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Table of Contents

May 06, 2014; vol. 111 no. 18

This Week in PNAS

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    In This Issue
    PNAS May 6, 2014 111 (18) 6529-6530; https://doi.org/10.1073/iti1814111

Letters (Online Only)

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    Human health risks of forest conservation
    Greet De Coster, Francisco Anaruma Filho, and Rozely Ferreira dos Santos
    PNAS May 6, 2014 111 (18) E1815; first published March 27, 2014. https://doi.org/10.1073/pnas.1401544111
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    Reply to De Coster et al.: Exploring the complexity of ecosystem–human health relationships
    Samuel S. Myers, Lynne Gaffikin, Christopher D. Golden, Richard S. Ostfeld, Kent H. Redford, Taylor H. Ricketts, Will R. Turner, and Steven A. Osofsky
    PNAS May 6, 2014 111 (18) E1816; first published March 27, 2014. https://doi.org/10.1073/pnas.1402671111

    See companion article:

    • Human health impacts of ecosystem alteration
      - Nov 11, 2013
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    Effective 2D model does not account for geometry sensing by self-organized proteins patterns
    Jacob Halatek and Erwin Frey
    PNAS May 6, 2014 111 (18) E1817; first published April 3, 2014. https://doi.org/10.1073/pnas.1220971111
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    Nrf2 target genes can be controlled by neuronal activity in the absence of Nrf2 and astrocytes
    Ruth F. Deighton, Nóra M. Márkus, Bashayer Al-Mubarak, Karen F. S. Bell, Sofia Papadia, Paul J. Meakin, Sudhir Chowdhry, John D. Hayes, and Giles E. Hardingham
    PNAS May 6, 2014 111 (18) E1818-E1820; first published April 21, 2014. https://doi.org/10.1073/pnas.1402097111
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    Reply to Deighton et al.: Neuronal activity regulates distinct antioxidant pathways in neurons and astrocytes
    Agata Habas, Junghyun Hahn, Xianhong Wang, and Marta Margeta
    PNAS May 6, 2014 111 (18) E1821-E1822; first published April 21, 2014. https://doi.org/10.1073/pnas.1403291111

    See companion article:

    • Nrf2 regulation by neuronal activity
      - Oct 21, 2013

Core Concepts

A brief introduction to emerging topics in science.
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    Mirror neurons
    • Front Matter
    Jessica Marshall
    PNAS May 6, 2014 111 (18) 6531; https://doi.org/10.1073/pnas.1404652111

QnAs

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    QnAs with Simon A. Levin
    Paul Gabrielsen
    PNAS May 6, 2014 111 (18) 6532; first published April 28, 2014. https://doi.org/10.1073/pnas.1406308111

Retrospective

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    David W. Talmage, 1919–2014
    Philippa Marrack, John C. Cambier, and Henry Claman
    PNAS May 6, 2014 111 (18) 6533; first published May 5, 2014. https://doi.org/10.1073/pnas.1405718111

Commentaries

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    Salmon, seabirds, and ecosystem dynamics
    James A. Estes
    PNAS May 6, 2014 111 (18) 6534-6535; first published April 16, 2014. https://doi.org/10.1073/pnas.1404905111

    See companion article:

    • Top-down control of open ocean ecosystem function
      - Mar 31, 2014
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    The trouble with (group II) introns
    W. Ford Doolittle
    PNAS May 6, 2014 111 (18) 6536-6537; first published April 22, 2014. https://doi.org/10.1073/pnas.1405174111

    See companion article:

    • Group II intron silences nuclear gene
      - Apr 10, 2014
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    Nature’s toolkit for microbial rhodopsin ion pumps
    Oded Béjà and Janos K. Lanyi
    PNAS May 6, 2014 111 (18) 6538-6539; first published April 15, 2014. https://doi.org/10.1073/pnas.1405093111

    See companion article:

