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  • Humans  (2)
  • 405; Center for Marine Environmental Sciences; Comment; DEPTH, sediment/rock; Gas chromatography; GC; GeoB13824-1; Gravity corer; M78/3A; MARUM; Meteor (1986); Methane  (1)
  • Atomic and molecular structure and dynamics  (1)
  • 2015-2019  (4)
  • 1950-1954
  • 2016  (4)
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Keywords
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  • 2015-2019  (4)
  • 1950-1954
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  • 1
    Publication Date: 2024-02-02
    Keywords: 405; Center for Marine Environmental Sciences; Comment; DEPTH, sediment/rock; Gas chromatography; GC; GeoB13824-1; Gravity corer; M78/3A; MARUM; Meteor (1986); Methane
    Type: Dataset
    Format: text/tab-separated-values, 42 data points
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  • 2
    Publication Date: 2016-06-03
    Description: Author(s): Lin Pan and Donald R. Beck This study reinterprets an earlier experimental photoelectron kinetic energy spectrum of the negative ion of lanthanum [A. M. Covington, D. Calabrese, J. S. Thompson, and T. J. Kvale, J. Phys. B 31 , L855 (1998) ] by carrying out relativistic configuration interaction (RCI) photodetachment calculation… [Phys. Rev. A 93, 062501] Published Wed Jun 01, 2016
    Keywords: Atomic and molecular structure and dynamics
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 3
    Publication Date: 2016-04-16
    Description: Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kosinski, Jan -- Mosalaganti, Shyamal -- von Appen, Alexander -- Teimer, Roman -- DiGuilio, Amanda L -- Wan, William -- Bui, Khanh Huy -- Hagen, Wim J H -- Briggs, John A G -- Glavy, Joseph S -- Hurt, Ed -- Beck, Martin -- 1R21AG047433-01/AG/NIA NIH HHS/ -- R21 AG047433/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 15;352(6283):363-5. doi: 10.1126/science.aaf0643.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. ; Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany. ; Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA. ; Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada. ; Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27081072" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Cryoelectron Microscopy ; Electron Microscope Tomography ; HeLa Cells ; Humans ; Mass Spectrometry ; Models, Molecular ; Nuclear Matrix/metabolism/ultrastructure ; Nuclear Pore/*metabolism/*ultrastructure ; Nuclear Pore Complex Proteins/chemistry/genetics/*metabolism
    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
    Publication Date: 2016-04-15
    Description: Promoters are DNA sequences that have an essential role in controlling gene expression. While recent whole cancer genome analyses have identified numerous hotspots of somatic point mutations within promoters, many have not yet been shown to perturb gene expression or drive cancer development. As such, positive selection alone may not adequately explain the frequency of promoter point mutations in cancer genomes. Here we show that increased mutation density at gene promoters can be linked to promoter activity and differential nucleotide excision repair (NER). By analysing 1,161 human cancer genomes across 14 cancer types, we find evidence for increased local density of somatic point mutations within the centres of DNase I-hypersensitive sites (DHSs) in gene promoters. Mutated DHSs were strongly associated with transcription initiation activity, in which active promoters but not enhancers of equal DNase I hypersensitivity were most mutated relative to their flanking regions. Notably, analysis of genome-wide maps of NER shows that NER is impaired within the DHS centre of active gene promoters, while XPC-deficient skin cancers do not show increased promoter mutation density, pinpointing differential NER as the underlying cause of these mutation hotspots. Consistent with this finding, we observe that melanomas with an ultraviolet-induced DNA damage mutation signature show greatest enrichment of promoter mutations, whereas cancers that are not highly dependent on NER, such as colon cancer, show no sign of such enrichment. Taken together, our analysis has uncovered the presence of a previously unknown mechanism linking transcription initiation and NER as a major contributor of somatic point mutation hotspots at active gene promoters in cancer genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perera, Dilmi -- Poulos, Rebecca C -- Shah, Anushi -- Beck, Dominik -- Pimanda, John E -- Wong, Jason W H -- England -- Nature. 2016 Apr 14;532(7598):259-63. doi: 10.1038/nature17437.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Australia, Sydney 2052, Australia. ; Department of Haematology, Prince of Wales Hospital, Sydney 2031, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27075100" target="_blank"〉PubMed〈/a〉
    Keywords: Colonic Neoplasms/genetics ; DNA Damage/genetics ; DNA Repair/*genetics/radiation effects ; Deoxyribonuclease I/metabolism ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Genome, Human/*genetics ; Humans ; Lung Neoplasms/genetics ; Melanoma/genetics ; Mutagenesis/*genetics ; *Mutation Rate ; Neoplasms/*genetics ; Point Mutation/genetics ; Promoter Regions, Genetic/*genetics ; *Transcription Initiation, Genetic ; Ultraviolet Rays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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