Table of Contents

Biological Sciences

• Applied Biological Sciences

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    Tumor radiation response enhancement by acoustical stimulation of the vasculature

    Gregory J. Czarnota, Raffi Karshafian, Peter N. Burns, Shun Wong, Azza Al Mahrouki, Justin W. Lee, Amanda Caissie, William Tran, Christina Kim, Melissa Furukawa, Emily Wong, and Anoja Giles

    PNAS July 24, 2012 109 (30) E2033-E2041; https://doi.org/10.1073/pnas.1200053109
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    Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation

    Dan Zheng, David A. Giljohann, David L. Chen, Matthew D. Massich, Xiao-Qi Wang, Hristo Iordanov, Chad A. Mirkin, and Amy S. Paller

    PNAS July 24, 2012 109 (30) 11975-11980; https://doi.org/10.1073/pnas.1118425109
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    Stabilization of vaccines and antibiotics in silk and eliminating the cold chain

    Jeney Zhang, Eleanor Pritchard, Xiao Hu, Thomas Valentin, Bruce Panilaitis, Fiorenzo G. Omenetto, and David L. Kaplan

    PNAS July 24, 2012 109 (30) 11981-11986; first published July 9, 2012. https://doi.org/10.1073/pnas.1206210109

• Biochemistry

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    Structural and functional characterization of the two phosphoinositide binding sites of PROPPINs, a β-propeller protein family

    Roswitha Krick, Ricarda A. Busse, Andreea Scacioc, Milena Stephan, Andreas Janshoff, Michael Thumm, and Karin Kühnel

    PNAS July 24, 2012 109 (30) E2042-E2049; https://doi.org/10.1073/pnas.1205128109
  • Open Access

    Structural study on the architecture of the bacterial ATP synthase F_o motor

    Jonna K. Hakulinen, Adriana L. Klyszejko, Jan Hoffmann, Luise Eckhardt-Strelau, Bernd Brutschy, Janet Vonck, and Thomas Meier

    PNAS July 24, 2012 109 (30) E2050-E2056; https://doi.org/10.1073/pnas.1203971109
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    Phenanthriplatin, a monofunctional DNA-binding platinum anticancer drug candidate with unusual potency and cellular activity profile

    Ga Young Park, Justin J. Wilson, Ying Song, and Stephen J. Lippard

    PNAS July 24, 2012 109 (30) 11987-11992; https://doi.org/10.1073/pnas.1207670109
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    Preparation of unnatural N-to-N and C-to-C protein fusions

    Martin D. Witte, Juan J. Cragnolini, Stephanie K. Dougan, Nicholas C. Yoder, Maximilian W. Popp, and Hidde L. Ploegh

    PNAS July 24, 2012 109 (30) 11993-11998; https://doi.org/10.1073/pnas.1205427109
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    ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote

    Artem Y. Lyubimov, Alessandro Costa, Franziska Bleichert, Michael R. Botchan, and James M. Berger

    PNAS July 24, 2012 109 (30) 11999-12004; https://doi.org/10.1073/pnas.1209406109
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    Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet

    Denis A. Malyshev, Kirandeep Dhami, Henry T. Quach, Thomas Lavergne, Phillip Ordoukhanian, Ali Torkamani, and Floyd E. Romesberg

    PNAS July 24, 2012 109 (30) 12005-12010; https://doi.org/10.1073/pnas.1205176109
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    A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end

    Ludovic Pecqueur, Christian Duellberg, Birgit Dreier, Qiyang Jiang, Chunguang Wang, Andreas Plückthun, Thomas Surrey, Benoît Gigant, and Marcel Knossow

    PNAS July 24, 2012 109 (30) 12011-12016; https://doi.org/10.1073/pnas.1204129109
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    Structural and energetic basis of ALS-causing mutations in the atypical proline–tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS)

    Zi Chao Zhang and Yuh Min Chook

    PNAS July 24, 2012 109 (30) 12017-12021; https://doi.org/10.1073/pnas.1207247109

• Biophysics and Computational Biology

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    Magnetic characterization of isolated candidate vertebrate magnetoreceptor cells

