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  • 1
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    The oldest articulated osteichthyan reveals mosaic gnathostome characters (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-03-28
    Description: The evolutionary history of osteichthyans (bony fishes plus tetrapods) extends back to the Ludlow epoch of the Silurian period. However, these Silurian forms have been documented exclusively by fragmentary fossils. Here we report the discovery of an exceptionally preserved primitive fish from the Ludlow of Yunnan, China, that represents the oldest near-complete gnathostome (jawed vertebrate). The postcranial skeleton of this fish includes a primitive pectoral girdle and median fin spine as in non-osteichthyan gnathostomes, but a derived macromeric squamation as in crown osteichthyans, and substantiates the unexpected mix of postcranial features in basal sarcopterygians, previously restored from the disarticulated remains of Psarolepis. As the oldest articulated sarcopterygian, the new taxon offers insights into the origin and early divergence of osteichthyans, and indicates that the minimum date for the actinopterygian-sarcopterygian split was no later than 419 million years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Min -- Zhao, Wenjin -- Jia, Liantao -- Lu, Jing -- Qiao, Tuo -- Qu, Qingming -- England -- Nature. 2009 Mar 26;458(7237):469-74. doi: 10.1038/nature07855.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences, PO Box 643, Beijing 100044, China. zhumin@ivpp.ac.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325627" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Fishes/*anatomy & histology/classification ; *Fossils ; Geography ; *Phylogeny ; Time Factors
    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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    SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-17
    Description: Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamason, Rebecca L -- Mohideen, Manzoor-Ali P K -- Mest, Jason R -- Wong, Andrew C -- Norton, Heather L -- Aros, Michele C -- Jurynec, Michael J -- Mao, Xianyun -- Humphreville, Vanessa R -- Humbert, Jasper E -- Sinha, Soniya -- Moore, Jessica L -- Jagadeeswaran, Pudur -- Zhao, Wei -- Ning, Gang -- Makalowska, Izabela -- McKeigue, Paul M -- O'donnell, David -- Kittles, Rick -- Parra, Esteban J -- Mangini, Nancy J -- Grunwald, David J -- Shriver, Mark D -- Canfield, Victor A -- Cheng, Keith C -- CA73935/CA/NCI NIH HHS/ -- EY11308/EY/NEI NIH HHS/ -- HD37572/HD/NICHD NIH HHS/ -- HD40179/HD/NICHD NIH HHS/ -- HG002154/HG/NHGRI NIH HHS/ -- HL077910/HL/NHLBI NIH HHS/ -- RR017441/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2005 Dec 16;310(5755):1782-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jake Gittlen Cancer Research Foundation, Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16357253" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/genetics ; African Continental Ancestry Group/genetics ; Alanine/genetics ; Alleles ; Amino Acid Sequence ; Animals ; Antiporters/chemistry/*genetics/physiology ; Asian Continental Ancestry Group/genetics ; Biological Evolution ; Calcium/metabolism ; European Continental Ancestry Group/genetics ; Gene Frequency ; Genes ; Genetic Variation ; Haplotypes ; Heterozygote ; Humans ; Ion Transport ; Melanins/analysis ; Melanosomes/chemistry/ultrastructure ; Mice ; Molecular Sequence Data ; Multifactorial Inheritance ; Mutation ; Pigment Epithelium of Eye/chemistry/ultrastructure ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Skin Pigmentation/*genetics ; Threonine/genetics ; Zebrafish/embryology/*genetics/metabolism ; Zebrafish Proteins/chemistry/*genetics/physiology
    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
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    A Silurian placoderm with osteichthyan-like marginal jaw bones (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-09-27
