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  • Springer Nature  (87)
  • Wiley  (54)
  • Cell Press  (21)
  • Public Library of Science  (18)
  • Copernicus  (17)
  • Oxford University Press  (16)
  • Institute of Electrical and Electronics Engineers (IEEE)
  • Springer Science + Business Media
  • 2015-2019  (134)
  • 2010-2014  (55)
  • 2005-2009  (24)
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  • 1
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    Comparative analysis of secretome profiles of manganese(II)-oxidizing Ascomycete fungi (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Description: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Description: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Common variants upstream of KDR encoding VEGFR2 and in TTC39B associate with endometriosis (2016)
    Springer Nature
    Details
    Publication Date: 2016-07-27
    Description: Article Endometriosis is a common gynaecological disease but the underlying pathogenesis is poorly understood, however there is a strong familial component. Here the authors conduct a genome wide association study and identify a novel susceptibility locus that correlates with disease severity. Nature Communications doi: 10.1038/ncomms12350 Authors: Valgerdur Steinthorsdottir, Gudmar Thorleifsson, Kristrun Aradottir, Bjarke Feenstra, Asgeir Sigurdsson, Lilja Stefansdottir, Anna M. Kristinsdottir, Florian Zink, Gisli H. Halldorsson, Nete Munk Nielsen, Frank Geller, Mads Melbye, Daniel F. Gudbjartsson, Reynir T. Geirsson, Unnur Thorsteinsdottir, Kari Stefansson
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 3
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    Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans (2016)
    Springer Nature
    In: Nature
    Details
    Publication Date: 2016-03-24
    Description: Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans Nature 531, 7595 (2016). doi:10.1038/nature16990 Authors: Katherine D. Zink & Daniel E. Lieberman The origins of the genus Homo are murky, but by H. erectus, bigger brains and bodies had evolved that, along with larger foraging ranges, would have increased the daily energetic requirements of hominins. Yet H. erectus differs from earlier hominins in having relatively smaller teeth, reduced chewing muscles, weaker maximum bite force capabilities, and a relatively smaller gut. This paradoxical combination of increased energy demands along with decreased masticatory and digestive capacities is hypothesized to have been made possible by adding meat to the diet, by mechanically processing food using stone tools, or by cooking. Cooking, however, was apparently uncommon until 500,000 years ago, and the effects of carnivory and Palaeolithic processing techniques on mastication are unknown. Here we report experiments that tested how Lower Palaeolithic processing technologies affect chewing force production and efficacy in humans consuming meat and underground storage organs (USOs). We find that if meat comprised one-third of the diet, the number of chewing cycles per year would have declined by nearly 2 million (a 13% reduction) and total masticatory force required would have declined by 15%. Furthermore, by simply slicing meat and pounding USOs, hominins would have improved their ability to chew meat into smaller particles by 41%, reduced the number of chews per year by another 5%, and decreased masticatory force requirements by an additional 12%. Although cooking has important benefits, it appears that selection for smaller masticatory features in Homo would have been initially made possible by the combination of using stone tools and eating meat.
