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  • 1
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    Crosslinking reactions of 4-amino-6-oxo-2-vinylpyrimidine with guanine derivatives and structural analysis of the adducts (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-19
    Description: DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl 2 , NiCl 2 , ZnCl 2 and MnCl 2 . In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Historical heterogeneity and emotional expression [Psychological and Cognitive Sciences] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-05-13
    Description: A small number of facial expressions may be universal in that they are produced by the same basic affective states and recognized as such throughout the world. However, other aspects of emotionally expressive behavior vary widely across culture. Just why do they vary? We propose that some cultural differences in...
    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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  • 3
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    Effects of aspect ratio and concentration on rheology of epoxy suspensions containing model plate-like nanoparticles (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-12-29
    Description: Hexagonal 2-dimensional α-zirconium phosphate crystals were prepared with lateral diameters ranging from 110 nm to 1.5 μm to investigate the effect of particle size on suspension rheology. The nanoplatelets were exfoliated to individual sheets with monodisperse thickness and dispersed in a Newtonian epoxy fluid. The steady shear response of dilute and semi-dilute suspensions was measured and compared to expressions obtained from theory for infinitely dilute suspensions. For suspensions containing the smaller nanoplatelets, aspect ratio ∼160, the low shear rate viscosity and transition to shear thinning behavior were well described by theory for loadings up to 0.5 vol. %. The agreement was improved by assuming a moderate polydispersity in lateral diameter, ∼30%–50%, which is consistent with experimental observation. For the higher aspect ratio nanoplatelets, good agreement between theory and experiment was observed only at high shear rates. At lower shear rate, theory consistently over-predicted viscosity, which was attributed to a progressive shift to non-isotropic initial conditions with increasing particle size. The results suggest that at a fixed Peclet number, there is an increasing tendency for the nanoplatelets to form transient, local stacks as particle size increases. The largest particles, aspect ratio ∼2200, showed unusual shear thinning and thickening behaviors that were attributed to particle flexibility. The findings demonstrate the surprising utility of theory for infinitely dilute suspensions to interpret, and in some cases quantitatively describe, the non-Newtonian viscosity of real suspensions containing high aspect ratio plate-like particles. A simple framework is proposed to interpret deviations from ideal behavior based on the local and collective behavior of the suspended nanoplatelets.
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    NMR evidence for an intimate relationship between antiferromagnetic spin fluctuations and extended s-wave superconductivity in monocrystalline SrFe_{2} (As_{1−x} P_{x} )_{2} (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-10-01
    Description: Author(s): M. Miyamoto, H. Mukuda, T. Kobayashi, M. Yashima, Y. Kitaoka, S. Miyasaka, and S. Tajima We report on a systematic P 31 -NMR study on an iron- (Fe-) based superconductor SrFe 2 ( As 1 − x P x ) 2 (Sr122AsP) in which a superconducting (SC) transition temperature T c at x = 0.35 increases from T c = 26 K up to 33 K by annealing an as-grown monocrystalline sample. The present NMR study has unraveled that T c … [Phys. Rev. B 92, 125154] Published Wed Sep 30, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Genes, Vol. 1, Pages 263-282: A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly (2012)
    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Details
    Publication Date: 2012-06-12
    Description: This study presents a new computer program for assessing the effects of different factors and sequencing strategies on de novo sequence assembly. The program uses reads from actual sequencing studies or from simulations with a reference genome that may also be real or simulated. The simulated reads can be created with our read simulator. They can be of differing length and coverage, consist of paired reads with varying distance, and include sequencing errors such as color space miscalls to imitate SOLiD data. The simulated or real reads are mapped to their reference genome and our assembly simulator is then used to obtain optimal assemblies that are limited only by the distribution of repeats. By way of this mapping, the assembly simulator determines which contigs are theoretically possible, or conversely (and perhaps more importantly), which are not. We illustrate the application and utility of our new simulation tools with several experiments that test the effects of genome complexity (repeats), read length and coverage, word size in De Bruijn graph assembly, and alternative sequencing strategies (e.g., BAC pooling) on sequence assemblies. These experiments highlight just some of the uses of our simulators in the experimental design of sequencing projects and in the further development of assembly algorithms.
    Electronic ISSN: 2073-4425
    Topics: Biology
    Published by Molecular Diversity Preservation International (MDPI)
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  • 6
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    Fukushima radionuclides in ocean [Environmental Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-04-18
    Description: The Tōhoku earthquake and tsunami of March 11, 2011, resulted in unprecedented radioactivity releases from the Fukushima Dai-ichi nuclear power plants to the Northwest Pacific Ocean. Results are presented here from an international study of radionuclide contaminants in surface and subsurface waters, as well as in zooplankton and fish, off Japan in June 2011. A major finding is detection of Fukushima-derived 134Cs and 137Cs throughout waters 30–600 km offshore, with the highest activities associated with near-shore eddies and the Kuroshio Current acting as a southern boundary for transport. Fukushima-derived Cs isotopes were also detected in zooplankton and mesopelagic fish, and unique to this study we also find 110mAg in zooplankton. Vertical profiles are used to calculate a total inventory of ∼2 PBq 137Cs in an ocean area of 150,000 km2. Our results can only be understood in the context of our drifter data and an oceanographic model that shows rapid advection of contaminants further out in the Pacific. Importantly, our data are consistent with higher estimates of the magnitude of Fukushima fallout and direct releases [Stohl et al. (2011) Atmos Chem Phys Discuss 11:28319–28394; Bailly du Bois et al. (2011) J Environ Radioact, 10.1016/j.jenvrad.2011.11.015]. We address risks to public health and marine biota by showing that though Cs isotopes are elevated 10–1,000× over prior levels in waters off Japan, radiation risks due to these radionuclides are below those generally considered harmful to marine animals and human consumers, and even below those from naturally occurring radionuclides.
