Table of Contents

Biological Sciences

• Anthropology

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    Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution

    • From the Cover

    Kevin E. Langergraber, Kay Prüfer, Carolyn Rowney, Christophe Boesch, Catherine Crockford, Katie Fawcett, Eiji Inoue, Miho Inoue-Muruyama, John C. Mitani, Martin N. Muller, Martha M. Robbins, Grit Schubert, Tara S. Stoinski, Bence Viola, David Watts, Roman M. Wittig, Richard W. Wrangham, Klaus Zuberbühler, Svante Pääbo, and Linda Vigilant

    PNAS September 25, 2012 109 (39) 15716-15721; https://doi.org/10.1073/pnas.1211740109

    See companion article:

    • Longer time scale for human evolution

      - Sep 14, 2012

    See companion article:

    • Divergences and mutation rates in humans and apes

      - Jan 31, 2013

• Biochemistry

  • Open Access

    Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

    Giedrius Gasiunas, Rodolphe Barrangou, Philippe Horvath, and Virginijus Siksnys

    PNAS September 25, 2012 109 (39) E2579-E2586; https://doi.org/10.1073/pnas.1208507109
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    Folate binding site of flavin-dependent thymidylate synthase

    Eric M. Koehn, Laura L. Perissinotti, Salah Moghram, Arjun Prabhakar, Scott A. Lesley, Irimpan I. Mathews, and Amnon Kohen

    PNAS September 25, 2012 109 (39) 15722-15727; https://doi.org/10.1073/pnas.1206077109
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    Selection of antibodies that regulate phenotype from intracellular combinatorial antibody libraries

    Hongkai Zhang, Ian A. Wilson, and Richard A. Lerner

    PNAS September 25, 2012 109 (39) 15728-15733; https://doi.org/10.1073/pnas.1214275109
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    Reversible cycling between cysteine persulfide-ligated [2Fe-2S] and cysteine-ligated [4Fe-4S] clusters in the FNR regulatory protein

    Bo Zhang, Jason C. Crack, Sowmya Subramanian, Jeffrey Green, Andrew J. Thomson, Nick E. Le Brun, and Michael K. Johnson

    PNAS September 25, 2012 109 (39) 15734-15739; https://doi.org/10.1073/pnas.1208787109
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    Revisiting the contribution of negative charges on the chaperonin cage wall to the acceleration of protein folding

    Fumihiro Motojima, Yuko Motojima-Miyazaki, and Masasuke Yoshida

    PNAS September 25, 2012 109 (39) 15740-15745; https://doi.org/10.1073/pnas.1204547109

• Biophysics and Computational Biology

  • Open Access

    Parameter-free model discrimination criterion based on steady-state coplanarity

    Heather A. Harrington, Kenneth L. Ho, Thomas Thorne, and Michael P.H. Stumpf

    PNAS September 25, 2012 109 (39) 15746-15751; https://doi.org/10.1073/pnas.1117073109
  • Open Access

    Domain–domain interactions in full-length p53 and a specific DNA complex probed by methyl NMR spectroscopy

    Michal Bista, Stefan M. Freund, and Alan R. Fersht

    PNAS September 25, 2012 109 (39) 15752-15756; https://doi.org/10.1073/pnas.1214176109
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    A kinetic model of rapidly reversible nonphotochemical quenching

    Julia Zaks, Kapil Amarnath, David M. Kramer, Krishna K. Niyogi, and Graham R. Fleming

    PNAS September 25, 2012 109 (39) 15757-15762; https://doi.org/10.1073/pnas.1211017109

    See companion article:

    • Modeling the protection of photosynthesis

      - Sep 18, 2012
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    Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

    Jin Wang, Ronaldo J. Oliveira, Xiakun Chu, Paul C. Whitford, Jorge Chahine, Wei Han, Erkang Wang, José N. Onuchic, and Vitor B.P. Leite

    PNAS September 25, 2012 109 (39) 15763-15768; https://doi.org/10.1073/pnas.1212842109
  • Open Access

    Evidence that viral RNAs have evolved for efficient, two-stage packaging

    Alexander Borodavka, Roman Tuma, and Peter G. Stockley

    PNAS September 25, 2012 109 (39) 15769-15774; https://doi.org/10.1073/pnas.1204357109
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    Supertertiary structure of the synaptic MAGuK scaffold proteins is conserved

