamaterials that can achieve large effective negative swelling ratios and tunable stress-strain curves, with desired isotropic/anisotropic features. This material system exploits horseshoe-shaped composite microstructures of hydrogel and passive materials as the building blocks, which extend into a periodic network, following the lattice constructions. The building block structure leverages a sandwiched configuration to convert the hydraulic swelling deformations of hydrogel into bending deformations, thereby resulting in an effective shrinkage (up to around –47% linear strain) of the entire network. By introducing spatially heterogeneous designs, we demonstrated a range of unusual, anisotropic swelling responses, including those with expansion in one direction and, simultaneously, shrinkage along the perpendicular direction. The design approach, as validated by experiments, allows the determination of tailored microstructure geometries to yield desired length/area changes. These design concepts expand the capabilities of existing soft materials and hold promising potential for applications in a diverse range of areas.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 5
    Publication Date: 2016-05-20
    Description: In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Yuan -- Yan, Chunli -- Fang, Jie -- Inouye, Carla -- Tjian, Robert -- Ivanov, Ivaylo -- Nogales, Eva -- GM110387/GM/NIGMS NIH HHS/ -- GM63072/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2016 May 11;533(7603):359-65. doi: 10.1038/nature17970.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA. ; Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA. ; Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA. ; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA. ; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27193682" target="_blank"〉PubMed〈/a〉
    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: 2016-04-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Louder, Robert K -- He, Yuan -- Lopez-Blanco, Jose Ramon -- Fang, Jie -- Chacon, Pablo -- Nogales, Eva -- Nature. 2016 Apr 20. doi: 10.1038/nature17984.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27096372" target="_blank"〉PubMed〈/a〉
    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: 2016-03-24
    Description: The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856295/" 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/PMC4856295/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Louder, Robert K -- He, Yuan -- Lopez-Blanco, Jose Ramon -- Fang, Jie -- Chacon, Pablo -- Nogales, Eva -- GM008295/GM/NIGMS NIH HHS/ -- GM63072/GM/NIGMS NIH HHS/ -- R01 GM063072/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2016 Mar 31;531(7596):604-9. doi: 10.1038/nature17394. Epub 2016 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biophysics Graduate Group, University of California, Berkeley, California 94720, USA. ; QB3 Institute, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. ; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; Department of Biological Physical Chemistry, Rocasolano Physical Chemistry Institute, CSIC, Serrano 119, Madrid 28006, Spain. ; Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27007846" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; DNA/chemistry/metabolism/ultrastructure ; Humans ; Models, Molecular ; Promoter Regions, Genetic/*genetics ; Protein Binding ; Substrate Specificity ; TATA Box/genetics ; TATA-Binding Protein Associated Factors/chemistry/metabolism/ultrastructure ; TATA-Box Binding Protein/chemistry/metabolism/ultrastructure ; Transcription Factor TFIIA/chemistry/metabolism/ultrastructure ; Transcription Factor TFIID/chemistry/*metabolism/*ultrastructure ; *Transcription Initiation, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2011-07-19
    Description: The terrestrial carbon sink has been large in recent decades, but its size and location remain uncertain. Using forest inventory data and long-term ecosystem carbon studies, we estimate a total forest sink of 2.4 +/- 0.4 petagrams of carbon per year (Pg C year(-1)) globally for 1990 to 2007. We also estimate a source of 1.3 +/- 0.7 Pg C year(-1) from tropical land-use change, consisting of a gross tropical deforestation emission of 2.9 +/- 0.5 Pg C year(-1) partially compensated by a carbon sink in tropical forest regrowth of 1.6 +/- 0.5 Pg C year(-1). Together, the fluxes comprise a net global forest sink of 1.1 +/- 0.8 Pg C year(-1), with tropical estimates having the largest uncertainties. Our total forest sink estimate is equivalent in magnitude to the terrestrial sink deduced from fossil fuel emissions and land-use change sources minus ocean and atmospheric sinks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Yude -- Birdsey, Richard A -- Fang, Jingyun -- Houghton, Richard -- Kauppi, Pekka E -- Kurz, Werner A -- Phillips, Oliver L -- Shvidenko, Anatoly -- Lewis, Simon L -- Canadell, Josep G -- Ciais, Philippe -- Jackson, Robert B -- Pacala, Stephen W -- McGuire, A David -- Piao, Shilong -- Rautiainen, Aapo -- Sitch, Stephen -- Hayes, Daniel -- New York, N.Y. -- Science. 2011 Aug 19;333(6045):988-93. doi: 10.1126/science.1201609. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Agriculture Forest Service, Newtown Square, PA 19073, USA. ypan@fs.fed.us〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764754" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; Biomass ; Carbon/analysis ; Carbon Dioxide/analysis ; *Carbon Sequestration ; Climate Change ; Conservation of Natural Resources ; *Ecosystem ; *Trees ; Tropical Climate
    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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  • 9
    Publication Date: 2013-03-01
    Description: Eukaryotic transcription initiation requires the assembly of general transcription factors into a pre-initiation complex that ensures the accurate loading of RNA polymerase II (Pol II) at the transcription start site. The molecular mechanism and function of this assembly have remained elusive due to lack of structural information. Here we have used an in vitro reconstituted system to study the stepwise assembly of human TBP, TFIIA, TFIIB, Pol II, TFIIF, TFIIE and TFIIH onto promoter DNA using cryo-electron microscopy. Our structural analyses provide pseudo-atomic models at various stages of transcription initiation that illuminate critical molecular interactions, including how TFIIF engages Pol II and promoter DNA to stabilize both the closed pre-initiation complex and the open-promoter complex, and to regulate start--initiation complexes, combined with the localization of the TFIIH helicases XPD and XPB, support a DNA translocation model of XPB and explain its essential role in promoter opening.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3612373/" 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/PMC3612373/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Yuan -- Fang, Jie -- Taatjes, Dylan J -- Nogales, Eva -- CA127364/CA/NCI NIH HHS/ -- GM63072/GM/NIGMS NIH HHS/ -- R01 CA127364/CA/NCI NIH HHS/ -- R01 GM063072/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Mar 28;495(7442):481-6. doi: 10.1038/nature11991. Epub 2013 Feb 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23446344" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cryoelectron Microscopy ; DNA/chemistry/genetics/metabolism ; DNA Helicases/chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Promoter Regions, Genetic/*genetics ; Protein Conformation ; RNA Polymerase II/*chemistry/metabolism/*ultrastructure ; TATA-Box Binding Protein/chemistry/metabolism ; Transcription Factor TFIIH/chemistry/metabolism ; Transcription Factors, TFII/*chemistry/metabolism/*ultrastructure ; Transcription Initiation Site ; Transcription Initiation, Genetic/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2018-03-06
    Description: Weyl points are the crossings of linearly dispersing energy bands of three-dimensional crystals, providing the opportunity to explore a variety of intriguing phenomena such as topologically protected surface states and chiral anomalies. However, the lack of an ideal Weyl system in which the Weyl points all exist at the same energy and are separated from any other bands poses a serious limitation to the further development of Weyl physics and potential applications. By experimentally characterizing a microwave photonic crystal of saddle-shaped metallic coils, we observed ideal Weyl points that are related to each other through symmetry operations. Topological surface states exhibiting helicoidal structure have also been demonstrated. Our system provides a photonic platform for exploring ideal Weyl systems and developing possible topological devices.
    Keywords: Physics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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