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 4
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    New basal cell carcinoma susceptibility loci (2015)
    Springer Nature
    Details
    Publication Date: 2015-04-11
    Description: Article Basal cell carcinoma is a common cancer among people of European ancestry, with associated high economic costs to monitor and treat. Here Stacey et al. conduct a genome-wide association study on Icelandic and other European populations, identifying four novel loci associated with cancer susceptibility. Nature Communications doi: 10.1038/ncomms7825 Authors: Simon N. Stacey, Hannes Helgason, Sigurjon A. Gudjonsson, Gudmar Thorleifsson, Florian Zink, Asgeir Sigurdsson, Birte Kehr, Julius Gudmundsson, Patrick Sulem, Bardur Sigurgeirsson, Kristrun R. Benediktsdottir, Kristin Thorisdottir, Rafn Ragnarsson, Victoria Fuentelsaz, Cristina Corredera, Yolanda Gilaberte, Matilde Grasa, Dolores Planelles, Onofre Sanmartin, Peter Rudnai, Eugene Gurzau, Kvetoslava Koppova, Bjørn A. Nexø, Anne Tjønneland, Kim Overvad, Jon G. Jonasson, Laufey Tryggvadottir, Hrefna Johannsdottir, Anna M. Kristinsdottir, Hreinn Stefansson, Gisli Masson, Olafur T. Magnusson, Bjarni V. Halldorsson, Augustine Kong, Thorunn Rafnar, Unnur Thorsteinsdottir, Ulla Vogel, Rajiv Kumar, Eduardo Nagore, José I. Mayordomo, Daniel F. Gudbjartsson, Jon H. Olafsson, Kari Stefansson
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 5
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    On the potentially dramatic history of the super-Earth {rho} 55 Cancri e (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-24
    Description: We demonstrate that tidal evolution of the inner planet (‘e’) of the system orbiting the star 55 Cancri could have led to passage through two secular resonances with other planets in the system. The consequence of this evolution is excitation of both the planetary eccentricity and inclination relative to the original orbital plane. The large mass ratio between the innermost planet and the others means that these excitations can be of substantial amplitude and can have dramatic consequences for the system organization. Such evolution can potentially explain the large observed mutual inclination between the innermost and outermost planets in the system, and implies that tidal heating could have substantially modified the structure of planet e, and possibly reduced its mass by Roche lobe overflow. Similar inner secular resonances may be found in many multiple planet systems and suggest that many of the innermost planets in these systems could have suffered similar evolutions.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Excited state mixed valence in a dual-bridged three-chromophore system (2012)
    Wiley
    Details
    Publication Date: 2012-04-15
    Description: The optical and resonance Raman spectra of the 2,2′: 6′,2″:6″,6-trioxytriphenyl-amine cation are measured and interpreted. This molecule contains two simultaneous types of coupling between three chromophores and two types of bridging atoms. The first and conventional coupling involves a single nitrogen bridge that couples all three aryl groups. The second is provided by the three oxygen atoms, each of which bridges two adjacent aryl groups. There are two bands in the visible region of the optical absorption spectrum; their assignment and the interpretation of the contributing orbitals and electronic states are described in terms of the neighboring orbital model that explains the effects of the two types of coupling. The bonding changes that take place in the excited electronic states are probed by resonance Raman spectroscopy intensities and analyzed using the time-dependent theory of resonance Raman spectroscopy. The optical absorption spectrum was fit using the measured vibrational frequencies and excited state distortions. The distortions correlate well with the bonding changes predicted by the neighboring orbital model. The resonance Raman data and neighboring orbital model analysis reveal that the two optical absorption bands correspond to charge transfers from aryl groups with different nodal structures in their pi orbitals. Copyright © 2012 John Wiley & Sons, Ltd. The three-chromophore cation (left) has a symmetric charge distribution in its ground state and three equivalent charge-bearing units in its lowest excited state. Coupling between the three units occurs through the central nitrogen and pair-wise through the oxygen. The effects of the coupling on the electronic and resonance Raman spectra are interpreted using the neighboring orbital model.