    James J. McCann, Liqiang Zheng, Daniel Rohrbeck, Suren Felekyan, Ralf Kühnemuth, R. Bryan Sutton, Claus A. M. Seidel, and Mark E. Bowen

    PNAS September 25, 2012 109 (39) 15775-15780; https://doi.org/10.1073/pnas.1200254109

• Cell Biology

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    Ultrastructural dynamics of proteins involved in endocytic budding

    Fatima-Zahra Idrissi, Anabel Blasco, Anna Espinal, and María Isabel Geli

    PNAS September 25, 2012 109 (39) E2587-E2594; https://doi.org/10.1073/pnas.1202789109
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    ECM microenvironment regulates collective migration and local dissemination in normal and malignant mammary epithelium

    Kim-Vy Nguyen-Ngoc, Kevin J. Cheung, Audrey Brenot, Eliah R. Shamir, Ryan S. Gray, William C. Hines, Paul Yaswen, Zena Werb, and Andrew J. Ewald

    PNAS September 25, 2012 109 (39) E2595-E2604; https://doi.org/10.1073/pnas.1212834109
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    Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity

    Julian Lai, Chuan Hock Koh, Monika Tjota, Laurent Pieuchot, Vignesh Raman, Karthik Balakrishna Chandrababu, Daiwen Yang, Limsoon Wong, and Gregory Jedd

    PNAS September 25, 2012 109 (39) 15781-15786; https://doi.org/10.1073/pnas.1207467109
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    TBC1D16 is a Rab4A GTPase activating protein that regulates receptor recycling and EGF receptor signaling

    Basem S. Goueli, Marianne Broome Powell, Elizabeth C. Finger, and Suzanne R. Pfeffer

    PNAS September 25, 2012 109 (39) 15787-15792; https://doi.org/10.1073/pnas.1204540109
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    Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

    Mathieu Beauchemin, Sougata Roy, Philippe Daoust, Steve Dagenais-Bellefeuille, Thierry Bertomeu, Louis Letourneau, B. Franz Lang, and David Morse

    PNAS September 25, 2012 109 (39) 15793-15798; https://doi.org/10.1073/pnas.1206683109
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    Dual modes of motility at the leading edge of migrating epithelial cell sheets

    Jes K. Klarlund

    PNAS September 25, 2012 109 (39) 15799-15804; https://doi.org/10.1073/pnas.1210992109
  • Open Access

    cAMP response element-binding protein promotes gliomagenesis by modulating the expression of oncogenic microRNA-23a

    Xiaochao Tan, Shan Wang, Liyuan Zhu, Chao Wu, Bin Yin, Jizong Zhao, Jiangang Yuan, Boqin Qiang, and Xiaozhong Peng

    PNAS September 25, 2012 109 (39) 15805-15810; https://doi.org/10.1073/pnas.1207787109
  • Open Access

    Compartmentalization of superoxide dismutase 1 (SOD1G93A) aggregates determines their toxicity

    Sarah J. Weisberg, Roman Lyakhovetsky, Ayelet-chen Werdiger, Aaron D. Gitler, Yoav Soen, and Daniel Kaganovich

    PNAS September 25, 2012 109 (39) 15811-15816; https://doi.org/10.1073/pnas.1205829109

• Developmental Biology

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    Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi

    Katherine D. Walton, Åsa Kolterud, Michael J. Czerwinski, Michael J. Bell, Ajay Prakash, Juhi Kushwaha, Ann S. Grosse, Santiago Schnell, and Deborah L. Gumucio

    PNAS September 25, 2012 109 (39) 15817-15822; https://doi.org/10.1073/pnas.1205669109

• Ecology

  • Open Access

    Models and tests of optimal density and maximal yield for crop plants

    • From the Cover

    Jianming Deng, Jinzhi Ran, Zhiqiang Wang, Zhexuan Fan, Genxuan Wang, Mingfei Ji, Jing Liu, Yun Wang, Jianquan Liu, and James H. Brown

    PNAS September 25, 2012 109 (39) 15823-15828; https://doi.org/10.1073/pnas.1210955109

    See companion article:

    • Scaling of crop systems

      - Sep 14, 2012
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    Allometric scaling of population variance with mean body size is predicted from Taylor’s law and density-mass allometry