    Description: The gnathostome (jawed vertebrate) crown group comprises two extant clades with contrasting character complements. Notably, Chondrichthyes (cartilaginous fish) lack the large dermal bones that characterize Osteichthyes (bony fish and tetrapods). The polarities of these differences, and the morphology of the last common ancestor of crown gnathostomes, are the subject of continuing debate. Here we describe a three-dimensionally preserved 419-million-year-old placoderm fish from the Silurian of China that represents the first stem gnathostome with dermal marginal jaw bones (premaxilla, maxilla and dentary), features previously restricted to Osteichthyes. A phylogenetic analysis places the new form near the top of the gnathostome stem group but does not fully resolve its relationships to other placoderms. The analysis also assigns all acanthodians to the chondrichthyan stem group. These results suggest that the last common ancestor of Chondrichthyes and Osteichthyes had a macromeric dermal skeleton, and provide a new framework for studying crown gnathostome divergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhu, Min -- Yu, Xiaobo -- Ahlberg, Per Erik -- Choo, Brian -- Lu, Jing -- Qiao, Tuo -- Qu, Qingming -- Zhao, Wenjin -- Jia, Liantao -- Blom, Henning -- Zhu, You'an -- England -- Nature. 2013 Oct 10;502(7470):188-93. doi: 10.1038/nature12617. Epub 2013 Sep 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. zhumin@ivpp.ac.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24067611" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; Fishes/*anatomy & histology/*classification ; *Fossils ; Jaw/*anatomy & histology ; *Phylogeny ; Species Specificity
    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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  • 4
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    Genome sequencing reveals insights into physiology and longevity of the naked mole rat (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-14
    Description: The naked mole rat (Heterocephalus glaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal. Although it is the size of a mouse, its maximum lifespan exceeds 30 years, making this animal the longest-living rodent. Naked mole rats show negligible senescence, no age-related increase in mortality, and high fecundity until death. In addition to delayed ageing, they are resistant to both spontaneous cancer and experimentally induced tumorigenesis. Naked mole rats pose a challenge to the theories that link ageing, cancer and redox homeostasis. Although characterized by significant oxidative stress, the naked mole rat proteome does not show age-related susceptibility to oxidative damage or increased ubiquitination. Naked mole rats naturally reside in large colonies with a single breeding female, the 'queen', who suppresses the sexual maturity of her subordinates. They also live in full darkness, at low oxygen and high carbon dioxide concentrations, and are unable to sustain thermogenesis nor feel certain types of pain. Here we report the sequencing and analysis of the naked mole rat genome, which reveals unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness and insensitivity to low oxygen, and altered visual function, circadian rythms and taste sensing. This information provides insights into the naked mole rat's exceptional longevity and ability to live in hostile conditions, in the dark and at low oxygen. The extreme traits of the naked mole rat, together with the reported genome and transcriptome information, offer opportunities for understanding ageing and advancing other areas of biological and biomedical research.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319411/" 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/PMC3319411/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Eun Bae -- Fang, Xiaodong -- Fushan, Alexey A -- Huang, Zhiyong -- Lobanov, Alexei V -- Han, Lijuan -- Marino, Stefano M -- Sun, Xiaoqing -- Turanov, Anton A -- Yang, Pengcheng -- Yim, Sun Hee -- Zhao, Xiang -- Kasaikina, Marina V -- Stoletzki, Nina -- Peng, Chunfang -- Polak, Paz -- Xiong, Zhiqiang -- Kiezun, Adam -- Zhu, Yabing -- Chen, Yuanxin -- Kryukov, Gregory V -- Zhang, Qiang -- Peshkin, Leonid -- Yang, Lan -- Bronson, Roderick T -- Buffenstein, Rochelle -- Wang, Bo -- Han, Changlei -- Li, Qiye -- Chen, Li -- Zhao, Wei -- Sunyaev, Shamil R -- Park, Thomas J -- Zhang, Guojie -- Wang, Jun -- Gladyshev, Vadim N -- AG021518/AG/NIA NIH HHS/ -- AG038004/AG/NIA NIH HHS/ -- CA080946/CA/NCI NIH HHS/ -- R01 AG021518/AG/NIA NIH HHS/ -- R01 AG021518-10/AG/NIA NIH HHS/ -- R01 AG038004/AG/NIA NIH HHS/ -- R01 AG038004-02/AG/NIA NIH HHS/ -- R01 CA080946/CA/NCI NIH HHS/ -- R01 CA080946-11/CA/NCI NIH HHS/ -- England -- Nature. 