Table of Contents

Biological Sciences

• Agricultural Sciences

  • Open Access

    A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs

    Wellington Muchero, Ndeye N. Diop, Prasanna R. Bhat, Raymond D. Fenton, Steve Wanamaker, Marti Pottorff, Sarah Hearne, Ndiaga Cisse, Christian Fatokun, Jeffrey D. Ehlers, Philip A. Roberts, and Timothy J. Close

    PNAS October 27, 2009 106 (43) 18159-18164; https://doi.org/10.1073/pnas.0905886106

• Anthropology

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    Age at first reproduction explains rate variation in the strepsirrhine molecular clock

    C. Tsantes and M. E. Steiper

    PNAS October 27, 2009 106 (43) 18165-18170; https://doi.org/10.1073/pnas.0906686106

• Applied Biological Sciences

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    Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor

    Keith Biggadike, Randy K. Bledsoe, Diane M. Coe, Tony W. J. Cooper, David House, Marie A. Iannone, Simon J. F. Macdonald, Kevin P. Madauss, Iain M. McLay, Tracy J. Shipley, Simon J. Taylor, Thuy B. Tran, Iain J. Uings, Victoria Weller, and Shawn P. Williams

    PNAS October 27, 2009 106 (43) 18114-18119; https://doi.org/10.1073/pnas.0909125106
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    Site-specific recombination for the modification of transgenic strains of the Mediterranean fruit fly Ceratitis capitata

    Marc F. Schetelig, Francesca Scolari, Alfred M. Handler, Sebastian Kittelmann, Giuliano Gasperi, and Ernst A. Wimmer

    PNAS October 27, 2009 106 (43) 18171-18176; https://doi.org/10.1073/pnas.0907264106

• Biochemistry

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    Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state

    Alphonse I. Arunkumar, Gregory C. Campanello, and David P. Giedroc

    PNAS October 27, 2009 106 (43) 18177-18182; https://doi.org/10.1073/pnas.0905558106
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    Endogenous nitric oxide regulates the recovery of the radiation-resistant bacterium Deinococcus radiodurans from exposure to UV light

    Bhumit A. Patel, Magali Moreau, Joanne Widom, Huan Chen, Longfei Yin, Yuejin Hua, and Brian R. Crane

    PNAS October 27, 2009 106 (43) 18183-18188; https://doi.org/10.1073/pnas.0907262106

    See companion article:

    • In This Issue

      - Oct 27, 2009
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    Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end-joining for cDNA ligation

    Fanglei Zhuang, Marta Mastroianni, Travis B. White, and Alan M. Lambowitz

    PNAS October 27, 2009 106 (43) 18189-18194; https://doi.org/10.1073/pnas.0910277106
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    Multistart simulated annealing refinement of the crystal structure of the 70S ribosome

    Andrei Korostelev, Martin Laurberg, and Harry F. Noller

    PNAS October 27, 2009 106 (43) 18195-18200; https://doi.org/10.1073/pnas.0909287106
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    An 8-oxo-guanine repair pathway coordinated by MUTYH glycosylase and DNA polymerase λ

    Barbara van Loon and Ulrich Hübscher

    PNAS October 27, 2009 106 (43) 18201-18206; https://doi.org/10.1073/pnas.0907280106
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    Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

    Karen Adelman, Megan A. Kennedy, Sergei Nechaev, Daniel A. Gilchrist, Ginger W. Muse, Yurii Chinenov, and Inez Rogatsky

    PNAS October 27, 2009 106 (43) 18207-18212; https://doi.org/10.1073/pnas.0910177106
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    Identification of a physiological E2 module for the human anaphase-promoting complex

    Adam Williamson, Katherine E. Wickliffe, Barbara G. Mellone, Ling Song, Gary H. Karpen, and Michael Rape

    PNAS October 27, 2009 106 (43) 18213-18218; https://doi.org/10.1073/pnas.0907887106
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    Highly error-free role of DNA polymerase η in the replicative bypass of UV-induced pyrimidine dimers in mouse and human cells

    Jung-Hoon Yoon, Louise Prakash, and Satya Prakash

    PNAS October 27, 2009 106 (43) 18219-18224; https://doi.org/10.1073/pnas.0910121106
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    Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct

    Jayvardhan Pandit, Michael D. Forman, Kimberly F. Fennell, Keith S. Dillman, and Frank S. Menniti

    PNAS October 27, 2009 106 (43) 18225-18230; https://doi.org/10.1073/pnas.0907635106

• Biophysics and Computational Biology

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    Water-mediated signal multiplication with Y-shaped carbon nanotubes