    Joel E. Cohen, Meng Xu, and William S. F. Schuster

    PNAS September 25, 2012 109 (39) 15829-15834; https://doi.org/10.1073/pnas.1212883109

• Evolution

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    Silurian horseshoe crab illuminates the evolution of arthropod limbs

    Derek E. G. Briggs, Derek J. Siveter, David J. Siveter, Mark D. Sutton, Russell J. Garwood, and David Legg

    PNAS September 25, 2012 109 (39) 15702-15705; https://doi.org/10.1073/pnas.1205875109
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    Phylogenies reveal predictive power of traditional medicine in bioprospecting

    C. Haris Saslis-Lagoudakis, Vincent Savolainen, Elizabeth M. Williamson, Félix Forest, Steven J. Wagstaff, Sushim R. Baral, Mark F. Watson, Colin A. Pendry, and Julie A. Hawkins

    PNAS September 25, 2012 109 (39) 15835-15840; https://doi.org/10.1073/pnas.1202242109
  • Open Access

    Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons

    Trees-Juen Chuang, Feng-Chi Chen, and Yen-Zho Chen

    PNAS September 25, 2012 109 (39) 15841-15846; https://doi.org/10.1073/pnas.1208214109

• Genetics

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    Epistasis dominates the genetic architecture of Drosophila quantitative traits

    • Inaugural Article

    Wen Huang, Stephen Richards, Mary Anna Carbone, Dianhui Zhu, Robert R. H. Anholt, Julien F. Ayroles, Laura Duncan, Katherine W. Jordan, Faye Lawrence, Michael M. Magwire, Crystal B. Warner, Kerstin Blankenburg, Yi Han, Mehwish Javaid, Joy Jayaseelan, Shalini N. Jhangiani, Donna Muzny, Fiona Ongeri, Lora Perales, Yuan-Qing Wu, Yiqing Zhang, Xiaoyan Zou, Eric A. Stone, Richard A. Gibbs, and Trudy F. C. Mackay

    PNAS September 25, 2012 109 (39) 15553-15559; https://doi.org/10.1073/pnas.1213423109
  • Open Access

    Genetic composition of yield heterosis in an elite rice hybrid

    Gang Zhou, Ying Chen, Wen Yao, Chengjun Zhang, Weibo Xie, Jinping Hua, Yongzhong Xing, Jinghua Xiao, and Qifa Zhang

    PNAS September 25, 2012 109 (39) 15847-15852; https://doi.org/10.1073/pnas.1214141109
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    p21-Activated kinase interacts with Wnt signaling to regulate tissue polarity and gene expression

    Kah Yee Goh, Natalie Weili Ng, Thilo Hagen, and Takao Inoue

    PNAS September 25, 2012 109 (39) 15853-15858; https://doi.org/10.1073/pnas.1120795109

• Immunology

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    Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development

    Jorge Galindo-Villegas, Diana García-Moreno, Sofia de Oliveira, José Meseguer, and Victoriano Mulero

    PNAS September 25, 2012 109 (39) E2605-E2614; https://doi.org/10.1073/pnas.1209920109
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    The immunodominant myeloperoxidase T-cell epitope induces local cell-mediated injury in antimyeloperoxidase glomerulonephritis

    Joshua D. Ooi, Janet Chang, Michael J. Hickey, Dorin-Bogdan Borza, Lars Fugger, Stephen R. Holdsworth, and A. Richard Kitching

    PNAS September 25, 2012 109 (39) E2615-E2624; https://doi.org/10.1073/pnas.1210147109
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    A mouse model for HIV-1 entry

    John Pietzsch, Henning Gruell, Stylianos Bournazos, Bridget M. Donovan, Florian Klein, Ron Diskin, Michael S. Seaman, Pamela J. Bjorkman, Jeffrey V. Ravetch, Alexander Ploss, and Michel C. Nussenzweig

    PNAS September 25, 2012 109 (39) 15859-15864; https://doi.org/10.1073/pnas.1213409109
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    Chromatin conformation governs T-cell receptor Jβ gene segment usage

    Wilfred Ndifon, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich-Zeliger, Ruth Arnon, and Nir Friedman