2011 Oct 12;479(7372):223-7. doi: 10.1038/nature10533.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioinspired Science, Ewha Womans University, Seoul, 120-750, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993625" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Aging/genetics ; Amino Acid Sequence ; Animals ; Body Temperature Regulation/genetics ; Carbon Dioxide/analysis/metabolism ; Circadian Rhythm/genetics ; Darkness ; Genes/genetics ; Genome/*genetics ; Genomic Instability/genetics ; Genomics ; Humans ; Ion Channels/genetics ; Longevity/*genetics/physiology ; Male ; Mitochondrial Proteins/genetics ; Mole Rats/*genetics/*physiology ; Molecular Sequence Data ; Mutagenesis/genetics ; Oxygen/analysis/metabolism ; Taste/genetics ; Transcriptome/genetics ; Visual Perception/genetics
    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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  • 5
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    Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-20
    Description: Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown. We demonstrated that central metabolism enzymes in Salmonella were acetylated extensively and differentially in response to different carbon sources, concomitantly with changes in cell growth and metabolic flux. The relative activities of key enzymes controlling the direction of glycolysis versus gluconeogenesis and the branching between citrate cycle and glyoxylate bypass were all regulated by acetylation. This modulation is mainly controlled by a pair of lysine acetyltransferase and deacetylase, whose expressions are coordinated with growth status. Reversible acetylation of metabolic enzymes ensure that cells respond environmental changes via promptly sensing cellular energy status and flexibly altering reaction rates or directions. It represents a metabolic regulatory mechanism conserved from bacteria to mammals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183141/" 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/PMC4183141/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Qijun -- Zhang, Yakun -- Yang, Chen -- Xiong, Hui -- Lin, Yan -- Yao, Jun -- Li, Hong -- Xie, Lu -- Zhao, Wei -- Yao, Yufeng -- Ning, Zhi-Bin -- Zeng, Rong -- Xiong, Yue -- Guan, Kun-Liang -- Zhao, Shimin -- Zhao, Guo-Ping -- R01 CA068377/CA/NCI NIH HHS/ -- R01 CA163834/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2010 Feb 19;327(5968):1004-7. doi: 10.1126/science.1179687.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20167787" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/chemistry/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*metabolism ; Citric Acid/*metabolism ; Energy Metabolism ; Enzymes/*metabolism ; Gene Expression Regulation, Bacterial ; *Gluconeogenesis ; Glucose/*metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; *Glycolysis ; Group III Histone Deacetylases/genetics/metabolism ; Isocitrate Lyase/metabolism ; Lysine/metabolism ; Metabolic Networks and Pathways ; Multienzyme Complexes/metabolism ; Mutation ; Protein Processing, Post-Translational ; Protein-Serine-Threonine Kinases/metabolism ; Recombinant Proteins/metabolism ; Salmonella typhimurium/enzymology/genetics/growth & development/*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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  • 6
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    Comparative analysis of bat genomes provides insight into the evolution of flight and immunity (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-22