    Stephan H.K. Eder, Hervé Cadiou, Airina Muhamad, Peter A. McNaughton, Joseph L. Kirschvink, and Michael Winklhofer

    PNAS July 24, 2012 109 (30) 12022-12027; https://doi.org/10.1073/pnas.1205653109
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    Mechanical elasticity as a physical signature of conformational dynamics in a virus particle

    Milagros Castellanos, Rebeca Pérez, Carolina Carrasco, Mercedes Hernando-Pérez, Julio Gómez-Herrero, Pedro J. de Pablo, and Mauricio G. Mateu

    PNAS July 24, 2012 109 (30) 12028-12033; https://doi.org/10.1073/pnas.1207437109
  • Open Access

    Speed, dissipation, and error in kinetic proofreading

    Arvind Murugan, David A. Huse, and Stanislas Leibler

    PNAS July 24, 2012 109 (30) 12034-12039; https://doi.org/10.1073/pnas.1119911109
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    Transcriptome and methylome interactions in rice hybrids

    Ramakrishna K. Chodavarapu, Suhua Feng, Bo Ding, Stacey A. Simon, David Lopez, Yulin Jia, Guo-Liang Wang, Blake C. Meyers, Steven E. Jacobsen, and Matteo Pellegrini

    PNAS July 24, 2012 109 (30) 12040-12045; https://doi.org/10.1073/pnas.1209297109

• Cell Biology

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    Rab27 and Rab3 sequentially regulate human sperm dense-core granule exocytosis

    Matías A. Bustos, Ornella Lucchesi, María C. Ruete, Luis S. Mayorga, and Claudia N. Tomes

    PNAS July 24, 2012 109 (30) E2057-E2066; https://doi.org/10.1073/pnas.1121173109
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    Cryoelectron tomography reveals doublet-specific structures and unique interactions in the I1 dynein

    Thomas Heuser, Cynthia F. Barber, Jianfeng Lin, Jeremy Krell, Matthew Rebesco, Mary E. Porter, and Daniela Nicastro

    PNAS July 24, 2012 109 (30) E2067-E2076; https://doi.org/10.1073/pnas.1120690109
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    Amyloid precursor protein (APP) traffics from the cell surface via endosomes for amyloid β (Aβ) production in the trans-Golgi network

    Regina Wai-Yan Choy, Zhiliang Cheng, and Randy Schekman

    PNAS July 24, 2012 109 (30) E2077-E2082; https://doi.org/10.1073/pnas.1208635109
  • Open Access

    JNK and PTEN cooperatively control the development of invasive adenocarcinoma of the prostate

    Anette Hübner, David J. Mulholland, Claire L. Standen, Maria Karasarides, Julie Cavanagh-Kyros, Tamera Barrett, Hongbo Chi, Dale L. Greiner, Cathy Tournier, Charles L. Sawyers, Richard A. Flavell, Hong Wu, and Roger J. Davis

    PNAS July 24, 2012 109 (30) 12046-12051; https://doi.org/10.1073/pnas.1209660109
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    Plasminogen activator inhibitor 1 - insulin-like growth factor binding protein 3 cascade regulates stress-induced senescence

    David J. Elzi, Yanlai Lai, Meihua Song, Kevin Hakala, Susan T. Weintraub, and Yuzuru Shiio

    PNAS July 24, 2012 109 (30) 12052-12057; https://doi.org/10.1073/pnas.1120437109
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    The Sin3a repressor complex is a master regulator of STAT transcriptional activity

    Laura Icardi, Raffaele Mori, Viola Gesellchen, Sven Eyckerman, Lode De Cauwer, Judith Verhelst, Koen Vercauteren, Xavier Saelens, Philip Meuleman, Geert Leroux-Roels, Karolien De Bosscher, Michael Boutros, and Jan Tavernier

    PNAS July 24, 2012 109 (30) 12058-12063; https://doi.org/10.1073/pnas.1206458109

• Developmental Biology

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    Tmem100, an ALK1 receptor signaling-dependent gene essential for arterial endothelium differentiation and vascular morphogenesis

