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  • 1
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    Structure of promoter-bound TFIID and model of human pre-initiation complex assembly (2016)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 2
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    Corrigendum: Structure of promoter-bound TFIID and model of human pre-initiation complex assembly (2016)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 3
    Electronic Resource
    Electronic Resource
    The role of soil organic matter in sustaining soil fertility (1994)
    [s.l.] : Nature Publishing Group
    Nature 371 (1994), S. 783-785 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The contribution to soil fertility from the mineralization of organic matter (OM) can be estimated from budgets of carbon and nutrients during agricultural use. A more detailed picture of the mineralization process can be obtained when coarse and fine, mineral-associated ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/371783a0
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  • 4
    Electronic Resource
    Electronic Resource
    Description of a new artificial diet for rearing ant colonies asIridomyrmex humilis, Monomorium pharaonis andWasmannia auropunctata (Hymenoptera; Formicidae) (1989)
    Springer
    Insectes sociaux 36 (1989), S. 348-352 
    Details
    ISSN: 1420-9098
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Description / Table of Contents: Resume Nous présentons la recette d'une nourriture artificielle élaborée pour élever des fourmis en laboratoire. Cette nourriture ne se dessèche pas et s'est avérée adéquate pour l'élevage de plusieur espèces telles queIridomyrmex humilis, Monomorium pharaonis etWasmannia auropunctata. Des sexués mâles et femelles ont été régulièrement produits dans ces sociétés.
    Notes: Summary A diet which does not desiccate was developed for rearing various ant species. this diet was found to be very attractive forIridomyrmex humilis. Monomorium pharaonis andWasmannia auropunctata in which species it permitted the rearing of colonies for long periods and the regular production of sexuals.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02224886
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  • 5
    Electronic Resource
    Electronic Resource
    Phosphorus and nitrogen status in soils and vegetation along a toposequence of dystrophic rainforests on the upper Rio Negro (1994)
    Springer
    Oecologia 99 (1994), S. 145-150 
    Details
    ISSN: 1432-1939
    Keywords: Amazon rainforests ; Nutrient cycling ; Soil nutrient status ; Toposequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Amazon forests along a toposequence at San Carlos de Rio Negro (Venezuela) show distinct nutrient limitations depending on slope position. Soils were collected by genetic horizons and analysed to provide information on the relationships between soil P and N status and the nutrition of natural forest at three locations along the toposequence. The upper-slope tierra firme sites had total P concentrations between 100 and 200 μg g−1 in the mineral soil fines and between 700 and 1100 μg g−1 in lateritic nodules. Hyphae were seen to explore lateritic nodules and may contribute to P nutrition. Total P in the mineral soil of the lower slope ranged from only 3 to 130 μg g−1. In both the organic mats of the tierra firme and the humic horizon at the lower-slope tall Amazon caatinga site, 50–60% of the P was in inorganic forms, which, in the absence of P-fixing mineral soil, maintain high levels of plant-available P. As a result, the litter mats and humic horizon accounted for over 70% of the total available P in these soils. The proportion of available P increased, and P sorption decreased, downslope, supporting ecological studies which found that tall Amazon caatinga was least P-limited. Soil N and C levels show a maximum at the mid-slope and a minimum at the lower slope. Distributions of biomass C, N and P closely follow those of soil C, N and available (but not total) P along the slope.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00317095
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  • 6
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    Conformational flexibility of bacterial RNA polymerase (2002)
    National Academy of Sciences
    Details
    Publication Date: 2002-03-19
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    FRODOCK 2.0: fast protein-protein docking server (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-30
    Description: : The prediction of protein–protein complexes from the structures of unbound components is a challenging and powerful strategy to decipher the mechanism of many essential biological processes. We present a user-friendly protein–protein docking server based on an improved version of FRODOCK that includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them against experimental distance constraints. The competitive success rates and efficiency achieved allow the retrieval of reliable potential protein–protein binding conformations that can be further refined with more computationally demanding strategies. Availability and Implementation: The server is free and open to all users with no login requirement at http://frodock.chaconlab.org Contact: pablo@chaconlab.org Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    RCD+: Fast loop modeling server (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service ( http://rcd.chaconlab.org ) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ~10-fold faster.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Cryo-EM structure of PRC1 bound to the microtubule [Biophysics and Computational Biology] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-08-24
    Description: Proteins that associate with microtubules (MTs) are crucial to generate MT arrays and establish different cellular architectures. One example is PRC1 (protein regulator of cytokinesis 1), which cross-links antiparallel MTs and is essential for the completion of mitosis and cytokinesis. Here we describe a 4-Å–resolution cryo-EM structure of monomeric PRC1...
    Keywords: Inaugural Articles
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Dissipative dynamics of a particle in a vibrating periodic potential: Chaos and control (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-12-24
    Description: Author(s): R. Chacón, P. J. Martínez, and J. A. Martínez The dissipative chaotic dynamics of a particle subjected to a horizontally vibrating periodic potential is characterized theoretically and confirmed numerically in the case of an external chaos-controlling periodic excitation also acting on the particle. Theoretical predictions concerning the chaoti… [Phys. Rev. E 92, 062921] Published Wed Dec 23, 2015
    Keywords: Nonlinear Dynamics and Chaos
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
    Published by American Physical Society (APS)
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