    Yusong Tu, Peng Xiu, Rongzheng Wan, Jun Hu, Ruhong Zhou, and Haiping Fang

    PNAS October 27, 2009 106 (43) 18120-18124; https://doi.org/10.1073/pnas.0902676106
  • Open Access

    Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis

    E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo

    PNAS October 27, 2009 106 (43) 18125-18130; https://doi.org/10.1073/pnas.0904721106
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    Kinetics of hyperpolarized ¹³C₁-pyruvate transport and metabolism in living human breast cancer cells

    Talia Harris, Galit Eliyahu, Lucio Frydman, and Hadassa Degani

    PNAS October 27, 2009 106 (43) 18131-18136; https://doi.org/10.1073/pnas.0909049106
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    Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging

    • From the Cover

    Joost van Mameren, Peter Gross, Geraldine Farge, Pleuni Hooijman, Mauro Modesti, Maria Falkenberg, Gijs J. L. Wuite, and Erwin J. G. Peterman

    PNAS October 27, 2009 106 (43) 18231-18236; https://doi.org/10.1073/pnas.0904322106

    See companion article:

    • Peeling back the mystery of DNA overstretching

      - Oct 21, 2009
    • In This Issue

      - Oct 27, 2009
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    Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

    Nobuyasu Koga, Tomoshi Kameda, Kei-ichi Okazaki, and Shoji Takada

    PNAS October 27, 2009 106 (43) 18237-18242; https://doi.org/10.1073/pnas.0904756106
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    Single-cell response to stiffness exhibits muscle-like behavior

    Démosthène Mitrossilis, Jonathan Fouchard, Axel Guiroy, Nicolas Desprat, Nicolas Rodriguez, Ben Fabry, and Atef Asnacios

    PNAS October 27, 2009 106 (43) 18243-18248; https://doi.org/10.1073/pnas.0903994106
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    Hidden dynamic allostery in a PDZ domain

    Chad M. Petit, Jun Zhang, Paul J. Sapienza, Ernesto J. Fuentes, and Andrew L. Lee

    PNAS October 27, 2009 106 (43) 18249-18254; https://doi.org/10.1073/pnas.0904492106
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    Myosin VI undergoes a 180° power stroke implying an uncoupling of the front lever arm

    Jeff G. Reifenberger, Erdal Toprak, HyeongJun Kim, Dan Safer, H. Lee Sweeney, and Paul R. Selvin

    PNAS October 27, 2009 106 (43) 18255-18260; https://doi.org/10.1073/pnas.0900005106
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    Mechanochemical model for myosin V

    Erin M. Craig and Heiner Linke

    PNAS October 27, 2009 106 (43) 18261-18266; https://doi.org/10.1073/pnas.0908192106
  • Open Access

    Fibronectin forms the most extensible biological fibers displaying switchable force-exposed cryptic binding sites

    Enrico Klotzsch, Michael L. Smith, Kristopher E. Kubow, Simon Muntwyler, William C. Little, Felix Beyeler, Delphine Gourdon, Bradley J. Nelson, and Viola Vogel

    PNAS October 27, 2009 106 (43) 18267-18272; https://doi.org/10.1073/pnas.0907518106
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    Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization

    Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentsev, Mikael Oliveberg, and Mikael Akke

    PNAS October 27, 2009 106 (43) 18273-18278; https://doi.org/10.1073/pnas.0907387106

• Cell Biology

  • Open Access

    Tracking lineages of single cells in lines using a microfluidic device

    Amy C. Rowat, James C. Bird, Jeremy J. Agresti, Oliver J. Rando, and David A. Weitz

    PNAS October 27, 2009 106 (43) 18149-18154; https://doi.org/10.1073/pnas.0903163106
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    Miz1 is a signal- and pathway-specific modulator or regulator (SMOR) that suppresses TNF-α-induced JNK1 activation

    Jing Liu, Yingming Zhao, Martin Eilers, and Anning Lin

    PNAS October 27, 2009 106 (43) 18279-18284; https://doi.org/10.1073/pnas.0906328106
  • Open Access

    Statins inhibit protein lipidation and induce the unfolded protein response in the non-sterol producing nematode Caenorhabditis elegans

    Catarina Mörck, Louise Olsen, Caroline Kurth, Annelie Persson, Nadia Jin Storm, Emma Svensson, John-Olov Jansson, Marika Hellqvist, Annika Enejder, Nils J. Faergeman, and Marc Pilon