    • New class of rhodopsin chloride pump in bacteria
      - Mar 31, 2014

PNAS Plus Significance Statements

Brief statements written by the authors about the significance of their papers.
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    PNAS Plus Significance Statements
    PNAS May 6, 2014 111 (18) 6540-6541; https://doi.org/10.1073/pnas.ss11118

Perspective

  • Open Access
    Changing the academic culture: Valuing patents and commercialization toward tenure and career advancement
    Paul R. Sanberg, Morteza Gharib, Patrick T. Harker, Eric W. Kaler, Richard B. Marchase, Timothy D. Sands, Nasser Arshadi, and Sudeep Sarkar
    PNAS May 6, 2014 111 (18) 6542-6547; first published April 28, 2014. https://doi.org/10.1073/pnas.1404094111

Physical Sciences

  • Applied Mathematics

    • Open Access
      Conceptual dynamical models for turbulence
      Andrew J. Majda and Yoonsang Lee
      PNAS May 6, 2014 111 (18) 6548-6553; first published April 21, 2014. https://doi.org/10.1073/pnas.1404914111
  • Applied Physical Sciences

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      Long-range repulsion of colloids driven by ion exchange and diffusiophoresis
      Daniel Florea, Sami Musa, Jacques M. R. Huyghe, and Hans M. Wyss
      PNAS May 6, 2014 111 (18) 6554-6559; first published April 18, 2014. https://doi.org/10.1073/pnas.1322857111
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      Theory for plasticity of face-centered cubic metals
      Minho Jo, Yang Mo Koo, Byeong-Joo Lee, Börje Johansson, Levente Vitos, and Se Kyun Kwon
      PNAS May 6, 2014 111 (18) 6560-6565; first published April 21, 2014. https://doi.org/10.1073/pnas.1400786111
    • Open Access
      Charge gradient microscopy
      Seungbum Hong, Sheng Tong, Woon Ik Park, Yoshiomi Hiranaga, Yasuo Cho, and Andreas Roelofs
      PNAS May 6, 2014 111 (18) 6566-6569; first published April 23, 2014. https://doi.org/10.1073/pnas.1324178111
  • Chemistry

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      Investigations of heme distortion, low-frequency vibrational excitations, and electron transfer in cytochrome c
      Yuhan Sun, Abdelkrim Benabbas, Weiqiao Zeng, Jesse G. Kleingardner, Kara L. Bren, and Paul M. Champion
      PNAS May 6, 2014 111 (18) 6570-6575; first published April 21, 2014. https://doi.org/10.1073/pnas.1322274111
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      How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases
      Philip Wulff, Christopher C. Day, Frank Sargent, and Fraser A. Armstrong
      PNAS May 6, 2014 111 (18) 6606-6611; first published April 8, 2014. https://doi.org/10.1073/pnas.1322393111
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      Effects of side chains in helix nucleation differ from helix propagation
      Stephen E. Miller, Andrew M. Watkins, Neville R. Kallenbach, and Paramjit S. Arora
      PNAS May 6, 2014 111 (18) 6636-6641; first published April 21, 2014. https://doi.org/10.1073/pnas.1322833111
  • Earth, Atmospheric, and Planetary Sciences

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      A bottom-up control on fresh-bedrock topography under landscapes
      Daniella M. Rempe and William E. Dietrich
      PNAS May 6, 2014 111 (18) 6576-6581; first published April 23, 2014. https://doi.org/10.1073/pnas.1404763111
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      Pronounced zonal heterogeneity in Eocene southern high-latitude sea surface temperatures
      Peter M. J. Douglas, Hagit P. Affek, Linda C. Ivany, Alexander J. P. Houben, Willem P. Sijp, Appy Sluijs, Stefan Schouten, and Mark Pagani
      PNAS May 6, 2014 111 (18) 6582-6587; first published April 21, 2014. https://doi.org/10.1073/pnas.1321441111
  • Engineering

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      Solid MRI contrast agents for long-term, quantitative in vivo oxygen sensing
      Vincent H. Liu, Christophoros C. Vassiliou, Syed M. Imaad, and Michael J. Cima
      PNAS May 6, 2014 111 (18) 6588-6593; first published April 21, 2014. https://doi.org/10.1073/pnas.1400015111
  • Environmental Sciences