    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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    Genome maps 10. Comparative genomics. Mammalian radiations. Wall chart (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-11-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, S J -- Eisenberg, J F -- Miyamoto, M -- Hedges, S B -- Kumar, S -- Wilson, D E -- Menotti-Raymond, M -- Murphy, W J -- Nash, W G -- Lyons, L A -- Menninger, J C -- Stanyon, R -- Wienberg, J -- Copeland, N G -- Jenkins, N A -- Gellin, J -- Yerle, M -- Andersson, L -- Womack, J -- Broad, T -- Postlethwait, J -- Serov, O -- Bailey, E -- James, M R -- Marshall Graves, J A -- New York, N.Y. -- Science. 1999 Oct 15;286(5439):463-78.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Cancer Institute, Frederick, MD, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10577209" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Chromosome Mapping ; Chromosome Painting ; *Genome ; *Genome, Human ; Humans ; Mammals/*genetics ; Nucleic Acid Hybridization ; Phylogeny
    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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  • 8
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    Molecular and morphological supertrees for eutherian (placental) mammals (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-07
    Description: A large body of diverse comparative data now exists for a major phylogenetic synthesis of the higher-level relationships among eutherian (placental) mammals. We present such a phylogenetic synthesis using the composite trees or supertrees from the combined and separate analyses of their published molecular and morphological source phylogenies. Our combined and separate supertrees largely support the same suprafamilial taxa and orders, but different interordinal clades. These similarities and differences reinforce the continuing contributions of morphological studies, while highlighting the growing influence of molecular information on the field. As current summaries of past research, our supertrees emphasize opportunities for future work, while providing a step toward the eventual integration of the data and characters themselves.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, F G -- Miyamoto, M M -- Freire, N P -- Ong, P Q -- Tennant, M R -- Young, T S -- Gugel, K F -- New York, N.Y. -- Science. 2001 Mar 2;291(5509):1786-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611-8525, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11230694" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Humans ; Mammals/anatomy & histology/*classification/genetics ; Pedigree ; *Phylogeny
    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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  • 9
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    Comment on "Population size does not influence mitochondrial genetic diversity in animals" (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-02
    Description: Bazin et al. (Reports, 28 April, 2006, p. 570) found no relationship between mitochondrial DNA (mtDNA) diversity and population size when comparing across large groups of animals. We show empirically that species with smaller populations, as represented by eutherian mammals, exhibit a positive correlation between mtDNA and allozyme variation, suggesting that mtDNA diversity may correlate with population size in these animals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mulligan, Connie J -- Kitchen, Andrew -- Miyamoto, Michael M -- New York, N.Y. -- Science. 2006 Dec 1;314(5804):1390.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anthropology, Box 103610, University of Florida, Gainesville, FL 32610, USA. mulligan@anthro.ufl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17138883" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Heterozygote ; Humans ; Invertebrates/genetics ; Isoenzymes/genetics ; Male ; Mammals/*genetics ; Population Density
    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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  • 10
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    Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region (1987)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1987-10-16
    Description: Sequences from the upstream and downstream flanking DNA regions of the psi eta-globin locus in Pan troglodytes (common chimpanzee), Gorilla gorilla (gorilla), and Pongo pygmaeus (orangutan, the closest living relative to Homo, Pan, and Gorilla) provided further data for evaluating the phylogenetic relations of humans and African apes. These newly sequenced orthologs [an additional 4.9 kilobase pairs (kbp) for each species] were combined with published psi eta-gene sequences and then compared to the same orthologous stretch (a continuous 7.1-kbp region) available for humans. Phylogenetic analysis of these nucleotide sequences by the parsimony method indicated (i) that human and chimpanzee are more closely related to each other than either is to gorilla and (ii) that the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans. These results indicate that features (for example, knuckle-walking) unique to African apes (but not to humans) are primitive and that even local molecular clocks should be applied with caution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miyamoto, M M -- Slightom, J L -- Goodman, M -- R01 HL 33940/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 1987 Oct 16;238(4825):369-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, MI 48201.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3116671" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Biological Evolution ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Gait ; Globins/*genetics ; Gorilla gorilla/*genetics ; Haplorhini/*genetics ; Humans ; Metacarpophalangeal Joint ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Pan troglodytes/*genetics ; *Phylogeny ; Polymorphism, Genetic ; Sequence Homology, Nucleic Acid
    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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