    PNAS October 27, 2009 106 (43) 18285-18290; https://doi.org/10.1073/pnas.0907117106

• Developmental Biology

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    Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring

    Joel Smith and Eric H. Davidson

    PNAS October 27, 2009 106 (43) 18291-18296; https://doi.org/10.1073/pnas.0910007106
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    Temporomandibular joint formation requires two distinct hedgehog-dependent steps

    Patricia Purcell, Brian W. Joo, Jimmy K. Hu, Pamela V. Tran, Monica L. Calicchio, Daniel J. O'Connell, Richard L. Maas, and Clifford J. Tabin

    PNAS October 27, 2009 106 (43) 18297-18302; https://doi.org/10.1073/pnas.0908836106
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    Dual role for the methyltransferase G9a in the maintenance of β-globin gene transcription in adult erythroid cells

    Chandra-Prakash Chaturvedi, Alison M. Hosey, Carmen Palii, Carolina Perez-Iratxeta, Yoshihiro Nakatani, Jeffrey A. Ranish, F. Jeffrey Dilworth, and Marjorie Brand

    PNAS October 27, 2009 106 (43) 18303-18308; https://doi.org/10.1073/pnas.0906769106
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    The keratin-related Ouroboros proteins function as immune antigens mediating tail regression in Xenopus metamorphosis

    Katsuki Mukaigasa, Akira Hanasaki, Mitsugu Maéno, Hiroshi Fujii, Shin-ichiro Hayashida, Mari Itoh, Makoto Kobayashi, Shin Tochinai, Masayuki Hatta, Kazuya Iwabuchi, Masanori Taira, Kazunori Onoé, and Yumi Izutsu

    PNAS October 27, 2009 106 (43) 18309-18314; https://doi.org/10.1073/pnas.0708837106

• Ecology

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    Divergent investment strategies of Acacia myrmecophytes and the coexistence of mutualists and exploiters

    Martin Heil, Marcia González-Teuber, Lars W. Clement, Stefanie Kautz, Manfred Verhaagh, and Juan Carlos Silva Bueno

    PNAS October 27, 2009 106 (43) 18091-18096; https://doi.org/10.1073/pnas.0904304106
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    Evidence that chytrids dominate fungal communities in high-elevation soils

    K. R. Freeman, A. P. Martin, D. Karki, R. C. Lynch, M. S. Mitter, A. F. Meyer, J. E. Longcore, D. R. Simmons, and S. K. Schmidt

    PNAS October 27, 2009 106 (43) 18315-18320; https://doi.org/10.1073/pnas.0907303106

• Evolution

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    Macroevolutionary chemical escalation in an ancient plant–herbivore arms race

    Judith X. Becerra, Koji Noge, and D. Lawrence Venable

    PNAS October 27, 2009 106 (43) 18062-18066; https://doi.org/10.1073/pnas.0904456106
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    Evidence for adaptive radiation from a phylogenetic study of plant defenses

    Anurag A. Agrawal, Mark Fishbein, Rayko Halitschke, Amy P. Hastings, Daniel L. Rabosky, and Sergio Rasmann

    PNAS October 27, 2009 106 (43) 18067-18072; https://doi.org/10.1073/pnas.0904862106
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    The evolution of antiherbivore defenses and their contribution to species coexistence in the tropical tree genus Inga

    Thomas A. Kursar, Kyle G. Dexter, John Lokvam, R. Toby Pennington, James E. Richardson, Marjorie G. Weber, Eric T. Murakami, Camilla Drake, Ruth McGregor, and Phyllis D. Coley

    PNAS October 27, 2009 106 (43) 18073-18078; https://doi.org/10.1073/pnas.0904786106
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    Plant sex and the evolution of plant defenses against herbivores

    Marc T. J. Johnson, Stacey D. Smith, and Mark D. Rausher

    PNAS October 27, 2009 106 (43) 18079-18084; https://doi.org/10.1073/pnas.0904695106
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    Macroevolutionary patterns of defense and pollination in Dalechampia vines: Adaptation, exaptation, and evolutionary novelty

    W. Scott Armbruster, Joongku Lee, and Bruce G. Baldwin

    PNAS October 27, 2009 106 (43) 18085-18090; https://doi.org/10.1073/pnas.0907051106
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    Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks

    Ian S. Pearse and Andrew L. Hipp

    PNAS October 27, 2009 106 (43) 18097-18102; https://doi.org/10.1073/pnas.0904867106
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    Repeated climate-linked host shifts have promoted diversification in a temperate clade of leaf-mining flies