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      Lead in ancient Rome’s city waters
      Hugo Delile, Janne Blichert-Toft, Jean-Philippe Goiran, Simon Keay, and Francis Albarède
      PNAS May 6, 2014 111 (18) 6594-6599; first published April 21, 2014. https://doi.org/10.1073/pnas.1400097111

Social Sciences

  • Anthropology

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      Lead in ancient Rome’s city waters
      Hugo Delile, Janne Blichert-Toft, Jean-Philippe Goiran, Simon Keay, and Francis Albarède
      PNAS May 6, 2014 111 (18) 6594-6599; first published April 21, 2014. https://doi.org/10.1073/pnas.1400097111
  • Psychological and Cognitive Sciences

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      Automatic ultrarapid activation and inhibition of cortical motor systems in spoken word comprehension
      Yury Shtyrov, Anna Butorina, Anastasia Nikolaeva, and Tatiana Stroganova
      PNAS May 6, 2014 111 (18) E1918-E1923; first published April 21, 2014. https://doi.org/10.1073/pnas.1323158111
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      Neural sensitivity to eudaimonic and hedonic rewards differentially predict adolescent depressive symptoms over time
      Eva H. Telzer, Andrew J. Fuligni, Matthew D. Lieberman, and Adriana Galván
      PNAS May 6, 2014 111 (18) 6600-6605; first published April 21, 2014. https://doi.org/10.1073/pnas.1323014111
    • Open Access
      The dynamic role of genetics on cortical patterning during childhood and adolescence
      J. Eric Schmitt, Michael C. Neale, Bilqis Fassassi, Javier Perez, Rhoshel K. Lenroot, Elizabeth M. Wells, and Jay N. Giedd
      PNAS May 6, 2014 111 (18) 6774-6779; first published April 21, 2014. https://doi.org/10.1073/pnas.1311630111

Biological Sciences

  • Applied Biological Sciences

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      Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis
      Zachary D. Nagel, Carrie M. Margulies, Isaac A. Chaim, Siobhan K. McRee, Patrizia Mazzucato, Anwaar Ahmad, Ryan P. Abo, Vincent L. Butty, Anthony L. Forget, and Leona D. Samson
      PNAS May 6, 2014 111 (18) E1823-E1832; first published April 22, 2014. https://doi.org/10.1073/pnas.1401182111
  • Biochemistry

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      Myosin-10 produces its power-stroke in two phases and moves processively along a single actin filament under low load
      Yasuharu Takagi, Rachel E. Farrow, Neil Billington, Attila Nagy, Christopher Batters, Yi Yang, James R. Sellers, and Justin E. Molloy
      PNAS May 6, 2014 111 (18) E1833-E1842; first published April 21, 2014. https://doi.org/10.1073/pnas.1320122111
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      GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state
      Erik C. Hansen, Kyle J. Seamon, Shannen L. Cravens, and James T. Stivers
      PNAS May 6, 2014 111 (18) E1843-E1851; first published April 21, 2014. https://doi.org/10.1073/pnas.1401706111
    • Open Access
      A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1
      Pierre Barraud, Silpi Banerjee, Weaam I. Mohamed, Michael F. Jantsch, and Frédéric H.-T. Allain
      PNAS May 6, 2014 111 (18) E1852-E1861; first published April 21, 2014. https://doi.org/10.1073/pnas.1323698111
    • You have access
      How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases
      Philip Wulff, Christopher C. Day, Frank Sargent, and Fraser A. Armstrong
      PNAS May 6, 2014 111 (18) 6606-6611; first published April 8, 2014. https://doi.org/10.1073/pnas.1322393111
    • You have access
      RNA–RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes
      • From the Cover
      Guosheng Qu, Xiaolong Dong, Carol Lyn Piazza, Venkata R. Chalamcharla, Sheila Lutz, M. Joan Curcio, and Marlene Belfort
      PNAS May 6, 2014 111 (18) 6612-6617; first published April 10, 2014. https://doi.org/10.1073/pnas.1404276111