    Satoshi Somekawa, Keiichi Imagawa, Hisaki Hayashi, Masahide Sakabe, Tomoko Ioka, Genki E. Sato, Ken Inada, Takaaki Iwamoto, Toshio Mori, Shiro Uemura, Osamu Nakagawa, and Yoshihiko Saito

    PNAS July 24, 2012 109 (30) 12064-12069; https://doi.org/10.1073/pnas.1207210109

• Ecology

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    Sensing and decision-making in random search

    Andrew M. Hein and Scott A. McKinley

    PNAS July 24, 2012 109 (30) 12070-12074; https://doi.org/10.1073/pnas.1202686109
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    Compensatory mechanisms for ameliorating the fundamental trade-off between predator avoidance and foraging

    • From the Cover

    Jennifer S. Thaler, Scott H. McArt, and Ian Kaplan

    PNAS July 24, 2012 109 (30) 12075-12080; https://doi.org/10.1073/pnas.1208070109

• Evolution

  • Open Access

    Evolution of music by public choice

    • From the Cover
    • Cozzarelli Prize Winner

    Robert M. MacCallum, Matthias Mauch, Austin Burt, and Armand M. Leroi

    PNAS July 24, 2012 109 (30) 12081-12086; https://doi.org/10.1073/pnas.1203182109

    See companion article:

    • Adaptive walks on the fitness landscape of music

      - Jul 24, 2012

    See companion article:

    • Reply to Claidière et al.: Role of psychological bias in evolution depends on the kind of culture

      - Dec 18, 2012

• Genetics

  • Open Access

    A public resource facilitating clinical use of genomes

    • Inaugural Article

    Madeleine P. Ball, Joseph V. Thakuria, Alexander Wait Zaranek, Tom Clegg, Abraham M. Rosenbaum, Xiaodi Wu, Misha Angrist, Jong Bhak, Jason Bobe, Matthew J. Callow, Carlos Cano, Michael F. Chou, Wendy K. Chung, Shawn M. Douglas, Preston W. Estep, Athurva Gore, Peter Hulick, Alberto Labarga, Je-Hyuk Lee, Jeantine E. Lunshof, Byung Chul Kim, Jong-Il Kim, Zhe Li, Michael F. Murray, Geoffrey B. Nilsen, Brock A. Peters, Anugraha M. Raman, Hugh Y. Rienhoff, Kimberly Robasky, Matthew T. Wheeler, Ward Vandewege, Daniel B. Vorhaus, Joyce L. Yang, Luhan Yang, John Aach, Euan A. Ashley, Radoje Drmanac, Seong-Jin Kim, Jin Billy Li, Leonid Peshkin, Christine E. Seidman, Jeong-Sun Seo, Kun Zhang, Heidi L. Rehm, and George M. Church

    PNAS July 24, 2012 109 (30) 11920-11927; https://doi.org/10.1073/pnas.1201904109

    See companion article:

    • Profile of George M. Church

      - Jul 24, 2012
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    Effects of a single nucleotide polymorphism in the chicken NK-lysin gene on antimicrobial activity and cytotoxicity of cancer cells

    Mi Ok Lee, Eun-Hee Kim, Hyun-Jun Jang, Mi Na Park, Hee-Jong Woo, Jae Yong Han, and James E. Womack

    PNAS July 24, 2012 109 (30) 12087-12092; https://doi.org/10.1073/pnas.1209161109
  • Open Access

    Molecular dissection of Neurospora Spore killer meiotic drive elements

    Thomas M. Hammond, David G. Rehard, Hua Xiao, and Patrick K. T. Shiu

    PNAS July 24, 2012 109 (30) 12093-12098; https://doi.org/10.1073/pnas.1203267109

    See companion article:

    • A fungal gene reinforces Mendel's laws by counteracting genetic cheating

      - Jul 24, 2012
  • Open Access

    Critical function for the Ras-GTPase activating protein RASA3 in vertebrate erythropoiesis and megakaryopoiesis

    Lionel Blanc, Steven L. Ciciotte, Babette Gwynn, Gordon J. Hildick-Smith, Eric L. Pierce, Kathleen A. Soltis, Jeffrey D. Cooney, Barry H. Paw, and Luanne L. Peters