    Isaac S. Winkler, Charles Mitter, and Sonja J. Scheffer

    PNAS October 27, 2009 106 (43) 18103-18108; https://doi.org/10.1073/pnas.0904852106

• Genetics

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    Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

    • From the Cover

    Stacie L. Bumgarner, Robin D. Dowell, Paula Grisafi, David K. Gifford, and Gerald R. Fink

    PNAS October 27, 2009 106 (43) 18321-18326; https://doi.org/10.1073/pnas.0909641106

    See companion article:

    • A transcription switch toggled by noncoding RNAs

      - Oct 21, 2009

• Immunology

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    Glycans on influenza hemagglutinin affect receptor binding and immune response

    Cheng-Chi Wang, Juine-Ruey Chen, Yung-Chieh Tseng, Che-Hsiung Hsu, Yu-Fu Hung, Shih-Wei Chen, Chin-Mei Chen, Kay-Hooi Khoo, Ting-Jen Cheng, Yih-Shyun E. Cheng, Jia-Tsrong Jan, Chung-Yi Wu, Che Ma, and Chi-Huey Wong

    PNAS October 27, 2009 106 (43) 18137-18142; https://doi.org/10.1073/pnas.0909696106

    See companion article:

    • In This Issue

      - Oct 27, 2009
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    Negative regulation of MyD88-dependent signaling by IL-10 in dendritic cells

    JiHoon Chang, Steven L. Kunkel, and Cheong-Hee Chang

    PNAS October 27, 2009 106 (43) 18327-18332; https://doi.org/10.1073/pnas.0905815106
  • Open Access

    Age-associated increase in lifespan of naïve CD4 T cells contributes to T-cell homeostasis but facilitates development of functional defects

    Hirotake Tsukamoto, Karen Clise-Dwyer, Gail E. Huston, Debra K. Duso, Amanda L. Buck, Lawrence L. Johnson, Laura Haynes, and Susan L. Swain

    PNAS October 27, 2009 106 (43) 18333-18338; https://doi.org/10.1073/pnas.0910139106
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    Aberrantly resolved RAG-mediated DNA breaks in Atm-deficient lymphocytes target chromosomal breakpoints in cis

    Grace K. Mahowald, Jason M. Baron, Michael A. Mahowald, Shashikant Kulkarni, Andrea L. Bredemeyer, Craig H. Bassing, and Barry P. Sleckman

    PNAS October 27, 2009 106 (43) 18339-18344; https://doi.org/10.1073/pnas.0902545106
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    Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1

    Hongmin Zhang, Jin-huan Liu, Wei Yang, Timothy Springer, Motomu Shimaoka, and Jia-huai Wang

    PNAS October 27, 2009 106 (43) 18345-18350; https://doi.org/10.1073/pnas.0909301106

• Medical Sciences

  • Open Access

    Identifying genotype-dependent efficacy of single and combined PI3K- and MAPK-pathway inhibition in cancer

    Martin L. Sos, Stefanie Fischer, Roland Ullrich, Martin Peifer, Johannes M. Heuckmann, Mirjam Koker, Stefanie Heynck, Isabel Stückrath, Jonathan Weiss, Florian Fischer, Kathrin Michel, Aviva Goel, Lucia Regales, Katerina A. Politi, Samanthi Perera, Matthäus Getlik, Lukas C. Heukamp, Sascha Ansén, Thomas Zander, Rameen Beroukhim, Hamid Kashkar, Kevan M. Shokat, William R. Sellers, Daniel Rauh, Christine Orr, Klaus P. Hoeflich, Lori Friedman, Kwok-Kin Wong, William Pao, and Roman K. Thomas

    PNAS October 27, 2009 106 (43) 18351-18356; https://doi.org/10.1073/pnas.0907325106
  • Open Access

    A wave of nascent transcription on activated human genes

    Youichiro Wada, Yoshihiro Ohta, Meng Xu, Shuichi Tsutsumi, Takashi Minami, Kenji Inoue, Daisuke Komura, Jun'ichi Kitakami, Nobuhiko Oshida, Argyris Papantonis, Akashi Izumi, Mika Kobayashi, Hiroko Meguro, Yasuharu Kanki, Imari Mimura, Kazuki Yamamoto, Chikage Mataki, Takao Hamakubo, Katsuhiko Shirahige, Hiroyuki Aburatani, Hiroshi Kimura, Tatsuhiko Kodama, Peter R. Cook, and Sigeo Ihara

    PNAS October 27, 2009 106 (43) 18357-18361; https://doi.org/10.1073/pnas.0902573106