    Description: Bats are the only mammals capable of sustained flight and are notorious reservoir hosts for some of the world's most highly pathogenic viruses, including Nipah, Hendra, Ebola, and severe acute respiratory syndrome (SARS). To identify genetic changes associated with the development of bat-specific traits, we performed whole-genome sequencing and comparative analyses of two distantly related species, fruit bat Pteropus alecto and insectivorous bat Myotis davidii. We discovered an unexpected concentration of positively selected genes in the DNA damage checkpoint and nuclear factor kappaB pathways that may be related to the origin of flight, as well as expansion and contraction of important gene families. Comparison of bat genomes with other mammalian species has provided new insights into bat biology and evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guojie -- Cowled, Christopher -- Shi, Zhengli -- Huang, Zhiyong -- Bishop-Lilly, Kimberly A -- Fang, Xiaodong -- Wynne, James W -- Xiong, Zhiqiang -- Baker, Michelle L -- Zhao, Wei -- Tachedjian, Mary -- Zhu, Yabing -- Zhou, Peng -- Jiang, Xuanting -- Ng, Justin -- Yang, Lan -- Wu, Lijun -- Xiao, Jin -- Feng, Yue -- Chen, Yuanxin -- Sun, Xiaoqing -- Zhang, Yong -- Marsh, Glenn A -- Crameri, Gary -- Broder, Christopher C -- Frey, Kenneth G -- Wang, Lin-Fa -- Wang, Jun -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):456-60. doi: 10.1126/science.1230835. Epub 2012 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Shenzhen, 518083, China. zhanggj@genomics.org.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258410" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Biological Evolution ; Chiroptera/*genetics/immunology/physiology ; DNA Damage/genetics ; DNA Repair/genetics ; Echolocation ; Evolution, Molecular ; *Flight, Animal ; Genetic Speciation ; *Genome ; Hibernation/genetics ; High-Throughput Nucleotide Sequencing ; Immunity, Innate/*genetics ; Male ; Molecular Sequence Data ; Phylogeny ; Reactive Oxygen Species/metabolism ; Selection, Genetic ; *Sequence Analysis, DNA ; Species Specificity
    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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  • 7
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    DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-09-01
    Description: DNA strand exchange plays a central role in genetic recombination across all kingdoms of life, but the physical basis for these reactions remains poorly defined. Using single-molecule imaging, we found that bacterial RecA and eukaryotic Rad51 and Dmc1 all stabilize strand exchange intermediates in precise three-nucleotide steps. Each step coincides with an energetic signature (0.3 kBT) that is conserved from bacteria to humans. Triplet recognition is strictly dependent on correct Watson-Crick pairing. Rad51, RecA, and Dmc1 can all step over mismatches, but only Dmc1 can stabilize mismatched triplets. This finding provides insight into why eukaryotes have evolved a meiosis-specific recombinase. We propose that canonical Watson-Crick base triplets serve as the fundamental unit of pairing interactions during DNA recombination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580133/" 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/PMC4580133/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Ja Yil -- Terakawa, Tsuyoshi -- Qi, Zhi -- Steinfeld, Justin B -- Redding, Sy -- Kwon, YoungHo -- Gaines, William A -- Zhao, Weixing -- Sung, Patrick -- Greene, Eric C -- CA146940/CA/NCI NIH HHS/ -- GM074739/GM/NIGMS NIH HHS/ -- R01 CA146940/CA/NCI NIH HHS/ -- R01 ES015252/ES/NIEHS NIH HHS/ -- R01 GM074739/GM/NIGMS NIH HHS/ -- R01ES015252/ES/NIEHS NIH HHS/ -- T32 GM007367/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Aug 28;349(6251):977-81. doi: 10.1126/science.aab2666.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. ; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Department of Biophysics, Kyoto University, Sakyo, Kyoto, Japan. ; Department of Chemistry, Columbia University, New York, NY, USA. ; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA. ; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Howard Hughes Medical Institute, Columbia University, New York, NY, USA. ecg2108@cumc.columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26315438" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Pairing ; Base Sequence ; Cell Cycle Proteins/chemistry/metabolism ; DNA/*chemistry/*metabolism ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; Evolution, Molecular ; *Homologous Recombination ; Humans ; Meiosis ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Rad51 Recombinase/chemistry/*metabolism ; Rec A Recombinases/chemistry/*metabolism ; Recombinases/chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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