    PNAS July 24, 2012 109 (30) 12099-12104; https://doi.org/10.1073/pnas.1204948109

• Immunology

  • Open Access

    Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120

    Anthony P. West Jr., Ron Diskin, Michel C. Nussenzweig, and Pamela J. Bjorkman

    PNAS July 24, 2012 109 (30) E2083-E2090; https://doi.org/10.1073/pnas.1208984109
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    Defect in regulatory B-cell function and development of systemic autoimmunity in T-cell Ig mucin 1 (Tim-1) mucin domain-mutant mice

    Sheng Xiao, Craig R. Brooks, Chen Zhu, Chuan Wu, Johanna M. Sweere, Sonia Petecka, Ada Yeste, Francisco J. Quintana, Takaharu Ichimura, Raymond A. Sobel, Joseph V. Bonventre, and Vijay K. Kuchroo

    PNAS July 24, 2012 109 (30) 12105-12110; https://doi.org/10.1073/pnas.1120914109
  • Open Access

    HIV-1 envelope trimer elicits more potent neutralizing antibody responses than monomeric gp120

    James M. Kovacs, Joseph P. Nkolola, Hanqin Peng, Ann Cheung, James Perry, Caroline A. Miller, Michael S. Seaman, Dan H. Barouch, and Bing Chen

    PNAS July 24, 2012 109 (30) 12111-12116; https://doi.org/10.1073/pnas.1204533109
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    Hematopoietic-specific targeting of influenza A virus reveals replication requirements for induction of antiviral immune responses

    Ryan A. Langlois, Andrew Varble, Mark A. Chua, Adolfo García-Sastre, and Benjamin R. tenOever

    PNAS July 24, 2012 109 (30) 12117-12122; https://doi.org/10.1073/pnas.1206039109
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    Interferon regulatory factor 8 integrates T-cell receptor and cytokine-signaling pathways and drives effector differentiation of CD8 T cells

    Fumi Miyagawa, Hong Zhang, Atshushi Terunuma, Keiko Ozato, Yutaka Tagaya, and Stephen I. Katz

    PNAS July 24, 2012 109 (30) 12123-12128; https://doi.org/10.1073/pnas.1201453109
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    Enhancement of dendritic cell activation via CD40 ligand-expressing γδ T cells is responsible for protective immunity to Plasmodium parasites

    Shin-Ichi Inoue, Mamoru Niikura, Satoru Takeo, Shoichiro Mineo, Yasushi Kawakami, Akihiko Uchida, Shigeru Kamiya, and Fumie Kobayashi

    PNAS July 24, 2012 109 (30) 12129-12134; https://doi.org/10.1073/pnas.1204480109

• Microbiology

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    Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine kinase photoreceptor

    Hernán R. Bonomi, Diana M. Posadas, Gastón Paris, Mariela del Carmen Carrica, Marcus Frederickson, Lía Isabel Pietrasanta, Roberto A. Bogomolni, Angeles Zorreguieta, and Fernando A. Goldbaum

    PNAS July 24, 2012 109 (30) 12135-12140; https://doi.org/10.1073/pnas.1121292109
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    Antisense RNA that affects Rhodopseudomonas palustris quorum-sensing signal receptor expression

    Hidetada Hirakawa, Caroline S. Harwood, Kieran B. Pechter, Amy L. Schaefer, and E. Peter Greenberg

    PNAS July 24, 2012 109 (30) 12141-12146; https://doi.org/10.1073/pnas.1200243109
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    Eradication of bacterial persisters with antibiotic-generated hydroxyl radicals

    Sarah Schmidt Grant, Benjamin B. Kaufmann, Nikhilesh S. Chand, Nathan Haseley, and Deborah T. Hung

    PNAS July 24, 2012 109 (30) 12147-12152; https://doi.org/10.1073/pnas.1203735109
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    Inactivation of a single gene enables microaerobic growth of the obligate anaerobe Bacteroides fragilis