    PNAS September 25, 2012 109 (39) 15865-15870; https://doi.org/10.1073/pnas.1203916109
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    Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo

    Sasan Zandi, Josefine Åhsberg, Panagiotis Tsapogas, Jenny Stjernberg, Hong Qian, and Mikael Sigvardsson

    PNAS September 25, 2012 109 (39) 15871-15876; https://doi.org/10.1073/pnas.1210144109
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    T cells engineered with a T cell receptor against the prostate antigen TARP specifically kill HLA-A2⁺ prostate and breast cancer cells

    Victoria Hillerdal, Berith Nilsson, Björn Carlsson, Fredrik Eriksson, and Magnus Essand

    PNAS September 25, 2012 109 (39) 15877-15881; https://doi.org/10.1073/pnas.1209042109
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    Altered Ig levels and antibody responses in mice deficient for the Fc receptor for IgM (FcμR)

    Kazuhito Honjo, Yoshiki Kubagawa, Dewitt M. Jones, Brian Dizon, Zilu Zhu, Hiroshi Ohno, Shozo Izui, John F. Kearney, and Hiromi Kubagawa

    PNAS September 25, 2012 109 (39) 15882-15887; https://doi.org/10.1073/pnas.1206567109

• Medical Sciences

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    Oral advanced glycation endproducts (AGEs) promote insulin resistance and diabetes by depleting the antioxidant defenses AGE receptor-1 and sirtuin 1

    • From the Cover

    Weijing Cai, Maya Ramdas, Li Zhu, Xue Chen, Gary E. Striker, and Helen Vlassara

    PNAS September 25, 2012 109 (39) 15888-15893; https://doi.org/10.1073/pnas.1205847109

    See companion article:

    • AGEs and diabetes

      - Sep 14, 2012
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    Collaborative interplay between FGF-2 and VEGF-C promotes lymphangiogenesis and metastasis

    Renhai Cao, Hong Ji, Ninghan Feng, Yin Zhang, Xiaojuan Yang, Patrik Andersson, Yuping Sun, Katerina Tritsaris, Anker Jon Hansen, Steen Dissing, and Yihai Cao

    PNAS September 25, 2012 109 (39) 15894-15899; https://doi.org/10.1073/pnas.1208324109

• Microbiology

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    Fusion activation by a headless parainfluenza virus 5 hemagglutinin-neuraminidase stalk suggests a modular mechanism for triggering

    Sayantan Bose, Aarohi Zokarkar, Brett D. Welch, George P. Leser, Theodore S. Jardetzky, and Robert A. Lamb

    PNAS September 25, 2012 109 (39) E2625-E2634; https://doi.org/10.1073/pnas.1213813109
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    Virulence and transmissibility of H1N2 influenza virus in ferrets imply the continuing threat of triple-reassortant swine viruses

    Philippe Noriel Q. Pascua, Min-Suk Song, Jun Han Lee, Yun Hee Baek, Hyeok-il Kwon, Su-Jin Park, Eun Hye Choi, Gyo-Jin Lim, Ok-Jun Lee, Si-Wook Kim, Chul-Joong Kim, Moon Hee Sung, Myung Hee Kim, Sun-Woo Yoon, Elena A. Govorkova, Richard J. Webby, Robert G. Webster, and Young-Ki Choi

    PNAS September 25, 2012 109 (39) 15900-15905; https://doi.org/10.1073/pnas.1205576109

    See companion article:

    • In This Issue

      - Sep 25, 2012
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    Activation of Escherichia coli antiterminator BglG requires its phosphorylation

    Fabian M. Rothe, Thomas Bahr, Jörg Stülke, Bodo Rak, and Boris Görke

    PNAS September 25, 2012 109 (39) 15906-15911; https://doi.org/10.1073/pnas.1210443109

• Neuroscience

  • Open Access

    Mechanism for Hypocretin-mediated sleep-to-wake transitions

    Matthew E. Carter, Julia Brill, Patricia Bonnavion, John R. Huguenard, Ramon Huerta, and Luis de Lecea

    PNAS September 25, 2012 109 (39) E2635-E2644; https://doi.org/10.1073/pnas.1202526109
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    Brain imaging reveals neuronal circuitry underlying the crow’s perception of human faces