    Print ISSN: 0894-3230
    Electronic ISSN: 1099-1395
    Topics: Chemistry and Pharmacology , Physics
    Published by Wiley
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  • 7
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    Perinuclear positioning of the inactive human cystic fibrosis gene depends on CTCF, A-type lamins and an active histone deacetylase (2012)
    Wiley
    Details
    Publication Date: 2012-04-16
    Description: The nuclear positioning of mammalian genes often correlates with their functional state. For instance, the human cystic fibrosis transmembrane conductance regulator (CFTR) gene associates with the nuclear periphery in its inactive state, but occupies interior positions when active. It is not understood how nuclear gene positioning is determined. Here, we investigated trichostatin A (TSA)-induced repositioning of CFTR in order to address molecular mechanisms controlling gene positioning. Treatment with the histone deacetylase (HDAC) inhibitor TSA induced increased histone acetylation and CFTR repositioning towards the interior within 20 minutes. When CFTR localized in the nuclear interior (either after TSA treatment or when the gene was active) consistent histone H3 hyperacetylation was observed at a CTCF site close to the CFTR promoter. Knockdown experiments revealed that CTCF was essential for perinuclear CFTR positioning and both, CTCF knockdown as well as TSA treatment had similar and CFTR-specific effects on radial positioning. Furthermore, knockdown experiments revealed that also A-type lamins were required for the perinuclear positioning of CFTR. Together, the results showed that CTCF, A-type lamins and an active HDAC were essential for perinuclear positioning of CFTR and these components acted on a CTCF site adjacent to the CFTR promoter. The results are consistent with the idea that CTCF bound close to the CFTR promoter, A-type lamins and an active HDAC form a complex at the nuclear periphery, which becomes disrupted upon inhibition of the HDAC, leading to the observed release of CFTR. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.
    Electronic ISSN: 0091-7419
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Wiley
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  • 8
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    Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman (2016)
    Springer Nature
    Details
    Publication Date: 2016-01-15
    Description: Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman Scientific Reports, Published online: 14 January 2016; doi:10.1038/srep18932
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 9
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    Integration of molecular and enzymatic catalysts on graphene for biomimetic generation of antithrombotic species (2014)
    Springer Nature
    Details
    Publication Date: 2014-02-13
    Description: Article Enzymatic mimics, capable of catalysing cascading reactions under physiological conditions, can be formed from integrating multiple components. Here, the authors report a graphene–haemin–glucose oxidase system capable of biomimetic generation of antithrombotic species from abundant glucose and L -arginine. Nature Communications doi: 10.1038/ncomms4200 Authors: Teng Xue, Bo Peng, Min Xue, Xing Zhong, Chin-Yi Chiu, Si Yang, Yongquan Qu, Lingyan Ruan, Shan Jiang, Sergey Dubin, Richard B. Kaner, Jeffrey I. Zink, Mark E. Meyerhoff, Xiangfeng Duan, Yu Huang
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 10
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    Excited state mixed valence in a dual-bridged three-chromophore system (2012)
    Wiley
    Details
    Publication Date: 2012-01-27
    Description: The optical and resonance Raman spectra of the 2,2′: 6′,2″:6″,6-trioxytriphenyl-amine cation are measured and interpreted. This molecule contains two simultaneous types of coupling between three chromophores and two types of bridging atoms. The first and conventional coupling involves a single nitrogen bridge that couples all three aryl groups. The second is provided by the three oxygen atoms, each of which bridges two adjacent aryl groups. There are two bands in the visible region of the optical absorption spectrum; their assignment and the interpretation of the contributing orbitals and electronic states are described in terms of the neighboring orbital model that explains the effects of the two types of coupling. The bonding changes that take place in the excited electronic states are probed by resonance Raman spectroscopy intensities and analyzed using the time-dependent theory of resonance Raman spectroscopy. The optical absorption spectrum was fit using the measured vibrational frequencies and excited state distortions. The distortions correlate well with the bonding changes predicted by the neighboring orbital model. The resonance Raman data and neighboring orbital model analysis reveal that the two optical absorption bands correspond to charge transfers from aryl groups with different nodal structures in their pi orbitals. Copyright © 2012 John Wiley & Sons, Ltd. The three-chromophore cation (left) has a symmetric charge distribution in its ground state and three equivalent charge-bearing units in its lowest excited state. Coupling between the three units occurs through the central nitrogen and pair-wise through the oxygen. The effects of the coupling on the electronic and resonance Raman spectra are interpreted using the neighboring orbital model.
    Print ISSN: 0894-3230
    Electronic ISSN: 1099-1395
    Topics: Chemistry and Pharmacology , Physics
    Published by Wiley
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