    Brian M. Meehan, Anthony D. Baughn, Rene Gallegos, and Michael H. Malamy

    PNAS July 24, 2012 109 (30) 12153-12158; https://doi.org/10.1073/pnas.1203796109
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    Chemotactic signaling via carbohydrate phosphotransferase systems in Escherichia coli

    Silke Neumann, Karin Grosse, and Victor Sourjik

    PNAS July 24, 2012 109 (30) 12159-12164; https://doi.org/10.1073/pnas.1205307109

• Neuroscience

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    Neuregulin 1-ErbB4-PI3K signaling in schizophrenia and phosphoinositide 3-kinase-p110δ inhibition as a potential therapeutic strategy

    • From the Cover

    Amanda J. Law, Yanhong Wang, Yoshitatsu Sei, Patricio O’Donnell, Patrick Piantadosi, Francesco Papaleo, Richard E. Straub, Wenwei Huang, Craig J. Thomas, Radhakrishna Vakkalanka, Aaron D. Besterman, Barbara K. Lipska, Thomas M. Hyde, Paul J. Harrison, Joel E. Kleinman, and Daniel R. Weinberger

    PNAS July 24, 2012 109 (30) 12165-12170; https://doi.org/10.1073/pnas.1206118109

    See companion article:

    • Finding a druggable target for schizophrenia

      - Jul 24, 2012
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    Sushi domains confer distinct trafficking profiles on GABA_B receptors

    Saad Hannan, Megan E. Wilkins, and Trevor G. Smart

    PNAS July 24, 2012 109 (30) 12171-12176; https://doi.org/10.1073/pnas.1201660109
  • Open Access

    Remote control of renal physiology by the intestinal neuropeptide pigment-dispersing factor in Drosophila

    Aaron D. Talsma, Christo P. Christov, Ana Terriente-Felix, Gerit A. Linneweber, Daniel Perea, Matthew Wayland, Orie T. Shafer, and Irene Miguel-Aliaga

    PNAS July 24, 2012 109 (30) 12177-12182; https://doi.org/10.1073/pnas.1200247109
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    Inositol hexakisphosphate suppresses excitatory neurotransmission via synaptotagmin-1 C2B domain in the hippocampal neuron

    Shao-Nian Yang, Yue Shi, Guang Yang, Yuxin Li, Lina Yu, Ok-Ho Shin, Taulant Bacaj, Thomas C. Südhof, Jia Yu, and Per-Olof Berggren

    PNAS July 24, 2012 109 (30) 12183-12188; https://doi.org/10.1073/pnas.1115070109
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    Interleukin-1R3 mediates interleukin-1–induced potassium current increase through fast activation of Akt kinase

    Jiang Qian, Ling Zhu, Qiming Li, Natalya Belevych, Qun Chen, Fangli Zhao, Scott Herness, and Ning Quan

    PNAS July 24, 2012 109 (30) 12189-12194; https://doi.org/10.1073/pnas.1205207109
  • Open Access

    Synapse type-independent degradation of the endocannabinoid 2-arachidonoylglycerol after retrograde synaptic suppression

    Asami Tanimura, Motokazu Uchigashima, Maya Yamazaki, Naofumi Uesaka, Takayasu Mikuni, Manabu Abe, Kouichi Hashimoto, Masahiko Watanabe, Kenji Sakimura, and Masanobu Kano

    PNAS July 24, 2012 109 (30) 12195-12200; https://doi.org/10.1073/pnas.1204404109
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    C-fiber activity-dependent maturation of glycinergic inhibition in the spinal dorsal horn of the postnatal rat

    Stephanie C. Koch, Keri K. Tochiki, Stefan Hirschberg, and Maria Fitzgerald

    PNAS July 24, 2012 109 (30) 12201-12206; https://doi.org/10.1073/pnas.1118960109

• Pharmacology

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    A soluble bone morphogenetic protein type IA receptor increases bone mass and bone strength

