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  • 1
    Publication Date: 2013-09-13
    Description: During DNA repair by homologous recombination (HR), DNA synthesis copies information from a template DNA molecule. Multiple DNA polymerases have been implicated in repair-specific DNA synthesis, but it has remained unclear whether a DNA helicase is involved in this reaction. A good candidate DNA helicase is Pif1, an evolutionarily conserved helicase in Saccharomyces cerevisiae important for break-induced replication (BIR) as well as HR-dependent telomere maintenance in the absence of telomerase found in 10-15% of all cancers. Pif1 has a role in DNA synthesis across hard-to-replicate sites and in lagging-strand synthesis with polymerase delta (Poldelta). Here we provide evidence that Pif1 stimulates DNA synthesis during BIR and crossover recombination. The initial steps of BIR occur normally in Pif1-deficient cells, but Poldelta recruitment and DNA synthesis are decreased, resulting in premature resolution of DNA intermediates into half-crossovers. Purified Pif1 protein strongly stimulates Poldelta-mediated DNA synthesis from a D-loop made by the Rad51 recombinase. Notably, Pif1 liberates the newly synthesized strand to prevent the accumulation of topological constraint and to facilitate extensive DNA synthesis via the establishment of a migrating D-loop structure. Our results uncover a novel function of Pif1 and provide insights into the mechanism of HR.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915060/" 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/PMC3915060/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, Marenda A -- Kwon, YoungHo -- Xu, Yuanyuan -- Chung, Woo-Hyun -- Chi, Peter -- Niu, Hengyao -- Mayle, Ryan -- Chen, Xuefeng -- Malkova, Anna -- Sung, Patrick -- Ira, Grzegorz -- ES007061/ES/NIEHS NIH HHS/ -- ES015632/ES/NIEHS NIH HHS/ -- GM057814/GM/NIGMS NIH HHS/ -- GM080600/GM/NIGMS NIH HHS/ -- GM084242/GM/NIGMS NIH HHS/ -- R01 ES007061/ES/NIEHS NIH HHS/ -- R01 ES015632/ES/NIEHS NIH HHS/ -- R01 GM057814/GM/NIGMS NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01 GM084242/GM/NIGMS NIH HHS/ -- R03 ES016434/ES/NIEHS NIH HHS/ -- T32 GM008307/GM/NIGMS NIH HHS/ -- T32GM07526-34/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Oct 17;502(7471):393-6. doi: 10.1038/nature12585. Epub 2013 Sep 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baylor College of Medicine, Department of Molecular & Human Genetics, One Baylor Plaza, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24025768" target="_blank"〉PubMed〈/a〉
    Keywords: *Crossing Over, Genetic ; DNA Helicases/deficiency/genetics/*metabolism ; DNA Polymerase III/*metabolism ; DNA Repair ; *DNA Replication ; DNA, Fungal/*biosynthesis/chemistry/metabolism ; Nucleic Acid Conformation ; Rad51 Recombinase/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-08-15
    Description: Most spontaneous DNA double-strand breaks (DSBs) result from replication-fork breakage. Break-induced replication (BIR), a genome rearrangement-prone repair mechanism that requires the Pol32/POLD3 subunit of eukaryotic DNA Poldelta, was proposed to repair broken forks, but how genome destabilization is avoided was unknown. We show that broken fork repair initially uses error-prone Pol32-dependent synthesis, but that mutagenic synthesis is limited to within a few kilobases from the break by Mus81 endonuclease and a converging fork. Mus81 suppresses template switches between both homologous sequences and diverged human Alu repetitive elements, highlighting its importance for stability of highly repetitive genomes. We propose that lack of a timely converging fork or Mus81 may propel genome instability observed in cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayle, Ryan -- Campbell, Ian M -- Beck, Christine R -- Yu, Yang -- Wilson, Marenda -- Shaw, Chad A -- Bjergbaek, Lotte -- Lupski, James R -- Ira, Grzegorz -- F31 NS083159/NS/NINDS NIH HHS/ -- GM080600/GM/NIGMS NIH HHS/ -- HG006542/HG/NHGRI NIH HHS/ -- NS058529/NS/NINDS NIH HHS/ -- NS083159/NS/NINDS NIH HHS/ -- R01 GM080600/GM/NIGMS NIH HHS/ -- R01 NS058529/NS/NINDS NIH HHS/ -- U54 HG006542/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2015 Aug 14;349(6249):742-7. doi: 10.1126/science.aaa8391.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. ; Department of Molecular Biology and Genetics, University of Aarhus, Aarhus 8000, Denmark. ; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Department of Pediatrics, and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. Texas Children's Hospital, Houston, TX 77030, USA. ; Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. gira@bcm.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26273056" target="_blank"〉PubMed〈/a〉
    Keywords: Alu Elements ; Base Sequence ; *DNA Breaks, Double-Stranded ; DNA Repair/*genetics ; DNA Replication/*genetics ; DNA-Binding Proteins/genetics/*metabolism ; DNA-Directed DNA Polymerase/metabolism ; Endonucleases/genetics/*metabolism ; *Genomic Instability ; Humans ; Molecular Sequence Data ; Neoplasms/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/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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  • 3
    Publication Date: 2014-01-21
    Description: We present an integrated palaeoecological and archaeobotanical study of pre-Columbian raised-field agriculture in the Llanos de Moxos , a vast seasonally inundated forest–savanna mosaic in the Bolivian Amazon. Phytoliths from excavated raised-field soil units, together with pollen and charcoal in sediment cores from two oxbow lakes, were analysed to provide a history of land use and agriculture at the El Cerro raised-field site. The construction of raised fields involved the removal of savanna trees, and gallery forest was cleared from the area by ad 310. Despite the low fertility of Llanos de Moxos soils, we determined that pre-Columbian raised-field agriculture sufficiently improved soil conditions for maize cultivation. Fire was used as a common management practice until ad 1300, at which point, the land-use strategy shifted towards less frequent burning of savannas and raised fields. Alongside a reduction in the use of fire, sweet potato cultivation and the exploitation of Inga fruits formed part of a mixed resource strategy from ad 1300 to 1450. The pre-Columbian impact on the landscape began to lessen around ad 1450, as shown by an increase in savanna trees and gallery forest. Although agriculture at the site began to decline prior to European arrival, the abandonment of raised fields was protracted, with evidence of sweet potato cultivation occurring as late as ad 1800.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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  • 4
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 470 (1986), S. 0 
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters B 219 (1989), S. 515-520 
    ISSN: 0370-2693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters B 203 (1988), S. 188-196 
    ISSN: 0370-2693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters B 317 (1993), S. 119-124 
    ISSN: 0370-2693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Applied physics 58 (1994), S. 35-43 
    ISSN: 1432-0649
    Keywords: 02.00 ; 32.00 ; 42.55.Vc
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract This paper describes the multi-dimensional Non-Local Thermodynamic Equilibrium (NLTE) simulation code GLF. GLF simulates those physical processes needed for modeling X-ray lasers: atomic kinetics, radiation transport, hydrodynamics and basic laser-plasma interactions. GLF is constructed to be modular, portable and efficient. This paper concentrates on the physical formulations and numerical methods used in GLF.
    Type of Medium: Electronic Resource
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  • 9
    Publication Date: 1994-01-01
    Print ISSN: 0946-2171
    Electronic ISSN: 1432-0649
    Topics: Physics
    Published by Springer
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  • 10
    Publication Date: 1986-03-01
    Print ISSN: 0004-637X
    Electronic ISSN: 1538-4357
    Topics: Physics
    Published by Institute of Physics
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