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  • Oxford University Press  (22)
  • Molecular Diversity Preservation International  (15)
  • American Association for the Advancement of Science (AAAS)
  • 2020-2022
  • 2015-2019  (43)
  • 2016  (43)
  • 1
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    MALDI Mass Spectrometry Imaging Reveals Decreased CK5 Levels in Vulvar Squamous Cell Carcinomas Compared to the Precursor Lesion Differentiated Vulvar Intraepithelial Neoplasia (2016)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2016-07-08
    Print ISSN: 1661-6596
    Electronic ISSN: 1422-0067
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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  • 2
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    Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-11
    Description: PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, we assessed the evolutionary interactions between TE and piRNAs in a statistical framework using three nonmodel laurasiatherian mammals as a study system: dog, horse, and a vesper bat. These three species diverged ~80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes, we aimed to identify clear relationships among TE content, expression, and piRNAs. We found that the TE subfamilies that are the most transcribed appear to elicit the strongest "ping-pong" response. This was most evident among long interspersed elements, but the relationships between expression and ping-pong pilRNA (piRNA-like) expression were more complex among SINEs. SINE transcripts were equally abundant in the dog and horse yet new SINE insertions were relatively rare in the horse genome, where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome. However, our results also suggest that the presence of a robust piRNA response is apparently not sufficient to stop TE mobilization and accumulation.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-07
    Description: Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and losses. Several studies also suggest that mammalian OR repertoires are influenced by life history traits. Sauropsida is a diverse group of vertebrates group that is the sister group to mammals, and includes birds, testudines, squamates, and crocodilians, and represents a natural system to explore predictions derived from mammalian studies. In this study, we analyzed olfactory receptor (OR) repertoire variation among several representative species and found that the number of intact OR genes in sauropsid genomes analyzed ranged over an order of magnitude, from 108 in the green anole to over 1,000 in turtles. Our results suggest that different sauropsid lineages have highly divergent OR repertoire composition that derive from lineage-specific combinations of gene expansions, losses, and retentions of ancestral OR genes. These differences also suggest that varying degrees of adaption related to life history have shaped the unique OR repertoires observed across sauropsid lineages.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Existentially closed fields with G-derivations (2016)
    Oxford University Press
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    Publication Date: 2016-05-29
    Description: We prove that the theories of fields with Hasse–Schmidt derivations corresponding to actions of formal groups admit model companions. We also give geometric axiomatizations of these model companions.
    Print ISSN: 0024-6107
    Electronic ISSN: 1469-7750
    Topics: Mathematics
    Published by Oxford University Press
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  • 5
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    Long-range transcriptional interference in E. coli used to construct a dual positive selection system for genetic switches (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-03
    Description: We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong 70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Cross-Study Comparison Reveals Common Genomic, Network, and Functional Signatures of Desiccation Resistance in Drosophila melanogaster (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-04
    Description: Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categories, genetic pathways, and interaction networks. Here we report on the genomic overlap for natural desiccation resistance from a Pool-genome-wide association study experiment and a selection experiment in flies collected from the same region in southeastern Australia in different years. We identified over 600 single nucleotide polymorphisms associated with desiccation resistance in flies derived from almost 1,000 wild-caught genotypes, a similar number of loci to that observed in our previous genomic study of selected lines, demonstrating the genetic complexity of this ecologically important trait. By harnessing the power of cross-study comparison, we narrowed the candidates from almost 400 genes in each study to a core set of 45 genes, enriched for stimulus, stress, and defense responses. In addition to gene-level overlap, there was higher order congruence at the network and functional levels, suggesting genetic redundancy in key stress sensing, stress response, immunity, signaling, and gene expression pathways. We also identified variants linked to different molecular aspects of desiccation physiology previously verified from functional experiments. Our approach provides insight into the genomic basis of a complex and ecologically important trait and predicts candidate genetic pathways to explore in multiple genetic backgrounds and related species within a functional framework.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Emerging solutions to the water challenges of an urbanizing world (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-05-21