• Microbiology

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    Bacillus subtilis spreads by surfing on waves of surfactant

    Thomas E. Angelini, Marcus Roper, Roberto Kolter, David A. Weitz, and Michael P. Brenner

    PNAS October 27, 2009 106 (43) 18109-18113; https://doi.org/10.1073/pnas.0905890106

• Neuroscience

  • Open Access

    Monkey visual behavior falls into the uncanny valley

    Shawn A. Steckenfinger and Asif A. Ghazanfar

    PNAS October 27, 2009 106 (43) 18362-18366; https://doi.org/10.1073/pnas.0910063106
  • Open Access

    Alzheimer's disease-like pathological features in transgenic mice expressing the APP intracellular domain

    Kaushik Ghosal, Daniel L. Vogt, Man Liang, Yong Shen, Bruce T. Lamb, and Sanjay W. Pimplikar

    PNAS October 27, 2009 106 (43) 18367-18372; https://doi.org/10.1073/pnas.0907652106

    See companion article:

    • In This Issue

      - Oct 27, 2009
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    Podosomes are present in a postsynaptic apparatus and participate in its maturation

    Tomasz J. Proszynski, Jacinthe Gingras, Gregorio Valdez, Konrad Krzewski, and Joshua R. Sanes

    PNAS October 27, 2009 106 (43) 18373-18378; https://doi.org/10.1073/pnas.0910391106
  • Open Access

    Gray and white matter changes associated with tool-use learning in macaque monkeys

    M. M. Quallo, C. J. Price, K. Ueno, T. Asamizuya, K. Cheng, R. N. Lemon, and A. Iriki

    PNAS October 27, 2009 106 (43) 18379-18384; https://doi.org/10.1073/pnas.0909751106
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    Ca²⁺-dependent release of Munc18-1 from presynaptic mGluRs in short-term facilitation

    Yoshiaki Nakajima, Sumiko Mochida, Katsuya Okawa, and Shigetada Nakanishi

    PNAS October 27, 2009 106 (43) 18385-18389; https://doi.org/10.1073/pnas.0910088106
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    Spatiotemporal precision and hemodynamic mechanism of optical point spreads in alert primates

    Yevgeniy B. Sirotin, Elizabeth M. C. Hillman, Clemence Bordier, and Aniruddha Das

    PNAS October 27, 2009 106 (43) 18390-18395; https://doi.org/10.1073/pnas.0905509106

• Pharmacology

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    Zyklophin, a systemically active selective kappa opioid receptor peptide antagonist with short duration of action

    • From the Cover

    Jane V. Aldrich, Kshitij A. Patkar, and Jay P. McLaughlin

    PNAS October 27, 2009 106 (43) 18396-18401; https://doi.org/10.1073/pnas.0910180106

    See companion article:

    • In This Issue

      - Oct 27, 2009

• Physiology

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    α-Actinin2 cytoskeletal protein is required for the functional membrane localization of a Ca²⁺-activated K⁺ channel (SK2 channel)

    Ling Lu, Valeriy Timofeyev, Ning Li, Sassan Rafizadeh, Anil Singapuri, Todd R. Harris, and Nipavan Chiamvimonvat

    PNAS October 27, 2009 106 (43) 18402-18407; https://doi.org/10.1073/pnas.0908207106
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    Nitric oxide permits hypoxia-induced lymphatic perfusion by controlling arterial-lymphatic conduits in zebrafish and glass catfish

    Lasse Dahl Ejby Jensen, Renhai Cao, Eva-Maria Hedlund, Iris Söll, Jon O. Lundberg, Giselbert Hauptmann, John Fleng Steffensen, and Yihai Cao

    PNAS October 27, 2009 106 (43) 18408-18413; https://doi.org/10.1073/pnas.0907608106

• Plant Biology

  • Open Access

    VIP1 response elements mediate mitogen-activated protein kinase 3-induced stress gene expression

    Andrea Pitzschke, Armin Djamei, Markus Teige, and Heribert Hirt

    PNAS October 27, 2009 106 (43) 18414-18419; https://doi.org/10.1073/pnas.0905599106

• Population Biolgoy

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    Peripatetic health-care workers as potential superspreaders

    Laura Temime, Lulla Opatowski, Yohan Pannet, Christian Brun-Buisson, Pierre Yves Boëlle, and Didier Guillemot

    PNAS October 27, 2009 106 (43) 18420-18425; https://doi.org/10.1073/pnas.0900974106

    See companion article:

    • In This Issue

      - Oct 27, 2009