    Marc Baud’huin, Nicolas Solban, Milton Cornwall-Brady, Dianne Sako, Yoshimi Kawamoto, Katia Liharska, Darren Lath, Mary L. Bouxsein, Kathryn W. Underwood, Jeffrey Ucran, Ravindra Kumar, Eileen Pobre, Asya Grinberg, Jasbir Seehra, Ernesto Canalis, R. Scott Pearsall, and Peter I. Croucher

    PNAS July 24, 2012 109 (30) 12207-12212; https://doi.org/10.1073/pnas.1204929109

• Plant Biology

  • Open Access

    Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the maize transcription factor R

    Que Kong, Sitakanta Pattanaik, Antje Feller, Joshua R. Werkman, Chenglin Chai, Yongqin Wang, Erich Grotewold, and Ling Yuan

    PNAS July 24, 2012 109 (30) E2091-E2097; https://doi.org/10.1073/pnas.1205513109
  • Open Access

    Modeling huanglongbing transmission within a citrus tree

    Christinah Chiyaka, Burton H. Singer, Susan E. Halbert, J. Glenn Morris Jr., and Ariena H. C. van Bruggen

    PNAS July 24, 2012 109 (30) 12213-12218; https://doi.org/10.1073/pnas.1208326109
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    Insights into salt tolerance from the genome of Thellungiella salsuginea

    Hua-Jun Wu, Zhonghui Zhang, Jun-Yi Wang, Dong-Ha Oh, Maheshi Dassanayake, Binghang Liu, Quanfei Huang, Hai-Xi Sun, Ran Xia, Yaorong Wu, Yi-Nan Wang, Zhao Yang, Yang Liu, Wanke Zhang, Huawei Zhang, Jinfang Chu, Cunyu Yan, Shuang Fang, Jinsong Zhang, Yiqin Wang, Fengxia Zhang, Guodong Wang, Sang Yeol Lee, John M. Cheeseman, Bicheng Yang, Bo Li, Jiumeng Min, Linfeng Yang, Jun Wang, Chengcai Chu, Shou-Yi Chen, Hans J. Bohnert, Jian-Kang Zhu, Xiu-Jie Wang, and Qi Xie

    PNAS July 24, 2012 109 (30) 12219-12224; https://doi.org/10.1073/pnas.1209954109
  • Open Access

    TCP transcription factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), is required for normal tassel branch angle formation in maize

    Fang Bai, Renata Reinheimer, Diego Durantini, Elizabeth A. Kellogg, and Robert J. Schmidt

    PNAS July 24, 2012 109 (30) 12225-12230; https://doi.org/10.1073/pnas.1202439109
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    A phytochrome–phototropin light signaling complex at the plasma membrane

    Katharina Jaedicke, Anna Lena Lichtenthäler, Rabea Meyberg, Mathias Zeidler, and Jon Hughes

    PNAS July 24, 2012 109 (30) 12231-12236; https://doi.org/10.1073/pnas.1120203109

• Psychological and Cognitive Sciences

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    Monkeys have a limited form of short-term memory in audition

    Brian H. Scott, Mortimer Mishkin, and Pingbo Yin

    PNAS July 24, 2012 109 (30) 12237-12241; https://doi.org/10.1073/pnas.1209685109
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    Resetting capacity limitations revealed by long-lasting elimination of attentional blink through training

    Hoon Choi, Li-Hung Chang, Kazuhisa Shibata, Yuka Sasaki, and Takeo Watanabe

    PNAS July 24, 2012 109 (30) 12242-12247; https://doi.org/10.1073/pnas.1203972109
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    Adiponectin is critical in determining susceptibility to depressive behaviors and has antidepressant-like activity

    Jing Liu, Ming Guo, Di Zhang, Shao-Ying Cheng, Meilian Liu, Jun Ding, Philipp E. Scherer, Feng Liu, and Xin-Yun Lu

    PNAS July 24, 2012 109 (30) 12248-12253; https://doi.org/10.1073/pnas.1202835109

• Systems Biology

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    Mechanism-independent method for predicting response to multidrug combinations in bacteria

    Kevin Wood, Satoshi Nishida, Eduardo D. Sontag, and Philippe Cluzel

    PNAS July 24, 2012 109 (30) 12254-12259; https://doi.org/10.1073/pnas.1201281109