    Description: The top priorities for urban water sustainability include the provision of safe drinking water, wastewater handling for public health, and protection against flooding. However, rapidly aging infrastructure, population growth, and increasing urbanization call into question current urban water management strategies, especially in the fast-growing urban areas in Asia and Africa. We review innovative approaches in urban water management with the potential to provide locally adapted, resource-efficient alternative solutions. Promising examples include new concepts for stormwater drainage, increased water productivity, distributed or on-site treatment of wastewater, source separation of human waste, and institutional and organizational reforms. We conclude that there is an urgent need for major transdisciplinary efforts in research, policy, and practice to develop alternatives with implications for cities and aquatic ecosystems alike.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larsen, Tove A -- Hoffmann, Sabine -- Luthi, Christoph -- Truffer, Bernhard -- Maurer, Max -- New York, N.Y. -- Science. 2016 May 20;352(6288):928-33. doi: 10.1126/science.aad8641.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dubendorf, Switzerland. tove.larsen@eawag.ch. ; Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dubendorf, Switzerland. ; Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dubendorf, Switzerland. Faculty of Geosciences, University of Utrecht, Heidelberglaan 2, NL-3584 CS, Utrecht, Netherlands. ; Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dubendorf, Switzerland. Institute of Environmental Engineering, ETH Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27199414" target="_blank"〉PubMed〈/a〉
    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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    Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-04-29
    Description: Ribose is the central molecular subunit in RNA, but the prebiotic origin of ribose remains unknown. We observed the formation of substantial quantities of ribose and a diversity of structurally related sugar molecules such as arabinose, xylose, and lyxose in the room-temperature organic residues of photo-processed interstellar ice analogs initially composed of H2O, CH3OH, and NH3 Our results suggest that the generation of numerous sugar molecules, including the aldopentose ribose, may be possible from photochemical and thermal treatment of cosmic ices in the late stages of the solar nebula. Our detection of ribose provides plausible insights into the chemical processes that could lead to formation of biologically relevant molecules in suitable planetary environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meinert, Cornelia -- Myrgorodska, Iuliia -- de Marcellus, Pierre -- Buhse, Thomas -- Nahon, Laurent -- Hoffmann, Soren V -- d'Hendecourt, Louis Le Sergeant -- Meierhenrich, Uwe J -- New York, N.Y. -- Science. 2016 Apr 8;352(6282):208-12. doi: 10.1126/science.aad8137.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite Nice Sophia Antipolis, Institut de Chimie de Nice, UMR 7272 CNRS, 28 Avenue Valrose, 06108 Nice, France. cornelia.meinert@unice.fr uwe.meierhenrich@unice.fr. ; Universite Nice Sophia Antipolis, Institut de Chimie de Nice, UMR 7272 CNRS, 28 Avenue Valrose, 06108 Nice, France. Synchrotron SOLEIL, L'Orme des Merisiers, St Aubin BP48, 91192 Gif-sur-Yvette, France. ; Institut d'Astrophysique Spatiale, CNRS, Universite Paris-Sud, Universite Paris-Saclay, bat 121, 91405 Orsay, France. ; Centro de Investigaciones Quimicas, Universidad Autonoma del Estado de Morelos, Avenida Universidad 1001, 62209 Cuernavaca, Mexico. ; Synchrotron SOLEIL, L'Orme des Merisiers, St Aubin BP48, 91192 Gif-sur-Yvette, France. ; Aarhus University, Department of Physics and Astronomy, Ny Munkegade 120, 8000 Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27124456" target="_blank"〉PubMed〈/a〉
    Keywords: Acetic Acid/chemistry ; Ammonia/chemistry ; Arabinose/chemical synthesis ; *Cosmic Radiation ; Extraterrestrial Environment ; *Ice ; Meteoroids ; *Origin of Life ; Pentoses/chemical synthesis ; Photochemical Processes ; RNA/*chemistry ; Ribose/*chemical synthesis ; Ultraviolet Rays ; Xylose/chemical synthesis
    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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    BIG DATA AND BIODIVERSITY. Filling in biodiversity threat gaps (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-04-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joppa, L N -- O'Connor, B -- Visconti, P -- Smith, C -- Geldmann, J -- Hoffmann, M -- Watson, J E M -- Butchart, S H M -- Virah-Sawmy, M -- Halpern, B S -- Ahmed, S E -- Balmford, A -- Sutherland, W J -- Harfoot, M -- Hilton-Taylor, C -- Foden, W -- Di Minin, E -- Pagad, S -- Genovesi, P -- Hutton, J -- Burgess, N D -- New York, N.Y. -- Science. 2016 Apr 22;352(6284):416-8. doi: 10.1126/science.aaf3565. Epub 2016 Apr 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉See supplementary materials for complete list of author affiliations. lujoppa@microsoft.com. ; See supplementary materials for complete list of author affiliations.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27102469" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; Datasets as Topic/*standards ; Endangered Species/*statistics & numerical data ; Human Activities ; Humans
    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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    Cryovolcanism on Ceres (2016)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2016-09-02
    Description: Volcanic edifices are abundant on rocky bodies of the inner solar system. In the cold outer solar system, volcanism can occur on solid bodies with a water-ice shell, but derived cryovolcanic constructs have proved elusive. We report the discovery, using Dawn Framing Camera images, of a landform on dwarf planet Ceres that we argue represents a viscous cryovolcanic dome. Parent material of the cryomagma is a mixture of secondary minerals, including salts and water ice. Absolute model ages from impact craters reveal that extrusion of the dome has occurred recently. Ceres’ evolution must have been able to sustain recent interior activity and associated surface expressions. We propose salts with low eutectic temperatures and thermal conductivities as key drivers for Ceres’ long-term internal evolution.
    Keywords: Geochemistry, Geophysics, Planetary Science
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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