      See companion article:

      • The trouble with (group II) introns
        - Apr 22, 2014
    • Open Access
      CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference
      Megan L. Hochstrasser, David W. Taylor, Prashant Bhat, Chantal K. Guegler, Samuel H. Sternberg, Eva Nogales, and Jennifer A. Doudna
      PNAS May 6, 2014 111 (18) 6618-6623; first published April 18, 2014. https://doi.org/10.1073/pnas.1405079111
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      Structural basis for diversity in the SAM clan of riboswitches
      Jeremiah J. Trausch, Zhenjiang Xu, Andrea L. Edwards, Francis E. Reyes, Phillip E. Ross, Rob Knight, and Robert T. Batey
      PNAS May 6, 2014 111 (18) 6624-6629; first published April 21, 2014. https://doi.org/10.1073/pnas.1312918111
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      Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its stimulator protein
      Aiguo Zhao, Ying Fang, Xuemin Chen, Shun Zhao, Wei Dong, Yajing Lin, Weimin Gong, and Lin Liu
      PNAS May 6, 2014 111 (18) 6630-6635; first published April 21, 2014. https://doi.org/10.1073/pnas.1400166111
  • Biophysics and Computational Biology

    • Open Access
      Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates
      Harshad Ghodke, Hong Wang, Ching L. Hsieh, Selamawit Woldemeskel, Simon C. Watkins, Vesna Rapić-Otrin, and Bennett Van Houten
      PNAS May 6, 2014 111 (18) E1862-E1871; first published April 23, 2014. https://doi.org/10.1073/pnas.1323856111
    • You have access
      Effects of side chains in helix nucleation differ from helix propagation
      Stephen E. Miller, Andrew M. Watkins, Neville R. Kallenbach, and Paramjit S. Arora
      PNAS May 6, 2014 111 (18) 6636-6641; first published April 21, 2014. https://doi.org/10.1073/pnas.1322833111
    • You have access
      Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms
      Volker Schweikhard, Cong Meng, Kenji Murakami, Craig D. Kaplan, Roger D. Kornberg, and Steven M. Block
      PNAS May 6, 2014 111 (18) 6642-6647; first published April 14, 2014. https://doi.org/10.1073/pnas.1405181111
    • You have access
      Structure of a mitochondrial cytochrome c conformer competent for peroxidase activity
      Levi J. McClelland, Tung-Chung Mou, Margaret E. Jeakins-Cooley, Stephen R. Sprang, and Bruce E. Bowler
      PNAS May 6, 2014 111 (18) 6648-6653; first published April 23, 2014. https://doi.org/10.1073/pnas.1323828111
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      Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry
      Tatsuya Ikenoue, Young-Ho Lee, József Kardos, Hisashi Yagi, Takahisa Ikegami, Hironobu Naiki, and Yuji Goto
      PNAS May 6, 2014 111 (18) 6654-6659; first published April 21, 2014. https://doi.org/10.1073/pnas.1322602111
  • Cell Biology

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      Control of MT1-MMP transport by atypical PKC during breast-cancer progression
      Carine Rossé, Catalina Lodillinsky, Laetitia Fuhrmann, Maya Nourieh, Pedro Monteiro, Marie Irondelle, Emilie Lagoutte, Sophie Vacher, François Waharte, Perrine Paul-Gilloteaux, Maryse Romao, Lucie Sengmanivong, Mark Linch, Johan van Lint, Graça Raposo, Anne Vincent-Salomon, Ivan Bièche, Peter J. Parker, and Philippe Chavrier
      PNAS May 6, 2014 111 (18) E1872-E1879; first published April 21, 2014. https://doi.org/10.1073/pnas.1400749111
  • Developmental Biology