    John M. Marzluff, Robert Miyaoka, Satoshi Minoshima, and Donna J. Cross

    PNAS September 25, 2012 109 (39) 15912-15917; https://doi.org/10.1073/pnas.1206109109
  • Open Access

    Progressive dopaminergic cell loss with unilateral-to-bilateral progression in a genetic model of Parkinson disease

    Maxime W. C. Rousseaux, Paul C. Marcogliese, Dianbo Qu, Sarah J. Hewitt, Sarah Seang, Raymond H. Kim, Ruth S. Slack, Michael G. Schlossmacher, Diane C. Lagace, Tak W. Mak, and David S. Park

    PNAS September 25, 2012 109 (39) 15918-15923; https://doi.org/10.1073/pnas.1205102109
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    Role of pro-brain-derived neurotrophic factor (proBDNF) to mature BDNF conversion in activity-dependent competition at developing neuromuscular synapses

    H. Shawn Je, Feng Yang, Yuanyuan Ji, Guhan Nagappan, Barbara L. Hempstead, and Bai Lu

    PNAS September 25, 2012 109 (39) 15924-15929; https://doi.org/10.1073/pnas.1207767109

• Pharmacology

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    Targeting blood-brain barrier sphingolipid signaling reduces basal P-glycoprotein activity and improves drug delivery to the brain

    Ronald E. Cannon, John C. Peart, Brian T. Hawkins, Christopher R. Campos, and David S. Miller

    PNAS September 25, 2012 109 (39) 15930-15935; https://doi.org/10.1073/pnas.1203534109

    See companion article:

    • In This Issue

      - Sep 25, 2012
  • Open Access

    Endochin-like quinolones are highly efficacious against acute and latent experimental toxoplasmosis

    J. Stone Doggett, Aaron Nilsen, Isaac Forquer, Keith W. Wegmann, Lorraine Jones-Brando, Robert H. Yolken, Claudia Bordón, Susan A. Charman, Kasiram Katneni, Tracey Schultz, Jeremy N. Burrows, David J. Hinrichs, Brigitte Meunier, Vern B. Carruthers, and Michael K. Riscoe

    PNAS September 25, 2012 109 (39) 15936-15941; https://doi.org/10.1073/pnas.1208069109

• Plant Biology

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    Pointillist structural color in Pollia fruit

    Silvia Vignolini, Paula J. Rudall, Alice V. Rowland, Alison Reed, Edwige Moyroud, Robert B. Faden, Jeremy J. Baumberg, Beverley J. Glover, and Ullrich Steiner

    PNAS September 25, 2012 109 (39) 15712-15715; https://doi.org/10.1073/pnas.1210105109

    See companion article:

    • Pointillist structural color on land and in water

      - Nov 06, 2012
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    Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway

    Benoît Derrien, Nicolas Baumberger, Mikhail Schepetilnikov, Corrado Viotti, Julia De Cillia, Véronique Ziegler-Graff, Erika Isono, Karin Schumacher, and Pascal Genschik

    PNAS September 25, 2012 109 (39) 15942-15946; https://doi.org/10.1073/pnas.1209487109
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    Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress

    Daisuke Todaka, Kazuo Nakashima, Kyonoshin Maruyama, Satoshi Kidokoro, Yuriko Osakabe, Yusuke Ito, Satoko Matsukura, Yasunari Fujita, Kyouko Yoshiwara, Masaru Ohme-Takagi, Mikiko Kojima, Hitoshi Sakakibara, Kazuo Shinozaki, and Kazuko Yamaguchi-Shinozaki

    PNAS September 25, 2012 109 (39) 15947-15952; https://doi.org/10.1073/pnas.1207324109

• Psychological and Cognitive Sciences

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    Auditory perception at the root of language learning

    Jutta L. Mueller, Angela D. Friederici, and Claudia Männel

    PNAS September 25, 2012 109 (39) 15953-15958; https://doi.org/10.1073/pnas.1204319109
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    Nonconscious activation of placebo and nocebo pain responses

    Karin B. Jensen, Ted J. Kaptchuk, Irving Kirsch, Jacqueline Raicek, Kara M. Lindstrom, Chantal Berna, Randy L. Gollub, Martin Ingvar, and Jian Kong

    PNAS September 25, 2012 109 (39) 15959-15964; https://doi.org/10.1073/pnas.1202056109