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      Interepithelial signaling with nephric duct is required for the formation of overlying coelomic epithelial cell sheet
      Takashi Yoshino, Daisuke Saito, Yuji Atsuta, Chihiro Uchiyama, Shinya Ueda, Kiyotoshi Sekiguchi, and Yoshiko Takahashi
      PNAS May 6, 2014 111 (18) 6660-6665; first published April 21, 2014. https://doi.org/10.1073/pnas.1316728111
  • Ecology

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      Climate change, pink salmon, and the nexus between bottom-up and top-down forcing in the subarctic Pacific Ocean and Bering Sea
      • From the Cover
      Alan M. Springer and Gus B. van Vliet
      PNAS May 6, 2014 111 (18) E1880-E1888; first published March 31, 2014. https://doi.org/10.1073/pnas.1319089111

      See companion article:

      • Salmon, seabirds, and ecosystem dynamics
        - Apr 16, 2014
  • Evolution

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      Patterns of coding variation in the complete exomes of three Neandertals
      Sergi Castellano, Genís Parra, Federico A. Sánchez-Quinto, Fernando Racimo, Martin Kuhlwilm, Martin Kircher, Susanna Sawyer, Qiaomei Fu, Anja Heinze, Birgit Nickel, Jesse Dabney, Michael Siebauer, Louise White, Hernán A. Burbano, Gabriel Renaud, Udo Stenzel, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajković, Željko Kucan, Ivan Gušic, Michael V. Shunkov, Anatoli P. Derevianko, Bence Viola, Matthias Meyer, Janet Kelso, Aida M. Andrés, and Svante Pääbo
      PNAS May 6, 2014 111 (18) 6666-6671; first published April 21, 2014. https://doi.org/10.1073/pnas.1405138111
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      Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns
      Fay-Wei Li, Juan Carlos Villarreal, Steven Kelly, Carl J. Rothfels, Michael Melkonian, Eftychios Frangedakis, Markus Ruhsam, Erin M. Sigel, Joshua P. Der, Jarmila Pittermann, Dylan O. Burge, Lisa Pokorny, Anders Larsson, Tao Chen, Stina Weststrand, Philip Thomas, Eric Carpenter, Yong Zhang, Zhijian Tian, Li Chen, Zhixiang Yan, Ying Zhu, Xiao Sun, Jun Wang, Dennis W. Stevenson, Barbara J. Crandall-Stotler, A. Jonathan Shaw, Michael K. Deyholos, Douglas E. Soltis, Sean W. Graham, Michael D. Windham, Jane A. Langdale, Gane Ka-Shu Wong, Sarah Mathews, and Kathleen M. Pryer
      PNAS May 6, 2014 111 (18) 6672-6677; first published April 14, 2014. https://doi.org/10.1073/pnas.1319929111
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      Exploration of sequence space as the basis of viral RNA genome segmentation
      Elena Moreno, Samuel Ojosnegros, Juan García-Arriaza, Cristina Escarmís, Esteban Domingo, and Celia Perales
      PNAS May 6, 2014 111 (18) 6678-6683; first published April 22, 2014. https://doi.org/10.1073/pnas.1323136111
  • Genetics

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      Hypermutable DNA chronicles the evolution of human colon cancer
      Kamila Naxerova, Elena Brachtel, Jesse J. Salk, Aaron M. Seese, Karen Power, Bardia Abbasi, Matija Snuderl, Sarah Chiang, Simon Kasif, and Rakesh K. Jain
      PNAS May 6, 2014 111 (18) E1889-E1898; first published April 21, 2014. https://doi.org/10.1073/pnas.1400179111
    • You have access
      Domain within the helicase subunit Mcm4 integrates multiple kinase signals to control DNA replication initiation and fork progression
      Yi-Jun Sheu, Justin B. Kinney, Armelle Lengronne, Philippe Pasero, and Bruce Stillman
      PNAS May 6, 2014 111 (18) E1899-E1908; first published April 16, 2014. https://doi.org/10.1073/pnas.1404063111
    • Open Access
      Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair
      Justin N. Vaughn and Jeffrey L. Bennetzen
      PNAS May 6, 2014 111 (18) 6684-6689; first published April 23, 2014. https://doi.org/10.1073/pnas.1321854111
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      Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1
      Danny Leung, Tingting Du, Ulrich Wagner, Wei Xie, Ah Young Lee, Preeti Goyal, Yujing Li, Keith E. Szulwach, Peng Jin, Matthew C. Lorincz, and Bing Ren
      PNAS May 6, 2014 111 (18) 6690-6695; first published April 22, 2014. https://doi.org/10.1073/pnas.1322273111
  • Immunology

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      Endoscopic photoconversion reveals unexpectedly broad leukocyte trafficking to and from the gut
      Angela M. Morton, Esen Sefik, Rabi Upadhyay, Ralph Weissleder, Christophe Benoist, and Diane Mathis
      PNAS May 6, 2014 111 (18) 6696-6701; first published April 21, 2014. https://doi.org/10.1073/pnas.1405634111
    • You have access
      Host-derived, pore-forming toxin–like protein and trefoil factor complex protects the host against microbial infection
      • From the Cover
      Yang Xiang, Chao Yan, Xiaolong Guo, Kaifeng Zhou, Sheng’an Li, Qian Gao, Xuan Wang, Feng Zhao, Jie Liu, Wen-Hui Lee, and Yun Zhang
      PNAS May 6, 2014 111 (18) 6702-6707; first published April 14, 2014. https://doi.org/10.1073/pnas.1321317111
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      Lytic immune synapse function requires filamentous actin deconstruction by Coronin 1A
      Emily M. Mace and Jordan S. Orange
      PNAS May 6, 2014 111 (18) 6708-6713; first published April 23, 2014. https://doi.org/10.1073/pnas.1314975111
    • You have access
      Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies
      Beatriz Trastoy, Joseph V. Lomino, Brian G. Pierce, Lester G. Carter, Sebastian Günther, John P. Giddens, Greg A. Snyder, Thomas M. Weiss, Zhiping Weng, Lai-Xi Wang, and Eric J. Sundberg
      PNAS May 6, 2014 111 (18) 6714-6719; first published April 21, 2014. https://doi.org/10.1073/pnas.1322908111
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      Emergence of the A20/ABIN-mediated inhibition of NF-κB signaling via modifying the ubiquitinated proteins in a basal chordate
      Shaochun Yuan, Xiangru Dong, Xin Tao, Liqun Xu, Jie Ruan, Jian Peng, and Anlong Xu
      PNAS May 6, 2014 111 (18) 6720-6725; first published April 21, 2014. https://doi.org/10.1073/pnas.1321187111
  • Medical Sciences

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      Modulation of a voltage-gated Na+ channel by sevoflurane involves multiple sites and distinct mechanisms
      Annika F. Barber, Vincenzo Carnevale, Michael L. Klein, Roderic G. Eckenhoff, and Manuel Covarrubias
      PNAS May 6, 2014 111 (18) 6726-6731; first published April 21, 2014. https://doi.org/10.1073/pnas.1405768111
  • Microbiology

    • Open Access
      Hassallidins, antifungal glycolipopeptides, are widespread among cyanobacteria and are the end-product of a nonribosomal pathway
      Johanna Vestola, Tania K. Shishido, Jouni Jokela, David P. Fewer, Olli Aitio, Perttu Permi, Matti Wahlsten, Hao Wang, Leo Rouhiainen, and Kaarina Sivonen
      PNAS May 6, 2014 111 (18) E1909-E1917; first published April 17, 2014. https://doi.org/10.1073/pnas.1320913111
    • Open Access
      Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria
      • From the Cover
      Susumu Yoshizawa, Yohei Kumagai, Hana Kim, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Iwasaki, Edward F. DeLong, and Kazuhiro Kogure
      PNAS May 6, 2014 111 (18) 6732-6737; first published March 31, 2014. https://doi.org/10.1073/pnas.1403051111

      See companion article:

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Proceedings of the National Academy of Sciences: 111 (18)
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